Publications by year, excluding conference proceedings.
Complete CV Google Scholar Page
2024
Neophytou, Andreas; Starr, Francis W.; Chakrabarti, Dwaipayan; Sciortino, Francesco
Hierarchy of topological transitions in a network liquid Journal Article
In: Proceedings of the National Academy of Sciences, vol. 121, no. 36, pp. e2406890121, 2024.
Abstract | BibTeX | Tags: | Links:
@article{nscs24,
title = {Hierarchy of topological transitions in a network liquid},
author = {Andreas Neophytou and Francis W. Starr and Dwaipayan Chakrabarti and Francesco Sciortino},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zds23.pdf},
doi = {10.1073/pnas.2406890121},
year = {2024},
date = {2024-01-01},
journal = {Proceedings of the National Academy of Sciences},
volume = {121},
number = {36},
pages = {e2406890121},
abstract = {Understanding the fundamental principles which govern the structure and layout of physical networks<E2><80><94>networks composed of nodes and edges that occupy space and cannot overlap with each other<E2><80><94>has recently emerged as an important open question. As a test case, we investigate the densification of physical networks formed by DNA-functionalized nanoparticles. These particles have the capability to self-assemble into three distinct networks with notably different densities, each separated by first-order phase transitions. We reveal that these phase transitions signify a series of hierarchical transitions driven by the topological linking of rings, which is the key to producing physical networks satisfying excluded volume constraints. The representation of complex systems as networks has become a critical tool across many fields of science. In the context of physical networks, such as biological neural networks, vascular networks, or network liquids where the nodes and edges occupy volume in three-dimensional space, the question of how they become densely packed is of special importance. Here, we investigate a model network liquid, which is known to densify via two successive liquid<E2><80><93>liquid phase transitions (LLPTs). We elucidate the importance of rings<E2><80<80><94>cyclic paths formed by bonded particles in the networks<E2><80><94>and their spatial disposition in understanding the structural changes that underpin the increase in density across the LLPTs. Our analyses demonstrate that the densification of these networks is primarily driven by the formation of linked rings, and the LLPTs correspond to a hierarchy of topological transitions where rings form the fundamental building blocks. We envisage entanglement to emerge as a general mechanism for densification, with wide implications for the embedding of physical networks, especially in confined spaces.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Understanding the fundamental principles which govern the structure and layout of physical networks<E2><80><94>networks composed of nodes and edges that occupy space and cannot overlap with each other<E2><80><94>has recently emerged as an important open question. As a test case, we investigate the densification of physical networks formed by DNA-functionalized nanoparticles. These particles have the capability to self-assemble into three distinct networks with notably different densities, each separated by first-order phase transitions. We reveal that these phase transitions signify a series of hierarchical transitions driven by the topological linking of rings, which is the key to producing physical networks satisfying excluded volume constraints. The representation of complex systems as networks has become a critical tool across many fields of science. In the context of physical networks, such as biological neural networks, vascular networks, or network liquids where the nodes and edges occupy volume in three-dimensional space, the question of how they become densely packed is of special importance. Here, we investigate a model network liquid, which is known to densify via two successive liquid<E2><80><93>liquid phase transitions (LLPTs). We elucidate the importance of rings<E2><80<80><94>cyclic paths formed by bonded particles in the networks<E2><80><94>and their spatial disposition in understanding the structural changes that underpin the increase in density across the LLPTs. Our analyses demonstrate that the densification of these networks is primarily driven by the formation of linked rings, and the LLPTs correspond to a hierarchy of topological transitions where rings form the fundamental building blocks. We envisage entanglement to emerge as a general mechanism for densification, with wide implications for the embedding of physical networks, especially in confined spaces.
2023
Rubio, Cesar A. Castro; Fan, Jinpeng; Hanrahan, Max K.; Douglas, Jack F.; Starr, Francis W.
Structure and Dynamics of Composites of Star Polymers in a Linear Polymer Matrix Journal Article
In: Macromolecules, vol. 56, no. 23, pp. 9324-9335, 2023.
BibTeX | Tags: | Links:
@article{cfhds23,
title = {Structure and Dynamics of Composites of Star Polymers in a Linear Polymer Matrix},
author = {Cesar A. Castro Rubio and Jinpeng Fan and Max K. Hanrahan and Jack F. Douglas and Francis W. Starr},
url = {https://fstarr.wescreates.wesleyan.edu/publications/cfhds23.pdf},
doi = {10.1021/acs.macromol.3c01558},
year = {2023},
date = {2023-01-01},
journal = {Macromolecules},
volume = {56},
number = {23},
pages = {9324-9335},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Jeong, Cheol; Starr, Francis W.; Beers, Kathryn L.; Douglas, Jack F.
Influence of Functionalization on the Crystallinity and Basic Thermodynamic Properties of Polyethylene Journal Article
In: Macromolecules, vol. 56, no. 11, pp. 3873-3883, 2023.
BibTeX | Tags: | Links:
@article{jsbd23,
title = {Influence of Functionalization on the Crystallinity and Basic Thermodynamic Properties of Polyethylene},
author = {Cheol Jeong and Francis W. Starr and Kathryn L. Beers and Jack F. Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/jsbd23.pdf},
doi = {10.1021/acs.macromol.2c02569},
year = {2023},
date = {2023-01-01},
journal = {Macromolecules},
volume = {56},
number = {11},
pages = {3873-3883},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
2022
Zhang, Wengang; Starr, Francis W.; Beers, Kathryn L.; Douglas, Jack F.
Reactive Molecular Dynamics Simulations of the Depolymerization of Polyethylene Using Graphene-Oxide-Supported Platinum Nanoparticles Journal Article
In: The Journal of Physical Chemistry A, vol. 126, no. 20, pp. 3167-3173, 2022, (PMID: 35533406).
BibTeX | Tags: Nanotechnology, Polymers | Links:
@article{zsbd22,
title = {Reactive Molecular Dynamics Simulations of the Depolymerization of Polyethylene Using Graphene-Oxide-Supported Platinum Nanoparticles},
author = {Wengang Zhang and Francis W. Starr and Kathryn L. Beers and Jack F. Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zsbd22.pdf},
doi = {10.1021/acs.jpca.2c01167},
year = {2022},
date = {2022-05-26},
urldate = {2022-01-01},
journal = {The Journal of Physical Chemistry A},
volume = {126},
number = {20},
pages = {3167-3173},
note = {PMID: 35533406},
keywords = {Nanotechnology, Polymers},
pubstate = {published},
tppubtype = {article}
}
Vargas-Lara, Fernando; Starr, Francis W.; Douglas, Jack F.
Solution properties of spherical gold nanoparticles with grafted DNA chains from simulation and theory Journal Article
In: Nanoscale Adv., 2022.
Abstract | BibTeX | Tags: | Links:
@article{vsd22,
title = {Solution properties of spherical gold nanoparticles with grafted DNA chains from simulation and theory},
author = {Fernando Vargas-Lara and Francis W. Starr and Jack F. Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/vsd22.pdf},
doi = {10.1039/D2NA00377E},
year = {2022},
date = {2022-01-01},
journal = {Nanoscale Adv.},
publisher = {RSC},
abstract = {There has been a rapidly growing interest in the use of functionalized Au nanoparticles (NPs) as platforms in multiple applications in medicine and manufacturing. The sensing and targeting characteristics of these NPs, and the realization of precisely organized structures in manufacturing applications using such NPs, depend on the control of their surface functionalization. NP functionalization typically takes the form of polymer grafted layers, and a detailed knowledge of the chemical and structural properties of these layers is required to molecularly engineer the particle characteristics for specific applications. However, the prediction and experimental determination of these properties to enable the rational engineering of these particles is a persistent problem in the development of this class of materials. To address this situation, molecular dynamic simulations were performed based on a previously established coarse-grained single-stranded DNA (ssDNA) model to determine basic solution properties of model ssDNA-grafted NP-layers under a wide range of conditions. In particular, we emphasize the calculation of the hydrodynamic radius for ssDNA-grafted Au NPs as a function of structural parameters such as ssDNA length, NP core size, and surface coverage. We also numerically estimate the radius of gyration and the intrinsic viscosity of these NPs, which in combination with hydrodynamic radius estimates, provide valuable information about the fluctuating structure of the grafted polymer layers. We may then understand the origin of the commonly reported variation in effective NP ``size'' by different measurement methods, and then exploit this information in connection to material design and characterization in connection with the ever-growing number of applications utilizing polymer-grafted NPs.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There has been a rapidly growing interest in the use of functionalized Au nanoparticles (NPs) as platforms in multiple applications in medicine and manufacturing. The sensing and targeting characteristics of these NPs, and the realization of precisely organized structures in manufacturing applications using such NPs, depend on the control of their surface functionalization. NP functionalization typically takes the form of polymer grafted layers, and a detailed knowledge of the chemical and structural properties of these layers is required to molecularly engineer the particle characteristics for specific applications. However, the prediction and experimental determination of these properties to enable the rational engineering of these particles is a persistent problem in the development of this class of materials. To address this situation, molecular dynamic simulations were performed based on a previously established coarse-grained single-stranded DNA (ssDNA) model to determine basic solution properties of model ssDNA-grafted NP-layers under a wide range of conditions. In particular, we emphasize the calculation of the hydrodynamic radius for ssDNA-grafted Au NPs as a function of structural parameters such as ssDNA length, NP core size, and surface coverage. We also numerically estimate the radius of gyration and the intrinsic viscosity of these NPs, which in combination with hydrodynamic radius estimates, provide valuable information about the fluctuating structure of the grafted polymer layers. We may then understand the origin of the commonly reported variation in effective NP ``size'' by different measurement methods, and then exploit this information in connection to material design and characterization in connection with the ever-growing number of applications utilizing polymer-grafted NPs.
Zhu, Yuwen; Giuntoli, Andrea; Zhang, Wengang; Lin, Zhongqin; Keten, Sinan; Starr, Francis W.; Douglas, Jack F.
The effect of nanoparticle softness on the interfacial dynamics of a model polymer nanocomposite Journal Article
In: The Journal of Chemical Physics, vol. 157, no. 9, pp. 094901, 2022.
BibTeX | Tags: | Links:
@article{zgzlksd22,
title = {The effect of nanoparticle softness on the interfacial dynamics of a model polymer nanocomposite},
author = {Yuwen Zhu and Andrea Giuntoli and Wengang Zhang and Zhongqin Lin and Sinan Keten and Francis W. Starr and Jack F. Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zgzlksd22.pdf},
doi = {10.1063/5.0101551},
year = {2022},
date = {2022-01-01},
journal = {The Journal of Chemical Physics},
volume = {157},
number = {9},
pages = {094901},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Douglas, Jack F.; Starr, Francis W.
How Dispersity from Step-Growth Polymerization Affects Polymer Dynamics from Coarse-Grained Molecular Simulations Journal Article
In: Macromolecules, vol. 55, no. 22, pp. 9901-9907, 2022.
BibTeX | Tags: | Links:
@article{zds22,
title = {How Dispersity from Step-Growth Polymerization Affects Polymer Dynamics from Coarse-Grained Molecular Simulations},
author = {Wengang Zhang and Jack F. Douglas and Francis W. Starr},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zds22.pdf},
doi = {10.1021/acs.macromol.2c01623},
year = {2022},
date = {2022-01-01},
journal = {Macromolecules},
volume = {55},
number = {22},
pages = {9901-9907},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
McKenzie-Smith, Thomas; Douglas, Jack F.; Starr, Francis W.
Relating dynamic free volume to cooperative relaxation in a glass-forming polymer composite Journal Article
In: The Journal of Chemical Physics, vol. 157, no. 13, pp. 131101, 2022, ISSN: 0021-9606.
Abstract | BibTeX | Tags: | Links:
@article{mds22,
title = {Relating dynamic free volume to cooperative relaxation in a glass-forming polymer composite},
author = {Thomas McKenzie-Smith and Jack F. Douglas and Francis W. Starr},
url = {https://fstarr.wescreates.wesleyan.edu/publications/mds22.pdf},
doi = {10.1063/5.0114902},
issn = {0021-9606},
year = {2022},
date = {2022-01-01},
journal = {The Journal of Chemical Physics},
volume = {157},
number = {13},
pages = {131101},
abstract = {There are a variety of complementary descriptions of the temperature dependence of the structural relaxation time <CF><84> in glass-forming materials, which we interpret positively as suggesting an underlying unified description. We examine the inter-relation between the string model, an outgrowth of the Adam and Gibbs approach that emphasizes collective particle exchange motion, and the localization model, which emphasizes the volume explored by particles in their caged states, a kind of dynamic <E2><80><9C>free volume.<E2><80><9D> Each model of liquid dynamics is described by a limited set of parameters that must be interrelated if both descriptions simultaneously describe the relaxation behavior. We pursue the consequences of this idea by performing coarse-grained molecular simulations of polymer melts with additives of variable size and interaction strength with the polymer matrix, thereby significantly altering the relaxation of the composite material. Both the string and localization models describe our relaxation time data well, and a comparison of the model parameters allows us to relate the local caging scale <E2><9F><A8>u2<E2><9F><A9> (the Debye-Waller parameter) to the entropy of activation for molecular rearrangements in the string model, thereby developing a bridge between these seemingly disparate approaches to liquid dynamics.},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
There are a variety of complementary descriptions of the temperature dependence of the structural relaxation time <CF><84> in glass-forming materials, which we interpret positively as suggesting an underlying unified description. We examine the inter-relation between the string model, an outgrowth of the Adam and Gibbs approach that emphasizes collective particle exchange motion, and the localization model, which emphasizes the volume explored by particles in their caged states, a kind of dynamic <E2><80><9C>free volume.<E2><80><9D> Each model of liquid dynamics is described by a limited set of parameters that must be interrelated if both descriptions simultaneously describe the relaxation behavior. We pursue the consequences of this idea by performing coarse-grained molecular simulations of polymer melts with additives of variable size and interaction strength with the polymer matrix, thereby significantly altering the relaxation of the composite material. Both the string and localization models describe our relaxation time data well, and a comparison of the model parameters allows us to relate the local caging scale <E2><9F><A8>u2<E2><9F><A9> (the Debye-Waller parameter) to the entropy of activation for molecular rearrangements in the string model, thereby developing a bridge between these seemingly disparate approaches to liquid dynamics.
2021
McKenzie-Smith, Thomas Q.; Douglas, Jack F.; Starr, Francis W.
Explaining the Sensitivity of Polymer Segmental Relaxation to Additive Size Based on the Localization Model Journal Article
In: Phys. Rev. Lett., vol. 127, pp. 277802, 2021.
BibTeX | Tags: Glass Formation, Nanocomposites, Nanotechnology | Links:
@article{mds21,
title = {Explaining the Sensitivity of Polymer Segmental Relaxation to Additive Size Based on the Localization Model},
author = {Thomas Q. McKenzie-Smith and Jack F. Douglas and Francis W. Starr},
url = {https://fstarr.wescreates.wesleyan.edu/publications/mds21.pdf},
doi = {10.1103/PhysRevLett.127.277802},
year = {2021},
date = {2021-12-30},
journal = {Phys. Rev. Lett.},
volume = {127},
pages = {277802},
publisher = {American Physical Society},
keywords = {Glass Formation, Nanocomposites, Nanotechnology},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Starr, Francis W.; Douglas, Jack F.
Activation free energy gradient controls interfacial mobility gradient in thin polymer films Journal Article
In: The Journal of Chemical Physics, vol. 155, no. 17, pp. 174901, 2021.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Nanotechnology, Thin Films | Links:
@article{zsd21,
title = {Activation free energy gradient controls interfacial mobility gradient in thin polymer films},
author = {Wengang Zhang and Francis W. Starr and Jack F. Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zsd21.pdf},
doi = {10.1063/5.0064866},
year = {2021},
date = {2021-11-07},
journal = {The Journal of Chemical Physics},
volume = {155},
number = {17},
pages = {174901},
keywords = {Dynamic Heterogeneity, Glass Formation, Nanotechnology, Thin Films},
pubstate = {published},
tppubtype = {article}
}
Emamy, Hamed; Starr, Francis W.; Kumar, Sanat K.
Detecting bound polymer layers in attractive polymeranoparticle hybrids Journal Article
In: Nanoscale, vol. 13, pp. 12910-12915, 2021.
BibTeX | Tags: Glass Formation, Nanocomposites, Nanotechnology | Links:
@article{esk21,
title = {Detecting bound polymer layers in attractive polymeranoparticle hybrids},
author = {Hamed Emamy and Francis W. Starr and Sanat K. Kumar},
url = {https://https://fstarr.wescreates.wesleyan.edu/publications/esk21.pdf},
doi = {10.1039/D1NR02395K},
year = {2021},
date = {2021-07-01},
journal = {Nanoscale},
volume = {13},
pages = {12910-12915},
publisher = {The Royal Society of Chemistry},
keywords = {Glass Formation, Nanocomposites, Nanotechnology},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Douglas, Jack F.; Chremos, Alexandros; Starr, Francis W.
Structure and Dynamics of Star Polymer Films from Coarse-Grained Molecular Simulations Journal Article
In: Macromolecules, vol. 54, no. 12, pp. 5344-5353, 2021.
BibTeX | Tags: Glass Formation, Nanotechnology, Thin Films | Links:
@article{zdcs21,
title = {Structure and Dynamics of Star Polymer Films from Coarse-Grained Molecular Simulations},
author = {Wengang Zhang and Jack F. Douglas and Alexandros Chremos and Francis W. Starr},
url = {https://https://fstarr.wescreates.wesleyan.edu/publications/zdcs21.pdf},
doi = {10.1021/acs.macromol.1c00504},
year = {2021},
date = {2021-06-04},
journal = {Macromolecules},
volume = {54},
number = {12},
pages = {5344-5353},
keywords = {Glass Formation, Nanotechnology, Thin Films},
pubstate = {published},
tppubtype = {article}
}
Liu, Ari Y.; Emamy, Hamed; Douglas, Jack F.; Starr, Francis W.
Effects of Chain Length on the Structure and Dynamics of Semidilute Nanoparticle-Polymer Composites Journal Article
In: Macromolecules, vol. 54, no. 7, pp. 3041-3051, 2021.
BibTeX | Tags: Glass Formation, Nanocomposites, Nanotechnology | Links:
@article{leds21,
title = {Effects of Chain Length on the Structure and Dynamics of Semidilute Nanoparticle-Polymer Composites},
author = {Ari Y. Liu and Hamed Emamy and Jack F. Douglas and Francis W. Starr},
url = {http://fstarr.wescreates.wesleyan.edu/publications/leds21.pdf},
doi = {10.1021/acs.macromol.0c02500},
year = {2021},
date = {2021-03-23},
journal = {Macromolecules},
volume = {54},
number = {7},
pages = {3041-3051},
keywords = {Glass Formation, Nanocomposites, Nanotechnology},
pubstate = {published},
tppubtype = {article}
}
2020
Giuntoli, Andrea; Puosi, Francesco; Leporini, Dino; Starr, Francis W; Douglas, Jack F
Predictive relation for the α-relaxation time of a coarse-grained polymer melt under steady shear Journal Article
In: Science Advances, vol. 6, no. 17, 2020.
Abstract | BibTeX | Tags: Glass Formation, Polymers | Links:
@article{gplsd20,
title = {Predictive relation for the α-relaxation time of a coarse-grained polymer melt under steady shear},
author = {Andrea Giuntoli and Francesco Puosi and Dino Leporini and Francis W Starr and Jack F Douglas},
url = {http://fstarr.wescreates.wesleyan.edu/publications/gplsd20.pdf},
doi = {10.1126/sciadv.aaz0777},
year = {2020},
date = {2020-04-24},
journal = {Science Advances},
volume = {6},
number = {17},
publisher = {American Association for the Advancement of Science},
abstract = {We examine the influence of steady shear on structural relaxation in a simulated coarse-grained unentangled polymer melt over a wide range of temperature and shear rates. Shear is found to progressively suppress the $alpha$-relaxation process observed in the intermediate scattering function, leading ultimately to a purely inertially dominated $alpha$-relaxation at high shear rates, a trend similar to increasing temperature. On the basis of a scaling argument emphasizing dynamic heterogeneity in cooled liquids and its alteration under material deformation, we deduce and validate a parameter-free scaling relation for both the structural relaxation time
$tau_alpha$ from the intermediate scattering function and the textquotedblleftstretching exponenttextquotedblright
$beta$ quantifying the extent of dynamic heterogeneity over the entire range of temperatures and shear rates that we can simulate.},
keywords = {Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
We examine the influence of steady shear on structural relaxation in a simulated coarse-grained unentangled polymer melt over a wide range of temperature and shear rates. Shear is found to progressively suppress the $alpha$-relaxation process observed in the intermediate scattering function, leading ultimately to a purely inertially dominated $alpha$-relaxation at high shear rates, a trend similar to increasing temperature. On the basis of a scaling argument emphasizing dynamic heterogeneity in cooled liquids and its alteration under material deformation, we deduce and validate a parameter-free scaling relation for both the structural relaxation time
$tau_alpha$ from the intermediate scattering function and the textquotedblleftstretching exponenttextquotedblright
$beta$ quantifying the extent of dynamic heterogeneity over the entire range of temperatures and shear rates that we can simulate.
$tau_alpha$ from the intermediate scattering function and the textquotedblleftstretching exponenttextquotedblright
$beta$ quantifying the extent of dynamic heterogeneity over the entire range of temperatures and shear rates that we can simulate.
Zhang, Wengang; Starr, Francis W; Douglas, Jack F
Reconciling computational and experimental trends in the temperature dependence of the interfacial mobility of polymer films Journal Article
In: The Journal of Chemical Physics, vol. 152, no. 12, pp. 124703, 2020.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers | Links:
@article{zsd20,
title = {Reconciling computational and experimental trends in the temperature dependence of the interfacial mobility of polymer films},
author = {Wengang Zhang and Francis W Starr and Jack F Douglas},
url = {https://fstarr.wescreates.wesleyan.edu/publications/zsd20.pdf},
doi = {10.1063/1.5144262},
year = {2020},
date = {2020-01-01},
journal = {The Journal of Chemical Physics},
volume = {152},
number = {12},
pages = {124703},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
Fan, Jinpeng; Emamy, Hamed; Chremos, Alexandros; Douglas, Jack F; Starr, Francis W
Dynamic heterogeneity and collective motion in star polymer melts Journal Article
In: The Journal of Chemical Physics, vol. 152, no. 5, pp. 054904, 2020.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers | Links:
@article{fecds20,
title = {Dynamic heterogeneity and collective motion in star polymer melts},
author = {Jinpeng Fan and Hamed Emamy and Alexandros Chremos and Jack F Douglas and Francis W Starr},
url = {https://fstarr.wescreates.wesleyan.edu/publications/fecds20.pdf},
doi = {10.1063/1.5135731},
year = {2020},
date = {2020-01-01},
journal = {The Journal of Chemical Physics},
volume = {152},
number = {5},
pages = {054904},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
Storey, Amber N; Zhang, Wengang; Douglas, Jack F; Starr, Francis W
How Does Monomer Structure Affect the Interfacial Dynamics of Supported Ultrathin Polymer Films? Journal Article
In: Macromolecules, vol. 53, no. 21, pp. 9654-9664, 2020.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films | Links:
@article{szds20,
title = {How Does Monomer Structure Affect the Interfacial Dynamics of Supported Ultrathin Polymer Films?},
author = {Amber N Storey and Wengang Zhang and Jack F Douglas and Francis W Starr},
url = {http://fstarr.wescreates.wesleyan.edu/publications/szds20.pdf},
doi = {10.1021/acs.macromol.0c01413},
year = {2020},
date = {2020-01-01},
journal = {Macromolecules},
volume = {53},
number = {21},
pages = {9654-9664},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films},
pubstate = {published},
tppubtype = {article}
}
Emamy, Hamed; Kumar, Sanat K; Starr, Francis W
Structural Properties of Bound Layer in Polymer-Nanoparticle Composites Journal Article
In: Macromolecules, vol. 53, no. 18, pp. 7845-7850, 2020.
BibTeX | Tags: Nanocomposites, Polymers | Links:
@article{eks20,
title = {Structural Properties of Bound Layer in Polymer-Nanoparticle Composites},
author = {Hamed Emamy and Sanat K Kumar and Francis W Starr},
url = {http://fstarr.wescreates.wesleyan.edu/publications/eks20.pdf},
doi = {10.1021/acs.macromol.0c01465},
year = {2020},
date = {2020-01-01},
journal = {Macromolecules},
volume = {53},
number = {18},
pages = {7845-7850},
keywords = {Nanocomposites, Polymers},
pubstate = {published},
tppubtype = {article}
}
2019
Giovambattista, Nicolas; Starr, Francis W; Poole, Peter H
State variables for glasses: The case of amorphous ice Journal Article
In: The Journal of Chemical Physics, vol. 150, no. 22, pp. 224502, 2019.
Abstract | BibTeX | Tags: Glass Formation, Water | Links:
@article{gsp19,
title = {State variables for glasses: The case of amorphous ice},
author = {Nicolas Giovambattista and Francis W Starr and Peter H Poole},
url = {http://fstarr.web.wesleyan.edu/publications/gsp19.pdf},
doi = {10.1063/1.5092586},
year = {2019},
date = {2019-06-10},
journal = {The Journal of Chemical Physics},
volume = {150},
number = {22},
pages = {224502},
abstract = {Glasses are out-of-equilibrium systems whose state cannot be uniquely defined by the usual set of equilibrium state variables. Here, we seek to identify an expanded set of variables that uniquely define the state of a glass. The potential energy landscape (PEL) formalism is a useful approach within statistical mechanics to describe supercooled liquids and glasses. We use the PEL formalism and computer simulations to study the transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA). We employ the ST2 water model, which exhibits an abrupt first-order-like phase transition from LDA to HDA, similar to that observed in experiments. We prepare a number of distinct samples of both LDA and HDA that have completely different preparation histories. We then study the evolution of these LDA and HDA samples during compression and decompression at temperatures sufficiently low that annealing is absent and also during heating. We find that the evolution of each glass sample, during compression/decompression or heating, is uniquely determined by six macroscopic properties of the initial glass sample. These six quantities consist of three conventional thermodynamic state variables, the number of molecules N, the system volume V, and the temperature T, as well as three properties of the PEL, the inherent structure (IS) energy EIS, the IS pressure PIS, and the average curvature of the PEL at the IS ?IS. In other words, (N,V,T,EIS,PIS,?IS) are state variables that define the glass state in the case of amorphous ice. An interpretation of our results in terms of the PEL formalism is provided. Since the behavior of water in the glassy state is more complex than for most substances, our results suggest that these six state variables may be applicable to amorphous solids in general and that there may be situations in which fewer than six variables would be sufficient to define the state of a glass.},
keywords = {Glass Formation, Water},
pubstate = {published},
tppubtype = {article}
}
Glasses are out-of-equilibrium systems whose state cannot be uniquely defined by the usual set of equilibrium state variables. Here, we seek to identify an expanded set of variables that uniquely define the state of a glass. The potential energy landscape (PEL) formalism is a useful approach within statistical mechanics to describe supercooled liquids and glasses. We use the PEL formalism and computer simulations to study the transformations between low-density amorphous ice (LDA) and high-density amorphous ice (HDA). We employ the ST2 water model, which exhibits an abrupt first-order-like phase transition from LDA to HDA, similar to that observed in experiments. We prepare a number of distinct samples of both LDA and HDA that have completely different preparation histories. We then study the evolution of these LDA and HDA samples during compression and decompression at temperatures sufficiently low that annealing is absent and also during heating. We find that the evolution of each glass sample, during compression/decompression or heating, is uniquely determined by six macroscopic properties of the initial glass sample. These six quantities consist of three conventional thermodynamic state variables, the number of molecules N, the system volume V, and the temperature T, as well as three properties of the PEL, the inherent structure (IS) energy EIS, the IS pressure PIS, and the average curvature of the PEL at the IS ?IS. In other words, (N,V,T,EIS,PIS,?IS) are state variables that define the glass state in the case of amorphous ice. An interpretation of our results in terms of the PEL formalism is provided. Since the behavior of water in the glassy state is more complex than for most substances, our results suggest that these six state variables may be applicable to amorphous solids in general and that there may be situations in which fewer than six variables would be sufficient to define the state of a glass.
Emamy, Hamed; Gang, Oleg; Starr, Francis W
The Stability of a Nanoparticle Diamond Lattice Linked by DNA Journal Article
In: Nanomaterials, vol. 9, no. 5, 2019, ISSN: 2079-4991.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{egs19,
title = {The Stability of a Nanoparticle Diamond Lattice Linked by DNA},
author = {Hamed Emamy and Oleg Gang and Francis W Starr},
url = {http://fstarr.web.wesleyan.edu/publications/egs19.pdf},
doi = {10.3390/nano9050661},
issn = {2079-4991},
year = {2019},
date = {2019-04-26},
journal = {Nanomaterials},
volume = {9},
number = {5},
abstract = {The functionalization of nanoparticles (NPs) with DNA has proven to be an effective strategy for self-assembly of NPs into superlattices with a broad range of lattice symmetries. By combining this strategy with the DNA origami approach, the possible lattice structures have been expanded to include the cubic diamond lattice. This symmetry is of particular interest, both due to the inherent synthesis challenges, as well as the potential valuable optical properties, including a complete band-gap. Using these lattices in functional devices requires a robust and stable lattice. Here, we use molecular simulations to investigate how NP size and DNA stiffness affect the structure, stability, and crystallite shape of NP superlattices with diamond symmetry. We use the Wulff construction method to predict the equilibrium crystallite shape of the cubic diamond lattice. We find that, due to reorientation of surface particles, it is possible to create bonds at the surface with dangling DNA links on the interior, thereby reducing surface energy. Consequently, the crystallite shape depends on the degree to which such surface reorientation is possible, which is sensitive to DNA stiffness. Further, we determine dependence of the lattice stability on NP size and DNA stiffness by evaluating relative Gibbs free energy. We find that the free energy is dominated by the entropic component. Increasing NP size or DNA stiffness increases free energy, and thus decreases the relative stability of lattices. On the other hand, increasing DNA stiffness results in a more precisely defined lattice structure. Thus, there is a trade off between structure and stability of the lattice. Our findings should assist experimental design for controlling lattice stability and crystallite shape.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
The functionalization of nanoparticles (NPs) with DNA has proven to be an effective strategy for self-assembly of NPs into superlattices with a broad range of lattice symmetries. By combining this strategy with the DNA origami approach, the possible lattice structures have been expanded to include the cubic diamond lattice. This symmetry is of particular interest, both due to the inherent synthesis challenges, as well as the potential valuable optical properties, including a complete band-gap. Using these lattices in functional devices requires a robust and stable lattice. Here, we use molecular simulations to investigate how NP size and DNA stiffness affect the structure, stability, and crystallite shape of NP superlattices with diamond symmetry. We use the Wulff construction method to predict the equilibrium crystallite shape of the cubic diamond lattice. We find that, due to reorientation of surface particles, it is possible to create bonds at the surface with dangling DNA links on the interior, thereby reducing surface energy. Consequently, the crystallite shape depends on the degree to which such surface reorientation is possible, which is sensitive to DNA stiffness. Further, we determine dependence of the lattice stability on NP size and DNA stiffness by evaluating relative Gibbs free energy. We find that the free energy is dominated by the entropic component. Increasing NP size or DNA stiffness increases free energy, and thus decreases the relative stability of lattices. On the other hand, increasing DNA stiffness results in a more precisely defined lattice structure. Thus, there is a trade off between structure and stability of the lattice. Our findings should assist experimental design for controlling lattice stability and crystallite shape.
Kennedy, Kiley E; Shafique, Neha; Douglas, Jack F; Starr, Francis W
Cooperative dynamics in a model DPPC membrane arise from membrane layer interactions Journal Article
In: Emergent Materials, vol. 2, no. 1, pp. 1-10, 2019.
Abstract | BibTeX | Tags: Biophysics, Dynamic Heterogeneity, Membranes | Links:
@article{ksds19,
title = {Cooperative dynamics in a model DPPC membrane arise from membrane layer interactions},
author = {Kiley E Kennedy and Neha Shafique and Jack F Douglas and Francis W Starr},
url = {http://fstarr.web.wesleyan.edu/publications/ksds19.pdf},
doi = {10.1007/s42247-018-0020-2},
year = {2019},
date = {2019-03-01},
journal = {Emergent Materials},
volume = {2},
number = {1},
pages = {1-10},
abstract = {The dynamics of model membranes can be highly heterogeneous, especially in more ordered dense phases. To better understand the origins of this heterogeneity, as well as the degree to which monolayer systems mimic the dynamical properties of bilayer membranes, we use molecular simulations to contrast the dynamical behavior of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid monolayer with that of a DPPC bilayer. DPPC is prevalent in both biological monolayers and bilayers, and we utilize the widely studied MARTINI model to describe the molecular interactions. As expected, our simulations confirm that the lateral structure of the monolayer and bilayer is nearly indistinguishable in both low- and high-density phases. Dynamically, the monolayer and bilayer both exhibit a drop in mobility for dense phases, but we find that there are substantial differences in the amplitude of these changes, as well as the nature of molecular displacements for these systems. Specifically, the monolayer exhibits no apparent cooperativity of the dynamics, while the bilayer shows substantial spatial and temporal heterogeneity in the dynamics. Consequently, the dynamical heterogeneity and cooperativity observed in the bilayer membrane case arises in part due to interlayer interactions. We indeed find a substantial interdigitation of the membrane leaflets which appears to impede molecular rearrangement. On the other hand, the monolayer, like the bilayer, does exhibit complex non-Brownian molecular displacements at intermediate time scales. For the monolayer system, the single particle motion can be well characterized by fractional Brownian motion, rather than being a consequence of strong correlations in the molecular motion previously observed in bilayer membranes. The significant differences in the dynamics of dense monolayers and bilayers suggest that care must be taken when making inferences about membrane dynamics on the basis of monolayer studies.},
keywords = {Biophysics, Dynamic Heterogeneity, Membranes},
pubstate = {published},
tppubtype = {article}
}
The dynamics of model membranes can be highly heterogeneous, especially in more ordered dense phases. To better understand the origins of this heterogeneity, as well as the degree to which monolayer systems mimic the dynamical properties of bilayer membranes, we use molecular simulations to contrast the dynamical behavior of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid monolayer with that of a DPPC bilayer. DPPC is prevalent in both biological monolayers and bilayers, and we utilize the widely studied MARTINI model to describe the molecular interactions. As expected, our simulations confirm that the lateral structure of the monolayer and bilayer is nearly indistinguishable in both low- and high-density phases. Dynamically, the monolayer and bilayer both exhibit a drop in mobility for dense phases, but we find that there are substantial differences in the amplitude of these changes, as well as the nature of molecular displacements for these systems. Specifically, the monolayer exhibits no apparent cooperativity of the dynamics, while the bilayer shows substantial spatial and temporal heterogeneity in the dynamics. Consequently, the dynamical heterogeneity and cooperativity observed in the bilayer membrane case arises in part due to interlayer interactions. We indeed find a substantial interdigitation of the membrane leaflets which appears to impede molecular rearrangement. On the other hand, the monolayer, like the bilayer, does exhibit complex non-Brownian molecular displacements at intermediate time scales. For the monolayer system, the single particle motion can be well characterized by fractional Brownian motion, rather than being a consequence of strong correlations in the molecular motion previously observed in bilayer membranes. The significant differences in the dynamics of dense monolayers and bilayers suggest that care must be taken when making inferences about membrane dynamics on the basis of monolayer studies.
Zhang, Wengang; Douglas, Jack F; Starr, Francis W
What does the instantaneous normal mode spectrum tell us about dynamical heterogeneity in glass-forming fluids? Journal Article
In: The Journal of Chemical Physics, vol. 151, no. 18, pp. 184904, 2019.
BibTeX | Tags: | Links:
@article{zsd19b,
title = {What does the instantaneous normal mode spectrum tell us about dynamical heterogeneity in glass-forming fluids?},
author = {Wengang Zhang and Jack F Douglas and Francis W Starr},
url = {http://fstarr.web.wesleyan.edu/publications/zds19.pdf},
doi = {10.1063/1.5127821},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Chemical Physics},
volume = {151},
number = {18},
pages = {184904},
keywords = {},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Emamy, Hamed; Betancourt, Beatriz A Pazmiño; Vargas-Lara, Fernando; Starr, Francis W; Douglas, Jack F
The interfacial zone in thin polymer films and around nanoparticles in polymer nanocomposites Journal Article
In: The Journal of Chemical Physics, vol. 151, no. 12, pp. 124705, 2019.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Nanocomposites, Nanotechnology | Links:
@article{zepvsd19,
title = {The interfacial zone in thin polymer films and around nanoparticles in polymer nanocomposites},
author = {Wengang Zhang and Hamed Emamy and Beatriz A Pazmiño Betancourt and Fernando Vargas-Lara and Francis W Starr and Jack F Douglas},
url = {http://fstarr.web.wesleyan.edu/publications/zepvsd19.pdf},
doi = {10.1063/1.5119269},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Chemical Physics},
volume = {151},
number = {12},
pages = {124705},
keywords = {Dynamic Heterogeneity, Glass Formation, Nanocomposites, Nanotechnology},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Starr, Francis W; Douglas, Jack F
Collective Motion in the Interfacial and Interior Regions of Supported Polymer Films and Its Relation to Relaxation Journal Article
In: The Journal of Physical Chemistry B, vol. 123, no. 27, pp. 5935-5941, 2019, (PMID: 31192601).
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers | Links:
@article{zsd19,
title = {Collective Motion in the Interfacial and Interior Regions of Supported Polymer Films and Its Relation to Relaxation},
author = {Wengang Zhang and Francis W Starr and Jack F Douglas},
url = {http://fstarr.web.wesleyan.edu/publications/zsd19.pdf},
doi = {10.1021/acs.jpcb.9b04155},
year = {2019},
date = {2019-01-01},
journal = {The Journal of Physical Chemistry B},
volume = {123},
number = {27},
pages = {5935-5941},
note = {PMID: 31192601},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
2018
Emamy, Hamed; Kumar, Sanat K; Starr, Francis W
Diminishing Interfacial Effects with Decreasing Nanoparticle Size in Polymer-Nanoparticle Composites Journal Article
In: Phys. Rev. Lett., vol. 121, pp. 207801, 2018.
BibTeX | Tags: Glass Formation, Nanocomposites, Polymers | Links:
@article{eks18,
title = {Diminishing Interfacial Effects with Decreasing Nanoparticle Size in Polymer-Nanoparticle Composites},
author = {Hamed Emamy and Sanat K Kumar and Francis W Starr},
url = {http://fstarr.web.wesleyan.edu/publications/eks18.pdf},
doi = {10.1103/PhysRevLett.121.207801},
year = {2018},
date = {2018-11-01},
journal = {Phys. Rev. Lett.},
volume = {121},
pages = {207801},
publisher = {American Physical Society},
keywords = {Glass Formation, Nanocomposites, Polymers},
pubstate = {published},
tppubtype = {article}
}
Zhang, Wengang; Douglas, Jack F.; Starr, Francis W.
Why we need to look beyond the glass transition temperature to characterize the dynamics of thin supported polymer films Journal Article
In: Proceedings of the National Academy of Sciences, 2018, ISSN: 0027-8424.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Thin Films | Links:
@article{zds18,
title = {Why we need to look beyond the glass transition temperature to characterize the dynamics of thin supported polymer films},
author = { Wengang Zhang and Jack F. Douglas and Francis W. Starr},
url = {http://fstarr.web.wesleyan.edu/publications/zds18.pdf},
doi = {10.1073/pnas.1722024115},
issn = {0027-8424},
year = {2018},
date = {2018-05-14},
journal = {Proceedings of the National Academy of Sciences},
publisher = {National Academy of Sciences},
abstract = {The disparate results for Tg shifts of polymer thin films raise the question of whether Tg provides a good metric to characterize changes in the overall dynamics of these films. Our work demonstrates how different techniques to measure Tg are influenced by the relaxation gradient across the film. We find that different measurement methods can provide contradictory Tg estimates, depending on their sensitivity to dynamics near the substrate, providing a possible explanation for prior contradictory results. We take advantage of these differences by combining Tg estimates to predict Tg near the substrate. Our findings should be useful for polymer thin film applications, including microelectronic devices, lithium battery technology, and the development of biomedical devices.There is significant variation in the reported magnitude and even the sign of Tg shifts in thin polymer films with nominally the same chemistry, film thickness, and supporting substrate. The implicit assumption is that methods used to estimate Tg in bulk materials are relevant for inferring dynamic changes in thin films. To test the validity of this assumption, we perform molecular simulations of a coarse-grained polymer melt supported on an attractive substrate. As observed in many experiments, we find that Tg based on thermodynamic criteria (temperature dependence of film height or enthalpy) decreases with decreasing film thickness, regardless of the polymer–substrate interaction strength ε. In contrast, we find that Tg based on a dynamic criterion (relaxation of the dynamic structure factor) also decreases with decreasing thickness when ε is relatively weak, but Tg increases when ε exceeds the polymer–polymer interaction strength. We show that these qualitatively different trends in Tg reflect differing sensitivities to the mobility gradient across the film. Apparently, the slowly relaxing polymer segments in the substrate region make the largest contribution to the shift of Tg in the dynamic measurement, but this part of the film contributes less to the thermodynamic estimate of Tg. Our results emphasize the limitations of using Tg to infer changes in the dynamics of polymer thin films. However, we show that the thermodynamic and dynamic estimates of Tg can be combined to predict local changes in Tg near the substrate, providing a simple method to infer information about the mobility gradient.},
keywords = {Dynamic Heterogeneity, Glass Formation, Thin Films},
pubstate = {published},
tppubtype = {article}
}
The disparate results for Tg shifts of polymer thin films raise the question of whether Tg provides a good metric to characterize changes in the overall dynamics of these films. Our work demonstrates how different techniques to measure Tg are influenced by the relaxation gradient across the film. We find that different measurement methods can provide contradictory Tg estimates, depending on their sensitivity to dynamics near the substrate, providing a possible explanation for prior contradictory results. We take advantage of these differences by combining Tg estimates to predict Tg near the substrate. Our findings should be useful for polymer thin film applications, including microelectronic devices, lithium battery technology, and the development of biomedical devices.There is significant variation in the reported magnitude and even the sign of Tg shifts in thin polymer films with nominally the same chemistry, film thickness, and supporting substrate. The implicit assumption is that methods used to estimate Tg in bulk materials are relevant for inferring dynamic changes in thin films. To test the validity of this assumption, we perform molecular simulations of a coarse-grained polymer melt supported on an attractive substrate. As observed in many experiments, we find that Tg based on thermodynamic criteria (temperature dependence of film height or enthalpy) decreases with decreasing film thickness, regardless of the polymer–substrate interaction strength ε. In contrast, we find that Tg based on a dynamic criterion (relaxation of the dynamic structure factor) also decreases with decreasing thickness when ε is relatively weak, but Tg increases when ε exceeds the polymer–polymer interaction strength. We show that these qualitatively different trends in Tg reflect differing sensitivities to the mobility gradient across the film. Apparently, the slowly relaxing polymer segments in the substrate region make the largest contribution to the shift of Tg in the dynamic measurement, but this part of the film contributes less to the thermodynamic estimate of Tg. Our results emphasize the limitations of using Tg to infer changes in the dynamics of polymer thin films. However, we show that the thermodynamic and dynamic estimates of Tg can be combined to predict local changes in Tg near the substrate, providing a simple method to infer information about the mobility gradient.
Audus, Debra J.; Starr, Francis W.; Douglas, Jack F.
Valence, loop formation and universality in self-assembling patchy particles Journal Article
In: Soft Matter, vol. 14, pp. 1622-1630, 2018.
Abstract | BibTeX | Tags: Self Assembly | Links:
@article{asd18,
title = {Valence, loop formation and universality in self-assembling patchy particles},
author = {Audus, Debra J. and Starr, Francis W. and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/asd18.pdf},
doi = {10.1039/C7SM02419C},
year = {2018},
date = {2018-01-31},
journal = {Soft Matter},
volume = {14},
pages = {1622-1630},
abstract = {Patchy particles have emerged as an attractive model for phase separation and self-assembly in globular proteins solutions, colloidal patchy particles, and molecular fluids where directional interactions are operative. In our previous work, we extensively explored the coupling of directional and isotropic interactions on both the phase separation and self-assembly in a system of patchy particles with five spots. Here, we extend this work to consider different patch valences and isotropic interaction strengths with an emphasis on self-assembly. Although the location of self-assembly transition lines in the temperature-density plane depend on a number of parameters, we find universal behavior of cluster size that is dependent only on the probability of a spot being bound, the patch valence, and the density. Using these principles, we quantify both the mass distribution and the shape for all clusters, as well as clusters containing loops. Following the logical implications of these results, combined with a simplified version of a mean-field theory that incorporates Flory-Stockmayer theory, we find a universal curve for the temperature dependence of cluster mass and a universal curve for the fraction of clusters that contain loops. As the curves are dependent on the patchy valence, such results provide a method for parameterizing patchy particles models using experimental data.},
keywords = {Self Assembly},
pubstate = {published},
tppubtype = {article}
}
Patchy particles have emerged as an attractive model for phase separation and self-assembly in globular proteins solutions, colloidal patchy particles, and molecular fluids where directional interactions are operative. In our previous work, we extensively explored the coupling of directional and isotropic interactions on both the phase separation and self-assembly in a system of patchy particles with five spots. Here, we extend this work to consider different patch valences and isotropic interaction strengths with an emphasis on self-assembly. Although the location of self-assembly transition lines in the temperature-density plane depend on a number of parameters, we find universal behavior of cluster size that is dependent only on the probability of a spot being bound, the patch valence, and the density. Using these principles, we quantify both the mass distribution and the shape for all clusters, as well as clusters containing loops. Following the logical implications of these results, combined with a simplified version of a mean-field theory that incorporates Flory-Stockmayer theory, we find a universal curve for the temperature dependence of cluster mass and a universal curve for the fraction of clusters that contain loops. As the curves are dependent on the patchy valence, such results provide a method for parameterizing patchy particles models using experimental data.
Betancourt, Beatriz A. Pazmino; Starr, Francis W.; Douglas, Jack F.
String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt Journal Article
In: The Journal of Chemical Physics, vol. 148, no. 10, pp. 104508, 2018.
BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers | Links:
@article{psd18,
title = {String-like collective motion in the α- and β-relaxation of a coarse-grained polymer melt},
author = {Beatriz A. Pazmino Betancourt and Francis W. Starr and Jack F. Douglas},
url = {http://fstarr.web.wesleyan.edu/publications/psd18.pdf},
doi = {10.1063/1.5009442},
year = {2018},
date = {2018-01-01},
journal = {The Journal of Chemical Physics},
volume = {148},
number = {10},
pages = {104508},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
2017
Vargas-Lara, Fernando; Starr, Francis W.; Douglas, Jack F.
Molecular rigidity and enthalpy-entropy compensation in DNA melting Journal Article
In: Soft Matter, vol. 13, pp. 8309-8330, 2017.
Abstract | BibTeX | Tags: Biophysics, DNA | Links:
@article{vsd17,
title = {Molecular rigidity and enthalpy-entropy compensation in DNA melting},
author = {Vargas-Lara, Fernando and Starr, Francis W. and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/vsd17.pdf},
doi = {10.1039/C7SM01220A},
year = {2017},
date = {2017-10-23},
journal = {Soft Matter},
volume = {13},
pages = {8309-8330},
publisher = {The Royal Society of Chemistry},
abstract = {Enthalpy-entropy compensation (EEC) is observed in diverse molecular binding processes of importance to living systems and manufacturing applications, but this widely occurring phenomenon is not sufficiently understood from a molecular physics standpoint. To gain insight into this fundamental problem, we focus on the melting of double-stranded DNA (dsDNA) since measurements exhibiting EEC are extensive for nucleic acid complexes and existing coarse-grained models of DNA allow us to explore the influence of changes in molecular parameters on the energetic parameters by using molecular dynamics simulations. Previous experimental and computational studies have indicated a correlation between EEC and changes in molecular rigidity in certain binding-unbinding processes, and, correspondingly, we estimate measures of DNA molecular rigidity under a wide range of conditions, along with resultant changes in the enthalpy and entropy of binding. In particular, we consider variations in dsDNA rigidity that arise from changes of intrinsic molecular rigidity such as varying the associative interaction strength between the DNA bases, the length of the DNA chains, and the bending stiffness of the individual DNA chains. We also consider extrinsic changes of molecular rigidity arising from the addition of polymer additives and geometrical confinement of DNA between parallel plates. All our computations confirm EEC and indicate that this phenomenon is indeed highly correlated with changes in molecular rigidity. However, two distinct patterns relating to how DNA rigidity influences the entropy of association emerge from our analysis. Increasing the intrinsic DNA rigidity increases the entropy of binding, but increases in molecular rigidity from external constraints decreases the entropy of binding. EEC arises in numerous synthetic and biological binding processes and we suggest that changes in molecular rigidity might provide a common origin of this ubiquitous phenomenon in the mutual binding and unbinding of complex molecules.},
keywords = {Biophysics, DNA},
pubstate = {published},
tppubtype = {article}
}
Enthalpy-entropy compensation (EEC) is observed in diverse molecular binding processes of importance to living systems and manufacturing applications, but this widely occurring phenomenon is not sufficiently understood from a molecular physics standpoint. To gain insight into this fundamental problem, we focus on the melting of double-stranded DNA (dsDNA) since measurements exhibiting EEC are extensive for nucleic acid complexes and existing coarse-grained models of DNA allow us to explore the influence of changes in molecular parameters on the energetic parameters by using molecular dynamics simulations. Previous experimental and computational studies have indicated a correlation between EEC and changes in molecular rigidity in certain binding-unbinding processes, and, correspondingly, we estimate measures of DNA molecular rigidity under a wide range of conditions, along with resultant changes in the enthalpy and entropy of binding. In particular, we consider variations in dsDNA rigidity that arise from changes of intrinsic molecular rigidity such as varying the associative interaction strength between the DNA bases, the length of the DNA chains, and the bending stiffness of the individual DNA chains. We also consider extrinsic changes of molecular rigidity arising from the addition of polymer additives and geometrical confinement of DNA between parallel plates. All our computations confirm EEC and indicate that this phenomenon is indeed highly correlated with changes in molecular rigidity. However, two distinct patterns relating to how DNA rigidity influences the entropy of association emerge from our analysis. Increasing the intrinsic DNA rigidity increases the entropy of binding, but increases in molecular rigidity from external constraints decreases the entropy of binding. EEC arises in numerous synthetic and biological binding processes and we suggest that changes in molecular rigidity might provide a common origin of this ubiquitous phenomenon in the mutual binding and unbinding of complex molecules.
Zhang, Wengang; Douglas, Jack F.; Starr, Francis W.
Effects of a “bound” substrate layer on the dynamics of supported polymer films Journal Article
In: The Journal of Chemical Physics, vol. 147, pp. 044901, 2017.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films | Links:
@article{zds17-2,
title = {Effects of a “bound” substrate layer on the dynamics of supported polymer films},
author = {Wengang Zhang and Jack F. Douglas and Francis W. Starr},
url = {http://fstarr.web.wesleyan.edu/publications/zds17-2.pdf},
doi = {10.1063/1.4994064},
year = {2017},
date = {2017-07-25},
journal = {The Journal of Chemical Physics},
volume = {147},
pages = {044901},
abstract = {It is widely appreciated that an attractive polymer-substrate interaction can slow relaxation in thin supported polymer films and polymer nanocomposites. Recent measurements and simulations on nancomposites have indicated that this slowing of polymer dynamics occurs more strongly near a highly attractive particle surface where a “bound” layer having a much lower mobility can form, strongly influencing the thermodynamics and dynamics of the film. Here we use molecular simulations to show that a bound interfacial layer having a very similar nature arises in thin supported polymer films when the polymer-polymer attraction is stronger than the polymer-polymer interaction strength. This bound polymer layer effectively insulates the remainder of the film from the strong interfacial interactions, and the resulting thermodynamically determined Tg is relatively insensitive to the polymer-substrate interaction strength when it exceeds that of the polymer-polymer interactions. The presence of this layer gives rise to an additional relaxation process in the self-intermediate scattering function that is not observed in the bulk material and leads to a slowing down of the average relaxation time of the film as a whole. On the other hand, the average relaxation time of the film outside the bound layer does not grow in proportion to the strength of the substrate attraction due to the weak coupling of the substrate relaxation to the relaxation in the interior of the film. At large substrate attraction, the bound layer effectively “cloaks” the substrate, reducing the effect of the polymer-surface interaction on Tg.},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films},
pubstate = {published},
tppubtype = {article}
}
It is widely appreciated that an attractive polymer-substrate interaction can slow relaxation in thin supported polymer films and polymer nanocomposites. Recent measurements and simulations on nancomposites have indicated that this slowing of polymer dynamics occurs more strongly near a highly attractive particle surface where a “bound” layer having a much lower mobility can form, strongly influencing the thermodynamics and dynamics of the film. Here we use molecular simulations to show that a bound interfacial layer having a very similar nature arises in thin supported polymer films when the polymer-polymer attraction is stronger than the polymer-polymer interaction strength. This bound polymer layer effectively insulates the remainder of the film from the strong interfacial interactions, and the resulting thermodynamically determined Tg is relatively insensitive to the polymer-substrate interaction strength when it exceeds that of the polymer-polymer interactions. The presence of this layer gives rise to an additional relaxation process in the self-intermediate scattering function that is not observed in the bulk material and leads to a slowing down of the average relaxation time of the film as a whole. On the other hand, the average relaxation time of the film outside the bound layer does not grow in proportion to the strength of the substrate attraction due to the weak coupling of the substrate relaxation to the relaxation in the interior of the film. At large substrate attraction, the bound layer effectively “cloaks” the substrate, reducing the effect of the polymer-surface interaction on Tg.
Giovambattista, Nicolas; Starr, Francis W.; Poole, Peter H.
Influence of sample preparation on the transformation of low-density to high-density amorphous ice: An explanation based on the potential energy landscape Journal Article
In: The Journal of Chemical Physics, vol. 147, no. 4, pp. 044501, 2017.
Abstract | BibTeX | Tags: Glass Formation, Polyamorphism, Water | Links:
@article{gsp17,
title = {Influence of sample preparation on the transformation of low-density to high-density amorphous ice: An explanation based on the potential energy landscape},
author = {Nicolas Giovambattista and Francis W. Starr and Peter H. Poole},
url = {http://fstarr.web.wesleyan.edu/publications/gsp17.pdf},
doi = {10.1063/1.499356},
year = {2017},
date = {2017-07-25},
journal = {The Journal of Chemical Physics},
volume = {147},
number = {4},
pages = {044501},
abstract = {Experiments and computer simulations of the transformations of amorphous ices display different behaviors depending on sample preparation methods and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to-HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from knowledge of the PEL of the system.},
keywords = {Glass Formation, Polyamorphism, Water},
pubstate = {published},
tppubtype = {article}
}
Experiments and computer simulations of the transformations of amorphous ices display different behaviors depending on sample preparation methods and on the rates of change of temperature and pressure to which samples are subjected. In addition to these factors, simulation results also depend strongly on the chosen water model. Using computer simulations of the ST2 water model, we study how the sharpness of the compression-induced transition from low-density amorphous ice (LDA) to high-density amorphous ice (HDA) is influenced by the preparation of LDA. By studying LDA samples prepared using widely different procedures, we find that the sharpness of the LDA-to-HDA transformation is correlated with the depth of the initial LDA sample in the potential energy landscape (PEL), as characterized by the inherent structure energy. Our results show that the complex phenomenology of the amorphous ices reported in experiments and computer simulations can be understood and predicted in a unified way from knowledge of the PEL of the system.
Zhang, Wengang; Douglas, Jack F.; Starr, Francis W.
Dynamical heterogeneity in a vapor-deposited polymer glass Journal Article
In: The Journal of Chemical Physics, vol. 146, no. 20, pp. 203310, 2017.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers | Links:
@article{zds17,
title = {Dynamical heterogeneity in a vapor-deposited polymer glass},
author = {Wengang Zhang and Jack F. Douglas and Francis W. Starr},
url = {http://fstarr.web.wesleyan.edu/publications/zds17.pdf},
doi = {10.1063/1.4976542},
year = {2017},
date = {2017-01-01},
journal = {The Journal of Chemical Physics},
volume = {146},
number = {20},
pages = {203310},
abstract = {Recently, there has been great interest in ?ultrastable? glasses formed via vapor deposition, both because of emerging engineering applications of these materials (e.g., active layers in light-emitting diodes and photovoltaics) and, theoretically, as materials for probing the equilibrium properties of glassy materials below their glass transition, based on the conjecture that these materials are equivalent to glassy materials aged over astronomical time scales. We use molecular dynamics simulations to examine the properties of ultrastable vapor-deposited and ordinary polymer glasses. Based on the difference in the energy of the deposited and ordinary films, we estimate the effective cooling rate for the vapor deposited films to be 1 to 3 orders of magnitude larger than that of the ordinary film, depending on the deposition temperature. Similarly, we find an increase in the average segmental relaxation time of the vapor-deposited film compared to the ordinary glass. On the other hand, the normal mode spectrum is essentially identical for the vapor-deposited and the ordinary glass film, suggesting that the high-frequency dynamics should be similar. In short, the segmental relaxation dynamics of the polymer vapor-deposited glass are consistent with those of an ordinary polymer glass with a somewhat slower effective cooling rate. Of course, one would expect a larger effect on dynamics approaching the experimental glass transition, where the cooling rates are much slower than accessible in simulation. To more precisely probe the relationship between the dynamics of these glasses, we examine dynamical heterogeneity within the film. Due to the substantial mobility gradient in the glassy films, we find that it is crucial to distinguish the dynamics of the middle part of the film from those of the entire film. Considering the film as a whole, the average dynamical heterogeneity is dominated by the mobility gradient, and as a consequence the heterogeneity is nearly indistinguishable between the ordinary and vapor deposited glass films. In contrast, in the middle part of the film, where there is almost no mobility gradient, we find the dynamical heterogeneity within the deposited film is somewhat larger than that of the ordinary film at the same temperature. We further show that the scale of the interfacial region grows on cooling in the equilibrium film, but this trend reverses in the glass state. We attribute this reversal in part to a shrinking ratio of the relaxation time in the middle of the film to that of the interfacial layer in the non-equilibrium state. The dynamics in this mobile interfacial layer for the ordinary and deposited film are nearly the same, suggesting that the interfacial region is always in a near-equilibrium state. These results emphasize the importance of distinguishing between interfacial and internal relaxation processes in this emerging class of materials.},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
Recently, there has been great interest in ?ultrastable? glasses formed via vapor deposition, both because of emerging engineering applications of these materials (e.g., active layers in light-emitting diodes and photovoltaics) and, theoretically, as materials for probing the equilibrium properties of glassy materials below their glass transition, based on the conjecture that these materials are equivalent to glassy materials aged over astronomical time scales. We use molecular dynamics simulations to examine the properties of ultrastable vapor-deposited and ordinary polymer glasses. Based on the difference in the energy of the deposited and ordinary films, we estimate the effective cooling rate for the vapor deposited films to be 1 to 3 orders of magnitude larger than that of the ordinary film, depending on the deposition temperature. Similarly, we find an increase in the average segmental relaxation time of the vapor-deposited film compared to the ordinary glass. On the other hand, the normal mode spectrum is essentially identical for the vapor-deposited and the ordinary glass film, suggesting that the high-frequency dynamics should be similar. In short, the segmental relaxation dynamics of the polymer vapor-deposited glass are consistent with those of an ordinary polymer glass with a somewhat slower effective cooling rate. Of course, one would expect a larger effect on dynamics approaching the experimental glass transition, where the cooling rates are much slower than accessible in simulation. To more precisely probe the relationship between the dynamics of these glasses, we examine dynamical heterogeneity within the film. Due to the substantial mobility gradient in the glassy films, we find that it is crucial to distinguish the dynamics of the middle part of the film from those of the entire film. Considering the film as a whole, the average dynamical heterogeneity is dominated by the mobility gradient, and as a consequence the heterogeneity is nearly indistinguishable between the ordinary and vapor deposited glass films. In contrast, in the middle part of the film, where there is almost no mobility gradient, we find the dynamical heterogeneity within the deposited film is somewhat larger than that of the ordinary film at the same temperature. We further show that the scale of the interfacial region grows on cooling in the equilibrium film, but this trend reverses in the glass state. We attribute this reversal in part to a shrinking ratio of the relaxation time in the middle of the film to that of the interfacial layer in the non-equilibrium state. The dynamics in this mobile interfacial layer for the ordinary and deposited film are nearly the same, suggesting that the interfacial region is always in a near-equilibrium state. These results emphasize the importance of distinguishing between interfacial and internal relaxation processes in this emerging class of materials.
Rivera, Jose L.; Villanueva-Mejia, Francisco; Navarro-Santos, Pedro; Starr, Francis W.
Desalination by dragging water using a low-energy nano-mechanical device of porous graphene Journal Article
In: RSC Adv., vol. 7, pp. 53729-53739, 2017.
Abstract | BibTeX | Tags: Nanotechnology, Thin Films, Water | Links:
@article{rvns17,
title = {Desalination by dragging water using a low-energy nano-mechanical device of porous graphene},
author = { Jose L. Rivera and Francisco Villanueva-Mejia and Pedro Navarro-Santos and Francis W. Starr},
url = {http://fstarr.web.wesleyan.edu/publications/rvns17.pdf},
doi = {10.1039/C7RA09847B},
year = {2017},
date = {2017-01-01},
journal = {RSC Adv.},
volume = {7},
pages = {53729-53739},
publisher = {The Royal Society of Chemistry},
abstract = {We propose a nano-structured suction system based on graphene sheets for water desalination processes. The desalination system modeled in this work is an alternative process to the commonly employed but energy intensive reverse osmosis process. The nano-structured system generates drag forces, which pull water molecules from the saline solution into a chamber. Our molecular simulations consist of two rigid walls of graphene: one wall with 5 A pores permeable to water molecules forms the membrane, while the other wall acts as a plunger to induce and control the transfer of desalinated water molecules, which accumulate in a chamber between the two walls. Prior to the desalination process, the chamber is saturated with one monolayer of water molecules. The desalination occurs when the plunger moves to create unsaturated space inside the chamber. At plunger speeds up to 10 cm s-1, the system desalinates saltwater films in the open part of the membrane. At higher plunger speeds, the desalination chamber expands faster than molecules can fill the chamber, resulting in cavitation and poor desalination. At plunger speeds of 0.5 cm s-1, the desalination occurs via a quasi-equilibrium process, which minimizes the energy necessary to drive desalination. Our findings suggest that the desalination process requires less energy than reverse osmosis methods at plunger speeds up to 0.15 cm s-1 (for the chosen pore density). The filling profile of desalinated water molecules inside the chamber occurs via three distinct regimes: the first two regimes correspond to the formation of one and then two monolayers adsorbed to the chamber's walls. The third regime corresponds to the filling of molecules between the adsorbed layers, which approaches a density close to the density of bulk liquid water. Including flexibility in the graphene sheets does not affect the energy consumption for desalination processes occurring after the formation of the second monolayer, but flexible membranes require a slightly larger pore diameter (7 A) than rigid membranes.},
keywords = {Nanotechnology, Thin Films, Water},
pubstate = {published},
tppubtype = {article}
}
We propose a nano-structured suction system based on graphene sheets for water desalination processes. The desalination system modeled in this work is an alternative process to the commonly employed but energy intensive reverse osmosis process. The nano-structured system generates drag forces, which pull water molecules from the saline solution into a chamber. Our molecular simulations consist of two rigid walls of graphene: one wall with 5 A pores permeable to water molecules forms the membrane, while the other wall acts as a plunger to induce and control the transfer of desalinated water molecules, which accumulate in a chamber between the two walls. Prior to the desalination process, the chamber is saturated with one monolayer of water molecules. The desalination occurs when the plunger moves to create unsaturated space inside the chamber. At plunger speeds up to 10 cm s-1, the system desalinates saltwater films in the open part of the membrane. At higher plunger speeds, the desalination chamber expands faster than molecules can fill the chamber, resulting in cavitation and poor desalination. At plunger speeds of 0.5 cm s-1, the desalination occurs via a quasi-equilibrium process, which minimizes the energy necessary to drive desalination. Our findings suggest that the desalination process requires less energy than reverse osmosis methods at plunger speeds up to 0.15 cm s-1 (for the chosen pore density). The filling profile of desalinated water molecules inside the chamber occurs via three distinct regimes: the first two regimes correspond to the formation of one and then two monolayers adsorbed to the chamber's walls. The third regime corresponds to the filling of molecules between the adsorbed layers, which approaches a density close to the density of bulk liquid water. Including flexibility in the graphene sheets does not affect the energy consumption for desalination processes occurring after the formation of the second monolayer, but flexible membranes require a slightly larger pore diameter (7 A) than rigid membranes.
2016
Shafique, Neha; Kennedy, Kiley E.; Douglas, Jack F.; Starr, Francis W.
Quantifying the Heterogeneous Dynamics of a Simulated DPPC Membrane Journal Article
In: JOURNAL OF PHYSICAL CHEMISTRY B, vol. 120, no. 23, pp. 5172–5182, 2016, (PMID: 27223339).
Abstract | BibTeX | Tags: Biophysics, Dynamic Heterogeneity, Membranes | Links:
@article{skds16,
title = {Quantifying the Heterogeneous Dynamics of a Simulated DPPC Membrane},
author = {Neha Shafique and Kiley E. Kennedy and Jack F. Douglas and Francis W. Starr},
url = {http://fstarr.web.wesleyan.edu/publications/skds16-links.pdf},
doi = {10.1021/acs.jpcb.6b02982},
year = {2016},
date = {2016-05-25},
journal = {JOURNAL OF PHYSICAL CHEMISTRY B},
volume = {120},
number = {23},
pages = {5172–5182},
abstract = {Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1–2 μs) and length (1–10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions.},
note = {PMID: 27223339},
keywords = {Biophysics, Dynamic Heterogeneity, Membranes},
pubstate = {published},
tppubtype = {article}
}
Heterogeneity of dynamics plays a vital role in membrane function, but the methods for quantifying this heterogeneity are still being developed. Here we examine membrane dynamical heterogeneity via molecular simulations of a single-component dipalmitoylphosphatidylcholine (DPPC) lipid bilayer using the MARTINI force field. We draw upon well-established analysis methods developed in the study of glass-forming fluids and find significant changes in lipid dynamics between the fluid (Lα), and gel (Lβ) phases. In particular, we distinguish two mobility groups in the more ordered Lβ phase: (i) lipids that are transiently trapped by their neighbors and (ii) lipids with displacements on the scale of the intermolecular spacing. These distinct mobility groups spatially segregate, forming dynamic clusters that have characteristic time (1–2 μs) and length (1–10 nm) scales comparable to those of proteins and other biomolecules. We suggest that these dynamic clusters could couple to biomolecules within the membrane and thus may play a role in many membrane functions. In the equilibrium membrane, lipid molecules dynamically exchange between the mobility groups, and the resulting clusters are not associated with a thermodynamic phase separation. Dynamical clusters having similar characteristics arise in many other condensed phase materials, placing membranes in a broad class of materials with strong intermolecular interactions.
Wang, Wujie; Nocka, Laura M.; Wiemann, Brianne Z.; Hinckley, Daniel M.; Mukerji, Ishita; Starr, Francis W.
Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments Journal Article
In: SCIENTIFIC REPORTS, vol. 6, pp. 22863, 2016.
Abstract | BibTeX | Tags: Biophysics, DNA | Links:
@article{wnwhms16,
title = {Holliday Junction Thermodynamics and Structure: Coarse-Grained Simulations and Experiments},
author = {Wang, Wujie and Nocka, Laura M. and Wiemann, Brianne Z. and Hinckley, Daniel M. and Mukerji, Ishita and Starr, Francis W.},
url = {http://www.nature.com/articles/srep22863.pdf},
doi = {http://dx.doi.org/10.1038/srep22863},
year = {2016},
date = {2016-03-01},
journal = {SCIENTIFIC REPORTS},
volume = {6},
pages = {22863},
publisher = {The Authors},
abstract = {Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior. },
keywords = {Biophysics, DNA},
pubstate = {published},
tppubtype = {article}
}
Holliday junctions play a central role in genetic recombination, DNA repair and other cellular processes. We combine simulations and experiments to evaluate the ability of the 3SPN.2 model, a coarse-grained representation designed to mimic B-DNA, to predict the properties of DNA Holliday junctions. The model reproduces many experimentally determined aspects of junction structure and stability, including the temperature dependence of melting on salt concentration, the bias between open and stacked conformations, the relative populations of conformers at high salt concentration, and the inter-duplex angle (IDA) between arms. We also obtain a close correspondence between the junction structure evaluated by all-atom and coarse-grained simulations. We predict that, for salt concentrations at physiological and higher levels, the populations of the stacked conformers are independent of salt concentration, and directly observe proposed tetrahedral intermediate sub-states implicated in conformational transitions. Our findings demonstrate that the 3SPN.2 model captures junction properties that are inaccessible to all-atom studies, opening the possibility to simulate complex aspects of junction behavior.
Liu, Wenyan; Tagawa, Miho; Xin, Huolin L.; Wang, Tong; Emamy, Hamed; Li, Huilin; Yager, Kevin G.; Starr, Francis W.; Tkachenko, Alexei V.; Gang, Oleg
Diamond family of nanoparticle superlattices Journal Article
In: SCIENCE, vol. 351, no. 6273, pp. 582-586, 2016, ISSN: 0036-8075.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{science16,
title = {Diamond family of nanoparticle superlattices},
author = {Liu, Wenyan and Tagawa, Miho and Xin, Huolin L. and Wang, Tong and Emamy, Hamed and Li, Huilin and Yager, Kevin G. and Starr, Francis W. and Tkachenko, Alexei V. and Gang, Oleg},
url = {http://fstarr.web.wesleyan.edu/publications/science16.pdf},
doi = {10.1126/science.aad2080},
issn = {0036-8075},
year = {2016},
date = {2016-02-01},
journal = {SCIENCE},
volume = {351},
number = {6273},
pages = {582-586},
abstract = {Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
Diamond lattices formed by atomic or colloidal elements exhibit remarkable functional properties. However, building such structures via self-assembly has proven to be challenging because of the low packing fraction, sensitivity to bond orientation, and local heterogeneity. We report a strategy for creating a diamond superlattice of nano-objects via self-assembly and demonstrate its experimental realization by assembling two variant diamond lattices, one with and one without atomic analogs. Our approach relies on the association between anisotropic particles with well-defined tetravalent binding topology and isotropic particles. The constrained packing of triangular binding footprints of truncated tetrahedra on a sphere defines a unique three-dimensional lattice. Hence, the diamond self-assembly problem is solved via its mapping onto two-dimensional triangular packing on the surface of isotropic spherical particles.
Audus, Debra J.; Starr, Francis W.; Douglas, Jack F.
Coupling of isotropic and directional interactions and its effect on phase separation and self-assembly Journal Article
In: THE JOURNAL OF CHEMICAL PHYSICS, vol. 144, no. 7, pp. 074901, 2016.
Abstract | BibTeX | Tags: Biophysics, Self Assembly | Links:
@article{asd16,
title = {Coupling of isotropic and directional interactions and its effect on phase separation and self-assembly},
author = {Audus, Debra J. and Starr, Francis W. and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/asd16.pdf},
doi = {http://dx.doi.org/10.1063/1.4941454},
year = {2016},
date = {2016-01-01},
journal = {THE JOURNAL OF CHEMICAL PHYSICS},
volume = {144},
number = {7},
pages = {074901},
abstract = {The interactions of molecules and particles in solution often involve an interplay between isotropic and highly directional interactions that lead to a mutual coupling of phase separation and self-assembly. This situation arises, for example, in proteins interacting through hydrophobic and charged patch regions on their surface and in nanoparticles with grafted polymer chains, such as DNA. As a minimal model of complex fluids exhibiting this interaction coupling, we investigate spherical particles having an isotropic interaction and a constellation of five attractive patches on the particle’s surface. Monte Carlo simulations and mean-field calculations of the phase boundaries of this model depend strongly on the relative strength of the isotropic and patch potentials, where we surprisingly find that analytic mean-field predictions become increasingly accurate as the directional interactions become increasingly predominant. We quantitatively account for this effect by noting that the effective interaction range increases with increasing relative directional to isotropic interaction strength. We also identify thermodynamic transition lines associated with self-assembly, extract the entropy and energy of association, and characterize the resulting cluster properties obtained from simulations using percolation scaling theory and Flory-Stockmayer mean-field theory. We find that the fractal dimension and cluster size distribution are consistent with those of lattice animals, i.e., randomly branched polymers swollen by excluded volume interactions. We also identify a universal functional form for the average molecular weight and a nearly universal functional form for a scaling parameter characterizing the cluster size distribution. Since the formation of branched clusters at equilibrium is a common phenomenon in nature, we detail how our analysis can be used in experimental characterization of such associating fluids. },
keywords = {Biophysics, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
The interactions of molecules and particles in solution often involve an interplay between isotropic and highly directional interactions that lead to a mutual coupling of phase separation and self-assembly. This situation arises, for example, in proteins interacting through hydrophobic and charged patch regions on their surface and in nanoparticles with grafted polymer chains, such as DNA. As a minimal model of complex fluids exhibiting this interaction coupling, we investigate spherical particles having an isotropic interaction and a constellation of five attractive patches on the particle’s surface. Monte Carlo simulations and mean-field calculations of the phase boundaries of this model depend strongly on the relative strength of the isotropic and patch potentials, where we surprisingly find that analytic mean-field predictions become increasingly accurate as the directional interactions become increasingly predominant. We quantitatively account for this effect by noting that the effective interaction range increases with increasing relative directional to isotropic interaction strength. We also identify thermodynamic transition lines associated with self-assembly, extract the entropy and energy of association, and characterize the resulting cluster properties obtained from simulations using percolation scaling theory and Flory-Stockmayer mean-field theory. We find that the fractal dimension and cluster size distribution are consistent with those of lattice animals, i.e., randomly branched polymers swollen by excluded volume interactions. We also identify a universal functional form for the average molecular weight and a nearly universal functional form for a scaling parameter characterizing the cluster size distribution. Since the formation of branched clusters at equilibrium is a common phenomenon in nature, we detail how our analysis can be used in experimental characterization of such associating fluids.
Giovambattista, Nicolas; Sciortino, Francesco; Starr, Francis W.; Poole, Peter H.
Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice Journal Article
In: The Journal of Chemical Physics, vol. 145, no. 22, pp. 224501, 2016.
BibTeX | Tags: Glass Formation, Polyamorphism, Water | Links:
@article{gssp16,
title = {Potential energy landscape of the apparent first-order phase transition between low-density and high-density amorphous ice},
author = {Giovambattista, Nicolas and Sciortino, Francesco and Starr, Francis W. and Poole, Peter H.},
url = {http://fstarr.web.wesleyan.edu/publications/gssp16.pdf},
doi = {http://dx.doi.org/10.1063/1.4968047},
year = {2016},
date = {2016-01-01},
journal = {The Journal of Chemical Physics},
volume = {145},
number = {22},
pages = {224501},
keywords = {Glass Formation, Polyamorphism, Water},
pubstate = {published},
tppubtype = {article}
}
Starr, Francis W.; Douglas, Jack F.; Meng, Dong; Kumar, Sanat K.
Bound Layers "Cloak" Nanoparticles in Strongly Interacting Polymer Nanocomposites Journal Article
In: ACS Nano, vol. 10, pp. 10960 - 10965, 2016.
Abstract | BibTeX | Tags: Glass Formation, Nanocomposites, Polymers | Links:
@article{sdmk16,
title = {Bound Layers "Cloak" Nanoparticles in Strongly Interacting Polymer Nanocomposites},
author = {Starr, Francis W. and Douglas, Jack F. and Meng, Dong and Kumar, Sanat K. },
url = {http://fstarr.web.wesleyan.edu/publications/sdmk16.pdf},
doi = {10.1021/acsnano.6b05683},
year = {2016},
date = {2016-01-01},
journal = {ACS Nano},
volume = {10},
pages = {10960 - 10965},
abstract = {Polymer-nanoparticle (NP) interfacial interactions are expected to strongly influence the properties of nanocomposites, but surprisingly, experiments often report small or no changes in the glass transition temperature, Tg. To understand this paradoxical situation, we simulate nanocomposites over a broad range of polymer-NP interaction strengths ε. When ε is stronger than the polymer-polymer interaction, a distinct relaxation that is slower than the main α-relaxation emerges, arising from an adsorbed "bound" polymer layer near the NP surface. This bound layer "cloaks" the NPs, so that the dynamics of the matrix polymer are largely unaffected. Consequently, Tg defined from the temperature dependence of the routinely measured thermodynamics or the polymer matrix relaxation is nearly independent of ε, in accord with many experiments. Apparently, quasi-thermodynamic measurements do not reliably reflect dynamical changes in the bound layer, which alter the overall composite dynamics. These findings clarify the relation between quasi-thermodynamic Tg measurements and nanocomposite dynamics, and should also apply to thin polymer films.},
keywords = {Glass Formation, Nanocomposites, Polymers},
pubstate = {published},
tppubtype = {article}
}
Polymer-nanoparticle (NP) interfacial interactions are expected to strongly influence the properties of nanocomposites, but surprisingly, experiments often report small or no changes in the glass transition temperature, Tg. To understand this paradoxical situation, we simulate nanocomposites over a broad range of polymer-NP interaction strengths ε. When ε is stronger than the polymer-polymer interaction, a distinct relaxation that is slower than the main α-relaxation emerges, arising from an adsorbed "bound" polymer layer near the NP surface. This bound layer "cloaks" the NPs, so that the dynamics of the matrix polymer are largely unaffected. Consequently, Tg defined from the temperature dependence of the routinely measured thermodynamics or the polymer matrix relaxation is nearly independent of ε, in accord with many experiments. Apparently, quasi-thermodynamic measurements do not reliably reflect dynamical changes in the bound layer, which alter the overall composite dynamics. These findings clarify the relation between quasi-thermodynamic Tg measurements and nanocomposite dynamics, and should also apply to thin polymer films.
2015
Hanakata, Paul Z.; Pazmiño Betancourt, Beatriz A.; Douglas, Jack F.; Starr, Francis W.
A unifying framework to quantify the effects of substrate interactions, stiffness, and roughness on the dynamics of thin supported polymer films Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 142, no. 23, pp. 234907, 2015, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films | Links:
@article{hpds15,
title = {A unifying framework to quantify the effects of substrate interactions, stiffness, and roughness on the dynamics of thin supported polymer films},
author = {Hanakata, Paul Z. and Pazmiño Betancourt, Beatriz A. and Douglas, Jack F. and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/hpds15.pdf},
doi = {10.1063/1.4922481},
issn = {0021-9606},
year = {2015},
date = {2015-06-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {142},
number = {23},
pages = {234907},
abstract = {Changes in the dynamics of supported polymer films in comparison to bulk materials involve a complex convolution of effects, such as substrate interactions, roughness, and compliance, in addition to film thickness. We consider molecular dynamics simulations of substrate-supported, coarse-grained polymer films where these parameters are tuned separately to determine how each of these variables influence the molecular dynamics of thin polymer films. We find that all these variables significantly influence the film dynamics, leading to a seemingly intractable degree of complexity in describing these changes. However, by considering how these constraining variables influence string-like collective motion within the film, we show that all our observations can be understood in a unified and quantitative way. More specifically, the string model for glass-forming liquids implies that the changes in the structural relaxation of these films are governed by the changes in the average length of string-like cooperative motions and this model is confirmed under all conditions considered in our simulations. Ultimately, these changes are parameterized in terms of just the activation enthalpy and entropy for molecular organization, which have predictable dependences on substrate properties and film thickness, offering a promising approach for the rational design of film properties. (C) 2015 AIP Publishing LLC.},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films},
pubstate = {published},
tppubtype = {article}
}
Changes in the dynamics of supported polymer films in comparison to bulk materials involve a complex convolution of effects, such as substrate interactions, roughness, and compliance, in addition to film thickness. We consider molecular dynamics simulations of substrate-supported, coarse-grained polymer films where these parameters are tuned separately to determine how each of these variables influence the molecular dynamics of thin polymer films. We find that all these variables significantly influence the film dynamics, leading to a seemingly intractable degree of complexity in describing these changes. However, by considering how these constraining variables influence string-like collective motion within the film, we show that all our observations can be understood in a unified and quantitative way. More specifically, the string model for glass-forming liquids implies that the changes in the structural relaxation of these films are governed by the changes in the average length of string-like cooperative motions and this model is confirmed under all conditions considered in our simulations. Ultimately, these changes are parameterized in terms of just the activation enthalpy and entropy for molecular organization, which have predictable dependences on substrate properties and film thickness, offering a promising approach for the rational design of film properties. (C) 2015 AIP Publishing LLC.
Pazmiño Betancourt, Beatriz A.; Hanakata, Paul Z.; Starr, Francis W.; Douglas, Jack F.
Quantitative relations between cooperative motion, emergent elasticity, and free volume in model glass-forming polymer materials Journal Article
In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 112, no. 10, pp. 2966-2971, 2015, ISSN: 0027-8424.
Abstract | BibTeX | Tags: Glass Formation, Polymers | Links:
@article{phsd15,
title = {Quantitative relations between cooperative motion, emergent elasticity, and free volume in model glass-forming polymer materials},
author = {Pazmiño Betancourt, Beatriz A. and Hanakata, Paul Z. and Starr, Francis W. and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/phsd15.pdf},
doi = {10.1073/pnas.1418654112},
issn = {0027-8424},
year = {2015},
date = {2015-03-01},
journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
volume = {112},
number = {10},
pages = {2966-2971},
abstract = {The study of glass formation is largely framed by semiempirical models that emphasize the importance of progressively growing cooperative motion accompanying the drop in fluid configurational entropy, emergent elasticity, or the vanishing of accessible free volume available for molecular motion in cooled liquids. We investigate the extent to which these descriptions are related through computations on a model coarse-grained polymer melt, with and without nanoparticle additives, and for supported polymer films with smooth or rough surfaces, allowing for substantial variation of the glass transition temperature and the fragility of glass formation. We find quantitative relations between emergent elasticity, the average local volume accessible for particle motion, and the growth of collective motion in cooled liquids. Surprisingly, we find that each of these models of glass formation can equally well describe the relaxation data for all of the systems that we simulate. In this way, we uncover some unity in our understanding of glass-forming materials from perspectives formerly considered as distinct.},
keywords = {Glass Formation, Polymers},
pubstate = {published},
tppubtype = {article}
}
The study of glass formation is largely framed by semiempirical models that emphasize the importance of progressively growing cooperative motion accompanying the drop in fluid configurational entropy, emergent elasticity, or the vanishing of accessible free volume available for molecular motion in cooled liquids. We investigate the extent to which these descriptions are related through computations on a model coarse-grained polymer melt, with and without nanoparticle additives, and for supported polymer films with smooth or rough surfaces, allowing for substantial variation of the glass transition temperature and the fragility of glass formation. We find quantitative relations between emergent elasticity, the average local volume accessible for particle motion, and the growth of collective motion in cooled liquids. Surprisingly, we find that each of these models of glass formation can equally well describe the relaxation data for all of the systems that we simulate. In this way, we uncover some unity in our understanding of glass-forming materials from perspectives formerly considered as distinct.
Vargas-Lara, Fernando; Stavis, Samuel M.; Strychalski, Elizabeth A.; Nablo, Brian J.; Geist, Jon; Starr, Francis W.; Douglas, Jack F.
Dimensional reduction of duplex DNA under confinement to nanofluidic slits Journal Article
In: SOFT MATTER, vol. 11, no. 42, pp. 8273-8284, 2015, ISSN: 1744-683X.
Abstract | BibTeX | Tags: Biophysics, DNA | Links:
@article{vssngsd15,
title = {Dimensional reduction of duplex DNA under confinement to nanofluidic slits},
author = {Vargas-Lara, Fernando and Stavis, Samuel M. and Strychalski, Elizabeth A. and Nablo, Brian J. and Geist, Jon and Starr, Francis W. and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/vssngsd15.pdf},
doi = {10.1039/c5sm01580d},
issn = {1744-683X},
year = {2015},
date = {2015-01-01},
journal = {SOFT MATTER},
volume = {11},
number = {42},
pages = {8273-8284},
abstract = {There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.},
keywords = {Biophysics, DNA},
pubstate = {published},
tppubtype = {article}
}
There has been much interest in the dimensional properties of double-stranded DNA (dsDNA) confined to nanoscale environments as a problem of fundamental importance in both biological and technological fields. This has led to a series of measurements by fluorescence microscopy of single dsDNA molecules under confinement to nanofluidic slits. Despite the efforts expended on such experiments and the corresponding theory and simulations of confined polymers, a consistent description of changes of the radius of gyration of dsDNA under strong confinement has not yet emerged. Here, we perform molecular dynamics (MD) simulations to identify relevant factors that might account for this inconsistency. Our simulations indicate a significant amplification of excluded volume interactions under confinement at the nanoscale due to the reduction of the effective dimensionality of the system. Thus, any factor influencing the excluded volume interaction of dsDNA, such as ionic strength, solution chemistry, and even fluorescent labels, can greatly influence the dsDNA size under strong confinement. These factors, which are normally less important in bulk solutions of dsDNA at moderate ionic strengths because of the relative weakness of the excluded volume interaction, must therefore be under tight control to achieve reproducible measurements of dsDNA under conditions of dimensional reduction. By simulating semi-flexible polymers over a range of parameter values relevant to the experimental systems and exploiting past theoretical treatments of the dimensional variation of swelling exponents and prefactors, we have developed a novel predictive relationship for the in-plane radius of gyration of long semi-flexible polymers under slit-like confinement. Importantly, these analytic expressions allow us to estimate the properties of dsDNA for the experimentally and biologically relevant range of contour lengths that is not currently accessible by state-of-the-art MD simulations.
2014
Starr, Francis W.
PHYSICS OF WATER Crystal-clear transition Journal Article
In: NATURE PHYSICS, vol. 10, no. 9, pp. 628-629, 2014, ISSN: 1745-2473.
BibTeX | Tags: Polyamorphism, Water | Links:
@article{snv14,
title = {PHYSICS OF WATER Crystal-clear transition},
author = {Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/snv14.pdf},
doi = {10.1038/nphys3059},
issn = {1745-2473},
year = {2014},
date = {2014-09-01},
journal = {NATURE PHYSICS},
volume = {10},
number = {9},
pages = {628-629},
keywords = {Polyamorphism, Water},
pubstate = {published},
tppubtype = {article}
}
Hanakata, Paul Z.; Douglas, Jack F.; Starr, Francis W.
Interfacial mobility scale determines the scale of collective motion and relaxation rate in polymer films Journal Article
In: NATURE COMMUNICATIONS, vol. 5, pp. 4163, 2014, ISSN: 2041-1723.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films | Links:
@article{hds14,
title = {Interfacial mobility scale determines the scale of collective motion and relaxation rate in polymer films},
author = {Hanakata, Paul Z. and Douglas, Jack F. and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/hds14.pdf},
doi = {10.1038/ncomms5163},
issn = {2041-1723},
year = {2014},
date = {2014-06-01},
journal = {NATURE COMMUNICATIONS},
volume = {5},
pages = {4163},
abstract = {Thin polymer films are ubiquitous in manufacturing and medical applications, and there has been intense interest in how film thickness and substrate interactions influence film dynamics. It is appreciated that a polymer-air interfacial layer with enhanced mobility plays an important role in the observed changes and recent studies suggest that the length scale x of this interfacial layer is related to film relaxation. In the context of the Adam-Gibbs and random first-order transition models of glass formation, these results provide indirect evidence for a relation between xi and the scale of collective molecular motion. Here we report direct evidence for a proportionality between xi and the average length L of string-like particle displacements in simulations of polymer films supported on substrates with variable interaction strength and rigidity. This relation explicitly links xi to the theoretical scale of cooperatively rearranging regions, offering a promising route to experimentally determine this scale of cooperative motion.},
keywords = {Dynamic Heterogeneity, Glass Formation, Polymers, Thin Films},
pubstate = {published},
tppubtype = {article}
}
Thin polymer films are ubiquitous in manufacturing and medical applications, and there has been intense interest in how film thickness and substrate interactions influence film dynamics. It is appreciated that a polymer-air interfacial layer with enhanced mobility plays an important role in the observed changes and recent studies suggest that the length scale x of this interfacial layer is related to film relaxation. In the context of the Adam-Gibbs and random first-order transition models of glass formation, these results provide indirect evidence for a relation between xi and the scale of collective molecular motion. Here we report direct evidence for a proportionality between xi and the average length L of string-like particle displacements in simulations of polymer films supported on substrates with variable interaction strength and rigidity. This relation explicitly links xi to the theoretical scale of cooperatively rearranging regions, offering a promising route to experimentally determine this scale of cooperative motion.
Pazmiño Betancourt, Beatriz A.; Douglas, Jack F.; Starr, Francis W.
String model for the dynamics of glass-forming liquids Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 140, no. 20, pp. 204509, 2014, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Dynamic Heterogeneity, Glass Formation | Links:
@article{pds14,
title = {String model for the dynamics of glass-forming liquids},
author = {Pazmiño Betancourt, Beatriz A. and Douglas, Jack F. and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/pds14.pdf},
doi = {10.1063/1.4878502},
issn = {0021-9606},
year = {2014},
date = {2014-05-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {140},
number = {20},
pages = {204509},
abstract = {We test the applicability of a living polymerization theory to describe cooperative string-like particle rearrangement clusters (strings) observed in simulations of a coarse-grained polymer melt. The theory quantitatively describes the interrelation between the average string length L, configurational entropy S-conf, and the order parameter for string assembly Phi without free parameters. Combining this theory with the Adam-Gibbs model allows us to predict the relaxation time tau in a lower temperature T range than accessible by current simulations. In particular, the combined theories suggest a return to Arrhenius behavior near T-g and a low T residual entropy, thus avoiding a Kauzmann ``entropy crisis.'' (C) 2014 AIP Publishing LLC.},
keywords = {Dynamic Heterogeneity, Glass Formation},
pubstate = {published},
tppubtype = {article}
}
We test the applicability of a living polymerization theory to describe cooperative string-like particle rearrangement clusters (strings) observed in simulations of a coarse-grained polymer melt. The theory quantitatively describes the interrelation between the average string length L, configurational entropy S-conf, and the order parameter for string assembly Phi without free parameters. Combining this theory with the Adam-Gibbs model allows us to predict the relaxation time tau in a lower temperature T range than accessible by current simulations. In particular, the combined theories suggest a return to Arrhenius behavior near T-g and a low T residual entropy, thus avoiding a Kauzmann ``entropy crisis.'' (C) 2014 AIP Publishing LLC.
Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas
Heating-induced glass-glass and glass-liquid transformations in computer simulations of water Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 140, no. 11, pp. 114504, 2014, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Glass Formation, Polyamorphism, Water | Links:
@article{csg14,
title = {Heating-induced glass-glass and glass-liquid transformations in computer simulations of water},
author = {Chiu, Janet and Starr, Francis W. and Giovambattista, Nicolas},
url = {http://fstarr.web.wesleyan.edu/publications/csg14.pdf},
doi = {10.1063/1.4868028},
issn = {0021-9606},
year = {2014},
date = {2014-03-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {140},
number = {11},
pages = {114504},
abstract = {Water exists in at least two families of glassy states, broadly categorized as the low-density (LDA) and high-density amorphous ice (HDA). Remarkably, LDA and HDA can be reversibly interconverted via appropriate thermodynamic paths, such as isothermal compression and isobaric heating, exhibiting first-order-like phase transitions. We perform out-of-equilibrium molecular dynamics simulations of glassy water using the ST2 model to study the evolution of LDA and HDA upon isobaric heating. Depending on pressure, glass-to-glass, glass-to-crystal, glass-to-vapor, as well as glass-to-liquid transformations are found. Specifically, heating LDA results in the following transformations, with increasing heating pressures: (i) LDA-to-vapor (sublimation), (ii) LDA-to-liquid (glass transition), (iii) LDA-to-HDA-to-liquid, (iv) LDA-to-HDA-to-liquid-to-crystal, and (v) LDA-to- HDA-to-crystal. Similarly, heating HDA results in the following transformations, with decreasing heating pressures: (a) HDA-to-crystal, (b) HDA-to-liquid-to-crystal, (c) HDA-to-liquid (glass transition), (d) HDA-to-LDA-to-liquid, and (e) HDA-to-LDA-to-vapor. A more complex sequence may be possible using lower heating rates. For each of these transformations, we determine the corresponding transformation temperature as function of pressure, and provide a P-T ``phase diagram'' for glassy water based on isobaric heating. Our results for isobaric heating dovetail with the LDA-HDA transformations reported for ST2 glassy water based on isothermal compression/decompression processes [ Chiu et al., J. Chem. Phys. 139, 184504 (2013)]. The resulting phase diagram is consistent with the liquid-liquid phase transition hypothesis. At the same time, the glass phase diagram is sensitive to sample preparation, such as heating or compression rates. Interestingly, at least for the rates explored, our results suggest that the LDA-to-liquid (HDA-to-liquid) and LDA-to-HDA (HDA-to-LDA) transformation lines on heating are related, both being associated with the limit of kinetic stability of LDA (HDA). (C) 2014 AIP Publishing LLC.},
keywords = {Glass Formation, Polyamorphism, Water},
pubstate = {published},
tppubtype = {article}
}
Water exists in at least two families of glassy states, broadly categorized as the low-density (LDA) and high-density amorphous ice (HDA). Remarkably, LDA and HDA can be reversibly interconverted via appropriate thermodynamic paths, such as isothermal compression and isobaric heating, exhibiting first-order-like phase transitions. We perform out-of-equilibrium molecular dynamics simulations of glassy water using the ST2 model to study the evolution of LDA and HDA upon isobaric heating. Depending on pressure, glass-to-glass, glass-to-crystal, glass-to-vapor, as well as glass-to-liquid transformations are found. Specifically, heating LDA results in the following transformations, with increasing heating pressures: (i) LDA-to-vapor (sublimation), (ii) LDA-to-liquid (glass transition), (iii) LDA-to-HDA-to-liquid, (iv) LDA-to-HDA-to-liquid-to-crystal, and (v) LDA-to- HDA-to-crystal. Similarly, heating HDA results in the following transformations, with decreasing heating pressures: (a) HDA-to-crystal, (b) HDA-to-liquid-to-crystal, (c) HDA-to-liquid (glass transition), (d) HDA-to-LDA-to-liquid, and (e) HDA-to-LDA-to-vapor. A more complex sequence may be possible using lower heating rates. For each of these transformations, we determine the corresponding transformation temperature as function of pressure, and provide a P-T ``phase diagram'' for glassy water based on isobaric heating. Our results for isobaric heating dovetail with the LDA-HDA transformations reported for ST2 glassy water based on isothermal compression/decompression processes [ Chiu et al., J. Chem. Phys. 139, 184504 (2013)]. The resulting phase diagram is consistent with the liquid-liquid phase transition hypothesis. At the same time, the glass phase diagram is sensitive to sample preparation, such as heating or compression rates. Interestingly, at least for the rates explored, our results suggest that the LDA-to-liquid (HDA-to-liquid) and LDA-to-HDA (HDA-to-LDA) transformation lines on heating are related, both being associated with the limit of kinetic stability of LDA (HDA). (C) 2014 AIP Publishing LLC.
Starr, Francis W.; Sciortino, Francesco
``Crystal-clear'' liquid-liquid transition in a tetrahedral fluid Journal Article
In: SOFT MATTER, vol. 10, no. 47, pp. 9413-9422, 2014, ISSN: 1744-683X.
Abstract | BibTeX | Tags: DNA, Polyamorphism | Links:
@article{ss14,
title = {``Crystal-clear'' liquid-liquid transition in a tetrahedral fluid},
author = {Starr, Francis W. and Sciortino, Francesco},
url = {http://fstarr.web.wesleyan.edu/publications/ss14.pdf},
doi = {10.1039/c4sm01835d},
issn = {1744-683X},
year = {2014},
date = {2014-01-01},
journal = {SOFT MATTER},
volume = {10},
number = {47},
pages = {9413-9422},
abstract = {For a model known to exhibit liquid-liquid transitions, we examine how varying the bond orientational flexibility affects the stability of the liquid-liquid transition relative to that of the crystal phases. For very rigidly oriented bonds, the crystal is favored over all amorphous phase transitions. We find that increasing the bond flexibility decreases both the critical temperature T-c for liquid-liquid phase separation and the melting temperature T-m. The effect of increasing flexibility is much stronger for melting, so that the distance between T-c and T-m progressively reduces and inverts sign. Under these conditions, a ``naked'' liquid-liquid critical point bulges out in the liquid phase and becomes accessible, without the possibility of crystallization. These results confirm that a crystal-clear, liquid-liquid transition can occur as a genuine, thermodynamically stable phenomenon for tetrahedral coordinated particles with flexible bond orientation, but that such a transition is hidden by crystallization when bonds are highly directional.},
keywords = {DNA, Polyamorphism},
pubstate = {published},
tppubtype = {article}
}
For a model known to exhibit liquid-liquid transitions, we examine how varying the bond orientational flexibility affects the stability of the liquid-liquid transition relative to that of the crystal phases. For very rigidly oriented bonds, the crystal is favored over all amorphous phase transitions. We find that increasing the bond flexibility decreases both the critical temperature T-c for liquid-liquid phase separation and the melting temperature T-m. The effect of increasing flexibility is much stronger for melting, so that the distance between T-c and T-m progressively reduces and inverts sign. Under these conditions, a ``naked'' liquid-liquid critical point bulges out in the liquid phase and becomes accessible, without the possibility of crystallization. These results confirm that a crystal-clear, liquid-liquid transition can occur as a genuine, thermodynamically stable phenomenon for tetrahedral coordinated particles with flexible bond orientation, but that such a transition is hidden by crystallization when bonds are highly directional.
Ko, Seung Hyeon; Vargas-Lara, Fernando; Patrone, Paul N.; Stavis, Samuel M.; Starr, Francis W.; Douglas, Jack F.; Liddle, J. Alexander
High-speed, high-purity separation of gold nanoparticle-DNA origami constructs using centrifugation Journal Article
In: SOFT MATTER, vol. 10, no. 37, pp. 7370-7378, 2014, ISSN: 1744-683X.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology | Links:
@article{kvpssdl14,
title = {High-speed, high-purity separation of gold nanoparticle-DNA origami constructs using centrifugation},
author = {Ko, Seung Hyeon and Vargas-Lara, Fernando and Patrone, Paul N. and Stavis, Samuel M. and Starr, Francis W. and Douglas, Jack F. and Liddle, J. Alexander},
url = {http://fstarr.web.wesleyan.edu/publications/kvpssdl14.pdf},
doi = {10.1039/c4sm01071j},
issn = {1744-683X},
year = {2014},
date = {2014-01-01},
journal = {SOFT MATTER},
volume = {10},
number = {37},
pages = {7370-7378},
abstract = {DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions have yields of <100%, requiring the development of methods to purify the desired product. We study the performance of centrifugation as a separation approach by combining optical and hydrodynamic measurements and computations. We demonstrate that bench-top microcentrifugation is a simple and efficient method of separating the reaction products, readily achieving purities of >90%. The gold nanoparticles play a number of critical roles in our system, functioning not only as integral components of the purified products, but also as hydrodynamic separators and optical indicators of the reaction products during the purification process. We find that separation resolution is ultimately limited by the polydispersity in the mass of the gold nanoparticles and by structural distortions of DNA origami induced by the gold nanoparticles. Our study establishes a methodology for determining the design rules for nanomanufacturing DNA origami-nanoparticle constructs.},
keywords = {Biophysics, DNA, Nanotechnology},
pubstate = {published},
tppubtype = {article}
}
DNA origami is a powerful platform for assembling gold nanoparticle constructs, an important class of nanostructure with numerous applications. Such constructs are assembled by the association of complementary DNA oligomers. These association reactions have yields of <100%, requiring the development of methods to purify the desired product. We study the performance of centrifugation as a separation approach by combining optical and hydrodynamic measurements and computations. We demonstrate that bench-top microcentrifugation is a simple and efficient method of separating the reaction products, readily achieving purities of >90%. The gold nanoparticles play a number of critical roles in our system, functioning not only as integral components of the purified products, but also as hydrodynamic separators and optical indicators of the reaction products during the purification process. We find that separation resolution is ultimately limited by the polydispersity in the mass of the gold nanoparticles and by structural distortions of DNA origami induced by the gold nanoparticles. Our study establishes a methodology for determining the design rules for nanomanufacturing DNA origami-nanoparticle constructs.
Starr, Francis W.; Hartmann, Benedikt; Douglas, Jack F.
Dynamical clustering and a mechanism for raft-like structures in a model lipid membrane Journal Article
In: SOFT MATTER, vol. 10, no. 17, pp. 3036-3047, 2014, ISSN: 1744-683X.
Abstract | BibTeX | Tags: Biophysics, Dynamic Heterogeneity, Membranes | Links:
@article{shd14,
title = {Dynamical clustering and a mechanism for raft-like structures in a model lipid membrane},
author = {Starr, Francis W. and Hartmann, Benedikt and Douglas, Jack F.},
url = {http://fstarr.web.wesleyan.edu/publications/shd14.pdf},
doi = {10.1039/c3sm53187b},
issn = {1744-683X},
year = {2014},
date = {2014-01-01},
journal = {SOFT MATTER},
volume = {10},
number = {17},
pages = {3036-3047},
abstract = {We use molecular dynamics simulations to examine the dynamical heterogeneity of a model single-component lipid membrane using a coarse-grained representation of lipid molecules. This model qualitatively reproduces the known phase transitions between disordered, ordered, and gel membrane phases, and the phase transitions are accompanied by significant changes in the nature of the lipid dynamics. In particular, lipid diffusion in the liquid-ordered phase is hindered by the transient trapping of molecules by their neighbors, similar to the dynamics of a liquid approaching its glass transition. This transient molecular caging gives rise to two distinct mobility groups within a single-component membrane: lipids that are transiently trapped, and lipids with displacements on the scale of the intermolecular spacing. Most significantly, lipids within these distinct mobility states spatially segregate, creating transient ``islands'' of enhanced mobility having a size and time scale compatible with lipid ``rafts,'' dynamical structures thought to be important for cell membrane function. Although the dynamic lipid clusters that we observe do not themselves correspond to rafts (which are more complex, multicomponent structures), we hypothesize that such rafts may develop from the same universal mechanism, explaining why raft-like regions should arise, regardless of lipid structural or compositional details. These clusters are strikingly similar to the dynamical clusters found in glass-forming fluids, and distinct from phase-separation clusters. We also show that mobile lipid clusters can be dissected into smaller clusters of cooperatively rearranging molecules. The geometry of these clusters can be understood in the context of branched equilibrium polymers, related to percolation theory. We discuss how these dynamical structures relate to a range observations on the dynamics of lipid membranes.},
keywords = {Biophysics, Dynamic Heterogeneity, Membranes},
pubstate = {published},
tppubtype = {article}
}
We use molecular dynamics simulations to examine the dynamical heterogeneity of a model single-component lipid membrane using a coarse-grained representation of lipid molecules. This model qualitatively reproduces the known phase transitions between disordered, ordered, and gel membrane phases, and the phase transitions are accompanied by significant changes in the nature of the lipid dynamics. In particular, lipid diffusion in the liquid-ordered phase is hindered by the transient trapping of molecules by their neighbors, similar to the dynamics of a liquid approaching its glass transition. This transient molecular caging gives rise to two distinct mobility groups within a single-component membrane: lipids that are transiently trapped, and lipids with displacements on the scale of the intermolecular spacing. Most significantly, lipids within these distinct mobility states spatially segregate, creating transient ``islands'' of enhanced mobility having a size and time scale compatible with lipid ``rafts,'' dynamical structures thought to be important for cell membrane function. Although the dynamic lipid clusters that we observe do not themselves correspond to rafts (which are more complex, multicomponent structures), we hypothesize that such rafts may develop from the same universal mechanism, explaining why raft-like regions should arise, regardless of lipid structural or compositional details. These clusters are strikingly similar to the dynamical clusters found in glass-forming fluids, and distinct from phase-separation clusters. We also show that mobile lipid clusters can be dissected into smaller clusters of cooperatively rearranging molecules. The geometry of these clusters can be understood in the context of branched equilibrium polymers, related to percolation theory. We discuss how these dynamical structures relate to a range observations on the dynamics of lipid membranes.
2013
Chiu, Janet; Starr, Francis W.; Giovambattista, Nicolas
Pressure-induced transformations in computer simulations of glassy water Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 139, no. 18, pp. 184504, 2013, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Glass Formation, Polyamorphism, Water | Links:
@article{csg13,
title = {Pressure-induced transformations in computer simulations of glassy water},
author = {Chiu, Janet and Starr, Francis W. and Giovambattista, Nicolas},
url = {http://fstarr.web.wesleyan.edu/publications/csg13.pdf},
doi = {10.1063/1.4829276},
issn = {0021-9606},
year = {2013},
date = {2013-11-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {139},
number = {18},
pages = {184504},
abstract = {Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a ``P-T phase diagram'' for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water. (C) 2013 AIP Publishing LLC.},
keywords = {Glass Formation, Polyamorphism, Water},
pubstate = {published},
tppubtype = {article}
}
Glassy water occurs in at least two broad categories: low-density amorphous (LDA) and high-density amorphous (HDA) solid water. We perform out-of-equilibrium molecular dynamics simulations to study the transformations of glassy water using the ST2 model. Specifically, we study the known (i) compression-induced LDA-to-HDA, (ii) decompression-induced HDA-to-LDA, and (iii) compression-induced hexagonal ice-to-HDA transformations. We study each transformation for a broad range of compression/decompression temperatures, enabling us to construct a ``P-T phase diagram'' for glassy water. The resulting phase diagram shows the same qualitative features reported from experiments. While many simulations have probed the liquid-state phase behavior, comparatively little work has examined the transitions of glassy water. We examine how the glass transformations relate to the (first-order) liquid-liquid phase transition previously reported for this model. Specifically, our results support the hypothesis that the liquid-liquid spinodal lines, between a low-density and high-density liquid, are extensions of the LDA-HDA transformation lines in the limit of slow compression. Extending decompression runs to negative pressures, we locate the sublimation lines for both LDA and hyperquenched glassy water (HGW), and find that HGW is relatively more stable to the vapor. Additionally, we observe spontaneous crystallization of HDA at high pressure to ice VII. Experiments have also seen crystallization of HDA, but to ice XII. Finally, we contrast the structure of LDA and HDA for the ST2 model with experiments. We find that while the radial distribution functions (RDFs) of LDA are similar to those observed in experiments, considerable differences exist between the HDA RDFs of ST2 water and experiment. The differences in HDA structure, as well as the formation of ice VII (a tetrahedral crystal), are a consequence of ST2 overemphasizing the tetrahedral character of water. (C) 2013 AIP Publishing LLC.