Publications by year, excluding conference proceedings.
Complete CV Google Scholar Page
2019
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.
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.
2016
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.
2015
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
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.; 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.
2012
Chi, Cheng; Vargas-Lara, Fernando; Tkachenko, Alexei V.; Starr, Francis W.; Gang, Oleg
Internal Structure of Nanoparticle Dimers Linked by DNA Journal Article
In: ACS NANO, vol. 6, no. 8, pp. 6793-6802, 2012, ISSN: 1936-0851.
Abstract | BibTeX | Tags: Biophysics, DNA | Links:
@article{cvtsg12,
title = {Internal Structure of Nanoparticle Dimers Linked by DNA},
author = {Chi, Cheng and Vargas-Lara, Fernando and Tkachenko, Alexei V. and Starr, Francis W. and Gang, Oleg},
url = {http://fstarr.web.wesleyan.edu/publications/cvtsg12.pdf},
doi = {10.1021/nn301528h},
issn = {1936-0851},
year = {2012},
date = {2012-08-01},
journal = {ACS NANO},
volume = {6},
number = {8},
pages = {6793-6802},
abstract = {We construct nanoparticle dimers linked by DNA. These dimers are basic units in a possible multiscale, hierarchical assembly and serve as a model system to understand DNA-mediated interactions, especially in the nontrivial regime when the nanoparticle and DNA are comparable in their sizes. We examine the structure of nanoparticle dimers in detail by a combination of scattering experiments and molecular simulations. We find that, for a given DNA length, the interparticle separation within the dimer is controlled primarily by the number of linking DNA. We summarize our findings in a simple model that captures the Interplay of the number of DNA bridges, their length, the particle's curvature, and the excluded volume effects. We demonstrate the applicability of the model to our results, without any free parameters. As a consequence, the increase of dimer separation with increasing temperature can be understood as a result of changing the number of connecting DNA.},
keywords = {Biophysics, DNA},
pubstate = {published},
tppubtype = {article}
}
We construct nanoparticle dimers linked by DNA. These dimers are basic units in a possible multiscale, hierarchical assembly and serve as a model system to understand DNA-mediated interactions, especially in the nontrivial regime when the nanoparticle and DNA are comparable in their sizes. We examine the structure of nanoparticle dimers in detail by a combination of scattering experiments and molecular simulations. We find that, for a given DNA length, the interparticle separation within the dimer is controlled primarily by the number of linking DNA. We summarize our findings in a simple model that captures the Interplay of the number of DNA bridges, their length, the particle's curvature, and the excluded volume effects. We demonstrate the applicability of the model to our results, without any free parameters. As a consequence, the increase of dimer separation with increasing temperature can be understood as a result of changing the number of connecting DNA.
2011
Padovan-Merhar, Olivia; Vargas Lara, Fernando; Starr, Francis W.
Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 134, no. 24, pp. 244701, 2011, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{pvs11,
title = {Stability of DNA-linked nanoparticle crystals: Effect of number of strands, core size, and rigidity of strand attachment},
author = {Padovan-Merhar, Olivia and Vargas Lara, Fernando and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/pvs11.pdf},
doi = {10.1063/1.3596745},
issn = {0021-9606},
year = {2011},
date = {2011-06-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {134},
number = {24},
pages = {244701},
abstract = {Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)]. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3596745]},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
Three-dimensional ordered lattices of nanoparticles (NPs) linked by DNA have potential applications in novel devices and materials, but most experimental attempts to form crystals result in amorphous packing. Here we use a coarse-grained computational model to address three factors that impact the stability of bcc and fcc crystals formed by DNA-linked NPs : (i) the number of attached strands to the NP surface, (ii) the size of the NP core, and (iii) the rigidity of the strand attachment. We find that allowing mobility in the attachment of DNA strands to the core NP can very slightly increase or decrease melting temperature T(M). Larger changes to T(M) result from increasing the number of strands, which increases T(M), or by increasing the core NP diameter, which decreases T(M). Both results are consistent with experimental findings. Moreover, we show that the behavior of T(M) can be quantitatively described by the model introduced previously [F. Vargas Lara and F. W. Starr, Soft Matter, 7, 2085 (2011)]. (C) 2011 American Institute of Physics. [doi: 10.1063/1.3596745]
Vargas Lara, Fernando; Starr, Francis W.
Stability of DNA-linked nanoparticle crystals I: Effect of linker sequence and length Journal Article
In: SOFT MATTER, vol. 7, no. 5, pp. 2085-2093, 2011, ISSN: 1744-683X.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{vs11,
title = {Stability of DNA-linked nanoparticle crystals I: Effect of linker sequence and length},
author = {Vargas Lara, Fernando and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/vs11.pdf},
doi = {10.1039/c0sm00989j},
issn = {1744-683X},
year = {2011},
date = {2011-01-01},
journal = {SOFT MATTER},
volume = {7},
number = {5},
pages = {2085-2093},
abstract = {The creation of three-dimensional, crystalline-ordered nanoparticle (NP) structures linked by DNA has proved experimentally challenging. Here we aim to systematically study parameters that influence the relative thermodynamic and kinetic stability of such crystals. To avoid experimental bottlenecks and directly control molecular-scale parameters, we carry out molecular dynamics simulations of a coarse-grained model in which short DNA strands (6 to 12 bp) are tethered to a NP core. We examine the influence of the number of bases per strand L, number of linking bases l and the number of spacer bases s on the stability of crystal states. We also consider the effect of using a single linking NP type versus a binary linking system. We explicitly compute the free energy, entropy, and melting point T(M) for BCC and FCC lattices. We show that binary systems are preferable for generating BCC lattices, while a single NP type generates the most stable FCC crystals. We propose a simple model for short DNA strands that can account for T(M) of all our data. The model also indicates that the heat of fusion between crystal and amorphous phases grows linearly with l, providing a route to maximize the relative crystal stability.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
The creation of three-dimensional, crystalline-ordered nanoparticle (NP) structures linked by DNA has proved experimentally challenging. Here we aim to systematically study parameters that influence the relative thermodynamic and kinetic stability of such crystals. To avoid experimental bottlenecks and directly control molecular-scale parameters, we carry out molecular dynamics simulations of a coarse-grained model in which short DNA strands (6 to 12 bp) are tethered to a NP core. We examine the influence of the number of bases per strand L, number of linking bases l and the number of spacer bases s on the stability of crystal states. We also consider the effect of using a single linking NP type versus a binary linking system. We explicitly compute the free energy, entropy, and melting point T(M) for BCC and FCC lattices. We show that binary systems are preferable for generating BCC lattices, while a single NP type generates the most stable FCC crystals. We propose a simple model for short DNA strands that can account for T(M) of all our data. The model also indicates that the heat of fusion between crystal and amorphous phases grows linearly with l, providing a route to maximize the relative crystal stability.
2010
Hsu, Chia Wei; Sciortino, Francesco; Starr, Francis W.
Theoretical Description of a DNA-Linked Nanoparticle Self-Assembly Journal Article
In: PHYSICAL REVIEW LETTERS, vol. 105, no. 5, pp. 055502, 2010, ISSN: 0031-9007.
Abstract | BibTeX | Tags: Biophysics, DNA, Self Assembly | Links:
@article{hss10,
title = {Theoretical Description of a DNA-Linked Nanoparticle Self-Assembly},
author = {Hsu, Chia Wei and Sciortino, Francesco and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/hss10.pdf},
doi = {10.1103/PhysRevLett.105.055502},
issn = {0031-9007},
year = {2010},
date = {2010-07-01},
journal = {PHYSICAL REVIEW LETTERS},
volume = {105},
number = {5},
pages = {055502},
abstract = {Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA-tethered nanoparticles.},
keywords = {Biophysics, DNA, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide theoretical descriptions for the equilibrium clustering and dynamics, as well as the self-assembly kinetics of DNA-linked nanoparticles. Striking agreement is observed between the theory and molecular modeling of DNA-tethered nanoparticles.
Dai, Wei; Hsu, Chia Wei; Sciortino, Francesco; Starr, Francis W.
Valency Dependence of Polymorphism and Polyamorphism in DNA-Functionalized Nanoparticles Journal Article
In: LANGMUIR, vol. 26, no. 5, pp. 3601-3608, 2010, ISSN: 0743-7463.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Polyamorphism | Links:
@article{dhss10,
title = {Valency Dependence of Polymorphism and Polyamorphism in DNA-Functionalized Nanoparticles},
author = {Dai, Wei and Hsu, Chia Wei and Sciortino, Francesco and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/dhss.pdf},
doi = {10.1021/la903031p},
issn = {0743-7463},
year = {2010},
date = {2010-03-01},
journal = {LANGMUIR},
volume = {26},
number = {5},
pages = {3601-3608},
abstract = {Nanoparticles (NP) functionalized with single-stranded DNA (ssDNA) offer a route to custom-designed, self-assembled nanomaterials with potentially unusual properties, The bonding, selectivity of DNA guarantees one-to-one binding to form double-stranded DNA (dsDNA), and an appropriate base sequence results in head-to-tail binding linking NP into networks. We explore the phase behavior and structure of a model for NP functionalized with between 3 and 6 short ssDNA through simulations of a coarse-grained molecular model, allowing us to examine both the role of the number of attached strands (valency) and their relative orientations. The NP assemble into networks where the number of NP links is controlled by the number of attached strands, The large length scale of the DNA links relative to the core NP size opens the possibility for the formation of interpenetrating networks that give rise 10 multiple thermodynamically distinct states. We find that the 3-functionalized NP have only a single phase transition between a dilute solution of NPs and an assembled network state. 4-Functionalized NP (with tetrahedral symmetry) exhibit four amorphous phases, or polyamorphism, each higher density phase consisting of an additional interpenetrating network. The two investigated geometries of 5-functionalized NP both exhibit two phase transitions and three amorphouos phases. Like the 4-functionalized NP, the highest density phase consists of interpenetrating networks, demonstrating that regular symmetry is not a prerequisite for interpenetration to produce thermodynamically distinct phases. The width of theh coexistence regions for all phase transitions increase with increasing functionality. Finally, for 6-functionalized NP with octahedral symmetry. the possibility of observing disordered phases with significantly bonded particles is preempted by the formation of ordered crystal phases, Interestingly, the extreme softness of the potential combined with the directional interaction allows for the formation of (at least) six distinct crystalline structures (ie., polymorphism) consisting of up to six interpenetrating simple cubic lattices.},
keywords = {Biophysics, DNA, Nanotechnology, Polyamorphism},
pubstate = {published},
tppubtype = {article}
}
Nanoparticles (NP) functionalized with single-stranded DNA (ssDNA) offer a route to custom-designed, self-assembled nanomaterials with potentially unusual properties, The bonding, selectivity of DNA guarantees one-to-one binding to form double-stranded DNA (dsDNA), and an appropriate base sequence results in head-to-tail binding linking NP into networks. We explore the phase behavior and structure of a model for NP functionalized with between 3 and 6 short ssDNA through simulations of a coarse-grained molecular model, allowing us to examine both the role of the number of attached strands (valency) and their relative orientations. The NP assemble into networks where the number of NP links is controlled by the number of attached strands, The large length scale of the DNA links relative to the core NP size opens the possibility for the formation of interpenetrating networks that give rise 10 multiple thermodynamically distinct states. We find that the 3-functionalized NP have only a single phase transition between a dilute solution of NPs and an assembled network state. 4-Functionalized NP (with tetrahedral symmetry) exhibit four amorphous phases, or polyamorphism, each higher density phase consisting of an additional interpenetrating network. The two investigated geometries of 5-functionalized NP both exhibit two phase transitions and three amorphouos phases. Like the 4-functionalized NP, the highest density phase consists of interpenetrating networks, demonstrating that regular symmetry is not a prerequisite for interpenetration to produce thermodynamically distinct phases. The width of theh coexistence regions for all phase transitions increase with increasing functionality. Finally, for 6-functionalized NP with octahedral symmetry. the possibility of observing disordered phases with significantly bonded particles is preempted by the formation of ordered crystal phases, Interestingly, the extreme softness of the potential combined with the directional interaction allows for the formation of (at least) six distinct crystalline structures (ie., polymorphism) consisting of up to six interpenetrating simple cubic lattices.
Dai, Wei; Kumar, Sanat K.; Starr, Francis W.
Universal two-step crystallization of DNA-functionalized nanoparticles Journal Article
In: SOFT MATTER, vol. 6, no. 24, pp. 6130-6135, 2010, ISSN: 1744-683X.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{dks10,
title = {Universal two-step crystallization of DNA-functionalized nanoparticles},
author = {Dai, Wei and Kumar, Sanat K. and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/dks10.pdf},
doi = {10.1039/c0sm00484g},
issn = {1744-683X},
year = {2010},
date = {2010-01-01},
journal = {SOFT MATTER},
volume = {6},
number = {24},
pages = {6130-6135},
abstract = {We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature ``slot'', and always proceeds via a two-step process, mediated by a highly-connected amorphous intermediate. For lower temperature quenches, the dynamics of unzipping strands in the amorphous state is sufficiently slow that crystallization is kinetically hindered. This accounts for the well-documented difficulty of forming crystals in these systems. The strong parallel to the crystallization behavior of proteins and colloids suggests that these disparate systems crystallize in an apparently universal manner.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature ``slot'', and always proceeds via a two-step process, mediated by a highly-connected amorphous intermediate. For lower temperature quenches, the dynamics of unzipping strands in the amorphous state is sufficiently slow that crystallization is kinetically hindered. This accounts for the well-documented difficulty of forming crystals in these systems. The strong parallel to the crystallization behavior of proteins and colloids suggests that these disparate systems crystallize in an apparently universal manner.
2008
Hsu, Chia Wei; Largo, Julio; Sciortino, Francesco; Starr, Francis W.
Hierarchies of networked phases induced by multiple liquid-liquid critical points Journal Article
In: PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 105, no. 37, pp. 13711-13715, 2008, ISSN: 0027-8424.
Abstract | BibTeX | Tags: Biophysics, DNA, Polyamorphism, Self Assembly, Water | Links:
@article{hlss08,
title = {Hierarchies of networked phases induced by multiple liquid-liquid critical points},
author = {Hsu, Chia Wei and Largo, Julio and Sciortino, Francesco and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/hlss.pdf},
doi = {10.1073/pnas.0804854105},
issn = {0027-8424},
year = {2008},
date = {2008-09-01},
journal = {PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA},
volume = {105},
number = {37},
pages = {13711-13715},
abstract = {Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network-forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid-gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus, bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in sing le-component systems, suggested to occur in some atomic and molecular network-forming fluids, including water and silica.},
keywords = {Biophysics, DNA, Polyamorphism, Self Assembly, Water},
pubstate = {published},
tppubtype = {article}
}
Nanoparticles and colloids functionalized by four single strands of DNA can be thought of as designed analogs to tetrahedral network-forming atoms and molecules, with a difference that the attached DNA strands allow for control of the length scale of bonding relative to the core size. We explore the behavior of an experimentally realized model for nanoparticles functionalized by four single strands of DNA (a tetramer), and show that this single-component model exhibits a rich phase diagram with at least three critical points and four thermodynamically distinct amorphous phases. We demonstrate that the additional critical points are part of the Ising universality class, like the ordinary liquid-gas critical point. The dense phases consist of a hierarchy of interpenetrating networks, reminiscent of a woven cloth. Thus, bonding specificity of DNA provides an effective route to generate new nano-networked materials with polyamorphic behavior. The concept of network interpenetration helps to explain the generation of multiple liquid phases in sing le-component systems, suggested to occur in some atomic and molecular network-forming fluids, including water and silica.
2007
Largo, Julio; Starr, Francis W.; Sciortino, Francesco
Self-assembling DNA dendrimers: A numerical study Journal Article
In: LANGMUIR, vol. 23, no. 11, pp. 5896-5905, 2007, ISSN: 0743-7463.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{lss,
title = {Self-assembling DNA dendrimers: A numerical study},
author = {Largo, Julio and Starr, Francis W. and Sciortino, Francesco},
url = {http://fstarr.web.wesleyan.edu/publications/lss.pdf},
doi = {10.1021/la063036z},
issn = {0743-7463},
year = {2007},
date = {2007-05-01},
journal = {LANGMUIR},
volume = {23},
number = {11},
pages = {5896-5905},
abstract = {DNA is increasingly used as a specific linker to template nanostructured materials. We present a molecular dynamics simulation study of a simple DNA-dendrimer model designed to capture the basic characteristics of the biological interactions, where selectivity and strong cooperativity play an important role. Exploring a large set of densities and temperatures, we follow the progressive formation of a percolating large-scale network whose connectivity can be described by random percolation theory. We identify the relative regions of network formation and kinetic arrest versus phase separation and show that the location of the two-phase region can be interpreted in the same framework as reduced valency models. This correspondence provides guidelines for designing stable, equilibrium self-assembled low-density networks. Finally, we demonstrate a relation between bonding and dynamics, by showing that the temperature dependence of the diffusion constant is controlled by the number of fully unbonded dendrimers.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
DNA is increasingly used as a specific linker to template nanostructured materials. We present a molecular dynamics simulation study of a simple DNA-dendrimer model designed to capture the basic characteristics of the biological interactions, where selectivity and strong cooperativity play an important role. Exploring a large set of densities and temperatures, we follow the progressive formation of a percolating large-scale network whose connectivity can be described by random percolation theory. We identify the relative regions of network formation and kinetic arrest versus phase separation and show that the location of the two-phase region can be interpreted in the same framework as reduced valency models. This correspondence provides guidelines for designing stable, equilibrium self-assembled low-density networks. Finally, we demonstrate a relation between bonding and dynamics, by showing that the temperature dependence of the diffusion constant is controlled by the number of fully unbonded dendrimers.
2006
Starr, Francis W.; Sciortino, Francesco
Model for assembly and gelation of four-armed DNA dendrimers Journal Article
In: JOURNAL OF PHYSICS-CONDENSED MATTER, vol. 18, no. 26, pp. L347-L353, 2006, ISSN: 0953-8984.
Abstract | BibTeX | Tags: Biophysics, DNA, Nanotechnology, Self Assembly | Links:
@article{ss06,
title = {Model for assembly and gelation of four-armed DNA dendrimers},
author = {Starr, Francis W. and Sciortino, Francesco},
url = {http://fstarr.web.wesleyan.edu/publications/ss.pdf},
doi = {10.1088/0953-8984/18/26/L02},
issn = {0953-8984},
year = {2006},
date = {2006-07-01},
journal = {JOURNAL OF PHYSICS-CONDENSED MATTER},
volume = {18},
number = {26},
pages = {L347-L353},
abstract = {We introduce and numerically study a model designed to mimic the bulk behaviour of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative intermolecular links. We find that in an extremely narrow temperature range the system forms a large-scale, low-density disordered network via a thermo-reversible gel transition. By controlling the strand length, the gel transition temperature can be made arbitrarily close to the percolation transition, in contrast with recent model systems of physical gelation. This study helps the understanding of self-assembly in this class of new biomaterials and provides a bridge between physical and chemical gels.},
keywords = {Biophysics, DNA, Nanotechnology, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
We introduce and numerically study a model designed to mimic the bulk behaviour of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative intermolecular links. We find that in an extremely narrow temperature range the system forms a large-scale, low-density disordered network via a thermo-reversible gel transition. By controlling the strand length, the gel transition temperature can be made arbitrarily close to the percolation transition, in contrast with recent model systems of physical gelation. This study helps the understanding of self-assembly in this class of new biomaterials and provides a bridge between physical and chemical gels.