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.
2018
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.
2016
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.
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; 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.
Rahedi, Andrew J.; Douglas, Jack F.; Starr, Francis W.
Model for reversible nanoparticle assembly in a polymer matrix Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 128, no. 2, pp. 024902, 2008, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Nanocomposites, Polymers, Self Assembly | Links:
@article{rds08,
title = {Model for reversible nanoparticle assembly in a polymer matrix},
author = {Rahedi, Andrew J. and Douglas, Jack F. and Starr, Francis W.},
url = {http://fstarr.web.wesleyan.edu/publications/rds.pdf},
doi = {10.1063/1.2815809},
issn = {0021-9606},
year = {2008},
date = {2008-01-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {128},
number = {2},
pages = {024902},
abstract = {The clustering of nanoparticles (NPs) in solutions and polymer melts depends sensitively on the strength and directionality of the NP interactions involved, as well as the molecular geometry and interactions of the dispersing fluids. Since clustering can strongly influence the properties of polymer-NP materials, we aim to better elucidate the mechanism of reversible self-assembly of highly symmetric NPs into clusters under equilibrium conditions. Our results are based on molecular dynamics simulations of icosahedral NP with a long-ranged interaction intended to mimic the polymer-mediated interactions of a polymer-melt matrix. To distinguish effects of polymer-mediated interactions from bare NP interactions, we compare the NP assembly in our coarse-grained model to the case where the NP interactions are purely short ranged. For the ``control'' case of NPs with short-ranged interactions and no polymer matrix, we find that the particles exhibit ordinary phase separation. By incorporating physically plausible long-ranged interactions, we suppress phase separation and qualitatively reproduce the thermally reversible cluster formation found previously in computations for NPs with short-ranged interactions in an explicit polymer-melt matrix. We further characterize the assembly process by evaluating the cluster properties and the location of the self-assembly transition. Our findings are consistent with a theoretical model for equilibrium clustering when the particle association is subject to a constraint. In particular, the density dependence of the average cluster mass exhibits a linear concentration dependence, in contrast to the square root dependence found in freely associating systems. The coarse-grained model we use to simulate NP in a polymer matrix shares many features of potentials used to model colloidal systems. The model should be practically valuable for exploring factors that control the dispersion of NP in polymer matrices where explicit simulation of the polymer matrix is too time consuming. (c) 2008 American Institute of Physics.},
keywords = {Nanocomposites, Polymers, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
The clustering of nanoparticles (NPs) in solutions and polymer melts depends sensitively on the strength and directionality of the NP interactions involved, as well as the molecular geometry and interactions of the dispersing fluids. Since clustering can strongly influence the properties of polymer-NP materials, we aim to better elucidate the mechanism of reversible self-assembly of highly symmetric NPs into clusters under equilibrium conditions. Our results are based on molecular dynamics simulations of icosahedral NP with a long-ranged interaction intended to mimic the polymer-mediated interactions of a polymer-melt matrix. To distinguish effects of polymer-mediated interactions from bare NP interactions, we compare the NP assembly in our coarse-grained model to the case where the NP interactions are purely short ranged. For the ``control'' case of NPs with short-ranged interactions and no polymer matrix, we find that the particles exhibit ordinary phase separation. By incorporating physically plausible long-ranged interactions, we suppress phase separation and qualitatively reproduce the thermally reversible cluster formation found previously in computations for NPs with short-ranged interactions in an explicit polymer-melt matrix. We further characterize the assembly process by evaluating the cluster properties and the location of the self-assembly transition. Our findings are consistent with a theoretical model for equilibrium clustering when the particle association is subject to a constraint. In particular, the density dependence of the average cluster mass exhibits a linear concentration dependence, in contrast to the square root dependence found in freely associating systems. The coarse-grained model we use to simulate NP in a polymer matrix shares many features of potentials used to model colloidal systems. The model should be practically valuable for exploring factors that control the dispersion of NP in polymer matrices where explicit simulation of the polymer matrix is too time consuming. (c) 2008 American Institute of Physics.
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.
2003
Starr, Francis W.; Douglas, Jack F.; Glotzer, Sharon C.
Origin of particle clustering in a simulated polymer nanocomposite and its impact on rheology Journal Article
In: JOURNAL OF CHEMICAL PHYSICS, vol. 119, no. 3, pp. 1777-1788, 2003, ISSN: 0021-9606.
Abstract | BibTeX | Tags: Nanocomposites, Polymers, Self Assembly | Links:
@article{sdg03,
title = {Origin of particle clustering in a simulated polymer nanocomposite and its impact on rheology},
author = {Starr, Francis W. and Douglas, Jack F. and Glotzer, Sharon C.},
url = {http://fstarr.web.wesleyan.edu/publications/sdg.pdf},
doi = {10.1063/1.1580099},
issn = {0021-9606},
year = {2003},
date = {2003-07-01},
journal = {JOURNAL OF CHEMICAL PHYSICS},
volume = {119},
number = {3},
pages = {1777-1788},
abstract = {Many nanoparticles have short-range interactions relative to their size, and these interactions tend to be ``patchy'' since the interatomic spacing is comparable to the nanoparticle size. For a dispersion of such particles, it is not a priori obvious what mechanism will control the clustering of the nanoparticles, and how the clustering will be affected by tuning various control parameters. To gain insight into these questions, we perform molecular dynamics simulations of polyhedral nanoparticles in a dense bead-spring polymer melt under both quiescent and steady shear conditions. We explore the mechanism that controls nanoparticle clustering and find that the crossover from dispersed to clustered states is consistent with the predictions for equilibrium particle association or equilibrium polymerization, and that the crossover does not appear to match the expectations for first-order phase separation typical for binary mixtures in the region of the phase diagram where we can equilibrate the system. At the same time, we cannot rule out the possibility of phase separation at a lower temperature. Utilizing the existing framework for dynamic clustering transitions offers the possibility of more rationally controlling the dispersion and properties of nanocomposite materials. Finally, we examine how nanocomposite rheology depends on the state of equilibrium clustering. We find that the shear viscosity for dispersed configurations is larger than that for clustered configurations, in contrast to expectations based on macroscopic colloidal dispersions. We explain this result by the alteration of the polymer matrix properties in the vicinity of the nanoparticles. We also show that shear tends to disperse clustered nanoparticle configurations in our system, an effect particularly important for processing. (C) 2003 American Institute of Physics.},
keywords = {Nanocomposites, Polymers, Self Assembly},
pubstate = {published},
tppubtype = {article}
}
Many nanoparticles have short-range interactions relative to their size, and these interactions tend to be ``patchy'' since the interatomic spacing is comparable to the nanoparticle size. For a dispersion of such particles, it is not a priori obvious what mechanism will control the clustering of the nanoparticles, and how the clustering will be affected by tuning various control parameters. To gain insight into these questions, we perform molecular dynamics simulations of polyhedral nanoparticles in a dense bead-spring polymer melt under both quiescent and steady shear conditions. We explore the mechanism that controls nanoparticle clustering and find that the crossover from dispersed to clustered states is consistent with the predictions for equilibrium particle association or equilibrium polymerization, and that the crossover does not appear to match the expectations for first-order phase separation typical for binary mixtures in the region of the phase diagram where we can equilibrate the system. At the same time, we cannot rule out the possibility of phase separation at a lower temperature. Utilizing the existing framework for dynamic clustering transitions offers the possibility of more rationally controlling the dispersion and properties of nanocomposite materials. Finally, we examine how nanocomposite rheology depends on the state of equilibrium clustering. We find that the shear viscosity for dispersed configurations is larger than that for clustered configurations, in contrast to expectations based on macroscopic colloidal dispersions. We explain this result by the alteration of the polymer matrix properties in the vicinity of the nanoparticles. We also show that shear tends to disperse clustered nanoparticle configurations in our system, an effect particularly important for processing. (C) 2003 American Institute of Physics.