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ABSTRACT: Technological applications of liquid crystals have generally relied on control of molecular orientation at a surface or an interface. Such control has been achieved through topography, chemistry and the adsorption of monolayers or surfactants. The role of the substrate or interface has been to impart order over visible length scales and to confine the liquid crystal in a device. Here, we report results from a computational study of a liquid-crystal-based system in which the opposite is true: the liquid crystal is used to impart order on the interfacial arrangement of a surfactant. Recent experiments on macroscopic interfaces have hinted that an interfacial coupling between bulk liquid crystal and surfactant can lead to a two-dimensional phase separation of the surfactant at the interface, but have not had the resolution to measure the structure of the resulting phases. To enhance that coupling, we consider the limit of nanodroplets, the interfaces of which are decorated with surfactant molecules that promote local perpendicular orientation of mesogens within the droplet. In the absence of surfactant, mesogens at the interface are all parallel to that interface. As the droplet is cooled, the mesogens undergo a transition from a disordered (isotropic) to an ordered (nematic or smectic) liquid-crystal phase. As this happens, mesogens within the droplet cause a transition of the surfactant at the interface, which forms new ordered nanophases with morphologies dependent on surfactant concentration. Such nanophases are reminiscent of those encountered in block copolymers, and include circular, striped and worm-like patterns.
Nature 05/2012; 485(7396):86-9. · 36.28 Impact Factor
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ABSTRACT: The structural evolution of surface gratings on a glassy material is investigated by means of molecular simulations. The gratings provide a means to probe surface diffusion in the vicinity of the glass transition temperature. A theory by Mullins [J. Appl. Phys. 30, 77 (1959)] is used to extract qu-antitative measures of surface diffusivity that rely on calculation of grating amplitude as a function of time. The simulations are implemented in the context of a model binary glass mixture [S. S. Ashwin and S. Sastry, J. Phys.: Condens. Matter 15, S1253 (2003)]. We find that surface diffusion is faster than bulk diffusion by several orders of magnitude, consistent with recent experimental data for an organic glass former. The diffusivities extracted by the grating-decay approach are consistent with those estimated on the basis of mean-squared particle displacements. The grating-decay approach, however, is more efficient than traditional techniques based on Einstein's diffusion equation. Grating decay is also more versatile and is shown to be applicable in a variety of sample geometries.
The Journal of chemical physics 05/2011; 134(19):194704. · 3.09 Impact Factor
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ABSTRACT: We present a coarse grain representation for Gaussian chains in the presence of hard surfaces. Whereas a Gaussian chain in the bulk can be represented by a bead-spring model with a quadratic potential between adjacent beads, the presence of a surface reduces the number of allowed chain configurations and modifies the effective potential between the beads. We derive the corrected potentials for several surface geometries: a single wall, two parallel walls (slit), and a spherical or cylindrical object (nanoparticle). Those potentials can be used in any model that includes a Gaussian chain, regardless of the simulation method. As an illustration, we consider a coarse grain model of a polymeric melt and, using Monte Carlo simulations, we compute the density profiles for (i) a melt confined in a slit and (ii) a melt in the vicinity of a nanoparticle. The case of a polymeric solution confined within a slit is also addressed, and the proposed approach is shown to yield results in qualitative agreement with those obtained with field-theoretic simulations.
The Journal of chemical physics 08/2010; 133(6):064905. · 3.09 Impact Factor
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ABSTRACT: DNA hybridization plays a central role in biology and, increasingly, in materials science. Yet, there is no precedent for examining the pathways by which specific single-stranded DNA sequences interact to assemble into a double helix. A detailed model of DNA is adopted in this work to examine such pathways and to determine the role of sequence, if any, on DNA hybridization. Transition path sampling simulations reveal that DNA rehybridization is prompted by a distinct nucleation event involving molecular sites with approximately four bases pairing with partners slightly offset from those involved in ideal duplexation. Nucleation is promoted in regions with repetitive base pair sequence motifs, which yield multiple possibilities for finding complementary base partners. Repetitive sequences follow a nonspecific pathway to renaturation consistent with a molecular "slithering" mechanism, whereas random sequences favor a restrictive pathway involving the formation of key base pairs before renaturation fully ensues.
Proceedings of the National Academy of Sciences 10/2009; 106(43):18125-30. · 9.68 Impact Factor
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ABSTRACT: A growing body of experimental evidence indicates that the interaction between amyloid beta peptide and lipid bilayer membranes plays an important role in the development of Alzheimer disease. Recent experimental evidence also suggests that trehalose, a simple disaccharide, reduces the toxicity of amyloid beta peptide. Molecular simulations are used to examine the effect of trehalose on the conformational stability of amyloid beta peptide in aqueous solution and its effect on the interaction between amyloid beta peptide and a model phospholipid bilayer membrane. It is found that, in aqueous solution, the peptide exhibits a random coil conformation but, in the presence of trehalose, it adopts an alpha helical conformation. It is then shown that the insertion of amyloid beta peptide into a membrane is more favorable when the peptide is folded into an alpha-helix than in a random coil conformation, thereby suggesting that trehalose promotes the insertion of alpha-helical amyloid beta into biological membranes.
The Journal of chemical physics 09/2009; 131(8):085101. · 3.09 Impact Factor
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ABSTRACT: A mesoscale model of DNA is presented (3SPN.1), extending the scheme previously developed by our group. Each nucleotide is mapped onto three interaction sites. Solvent is accounted for implicitly through a medium-effective dielectric constant and electrostatic interactions are treated at the level of Debye-Hückel theory. The force field includes a weak, solvent-induced attraction, which helps mediate the renaturation of DNA. Model parameterization is accomplished through replica exchange molecular dynamics simulations of short oligonucleotide sequences over a range of composition and chain length. The model describes the melting temperature of DNA as a function of composition as well as ionic strength, and is consistent with heat capacity profiles from experiments. The dependence of persistence length on ionic strength is also captured by the force field. The proposed model is used to examine the renaturation of DNA. It is found that a typical renaturation event occurs through a nucleation step, whereby an interplay between repulsive electrostatic interactions and colloidal-like attractions allows the system to undergo a series of rearrangements before complete molecular reassociation occurs.
Biophysical Journal 04/2009; 96(5):1675-90. · 3.65 Impact Factor
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ABSTRACT: The renaturation/denaturation of DNA oligonucleotides is characterized in the context of expanded ensemble (EXE) and transition path sampling (TPS) simulations. Free energy profiles have been determined from EXE for DNA sequences of varying composition, chain length, and ionic strength. TPS simulations within a Langevin dynamics formalism have been carried out to obtain further information of the transition state for renaturation. Simulation results reveal that free energy profiles are strikingly similar for the various DNA sequences considered in this work. Taking intact double-stranded DNA to have an extent of reaction ξ = 1.0, the maximum of the free energy profile appears at ξ≈0.15, corresponding to ∼2 base pairs. In terms of chain length, the free energy barrier of longer oligonucleotides (30 versus 15 base pairs) is higher and slightly narrower, due to increased sharpness associated with the transition. Low ionic strength tends to decrease free energy barriers, whereby increasing strand rigidity facilitates reassociation. Two mechanisms for DNA reassociation emerge from our analysis of the transition state ensemble. Repetitive sequences tend to reassociate through a non-specific pathway involving molecular slithering. In contrast, random sequences associate through a more restrictive pathway involving the formation of specific contacts, which then leads to overall molecular zippering. In both random and repetitive sequences, the distribution of contacts suggests that nucleation is favored for sites located within the middle region of the chain. The prevalent extent of reaction for the transition state is ξ≈0.25, and the critical size of the nucleus as obtained from our analysis involves ∼4 base pairs.
Journal of Physics Condensed Matter 01/2009; 21(3):034105. · 2.55 Impact Factor
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ABSTRACT: Long polyglutamine chains have been associated with a number of neurodegenerative diseases. These include Huntington's disease, where expanded polyglutamine (PolyQ) sequences longer than 36 residues are correlated with the onset of symptoms. In this paper we study the folding pathway of a 54-residue PolyQ chain into a beta-helical structure. Transition path sampling Monte Carlo simulations are used to generate unbiased reactive pathways between unfolded configurations and the folded beta-helical structure of the polyglutamine chain. The folding process is examined in both explicit water and an implicit solvent. Both models reveal that the formation of a few critical contacts is necessary and sufficient for the molecule to fold. Once the primary contacts are formed, the fate of the protein is sealed and it is largely committed to fold. We find that, consistent with emerging hypotheses about PolyQ aggregation, a stable beta-helical structure could serve as the nucleus for subsequent polymerization of amyloid fibrils. Our results indicate that PolyQ sequences shorter than 36 residues cannot form that nucleus, and it is also shown that specific mutations inferred from an analysis of the simulated folding pathway exacerbate its stability.
The Journal of chemical physics 11/2008; 129(13):135102. · 3.09 Impact Factor
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ABSTRACT: • Stem cell tissue engineering– Potential cell sources– Incorporation of hESCs• Undifferentiated hESC culture engineering• Ectodermal tissues– Skin– Cornea– Neural lineages• Mesodermal tissues– Heart– Bone and cartilage– Circulatory system• Endodermal tissues– Pancreas– Liver• Future challengesAbstractRecent advances in human embryonic stem cell (hESC) biology now offer an alternative cell source for tissue engineers, as these cells are capable of proliferating indefinitely and differentiating to many clinically relevant cell types. Novel culture methods capable of exerting spatial and temporal control over the stem cell microenvironment allow for more efficient expansion of hESCs, and significant advances have been made toward improving our understanding of the biophysical and biochemical cues that direct stem cell fate choices. Effective production of lineage specific progenitors or terminally differentiated cells enables researchers to incorporate hESC derivatives into engineered tissue constructs. Here, we describe current efforts using hESCs as a cell source for tissue engineering applications, highlighting potential advantages of hESCs over current practices as well as challenges which must be overcome.
Journal of Cellular and Molecular Medicine 05/2008; 12(3):709 - 729. · 4.13 Impact Factor
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ABSTRACT: The free energy surfaces of a wide variety of systems encountered in physics, chemistry, and biology are characterized by the existence of deep minima separated by numerous barriers. One of the central aims of recent research in computational chemistry and physics has been to determine how transitions occur between deep local minima on rugged free energy landscapes, and transition path sampling (TPS) Monte-Carlo methods have emerged as an effective means for numerical investigation of such transitions. Many of the shortcomings of TPS-like approaches generally stem from their high computational demands. Two new algorithms are presented in this work that improve the efficiency of TPS simulations. The first algorithm uses biased shooting moves to render the sampling of reactive trajectories more efficient. The second algorithm is shown to substantially improve the accuracy of the transition state ensemble by introducing a subset of local transition path simulations in the transition state. The system considered in this work consists of a two-dimensional rough energy surface that is representative of numerous systems encountered in applications. When taken together, these algorithms provide gains in efficiency of over two orders of magnitude when compared to traditional TPS simulations.
The Journal of Chemical Physics 05/2008; 128(14):144104. · 3.33 Impact Factor
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ABSTRACT: A high-flux backscattering spectrometer and a time-of-flight disk chopper spectrometer are used to probe the molecular mobility of model freeze-dried phospholipid liposomes at a range of temperatures surrounding the main melting transition. Using specific deuteration, quasielastic neutron scattering provides evidence that, in contrast to the hydrocarbon chains, the headgroups of the phospholipid molecules do not exhibit a sharp melting transition. The onset of motion in the tails is located at temperatures far below the calorimetric transition. Long-range motion is achieved through the onset of whole-lipid translation at the melting temperature. Atomistic simulations are performed on a multibilayer model at conditions corresponding to the scattering experiments. The model provides a good description of the dynamics of the system, with predictions of the scattering functions that agree with experimental results. The analysis of both experimental data and results of simulations supports a picture of a gradual melting of the heterogeneous hydrophobic domain, with part of the chains spanning increasingly larger volumes and part of them remaining effectively immobile until the thermodynamic phase transition occurs.
Biophysical Journal 02/2007; 92(1):147-61. · 3.65 Impact Factor
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ABSTRACT: Gibbs-Duhem integrations are performed to trace the vapor-liquid coexistence curves of homopolymers on a lattice. The integration entails simultaneous grand canonical simulations for the two coexisting phases and, consequently, no pressure evaluations or volume moves are necessary. Since mechanical equilibration of lattice systems can be troublesome, the proposed method offers some advantages over alternative approaches for phase equilibrium simulation, such as the integration of Clapeyron's equation and the Gibbs ensemble. Simulation results are presented for homopolymers and block copolymers; good agreement is found with previous Gibbs-ensemble results for homopolymers.
EPL (Europhysics Letters) 01/2007; 40(2):111. · 2.17 Impact Factor
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ABSTRACT: A Monte Carlo simulation method is presented for simulation of phase transitions, with emphasis on the study of crystallization. The method relies on a random walk in order parameter Phi(q(N)) space to calculate a free energy profile between the two coexisting phases. The energy and volume data generated over the course of the simulation are subsequently reweighed to identify the precise conditions for phase coexistence. The usefulness of the method is demonstrated in the context of crystallization of a purely repulsive Lennard-Jones system. A systematic analysis of precritical and critical nuclei as a function of supercooling reveals a gradual change from a bcc to a fcc structure inside the crystalline nucleus as it grows at large degrees of supercooling. The method is generally applicable and is expected to find applications in systems for which two or more coexisting phases can be distinguished through one or more order parameters.
The Journal of Chemical Physics 05/2006; 124(13):134102. · 3.33 Impact Factor
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ABSTRACT: In this paper a new algorithm is presented that improves the efficiency of Wang and Landau algorithm or density of states (DOS) Monte Carlo simulations by employing rejected states. The algorithm is shown to have a performance superior to that of the original Wang-Landau [F. Wang and D. P. Landau, Phys. Rev. Lett. 86, 2050 (2001)] algorithm and the more recent configurational temperature DOS algorithm. The performance of the method is illustrated in the context of results for the Lennard-Jones fluid.
The Journal of Chemical Physics 04/2006; 124(11):114102. · 3.33 Impact Factor
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Advanced Functional Materials 02/2006; 16(5):618 - 624. · 10.18 Impact Factor
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ABSTRACT: In this paper we present our approach for integrating block copolymers into the lithographic process so as to enable molecular-level control over the dimensions and shapes of nanoscale patterned resist features and simultaneously retain essential process attributes such as pattern perfection, registration, and the ability to create non-regular device-oriented structures. Combining self-assembling materials with advanced lithographic tools may allow current manufacturing techniques to be extended to the scale of 10 nm and below and meet the long-term requirements detailed in the International Technology Roadmap for Semiconductors (2004)
Electron Devices Meeting, 2005. IEDM Technical Digest. IEEE International; 01/2006
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ABSTRACT: Expanded ensemble density-of-states simulations and a connectivity altering algorithm are used to investigate the effective interactions that arise between nanoparticles suspended in polymer solutions. Our calculations with systems of long polymeric chains reveal oscillations in the effective polymer-induced interactions between the particles, even at low concentrations. The range of these interactions is considerably longer than originally anticipated, and their origin is traced back to the chain-end effects and density fluctuations that were absent in previous treatments of these systems.
The Journal of Chemical Physics 08/2005; 123(3):34901. · 3.33 Impact Factor
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ABSTRACT: We analyze the response of a nematic liquid-crystal film, confined between parallel walls, to the presence of nanoscopic particles adsorbed at the walls. This is done for a variety of patterns of adsorption (random and periodic) and operational conditions of the system that can be controlled in experimental liquid-crystal-based devices. We compute simulated optical textures and the total optical output of the sensor between crossed polars, as well as the correlation function for the liquid-crystal tensor order parameter; we use these observables to discuss the gradual destruction of the original uniform orientation. For large concentrations of particles adsorbed in random patterns, the liquid crystal at the center of the sensor adopts a multidomain state, characterized by a small correlation length of the tensor order parameter, and also by a loss of optical anisotropy under observation through crossed polars. In contrast, for particles adsorbed in periodic patterns, the nematic at the center of the cell can remain in a monodomain orientation state, provided the patterns in opposite walls are synchronized.
The Journal of Chemical Physics 06/2005; 122(18):184711. · 3.33 Impact Factor
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ABSTRACT: We have investigated the defect structures and potential of mean force (PMF) of three colloidal spheres immersed in a nematic liquid crystal (for linear and equilateral-triangular configurations), using a coarse-grained theory for the tensor order parameter. At large separations, each sphere is surrounded by an equatorial Saturn ring defect; at short separations, the theory predicts a drastic reorganization of the disclination lines: additional disclination rings are observed in planes perpendicular to the original ones. For both types of configurations, the PMF is attractive and always greater than a pairwise sum of binary PMFs. Comparing the PMFs of linear and equilateral-triangular configurations, we have found the triangular configuration to be more stable than the linear configuration. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1033-1040, 2005
Journal of Polymer Science Part B Polymer Physics 03/2005; 43(8):1033 - 1040. · 1.53 Impact Factor
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ABSTRACT: The conformation and dynamics of a single DNA molecule undergoing oscillatory pressure-driven flow in microfluidic channels is studied using Brownian dynamics simulations, accounting for hydrodynamic interactions between segments in the bulk and between the chain and the walls. Oscillatory flow provides a scenario under which the polymers may remain in the channel for an indefinite amount of time as they are stretched and migrate away from the channel walls. We show that by controlling the chain length, flow rate and oscillatory flow frequency, we are able to manipulate the chain extension and the chain migration from the channel walls. The chain stretch and the chain depletion layer thickness near the wall are found to increase as the Weissenberg number increases and as the oscillatory frequency decreases.
Macromolecules 02/2005; 38(15):6680-6687. · 5.17 Impact Factor
