E. Sambriski - Academia.edu (original) (raw)

Papers by E. Sambriski

Journal of Physics: Condensed Matter, 2022

The Generalized Continuous Multiple Step (GCMS) potential is presented in this work. Due to its f... more The Generalized Continuous Multiple Step (GCMS) potential is presented in this work. Due to its flexibility, repulsive and/or attractive contributions are encodable through adjustable energy and length scales. The GCMS interaction provides a continuous representation of square-well, square-shoulder potentials and their variants for implementation in computer simulations. A continuous and differentiable energy representation is required to derive forces in conventional simulation algorithms. Molecular Dynamics simulations are of particular interest when considering the dynamic properties of a system. The GCMS potential can mimic other interactions with a judicious choice of parameters due to the versatile sigmoid form. In this study, our benchmarks for the GCMS representation include triangular, Yukawa, Franzese, and Lennard-Jones potentials. Comparisons made with published data on volumetric phase diagrams, liquid structure, and diffusivity from model systems are in excellent agreem...

Journal of Molecular Liquids, 2021

Abstract Hierarchical self-assembly provides a versatile pathway for generating new functional ma... more Abstract Hierarchical self-assembly provides a versatile pathway for generating new functional materials. In this work, we show that confining core-corona colloids in a cylindrical cavity leads to an interesting repertoire of self-organized structures, some of which display hierarchical organization. Particle density, corona size, and cylinder radius were varied systematically to elucidate their role in colloidal arrangements. Extensive Monte Carlo simulations were performed to attain structural phase diagrams for the systems studied: complex mesophases are observed for certain model parameters. Among the observed morphologies are helical arrangements: simple and double helices consisting of particle stripes ordered around a cylindrical axis with a pitch dictated by the corona size. We also report the structural analysis of morphologies displaying stratified packing. Length scales of the core-corona particles and confining cylinders studied in this work are comparable to reported experimental systems. Our results offer practicable molecular design principles to obtain specific colloidal nanocrystalline arrangements for targeted applications.

Frontiers in Physics, 2021

A bidimensional (2D) thermotropic liquid crystal (LC) is investigated with Molecular Dynamics (MD... more A bidimensional (2D) thermotropic liquid crystal (LC) is investigated with Molecular Dynamics (MD) simulations. The Gay-Berne mesogen with parameterization GB(3, 5, 2, 1) is used to model a calamitic system. Spatial orientation of the LC samples is probed with the nematic order parameter: a sharp isotropic-smectic (I-Sm) transition is observed at lower pressures. At higher pressures, the I-Sm transition involves an intermediate nematic phase. Topology of the orthobaric phase diagram for the 2D case differs from the 3D case in two important respects: 1) the nematic region appears at lower temperatures and slightly lower densities, and 2) the critical point occurs at lower temperature and slightly higher density. The 2D calamitic model is used to probe the structural behavior of LC samples under strong confinement when either planar or homeotropic anchoring prevails. Samples subjected to circular, square, and triangular boundaries are gradually cooled to study how orientational order ...

RSC Advances, 2019

Saturn ring dyads (left) mediate more stable colloidal interactions than Saturn ring triads (righ... more Saturn ring dyads (left) mediate more stable colloidal interactions than Saturn ring triads (right) in nematic-phase discotic dispersions.

Soft Matter, 2016

The stability of columnar mesophases in binary discotic mixtures can be induced by varying the bi... more The stability of columnar mesophases in binary discotic mixtures can be induced by varying the bidispersity in molecular thickness.

Environmental Science and Engineering, 2011

ABSTRACT Structures and self-diffusion coefficients of Gay-Berne (GB) mesogens with parameterizat... more ABSTRACT Structures and self-diffusion coefficients of Gay-Berne (GB) mesogens with parameterizations GB(3.0, 5.0, 2.0, 1.0) and GB(4.4, 20.0, 1.0, 1.0) were extracted from NVT Molecular Dynamics simulations. These parameterizations are commonly used in the study of mesogenic systems. Structural features of accessible phases were characterized through translational [ g||(r||)g_{\parallel}(r_{\parallel}) ] and positional [ g^(r^)g_{\perp}(r_{\perp}) ] radial distribution functions. Translational self-diffusion coefficients parallel ( D||D_{\parallel} ) and perpendicular ( D^D_{\perp} ) to the global director were determined. Upon cooling a mesogenic system with parameterization GB(3.0, 5.0, 2.0, 1.0), a solid-like phase forms (as deduced from diffusivity) without attaining a smectic phase. Instead, the GB(4.4, 20.0, 1.0, 1.0) parameterization yields a range of liquid crystalline phases that follows the sequence isotropic ®\to nematic ®\to smectic A ®\to smectic B, for which the smectic B phase exhibits small, but measurable diffusivity. Collectively, results point to the GB(4.4, 20.0, 1.0, 1.0) parameterization as being a better candidate in capturing the typical gamut of liquid crystalline phases.

Soft Matter, 2014

Molecular Dynamics simulations were performed for the Gay-Berne discotic fluid parameterized by G... more Molecular Dynamics simulations were performed for the Gay-Berne discotic fluid parameterized by GB(0.345, 0.2, 1.0, 2.0). The volumetric phase diagram exhibits isotropic (IL), nematic (ND), and two columnar phases characterized by radial distribution functions: the transversal fluid structure varies between a hexagonal columnar (CD) phase (at higher temperatures and pressures) and a rectangular columnar (CO) phase (at lower temperatures and pressures). The slab-wise analysis of fluid dynamics suggests the formation of grain-boundary defects in the CO phase. Longitudinal fluid structure is highly periodic with narrow peaks for the CO phase, suggestive of a near-crystalline (yet diffusive) system, but is only short-ranged for the CD phase. The IL phase does not exhibit anisotropic diffusion. Transversal diffusion is more favorable in the ND phase at all times, but only favorable at short times for the columnar phases. In the columnar phases, a crossover occurs where longitudinal diffusion is favored over transversal diffusion at intermediate-to-long timescales. The anomalous diffusivity is pronounced in both columnar phases, with three identifiable contributions: (a) the rattling of discogens within a transient &amp;amp;amp;amp;amp;amp;amp;quot;interdigitation&amp;amp;amp;amp;amp;amp;amp;quot; cage, (b) the hopping of discogens across columns, and (c) the drifting motion of discogens along the orientation of the director.

Soft Matter, 2011

ABSTRACT A molecular model of DNA, that has been shown to reproduce hybridization, is used here t... more ABSTRACT A molecular model of DNA, that has been shown to reproduce hybridization, is used here to study the transition from two single-stranded molecules to a double-helical complex in situations where one strand is attached to a surface. Transition Path Sampling simulations reveal that hybridization is initiated by forming specific contacts between distinct bases of the molecule. Molecules with repetitive sequences form double helices by sliding along each other after having formed initial contacts. For random sequences, it is shown that the pathway that molecules follow to hybridization depends on the linker length as well as the temperature, and is significantly different from that observed in the bulk.

Nature, 2012

Technological applications of liquid crystals have generally relied on control of molecular orien... more 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.

Molecular Physics, 2013

ABSTRACT Phase diagrams for Gay–Berne (GB) fluids were obtained from molecular dynamics simulatio... more ABSTRACT Phase diagrams for Gay–Berne (GB) fluids were obtained from molecular dynamics simulations for GB(2, 5, 1, 2) (i.e. short mesogens) and GB(3, 5, 1, 2) (i.e. long mesogens), which yield isotropic, nematic, and smectic-B phases. The long-mesogen fluid also yields the smectic-A phase. Ordered phases of the long-mesogen fluid form at higher temperatures and lower densities when compared to those of the short-mesogen fluid. The effect of confinement under weak and strong substrate couplings in slab geometry was investigated. Compared to the bulk, the isotropic–nematic transition does not shift in temprature significantly for the weakly coupled substrate in either mesogen fluid. However, the strongly coupled substrate shifts the transition to lower temperature. Confinement induces marked stratification in the short-mesogen fluid. This effect diminishes with distance from the substrate, yielding bulk-like behaviour in the slab central region. Fluid stratification is very weak for the long-mesogen fluid, but the strongly coupled substrate induces ‘smectisation’, an ordering effect that decays with distance. Orientation of the fluid on the substrate depends on the mesogen. There is no preferred orientation in a plane parallel to the substrate for the weakly coupled case. In the strongly coupled case, the mesogen orientation mimics that of adjacent fluid layers. Planar anchoring is observed with a broad distribution of orientations in the weakly coupled case. In the strongly coupled case, the distribution leans toward planar orientations for the short-mesogen fluid, while a marginal preference for tilting persists in the long-mesogen fluid.

97403-We extend our previous analytical coarse-graining (CG) procedure 1 , which maps polymer liq... more 97403-We extend our previous analytical coarse-graining (CG) procedure 1 , which maps polymer liquids onto a system of interacting soft-colloidal particles. First, we present an optimized representation of the effective pair potential, v cc (r) [initially determined via the hypernetted-chain closure], by carrying out an interative predictor-corrector (PC) scheme. Then, we compare the thermodynamics obtained through the virial and compressibility routes, for which we observe an improvement in their consistency when using the PC result. Finally, we present an intermediate length-scale CG treatment for polymers by performing an analytical remapping of the chain onto "blobs" (monomer aggregates). The derived expression for the blobblob total correlation function, h bb (r), is seen to be in agreement with data from united-atom molecular dynamics simulations.

Journal of Physics: Condensed Matter, 2007

We extend our generalized Langevin equation for cooperative dynamics (CDGLE), a many-chain approa... more We extend our generalized Langevin equation for cooperative dynamics (CDGLE), a many-chain approach, to investigate liquids composed of macromolecules with different local chemical structure. In particular, the specific role of semiflexibility and local architecture on the overall polymer dynamics is explored. The theory predicts centre-of-mass diffusion in good agreement with simulations for liquids of macromolecules with slightly branched monomeric architectures.

Expanded ensembles were used to obtain the association free energy, in which the number of ideal ... more Expanded ensembles were used to obtain the association free energy, in which the number of ideal basepair contacts formed served as the order parameter, for DNA oligonucleotides of varying composition, chain length, and ionic strength. Although free energy profiles are unique to each sequence, all exhibit a pronounced response for low contact numbers dominated largely by an increase in system entropy. Short oligonucleotides with sequence periodicity exhibit a rather smooth free energy profile that increases in complexity as chain length increases. The complexity in non-periodic sequences arises even in short oligonucleotides. Taking intact dsDNA with an extent of reaction &amp;xgr; = 1.0, the maximum of the free energy profile appears at &amp;xgr;&amp;ap;0.1, representing two to four basepair contacts. In terms of chain length, the free energy barrier of longer oligonucleotides is higher and slightly narrower, due to the ensuant sharpness of the single-to-double stranded transition. Low ionic strength conditions induce an instability along the sugar-phosphate backbone of DNA, resulting in a decrease of the free energy barrier toward molecular dissociation.

Proceedings of the National Academy of Sciences, 2009

DNA hybridization plays a central role in biology and, increasingly, in materials science. Yet, t... more 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. mesoscale modeling ͉ nucleic acids ͉ self-assembly www.

Physical Review Letters, 2004

An analytical description of polymer melts and their mixtures as liquids of interacting soft coll... more An analytical description of polymer melts and their mixtures as liquids of interacting soft colloidal particles is obtained from liquid-state theory. The derived center-of-mass pair correlation functions with no adjustable parameters reproduce those computed from united atom molecular dynamics simulations. The coarse-grained description correctly bridges micro-and mesoscopic fluid properties. Molecular dynamics simulations of soft colloidal particles interacting through the calculated effective pair potentials are consistent with data from microscale simulations and analytical formulas.