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ESPResSo es un software especializado para realizar simulaciones computacionales de dinamica molecular en el area de la materia condensada blanda; en particular fue creado para simulaciones del tipo grano grueso. Tradicionalmente, este software, ha sido utilizado como una poderosa herramienta para investigacion basica , aplicada y como una plataforma facil de extender acorde a las necesidades del usuario. Sin embargo, dada su inherente versatilidad y facilidad para implementar un sistema, es posible tambien u tilizarlo como una plataforma didactica que sirva como un primer acercamiento a la simulacion computacional, o bien, como herramienta de apoyo en la docencia. En este trabajo mostraremos las caracteristicas y uso basico d el software, a traves de la implementacion de algunos sistemas basicos y del calculo de observables estandar como la funcion de distribucion radial y el desplazamiento cuadratico medio .

We present a molecular dynamics and theoretical study on the diffusion of interacting particles embedded on the surface of a sphere. By proposing five different interaction potentials among particles, we perform molecular dynamics simulations and calculate the mean square displacement (MSD) of tracer particles under a crowded regime of high surface density. Results for all the potentials show four different behaviors passing from ballistic and transitory at very short times, to sub-diffusive and saturation behaviors at intermediary and long times. Making use of irreversible thermodynamics theory, we also model the last two stages showing that the crowding induces a sub-diffusion process similar to that caused by particles trapped in cages, and that the saturation of the MSD is due to the existence of an entropic potential that limits the number of accessible states to the particles. By discussing the convenience of projecting the motions of the particles over a plane of observation, consistent with experimental capabilities, we compare the predictions of our theoretical model with the simulations showing that these stages are remarkably well described in qualitative and quantitative terms.

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 emerges. Depending on anchoring mode and confining geometry, characteristic topological defects emerge. Textures in these systems are similar to those observed in experiments and simulations of lyotropic LCs.

HIV-1 Gag is a large multidomain poly-protein with flexible unstructured linkers connecting its globular subdomains. It is compact when in solution but assumes an extended conformation when assembled within the immature HIV-1 virion. Here, we use molecular dynamics (MD) simulations to quantitatively characterize the intra-domain interactions of HIV-1 Gag. We find that the matrix (MA) domain and the C-terminal subdomain CActd of the CA capsid domain can form a bound state. The bound state, which is held together primarily by interactions between complementary charged and polar residues, stabilizes the compact state of HIV-1 Gag. We calculate the depth of the attractive free energy potential between the MA/ CActd sites and find it to be about three times larger than the dimerization interaction between the CActd domains. Sequence analysis shows high conservation within the newly-found intra-Gag MA/CActd binding site, as well as its spatial proximity to other well known elements of Gag -such as CActd's SP1 helix region, its inositol hexaphosphate (IP6) binding site and major homology region (MHR), as well as the MA trimerization site. Our results point to a high, but yet undetermined, functional significance of the intra-Gag binding site. Recent biophysical experiments that address the binding specificity of Gag are interpreted in the context of the MA/CActd bound state, suggesting an important role in selective packaging of genomic RNA by Gag.

Molecular simulations in the canonical and isothermal-isobaric ensembles were performed for a two-dimensional simple fluid using a set of non conformal molecular interactions. The specific characteristics of this interaction model give it some advantages over other well known interaction potentials employed traditionally in the study of thermodynamic properties of soft matter systems. The functional form employed for modelling the effective potentials is the one proposed by the so-called ANC theory (Approximate Non-Conformal Theory), which allows to modify separately the contributions of the repulsive and attractive terms by means of a molecular parameter called softness. The effect of both, repulsive and attractive softness, on the liquid-vapour coexistence, liquid-solid transition and vaporization curve as well as on the value of the critical properties were explored. In fact, the linear dependence on the softness parameters exhibited by the critical properties, allows to extrapolate the linear correlations presented in this work, to reproduce the critical point of a two-dimensional Lennard-Jones fluid. With the aim of showing how versatile is the interaction model presented in this work, adequate values of the softness parameters were selected to reproduce qualitatively the liquid-vapour coexistence and critical points for both, a two-dimensional model fluid with a double exponential interaction potential, widely employed in molecular simulations of simple fluids; and a thin monolayer of methane molecules adsorbed on a planar graphite substrate, a system that can be considered in good approximation as two-dimensional and that has been studied in a lot of work for four decades. Finally, the effects of the dimensionality of the system was evaluated by quantifying the relative percentage differences exhibited by the thermodynamic properties explored in this paper with respect to its three-dimensional counterpart. The results presented in this work show not only the predictive capacity of the linear correlations mentioned, but the robustness of the ANC interactions to reproduce thermophysical properties and phase equilibria for model and real two-dimensional fluids. Discriminating the influence of repulsive and attractive contributions in molecular interaction models is undoubtedly of great relevance to have a better understanding of thermodynamic properties of simple and complex fluids.

Three discotic liquid-crystalline binary mixtures, characterized by their extent of bidispersity in molecular thickness, were investigated with molecular dynamics simulations. Each equimolar mixture contained A-type (thin) and B-type (thick) discogens. The temperature-dependence of the orientational order parameter reveals that A-type liquid samples produce ordered phases more readily, with the (hexagonal) columnar phase being the most structured variant. Moderately and strongly bidisperse mixtures produce globally-segregated samples for temperatures corresponding to ordered phases; the weakly bidisperse mixture displays microheterogeneities. Ordered phases in the B-type liquid are induced partially by the presence of the A-type fluid. In the moderately bidisperse mixture, order is induced through orientational frustration: a mixed prenematic-like phase precedes global segregation to yield nematic and columnar mesophases upon further cooling. In the strongly bidisperse mixture, order is induced less efficiently through a paranematic-like mechanism: a highly-ordered A-type fluid imparts order to B-type discogens found at the interface of a fully-segregated sample. This ordering effect permeates into the disordered B-type domain until nematic and columnar phases emerge upon further cooling. At sufficiently low temperatures, all samples investigated exhibit the (hexagonal) columnar mesophase.

Upon compression, the equilibrium hard-sphere liquid [pair potential uHS(r)] freezes at a packing fraction ϕf = 0.494 or, if crystallization is prevented, becomes metastable up to its glass transition at ϕg ≈ 0.58. Throughout the fluid regime (ϕ < ϕg), we are, thus, certain that this model liquid does not exhibit any form of kinetic arrest. If, however, a small portion of these spheres (packing fraction ϕ2 ≪ ϕ) happen to ignore each other [u22(r) = 0] but do not ignore the remaining “normal” hard spheres [u12(r) = u21(r) = u11(r) = uHS(r)], whose packing fraction is thus ϕ1 = ϕ − ϕ2, they run the risk of becoming dynamically arrested before they demix from the “normal” particles. This unexpected and counterintuitive scenario was first theoretically predicted and then confirmed by simulations.

Molecular dynamics simulations were performed for a Gay-Berne discotic fluid confined in a slab geometry for two different anchorings: homeotropic (face-on) and planar (edge-on), and for two different confinement lengths. Our results show that the behaviour of the more confined system in the temperature region of the isotropic–nematic transition is critically influenced by the presence of the walls: the growth of the solid–liquid crystal interface spans over the entire width of the cell, and the character of the transition is changed from first order to continuous. For all the confined systems studied, we observe a higher nematic–columnar transition temperature and a smaller nematic phase region in the phase diagram, as compared with the behaviour of the infinite system.

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 ...

Molecular dynamics simulations of a coarse grain model are used to explore the morphology of thermotropic liquid crystal nanodroplets. The characteristic length of the droplets is such that different contributions to the energy, including interfacial and bulk-like terms, have comparable magnitudes. Depending on the relative strength of such contributions, a wide variety of mesophases can be identified. These range from a completely disordered isotropic phase at elevated temperatures, to ordered radial and smectic phases at low temperatures. Bipolar, uniaxial and axial phases are also observed. Our results suggest that according to the ratio between perpendicular and planar anchoring strengths, an isotropic–radial transition may occur through several intermediate phases. In contrast, a direct bipolar–radial transition is never observed. Our results are summarized in the form of a generic phase diagram for spherical nanodroplets as a function of anchoring strength. The diagram exhibits a number of common features with phase transitions that have been observed in experiments with larger, micron-sized droplets. Perhaps more importantly, it serves to emphasize the balance that exists in nanodroplets between surface and bulk interactions, droplet size and temperature, and how that balance influences the behavior of the system.

This letter reports that darkfield microscopy can be used to track the trajectories of chemically functionalized gold nanoparticles in nematic liquid crystals (LCs), thus leading to measurements of the diffusion coefficients of the nanoparticles in the LCs. These measurements reveal that the diffusion coefficients of the nanoparticles dispersed in the LC are strongly dependent on the surface chemistry of the nanoparticles. Because the changes in surface chemistry are measured to have negligible influence on the diffusion coefficients of the same nanoparticles dispersed in isotropic solvents, we conclude that surface chemistry-induced changes in the local order of LCs underlie the behavior of the diffusion coefficients of the nanoparticles in the LC. Surface chemistry-dependent ordering of the LCs near the surfaces of the nanoparticles was also found to influence diffusion coefficients measured when the LC was heated above the bulk nematic-to-isotropic transition temperature. These experimental measurements are placed into the context of past theoretical predictions regarding the impact of local ordering of LCs on diffusion coefficients. The results that emerge from this study provide important insights into the mobility of nanoparticles in LCs and suggest new approaches based on measurements of nanoparticle dynamics that can yield information on the ordering of LCs near nanoparticles.

We use Molecular Dynamics simulations to study the effect of interactions and confinement (walls) on particle diffusion. We extend previous studies by analyzing the mean squared displacement (MSD) of an interacting fluid constrained to a circular, square and triangular cavity of nanometric size. The interactions among particles and walls are modeled by means of three classic potentials namely, Lenard-Jones (CLJ), soft Lenard-Jones (SLJ) and hard Lenard-Jones (HLJ) potentials. For hard spheres, for all cavities, and for very diluted densities, diffusion is shown to be less favorable in comparison with particles interacting with a CLJ. It is also observed that HLJ particles do not show difference in their MSD with SLJ particles at these densities. Confinement effects also appear at these densities and it is shown that diffusion decreases in the following cavity shape order: triangular, square and circular. For moderated densities, the combination of confinement and interactions shows a non-trivial effect. It is observed that particles inside a triangular cavity interacting by means of HLJ, reduce their MSD in comparison with CLJ or SLJ particles, since for this cavity shape, hard collisions reduce the particles’ speed. For higher densities, another non-trivial effect appears. Once again, the combination of interactions and confinement gives rise to order in the system that clearly reduces the system MSD. It is also shown that order appears for SLJ particles but it is absent for CLJ or HLJ particles.

Using strongly interacting, three-dimensional dipolar fluids as model systems we compare computer simulation results obtained with the full, conventional Ewald summation with results based on a truncated Ewald sum. The truncation consists of entirely neglecting the Fourier part of the full Ewald expression, which saves a large amount of the otherwise required computational time. In order to test the truncated version we consider two types of dipole-driven phase transitions: the isotropic-to-ferroelectric transition of one-component dipolar soft sphere fluids, on one hand, and the demixing transition in mixtures of dipolar and neutral soft spheres, on the other. Comparing various thermodynamic and structural data we find that the truncated Ewald sum yields surprisingly accurate results even at large dipolar coupling strength and even when subtle quantities such as the dielectric constant and the pressure tensor are considered. Our work thus suggests that the truncated version can safely be used to obtain a...

Density of states Monte Carlo simulations have been performed to study the isotropic–nematic (IN) transition of the Lebwohl–Lasher model for liquid crystals. The IN transition temperature was calculated as a function of system size using expanded ensemble density of states simulations with histogram reweighting. The IN temperature for infinite system size was obtained by extrapolation of three independent measures. A subsequent analysis of the kinetics in the model showed that the transition occurs via spinodal decomposition through aggregation of clusters of liquid crystal molecules.

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.

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 [\(g_{\parallel}(r_{\parallel})\)] and positional [\(g_{\perp}(r_{\perp})\)] radial distribution functions. Translational self-diffusion coefficients parallel (\(D_{\parallel}\)) and perpendicular (\(D_{\perp}\)) 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.

We present the phase diagram of Gay‐Berne potential for discotic symmetry using a particular set of parameters. We show evidence of isotropic, nematic and columnar phases. These results were obtained using two different Molecular Dynamics ensembles to get complementary information. The canonical ensemble to produce interphases between coexisting phases and isothermal‐isobaric ensemble to calculate homogeneous properties. The phase diagram was constructed using 2048 particles. For the lower part of the phase diagram, corresponding to low range of temperatures, we present evidence of coexistence lines for isotropic and columnar phases, We support our conclusions on distribution functions and nematic order parameter results.

We present a constant-pressure molecular dynamics simulation study of the phase behavior of binary (50:50) Gay-Berne liquid crystal mixtures consisting of elongated particles with different lengths $({L}_{A}g{L}_{B})$ and equal diameters. We focus on systems at dense liquid-state conditions. Considering three mixtures characterized by different values of ${L}_{A(B)}$ and different length ratios $q={L}_{B}∕{L}_{A}l1$, we find complex fluid-fluid phase behavior resulting from the interplay between nematic, smectic-$A$-type, or smectic-$B$-type orientational ordering, on the one hand, and demixing into two phases of different composition (fractionation), on the other hand. The driving ``forces'' of demixing transitions are the temperature and the length ratio. Indeed, in the system characterized by the largest value of $q$ $(q=0.86)$ orientational order occurs already in mixed states, whereas full fractionation is found at $q=0.71$. The two resulting states are either of type smectic-$B$-nematic (intermediate temperatures) or smectic-$B$-smectic-$B$ (low temperatures). In the intermediate case $q=0.80$ we observe a stepwise ordering and demixing behavior on cooling the system from high temperatures. Moreover, our results show that the stability range of (partially) nematic structures in mixtures of sufficiently small $q$ can be significantly larger than in the pure counterparts, in qualitative agreement with experimental observations.

We have carried out extensive equilibrium molecular dynamics (MD) simulations to study the structure and the interfacial properties in the liquid-vapor (LV) phase coexistence of partially miscible binary Lennard-Jones (LJ) mixtures. By analyzing the structural properties as a function of the miscibility parameter, $ \alpha $, we found that at relatively low temperatures the system separates forming a liquid A-liquid B interface in coexistence with the vapor phase. At higher temperatures and, $ 0, Comment: Enlarged version that include results of more extensive simulations. A total of 24 LaTeX pages that include 12 encapsulated poscript figures. To appear in PRE, Vol. 70, issue Sept. 1st (2004)

We have carried out extensive equilibrium molecular dynamics (MD) simulations to investigate the Liquid-Vapor coexistence in partially miscible binary and ternary mixtures of Lennard-Jones (LJ) fluids. We have studied in detail the time evolution of the density profiles and the interfacial properties in a temperature region of the phase diagram where the condensed phase is demixed. The composition of the mixtures are fixed, 50% for the binary mixture and 33.33% for the ternary mixture. The results of the simulations clearly indicate that in the range of temperatures $78 < T < 102 ^{\rm o}$K, --in the scale of argon-- the system evolves towards a metastable alternated liquid-liquid lamellar state in coexistence with its vapor phase. These states can be achieved if the initial configuration is fully disordered, that is, when the particles of the fluids are randomly placed on the sites of an FCC crystal or the system is completely mixed. As temperature decreases these states become very well defined and more stables in time. We find that below $90 ^{\rm o}$K, the alternated liquid-liquid lamellar state remains alive for 80 ns, in the scale of argon, the longest simulation we have carried out. Nonetheless, we believe that in this temperature region these states will be alive for even much longer times., 18 Latex-RevTex pages including 12 encapsulated postscript figures. Figures with better resolution available upon request. Accepted for publication in Phys. Rev. E Dec. 1st issue

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 "interdigitation" cage, (b) the hopping of discogens across columns, and (c) the drifting motion of discogens along the orientation of the director.

We developed an explicit equation of state (EOS) for small non polar molecules by means of an effective two-body potential. The average effect of three-body forces was incorporated as a perturbation, which results in rescaled values for the parameters of the two-body potential. These values replace the original ones in the EOS corresponding to the two-body interaction. We applied this procedure to the heavier noble gases and used a modified Kihara function with an effective Axilrod-Teller-Muto (ATM) term to represent the two- and three-body forces. We also performed molecular dynamics simulations with two- and three-body forces. There was good agreement between predicted, simulated, and experimental thermodynamic properties of neon, argon, krypton, and xenon, up to twice the critical density and up to five times the critical temperature. In order to achieve 1% accuracy of the pressure at liquid densities, the EOS must incorporate the effect of ATM forces. The ATM factor in the rescaled two-body energy is most important at temperatures around and lower than the critical one. Nonetheless, the rescaling of two-body diameter cannot be neglected at liquid-like densities even at high temperature. This methodology can be extended straightforwardly to deal with other two- and three-body potentials. It could also be used for other nonpolar substances where a spherical two-body potential is still a reasonable coarse-grain approximation.

The diffusivity of a nanoparticle suspended in a liquid crystal is investigated in the limit of nematic ordering and under isotropic conditions. Molecular simulations are performed with the liquid-crystalline solvent represented at the level of Gay–Berne mesogens in the canonical (N,V,T) ensemble. The mesogen–colloid interaction strength is varied to induce anchoring that ranges from parallel to perpendicular. Mean square displacements, orientational correlation functions, and relative colloidal diffusivities are reported for different types of mesogenic anchoring on the nanoparticle. The Gay–Berne parametrization is contextualized with respect to experimental observations, and a specific set of parameters is found to reproduce the characteristic ratio of mesogenic diffusivities observed in recent experiments. The results presented in this work provide a means to determine anchoring strength at small length scales, and the parameterizations provided in this work could serve as a starting point to interpret experimental data for nanoparticle suspensions in liquid-crystals at a molecular level.

A three-dimensional molecular theory is used to describe the effect of flow on the defects that arise around nanoparticles and nanodroplets suspended in a nematic liquid crystal. It is observed that flow displaces the Saturn ring line defect that forms around a nanoparticle at equilibrium in the upstream direction; it is eventually closed by the flow and becomes a Hedgehog point defect. In contrast, the Saturn ring that forms around a nanodroplet is slightly displaced in the downstream direction. Experimental measurements of defects around nanoparticles have not been reported in the literature. In the absence of experiments, the validity of theoretical predictions is assessed through a direct comparison to results of many-body molecular dynamics simulations of a coarse grain liquid crystal model. Theoretical predictions and molecular simulations are in quantitative agreement, thereby lending credibility to the predictions presented in this work and suggesting that flow can be used to manipulate defect structure and aggregation of nanoparticles in nematic liquid crystals.

We have carried out extensive equilibrium molecular-dynamics simulations to study quantitatively the topology of the temperature versus density phase diagrams and related interfacial phenomena in a partially miscible symmetric Lennard-Jones binary mixture. The topological features are studied as a function of miscibility parameter, alpha = epsilonAB/epsilonAA. Here epsilonAA = epsilonBB and epsilonAB stand for the parameters related to the attractive part of the intermolecular interactions for similar and dissimilar particles, respectively. When the miscibility varies in the range 0alpha1, a continuous critical line of consolute points Tcons(rho)--critical demixing transition line--appears. This line intersects the liquid-vapor coexistence curve at different positions depending on the values of alpha, yielding mainly three different topologies for the phase diagrams. These results are in qualitative agreement to those found previously for square-well and hard-core Yukawa binary mixtures. The main contributions of the present paper are (i) a quantitative analysis of the phase behavior and (ii) a detailed study of the liquid-liquid interfacial and liquid-vapor surface tensions, as function of temperature and miscibility as well as its relationship to the topological features of the phase diagrams.