Gay-Berne Research Articles

GPU-Accelerated Molecular Dynamics Simulation to Study Liquid Crystal Phase Transition Using Coarse-Grained Gay-Berne Anisotropic Potential.

Gay-Berne (GB) potential is regarded as an accurate model in the simulation of anisotropic particles, especially for liquid crystal (LC) mesogens. However, its computational complexity leads to an extremely time-consuming process for large systems. Here, we developed a GPU-accelerated molecular dynamics (MD) simulation with coarse-grained GB potential implemented in GALAMOST package to investigate the LC phase transitions for mesogens in small molecules, main-chain or side-chain polymers. For identical mesogens in three different molecules, on cooling from fully isotropic melts, the small molecules form a single-domain smectic-B phase, while the main-chain LC polymers prefer a single-domain nematic phase as a result of connective restraints in neighboring mesogens. The phase transition of side-chain LC polymers undergoes a two-step process: nucleation of nematic islands and formation of multi-domain nematic texture. The particular behavior originates in the fact that the rotational orientation of the mesogenes is hindered by the polymer backbones. Both the global distribution and the local orientation of mesogens are critical for the phase transition of anisotropic particles. Furthermore, compared with the MD simulation in LAMMPS, our GPU-accelerated code is about 4 times faster than the GPU version of LAMMPS and at least 200 times faster than the CPU version of LAMMPS. This study clearly shows that GPU-accelerated MD simulation with GB potential in GALAMOST can efficiently handle systems with anisotropic particles and interactions, and accurately explore phase differences originated from molecular structures.

Density functional theory of freezing of a system of conjugated oligomers parameterised via Gay–Berne potential

ABSTRACTDensity functional theory (DFT) of freezing is used to study the isotropic–nematic, isotropic–smectic A and nematic–smectic A phase transitions in a system of large, semi-flexible conjugated oligomers parameterised within Gay–Berne (GB) potential. The pair correlation functions of the isotropic fluid, used as structural inputs in the DFT, are calculated by solving the Percus–Yevick integral equation theory. Large number of spherical harmonic coefficients of each orientation-dependent functions has been considered to ensure the numerical accuracy at different densities and temperatures for the system of these model GB ellipsoids having large aspect ratio (length-to-breadth ratio). We found that the system of GB ellipsoids parameterised for conjugated oligomers shows stable isotropic, nematic and smectic A phases. At low temperatures, on increasing the density, isotropic fluid makes a direct transition to smectic A phase. Nematic phase get stabilised in between the isotropic and smectic A phases on increasing the temperature. Using the transition parameter obtained through the DFT, we have plotted the temperature–density and pressure–temperature phase diagrams which are found to be qualitatively similar to the one obtained in simulations for the systems with low aspect ratio GB particles.

An anisotropic coarse-grained model based on Gay-Berne and electric multipole potentials and its application to simulate a DMPC bilayer in an implicit solvent model.

In this work, we aim at optimizing the performance of the anisotropic GBEMP model, which adopts a framework by combining a Gay-Berne (GB) anisotropic potential with an electric multipole (EMP) potential, in simulating a DMPC lipid bilayer in an implicit solvent model. First, the Gay-Berne parameters were initially obtained by fitting to atomistic profiles of van der Waals interactions between homodimers of molecular fragments while EMP parameters was directly derived from the expansion of point multipoles at predefined EMP sites. Second, the GB and EMP parameters for DMPC molecule were carefully optimized to be comparable to AMBER atomistic model in the calculations of the dipole moments of DMPC monomers adopting different conformations as well as the nonbonded interactions between two DMPC molecules adopting different conformations and separated at various distances. Finally, the GB parameters for DMPC were slightly adjusted in simulating a 72 DMPC bilayer system so that our GBEMP model would be able to reproduce a few important structural properties, namely, thickness (DHH), area per lipid ( AL) and volume per lipid ( VL). Meanwhile, the atomistic and experimental results for electron density profiles and order parameters were reproduced reasonably well by the GBEMP model, demonstrating the promising feature of GBEMP model in modeling lipid systems. Finally, we have shown that current GBEMP model is more efficient by a factor of about 25 than AMBER atomistic point charge model.

SOLVATION FORCE OF ELLIPSE-SHAPED MOLECULES MOVING IN ONE DIMENSION AND CONFINED BETWEEN TWO PARALLEL PLANAR WALLS

The model fluids containing hard ellipses (HEs) and Gay-Berne (GB) particles where their center is moving in one dimension and confined between two parallel walls with different interactions are investigated using Monte Carlo simulation, NVT ensemble. The dependency of fluid pressure with respect to the wall distances is studied. The oscillatory behaviors are seen in this quantity against wall separations. The total average number density profile of particles is calculated using the angular number density. For both HE and GB particles confined between hard walls the total average number density at the wall shows a similar oscillatory behavior. We also related the pressure of these systems to the relevant solvation force between two colloidal particles. We have investigated the dependency of this quantity to the packing fraction, temperature, structure of the walls confining the particles and the interaction between ellipses of the fluid. Finally it is possible to reach the required solvation forces by changing the thermodynamic or structural properties.

Mesoscale modeling of cement matrix using the concept of building block

ABSTRACTCalcium silicate hydrate (C-S-H) gel is the cohesive phase in cement paste and critically controls the cement hydration. Atomistic models can reproduce reasonable structural and mechanical properties of C-S-H gel at the nano scale. However, the length and time scale of such all-atom modeling technique are restrained by limited computing power. Under this context, coarse-grained modeling technique emerges as a useful alternative for investigating cement paste at extended length and time scale. Here, we regard the building block of cement as ellipsoid and develop a coarse-grained model of cement matrix based on the Gay-Berne (GB) potential. Emphasis of the present paper is on the parameterization and interpretation of the GB potential formula.

Dissipative particle dynamics thermostat: a novel thermostat for molecular dynamics simulation of liquid crystals with Gay-Berne potential

The Gay-Berne (GB) model has been proved to be highly successful in the simulation of liquid crystal phases via both molecular dynamics (MD) and nonequilibrium molecular dynamics (NEMD). However, the conventional thermostats used in the simulations of GB systems, such as Nose-Hoover and Langevin thermostats, have serious shortcomings especially in NEMD simulations. Recently, dissipative particle dynamics (DPD) has established itself as a useful thermostat for soft matter simulations, whereas the application of DPD thermostat in (NE)MD simulations is limited to the spherically isotropic potential models, such as the Lennard-Jones model. Considering the virtues of the DPD thermostat, that is, local, momentum conserved, and Galilean invariant, we extend the DPD thermostat to the non-spherical GB model. It is interesting to find that the translational DPD and rotational DPD thermostats can be used in the GB system independently and both can achieve the thermostatting effects. Also, we compared the performance of the DPD thermostat with other commonly used thermostats in NEMD simulations by investigating the streaming velocity profiles and the dynamics of phase separation in a typical but simple binary GB mixture under shear field. It is revealed that the known virtues of DPD thermostats, such as Galilean invariant, shear velocity profile-unbiased, and unscreened hydrodynamic interactions, are still intact when applying to GB systems. Finally, the appropriate parameters for the DPD thermostat in the GB system are identified for future investigations.

Molecular aspect ratio and anchoring strength effects in a confined Gay–Berne liquid crystal

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.

“Ideal glassformers” vs “ideal glasses”: Studies of crystal-free routes to the glassy state by “potential tuning” molecular dynamics, and laboratory calorimetry

The ability of some liquids to vitrify during supercooling is usually seen as a consequence of the rates of crystal nucleation (and∕or crystal growth) becoming small [D. R. Uhlmann, J. Non-Cryst. Solids 7, 337 (1972)]--and thus a matter of kinetics. However, there is evidence dating back to the empirics of coal briquetting for maximum trucking efficiency [D. Frenkel, Physics 3, 37 (2010)] that some object shapes find little advantage in self-assembly to ordered structures--meaning random packings prevail. Noting that key studies of non-spherical object packing have never been followed from hard ellipsoids [A. Donev, F. H. Stillinger, P. M. Chaikin, and S. Torquato, Phys. Rev. Lett. 92, 255506 (2004); A. Donev, I. Cisse, D. Sachs, E. A. Variano, F. H. Stillinger, R. Connelly, S. Torquato, and P. M. Chaikin, Science 303, 990 (2004)] or spherocylinders [S. R. Williams and A. P. Philipse, Phys. Rev. E 67, 051301 (2003)] (diatomics excepted [S.-H. Chong, A. J. Moreno, F. Sciortino, and W. Kob, Phys. Rev. Lett. 94, 215701 (2005)] into the world of molecules with attractive forces, we have made a molecular dynamics study of crystal melting and glass formation on the Gay-Berne (G-B) model of ellipsoidal objects [J. G. Gay and B. J. Berne, J. Chem. Phys. 74, 3316 (1981)] across the aspect ratio range of the hard ellipsoid studies. Here, we report that in the aspect ratio range of maximum ellipsoid packing efficiency, various G-B crystalline states that cannot be obtained directly from the liquid, disorder spontaneously near 0 K and transform to liquids without any detectable enthalpy of fusion. Without claiming to have proved the existence of single component examples, we use the present observations, together with our knowledge of non-ideal mixing effects, to discuss the probable existence of "ideal glassformers"--single or multicomponent liquids that vitrify before ever becoming metastable with respect to crystals. We find evidence that "ideal glassformer" systems might also be highly fragile systems, approaching the "ideal glass" condition. We link this to the high "volume fragility" behavior observed in recent hard dumbbell studies at similar length∕diameter ratios [R. Zhang and K. S. Schweitzer, J. Chem. Phys. 133, 104902 (2010)]. The discussion suggests some unusual systems for laboratory study. Using differential scanning calorimetry detection of fusion points T(m), liquidus temperatures T(l), and glass transition temperatures T(g), we describe a system that would seem incapable of crystallizing before glass transition, i.e., an "ideal glassformer." The existence of crystal-free routes to the glassy state will eliminate precrystalline fluctuations as a source of the dynamic heterogeneities that are generally considered important in the discussion of the "glassy state problem [P. W. Anderson, Science 267, 1615 (1995)]."

Mesogen polarity effects on biaxial nematics. Centrally located dipoles

We investigate the phase organisation of thermotropic biaxial Gay-Berne (GB) mesogens yielding a biaxial nematic (Nb) phase upon endowing them with a central point dipole. We study the effects of changing the strength and orientation of the dipole on the phase behaviour, and in particular we examine, using molecular dynamics (MD) simulations, the possibility of improving the stability of the Nb phase. After mapping the boundaries of the Nb phase, we find that the strength of the embedded dipole is the parameter with the strongest influence on the mesogenic properties, while its orientation plays a minor role. For these central dipole systems, we find that the Nb phase organisation is stable only for mesogens with relatively weak dipole moments, while it disappears if electrostatic interactions become comparable in magnitude with dispersion interactions.

Coarse-grained simulations for organic molecular liquids based on Gay-Berne and electric multipole potentials

Coarse-grained studies of CH(3)SH, CH(3)CHO and CHCl(3) liquids, based on anisotropic Gay-Berne (GB) and electric multipole potentials (EMP), demonstrate that the coarse-grained model is able to qualitatively reproduce the results obtained from the atomistic model (AMOEBA polarizable force field) and allows for significant saving in computation time. It should be pointed out that the accuracy of the coarse-grained model is very sensitive to how well the anisotropic GB particle is defined and how satisfactorily the EMP sites are chosen.

Note: Modification of the Gay-Berne potential for improved accuracy and speed

A modification of the Gay-Berne (GB) potential is proposed which is about 10% to 20% more speed efficient and statistically more accurate in reproducing the energy of interaction of two linear Lennard-Jones tetratomics when averaged over all orientations. For the special cases of end-to-end and side-by-side configurations, the new potential is equivalent to the GB one. A simple generalization to dissimilar particles of D∞h symmetry is presented but does not retain the superior agreement with respect to its GB counterpart, except at close range.

Shear viscosity of binary mixtures: The Gay–Berne potential

The Gay–Berne (GB) potential model is an interesting and useful model to study the real systems. Using the potential model, we intend to examine the thermodynamical properties of some anisotropic binary mixtures in two different phases, liquid and gas. For this purpose, we apply the integral equation method and solve numerically the Percus–Yevick (PY) integral equation. Then, we obtain the expansion coefficients of correlation functions to calculate the thermodynamical properties. Finally, we compare our results with the available experimental data [e.g., HFC-125+propane, R-125/143a, methanol+toluene, benzene+methanol, cyclohexane+ethanol, benzene+ethanol, carbon tetrachloride+ethyl acetate, and methanol+ethanol]. The results show that the GB potential model is capable for predicting the thermodynamical properties of binary mixtures with acceptable accuracy.

A modified Gay–Berne model for liquid crystal molecular dynamics simulation

We present a modified Gay–Berne (GB) potential, in which the attraction force can be tuned by adjusting one parameter only. An attractive parameter Ps is introduced for describing the strength of attractive force relative to its repulsive counterpart between large particles. Using the proposed model, the phase transition phenomena of liquid crystal molecules as the density varies from 0.32 to 0.24, have been investigated. Simulation results are compared with the results of using traditional GB potential. The phases and phase transitions observed by using different attractive parameters show the importance of studying the variation of attractive forces, which resulted in dramatic different phase transition phenomena.

Investigation of anisotropic thermal conductivity of uniaxial and biaxial Gay–Berne particles with molecular dynamics simulation

In this study, we investigated uniaxial and biaxial Gay–Berne (GB) particles with the help of the molecular dynamics (MD) simulation. Anisotropic thermal conductivities of the uniaxial and biaxial GB liquid crystal molecules were calculated both in the random molecular orientation and in the molecular orientations of 0°, 45° and 90° using the Müller-Plathe method. In the uniaxial molecules, it was found that the thermal conductivity ratios between the parallel and perpendicular components for the smectic and nematic phases are about 2.2:1 and 2.8:1, respectively. As for biaxial molecules, these ratios between the parallel and perpendicular components of molecules for the smectic and nematic phases are about 3.9:1 and 3.8:1, respectively.

A study of isotropic–nematic transition of quadrupolar Gay–Berne fluid using density-functional theory approach

The effects of quadrupole moments on the isotropic–nematic (IN) phase transitions are studied using the density-functional theory (DFT) for a Gay–Berne (GB) fluid for a range of length-to-breadth parameters in the reduced temperature range . The pair-correlation functions of the isotropic phase, which enter into the DFT as input parameters are found by solving the Percus–Yevick integral equation theory. The method used involves an expansion of angle-dependent functions appearing in the integral equations in terms of spherical harmonics and the harmonic coefficients are obtained by an iterative algorithm. All the terms of harmonic coefficients which involve l indices up to less than or equal to 6 are considered. The numerical accuracy of the results depends on the number of spherical harmonic coefficients considered for each orientation-dependent function. As the length-to-breadth ratio of quadrupolar GB molecules is increased, the IN transition is seen to move to lower density (and pressure) at a given temperature. It has been observed that the DFT is good to study the IN transitions in such fluids. The theoretical results have also been compared with the computer simulation results wherever they are available.

Molecular Dynamics Simulation of Organic Solvents Based on the Coarse-Grained Model

To obtain Gay-Berne (GB) parameters, we carried out Monte Carlo sampling of four reference configurations based on the Boltzmann distribution. After comparing with the van der Waals potential within the all-atom model we obtained the GB parameters. Also by fitting the charge, dipole, and quadrupole with the electric potential obtained from quantum chemical computations with Gaussian 03 we obtained the electric multipole potential (EMP) parameters. With the GB-EMP parameters we then carried out molecular dynamics simulations (MDS) for CHCl3 and tetrahydrofuran (THF) based on the coarse-grained (CG) model. Compared with the all-atom model, the CG model can reproduce the simulation results on the whole, but there are some deviations in the simulations in some details. The reason is that we only take one interaction site into account in this work. Therefore, for more complicated molecules it is necessary to take the placement of the interaction sites into account. Additionally, the multi-sites situation is also considered in the MDS within the frame of the coarse-grained model.

STUDY OF THE INHOMOGENEOUS SOFT GAUSSIAN OVERLAP FLUID

This paper has two parts. First, the classical density functional theory (DFT) has been applied to a system of soft ellipsoidal particles confined between two planar walls. For this system, both the isotropic and nematic phases are considered. To evaluate the excess free energy, two different direct correlation functions (DCF) are applied. The first is a numerical DCF calculated from the Percus–Yevick (PY) approximation (for the isotropic phase) and the second DCF is taken from the hypernetted-chain (HNC) approximation (for the nematic phase). The second part of this paper corresponds to the evaluation of the elastic constants of the Gay–Berne (GB) fluid using the DCF obtained from the HNC approximation. Our results are in good agreement with the simulation data.

Parametrization of the Gay–Berne potential for conjugated oligomer with a high aspect ratio

The Gay-Berne (GB) potential has been a popular semiempirical model for describing the short-range intermolecular forces for a wide variety of aspherical molecules, including liquid crystals and anisotropic colloids, with generally small molecular dimensions and low aspect ratios (<5). This study evaluates the parametrization of the GB potential for a high-aspect-ratio (=10) oligomer belonging to a model conjugated polymer. We elaborate that the semiflexibility associated with a large oligomer species demands a variant umbrella-sampling scheme in establishing the potentials of mean force (PMFs) for four pair ellipsoid arrangements typically utilized to parametrize the GB potential. The model ellipsoid so constructed is shown to capture the PMFs of essential intermediate arrangements as well, and, according to the results of simplex optimizations, recommendations are given for the minimum set of parameters to be included in the optimization of a large oligomer or particulate species. To further attest the parametrized GB potential, the coarse-grained (CG) Monte Carlo simulations employing the GB potential and the back-mapped, full-atom atomistic molecular dynamics (AMD) simulations were performed for a dense oligomer system at two representative system temperatures. The results indicated that the CG simulations can capture, with exceptional computational efficiency, the AMD predictions with good thermal transferability. In future perspectives, we remark on potential applications to construct efficient, parameter-free CG models for capturing fundamental material properties of large oligomer/particulate species as well as long-chain conjugated polymers.

Brownian dynamics simulation of multiphase suspension of disc-like particles and polymers

A computational model is proposed for simulating the flow of polymer nanocomposites. This model is based on a multiphase suspension of disc-like particles and polymers. The particles are represented by oblate spheroid particles that interact with each other via the Gay-Berne (GB) potential, and the polymers are modeled by finitely extensible nonlinear elastic (FENE) chains that interact with each other via the repulsive Lennard-Jones potential. The interaction between an oblate spheroid particle and a FENE chain is also considered using a modified GB potential. A Brownian dynamics simulation of the shear flows of this system was conducted to investigate the orientation behavior of disc-like particles and the rheological properties of this system. The orientation of disc-like particles was affected by polymers, and the particles in a suspension were well aligned in flows because of the flow orientation property of polymers. The predicted shear viscosity exhibited shear thinning, and the normal stress differences agree qualitatively with experimental measurements of polymer/clay nanocomposites. The simulation results suggest that the present model has the potential to be used as a computational model for polymer nanocomposites.

A soft-core Gay–Berne model for the simulation of liquid crystals by Hamiltonian replica exchange

The Gay-Berne (GB) potential has proved highly successful in the simulation of liquid crystal phases, although it is fairly demanding in terms of resources for simulations of large (e.g., N>10(5)) systems, as increasingly required in applications. Here, we introduce a soft-core GB model, which exhibits both liquid crystal phase behavior and rapid equilibration. We show that the Hamiltonian replica exchange method, coupled with the newly introduced soft-core GB model, can effectively speed up the equilibration of a GB liquid crystal phase by frequent exchange of configurations between replicas, while still recovering the mesogenic properties of the standard GB potential.