Shear-induced parallel-to-perpendicular orientation transition in the amphiphilic lamellar phase: a nonequilibrium molecular-dynamics simulation study

The present work is devoted to a study of the shear-induced parallel-to-perpendicular orientation transition in the lamellar system by the large-scale nonequilibrium molecular-dynamics (NEMD) simulation. An effective generic model-A2B2 tetramer for amphiphilies is used. The NEMD simulation produces unambiguous evidence that undulation instability along the vorticity direction sets in well above a critical shear rate and grows in magnitude as the shear rate is further increased. At a certain high shear rate, the coherent undulation instability grows so large that defects are nucleated and the global lamellar monodomain breaks into several aligned lamellar domains. Subsequently layers in these domains rotate into the perpendicular orientation with the rotation of chains towards the y direction, merge into a global perpendicular-aligned lamellar monodomain, and organize into a perfect well-aligned perpendicular lamellar phase by the migration and annihilation of edge dislocations and disclinations. The macroscopic observable viscosity as a function of time or shear rate is correlated with the structural response such as the mesoscopic domain morphology and the microscopic chain conformation. The onset of undulation instability concurs with the start-up of shear-thinning behavior. During the orientation transformation at the high shear rate, the complex time-dependent thixotropic behavior is observed. The smaller viscosity in the perpendicular lamellar phase gives an energetic reason for the shear-induced orientation transition.     

Measure of accuracy for multicanonical molecular-dynamics simulation

A measure of the flatness of the energy probability distribution for multicanonical molecular-dynamics (MMD) simulation is presented. It (the flatness measure) can be introduced by a slight change in the renewing scheme of the MMD potential energy. Our proposed measure is applied to liquid Ar with a Lennard-Jones potential system in order to investigate the influence of flatness on the simulation results such as internal energy and specific heat at constant volume. We find that the accuracy of MMD simulation is influenced not only by the flatness of the energy probability distribution but also by the width of the energy region that is accessible during the MMD simulation.     

Constant surface-tension molecular-dynamics simulation methods for anisotropic systems

We propose a simulation method for liquid-liquid interface under constant surface tension and constant normal pressure. The method introduces an anisotropic factor in the cell dynamics which avoids artifacts such as continuous expansion or contraction of the cell lengths. This allows simulation of a full range of surface tensions including when the value is 0, i. e, hydrostatic pressure.     

Shear viscosity of molten alkali halides from equilibrium and nonequilibrium molecular-dynamics simulations

The shear viscosity of molten NaCl and KCl was calculated through equilibrium (EMD) and nonequilibrium molecular-dynamics (NEMD) simulations in the canonical (N,V,T) ensemble. Two rigid-ion potentials were investigated, namely, the Born-Mayer-Huggins-Tosi-Fumi potential and the Michielsen-Woerlee-Graaf-Ketelaar potential with the parameters proposed by Ladd. The NEMD simulations were performed using the SLLOD equations of motion [D. J. Evans and G. P. Morriss, Phys. Rev. A 30, 1528 (1984)] with a Gaussian isokinetic thermostat and the results are compared with those obtained from Green-Kubo EMD (N,V,T) simulations and experimental shear viscosity data. The NEMD zero strain rate shear viscosity, eta(0), was obtained by fitting a simplified Carreau-type equation and by application of mode-coupling theory, i.e., a eta-gamma(1/2) linear relationship. The values obtained from the first method are found to be significantly lower than those predicted by the second. The agreement between the EMD and NEMD results with experimental data is satisfactory for the two potentials investigated. The ion-ion radial distribution functions obtained with the two rigid-ion potentials for both molten salts are discussed in terms of the differences between the two models.     

Calculating fifth-order Raman signals for various molecular liquids by equilibrium and nonequilibrium hybrid molecular dynamics simulation algorithms

The fifth-order two-dimensional (2D) Raman signals have been calculated from the equilibrium and nonequilibrium (finite field) molecular dynamics simulations. The equilibrium method evaluates response functions with equilibrium trajectories, while the nonequilibrium method calculates a molecular polarizability from nonequilibrium trajectories for different pulse configurations and sequences. In this paper, we introduce an efficient algorithm which hybridizes the existing two methods to avoid the time-consuming calculations of the stability matrices which are inherent in the equilibrium method. Using nonequilibrium trajectories for a single laser excitation, we are able to dramatically simplify the sampling process. With this approach, the 2D Raman signals for liquid xenon, carbon disulfide, water, acetonitrile, and formamide are calculated and discussed. Intensities of 2D Raman signals are also estimated and the peak strength of formamide is found to be only five times smaller than that of carbon disulfide.     

Reverse nonequilibrium molecular-dynamics calculation of the Soret coefficient in liquid benzene/cyclohexane mixtures

Reverse nonequilibrium molecular dynamics is the method applied here for the investigation of thermal diffusion in realistic molecular fluids. The Soret coefficients of benzene/cyclohexane mixtures are calculated using an all-atom model. The autocorrelation functions indicate that the mole fraction gradient converges much slower than the temperature gradient. Compared to experimental data, the results show the same tendency of the Soret coefficient variation versus the mole fraction. Although a systematic error exists for the magnitude of the Soret coefficient, a meanwhile systematic error for both the mutual diffusion and thermal diffusion coefficients provides some explanation of it; and the calculation with different force field parameters indicates a possibility to annihilate the systematic error. The influences of algorithm variables such as cutoff lengths and perturbation intensities are tested. Furthermore the temperature dependence of the Soret effect is observed, yielding the same trend as previous studies.     

Classical molecular-dynamics simulation of the hydroxyl radical in water

We have studied the hydration and diffusion of the hydroxyl radical OH0 in water using classical molecular dynamics. We report the atomic radial distribution functions, hydrogen-bond distributions, angular distribution functions, and lifetimes of the hydration structures. The most frequent hydration structure in the OH0 has one water molecule bound to the OH0 oxygen (57% of the time), and one water molecule bound to the OH0 hydrogen (88% of the time). In the hydrogen bonds between the OH0 and the water that surrounds it the OH0 acts mainly as proton donor. These hydrogen bonds take place in a low percentage, indicating little adaptability of the molecule to the structure of the solvent. All hydration structures of the OH0 have shorter lifetimes than those corresponding to the hydration structures of the water molecule. The value of the diffusion coefficient of the OH0 obtained from the simulation was 7.1x10(-9) m2 s(-1), which is higher than those of the water and the OH-.     

Test of classical nucleation theory via molecular-dynamics simulation

A direct test of classical nucleation theory (CNT) is made using molecular-dynamics simulations. The relation between critical nucleus size and undercooling temperature is extracted and the result yields the solid-liquid interfacial energy. It is shown that the CNT, within the assumptions made for spherical nucleus in supercooled liquid, is valid in the critical regime of nucleation for a large range of undercooling and nucleus size.     

A validation of the p-SLLOD equations of motion for homogeneous steady-state flows

A validation of the p-SLLOD equations of motion for nonequilibrium molecular dynamics simulation under homogeneous steady-state flow is presented. We demonstrate that these equations generate the correct center-of-mass trajectory of the system, are completely compatible with (and derivable from) Hamiltonian dynamics, satisfy an appropriate energy balance, and require no fictitious external force to generate the required homogeneous flow. It is also shown that no rigorous derivation of the SLLOD equations exists to date.     

A temperature control technique for nonequilibrium molecular simulation

We describe a dynamical approach to thermal regulation in molecular dynamics. Temperature is moderated by a control law and an additional variable, as in Nose dynamics, but whose influence on the system decreases as the system approaches equilibrium. This device enables approximation of microcanonical averages and autocorrelation functions consistent with a given target temperature. Moreover, we demonstrate that the suggested technique is effective for the control of heat dissipation in a nonequilibrium setting, first by showing that the temperature control correctly regulates heat introduced by a rapid change to the system, and then by studying the slow relaxation of vibrational degrees of freedom (e.g., due to bonded atoms) in a solvent bath.     

Langevin stabilization of molecular-dynamics simulations of polymers by means of quasisymplectic algorithms

Algorithms for the numerical integration of Langevin equations are compared in detail from the point of view of their accuracy, numerical efficiency, and stability to assess them as potential candidates for molecular-dynamics simulations of polymeric systems. Some algorithms are symplectic in the deterministic frictionless limit and prove to stabilize long time-step integrators. They are tested against other popular algorithms. The optimal algorithm depends on the main goal: accuracy or efficiency. The former depends on the observable of interest. A recently developed quasisymplectic algorithm with great accuracy in the position evaluation exhibits better overall accuracy and stability than the other ones. On the other hand, the well-known BrunGer-Brooks-Karplus [Chem. Phys. Lett. 105, 495 (1982)] algorithm is found to be faster with limited accuracy loss but less stable. It is also found that using higher-order algorithms does not necessarily improve the accuracy. Moreover, they usually require more force evaluations per single step, thus leading to poorer performances.     

Equivalence of nonequilibrium algorithms for simulations of planar Couette flow in confined fluids

Shear flow in fluids confined between planar solid walls is conventionally simulated by moving the walls past each other at constant relative velocity. In infinite fluids (in periodic boundary conditions), it is simulated using one of the "synthetic" nonequilibrium algorithms (the so-called Sllod and Dolls algorithms). Here I formulate the boundary conditions for the motion of confining walls that make these three algorithms equivalent in the weak-field limit.     

Large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction and nanobubble formation

We performed large-scale molecular-dynamics simulation of nanoscale hydrophobic interaction manifested by the formation of nanobubble between nanometer-sized hydrophobic clusters at constrained equilibrium. Particular attention is placed on the tendency of formation and stability of nanobubbles in between model nanoassemblies which are composed of hydrophobic clusters (or patches) embedded in a hydrophilic substrate. On the basis of physical behavior of nanobubble formation, we observed a change from short-range molecular hydrophobic interaction to midrange nanoscopic interaction when the length scale of hydrophobe approaches to about 1 nm. We investigated the behavior of nanobubble formation with several different patterns of nonpolar-site distribution on the nanoassemblies but always keeping a constant ratio of nonpolar to polar monomer sites. Dynamical properties of confined water molecules in between nanoassemblies are also calculated.     

Ab initio molecular-dynamics simulation of aqueous proton solvation and transport revisited

The solvation and transport of the hydrated excess proton is studied using the Car-Parrinello molecular-dynamics (CPMD) simulation method. The simulations were performed using BLYP and HCTH gradient-corrected exchange-correlation energy functionals. The fictitious electronic mass was chosen to be small enough so that the underlying water structural and dynamical properties were converged with respect to this important CPMD simulation parameter. An unphysical overstructuring of liquid water in the CPMD simulations using the BLYP functional resulted in the formation of long-lived hydrogen-bonding structures involving the excess proton and a particular (special) water oxygen. The excess proton was observed to be attracted to the special oxygen through the entire length of the BLYP CPMD simulations. Consequently, the excess proton diffusion was limited by the mobility of the special oxygen in the slowly diffusing water network and, in turn, the excess proton self-diffusion coefficient was found to be significantly below the experimental value. On the other hand, the structural properties of liquid water in the HCTH CPMD simulation were seen to be in better agreement with experiment, although the water and excess proton diffusions were still well below the experimental value.     

Semi-classical generalized Langevin equation for equilibrium and nonequilibrium molecular dynamics simulation

Molecular dynamics (MD) simulation based on Langevin equation has been widely used in the study of structural, thermal properties of matter in different phases. Normally, the atomic dynamics are described by classical equations of motion and the effect of the environment is taken into account through the fluctuating and frictional forces. Generally, the nuclear quantum effects and their coupling to other degrees of freedom are difficult to include in an efficient way. This could be a serious limitation on its application to the study of dynamical properties of materials made from light elements, in the presence of external driving electrical or thermal fields. One example of such system is single molecule dynamics on metal surface, an important system that has received intense study in surface science. In this review, we summarize recent effort in extending the Langevin MD to include nuclear quantum effect and their coupling to flowing electrical current. We discuss its applications in the study of adsorbate dynamics on metal surface, current-induced dynamics in molecular junctions, and quantum thermal transport between different reservoirs.     

Ion trajectory simulation for electrode configurations with arbitrary geometries

A multi-particle ion trajectory simulation program ITSIM 6.0 is described, which is capable of ion trajectory simulations for electrode configurations with arbitrary geometries. The electrode structures are input from a 3D drawing program AutoCAD and the electric field is calculated using a 3D field solver COMSOL. The program CreatePot acts as interface between the field solver and ITSIM 6.0. It converts the calculated electric field into a field array file readable by ITSIM 6.0 and ion trajectories are calculated by solving Newton's equation using Runge-Kutta integration methods. The accuracy of the field calculation is discussed for the ideal quadrupole ion trap in terms of applied mesh density. Electric fields of several different types of devices with 3D geometry are simulated, including ion transport through an ion optical system as a function of pressure. Ion spatial distributions, including the storage of positively charged ions only and simultaneous storage of positively/negatively charged ions in commercial linear ion traps with various geometries, are investigated using different trapping modes. Inelastic collisions and collision induced dissociation modeled using RRKM theory are studied, with emphasis on the fragmentation of n-butylbenzene inside an ideal quadrupole ion trap. The mass spectrum of 1,3-dichlorobenzene is simulated for the rectilinear ion trap device and good agreement is observed between the simulated and the experimental mass spectra. Collisional cooling using helium at different pressures is found to affect mass resolution in the rectilinear ion trap.     

Geometric structure of a molecule of Epitalon tetrapeptide: A molecular-dynamics simulation

Variation of the geometric parameters of a molecule of Epitalon tetrapeptide (Ala-Glu-Asp-Gly) over a period of 1500 ps was simulated by the method of molecular dynamics using AMBER force field. The structure of the molecule is stabilized by two salt bridges formed by the N-terminal nitrogen atom and oxygen atoms of Asp and Glu side chains. The biological effect of Epitalon was attributed to formation of salt or hydrogen bonds involving one or several ionizable functional groups of the molecules.     

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.     

Rosenbluth-sampled nonequilibrium work method for calculation of free energies in molecular simulation

We present methods that introduce concepts from Rosenbluth sampling [M. N. Rosenbluth and A. W. Rosenbluth, J. Chem. Phys. 23, 356 (1955)] into the Jarzynski nonequilibrium work (NEW) free-energy calculation technique [C. Jarzynski, Phys. Rev. Lett. 78, 2690 (1997)]. The proposed hybrid modifies the way steps are taken in the NEW process. With it, each step is selected from a range of alternatives, with bias given to steps that contribute the least work. The definition of the work average is modified to account for the bias. We introduce two variants of this method, lambda-bias sampling and configuration-bias sampling, respectively; a combined lambda- and configuration-bias method is also considered. By reducing the likelihood that large nonequilibrated work values enter the ensemble average, the Rosenbluth sampling aids in remedying problems of inaccuracy of the calculation. We demonstrate the performance of the proposed methods through a model system of N independent harmonic oscillators. This model captures the difficulties involved in calculating free energies in real systems while retaining many tractable features that are helpful to the study. We examine four variants of this model that differ qualitatively in the nature of their phase-space overlap. Results indicate that the lambda-bias sampling method is most useful for systems with entropic sampling barriers, while the configuration-bias methods are best for systems with energetic sampling barriers. The Rosenbluth-sampling schemes yield much more accurate results than the unbiased nonequilibrium work method. Typically the accuracy can be improved by about an order of magnitude for a given amount of sampling; this improvement translates into two or more orders of magnitude less sampling required to obtain a given level of accuracy, owing to the generally slow convergence of the NEW calculation when the inaccuracy is large.