Classical Simulation Model Research Articles

Quantitative predictions from molecular simulations using explicit or implicit interactions

AbstractEquilibrium simulations of molecular systems allow to extract many physicochemical properties. Given an “accurate enough” model, a “large enough” simulation system and “long enough” simulations, such calculations should yield accurate predictions of properties that can be tested by experimental measurements. Non‐equilibrium simulations can be used as a tool to obtain specific properties like viscosity or conductivity, but they have the drawback that in general only one property per simulation is produced. In addition, a range of methods is available for computing free energy differences. We here review the state of the art of using classical simulation models for generating quantitative predictions. Popular force fields have significant predictive power already but there is room for improvement. Bonded force potentials may need to be replaced by more accurate ones to better reproduce vibrational frequencies. Simplification of non‐bonded force terms, such as cut‐offs for electrostatic or dispersion interactions, should be avoided. Routine usage of force field methods will therefore require some tuning of parameters. Despite the extensive toolbox that is available for producing quantitative results, the computational cost of explicit solvent simulation is significant and therefore, approximate methods like implicit solvent models remain popular and are still being developed. Based on fundamental arguments as well as on examples of solvation free energies, host–guest complexation and non‐covalent association of molecules in solution, we conclude that implicit solvents as well as algorithmic simplifications are most useful when validation using experimental data or rigorous theoretical treatments is possible.This article is categorized under:Molecular and Statistical Mechanics > Molecular Dynamics and Monte‐Carlo MethodsTheoretical and Physical Chemistry > Statistical MechanicsSoftware > Simulation Methods

Harnessing aspect-oriented programming on GPU: application to warp-level parallelism

Stochastic simulations involve multiple replications in order to build confidence intervals for their results, and designs of experiments (DOEs) to explore their parameters set. In this paper, we propose warp–level parallelism (WLP), a GPU–enabled solution to compute multiple replications in parallel (MRIP) on GPUs (graphics processing units). GPUs are intrinsically tuned to process efficiently the same operation on several data, which is not suited to parallelise MRIP or DOEs. Our approach proposes to rely on small thread groups, called warps, to perform independent computations such as replications. This approach has proved to be efficient on three classical simulation models, but originally lacked the transparency users might expect. In this work, we enhance WLP using aspect oriented programming (AOP). Our work describes the way to combine CUDA and AOP, and brings forward the techniques available to exploit AOP in a CUDA–enabled development.

Improved pump turbine transient behaviour prediction using a Thoma number-dependent hillchart model

Water hammer phenomena are important issues for high head hydro power plants. Especially, if several reversible pump-turbines are connected to the same waterways there may be strong interactions between the hydraulic machines. The prediction and coverage of all relevant load cases is challenging and difficult using classical simulation models. On the basis of a recent pump-storage project, dynamic measurements motivate an improved modeling approach making use of the Thoma number dependency of the actual turbine behaviour. The proposed approach is validated for several transient scenarios and turns out to increase correlation between measurement and simulation results significantly. By applying a fully automated simulation procedure broad operating ranges can be covered which provides a consistent insight into critical load case scenarios. This finally allows the optimization of the closing strategy and hence the overall power plant performance.

Modeling of the Particles Pinning Effect on Grain Growth

In silicon steels, interaction of grain boundaries with particles occurs in a selective way. Currently, it is very difficult to include this preferential interaction directly in the classical simulation models. A new approach of grain growth simulation based on the concept of curvature-driven migration of the grain boundaries in the presence of particles has been used to study the abnormal grain growth (AGG) in Fe-3%Si alloy.

Modeling of the neighborhood topological effect on grain growth in presence of particles pinning

A model for grain growth with the particles effect is suggested. This model, which presents an extension of the von Neumann–Mullins law in presence of pinning particles, predicts two-grain critical numbers. Greater than the minimal critical number or less than the maximal critical number the grain boundary can be moving. Between the two limiting numbers no grain growth takes place. These limiting numbers permit us to introduce the preferential influence of particles on grain boundaries in the simulation procedure. Currently, it is very difficult to include this preferential interaction directly in the classical simulation models. A computer simulation by a modified Monte-Carlo potts technique is used to test our proposed model.

Nanoscale Tensile, Shear, and Failure Properties of Layered Silicates as a Function of Cation Density and Stress

Mechanical properties of layered silicates on the nanometer scale have been associated with large uncertainty. We attempt to clarify the linear elastic properties including tensile moduli, shear moduli, and potential failure mechanisms for the minerals pyrophyllite, montmorillonite, and mica in the order of increasing cation exchange capacity (CEC) under a broad range of stress using electronic structure calculations, semiempirical classical molecular dynamics simulation, and the comparison to available macroscopic experimental data. In-plane tensile moduli (xx and yy) are ∼160 GPa independent of CEC and stress, whereas perpendicular tensile moduli (zz) range from 5 to 60 GPa as a function of CEC at low stress (0.01 to 1 GPa) and approach in-plane values at high stress. In-plane shear moduli (xy) are ∼70 GPa independent of CEC and the shear strength increases from ∼1 to ∼3 GPa with increasing cation density. Shear moduli parallel to the layers (xz and yz) are between 2 and 20 GPa as a function of CEC, with a shear strength of 0.2 to 1 GPa beyond which the layers exhibit lateral shear flow. Tensile zz moduli, shear moduli, and shear strength in the xz and yz direction reach a local minimum at a cation density of 0.3 relative to mica. The simulation suggests sliding of the layers, in-plane kinks, and cation intrusion into the layers as potential failure mechanisms equal to amorphization on the macroscale. The anisotropy and stress-dependence of the mechanical properties is determined by the presence of rigid layers and flexible interlayer spaces of variable cation density. Current classical simulation models tend to overestimate in-plane moduli (xx, yy, xy) in a systematic way relative to electronic structure (DFT) and experimental results.

Water Simulation Model with Explicit Three-Molecule Interactions

Much effort has been directed at developing models for the computer simulation of liquid water. The simplest models involve effective two-molecule interactions, parametrized from experiment, for use in classical molecular dynamics simulations. These models have been very successful in describing the structure and dynamics of liquid water at room temperature and one atmosphere pressure. A completely successful model, however, should be robust enough to describe the properties of liquid water at other thermodynamic points, water's complicated phase diagram, heterogeneous situations like the liquid/vapor interface, ionic, and other aqueous solutions, and confined and biological water. In this paper, we develop a new classical simulation model with explicit three-molecule interactions. These interactions presumably make the model more robust in the senses described above, and since they are short-ranged, the model is efficient to simulate. The model is formulated as a perturbation from a classical two-molecule interaction model, where the forms of the correction to the two-molecule term and the three-molecule terms result from electronic structure calculations on dimers and trimers. The magnitudes of these perturbations, however, are determined empirically. The resulting model improves upon the well-known two-molecule interaction models for both static and dynamic properties.

Accurate FEM/BEM Simulation of Wireless Passive Surface Acoustic Wave Sensors

The wireless passive surface acoustic wave (SAW) impedance-loaded sensors offer new and exciting perspectives for remote monitoring and controlling of moving parts, even in harsh environments. However, the classical simulation models such as equivalent circuit model (ECM) and coupling of modes (COM) model are not rigorous enough for these sensors since these sensors usually work in the RF band. We try to make it more accurate by using FEM/BEM (combined finite element method and boundary element method) model to determine some key parameters used in the COM model of impedance-loaded SAW sensors. In this paper, we use periodic Green function which is the basis of FEM/BEM model to determine the key parameters. The result of measurements on real SAW is nearly in accordance with that of simulations.

Are water simulation models consistent with steady-state and ultrafast vibrational spectroscopy experiments?

Vibrational spectroscopy can provide important information about structure and dynamics in liquids. In the case of liquid water, this is particularly true for isotopically dilute HOD/D 2O and HOD/H 2O systems. Infrared and Raman line shapes for these systems were measured some time ago. Very recently, ultrafast three-pulse vibrational echo experiments have been performed on these systems, which provide new, exciting, and important dynamical benchmarks for liquid water. There has been tremendous theoretical effort expended on the development of classical simulation models for liquid water. These models have been parameterized from experimental structural and thermodynamic measurements. The goal of this paper is to determine if representative simulation models are consistent with steady-state, and especially with these new ultrafast, experiments. Such a comparison provides information about the accuracy of the dynamics of these simulation models. We perform this comparison using theoretical methods developed in previous papers, and calculate the experimental observables directly, without making the Condon and cumulant approximations, and taking into account molecular rotation, vibrational relaxation, and finite excitation pulses. On the whole, the simulation models do remarkably well; perhaps the best overall agreement with experiment comes from the SPC/E model.

Molecular structure of the outer bacterial membrane of Pseudomonas aeruginosa via classical simulation.

A detailed structural analysis has been performed of the outer bacterial membrane of Pseudomonas aeruginosa using a parameterized classical simulation model (R. D. Lins and T. P. Straatsma, Biophysical Journal, 2001, Vol. 81, pp. 1037-1046) with modest modifications. The structural analysis of the membrane is presented and newly discovered characteristics of the membrane are discussed. Simulations indicate that the relative contribution of different ligands to calcium ion coordination varies across the membrane, while maintaining a constant average coordination number of 6.1. Water penetrates the surface of the membrane to a depth of about 30 A. The hydration of ions and phosphate groups is shown to depend on location within the membrane. A measure of saccharide residue orientation is defined and average orientations are presented. Saccharide residues possess varying degrees of motion with a trend of greater mobility at the membrane surface. However, their motion is limited and even in the membrane outer core region the average structure appears fairly rigid over a period of 1 ns.

Systems Analysis in Water‐Distribution Network Design: From Theory to Practice

Review of the use of system‐analysis techniques, and in particular optimization, to design water‐distribution networks reveals that in spite of the considerable development of models in the literature they have not been accepted into practice. This lack of acceptance is present even though a competitive evaluation of the component design models has shown them to be capable of designing realistic networks. The lack of acceptance is attributed primarily to the absence of suitable packaging to make the algorithms useful in a design office environment. This evidence suggests that, from a practice point of view, there is relatively little need for further development of these component design models, other than the packaging. Reliability analysis in water‐distribution network design has not yet entered practice either. In contrast to the component size problem, reliability analysis has not been accepted primarily because of a lack of reliability measure that is both comprehensive in its interpretation of reliability and computationally feasible. More research is needed in this area before reliability can be explicitly incorporated into design procedures. Development of decision support systems (DSS) incorporating optimization and classical simulation models with an interactive graphics capability is seen as being a major priority for future research in the field, particularly if optimization approaches are to become more common in design practice. These DSSs can assist the designer in including and evaluating reliability and generating alternative solutions.