Simulation of low speed 3D nanochannel flow

This paper presents a new technique of simulating low speed nanochannel flows using molecular dynamics simulation (MDS) method. When using the molecular dynamics simulation method to study low speed nanoscale flow problems, a major difficulty is the extraction of the true flow velocity because of the highly nonlinear coupling of the low bulk flow velocity and the high velocity of molecules’ thermal motion. In all published papers the reported flow velocity is the average value of the sum of these two velocities over time. For high speed flow problems the conventional MDS method can give satisfactory result. However, when the flow velocity is much smaller than the thermal velocity, the conventional molecular dynamics simulation method cannot predict the true flow velocity. To overcome this difficulty, in this study, a new linearized algorithm is developed. The new algorithm separates the flow velocity increment caused by external forces from the thermal motion velocity at each time step. The detailed process of the new algorithm is derived in this paper and several cases of 3D nanochannel flows of liquid argon are simulated by using this method. The numerical results show that the new algorithm is valid for nanoscale flows.     

Effects of surface roughness and interface wettability on nanoscale flow in a nanochannel

Non-equilibrium molecular dynamics simulations have been carried out to investigate the effect of surface roughness and interface wettability on the nanorheology and slip boundary condition of simple fluids in a nanochannel of several atomic diameters width. The solid surfaces decorated with periodic nanostrips are considered as the rough surface in this study. The simulation results showed that the interface wettability and the surface roughness are important in determining the nanorheology of the nanochannel and fluid slip at solid–fluid interface. It is observed that the presence of surface roughness always suppresses the fluid slip for hydrophilic and hydrophobic surface nanochannels. For fluids over smooth and hydrophobic surfaces, the snapshots of fluid molecules show that an air gap or nanobubble exists at the fluid–solid interface, resulting in the apparent slip velocity. For a given surface with fixed interface wettability, the fluid velocities increase by increasing the driving force, while the driving force has no significant influence on the density structure of fluid molecules. The fluid slip and the flow rate are measured for hydrophilic and hydrophobic nanochannels. The flow rates in rough surface nanochannels are smaller than those of smooth surface walls due to the increase of drag resistance at the solid–fluid interface. The dependence between fluid slip and flow rate showed that the slip length increases approximately linearly with the flow rate for both the hydrophobic and hydrophilic surface nanochannels.     

Couette–Poiseuille flow of a gas in long microchannels

The flow of a compressible, isothermal gas under slightly rarefied conditions in a 2D planar geometry is considered. The gas is shear driven and is also subject to an applied pressure gradient, which is also known as Couette–Poiseuille (CP) flow. In this paper, the full Navier-Stokes (NS) equations are solved using a perturbation expansion up to the first order. The pressure profile is solved numerically. On the basis of the solutions, effects of rarefaction and compressibility on the flow characteristics are investigated in detail. The results show the parallel flow assumption to be invalid for cases with slight rarefaction. The axial and vertical velocity components are found to depend on the degree of rarefaction, applied pressure gradient and wall velocity. The effects of rarefaction on the occurrence of back flow are also discussed. In addition, the results for the Poiseuille and CP flow with and without rarefaction can be easily obtained from our results.     

Molecular dynamics simulation of flow past a plate

Molecular dynamics simulations with a soft-sphere potential have been carried out to model two dimensional fluid flow obstructed by a plate. At fluid velocities large enough to obtain adequate signal to noise resolution, two counter-circulating vortices are observed behind the obstruction. The stationary state length scale of these vortices is found to be roughly proportional to the average velocity in the system, as predicted by the hydrodynamic theory.     

Direct numerical simulations of localized disturbances in pipe Poiseuille flow

We consider pipe Poiseuille flow subjected to a disturbance which is highly localized in space. Experiments by Peixinho and Mullin have shown this disturbance to be efficient in triggering turbulence, yielding a threshold dependence on the required amplitude as R^-1.5 on the Reynolds number, R. The experiments also indicate an initial formation of hairpin vortices, with each hairpin having a length of approximately one pipe radius, independent of the Reynolds number in the range of R=2000-3000. We perform direct numerical simulations for R=5000. The results show a packet of hairpin vortices traveling downstream, each having a length of approximately one pipe radius. The perturbation remains highly localized in space while being advected downstream for approximately 10 pipe diameters. Beyond that distance from the disturbance origin, the flow becomes severely disordered.     

Numerical simulations of particle migration in a viscoelastic fluid subjected to Poiseuille flow

In this work we present 2D numerical simulations on the migration of a particle suspended in a viscoelastic fluid under Poiseuille flow. A Giesekus model is chosen as constitutive equation of the suspending liquid. In order to study the sole effect of the fluid viscoelasticity, both fluid and particle inertia are neglected.The governing equations are solved through the finite element method with proper stabilization techniques to get convergent solutions at relatively large flow rates. An Arbitrary Lagrangian–Eulerian (ALE) formulation is adopted to manage the particle motion. The mesh grid is moved along the flow so as to limit particle motion only in the gradient direction to substantially reduce mesh distortion and remeshing.Viscoelasticity of the suspending fluid induces particle cross-streamline migration. Both large Deborah number and shear thinning speed up the migration velocity. When the particle is small compared to the gap (small confinement), the particle migrates towards the channel centerline or the wall depending on its initial position. Above a critical confinement (large particles), the channel centerline is no longer attracting, and the particle is predicted to migrate towards the closest wall when its initial position is not on the channel centerline. As the particle approaches the wall, the translational velocity in the flow direction is found to become equal to the linear velocity corresponding to the rolling motion over the wall without slip.     

A variational path integral molecular dynamics study of a solid helium-4

In the present study, a variational path integral molecular dynamics method developed by the author [Chem. Phys. Lett. 482 (2009) 165] is applied to a solid helium-4 in the ground state. The method is a molecular dynamics algorithm for a variational path integral method which can be used to generate the exact ground state numerically. The solid state is shown to successfully be realized by the method, although a poor trial wavefunction that cannot describe the solid state is used.     

Scalability study of molecular dynamics simulation on Godson-T many-core architecture

Molecular dynamics (MD) simulation has broad applications, and an increasing amount of computing power is needed to satisfy the large scale of the real world simulation. The advent of the many-core paradigm brings unprecedented computing power, but it remains a great challenge to harvest the computing power due to MD’s irregular memory-access pattern. To address this challenge, this paper presents a joint application/architecture study to enhance the scalability of MD on Godson-T-like many-core architecture. First, a preprocessing approach leveraging an adaptive divide-and-conquer framework is designed to exploit locality through memory hierarchy with software controlled memory. Then three incremental optimization strategies–a novel data-layout to improve data locality, an on-chip locality-aware parallel algorithm to enhance data reuse, and a pipelining algorithm to hide latency to shared memory–are proposed to enhance on-chip parallelism for Godson-T many-core processor. Experiments on Godson-T simulator exhibit strong-scaling parallel efficiency of 0.99 on 64 cores, which is confirmed by a field-programmable gate array emulator. Also the performance per watt of MD on Godson-T is much higher than MD on a 16-cores Intel core i7 symmetric multiprocessor (SMP) and 26 times higher than MD on an 8-core 64-thread Sun T2 processor. Detailed analysis shows that optimizations utilizing architectural features to maximize data locality and to enhance data reuse benefit scalability most. Furthermore, a hierarchical parallelization scheme is designed to map the MD algorithm to Godson-T many-core cluster and a simple performance model is derived, which suggests that the optimization scheme is likely to scale well toward exascale. Certain architectural features are found essential for these optimizations, which could guide future hardware developments.     

A direct two-dimensional pressure formulation in molecular dynamics

Two-dimensional (2D) pressure field estimation in molecular dynamics (MD) simulations has been done using three-dimensional (3D) pressure field calculations followed by averaging, which is computationally expensive due to 3D convolutions. In this work, we develop a direct 2D pressure field estimation method which is much faster than 3D methods without losing accuracy. The method is validated with MD simulations on two systems: a liquid film and a cylindrical drop of argon suspended in surrounding vapor.     

Exploring the molecular basis of the enantioselective binding of penicillin G acylase towards a series of 2-aryloxyalkanoic acids: a docking and molecular dynamics study

In the present paper, molecular modeling studies were undertaken in order to shed light on the molecular basis of the observed enantioselectivity of penicillin G acylase (PGA), a well known enzyme for its industrial applications, towards 16 racemic 2-aryloxyalkanoic acids, which have been reported to affect several biological systems. With this intention docking calculations and MD simulations were performed. Docking results indicated that the (S)-enantiomers establish several electrostatic interactions with SerB1, SerB386 and ArgB263 of PGA. Conversely, the absence of specific polar interactions between the (R)-enantiomers and ArgB263 seems to be the main reason for the different binding affinities observed between the two enantiomers. Results of molecular dynamics simulations demonstrated that polar interactions are responsible for both the ligand affinity and PGA enantiospecificity. Modeling calculations provided possible explanations for the observed enantioselectivity of the enzyme that rationalize available experimental data and could be the basis for future protein engineering efforts.     

Algorithm optimization in molecular dynamics simulation

Establishing the neighbor list to efficiently calculate the inter-atomic forces consumes the majority of computation time in molecular dynamics (MD) simulation. Several algorithms have been proposed to improve the computation efficiency for short-range interaction in recent years, although an optimized numerical algorithm has not been provided. Based on a rigorous definition of Verlet radius with respect to temperature and list-updating interval in MD simulation, this paper has successfully developed an estimation formula of the computation time for each MD algorithm calculation so as to find an optimized performance for each algorithm. With the formula proposed here, the best algorithm can be chosen based on different total number of atoms, system average density and system average temperature for the MD simulation. It has been shown that the Verlet Cell-linked List (VCL) algorithm is better than other algorithms for a system with a large number of atoms. Furthermore, a generalized VCL algorithm optimized with a list-updating interval and cell-dividing number is analyzed and has been verified to reduce the computation time by 30∼60% in a MD simulation for a two-dimensional lattice system. Due to similarity, the analysis in this study can be extended to other many-particle systems.     

Structural analysis of a novel N-carbamoyl-d-amino acid amidohydrolase from a Brazilian Bradyrhizobium japonicum strain: In silico insights by molecular modelling,docking and molecular dynamics

In this work we performed several in silico analyses to describe the relevant structural aspects of an enzyme N-Carbamoyl-d-amino acid amidohydrolase (d-NCAase) encoded on the genome of the Brazilian strain CPAC 15 (=SEMIA 5079) of Bradyrhizobium japonicum, a nonpathogenic species belonging to the order Rhizobiales. d-NCAase has wide applications particularly in the pharmaceutical industry, since it catalyzes the production of d-amino acids such as D-p-hydroxyphenylglycine (D-HPG), an intermediate in the synthesis of β-lactam antibiotics. We applied a homology modelling approach and 50 ns of molecular dynamics simulations to predict the structure and the intersubunit interactions of this novel d-NCAase. Also, in order to evaluate the substrate binding site, the model was subjected to 50 ns of molecular dynamics simulations in the presence of N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) (a d-NCAase canonical substrate) and water-protein/water-substrate interactions analyses were performed. Overall, the structural analysis and the molecular dynamics simulations suggest that d-NCAase of B. japonicum CPAC-15 has a homodimeric structure in solution. Here, we also examined the substrate specificity of the catalytic site of our model and the interactions with water molecules into the active binding site were comprehensively discussed. Also, these simulations showed that the amino acids Lys123, His125, Pro127, Cys172, Asp174 and Arg176 are responsible for recognition of ligand in the active binding site through several chemical associations, such as hydrogen bonds and hydrophobic interactions. Our results show a favourable environment for a reaction of hydrolysis that transforms N-Carbamoyl-d-p-hydroxyphenylglycine (Cp-HPG) into the active compound D-p-hydroxyphenylglycine (D-HPG). This work envisage the use of d-NCAase from the Brazilian Bradyrhizobium japonicum strain CPAC-15 (=SEMIA 5079) for the industrial production of D-HPG, an important intermediate for semi-synthesis of β-lactam antibiotics such as penicillins, cephalosporins and amoxicillin.     

Ordinary differential equations of molecular dynamics

The ordinary differential equations of Newtonian dynamics are used in atomic simulations with the method of molecular dynamics. The basic issues are surveyed and standard algorithms are described. Several algorithmic variants are discussed. Some advanced ideas relating to parallel computation are considered.     

A parallel algorithm for molecular dynamics simulation of branched molecules

To get an insight into the effects of molecular architecture in the behaviour of thin lubricant films we have devised an algorithm for simulation of branched molecules. We have used this algorithm successfully to simulate branched isomers of C₃₀. However the algorithm is flexible enough to be used for the simulation of more complex branched molecules. The resulting algorithm can be used in molecular dynamics simulation of branched molecules and could be helpful in designing new materials at the molecular level.     

Molecular modeling and molecular dynamics simulation study of archaeal leucyl-tRNA synthetase in complex with different mischarged tRNA in editing conformation

Aminoacyl-tRNA synthetases (aaRSs) play important roles in maintaining the accuracy of protein synthesis. Some aaRSs accomplish this via editing mechanisms, among which leucyl-tRNA synthetase (LeuRS) edits non-cognate amino acid norvaline mainly by post-transfer editing. However, the molecular basis for this pathway for eukaryotic and archaeal LeuRS remain unclear. In this study, a complex of archaeal P. horikoshii LeuRS (PhLeuRS) with misacylated tRNA^Leu was modeled wherever tRNA’s acceptor stem was oriented directly into the editing site. To understand the distinctive features of organization we reconstructed a complex of PhLeuRS with tRNA and visualize post-transfer editing interactions mode by performing molecular dynamics (MD) simulation studies. To study molecular basis for substrate selectivity by PhLeuRS’s editing site we utilized MD simulation of the entire LeuRS complexes using a diverse charged form of tRNAs, namely norvalyl-tRNA^Leu and isoleucyl-tRNA^Leu. In general, the editing site organization of LeuRS from P.horikoshii has much in common with bacterial LeuRS. The MD simulation results revealed that the post-transfer editing substrate norvalyl-A76, binds more strongly than isoleucyl-A76. Moreover, the branched side chain of isoleucine prevents water molecules from being closer and hence the hydrolysis reaction slows significantly. To investigate a possible mechanism of the post-transfer editing reaction, by PhLeuRS we have determined that two water molecules (the attacking and assisting water molecules) are localized near the carbonyl group of the amino acid to be cleaved off. These water molecules approach the substrate from the opposite side to that observed for Thermus thermophilus LeuRS (TtLeuRS). Based on the results obtained, it was suggested that the post-transfer editing mechanism of PhLeuRS differs from that of prokaryotic TtLeuRS.     

Effect of solvent model when probing protein dynamics with molecular dynamics

We probe the dynamics of the Bpti and Galectin-3 proteins using molecular dynamics simulations employing three water models at different levels of resolution, viz. the atomistic TIP4P-Ewald, the coarse-grained Elba and an implicit generalised Born model. The dynamics are quantified indirectly by model-free order parameters, S² of the backbone NH and selected side-chain bond vectors, which also have been determined experimentally through NMR relaxation measurements. For the backbone, the order parameters produced with the three solvent models agree to a large extent with experiments, giving average unsigned deviations between 0.03 and 0.06. For the side-chains, for which the experimental data is incomplete, the deviations are considerably larger with mean deviations between 0.13 and 0.17. However, for both backbone and side-chains, it is difficult to pick a winner, as all models perform equally well overall. For a more complete set of side-chain vectors, we resort to analysing the variation among the estimates from different solvent models. Unfortunately, the variations are found to be sizeable with mean deviations between 0.11 and 0.15. Implications for computational assessment of protein dynamics are discussed.     

The MOLDY short-range molecular dynamics package

We describe a parallelised version of the MOLDY molecular dynamics program. This Fortran code is aimed at systems which may be described by short-range potentials and specifically those which may be addressed with the embedded atom method. This includes a wide range of transition metals and alloys. MOLDY provides a range of options in terms of the molecular dynamics ensemble used and the boundary conditions which may be applied. A number of standard potentials are provided, and the modular structure of the code allows new potentials to be added easily. The code is parallelised using OpenMP and can therefore be run on shared memory systems, including modern multicore processors. Particular attention is paid to the updates required in the main force loop, where synchronisation is often required in OpenMP implementations of molecular dynamics. We examine the performance of the parallel code in detail and give some examples of applications to realistic problems, including the dynamic compression of copper and carbon migration in an iron–carbon alloy.

Program summary

Program title: MOLDYCatalogue identifier: AEJU_v1_0Program summary URL:http://cpc.cs.qub.ac.uk/summaries/AEJU_v1_0.htmlProgram obtainable from: CPC Program Library, Queen?s University, Belfast, N. IrelandLicensing provisions: GNU General Public License version 2No. of lines in distributed program, including test data, etc.: 382 881No. of bytes in distributed program, including test data, etc.: 6 705 242Distribution format: tar.gzProgramming language: Fortran 95/OpenMPComputer: AnyOperating system: AnyHas the code been vectorised or parallelized?: Yes. OpenMP is required for parallel executionRAM: 100 MB or moreClassification: 7.7Nature of problem: Moldy addresses the problem of many atoms (of order 10⁶) interacting via a classical interatomic potential on a timescale of microseconds. It is designed for problems where statistics must be gathered over a number of equivalent runs, such as measuring thermodynamic properities, diffusion, radiation damage, fracture, twinning deformation, nucleation and growth of phase transitions, sputtering etc. In the vast majority of materials, the interactions are non-pairwise, and the code must be able to deal with many-body forces.Solution method: Molecular dynamics involves integrating Newton?s equations of motion. MOLDY uses verlet (for good energy conservation) or predictor–corrector (for accurate trajectories) algorithms. It is parallelised using open MP. It also includes a static minimisation routine to find the lowest energy structure. Boundary conditions for surfaces, clusters, grain boundaries, thermostat (Nose), barostat (Parrinello–Rahman), and externally applied strain are provided. The initial configuration can be either a repeated unit cell or have all atoms given explictly. Initial velocities are generated internally, but it is also possible to specify the velocity of a particular atom. A wide range of interatomic force models are implemented, including embedded atom, Morse or Lennard-Jones. Thus the program is especially well suited to calculations of metals.Restrictions: The code is designed for short-ranged potentials, and there is no Ewald sum. Thus for long range interactions where all particles interact with all others, the order-N scaling will fail. Different interatomic potential forms require recompilation of the code.Additional comments: There is a set of associated open-source analysis software for postprocessing and visualisation. This includes local crystal structure recognition and identification of topological defects.Running time: A set of test modules for running time are provided. The code scales as order N. The parallelisation shows near-linear scaling with number of processors in a shared memory environment. A typical run of a few tens of nanometers for a few nanoseconds will run on a timescale of days on a multiprocessor desktop.     

Exploiting hierarchy parallelism for molecular dynamics on a petascale heterogeneous system

Heterogeneous systems with nodes containing more than one type of computation units, e.g., central processing units (CPUs) and graphics processing units (GPUs), are becoming popular because of their low cost and high performance. In this paper, we have developed a Three-Level Parallelization Scheme (TLPS) for molecular dynamics (MD) simulation on heterogeneous systems. The scheme exploits multi-level parallelism combining (1) inter-node parallelism using spatial decomposition via message passing, (2) intra-node parallelism using spatial decomposition via dynamically scheduled multi-threading, and (3) intra-chip parallelism using multi-threading and short vector extension in CPUs, and employing multiple CUDA threads in GPUs. By using a hierarchy of parallelism with optimizations such as communication hiding intra-node, and memory optimizations in both CPUs and GPUs, we have implemented and evaluated a MD simulation on a petascale heterogeneous supercomputer TH-1A. The results show that MD simulations can be efficiently parallelized with our TLPS scheme and can benefit from the optimizations.     

Hardware accelerator for molecular dynamics: MDGRAPE-2

We developed MDGRAPE-2, a hardware accelerator that calculates forces at high speed in molecular dynamics (MD) simulations. MDGRAPE-2 is connected to a PC or a workstation as an extension board. The sustained performance of one MDGRAPE-2 board is 15 Gflops, roughly equivalent to the peak performance of the fastest supercomputer processing element. One board is able to calculate all forces between 10 000 particles in 0.28 s (i.e. 310000 time steps per day). If 16 boards are connected to one computer and operated in parallel, this calculation speed becomes ∼10 times faster. In addition to MD, MDGRAPE-2 can be applied to gravitational N-body simulations, the vortex method and smoothed particle hydrodynamics in computational fluid dynamics.     

Multi-scale molecular dynamics study of cholera pentamer binding to a GM1-phospholipid membrane

The AB₅ type toxin produced by the Vibrio cholerae bacterium is the causative agent of the cholera disease. The cholera toxin (CT) has been shown to bind specifically to GM1 glycolipids on the membrane surface. This binding of CT to the membrane is the initial step in its endocytosis and has been postulated to cause significant disruption to the membrane structure. In this work, we have carried out a combination of coarse-grain and atomistic simulations to study the binding of CT to a membrane modelled as an asymmetrical GM1-DPPC bilayer. Simulation results indicate that the toxin binds to the membrane through only three of its five B subunits, in effect resulting in a tilted bound configuration. Additionally, the binding of the CT can increase the area per lipid of GM1 leaflet, which in turn can cause the membrane regions interacting with the bound subunits to experience significant bilayer thinning and lipid tail disorder across both the leaflets.