Three parallel algorithms for classical molecular dynamics are presented. The first assigns each processor a fixed subset of atoms; the second assigns each a fixed subset of inter-atomic forces to compute; the third assigns each a fixed spatial region. The algorithms are suitable for molecular dynamics models which can be difficult to parallelize efficiently—those with short-range forces where the neighbors of each atom change rapidly. They can be implemented on any distributed-memory parallel machine which allows for message-passing of data between independently executing processors. The algorithms are tested on a standard Lennard-Jones benchmark problem for system sizes ranging from 500 to 100,000,000 atoms on several parallel supercomputers--the nCUBE 2, Intel iPSC/860 and Paragon, and Cray T3D. Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems. For large problems, the spatial algorithm achieves parallel efficiencies of 90% and a 1840-node Intel Paragon performs up to 165 faster than a single Cray C9O processor. Trade-offs between the three algorithms and guidelines for adapting them to more complex molecular dynamics simulations are also discussed.

Fast parallel algorithms for short-range molecular dynamics

Understanding and controlling the flow of water confined in nanopores has tremendous implications in theoretical studies and industrial applications. Here, we propose a simple model for the confined water flow based on the concept of effective slip, which is a linear sum of true slip, depending on a contact angle, and apparent slip, caused by a spatial variation of the confined water viscosity as a function of wettability as well as the nanopore dimension. Results from this model show that the flow capacity of confined water is 10 −1 ∼10 7 times that calculated by the no-slip Hagen–Poiseuille equation for nanopores with various contact angles and dimensions, in agreement with the majority of 53 different study cases from the literature. This work further sheds light on a controversy over an increase or decrease in flow capacity from molecular dynamics simulations and experiments.

https://www.pnas.org/content/pnas/114/13/3358.full.pdf

Wettability effect on nanoconfined water flow

We report high magnetic field scanning tunneling microscopy and Landau level spectroscopy of twisted graphene layers grown by chemical vapor deposition. For twist angles exceeding ~3° the low energy carriers exhibit Landau level spectra characteristic of massless Dirac fermions. Above 20° the layers effectively decouple and the electronic properties are indistinguishable from those in single-layer graphene, while for smaller angles we observe a slowdown of the carrier velocity which is strongly angle dependent. At the smallest angles the spectra are dominated by twist-induced van Hove singularities and the Dirac fermions eventually become localized. An unexpected electron-hole asymmetry is observed which is substantially larger than the asymmetry in either single or untwisted bilayer graphene.

Single-Layer Behavior and Its Breakdown in Twisted Graphene Layers

Hydrodynamic and hydromagnetic stability

Motivated by experiments in which a polynucleotide is driven through a proteinaceous pore by an electric field, we study the diffusive motion of a polymer threaded through a narrow channel with which it may have strong interactions. We show that there is a range of polymer lengths in which the system is approximately translationally invariant, and we develop a coarse-grained description of this regime. From this description, general features of the distribution of times for the polymer to pass through the pore may be deduced. We also introduce a more microscopic model. This model provides a physically reasonable scenario in which, as in experiments, the polymer's speed depends sensitively on its chemical composition, and even on its orientation in the channel. Finally, we point out that the experimental distribution of times for the polymer to pass through the pore is much broader than expected from simple estimates, and speculate on why this might be.

Driven Polymer Translocation Through a Narrow Pore

Viscosity variation of solvent in local regions near a solid surface, be it a biological surface of a protein or an engineered surface of a nanoconfinement, is a direct consequence of intermolecular interactions between the solid body and the solvent. The current coarse-grained molecular dynamics study takes advantage of this phenomenon to investigate the anomaly in a solvated protein's rotational dynamics confined using a representative solid matrix. The concept of persistence time, the characteristic time of structural reordering in liquids, is used to compute the solvent's local viscosity. With an increase in the degree of confinement, the confining matrix significantly influences the solvent molecule's local viscosity present in the protein hydration layer through intermolecular interactions. This effect contributes to the enhanced drag force on protein motion, causing a reduction in the rotational diffusion coefficient. Simulation results suggest that the direct matrix-protein non-bonded interaction is responsible for the occasional jump and discontinuity in orientational motion when the protein is in very tight confinement.

https://iopscience.iop.org/article/10.1088/1361-6528/abe906/pdf

Rotational dynamics of proteins in nanochannels: role of solvent’s local viscosity

Eyring theory employs the statistical mechanical theory of absolute reaction rates to analyse the transport mechanisms in fluids. A physicochemical methodology combining molecular dynamics (MD) and Eyring theory of reaction rates is proposed for investigating the liquid slip on a solid wall in the nanoscale domain. The method involves the determination of activation energy required for the flow process directly from the MD trajectory information and then calculate the important transport properties of the confined fluid from the activation energy. In order to demonstrate the universal applicability of the proposed methodology in nanofluidics, the slip flow behavior of argon, water and ionic liquid confined in various nanostructures has been investigated. The slip length is found to be size dependent in all the cases. The novelty of this method is that the variations in slip length are explained on the basis of molecular interactions and the subsequent changes in the activation energy.

Physicochemical analysis of slip flow phenomena in liquids under nanoscale confinement

The details of laser reflection method (LRM) for the determination of shear stress in low density transitional flows are presented. The method is employed to determine the shear stress due to impingement of a low density supersonic free jet issuing out from a convergent divergent nozzle on a flat plate. The plate is smeared with a thin oil film and kept parallel to the nozzle axis. For a thin oil film moving under the action of aerodynamic boundary layer, the shear stress at the air–oil interface is equal to the shear stress between the surface and air. A direct and dynamic measurement of the oil film slope generated by the shear force is done using a position sensing detector (PSD). The thinning rate of the oil film is directly measured which is the major advantage of the LRM. From the oil film slope history, calculation of the shear stress is done using a three-point formula. The range of Knudsen numbers investigated is from 0.028 to 0.516. Pressure ratio across the nozzle varied from 3,500 to 8,500 giving highly under expanded free jets. The measured values of shear, in the overlapping region of experimental parameters, show fair agreement with those obtained by force balance method and laser interferometric method.

Laser reflection method for determination of shear stress in low density transitional flows

Nanoporous carbon materials are extensively studied for various separation applications. Among them, water desalination by means of Reverse Osmosis (RO) stands out due to it’s large socio-economic relevance. Many studies are carried out in this area both computationally and experimentally. In computational studies the water simulated using different water models are prone to produce inconsistent results. In this study water desalination through hydrogen functionalized graphene nanopore is studied using different water models (SPC, SPC/E, TIP3P, TIP4P/2005). Up to 81% difference was observed in the flux estimates among the models. The water permeation rate was found to be closely related to the bulk transport properties of the simulated water.

/pdf/the-effect-of-water-models-on-desalination-through-graphene-1zzjpvzdyw.pdf

The Effect of Water Models on Desalination Through Graphene Nanopores

Combined kinetic theory-hydrodynamics treatment has been proven effective in the prediction of biomolecule dynamics, generally if a single biomolecule is present in the bulk solvent. But the validity of such a theory in many physiological conditions is controversial. In the present study, a sample protein surrounded by other large biomolecules is approximated as the protein in a cylindrical nanopore. The hydrodynamic radius of the protein is chosen as an indicator to check whether one of the widely used kinetic theoryhydrodynamics relation namely Stokes-Einstein-Debye relation, is genuine for confined conditions of the protein. It has been found that Stokes-Einstein-Debye relation cannot be satisfied by the protein if confinement dimensions are very close. The reason for the violation can be attributed to van der Waals interaction between pore and the protein.

Sarith P. Sathian

Papers

Rotational dynamics of proteins in nanochannels: role of solvent’s local viscosity

Physicochemical analysis of slip flow phenomena in liquids under nanoscale confinement

Laser reflection method for determination of shear stress in low density transitional flows

The Effect of Water Models on Desalination Through Graphene Nanopores

Stokes-EInstein-Debye Relation: A Check of Validity for Proteins in Nanoconfinements