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

Statics and kinematics of granular materials

Shear thickening is a type of non-Newtonian behavior in which the stress required to shear a fluid increases faster than linearly with shear rate. Many concentrated suspensions of particles exhibit an especially dramatic version, known as Discontinuous Shear Thickening (DST), in which the stress suddenly jumps with increasing shear rate and produces solid-like behavior. The best known example of such counter-intuitive response to applied stresses occurs in mixtures of cornstarch in water. Over the last several years, this shear-induced solid-like behavior together with a variety of other unusual fluid phenomena has generated considerable interest in the physics of densely packed suspensions. In this review, we discuss the common physical properties of systems exhibiting shear thickening, and different mechanisms and models proposed to describe it. We then suggest how these mechanisms may be related and generalized, and propose a general phase diagram for shear thickening systems. We also discuss how recent work has related the physics of shear thickening to that of granular materials and jammed systems. Since DST is described by models that require only simple generic interactions between particles, we outline the broader context of other concentrated many-particle systems such as foams and emulsions, and explain why DST is restricted to the parameter regime of hard-particle suspensions. Finally, we discuss some of the outstanding problems and emerging opportunities.

https://iopscience.iop.org/article/10.1088/0034-4885/77/4/046602/pdf

Shear thickening in concentrated suspensions: phenomenology, mechanisms and relations to jamming

BACKGROUND Transmission electron microscopy offers structural and compositional information with atomic resolution, but its use is restricted to thin, solid samples. Liquid samples, particularly those involving water, have been challenging because of the need to form a thin liquid layer that is stable within the microscope vacuum. Liquid cell electron microscopy is a developing technique that allows us to apply the powerful capabilities of the electron microscope to the imaging and analysis of liquid specimens. We can examine liquid-based processes in materials science and physics that are traditionally inaccessible to electron microscopy, and image biological structures at high resolution without the need for freezing or drying. The changes that occur inside batteries during operation, the attachment of atoms during the self-assembly of nanocrystals, and the structures of biological materials in liquid water are examples in which a microscopic view is providing unique insights. ADVANCES The difficulty of imaging water and other liquids was recognized from the earliest times in the development of transmission electron microscopy. Achieving a practical solution, however, required the use of modern microfabrication techniques to build liquid cells with thin but strong windows. Usually made of silicon nitride on a silicon support, these liquid cells perform two jobs: They separate the liquid from the microscope vacuum while also confining it into a layer that is thin enough for imaging with transmitted electrons. Additional functionality such as liquid flow, electrodes, or heating can be incorporated in the liquid cell. The first experiments to make use of modern liquid cells provided information on electrochemical deposition, nanomaterials synthesis, diffusion in liquids, and the structure of biological assemblies. Materials and processes now under study include corrosion, biomolecular structure, bubble dynamics, radiation effects, and biomineralization. New window materials such as graphene can improve resolution, and elemental analysis is possible by measuring energy loss or x-ray signals. Advances in electron optics and detectors, and the correlation of liquid cell microscopy data with probes such as fluorescence, have increased the range of information available from the sample. Because the equipment is not too expensive and works in existing electron microscopes, liquid cell microscopy programs have developed around the world. OUTLOOK Liquid cell electron microscopy is well positioned to explore new frontiers in electrochemistry and catalysis, nanomaterial growth, fluid physics, diffusion, radiation physics, geological and environmental processes involving clays and aerosols, complex biomaterials and polymers, and biological functions in aqueous environments. Continuing improvements in equipment and technique will allow materials and processes to be studied under different stimuli—for example, in extreme temperatures, during gas/liquid mixing, or in magnetic or electric fields. Correlative approaches that combine liquid cell electron microscopy with light microscope or synchrotron data promise a deeper study of chemical, electrochemical, and photochemical reactions; analytical electron microscopy will provide details of composition and chemical bonding in water; high-speed and aberration-corrected imaging extend the scales of the phenomena that can be examined. As liquid cell microscopy becomes more capable and quantitative, it promises the potential to extend into new areas, adopt advanced imaging modes such as holography, and perhaps even solve grand challenge problems such as the structure of the electrochemical double layer or molecular movements during biological processes.

/pdf/opportunities-and-challenges-in-liquid-cell-electron-3oawvph8aq.pdf

Opportunities and challenges in liquid cell electron microscopy

Cell membranes contain a large variety of lipid types and are crowded with proteins, endowing them with the plasticity needed to fulfill their key roles in cell functioning. The compositional complexity of cellular membranes gives rise to a heterogeneous lateral organization, which is still poorly understood. Computational models, in particular molecular dynamics simulations and related techniques, have provided important insight into the organizational principles of cell membranes over the past decades. Now, we are witnessing a transition from simulations of simpler membrane models to multicomponent systems, culminating in realistic models of an increasing variety of cell types and organelles. Here, we review the state of the art in the field of realistic membrane simulations and discuss the current limitations and challenges ahead.

Computational Modeling of Realistic Cell Membranes

Dry, frictional, steady-state granular flows down an inclined, rough surface are studied with discrete particle simulations. From this exemplary flow situation, macroscopic fields, consistent with the conservation laws of continuum theory, are obtained from microscopic data by time-averaging and spatial smoothing (coarse-graining). Two distinct coarse-graining length scale ranges are identified, where the fields are almost independent of the smoothing length w. The smaller, sub-particle length scale, w ≪ d, resolves layers in the flow near the base boundary that cause oscillations in the macroscopic fields. The larger, particle length scale, w ≈ d, leads to smooth stress and density fields, but the kinetic stress becomes scale-dependent; however, this scale-dependence can be quantified and removed. The macroscopic fields involve density, velocity, granular temperature, as well as strain-rate, stress, and fabric (structure) tensors. Due to the plane strain flow, each tensor can be expressed in an inherently anisotropic form with only four objective, coordinate frame invariant variables. For example, the stress is decomposed as: (i) the isotropic pressure, (ii) the “anisotropy” of the deviatoric stress, i.e., the ratio of deviatoric stress (norm) and pressure, (iii) the anisotropic stress distribution between the principal directions, and (iv) the orientation of its eigensystem. The strain rate tensor sets the reference system, and each objective stress (and fabric) variable can then be related, via discrete particle simulations, to the inertial number, I. This represents the plane strain special case of a general, local, and objective constitutive model. The resulting model is compared to existing theories and clearly displays small, but significant deviations from more simplified theories in all variables – on both the different length scales.

/pdf/coarse-grained-local-and-objective-continuum-description-of-3402gh297o.pdf

Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface

The viscosity-temperature relation is determined for the water models SPC/E, TIP4P, TIP4P/Ew, and TIP4P/2005 by considering Poiseuille flow inside a nano-channel using molecular dynamics. The viscosity is determined by fitting the resulting velocity profile (away from the walls) to the continuum solution for a Newtonian fluid and then compared to experimental values. The results show that the TIP4P/2005 model gives the best prediction of the viscosity for the complete range of temperatures for liquid water, and thus it is the preferred water model of these considered here for simulations where the magnitude of viscosity is crucial. On the other hand, with the TIP4P model, the viscosity is severely underpredicted, and overall the model performed worst, whereas the SPC/E and TIP4P/Ew models perform moderately.

/pdf/a-comparison-of-the-value-of-viscosity-for-several-water-1hjjobdhyy.pdf

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

We present molecular dynamics simulations of planar Poiseuille flow of a Lennard-Jones fluid at various temperatures and body forces. Local thermostatting is used close to the walls to reach steady-state up to a limit body force. Macroscopic fields are obtained from microscopic data by time- and space-averaging and smoothing the data with a self-consistent coarse-graining method based on kernel interpolation. Two phenomena make the system interesting: (i) strongly confined fluids show layering, i.e., strong oscillations in density near the walls, and (ii) the stress deviates from the Newtonian fluid assumption, not only in the layered regime, but also much further away from the walls. Various scalar, vectorial, and tensorial fields are analyzed and related to each other in order to understand better the effects of both the inhomogeneous density and the anisotropy on the flow behavior and rheology. The eigenvalues and eigendirections of the stress tensor are used to quantify the anisotropy in stress and form the basis of a newly proposed objective, inherently anisotropic constitutive model that allows for non-collinear stress and strain gradient by construction.

/pdf/a-study-of-the-anisotropy-of-stress-in-a-fluid-confined-in-a-4i9deb5oik.pdf

A study of the anisotropy of stress in a fluid confined in a nanochannel

Although the importance of temperature control in nonequilibrium molecular dynamics simulations is widely accepted, the consequences of the thermostatting approach in the case of strongly confined fluids are underappreciated. We show the strong influence of the thermostatting method on the water transport in carbon nanotubes (CNTs) by considering simulations in which the system temperature is controlled via the walls or via the fluid. Streaming velocities and mass flow rates are found to depend on the tube flexibility and on the thermostatting algorithm, with flow rates up to 20% larger when the walls are flexible. The larger flow rates in flexible CNTs are explained by a lower friction coefficient between water and the wall. Despite the lower friction, a larger solid-fluid interaction energy is found for flexible CNTs than for rigid ones. Furthermore, a comparison of thermostat schemes has shown that the Berendsen and Nose-Hoover thermostats result in very similar transport rates, while lower flow rates are found under the influence of the Langevin thermostat. These findings illustrate the significant influence of the thermostatting methods on the simulated confined fluid transport.

/pdf/water-flow-in-carbon-nanotubes-the-effect-of-tube-l4psa6t0a1.pdf

Water flow in carbon nanotubes: The effect of tube flexibility and thermostat.

Monovalent and divalent aqueous electrolytes confined in negatively charged porous silica are studied by means of molecular simulations including free energy calculations. Owing to the strong cation adsorption at the surface, surface charge overcompensation (overscreening) occurs which leads to an effective positive surface next to the Stern layer, followed by a negatively charged diffuse layer. A simple Poisson–Boltzmann model in which the single-ion potential of mean force is introduced is shown to capture the most prominent features of ion density profiles near an amorphous silica surface. Nevertheless, due to its mean-field nature, which fails to account for correlations, this simple model does not predict overscreening corresponding to charge inversion at the surface. Such an overscreening drastically affects the transport of confined electrolytes as it leads to flow reversal when subjected to an electric field. A simple continuum theory is shown to capture how the electro-osmotic flow is affected by overscreening and by the apparent enhanced viscosity of the confined electrolytes. Comparison with available experimental data is discussed, as well as the implications of these phenomena for ζ-potential measurements.

/pdf/ion-specific-adsorption-and-electroosmosis-in-charged-50y92gp39s.pdf

Remco Hartkamp

Papers

Coarse-grained local and objective continuum description of three-dimensional granular flows down an inclined surface

A comparison of the value of viscosity for several water models using Poiseuille flow in a nano-channel

A study of the anisotropy of stress in a fluid confined in a nanochannel

Water flow in carbon nanotubes: The effect of tube flexibility and thermostat.

Ion-specific adsorption and electroosmosis in charged amorphous porous silica.