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

Facemasks and Hand Hygiene to Prevent Influenza Transmission in Households: A Cluster Randomized Trial

We present the results of molecular dynamics computer simulations of a binary Lennard-Jones liquid confined between two parallel rough walls. These walls are realized by frozen amorphous configurations of the same liquid and therefore the structural properties of the confined fluid are identical to the ones of the bulk system. Hence this setup allows us to study how the relaxation dynamics is affected by the pure effect of confinement, i.e. if structural changes are completely avoided. We find that the local relaxation dynamics is a strong function of z, the distance of the particles from the wall, and that close to the surface the typical relaxation times are orders of magnitude larger than the ones in the bulk. Because of the cooperative nature of the particle dynamics, the slow dynamics also affects the dynamics of the particles for large values of z. Using various empirical laws, we are able to parameterize accurately the z-dependence of the generalized incoherent intermediate scattering function F_s(q,z,t) and also the spatial dependence of structural relaxation times. These laws allow us to determine various dynamical length scales and we find that their temperature dependence is compatible with an Arrhenius law. Furthermore, we find that at low temperatures time and space dependent correlation function fulfill a generalized factorization property similar to the one predicted by mode-coupling theory for bulk systems. For thin films and/or at sufficiently low temperatures, we find that the relaxation dynamics is influenced by the two walls in a strongly non-linear way in that the slowing down is much stronger than the one expected from the presence of only one confining wall. ....

http://arxiv.org/pdf/cond-mat/0309025.pdf

The relaxation dynamics of a supercooled liquid confined by rough walls

In this paper, we develop a first principles model that connects respiratory droplet physics with the evolution of a pandemic such as the ongoing Covid-19. The model has two parts. First, we model the growth rate of the infected population based on a reaction mechanism. The advantage of modeling the pandemic using the reaction mechanism is that the rate constants have sound physical interpretation. The infection rate constant is derived using collision rate theory and shown to be a function of the respiratory droplet lifetime. In the second part, we have emulated the respiratory droplets responsible for disease transmission as salt solution droplets and computed their evaporation time, accounting for droplet cooling, heat and mass transfer, and finally, crystallization of the dissolved salt. The model output favourably compares with the experimentally obtained evaporation characteristics of levitated droplets of pure water and salt solution, respectively, ensuring fidelity of the model. The droplet evaporation/desiccation time is, indeed, dependent on ambient temperature and is also a strong function of relative humidity. The multi-scale model thus developed and the firm theoretical underpinning that connects the two scales-macro-scale pandemic dynamics and micro-scale droplet physics-thus could emerge as a powerful tool in elucidating the role of environmental factors on infection spread through respiratory droplets.

/pdf/modeling-the-role-of-respiratory-droplets-in-covid-19-type-5060qb77yf.pdf

Modeling the role of respiratory droplets in Covid-19 type pandemics

A great success of solid state physics comes from the characterization of crystal structures in the reciprocal (wave vector) space. The power of structural characterization in Fourier space originates from the breakdown of translational and rotational symmetries. However, unlike crystals, liquids and amorphous solids possess continuous translational and rotational symmetries on a macroscopic scale, which makes Fourier space analysis much less effective. Lately, several studies have revealed local breakdown of translational and rotational symmetries even for liquids and glasses. Here, we review several mathematical methods used to characterize local structural features of apparently disordered liquids and glasses in real space. We distinguish two types of local ordering in liquids and glasses: energy-driven and entropy-driven. The former, which is favoured energetically by symmetry-selective directional bonding, is responsible for anomalous behaviours commonly observed in water-type liquids such as water, silicon, germanium and silica. The latter, which is often favoured entropically, shows connections with the heterogeneous, slow dynamics found in hard-sphere-like glass-forming liquids. We also discuss the relationship between such local ordering and crystalline structures and its impact on glass-forming ability. The knowledge of local structures of non-crystalline materials is of fundamental importance in the understanding of their physical properties. This Review describes recent advances in local structural analysis methods, which shed new light on mysterious phenomena in liquids and glasses.

Revealing key structural features hidden in liquids and glasses

Drying and crystallization of solution droplets is a problem of broad relevance, determining the microstructures of particles formed in spray-drying, the phase of particles delivered by, for example, aerosol formulations for inhalation therapies, and the impact of aerosols on radiative forcing and climate. The ephemeral nature of free droplets, particularly when considering the drying kinetics of droplets with highly volatile constituents, has often precluded the accurate measurement of transient properties such as droplet size and composition, preventing the robust assessment of predictive models of droplet-drying rates, nucleation, and crystallization. Here, we report novel measurements of the drying kinetics of individual aqueous sodium chloride solution droplets using an electrodynamic balance to isolate and trap single aerosol droplets (radius ≈ 25 μm). The initial solution droplet size and composition are shown to be highly reproducible in terms of drying rate and crystallization time when examined over hundreds of identical evaporating droplets. We introduce a numerical model that determines the concentration gradient across the radial profile of the droplet as it dries, considering both the surface recession because of evaporation and the diffusion of components within the droplet. Drying-induced crystallization is shown to be fully determined for this system, with nucleation and instantaneous crystallization occurring once a critical supersaturation level of 2.04 ± 0.02 is achieved at the surface of the evaporating droplet. This phenomenological model provides a consistent account of the timescale and surface concentration of free-droplet crystallization on drying for the different drying conditions studied, a necessary step in progress toward achieving control over rates of crystallization and the competitive formation of amorphous particles.

/pdf/drying-kinetics-of-salt-solution-droplets-water-evaporation-4sdc644uce.pdf

Drying Kinetics of Salt Solution Droplets: Water Evaporation Rates and Crystallization.

Key to resolving the scientific challenge of the glass transition is to understand the origin of the massive increase in viscosity of liquids cooled below their melting temperature (avoiding crystallisation). A number of competing and often mutually exclusive theoretical approaches have been advanced to describe this phenomenon. Some posit a bona fide thermodynamic phase to an 'ideal glass', an amorphous state with exceptionally low entropy. Other approaches are built around the concept of the glass transition as a primarily dynamic phenomenon. These fundamentally different interpretations give equally good descriptions of the data available, so it is hard to determine which-if any-is correct. Recently however this situation has begun to change. A consensus has emerged that one powerful means to resolve this longstanding question is to approach the putative thermodynamic transition sufficiently closely, and a number of techniques have emerged to meet this challenge. Here we review the results of some of these new techniques and discuss the implications for the existence-or otherwise-of the thermodynamic transition to an ideal glass.

/pdf/the-race-to-the-bottom-approaching-the-ideal-glass-4y8wzbzz9l.pdf

The race to the bottom: approaching the ideal glass?

Key to resolving the scientific challenge of the glass transition is to understand the origin of the massive increase in viscosity of liquids cooled below their melting temperature (avoiding crystallisation). A number of competing and often mutually exclusive theoretical approaches have been advanced to describe this phenomenon. Some posit a bona fide thermodynamic phase to an "ideal glass", an amorphous state with exceptionally low entropy. Other approaches are built around the concept of the glass transition as a primarily dynamic phenomenon. These fundamentally different interpretations give equally good descriptions of the data available, so it is hard to determine which -- if any -- is correct. Recently however this situation has begun to change. A consensus has emerged that one powerful means to resolve this longstanding question is to approach the putative thermodynamic transition sufficiently closely, and a number of techniques have emerged to meet this challenge. Here we review the results of some of these new techniques and discuss the implications for the existence -- or otherwise -- of the thermodynamic transition to an ideal glass.

/pdf/the-race-to-the-bottom-approaching-the-ideal-glass-1thfh7fux9.pdf

Disks moving in a narrow channel have many features in common with the glassy behavior of hard spheres in three dimensions. In this paper we study the caging behavior of the disks that sets in at characteristic packing fraction ϕ(d). Four-point overlap functions similar to those studied when investigating dynamical heterogeneities have been determined from event-driven molecular dynamics simulations and the time-dependent dynamical length scale has been extracted from them. The dynamical length scale increases with time and, on the equilibration time scale, it is proportional to the static length scale associated with the zigzag ordering in the system, which grows rapidly above ϕ(d). The structural features responsible for the onset of caging and the glassy behavior are easy to identify as they show up in the structure factor, which we have determined exactly from the transfer-matrix approach.

Glasslike behavior of a hard-disk fluid confined to a narrow channel

We model the thermodynamics of local structures within the hard sphere liquid at arbitrary volume fractions through the morphometric calculation of n-body correlations. We calculate absolute free energies of local geometric motifs in excellent quantitative agreement with molecular dynamics simulations across the liquid and supercooled liquid regimes. We find a bimodality in the density library of states where fivefold symmetric structures appear lower in free energy than fourfold symmetric structures and from a single reaction path predict a dynamical barrier which scales linearly in the compressibility factor. The method provides a new route to assess changes in the free energy landscape at volume fractions dynamically inaccessible to conventional techniques.

/pdf/morphometric-approach-to-many-body-correlations-in-hard-1e8as9y6ww.pdf

Joshua F. Robinson

Papers

Drying Kinetics of Salt Solution Droplets: Water Evaporation Rates and Crystallization.

The race to the bottom: approaching the ideal glass?

The race to the bottom: approaching the ideal glass?

Glasslike behavior of a hard-disk fluid confined to a narrow channel

Morphometric Approach to Many-Body Correlations in Hard Spheres