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

Differently from passive Brownian particles, active particles, also known as self-propelled Brownian particles or microswimmers and nanoswimmers, are capable of taking up energy from their environment and converting it into directed motion. Because of this constant flow of energy, their behavior can be explained and understood only within the framework of nonequilibrium physics. In the biological realm, many cells perform directed motion, for example, as a way to browse for nutrients or to avoid toxins. Inspired by these motile microorganisms, researchers have been developing artificial particles that feature similar swimming behaviors based on different mechanisms. These man-made micromachines and nanomachines hold a great potential as autonomous agents for health care, sustainability, and security applications. With a focus on the basic physical features of the interactions of self-propelled Brownian particles with a crowded and complex environment, this comprehensive review will provide a guided tour through its basic principles, the development of artificial self-propelling microparticles and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

/pdf/active-particles-in-complex-and-crowded-environments-4pyirdi1aj.pdf

Active Particles in Complex and Crowded Environments

Annual review of condensed matter physics

L E Reichl 1980 Austin: University of Texas Press xii + 709 pp price $29.95 I can thoroughly recommend this book and congratulate the author for having brought together so many aspects of statistical physics in a comprehensible manner. The subject matter is modern; all the recent developments such as stochastic theory, theories of quantum fluids and critical phenomena, nonlinear chemical physics and hydrodynamics are included and yet each topic is built up from its foundations.

A Modern Course in Statistical Physics

Active Brownian particles, also referred to as microswimmers and nanoswimmers, are biological or manmade microscopic and nanoscopic particles that can self-propel. Because of their activity, their behavior can only be explained and understood within the framework of nonequilibrium physics. In the biological realm, many cells perform active Brownian motion, for example, when moving away from toxins or towards nutrients. Inspired by these motile microorganisms, researchers have been developing artificial active particles that feature similar swimming behaviors based on different mechanisms; these manmade micro- and nanomachines hold a great potential as autonomous agents for healthcare, sustainability, and security applications. With a focus on the basic physical features of the interactions of active Brownian particles with a crowded and complex environment, this comprehensive review will put the reader at the very forefront of the field of active Brownian motion, providing a guided tour through its basic principles, the development of artificial self-propelling micro- and nanoparticles, and their application to the study of nonequilibrium phenomena, as well as the open challenges that the field is currently facing.

/pdf/active-brownian-particles-in-complex-and-crowded-3ym4we2m8l.pdf

Active Brownian Particles in Complex and Crowded Environments

In this review, we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field, with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and we suggest possible strategies for how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise to the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.

An Active Approach to Colloidal Self-Assembly.

In this review we discuss recent advances in the self-assembly of self-propelled colloidal particles and highlight some of the most exciting results in this field with a specific focus on dry active matter. We explore this phenomenology through the lens of the complexity of the colloidal building blocks. We begin by considering the behavior of isotropic spherical particles. We then discuss the case of amphiphilic and dipolar Janus particles. Finally, we show how the geometry of the colloids and/or the directionality of their interactions can be used to control the physical properties of the assembled active aggregates, and suggest possible strategies on how to exploit activity as a tunable driving force for self-assembly. The unique properties of active colloids lend promise for the design of the next generation of functional, environment-sensing microstructures able to perform specific tasks in an autonomous and targeted manner.

An active approach to colloidal self-assembly

Here, we describe a method for the enhanced self-assembly of triblock Janus colloids targeted to form a kagome lattice. Using computer simulations, we demonstrate that the formation of this elusive structure can be significantly improved by self-propelling or activating the colloids along the axis connecting their hydrophobic hemispheres. The process by which metastable aggregates are destabilized and transformed into the favored kagome lattice is quite general, and we argue this active approach provides a systematic pathway to improving the self-assembly of a large number of colloidal structures.

/pdf/activity-enhanced-self-assembly-of-a-colloidal-kagome-3hmeikyw2a.pdf

Activity-Enhanced Self-Assembly of a Colloidal Kagome Lattice.

Using numerical simulations, we characterized the behavior of an elastic membrane immersed in an active fluid. Our findings reveal a nontrivial folding and re-expansion of the membrane that is controlled by the interplay of its resistance to bending and the self-propulsion strength of the active components in solution. We show how flexible membranes tend to collapse into multifolded states, whereas stiff membranes fluctuate between an extended configuration and a singly folded state. This study provides a simple example of how to exploit the random motion of active particles to perform mechanical work at the microscale.

Anomalous dynamics of an elastic membrane in an active fluid.

Postdoctoral researchers play a crucial role in many research groups, serving as mentors, teachers, and leaders as they develop their skills and prepare for scientific careers (1). However, the coronavirus disease 2019 (COVID-19) crisis has put funding and support for postdoc positions at risk, threatening to upend the career paths available to these junior scientists.

https://science.sciencemag.org/content/sci/368/6494/957.2.full.pdf

The precarious position of postdocs during COVID-19.

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