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

N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

https://iopscience.iop.org/article/10.1088/0031-9112/34/4/040/pdf

Stochastic Processes in Physics and Chemistry

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method.

https://biblio.ugent.be/publication/8514189/file/8514192.pdf

The ReaxFF reactive force-field: development, applications and future directions

Spintronics refers commonly to phenomena in which the spin of electrons in a solid state environment plays the determining role In a more narrow sense spintronics is an emerging research field of electronics: spintronics devices are based on a spin control of electronics, or on an electrical and optical control of spin or magnetism This review presents selected themes of semiconductor spintronics, introducing important concepts in spin transport, spin injection, Silsbee-Johnson spin-charge coupling, and spindependent tunneling, as well as spin relaxation and spin dynamics The most fundamental spin-dependent nteraction in nonmagnetic semiconductors is spin-orbit coupling Depending on the crystal symmetries of the material, as well as on the structural properties of semiconductor based heterostructures, the spin-orbit coupling takes on different functional forms, giving a nice playground of effective spin-orbit Hamiltonians The effective Hamiltonians for the most relevant classes of materials and heterostructures are derived here from realistic electronic band structure descriptions Most semiconductor device systems are still theoretical concepts, waiting for experimental demonstrations A review of selected proposed, and a few demonstrated devices is presented, with detailed description of two important classes: magnetic resonant tunnel structures and bipolar magnetic diodes and transistors In most cases the presentation is of tutorial style, introducing the essential theoretical formalism at an accessible level, with case-study-like illustrations of actual experimental results, as well as with brief reviews of relevant recent achievements in the field

/pdf/semiconductor-spintronics-1ed0d0goer.pdf

Semiconductor Spintronics

The current understanding of some important nonlinear collective processes in quantum plasmas with degenerate electrons is presented. After reviewing the basic properties of quantum plasmas, model equations (e.g., the quantum hydrodynamic and effective nonlinear Schrodinger-Poisson equations) are presented that describe collective nonlinear phenomena at nanoscales. The effects of the electron degeneracy arise due to Heisenberg’s uncertainty principle and Pauli’s exclusion principle for overlapping electron wave functions that result in tunneling of electrons and the electron degeneracy pressure. Since electrons are Fermions (spin-1/2 quantum particles), there also appears an electron spin current and a spin force acting on electrons due to the Bohr magnetization. The quantum effects produce new aspects of electrostatic (ES) and electromagnetic (EM) waves in a quantum plasma that are summarized in here. Furthermore, nonlinear features of ES ion waves and electron plasma oscillations are discussed, as well as the trapping of intense EM waves in quantum electron-density cavities. Specifically, simulation studies of the coupled nonlinear Schrodinger and Poisson equations reveal the formation and dynamics of localized ES structures at nanoscales in a quantum plasma. The effect of an external magnetic field on the plasma wave spectra and develop quantum magnetohydrodynamic equations are also discussed. The results are useful for understanding numerous collective phenomena in quantum plasmas, such as those in compact astrophysical objects (e.g., the cores of white dwarf stars and giant planets), as well as in plasma-assisted nanotechnology (e.g., quantum diodes, quantum free-electron lasers, nanophotonics and nanoplasmonics, metallic nanostructures, thin metal films, semiconductor quantum wells, and quantum dots, etc.), and in the next generation of intense laser-solid density plasma interaction experiments relevant for fast ignition in inertial confinement fusion schemes.

/pdf/colloquium-nonlinear-collective-interactions-in-quantum-1nqlatefgo.pdf

Colloquium : nonlinear collective interactions in quantum plasmas with degenerate electron fluids

We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA-molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH-radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen-abstraction as well as formation of carbonyl- and hydroxyl-groups in the sugar-moiety that create holes in the sugar-rings. These holes grow up slowly between DNA-bases and DNA-backbone and the damage collectively propagate to DNA single and double strand break.

/pdf/reactive-molecular-dynamics-study-on-the-first-steps-of-dna-2t2vlnstow.pdf

Reactive Molecular Dynamics study on the first steps of DNA-damage by free hydroxyl radicals

We employ a large scale molecular simulation based on bond-order ReaxFF to simulate the chemical reaction and study the damage to a large fragment of DNA molecule in the solution by ionizing radiation. We illustrate that the randomly distributed clusters of diatomic OH radicals that are primary products of megavoltage ionizing radiation in water-based systems are the main source of hydrogen abstraction as well as formation of carbonyl and hydroxyl groups in the sugar moiety that create holes in the sugar rings. These holes grow up slowly between DNA bases and DNA backbone, and the damage collectively propagates to a DNA single and double strand break.

Reactive molecular dynamics study on the first steps of DNA damage by free hydroxyl radicals.

Understanding the damage of DNA bases from hydrogen abstraction by free OH radicals is of particular importance to understanding the indirect effect of ionizing radiation. Previous studies address the problem with truncated DNA bases as ab initio quantum simulations required to study such electronic-spin-dependent processes are computationally expensive. Here, for the first time, we employ a multiscale and hybrid quantum mechanical–molecular mechanical simulation to study the interaction of OH radicals with a guanine-deoxyribose-phosphate DNA molecular unit in the presence of water, where all of the water molecules and the deoxyribose-phosphate fragment are treated with the simplistic classical molecular mechanical scheme. Our result illustrates that the presence of water strongly alters the hydrogen-abstraction reaction as the hydrogen bonding of OH radicals with water restricts the relative orientation of the OH radicals with respect to the DNA base (here, guanine). This results in an angular anisotropy...

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

/pdf/tailoring-magnetism-in-quantum-dots-2866wi3czd.pdf

Tailoring Magnetism in Quantum Dots

We study the influence of deformations on magnetic ordering in quantum dots doped with magnetic impurities. The reduction of symmetry and the associated deformation from circular to elliptical quantum confinement lead to the formation of piezomagnetic quantum dots. The strength of elliptical deformation can be controlled by the gate voltage to change the magnitude of magnetization, at a fixed number of carriers and in the absence of an applied magnetic field. We reveal a reentrant magnetic ordering with the increase of elliptical deformation and suggest that the piezomagnetic quantum dots can be used as nanoscale magnetic switches.

Ramin M. Abolfath

Papers

Reactive Molecular Dynamics study on the first steps of DNA-damage by free hydroxyl radicals

Reactive molecular dynamics study on the first steps of DNA damage by free hydroxyl radicals.

Multiscale QM/MM molecular dynamics study on the first steps of guanine damage by free hydroxyl radicals in solution.

Tailoring Magnetism in Quantum Dots

Piezomagnetic Quantum Dots