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

抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the-art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudopotential and projector-augmented-wave approaches Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement their ideas In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-40poaosrve.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO.

Quantum ESPRESSO is an integrated suite of open-source computer codes for quantum simulations of materials using state-of-the art electronic-structure techniques, based on density-functional theory, density-functional perturbation theory, and many-body perturbation theory, within the plane-wave pseudo-potential and projector-augmented-wave approaches. Quantum ESPRESSO owes its popularity to the wide variety of properties and processes it allows to simulate, to its performance on an increasingly broad array of hardware architectures, and to a community of researchers that rely on its capabilities as a core open-source development platform to implement theirs ideas. In this paper we describe recent extensions and improvements, covering new methodologies and property calculators, improved parallelization, code modularization, and extended interoperability both within the distribution and with external software.

/pdf/advanced-capabilities-for-materials-modelling-with-quantum-1mm65lmkt8.pdf

Advanced capabilities for materials modelling with Quantum ESPRESSO

Advances in theory and algorithms for electronic structure calculations must be incorporated into program packages to enable them to become routinely used by the broader chemical community. This work reviews advances made over the past five years or so that constitute the major improvements contained in a new release of the Q-Chem quantum chemistry package, together with illustrative timings and applications. Specific developments discussed include fast methods for density functional theory calculations, linear scaling evaluation of energies, NMR chemical shifts and electric properties, fast auxiliary basis function methods for correlated energies and gradients, equation-of-motion coupled cluster methods for ground and excited states, geminal wavefunctions, embedding methods and techniques for exploring potential energy surfaces.

/pdf/advances-in-methods-and-algorithms-in-a-modern-quantum-29c5vso11m.pdf

Advances in methods and algorithms in a modern quantum chemistry program package

Radical pair recombination reactions are normally described using a quantum mechanical master equation for the electronic and nuclear spin density operator. The electron spin state selective (singlet and triplet) recombination processes are described with a Haberkorn reaction term in this master equation. Here we consider a general spin state selective electron transfer reaction of a radical pair and use Nakajima-Zwanzig theory to derive the master equation for the spin density operator, thereby elucidating the relationship between non-adiabatic reaction rate theory and the Haberkorn reaction term. A second order perturbation theory treatment of the diabatic coupling naturally results in the Haberkorn master equation with an additional reactive scalar electron spin coupling term. This term has been neglected in previous spin chemistry calculations, but we show that it will often be quite significant. We also show that beyond the second order in perturbation theory, i.e., beyond the Fermi golden rule limit, an additional reactive singlet-triplet dephasing term appears in the master equation. A closed form expression for the reactive scalar electron spin coupling in terms of the Marcus theory parameters that determine the singlet and triplet recombination rates is presented. By performing simulations of radical pair reactions with the exact hierarchical equations of motion method, we demonstrate that our master equations provide a very accurate description of radical pairs undergoing spin-selective non-adiabatic electron transfer reactions. The existence of a reactive electron spin coupling may well have implications for biologically relevant radical pair reactions such as those which have been suggested to play a role in avian magnetoreception.

/pdf/spin-selective-electron-transfer-reactions-of-radical-pairs-4kx3lowm2f.pdf

Spin-selective electron transfer reactions of radical pairs: Beyond the Haberkorn master equation

/pdf/electronic-structure-software-22lpaq4o47.pdf

Electronic structure software

The water molecule, rotationally state selected in the third and fourth OH stretching overtone (‖04〉−, ‖05〉−) and stretch–bend combination (‖04−2〉) levels, has been photodissociated via the A state at λ≂282 nm. The photofragment rotational state distributions, determined by OH(A–X) laser induced fluorescence (LIF), differ from those reported previously by Andresen and co‐workers, in which water was initially prepared in the ‖01〉− level and photodissociated at 193 nm, and from those by Crim and co‐workers, in which H2O was photodissociated via the ‖04〉− level at wavelengths shorter than 282 nm. These differences become more pronounced with increasing angular momentum in the parent water molecule and with an increasing number of quanta in the intermediate OH stretching overtone state. The Franck–Condon theory of Balint‐Kurti, previously employed successfully to account for the product state distributions arising from the 193 nm photodissociation of H2O‖01〉−, qualitatively reproduces the trends observed in the present study if it is assumed that dissociation occurs preferentially from extended RH‐OH configurations of the ‖04〉− and ‖05〉− overtones. The product OH state distributions are thus shown to be sensitive indicators of the bending and rotational motions of H2O(X) in the wide amplitude stretching region of the ground state surface.

New trends in the state‐to‐state photodissociation dynamics of H2O(Ã)

Graph-theoretical and semi-empirical quantum-chemical results are combined to give a picture of the energetics and isomerisations of a typical lower fullerene, C40. 38 of the 40 distinct fullerene isomers of C40 are connected by Stone–Wales (pyracylene) transformations; the isomer of lowest total energy (as calculated by the QCFF/PI method) has the smallest number of fused pentagon pairs, and elimination of pentagon adjacencies by successive pyracylene rearrangements takes all other connected C40 fullerenes downhill to the optimal isomer.

Energetics and isomerisation pathways of a lower fullerene. The Stone–Wales map for C40

C 76 has 19151 possible fullerene structural isomers of which up to 55 are compatible with the experimental 19-line 13 C NMR spectrum, but only two have isolated pentagons. Calculations of the relative energies of all 55 candidates within the semi-empirical QCFF/PI model pick out the isolated-pentagon D 2 isomer as the structure of lowest energy for C 76 , confirming previous calculations and providing support for the isolated-pentagon rule. Energy differences between isomers of C 76 are interpreted in the model as torsional strains induced by pentagon adjacencies.

David E. Manolopoulos

Papers

Spin-selective electron transfer reactions of radical pairs: Beyond the Haberkorn master equation

Electronic structure software

New trends in the state‐to‐state photodissociation dynamics of H2O(Ã)

Energetics and isomerisation pathways of a lower fullerene. The Stone–Wales map for C40

Relative stabilities of C76 isomers. A numerical test of the fullerene isolated-pentagon rule