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

We present a new method for calculating the product yield of a radical pair recombination reaction in the presence of a weak time-dependent magnetic field. This method successfully circumvents the computational difficulties presented by a direct solution of the Liouville-von Neumann equation for a long-lived radical pair containing many hyperfine-coupled nuclear spins. Using a modified formulation of Floquet theory, treating the time-dependent magnetic field as a perturbation, and exploiting the slow radical pair recombination, we show that one can obtain a good approximation to the product yield by considering only nearly degenerate sub-spaces of the Floquet space. Within a significant parameter range, the resulting method is found to give product yields in good agreement with exact quantum mechanical results for a variety of simple model radical pairs. Moreover it is considerably more efficient than the exact calculation, and it can be applied to radical pairs containing significantly more nuclear spins. This promises to open the door to realistic theoretical investigations of the effect of radiofrequency electromagnetic radiation on the photochemically induced radical pair recombination reactions in the avian retina which are believed to be responsible for the magnetic compass sense of migratory birds.

Floquet theory of radical pairs in radiofrequency magnetic fields

The magnetoelectroluminescence of conjugated organic polymer films is widely accepted to arise from a polaron pair mechanism, but their magnetoconductance is less well understood. Here we derive a new relationship between the experimentally measurable magnetoelectroluminescence and magnetoconductance and the theoretically calculable singlet yield of the polaron pair recombination reaction. This relationship is expected to be valid regardless of the mechanism of the magnetoconductance, provided the mobilities of the free polarons are independent of the applied magnetic field (i.e., provided one discounts the possibility of spin-dependent transport). We also discuss the semiclassical calculation of the singlet yield of the polaron pair recombination reaction for materials such as poly(2,5-dioctyloxy-paraphenylene vinylene) (DOO-PPV), the hyperfine fields in the polarons of which can be extracted from light-induced electron spin resonance measurements. The resulting theory is shown to give good agreement with experimental data for both normal (H-) and deuterated (D-) DOO-PPV over a wide range of magnetic field strengths once singlet-triplet dephasing is taken into account. Without this effect, which has not been included in any previous simulation of magnetoelectroluminescence, it is not possible to reproduce the experimental data for both isotopologues in a consistent fashion. Our results also indicate that the magnetoconductance of DOO-PPV cannot be solely due to the effect of the magnetic field on the dissociation of polaron pairs.

Magnetoelectroluminescence in organic light emitting diodes

We analyze the golden rule limit of the recently proposed isomorphic ring polymer (iso-RP) method. This method aims to combine an exact expression for the quantum mechanical partition function of a system with multiple electronic states with a pre-existing mixed quantum-classical (MQC) dynamics approximation, such as fewest switches surface hopping. Since the choice of the MQC method adds a degree of flexibility, we simplify the analysis by assuming that the dynamics used correctly reproduces the exact golden rule rate for a nonadiabatic (e.g., electron transfer) reaction in the high temperature limit. Having made this assumption, we obtain an expression for the iso-RP rate in the golden rule limit that is valid at any temperature. We then compare this rate with the exact rate for a series of simple spin-boson models. We find that the iso-RP method does not correctly predict how nuclear quantum effects affect the reaction rate in the golden rule limit. Most notably, it does not capture the quantum asymmetry in a conventional (Marcus) plot of the logarithm of the reaction rate against the thermodynamic driving force, and it also significantly overestimates the correct quantum mechanical golden rule rate for activationless electron transfer reactions. These results are analyzed and their implications discussed for the applicability of the iso-RP method to more general nonadiabatic reactions.

/pdf/an-analysis-of-isomorphic-rpmd-in-the-golden-rule-limit-4x5qx0zc4x.pdf

An analysis of isomorphic RPMD in the golden rule limit.

The isomer problem for fullerene derivatives: structural proposals for C70H36

Relaxation processes can have a large effect on the spin selective electron transfer reactions of radical pairs. These processes are often treated using phenomenological relaxation superoperators or with some model for the microscopic relaxation mechanism treated within Bloch-Redfield-Wangsness theory. Here, we demonstrate that an alternative perturbative relaxation theory, based on the Nakajima-Zwanzig equation, has certain advantages over Redfield theory. In particular, the Nakajima-Zwanzig equation does not suffer from the severe positivity problem of Redfield theory in the static disorder limit. Combining the Nakajima-Zwanzig approach consistently with the Schulten-Wolynes semiclassical method, we obtain an efficient method for modeling the spin dynamics of radical pairs containing many hyperfine-coupled nuclear spins. This is then used to investigate the spin-dependent electron transfer reactions and intersystem crossing of dimethyljulolidine-naphthalenediimide (DMJ-NDI) radical ion pairs. By comparing our simulations with experimental data, we find evidence for a field-independent contribution to the triplet quantum yields of these reactions which cannot be explained by electron spin relaxation alone.

David E. Manolopoulos

Papers

Floquet theory of radical pairs in radiofrequency magnetic fields

Magnetoelectroluminescence in organic light emitting diodes

An analysis of isomorphic RPMD in the golden rule limit.

The isomer problem for fullerene derivatives: structural proposals for C70H36

Electron spin relaxation in radical pairs: Beyond the Redfield approximation.