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

다중혈관 관상동맥 환자에서 y-문합을 이용하여 양쪽 내흉동맥만을 사용한 우회술의 조기 성적

We present two new hybrid meta exchange- correlation functionals, called M06 and M06-2X. The M06 functional is parametrized including both transition metals and nonmetals, whereas the M06-2X functional is a high-nonlocality functional with double the amount of nonlocal exchange (2X), and it is parametrized only for nonmetals.The functionals, along with the previously published M06-L local functional and the M06-HF full-Hartree–Fock functionals, constitute the M06 suite of complementary functionals. We assess these four functionals by comparing their performance to that of 12 other functionals and Hartree–Fock theory for 403 energetic data in 29 diverse databases, including ten databases for thermochemistry, four databases for kinetics, eight databases for noncovalent interactions, three databases for transition metal bonding, one database for metal atom excitation energies, and three databases for molecular excitation energies. We also illustrate the performance of these 17 methods for three databases containing 40 bond lengths and for databases containing 38 vibrational frequencies and 15 vibrational zero point energies. We recommend the M06-2X functional for applications involving main-group thermochemistry, kinetics, noncovalent interactions, and electronic excitation energies to valence and Rydberg states. We recommend the M06 functional for application in organometallic and inorganometallic chemistry and for noncovalent interactions.

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The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals

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

Multiwfn is a multifunctional program for wavefunction analysis. Its main functions are: (1) Calculating and visualizing real space function, such as electrostatic potential and electron localization function at point, in a line, in a plane or in a spatial scope. (2) Population analysis. (3) Bond order analysis. (4) Orbital composition analysis. (5) Plot density-of-states and spectrum. (6) Topology analysis for electron density. Some other useful utilities involved in quantum chemistry studies are also provided. The built-in graph module enables the results of wavefunction analysis to be plotted directly or exported to high-quality graphic file. The program interface is very user-friendly and suitable for both research and teaching purpose. The code of Multiwfn is substantially optimized and parallelized. Its efficiency is demonstrated to be significantly higher than related programs with the same functions. Five practical examples involving a wide variety of systems and analysis methods are given to illustrate the usefulness of Multiwfn. The program is free of charge and open-source. Its precompiled file and source codes are available from http://multiwfn.codeplex.com.

Multiwfn: a multifunctional wavefunction analyzer.

Traditionally, the discovery of new solid-state materials with user-defined properties is driven either by human intuition, heuristic chemical rules, and/or density functional theory (DFT). However, these methods have limitations, either in accessibly (domain expertise), accuracy, and/or throughput  [1]. Consequently, the material search space remains underexplored, given order 105 reported compounds compared to order 1010 theorized ternary compounds [2]. To accelerate the exploration of new solid-state materials, a framework capable of inverse design for materials with user-defined properties is needed. Herein, we present a generalized framework for inverse design of crystals with user-defined properties, which include both ground-state and excited-state properties (e.g., thermoelectric power factor) using sparsely labelled training data. The key enabler of this inverse-design framework is a general and invertible crystallographic representation that encodes the crystallographic information into the representations in both real space and reciprocal space. The trained surrogate model achieves similar property prediction accuracy and precision as DFT calculations within seconds. Using the developed inverse-design framework, we design 79 new crystals with user-targeted formation energies, 17 crystals with targeted bandgap, and 27 crystals for potential thermoelectric applications. The compositions of those designed materials are unique and cannot be found in the training or test sets. We validate our predictions using first-principle calculations. ­­Toward bridging the gap between simulation and experiment, we demonstrate a naive synthesizability metric — predicting the existence of an ICSD record — and show this methodology can, in principle, include stability and/or synthesizability as a target metric, once consensus metrics are agreed upon by the field.

An Invertible Crystallographic Representation for General Inverse Design of Inorganic Crystals with Targeted Properties

A simplified approach to treating the electron correlation energy is suggested in which only the alpha-beta component of the second order Moller-Plesset energy is evaluated, and then scaled by an empirical factor which is suggested to be 1.3. This scaled opposite spin second order energy (SOS-MP@) yields results for relative energies and derivative properties that are statistically improved over the conventional MP2 method. Furthermore, the SOS-MP2 energy can be evaluated without the 5th order computational steps associated with MP2 theory, even without exploiting any spatial locality. A 4th order algorithm is given for evaluating the opposite spin MP2 energy using auxiliary basis expansions, and a Laplace aproach, and timing comparisons are given.

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Scaled Opposite Spin Second Order Moller-Plesset Correlation Energy: An Economical Electronic Structure Method - eScholarship

Sodium ion batteries (SIBs) have many advantages such as the low price and abundance of sodium raw materials that are suitable for large-scale energy storage applications. Herein, we report an Mn-based pyrophosphate, Na(2)MnP(2)O(7), as a new SIB cathode material. Unlike most Mn-based cathode materials, which suffer severely from sluggish kinetics, Na(2)MnP(2)O(7) exhibits good electrochemical activity at ~3.8 V vs Na/Na(+) with a reversible capacity of 90 mAh g(-1) at room temperature. It also shows an excellent cycling and rate performance: 96% capacity retention after 30 cycles and 70% capacity retention at a c-rate increase from 0.05C to 1C. These electrochemical activities of the Mn-containing cathode material even at room temperature with relatively large particle sizes are remarkable considering an almost complete inactivity of the Li counterpart, Li(2)MnP(2)O(7). Using first-principles calculations, we find that the significantly enhanced kinetics of Na(2)MnP(2)O(7) is mainly due to the locally flexible accommodation of Jahn-Teller distortions aided by the corner-sharing crystal structure in triclinic Na(2)MnP(2)O(7). By contrast, in monoclinic Li(2)MnP(2)O(7), the edge-sharing geometry causes multiple bonds to be broken and formed during charging reaction with a large degree of atomic rearrangements. We expect that the similar computational strategy to analyze the atomic rearrangements can be used to predict the kinetics behavior when exploring new cathode candidates.

Anomalous Manganese Activation of a Pyrophosphate Cathode in Sodium Ion Batteries: A Combined Experimental and Theoretical Study.

Dirhodium acetates or copper triflate catalyze the highly regioisomeric formation of the fluorenes from appropriately substituted biaryldiazoacetates, whereas under thermal conditions a significantly reduced regioselectivity is observed.

Intramolecular Aromatic Carbenoid Insertion of Biaryldiazoacetates for the Regioselective Synthesis of Fluorenes.

https://pubs.acs.org/doi/pdf/10.1021/acsenergylett.6b00640

Yousung Jung

Papers

An Invertible Crystallographic Representation for General Inverse Design of Inorganic Crystals with Targeted Properties

Scaled Opposite Spin Second Order Moller-Plesset Correlation Energy: An Economical Electronic Structure Method - eScholarship

Anomalous Manganese Activation of a Pyrophosphate Cathode in Sodium Ion Batteries: A Combined Experimental and Theoretical Study.

Intramolecular Aromatic Carbenoid Insertion of Biaryldiazoacetates for the Regioselective Synthesis of Fluorenes.

EEWS 2016: Progress and Perspectives of Energy Science and Technology