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

6.2.2. Definition of Effective Properties 3064 6.3. Response Properties to Magnetic Fields 3066 6.3.1. Nuclear Shielding 3066 6.3.2. Indirect Spin−Spin Coupling 3067 6.3.3. EPR Parameters 3068 6.4. Properties of Chiral Systems 3069 6.4.1. Electronic Circular Dichroism (ECD) 3069 6.4.2. Optical Rotation (OR) 3069 6.4.3. VCD and VROA 3070 7. Continuum and Discrete Models 3071 7.1. Continuum Methods within MD and MC Simulations 3072

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Quantum mechanical continuum solvation models.

Nanocrystals are fundamental to modern science and technology. Mastery over the shape of a nanocrystal enables control of its properties and enhancement of its usefulness for a given application. Our aim is to present a comprehensive review of current research activities that center on the shape-controlled synthesis of metal nanocrystals. We begin with a brief introduction to nucleation and growth within the context of metal nanocrystal synthesis, followed by a discussion of the possible shapes that a metal nanocrystal might take under different conditions. We then focus on a variety of experimental parameters that have been explored to manipulate the nucleation and growth of metal nanocrystals in solution-phase syntheses in an effort to generate specific shapes. We then elaborate on these approaches by selecting examples in which there is already reasonable understanding for the observed shape control or at least the protocols have proven to be reproducible and controllable. Finally, we highlight a number of applications that have been enabled and/or enhanced by the shape-controlled synthesis of metal nanocrystals. We conclude this article with personal perspectives on the directions toward which future research in this field might take.

Shape‐Controlled Synthesis of Metal Nanocrystals: Simple Chemistry Meets Complex Physics?

Summary Background Since December, 2019, Wuhan, China, has experienced an outbreak of coronavirus disease 2019 (COVID-19), caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Epidemiological and clinical characteristics of patients with COVID-19 have been reported but risk factors for mortality and a detailed clinical course of illness, including viral shedding, have not been well described. Methods In this retrospective, multicentre cohort study, we included all adult inpatients (≥18 years old) with laboratory-confirmed COVID-19 from Jinyintan Hospital and Wuhan Pulmonary Hospital (Wuhan, China) who had been discharged or had died by Jan 31, 2020. Demographic, clinical, treatment, and laboratory data, including serial samples for viral RNA detection, were extracted from electronic medical records and compared between survivors and non-survivors. We used univariable and multivariable logistic regression methods to explore the risk factors associated with in-hospital death. Findings 191 patients (135 from Jinyintan Hospital and 56 from Wuhan Pulmonary Hospital) were included in this study, of whom 137 were discharged and 54 died in hospital. 91 (48%) patients had a comorbidity, with hypertension being the most common (58 [30%] patients), followed by diabetes (36 [19%] patients) and coronary heart disease (15 [8%] patients). Multivariable regression showed increasing odds of in-hospital death associated with older age (odds ratio 1·10, 95% CI 1·03–1·17, per year increase; p=0·0043), higher Sequential Organ Failure Assessment (SOFA) score (5·65, 2·61–12·23; p Interpretation The potential risk factors of older age, high SOFA score, and d-dimer greater than 1 μg/mL could help clinicians to identify patients with poor prognosis at an early stage. Prolonged viral shedding provides the rationale for a strategy of isolation of infected patients and optimal antiviral interventions in the future. Funding Chinese Academy of Medical Sciences Innovation Fund for Medical Sciences; National Science Grant for Distinguished Young Scholars; National Key Research and Development Program of China; The Beijing Science and Technology Project; and Major Projects of National Science and Technology on New Drug Creation and Development.

Clinical course and risk factors for mortality of adult inpatients with COVID-19 in Wuhan, China: a retrospective cohort study

Applications of Combinatorics and Graph Theory to Spectroscopy and Quantum Chemistry

An alloy cluster containing a 13-atom core, with a composition Ag 7 Au 6 (H 2 MSA) 10 (H 2 MSA=mercaptosuccinic acid) was synthesized from silver clusters by a galvanic exchange reaction. The clusters were characterized by several spectroscopic and microscopic methods. The alloy cluster shows luminescence with a quantum yield of 3.5×10 -2 at room temperature. Theoretical calculations for Ag 7 Au 6 (SCH 3 ) 10 suggest a distorted icosahedral core.

Ag7Au6: A 13-Atom Alloy Quantum Cluster

CAS SCF/CI calculations of low-lying states of SnH2

A relativistic configuration interaction scheme is described for polyatomic molecules containing heavy atoms. In this method first complete active space MCSCF followed by large scale configuration interaction calculations are carried out. The natural orbitals generated in the large scale CI are then used in the relativistic CI (RCI) calculations, which include the spin–orbit integrals. The spin–orbit integrals are obtained using large Gaussian basis sets, with the operator expressed as a difference of relativistic effective core potentials, and then transformed over the natural orbitals. The transformed integrals are included as one‐electron matrix elements in the RCI. This procedure thus takes into account both electron correlation and spin–orbit effects. The method is applied to the spin–orbit states derived from the three low‐lying states of PbH2, SnH2, and GeH2 (1A1, 3B1, and 1B1). The spin–orbit mixings of the 1A1 and 3B1(A1) states in the RCI wave functions of PbH2 and SnH2 were found to be quite si...

Relativistic configuration interaction calculations for polyatomics: Applications to PbH2, SnH2, and GeH2

It is demonstrated by using high-level ab initio computations that the yellow curcumin pigment, bis(4-hydroxy-3-methoxyphenyl)-1,6-diene-3,5-dione, in the east Indian root plant turmeric (Curcuma longa) exhibits unique charge and bonding characteristics that facilitate penetration into the blood−brain barrier and binding to amyloid β (Aβ). Alzheimer's disease is caused by Aβ accumulation in the brain cells combined with oxidative stress and inflammation. Consistent with the recent experimental work by Cole and co-workers (Yang, F., et al. J. Biol. Chem. 2004, 280, 5892−5901) that demonstrates curcumin pigment's binding ability to Aβ both in vivo and in vitro, it is shown here that curcumin possesses suitable charge and bonding features to facilitate the binding to Aβ. In addition, curcumin's anti-inflammatory and antioxidant properties are also attributed to electronic and structural features. It is shown that the presence of an enolic center and two phenolic polar groups separated by an essentially hydro...

Krishnan Balasubramanian

Papers

Applications of Combinatorics and Graph Theory to Spectroscopy and Quantum Chemistry

Ag7Au6: A 13-Atom Alloy Quantum Cluster

CAS SCF/CI calculations of low-lying states of SnH2

Relativistic configuration interaction calculations for polyatomics: Applications to PbH2, SnH2, and GeH2

Molecular Orbital Basis for Yellow Curry Spice Curcumin's Prevention of Alzheimer's Disease