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

NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. NAMD scales to hundreds of processors on high-end parallel platforms, as well as tens of processors on low-cost commodity clusters, and also runs on individual desktop and laptop computers. NAMD works with AMBER and CHARMM potential functions, parameters, and file formats. This article, directed to novices as well as experts, first introduces concepts and methods used in the NAMD program, describing the classical molecular dynamics force field, equations of motion, and integration methods along with the efficient electrostatics evaluation algorithms employed and temperature and pressure controls used. Features for steering the simulation across barriers and for calculating both alchemical and conformational free energy differences are presented. The motivations for and a roadmap to the internal design of NAMD, implemented in C++ and based on Charm++ parallel objects, are outlined. The factors affecting the serial and parallel performance of a simulation are discussed. Finally, typical NAMD use is illustrated with representative applications to a small, a medium, and a large biomolecular system, highlighting particular features of NAMD, for example, the Tcl scripting language. The article also provides a list of the key features of NAMD and discusses the benefits of combining NAMD with the molecular graphics/sequence analysis software VMD and the grid computing/collaboratory software BioCoRE. NAMD is distributed free of charge with source code at www.ks.uiuc.edu.

/pdf/scalable-molecular-dynamics-with-namd-51o1z7rwp8.pdf

Scalable molecular dynamics with NAMD

/pdf/scalable-molecular-dynamics-with-namd-3j7xyc70g4.pdf

Scalable Molecular Dynamics with NAMD

The 1000 Genomes Project set out to provide a comprehensive description of common human genetic variation by applying whole-genome sequencing to a diverse set of individuals from multiple populations. Here we report completion of the project, having reconstructed the genomes of 2,504 individuals from 26 populations using a combination of low-coverage whole-genome sequencing, deep exome sequencing, and dense microarray genotyping. We characterized a broad spectrum of genetic variation, in total over 88 million variants (84.7 million single nucleotide polymorphisms (SNPs), 3.6 million short insertions/deletions (indels), and 60,000 structural variants), all phased onto high-quality haplotypes. This resource includes >99% of SNP variants with a frequency of >1% for a variety of ancestries. We describe the distribution of genetic variation across the global sample, and discuss the implications for common disease studies.

https://cdr.lib.unc.edu/downloads/v692t8920

A global reference for human genetic variation.

Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.

The authors report the results of electrooptic (EO) and nonlinear optical (NLO) studies in several thin-film materials deposited on fused silica substrates. Using a transparent substrate allowed observation of the EO and NLO effects easily by using optical-transmission-type measurements. PLZT, BaTiO/sub 3/, SBN, BNN, and beta-BBO thin-film materials were studied. The material properties and the potential applications of these films are discussed. >

Electro-optic and non-linear optical properties of (Pb,La)(Zr,Ti)O/sub 3/, BaTiO/sub 3/ (Sr,Ba)Nb/sub 2/O/sub 6/, Ba/sub 2/NaNb/sub 5/O/sub 15/, and beta-BaB/sub 2/O/sub 4/ thin films

Both strands of a diploid genome can now be efficiently sequenced de novo, unlocking the diversity of the human gene pool.

Beyond the reference genome.

Simultaneous Force and Fluorescence Measurements on Single Ribosomes Demonstrate that mRNA Secondary Structures do not Restrict EF-G Catalyzed Translocation

ESCRT Membrane Scission Revealed by Optical Tweezers

RNA Polymerase Translocation in Processive Transcription Elongation and Pausing: Dynamics, Force-Dependence, and Modulation by Sequence-Specific RNAP-DNA Interactions

Carlos Bustamante

Papers

Electro-optic and non-linear optical properties of (Pb,La)(Zr,Ti)O/sub 3/, BaTiO/sub 3/ (Sr,Ba)Nb/sub 2/O/sub 6/, Ba/sub 2/NaNb/sub 5/O/sub 15/, and beta-BaB/sub 2/O/sub 4/ thin films

Beyond the reference genome.

Simultaneous Force and Fluorescence Measurements on Single Ribosomes Demonstrate that mRNA Secondary Structures do not Restrict EF-G Catalyzed Translocation

ESCRT Membrane Scission Revealed by Optical Tweezers

RNA Polymerase Translocation in Processive Transcription Elongation and Pausing: Dynamics, Force-Dependence, and Modulation by Sequence-Specific RNAP-DNA Interactions