Carlos Bustamante

Bio: Carlos Bustamante is an academic researcher from Stanford University. The author has contributed to research in topics: Population & Optical tweezers. The author has an hindex of 161, co-authored 770 publications receiving 106053 citations. Previous affiliations of Carlos Bustamante include Lawrence Berkeley National Laboratory & University of California.

Physical parameters that control the imaging of purple membranes with the scanning tunneling microscope

Abstract: The dominant physical and geometrical parameters for imaging hydrated purple membranes with the scanning tunneling microscope are identified and characterized. These are sample voltage, current density, and tip radius. Purple membranes are imaged with vertical and lateral resolution of 0.7 nm and 15 nm, respectively. We also found that the apparent height of the membranes depends on the tip-substrate separation. These experiments pose the problem of electron transport through 5-10 nm thick insulating materials. We propose a model where the contrast mechanism is controlled by two factors, the electric field at the interface and the transmission through empty states in the membrane.

Electro-Optic and Non-Linear Optical Coefficients of (Pb,La)(Zr,Ti)O3, BaTiO3, (Sr,Ba)Nb2O6 and Ba2NaNb5O15 Thin Films

Abstract: The electro-optic properties of sputter-deposited PLZT, BaTiO 3 , SBN, and BNN films on fused silica substrates have been studied using a confocal scanning optical polarization microscope. The Pockels, Kerr, and higher order electro-optic coefficients and their relations to the non-linear optical coefficients in the films are presented. The materials and physical properties of the films are discussed.

Differential polarization microscope using an image dissector camera and phase‐lock detection

Abstract: A polarization modulation microscope designed to detect and spatially resolve the distribution of optically anisotropic domains in microscopic objects is described. An image dissector camera is used as the detection device. The polarization of the light is modulated by means of a photoelastic modulator and a synchronous demodulation amplifier (lock‐in) is utilized to obtain the difference image between the images formed using two orthogonal forms of the incident polarization on the sample. Preliminary results are described for the linear dichroism imaging measurements of polymerized hemoglobin (HbS) in red blood sickle cells. The present limitations of this design are discussed along with various strategies to improve its performance.

A very low current scanning tunneling microscope

Abstract: The applications of the scanning tunneling microscope (STM) in air are usually restricted to good conducting materials as clean metals, doped and passivated semiconductors, or to some molecular adsorbates deposited onto graphite. In order to study poor conducting materials as biological molecules, we have built a very low current STM. This instrument can routinely be operated at 0.1 pA while having a bandwidth of 7 kHz. The advantages of using very low currents are illustrated by imaging 5‐nm‐thick purple membranes. These membranes can only be imaged at currents smaller than 2 pA.

Whole-genome sequencing reveals the extent of heterozygosity in a preferentially self-fertilizing hermaphroditic vertebrate.

Abstract: The mangrove rivulus, Kryptolebias marmoratus, is one of only two self-fertilizing hermaphroditic fish species and inhabits mangrove forests. While selfing can be advantageous, it reduces heterozygosity and decreases genetic diversity. Studies using microsatellites found that there are variable levels of selfing among populations of K. marmoratus, but overall, there is a low rate of outcrossing and, therefore, low heterozygosity. In this study, we used whole-genome data to assess the levels of heterozygosity in different lineages of the mangrove rivulus and infer the phylogenetic relationships among those lineages. We sequenced whole genomes from 15 lineages that were completely homozygous at microsatellite loci and used single nucleotide polymorphisms (SNPs) to determine heterozygosity levels. More variation was uncovered than in studies using microsatellite data because of the resolution of full genome sequencing data. Moreover, missense polymorphisms were found most often in genes associated with immune function and reproduction. Inferred phylogenetic relationships suggest that lineages largely group by their geographic distribution. The use of whole-genome data provided further insight into genetic diversity in this unique species. Although this study was limited by the number of lineages that were available, these data suggest that there is previously undescribed variation within lineages of K. marmoratus that could have functional consequences and (or) inform us about the limits to selfing (e.g., genetic load, accumulation of deleterious mutations) and selection that might favor the maintenance of heterozygosity. These results highlight the need to sequence additional individuals within and among lineages.

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

Abstract: 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。

Scalable molecular dynamics with NAMD

Abstract: 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.

A global reference for human genetic variation.

Abstract: 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.