scispace - formally typeset
Search or ask a question
Author

Peter T. Cummings

Bio: Peter T. Cummings is an academic researcher from Vanderbilt University. The author has contributed to research in topics: Molecular dynamics & Supercritical fluid. The author has an hindex of 69, co-authored 521 publications receiving 18942 citations. Previous affiliations of Peter T. Cummings include University of Guelph & Oak Ridge National Laboratory.


Papers
More filters
Journal ArticleDOI
01 Dec 2006-Cell
TL;DR: The genetic make-up of a cancer cell may realize its invasive potential through a clonal evolution process driven by definable microenvironmental selective forces, and this mathematical model provides a theoretical/experimental framework to quantitatively characterize this selective pressure for invasion and test ways to eliminate it.

751 citations

Journal Article
TL;DR: In this article, the authors propose a method for measuring the performance of a single node in a set of images.ING and INDEXING, e.g., this article.

490 citations

Journal ArticleDOI
TL;DR: The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces and the attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.
Abstract: Knowing how motile bacteria move near and along a solid surface is crucial to understanding such diverse phenomena as the migration of infectious bacteria along a catheter, biofilm growth, and the movement of bacteria through the pore spaces of saturated soil, a critical step in the in situ bioremediation of contaminated aquifers. In this study, a tracking microscope is used to record the three-dimensional motion of Escherichia coli near a planar glass surface. Data from the tracking microscope are analyzed to quantify the effects of bacteria-surface interactions on the swimming behavior of bacteria. The speed of cells approaching the surface is found to decrease in agreement with the mathematical model of Ramia et al. [Ramia, M., Tullock, D. L. & Phan-Tien, N. (1993) Biophys J. 65,755-778], which represents the bacteria as spheres with a single polar flagellum rotating at a constant rate. The tendency of cells to swim adjacent to the surface is shown in computer-generated reproductions of cell traces. The attractive interaction potential between the cells and the solid surface is offered as one of several possible explanations for this tendency.

354 citations

Journal ArticleDOI
TL;DR: By analogy to the wave interference, it is demonstrated that the interference of two electrical double layers near each slit wall does not only explain the entire C–d curve, including the anomalous character, but also predicts the oscillatory behavior of C-d curve beyond 1.8 nm.
Abstract: Supercapacitors composed of slit-shaped micropores ranging in size from 0.67 to 1.8 nm in a room-temperature ionic liquid were studied to investigate the dependence of capacitance (C) on the pore size (d) using molecular dynamics simulations. The capacitance versus pore size (i.e., the C–d curve) was found to exhibit two peaks located at 0.7 and 1.4 nm, respectively. Specifically, as the pore shrinks from 1.0 to 0.7 nm, the capacitance of the micropore increases anomalously, in good agreement with experimental observations. We report herein that the second peak within 1.0 to 1.8 nm is a new feature of the C–d curve. Furthermore, by analogy to the wave interference, we demonstrate that the interference of two electrical double layers near each slit wall does not only explain the entire C–d curve, including the anomalous character, but also predicts the oscillatory behavior of C–d curve beyond 1.8 nm.

322 citations

Journal ArticleDOI
07 May 2004-Langmuir
TL;DR: This multitechnique and multiscale approach demonstrates the compatibility of bond-valence models of surface oxygen proton affinities and Stern-based models of the EDL structure, with the actual molecular interfacial distributions observed experimentally, revealing new insight into EDL properties including specific binding sites and hydration states of sorbed ions, interfacial solvent properties, and the effect of solution ionic strength.
Abstract: A comprehensive picture of the interface between aqueous solutions and the (110) surface of rutile (α-TiO2) is being developed by combining molecular-scale and macroscopic approaches, including experimental measurements, quantum calculations, molecular simulations, and Gouy−Chapman−Stern models. In situ X-ray reflectivity and X-ray standing-wave measurements are used to define the atomic arrangement of adsorbed ions, the coordination of interfacial water molecules, and substrate surface termination and structure. Ab initio calculations and molecular dynamics simulations, validated through direct comparison with the X-ray results, are used to predict ion distributions not measured experimentally. Potentiometric titration and ion adsorption results for rutile powders having predominant (110) surface expression provide macroscopic constraints of electrical double layer (EDL) properties (e.g., proton release) which are evaluated by comparison with a three-layer EDL model including surface oxygen proton affini...

305 citations


Cited by
More filters
01 May 1993
TL;DR: 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.
Abstract: 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.

29,323 citations

28 Jul 2005
TL;DR: PfPMP1)与感染红细胞、树突状组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�ly.
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。

18,940 citations

Journal ArticleDOI
TL;DR: Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules.
Abstract: In this article, we present a new LINear Constraint Solver (LINCS) for molecular simulations with bond constraints. The algorithm is inherently stable, as the constraints themselves are reset instead of derivatives of the constraints, thereby eliminating drift. Although the derivation of the algorithm is presented in terms of matrices, no matrix matrix multiplications are needed and only the nonzero matrix elements have to be stored, making the method useful for very large molecules. At the same accuracy, the LINCS algorithm is three to four times faster than the SHAKE algorithm. Parallelization of the algorithm is straightforward. (C) 1997 John Wiley & Sons, Inc.

12,699 citations

Journal ArticleDOI
TL;DR: Van Kampen as mentioned in this paper provides an extensive graduate-level introduction which is clear, cautious, interesting and readable, and could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes.
Abstract: N G van Kampen 1981 Amsterdam: North-Holland xiv + 419 pp price Dfl 180 This is a book which, at a lower price, could be expected to become an essential part of the library of every physical scientist concerned with problems involving fluctuations and stochastic processes, as well as those who just enjoy a beautifully written book. It provides an extensive graduate-level introduction which is clear, cautious, interesting and readable.

3,647 citations

Journal ArticleDOI
TL;DR: The atomic force microscope (AFM) is not only used to image the topography of solid surfaces at high resolution but also to measure force-versus-distance curves as discussed by the authors, which provide valuable information on local material properties such as elasticity, hardness, Hamaker constant, adhesion and surface charge densities.

3,281 citations