Search Results - "Lippert, Ross A."

Accurate and efficient integration for molecular dynamics simulations at constant temperature and pressure by Lippert, Ross A, Predescu, Cristian, Ierardi, Douglas J, Mackenzie, Kenneth M, Eastwood, Michael P, Dror, Ron O, Shaw, David E

“…In molecular dynamics simulations, control over temperature and pressure is typically achieved by augmenting the original system with additional dynamical…”
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A common, avoidable source of error in molecular dynamics integrators by Lippert, Ross A, Bowers, Kevin J, Dror, Ron O, Eastwood, Michael P, Gregersen, Brent A, Klepeis, John L, Kolossvary, Istvan, Shaw, David E

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Equipartition and the Calculation of Temperature in Biomolecular Simulations by Eastwood, Michael P., Stafford, Kate A., Lippert, Ross A., Jensen, Morten Ø., Maragakis, Paul, Predescu, Cristian, Dror, Ron O., Shaw, David E.

“…Since the behavior of biomolecules can be sensitive to temperature, the ability to accurately calculate and control the temperature in molecular dynamics (MD)…”
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Distributional Regimes for the Number of k-Word Matches between Two Random Sequences by Lippert, Ross A., Huang, Haiyan, Waterman, Michael S.

“…When comparing two sequences, a natural approach is to count the number of k-letter words the two sequences have in common. No positional information is used…”
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A space-efficient construction of the Burrows-Wheeler transform for genomic data by Lippert, Ross A, Mobarry, Clark M, Walenz, Brian P

“…Algorithms for exact string matching have substantial application in computational biology. Time-efficient data structures which support a variety of exact…”
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Fixing multiple eigenvalues by a minimal perturbation by Lippert, Ross A.

“…Suppose we are given an n × n matrix, M , and a set of values, { λ i } i = 1 m ( m ⩽ n ), and we wish to find the smallest perturbation in the 2-norm (i.e.,…”
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Computationally efficient molecular dynamics integrators with improved sampling accuracy by Predescu, Cristian, Lippert, Ross A., Eastwood, Michael P., Ierardi, Douglas, Xu, Huafeng, Jensen, Morten Ø., Bowers, Kevin J., Gullingsrud, Justin, Rendleman, Charles A., Dror, Ron O., Shaw, David E.

“…The design of numerical integrators for particle simulations with arbitrary potentials entails fundamental trade-offs between the accuracy achieved and the…”
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Improved Twiddle Access for Fast Fourier Transforms by Bowers, K.J., Lippert, R.A., Dror, R.O., Shaw, D.E.

“…Optimizing the number of arithmetic operations required in fast Fourier transform (FFT) algorithms has been the focus of extensive research, but memory…”
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Space-efficient whole genome comparisons with Burrows-Wheeler transforms by Lippert, Ross A

“…The starting point for any alignment of mammalian genomes is the computation of exact matches satisfying various criteria. Time-efficient, O(n), data…”
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Fixing two eigenvalues by a minimal perturbation by Lippert, Ross A.

“…The optimal perturbation, Δ M, to a matrix, M, such that M − Δ M has a given eigenvalue λ 0 is given by the Eckart–Young theorem. This perturbation is optimal…”
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The linkage disequilibrium maps of three human chromosomes across four populations reflect their demographic history and a common underlying recombination pattern by De La Vega, Francisco M, Isaac, Hadar, Collins, Andrew, Scafe, Charles R, Halldórsson, Bjarni V, Su, Xiaoping, Lippert, Ross A, Wang, Yu, Laig-Webster, Marion, Koehler, Ryan T, Ziegle, Janet S, Wogan, Lewis T, Stevens, Junko F, Leinen, Kyle M, Olson, Sheri J, Guegler, Karl J, You, Xiaoqing, Xu, Lily H, Hemken, Heinz G, Kalush, Francis, Itakura, Mitsuo, Zheng, Yi, de Thé, Guy, O'Brien, Stephen J, Clark, Andrew G, Istrail, Sorin, Hunkapiller, Michael W, Spier, Eugene G, Gilbert, Dennis A

“…The extent and patterns of linkage disequilibrium (LD) determine the feasibility of association studies to map genes that underlie complex traits. Here we…”
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Discrete Approximations to Continuum Optimal Flow Problems by Lippert, Ross A.

“…Problems in partial differential equations with inequality constraints can be used to describe a continuum analog to various optimal flow/cut problems. While…”
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The multimode Procrustes problem by Trendafilov, Nickolay T., Lippert, Ross A.

“…In this paper, we consider a generalization of the well-known Procrustes problem relevant to principal component analysis of multidimensional data arrays. This…”
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Finding anchors for genomic sequence comparison by Lippert, Ross A, Zhao, Xiaoyue, Florea, Liliana, Mobarry, Clark, Istrail, Sorin

“…Recent sequencing of the human and other mammalian genomes has brought about the necessity to align them, to identify and characterize their commonalities and…”
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Flandersʼ theorem for many matrices under commutativity assumptions by De Terán, Fernando, Lippert, Ross A., Nakatsukasa, Yuji, Noferini, Vanni

“…We analyze the relationship between the Jordan canonical form of products, in different orders, of k square matrices A1,…,Ak. Our results extend some classical…”
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Multiscale Computation with Interpolating Wavelets by Lippert, Ross A., Arias, T.A., Edelman, Alan

“…Multiresolution analyses based upon interpolets, interpolating scaling functions introduced by Deslauriers and Dubuc, are particularly well-suited to physical…”
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The $\textit{u}$-series: A separable decomposition for electrostatics computation with improved accuracy by Predescu, Cristian, Lerer, Adam K, Lippert, Ross A, Towles, Brian, Grossman, J. P, Dirks, Robert M, Shaw, David E

“…The evaluation of electrostatic energy for a set of point charges in a periodic lattice is a computationally expensive part of molecular dynamics simulations…”
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Asymptotic convergence for iterative optimization in electronic structure by Lippert, Ross A., Sears, Mark P.

“…There have recently been a number of proposals for solving large electronic structure problems (local-density approximation, Hartree-Fock, and tight-binding…”
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Multiscale Computation with Interpolating Wavelets by Lippert, Ross A, Arias, T. A, Edelman, Alan

“…Journal of Computational Physics 140, 278 (1998) Multiresolution analyses based upon interpolets, interpolating scaling functions introduced by Deslauriers and…”
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