Search Results - "Straatsma, T.P."

Characterization of the outer membrane protein OprF of Pseudomonas aeruginosa in a lipopolysaccharide membrane by computer simulation by Straatsma, T.P., Soares, T.A.

“…The N‐terminal domain of outer membrane protein OprF of Pseudomonas aeruginosa forms a membrane spanning eight‐stranded antiparallel β‐barrel domain that folds…”
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High performance computational chemistry: An overview of NWChem a distributed parallel application by Kendall, Ricky A., Aprà, Edoardo, Bernholdt, David E., Bylaska, Eric J., Dupuis, Michel, Fann, George I., Harrison, Robert J., Ju, Jialin, Nichols, Jeffrey A., Nieplocha, Jarek, Straatsma, T.P., Windus, Theresa L., Wong, Adrian T.

“…NWChem is the software package for computational chemistry on massively parallel computing systems developed by the High Performance Computational Chemistry…”
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From NWChem to NWChemEx: Evolving with the Computational Chemistry Landscape by Straatsma, T.P.

“…Since the advent of the first computers, chemists have been at the forefront of using computers to understand and solve complex chemical problems. As the…”
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Retention of Conformational Entropy upon Calmodulin Binding to Target Peptides Is Driven by Transient Salt Bridges by Smith, Dayle M.A., Straatsma, T.P., Squier, Thomas C.

“…Calmodulin (CaM) is a highly flexible calcium-binding protein that mediates signal transduction through an ability to differentially bind to highly variable…”
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Molecular docking of balanol to dynamics snapshots of protein kinase A by Wong, Chung F., Kua, Jeremy, Zhang, Yingkai, Straatsma, T.P., McCammon, J. Andrew

“…Even if the structure of a receptor has been determined experimentally, it may not be a conformation to which a ligand would bind when induced fit effects are…”
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Computer Simulation of the Rough Lipopolysaccharide Membrane of Pseudomonas aeruginosa by Lins, Roberto D., Straatsma, T.P.

“…Lipopolysaccharides (LPSs) form the major constituent of the outer membrane of Gram-negative bacteria, and are believed to play a key role in processes that…”
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NWChem: scalable parallel computational chemistry by van Dam, H.J.J., de Jong, W.A., Bylaska, E., Govind, N., Kowalski, K., Straatsma, T.P., Valiev, M.

“…NWChem is a general‐purpose computational chemistry code specifically designed to run on distributed memory parallel computers. The core functionality of the…”
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Molecular basis of the structural stability of a Top7-based scaffold at extreme pH and temperature conditions by Soares, Thereza A., Boschek, Curt B., Apiyo, David, Baird, Cheryl, Straatsma, T.P.

“…The development of stable biomolecular scaffolds that can tolerate environmental extremes has considerable potential for industrial and defense-related…”
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Molecular Basis for Microbial Adhesion to Geochemical Surfaces: Computer Simulation of Pseudomonas aeruginosa Adhesion to Goethite by Shroll, Robert M., Straatsma, T.P.

“…The adhesion of Pseudomonas aeruginosa to the goethite mineral is investigated using classical molecular simulation. A fragment model for goethite has been…”
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Structural and Electronic Property Study of (ZnO) n , n ≤ 168: Transition from Zinc Oxide Molecular Clusters to Ultrasmall Nanoparticles by Chen, Mingyang, Straatsma, T. P, Fang, Zongtang, Dixon, David A

“…Global minimum energy structures of (ZnO) n , n ≤ 168, were determined by using a hybrid genetic algorithm followed by a local geometry optimization at the…”
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NWChem: A comprehensive and scalable open-source solution for large scale molecular simulations by Valiev, M., Bylaska, E.J., Govind, N., Kowalski, K., Straatsma, T.P., Van Dam, H.J.J., Wang, D., Nieplocha, J., Apra, E., Windus, T.L., de Jong, W.A.

“…The latest release of NWChem delivers an open-source computational chemistry package with extensive capabilities for large scale simulations of chemical and…”
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Non-orthogonal Configuration Interaction Study on the Effect of Thermal Distortions on the Singlet Fission Process in Photoexcited Pure and B,N-Doped Pentacene Crystals by López, Xavier, Straatsma, Tjerk P., Sánchez-Mansilla, Aitor, de Graaf, Coen

“…The present computational work analyzes singlet fission (SF) as a pathway for multiplication of photogenerated excitons in crystalline polyacenes. Our study…”
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Multilayer Divide-Expand-Consolidate Coupled-Cluster Method: Demonstrative Calculations of the Adsorption Energy of Carbon Dioxide in the Mg-MOF-74 Metal–Organic Framework by Barnes, Ashleigh L, Bykov, Dmytro, Lyakh, Dmitry I, Straatsma, Tjerk P

“…The implementation and evaluation of a multilayer extension of the divide-expand-consolidate (DEC) scheme within the LSDalton program is presented. The DEC…”
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Calmodulin Conformational Binding Entropy Is Driven by Transient Salt Bridges by Smith, Dayle, Straatsma, T.P., Squier, Thomas C.

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Classical Force Field Development and Molecular Dynamics of [Nife] Hydrogenase by Smith, Dayle, Squier, Thomas C., Straatsma, T.P.

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Molecular Dynamics Study of Calmodulin-Target Complexes by Smith, Dayle, Straatsma, T.P., Squier, Thomas C.

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On eliminating synchronous communication in molecular simulations to improve scalability by Straatsma, T.P., Chavarría-Miranda, Daniel G.

“…Molecular dynamics simulation, as a complementary tool to experimentation, has become an important methodology for the understanding and design of molecular…”
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Assessment of the convergence of molecular dynamics simulations of lipopolysaccharide membranes by Soares, T.A., Straatsma, T.P.

“…The outer membrane of Gram-negative bacteria is composed of a phospholipid inner leaflet and a lipopolysaccharide (LPS) outer leaflet. The chemical structure…”
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Revisiting the structural flexibility of the complex p21 ras ‐GTP: The catalytic conformation of the molecular switch II by Soares, T.A., Miller, J.H., Straatsma, T.P.

“…Abstract The hydrolysis of GTP in p21 ras triggers conformational changes that regulate the ras/ERK signaling pathway. An important active site residue is…”
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Revisiting the structural flexibility of the complex p21ras-GTP: The catalytic conformation of the molecular switch II by Soares, T.A., Miller, J.H., Straatsma, T.P.

“…The hydrolysis of GTP in p21ras triggers conformational changes that regulate the ras/ERK signaling pathway. An important active site residue is Gln61, which…”
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