Search Results - "Herman, C J"

GROMACS: Fast, flexible, and free by Van Der Spoel, David, Lindahl, Erik, Hess, Berk, Groenhof, Gerrit, Mark, Alan E., Berendsen, Herman J. C.

“…This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The…”
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High-Throughput Simulations Reveal Membrane-Mediated Effects of Alcohols on MscL Gating by Melo, Manuel N, Arnarez, Clément, Sikkema, Hendrik, Kumar, Neeraj, Walko, Martin, Berendsen, Herman J. C, Kocer, Armagan, Marrink, Siewert J, Ingólfsson, Helgi I

“…The mechanosensitive channels of large conductance (MscL) are bacterial membrane proteins that serve as last resort emergency release valves in case of severe…”
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Photoactivation of the Photoactive Yellow Protein:  Why Photon Absorption Triggers a Trans-to-Cis Isomerization of the Chromophore in the Protein by Groenhof, Gerrit, Bouxin-Cademartory, Mathieu, Hess, Berk, de Visser, Sam P., Berendsen, Herman J. C., Olivucci, Massimo, Mark, Alan E., Robb, Michael A.

“…Atomistic QM/MM simulations have been carried out on the complete photocycle of Photoactive Yellow Protein, a bacterial photoreceptor, in which blue light…”
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Phantasmidine: An Epibatidine Congener from the Ecuadorian Poison Frog Epipedobates anthonyi by Fitch, Richard W, Spande, Thomas F, Garraffo, H. Martin, Yeh, Herman J. C, Daly, John W

“…The skin of the Ecuadorian poison frog Epipedobates anthonyi contains the potent nicotinic agonists epibatidine (1) and N-methylepibatidine (3). In addition, a…”
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Dynamic Conformations of Flavin Adenine Dinucleotide:  Simulated Molecular Dynamics of the Flavin Cofactor Related to the Time-Resolved Fluorescence Characteristics by van den Berg, Petra A. W, Feenstra, K. Anton, Mark, Alan E, Berendsen, Herman J. C, Visser, Antonie J. W. G

“…Molecular dynamics (MD) simulations and polarized subnanosecond time-resolved flavin fluorescence spectroscopy have been used to study the conformational…”
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Considerations on corrosion and weld repair effects on the fatigue strength of a steel structure critical to the flight-safety by Nascimento, Marcelino P., Voorwald, Herman J.C.

“…The aim of this study is to analyze the effects of corrosion and successive tungsten inert gas (TIG) welding repairs on the reverse bending fatigue strength of…”
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Bioassay-Guided Isolation of Epiquinamide, a Novel Quinolizidine Alkaloid and Nicotinic Agonist from an Ecuadoran Poison Frog, Epipedobates tricolor by FITCH, Richard W., GARRAFFO, H. Martin, SPANDE, Thomas F., YEH, Herman J. C., DALY, John W.

“…Analytical HPLC fractionation, combined with an off-line 96-well fluorescent bioassay screen, has been developed and used for the separation and screening of a…”
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Calculation of the Redox Potential of the Protein Azurin and Some Mutants by van den Bosch, Marieke, Swart, Marcel, Snijders†, Jaap G, Berendsen, Herman J.C, Mark, Alan E, Oostenbrink, Chris, van Gunsteren, Wilfred F, Canters, Gerard W

“…Azurin from Pseudomonas aeruginosa is a small 128-residue, copper-containing protein. Its redox potential can be modified by mutating the protein. Free-energy…”
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Signal transduction in the photoactive yellow protein. I. Photon absorption and the isomerization of the chromophore by Groenhof, Gerrit, Lensink, Marc F., Berendsen, Herman J. C., Snijders, Jaap G., Mark, Alan E.

“…Molecular dynamics simulation techniques together with time‐dependent density functional theory calculations have been used to investigate the effect of photon…”
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The AUUCU Repeats Responsible for Spinocerebellar Ataxia Type 10 Form Unusual RNA Hairpins by Handa, Vaishali, Yeh, Herman J.C., McPhie, Peter, Usdin, Karen

“…Spinocerebellar ataxia type 10 is an autosomal dominant disorder caused by expansion of a pentameric repeat tract (ATTCT·AGAAT)n in intron 9 of the gene that…”
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A Glimpse of the Holy Grail? by BERENDSEN, H. J. C

“…Amino acid genetic sequencing reamins a daunting task. Research success in folding a 36-residue protein with dynamics simulation, dependent on huge computing…”
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Sugarcane bagasse cellulose/HDPE composites obtained by extrusion by Mulinari, Daniella Regina, Voorwald, Herman J.C., Cioffi, Maria Odila H., da Silva, Maria Lúcia C.P., da Cruz, Tessie Gouvêa, Saron, Clodoaldo

“…Natural fibers used in this study were both pre-treated and modified residues from sugarcane bagasse. Polymer of high density polyethylene (HDPE) was employed…”
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Improving efficiency of large time-scale molecular dynamics simulations of hydrogen-rich systems by Feenstra, K. Anton, Hess, Berk, Berendsen, Herman J. C.

“…A systematic analysis is performed on the effectiveness of removing degrees of freedom from hydrogen atoms and/or increasing hydrogen masses to increase the…”
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Molecular dynamics simulation of a membrane/water interface: the ordering of water and its relation to the hydration force by Marrink, Siewert Jan, Berkowitz, Max, Berendsen, Herman J. C

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Signal transduction in the photoactive yellow protein. II. Proton transfer initiates conformational changes by Groenhof, Gerrit, Lensink, Marc F., Berendsen, Herman J. C., Mark, Alan E.

“…Molecular dynamics simulation techniques, together with semiempirical PM3 calculations, have been used to investigate the effect of photoisomerization of the…”
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Determining equilibrium constants for dimerization reactions from molecular dynamics simulations by De Jong, Djurre H., Schäfer, Lars V., De Vries, Alex H., Marrink, Siewert J., Berendsen, Herman J. C., Grubmüller, Helmut

“…With today's available computer power, free energy calculations from equilibrium molecular dynamics simulations “via counting” become feasible for an…”
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Reality Simulation: Observe While It Happens by Berendsen, Herman J. C.

“…Decades of method development, together with rapid growth in computational power, are enabling researchers to simulate complex biological processes on…”
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Simulation of water transport through a lipid membrane by Marrink, Siewert-Jan, Berendsen, Herman J. C

“…To obtain insight in the process of water permeation through a lipid membrane we performed molecular dynamics simulations on a phospholipid (DPPC)/water system…”
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Preparation and properties of HDPE/sugarcane bagasse cellulose composites obtained for thermokinetic mixer by Mulinari, Daniella R., Voorwald, Herman J.C., Cioffi, Maria Odila H., da Silva, Maria Lúcia C.P., Luz, Sandra M.

“…The use of natural fibers as reinforcement for thermoplastics has generated much interest due to their low cost, possibility of environmental protection and…”
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Methyl Group-Induced Helicity in 1,4-Dimethylbenzo[c]phenanthrene and Its Metabolites:  Synthesis, Physical, and Biological Properties by Lakshman, Mahesh K, Kole, Panna L, Chaturvedi, Surendrakumar, Saugier, Joseph H, Yeh, Herman J. C, Glusker, Jenny P, Carrell, H. L, Katz, Amy K, Afshar, Carol E, Dashwood, Won-Mohaiza, Kenniston, Gary, Baird, William M

“…1,4-Dimethylbenzo[c]phenanthrene (1,4-DMBcPh) is the dimethylated analogue of the benzo[c]phenanthrene (BcPh), where one of its two methyl groups resides in…”
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