Results 41 to 50 of about 602,983 (281)

Molecular Dynamics Simulation of Collisions between Hydrogen and Graphite [PDF]

, 2006
Hydrogen adsorption by graphite is examined by classical molecular dynamics simulation using a modified Brenner REBO potential. Such interactions are typical in chemical sputtering experiments, and knowledge of the fundamental behavior of hydrogen and ...
Ito, A., Nakamura, H.
core   +1 more source

A methionine‐lined active site governs carbocation stabilization and product specificity in a bacterial terpene synthase

FEBS Letters, EarlyView.
This study reveals a unique active site enriched in methionine residues and demonstrates that these residues play a critical role by stabilizing carbocation intermediates through novel sulfur–cation interactions. Structure‐guided mutagenesis further revealed variants with significantly altered product profiles, enhancing pseudopterosin formation. These
Marion Ringel, Carl P. O. Helmer, Shani Zev, Ronja Driller, Emily Buhr, Markus Reinbold, Renana Schwartz, Gabriel Foley, Mikael Boden, Daniel Garbe, Gerhard Schenk, Dan Thomas Major, Bernhard Loll, Thomas Brück   +13 more
wiley   +1 more source

Computational prediction of L_{3} EXAFS spectra of gold nanoparticles from classical molecular dynamics simulations

, 2011
We present a computational approach for the simulation of extended x-ray absorption fine structure (EXAFS) spectra of nanoparticles directly from molecular dynamics simulations without fitting any of the structural parameters of the nanoparticle to ...
Comaschi, Tatiana, Price, Stephen W.T., Roscioni, Otello Maria, Russell, Andrea E., Skylaris, Chris-Kriton, Zonias, Nicholas   +5 more
core   +1 more source

Simulation of Claylike Colloids [PDF]

, 2005
We investigate properties of dense suspensions and sediments of small spherical silt particles by means of a combined Molecular Dynamics (MD) and Stochastic Rotation Dynamics (SRD) simulation.
D. J. Shaw, G. Lagaly, G. Wang, Hans J. Herrmann, I. D. Morrison, J. A. Lewis, J. F. Richardson, J. Mahanty, Jens Harting, K. S. Schmitz, M. P. Allen, Martin Hecht, R. J. Hunter, R. Oberacker, Thomas Ihle, W. B. Russel   +15 more
core   +2 more sources

pH‐mediated activation of the lysosomal arginine sensor SLC38A9

FEBS Letters, EarlyView.
Cells monitor nutrient levels via the lysosomal transporter SLC38A9 to activate the mechanistic target of rapamycin complex 1 (mTORC1). This study reveals that SLC38A9 function is regulated by pH. We identified histidine 544 as a critical pH sensor that undergoes conformational changes to control amino acid efflux from lysosomes; therefore, it ...
Xuelang Mu, Ampon Sae Her, Tamir Gonen
wiley   +1 more source

Applications of Molecular Dynamics Simulation in Protein Study

Membranes, 2022
Molecular Dynamics (MD) Simulations is increasingly used as a powerful tool to study protein structure-related questions. Starting from the early simulation study on the photoisomerization in rhodopsin in 1976, MD Simulations has been used to study ...
Siddharth Sinha, Benjamin Tam, San Ming Wang   +2 more
doaj   +1 more source

Ab-Initio Molecular Dynamics

, 2013
Computer simulation methods, such as Monte Carlo or Molecular Dynamics, are very powerful computational techniques that provide detailed and essentially exact information on classical many-body problems.
Alavi, Alder, Almlöf, Alonso, Andrade, Arias, Baroni, Bendt, Benoit, Berendsen, Berne, Binder, Binder, Blöchl, Blöchl, Blöchl, Born, Bornemann, Briggs, Camellone, Car, Caravati, Caravati, Caravati, Caravati, Caravati, Caravati, Ceperley, Ceperley, Ceriotti, Ceriotti, Chandler, Cucinotta, Dai, Dreizler, Ehrenfest, Engel, Ferguson, Fermi, Feynman, Feynman, Foulkes, Frenkel, Galli, Gan, Gilbert, Gillan, Goedecker, Goedecker, Guidon, Guidon, Guidon, Habershon, Harriman, Harris, Hartree, Hassanali, Hellmann, Herbert, Hohenberg, Hutter, Iannuzzi, Jones, Kalos, Khaliullin, Khaliullin, Koch, Kohanoff, Kohn, Kohn, Kolafa, Kolafa, Krack, Krack, Krack, Krajewski, Kresse, Kresse, Kresse, Kühne, Kühne, Kühne, Kühne, Laasonen, Landau, Levy, Lieb, Lippert, Lippert, Liu, Los, Los, Luduena, Luduena, Martin, Martyna, Marx, Marx, Marzari, McWeeny, Mermin, Metropolis, Modine, Morrone, Mostofi, Niklasson, Niklasson, Palser, Parr, Parrinello, Pascal, Pastore, Payne, Perdew, Pulay, Putrino, Rahman, Rapacioli, Rapaport, Ricci, Richters, Röhrig, Scheffler, Schlegel, Schmid, Selloni, Sharma, Smargiassi, Tangney, Tangney, Thomas, Thomas, Todorova, Tuckerman, Tuckerman, Tymczak, VandeVondele, VandeVondele, VandeVondele, Yang, Zhang   +140 more
core   +1 more source

Peroxidasin enables melanoma immune escape by inhibiting natural killer cell cytotoxicity

Molecular Oncology, EarlyView.
Peroxidasin (PXDN) is secreted by melanoma cells and binds the NK cell receptor NKG2D, thereby suppressing NK cell activation and cytotoxicity. PXDN depletion restores NKG2D signaling and enables effective NK cell–mediated melanoma killing. These findings identify PXDN as a previously unrecognized immune evasion factor and a potential target to improve
Hsu‐Min Sung, David Bickel, Lena C. M. Krause, Daria Ezeriņa, Christian Ickes, Julian Wojtachnia, Christine S. Gibhardt, Magdalena Shumanska, Khadija Wahni, Andrea Paluschkiwitz, Julia Malo Pueyo, Ekaterina Baranova, Wim Vranken, Hedwig Stanisz, Ioana Stejerean‐Todoran, Michael P. Schön, Joris Messens, Ivan Bogeski   +17 more
wiley   +1 more source

Molecular dynamics simulation of multi-pass nano-grinding process

MATEC Web of Conferences, 2018
Grinding involves the use of a large number of micrometric abrasive grains in order to remove material from workpiece surface efficiently and finally render a high quality surface. More specifically, grinding in the nano-metric level serves for attaining
Karkalos Nikolaos E., Markopoulos Angelos P.   +1 more
doaj   +1 more source

Keratin 19 as a prognostic marker and contributing factor of metastasis and chemoresistance in high‐grade serous ovarian cancer

Molecular Oncology, EarlyView.
Keratin 19 (KRT19) is overexpressed in high‐grade serous ovarian cancer with high levels of Kallikrein‐related peptidases (KLK) 4–7 and is associated with poor survival. In vivo analyses demonstrate that elevated KRT19 increases peritoneal tumour burden.
Sophia Bielesch, Isabel Vogel, Sina Nokodian, Johanna Moeller, Antonia Blechschmidt, Vicky Hecht, Vanessa Kuentzel, Katharina Thiedig, Melissa Schwab, Oliver Schilling, Holger Bronger, Marion Kiechle, Viktor Magdolen, Tobias Dreyer   +13 more
wiley   +1 more source