Results 41 to 50 of about 8,517,557 (393)

Coarse graining molecular dynamics with graph neural networks. [PDF]

Journal of Chemical Physics, 2020
Coarse graining enables the investigation of molecular dynamics for larger systems and at longer timescales than is possible at an atomic resolution.
B. Husic, N. Charron, Dominik Lemm, Jiang Wang, Adrià Pérez, Maciej Majewski, Andreas Krämer, Yaoyi Chen, S. Olsson, G. de Fabritiis, F. Noé, C. Clementi   +11 more
semanticscholar   +1 more source

Relationship Between Homodimeric Glucocorticoid Receptor and Transcriptional Regulation Assessed via an In Vitro Fluorescence Correlation Spectroscopy-Microwell System

Scientific Reports, 2018
Glucocorticoid receptor (GR) is a hormone-activated transcription regulatory protein involved in metabolism as well as adrenocortical responses to psychosocial stress.
Sho Oasa, Shintaro Mikuni, Johtaro Yamamoto, Tsumugi Kurosaki, Daisuke Yamashita, Masataka Kinjo   +5 more
doaj   +1 more source

Spin blockade and phonon bottleneck for hot electron relaxation observed in n-doped colloidal quantum dots

Nature Communications, 2021
Hot electrons in bulk semiconductors usually relax via electron-phonon scattering on a sub-picosecond timescale. Here, the authors observe hot electron lifetime as long as 320 picoseconds by performing a photochemical reduction reaction on colloidal ...
Junhui Wang, Lifeng Wang, Shuwen Yu, Tao Ding, Dongmei Xiang, Kaifeng Wu   +5 more
doaj   +1 more source

Event-Driven Molecular Dynamics in Parallel [PDF]

, 2003
Although event-driven algorithms have been shown to be far more efficient than time-driven methods such as conventional molecular dynamics, they have not become as popular.
Alder, Allen, Dokholyan, Knuth, Korniss, Lubachevsky, Lubachevsky, Lubachevsky, Luding, Luding, Luding, Luding, Luding, Marı́n, Marı́n, Rapaport, S. Luding, S. Miller, Smith   +18 more
core   +2 more sources

OpenMM 7: Rapid development of high performance algorithms for molecular dynamics

bioRxiv, 2016
OpenMM is a molecular dynamics simulation toolkit with a unique focus on extensibility. It allows users to easily add new features, including forces with novel functional forms, new integration algorithms, and new simulation protocols.
P. Eastman, Jason M. Swails, J. Chodera, R. McGibbon, Yutong Zhao, Kyle A. Beauchamp, Lee‐Ping Wang, Andrew C. Simmonett, M. Harrigan, Chaya D. Stern, Rafal P. Wiewiora, B. Brooks, V. Pande   +12 more
semanticscholar   +1 more source

Molecular dynamics as an approach to study prion protein misfolding and the effect of pathogenic mutations [PDF]

, 2011
Computer simulation of protein dynamics offers unique high-resolution information that complements experiment. Using experimentally derived structures of the natively folded prion protein (PrP), physically realistic dynamics and conformational changes ...
Daggett, Valerie, van der Kamp, Marc W
core   +2 more sources

On the dynamics of molecular conformation [PDF]

Proceedings of the National Academy of Sciences, 2006
Understanding the mechanism of fast transitions between conformed states of large biomolecules is central to reconciling the dichotomy between the relatively high speed of metabolic processes and slow (random-walk based) estimates on the speed of biomolecular processes.
openaire   +2 more sources

Near-field transmission matrix microscopy for mapping high-order eigenmodes of subwavelength nanostructures

Nature Communications, 2020
Nanoscale integrated photonic devices have complicated combinations of optical eigenmodes. Here, the authors develop a far- to near-field transmission matrix microscopy that enables measuring higher-order modes of nanostructures beyond the capabilities ...
Eunsung Seo, Young-Ho Jin, Wonjun Choi, Yonghyeon Jo, Suyeon Lee, Kyung-Deok Song, Joonmo Ahn, Q.-Han Park, Myung-Ki Kim, Wonshik Choi   +9 more
doaj   +1 more source

Coupling Constant pH Molecular Dynamics with Accelerated Molecular Dynamics [PDF]

Journal of Chemical Theory and Computation, 2010
An extension of the constant pH method originally implemented by Mongan et al. (J. Comput. Chem.2004, 25, 2038-2048) is proposed in this study. This adapted version of the method couples the constant pH methodology with the enhanced sampling technique of accelerated molecular dynamics, in an attempt to overcome the sampling issues encountered with ...
Williams, Sarah L, de Oliveira, César Augusto F, McCammon, J Andrew   +2 more
openaire   +3 more sources

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