Results 31 to 40 of about 1,038,801 (318)

GPU-SD and DPD Parallelization for Gromacs tools for molecular dynamics simulations [PDF]

, 2012
This article presents the GPU parallelization of new algorithms SD and DPD types for molecular dynamics systems developed by the Molecular Dynamics Group, University of Groningen, the Netherlands.
Marrink, Siewert,, Nicolae Goga, Cioromela, Ruxandra, Siewert Marrink, Goga, Nicolae, Marrink, Siewert, Goga, Nicolae,, Cioromela, Ruxandra,, Florica Moldoveanu, Marrink, Siewert; id_orcid, Moldoveanu, Florica, Ruxandra Cioromela, Moldoveanu, Florica,   +12 more
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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

Ring polymer molecular dynamics

, 2006
This thesis presents the ring polymer molecular dynamics (RPMD) approximation to the Kubo-transformed time correlation function and shows how it may be used as the basis of an approximate quantum-mechanical method for determining the dynamical properties
Craig, Ian R.
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Combining an Elastic Network With a Coarse-Grained Molecular Force Field: Structure, Dynamics, and Intermolecular Recognition [PDF]

, 2009
Structure-based and physics-based coarse-grained molecular force fields have become attractive approaches to gain mechanistic insight into the function of large biomolecular assemblies.
Marrink, Siewert-Jan, Ceruso, Marco A., Marco Cavalli, Marrink, Siewert-Jan; id_orcid, Periole, Xavier, Siewert-Jan Marrink, Xavier Periole, Marco A. Ceruso, Cavalli, Marco   +8 more
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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

Fermionic molecular dynamics [PDF]

Nuclear Physics A, 1989
Abstract A new type of molecular dynamics is proposed to solve approximately the many-body problem of interacting identical fermions with spin 1 2 . The interacting system is represented by an antisymmetrized many-body wave function consisting of single-particle states which are localized in phase space.
openaire   +1 more source

Validation of molecular dynamics simulation [PDF]

, 1998
How the results obtained by computer simulation of molecular systems can be validated is considered. The overall quality of the simulated properties of a molecular system will depend on (i) the quality of the theory or model, (ii) the accuracy of the ...
van Gunsteren, Wilfred F., Mark, A. E., van Gunsteren, W. F., Wilfred F. van Gunsteren, Mark, Alan E., Alan E. Mark   +5 more
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Characterization of thylakoid lipid membranes from cyanobacteria and higher plants by molecular dynamics simulations [PDF]

, 2015
The thylakoid membrane is mainly composed of non-common lipids, so called galactolipids. Despite the importance of these lipids for the function of the photosynthetic reaction centers, the molecular organization of these membranes is largely unexplored ...
van Eerden, Floris J., Marrink, Siewert J.; id_orcid, Wassenaar, Tsjerk A., de Jong, Djurre H., de Vries, Alex H.; id_orcid, de Vries, Alex H., Marrink, Siewert J.   +6 more
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Metagenomic analysis of human, animal, and environmental samples identifies potential emerging pathogens, profiles antibiotic resistance genes, and reveals horizontal gene transfer dynamics

Scientific Reports
Antimicrobial resistance (AMR) poses a significant threat to global health. The indiscriminate use of antibiotics has accelerated the emergence and spread of drug-resistant bacteria, compromising our ability to treat infectious diseases.
Rajindra Napit, Anupama Gurung, Ajit Poudel, Ashok Chaudhary, Prajwol Manandhar, Ajay Narayan Sharma, Samita Raut, Saman Man Pradhan, Jyotsna Joshi, Mathilde Poyet, Mathieu Groussin, Rajesh M. Rajbhandari, Dibesh B. Karmacharya   +12 more
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A Quantitative Study of Internal and External Interactions of Homodimeric Glucocorticoid Receptor Using Fluorescence Cross-Correlation Spectroscopy in a Live Cell

Scientific Reports, 2017
Glucocorticoid receptor (GRα) is a well-known ligand-dependent transcription-regulatory protein. The classic view is that unliganded GRα resides in the cytoplasm, relocates to the nucleus after ligand binding, and then associates with a specific DNA ...
Manisha Tiwari, Sho Oasa, Johtaro Yamamoto, Shintaro Mikuni, Masataka Kinjo   +4 more
doaj   +1 more source