Results 101 to 110 of about 8,517,557 (393)

Molecular Dynamics Simulations of Detonation Instability

, 2008
After making modifications to the Reactive Empirical Bond Order potential for Molecular Dynamics (MD) of Brenner et al. in order to make the model behave in a more conventional manner, we discover that the new model exhibits detonation instability, a ...
Andrew J. Heim, Edward M. Kober, Niels Grønbech-Jensen, Timothy C. Germann, W. Fickett   +4 more
core   +1 more source

MDAnalysis: A Python Package for the Rapid Analysis of Molecular Dynamics Simulations

SciPy, 2016
MDAnalysis (http://mdanalysis.org) is a library for structural and temporal analysis of molecular dynamics (MD) simulation trajectories and individual protein structures.
Richard J. Gowers, Max Linke, J. Barnoud, T. Reddy, M. Melo, Sean L. Seyler, J. Domanski, David L. Dotson, Sébastien Buchoux, Ian M. Kenney, O. Beckstein   +10 more
semanticscholar   +1 more source

Interplay between circadian and other transcription factors—Implications for cycling transcriptome reprogramming

FEBS Letters, EarlyView.
This perspective highlights emerging insights into how the circadian transcription factor CLOCK:BMAL1 regulates chromatin architecture, cooperates with other transcription factors, and coordinates enhancer dynamics. We propose an updated framework for how circadian transcription factors operate within dynamic and multifactorial chromatin landscapes ...
Xinyu Y. Nie, Jerome S. Menet
wiley   +1 more source

Deep tissue space-gated microscopy via acousto-optic interaction

Nature Communications, 2020
In ideal diffraction-limited optical microscopy imaging depth is limited by the multiply scattered wave. Here, the authors present a space gating method, based on an acoustic focus in the object plane and reconstruction using only the acousto-optically ...
Mooseok Jang, Hakseok Ko, Jin Hee Hong, Won Kyu Lee, Jae-Seung Lee, Wonshik Choi   +5 more
doaj   +1 more source

Hydrodynamic model for picosecond propagation of laser-created nanoplasmas

, 2015
The interaction of a free-electron-laser pulse with a moderate or large size cluster is known to create a quasi-neutral nanoplasma, which then expands on hydrodynamic timescale, i.e., $>1$ ps.
Jurek, Zoltan, Santra, Robin, Saxena, Vikrant, Ziaja, Beata   +3 more
core   +1 more source

Real‐time assay of ribonucleotide reductase activity with a fluorescent RNA aptamer

FEBS Letters, EarlyView.
Ribonucleotide reductases (RNR) synthesize DNA building blocks de novo, making them crucial in DNA replication and drug targeting. FLARE introduces the first single‐tube real‐time coupled RNR assay, which enables isothermal tracking of RNR activity at nanomolar enzyme levels and allows the reconstruction of allosteric regulatory patterns and rapid ...
Jacopo De Capitani, Noemi E. Nwosu, Viktoria Gocke, Müge Kasanmascheff, Hannes Mutschler   +4 more
wiley   +1 more source

Mechanistic insight into the dynamics of Mur ligase through a comprehensive timescale-specific approach

Communications Chemistry
Muramyl ligases are multidomain enzymes involved in intracellular steps of bacterial peptidoglycan synthesis and are considered promising targets for the development of new antibacterial agents.
Iza Ogris, Barbara Zupančič, Izidor Sosič, Franci Merzel, Simona Golič Grdadolnik   +4 more
doaj   +1 more source

Programming an interpreter using molecular dynamics [PDF]

, 2007
PGA (ProGram Algebra) is an algebra of programs which concerns programs in their simplest form: sequences of instructions. Molecular dynamics is a simple model of computation developed in the setting of PGA, which bears on the use of dynamic data ...
C. A. Middelburg, C. A. Middelburg, C. A. Middelburg, J. A. Bergstra, J. A. Bergstra, J. A. Bergstra   +5 more
core   +4 more sources

Advances in Molecular Dynamics Simulations and Enhanced Sampling Methods for the Study of Protein Systems

International Journal of Molecular Sciences, 2020
Molecular dynamics (MD) simulation is a rigorous theoretical tool that when used efficiently could provide reliable answers to questions pertaining to the structure-function relationship of proteins.
Raudah Lazim, Donghyuk Suh, Sun Choi
semanticscholar   +1 more source

Disordered but rhythmic—the role of intrinsic protein disorder in eukaryotic circadian timing

FEBS Letters, EarlyView.
Unstructured domains known as intrinsically disordered regions (IDRs) are present in nearly every part of the eukaryotic core circadian oscillator. IDRs enable many diverse inter‐ and intramolecular interactions that support clock function. IDR conformations are highly tunable by post‐translational modifications and environmental conditions, which ...
Emery T. Usher, Jacqueline F. Pelham
wiley   +1 more source