scholarly journals Atomistic Simulations of Wimley–White Pentapeptides: Sampling of Structure and Dynamics in Solution

2013 ◽  
Vol 9 (3) ◽  
pp. 1657-1666 ◽  
Author(s):  
Gurpreet Singh ◽  
D. Peter Tieleman
Keyword(s):  
Atomistic Simulations ◽  
Structure And Dynamics

Micromechanics and Microdynamics Via Atomistic Simulations

1988 ◽  
Vol 140 ◽  
Author(s):  
Uzi Landman ◽  
W. D. Luedtke ◽  
M. W. Ribarsky
Keyword(s):  
Microscopic Level ◽  
Atomistic Simulations ◽  
Dynamical Response ◽  
Natural Phenomena ◽  
Force Microscopy ◽  
Structure And Dynamics ◽  
External Perturbations ◽  
Atomic Force ◽  
Basic Understanding ◽  
Dynamics Simulations

AbstractBasic understanding of the structure and dynamics of materials and their response to external perturbations requires knowledge on the microscopic level, of the underlying energetics and atomic dynamics, whose consequences we observe and measure. Coupled with the above is the everlasting quest to observe and understand natural phenomena on refined microscopic scales, which provides the impetus for the development of experimental and theoretical techniques for the interrogation of materials with refined spatial and temporal resolution. In this paper we review the development of molecular dynamics simulations for studies of the energetics and dynamical response of materials to external mechanical perturbations. Applications to investigations of solid and liquid interfacial systems under stress and to studies of the consequences of tip-substrate interactions in atomic force microscopy are demonstrated.

scholarly journals A perspective on the molecular simulation of DNA from structural and functional aspects

2021 ◽  
Author(s):  
Manas Mondal ◽  
Lijiang Yang ◽  
Zhicheng Cai ◽  
Piya Patra ◽  
Yi Qin Gao
Keyword(s):  
Gene Regulation ◽  
Environmental Factors ◽  
Protein Binding ◽  
Structural Organization ◽  
Atomistic Simulations ◽  
Dna Interactions ◽  
Structure And Dynamics ◽  
Functional Aspects ◽  
Protein Dna Interactions ◽  
Base Modifications

An overview of atomistic simulations on the effect of sequences, base modifications, environmental factors and protein binding on DNA’s hierarchical structure and dynamics in the context of protein–DNA interactions, gene regulation and structural organization of chromatin.

scholarly journals Long Time-Scale Atomistic Simulations of the Structure and Dynamics of Transcription Factor-DNA Recognition

2019 ◽  
Vol 123 (17) ◽  
pp. 3576-3590 ◽  
Author(s):  
Qinghua Liao ◽  
Malin Lüking ◽  
Dennis M. Krüger ◽  
Sebastian Deindl ◽  
Johan Elf ◽  
...  
Keyword(s):  
Transcription Factor ◽  
Time Scale ◽  
Dna Recognition ◽  
Atomistic Simulations ◽  
Structure And Dynamics ◽  
Long Time

scholarly journals Integrating NMR, SAXS, and Atomistic Simulations: Structure and Dynamics of a Two-Domain Protein

2018 ◽  
Vol 114 (4) ◽  
pp. 839-855 ◽  
Author(s):  
Karl T. Debiec ◽  
Matthew J. Whitley ◽  
Leonardus M.I. Koharudin ◽  
Lillian T. Chong ◽  
Angela M. Gronenborn
Keyword(s):  
Atomistic Simulations ◽  
Structure And Dynamics ◽  
Domain Protein

Nucleosome dynamics

2006 ◽  
Vol 73 ◽  
pp. 109-119 ◽  
Author(s):  
Chris Stockdale ◽  
Michael Bruno ◽  
Helder Ferreira ◽  
Elisa Garcia-Wilson ◽  
Nicola Wiechens ◽  
...  
Keyword(s):  
High Resolution ◽  
Chromatin Structure ◽  
Current Knowledge ◽  
Dynamic Properties ◽  
Structure And Dynamics ◽  
Nucleosome Dynamics ◽  
Sharp Focus ◽  
Recent Advances ◽  
Insight Into ◽  
Chromatin Structure And Dynamics

In the 30 years since the discovery of the nucleosome, our picture of it has come into sharp focus. The recent high-resolution structures have provided a wealth of insight into the function of the nucleosome, but they are inherently static. Our current knowledge of how nucleosomes can be reconfigured dynamically is at a much earlier stage. Here, recent advances in the understanding of chromatin structure and dynamics are highlighted. The ways in which different modes of nucleosome reconfiguration are likely to influence each other are discussed, and some of the factors likely to regulate the dynamic properties of nucleosomes are considered.

Structure and dynamics of phosphate glasses

1998 ◽  
Vol 77 (2) ◽  
pp. 357-362 ◽  
Author(s):  
A. Matic, L. Borjesson
Keyword(s):  
Phosphate Glasses ◽  
Structure And Dynamics
Sign in / Sign up

Export Citation Format

Share Document