Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
Reads0
Chats0
TLDR
In this paper, a numerical algorithm integrating the 3N Cartesian equations of motion of a system of N points subject to holonomic constraints is formulated, and the relations of constraint remain perfectly fulfilled at each step of the trajectory despite the approximate character of numerical integration.About:
This article is published in Journal of Computational Physics.The article was published on 1977-03-01 and is currently open access. It has received 18394 citations till now. The article focuses on the topics: Generalized coordinates & Holonomic constraints.read more
Citations
More filters
Journal ArticleDOI
Src activation by adrenoreceptors is a key switch for tumour metastasis
Guillermo N. Armaiz-Pena,Julie K. Allen,Julie K. Allen,Anthony Cruz,Rebecca L. Stone,Alpa M. Nick,Yvonne G. Lin,Liz Y. Han,Lingegowda S. Mangala,Gabriel J. Villares,Gabriel J. Villares,Pablo E. Vivas-Mejia,Pablo E. Vivas-Mejia,Cristian Rodriguez-Aguayo,Archana S. Nagaraja,Archana S. Nagaraja,Kshipra M. Gharpure,Kshipra M. Gharpure,Zheng Wu,Robert D. English,Kizhake V. Soman,Mian M.K. Shahzad,Maya Zigler,Maya Zigler,Michael T. Deavers,Alexander Zien,Theodoros G. Soldatos,David B. Jackson,John E. Wiktorowicz,Madeline Torres-Lugo,Tom Young,Koen De Geest,Gary E. Gallick,Menashe Bar-Eli,Gabriel Lopez-Berestein,Steve W. Cole,Gustavo E. López,Susan K. Lutgendorf,Anil K. Sood +38 more
TL;DR: These results identify a new mechanism of Src phosphorylation that mediates beta-adrenergic/PKA regulation of downstream networks, thereby enhancing tumor cell migration, invasion and growth and provide a pivotal molecular target for disrupting neural signaling in the tumor microenvironment.
Journal ArticleDOI
Interaction of the Disaccharide Trehalose with a Phospholipid Bilayer: A Molecular Dynamics Study
Cristina Silva Pereira,Roberto D. Lins,Indira Chandrasekhar,Luiz C. G. Freitas,Philippe H. Hünenberger +4 more
TL;DR: In this study, molecular dynamics simulations are used to investigate the interaction of trehalose with a phospholipid bilayer at atomistic resolution and show that trehalOSE is able to minimize the disruptive effect of the elevated temperature and stabilize the bilayer structure.
Journal ArticleDOI
Molecular dynamics simulations of the unfolding of barnase in water and 8 m aqueous urea
TL;DR: The results of the simulations in urea suggest a mechanism at the molecular level for its well-known enhancement of the denaturation of proteins in terms of site-directed mutagenesis and the relative stability of the different elements of secondary structure.
Journal ArticleDOI
The role of tryptophan side chains in membrane protein anchoring and hydrophobic mismatch.
TL;DR: Calculations provide quantitative measures that explain Trp's role as a modulator of responses to hydrophobic mismatch, providing a deeper understanding of how lipid composition may control a range of membrane active peptides and proteins.
Journal ArticleDOI
Unveiling the Active Structure of Single Nickel Atom Catalysis: Critical Roles of Charge Capacity and Hydrogen Bonding.
Xunhua Zhao,Yuanyue Liu +1 more
TL;DR: This work explains a long-standing puzzle for an important catalyst, and highlights the crucial roles of charge capacity and hydrogen bonding, which can help elucidate the mechanisms of other heterogeneous electrocatalysts in aqueous solution and enable more effective catalyst design.
References
More filters
Journal ArticleDOI
Computer "Experiments" on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules
TL;DR: In this article, the equilibrium properties of a system of 864 particles interacting through a Lennard-Jones potential have been integrated for various values of the temperature and density, relative, generally, to a fluid state.
Journal ArticleDOI
Improved simulation of liquid water by molecular dynamics
TL;DR: In this paper, a four-charge model for each molecule and a modification of the prior ''BNS'' interaction was proposed to improve the fidelity of the molecular dynamics simulation, leading to a density maximum near 27°C for the liquid in coexistence with its vapor and to molecular distribution functions in better agreement with x-ray scattering experiments.
Journal ArticleDOI
Molecular Dynamics Study of Liquid Water
TL;DR: In this paper, a sample of water, consisting of 216 rigid molecules at mass density 1 gm/cm3, has been simulated by computer using the molecular dynamics technique, subject to an effective pair potential that incorporates the principal structural effects of manybody interactions in real water.
Journal ArticleDOI
Molecular dynamics of liquid n-butane near its boiling point
TL;DR: The self-diffusion coefficient of n-butane is approximately 6.0 × 10−5 cm2/s and the corresponding velocity autocorrelation function displays practically no cage effect, differing markedly from argon and other simple fluids.
Journal ArticleDOI
Simulation of Diatomic Homonuclear Liquids
TL;DR: In this paper, the authors used the molecular-dynamic method to simulate a fluid of 500 rigid diatomic homo-nuclear molecules interacting by a double Lennard-Jones potential.