Numerical Integration of the Cartesian Equations of Motion of a System with Constraints: Molecular Dynamics of n-Alkanes
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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
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5-N-methylated quindoline derivatives as telomeric g-quadruplex stabilizing ligands: effects of 5-N positive charge on quadruplex binding affinity and cell proliferation.
Yu Jing Lu,Tian Miao Ou,Jia Heng Tan,Jin-Qiang Hou,Wei Yan Shao,Dan Peng,Ning Sun,Xiaodong Wang,Wei Bin Wu,Xian Zhang Bu,Zhi Shu Huang,Dik-Lung Ma,Kwok Yin Wong,Lian Quan Gu +13 more
TL;DR: A series of 5-N-methyl quindoline (cryptolepine) derivatives as telomeric quadruplex ligands was synthesized and evaluated, showing a remarkable cessation in population growth and cellular senescence phenotype and accompanied by a shortening of the telomere length.
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Protein structure and dynamics in nonaqueous solvents: insights from molecular dynamics simulation studies.
TL;DR: Water and counterions play a fundamental and dynamic role on protein stabilization, but they also seem to be important for protein unfolding at high percentages of bound water.
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An improved method to predict the entropy term with the MM/PBSA approach
Jacob Kongsted,Ulf Ryde +1 more
TL;DR: A method is suggested to calculate improved entropies within the MM/PBSA approach (molecular mechanics combined with Poisson–Boltzmann and surface area calculations) to estimate protein–ligand binding affinities, and it is shown that it gives more stable results and often improved predictions of the relative binding Affinities.
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Molecular structure and OH-stretch spectra of liquid water surface.
TL;DR: The low-frequency wing of the OH-stretch band, near 3200 cm(-1) in the SFG spectrum, is proposed to be due to collective excitations of a relatively small number of intermolecularly coupled O-H bond vibrations.
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Structural and functional characterization of the aryl hydrocarbon receptor ligand binding domain by homology modeling and mutational analysis
TL;DR: The physicochemical characteristics of some residues and of their mutants, along with the effects of mutagenesis on TCDD and DNA binding, suggest some key features that are required for ligand binding and activation of mAhR at a molecular level, thus providing a framework for further studies.
References
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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.
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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.
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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.
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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.
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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.