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Scalable Molecular Dynamics with NAMD
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The article was published on 2012-12-14 and is currently open access. It has received 13375 citations till now.read more
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Histone H2A C-terminus regulates chromatin dynamics, remodeling, and histone H1 binding.
Christine Vogler,Claudia Huber,Tanja Waldmann,Ramona Ettig,Lora Braun,Annalisa Izzo,Sylvain Daujat,Isabelle Chassignet,Andrés J. López-Contreras,Oscar Fernandez-Capetillo,Miroslav Dundr,Karsten Rippe,Gernot Längst,Robert Schneider +13 more
TL;DR: It is suggested that the H2A C-terminal tail has a bipartite function: stabilisation of the nucleosomal core particle, as well as mediation of the protein interactions that control chromatin dynamics and conformation.
Journal ArticleDOI
Drude Polarizable Force Field for Molecular Dynamics Simulations of Saturated and Unsaturated Zwitterionic Lipids.
TL;DR: The iterative optimization protocol employed in this effort led to lipid models that achieve a good balance between reproducing quantum mechanical data on model compound representative of phospholipids and reproducing a range of experimental condensed phase properties of bilayers.
Journal ArticleDOI
Atomistic Simulations of Membrane Ion Channel Conduction, Gating, and Modulation
TL;DR: Modern simulations offer a range of molecular-level insights into ion channel function and modulation as a learning platform for mechanistic discovery and drug development.
Journal ArticleDOI
Interfacing Graphene-Based Materials With Neural Cells.
Mattia Bramini,Giulio Alberini,Giulio Alberini,Elisabetta Colombo,Martina Chiacchiaretta,Martina Chiacchiaretta,Mattia L. DiFrancesco,José Fernando Maya-Vetencourt,Luca Maragliano,Fabio Benfenati,Fabio Benfenati,Fabrizia Cesca +11 more
TL;DR: In this paper, the state-of-the-art in the use of graphene materials to engineer three-dimensional scaffolds to drive neuronal growth and regeneration in vivo, and the possibility of using graphene as a component of hybrid composites/multi-layer organic electronics devices.
Journal ArticleDOI
Both Genome Segments Contribute to the Pathogenicity of Very Virulent Infectious Bursal Disease Virus
Olivier Escaffre,Cyril Le Nouën,Michel Amelot,Xavier Ambroggio,Kristen M. Ogden,Olivier Guionie,Didier Toquin,Hermann J. Müller,Mohammed Rafiqul Islam,Nicolas Eterradossi +9 more
TL;DR: It is found that a valine that modifies the most exposed part of the capsid protein VP2 critically modified the antigenicity and partially reduced the pathogenicity of isolate 94432.
References
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Journal ArticleDOI
Generalized Gradient Approximation Made Simple
TL;DR: A simple derivation of a simple GGA is presented, in which all parameters (other than those in LSD) are fundamental constants, and only general features of the detailed construction underlying the Perdew-Wang 1991 (PW91) GGA are invoked.
Journal ArticleDOI
Self-Consistent Equations Including Exchange and Correlation Effects
Walter Kohn,L. J. Sham +1 more
TL;DR: In this paper, the Hartree and Hartree-Fock equations are applied to a uniform electron gas, where the exchange and correlation portions of the chemical potential of the gas are used as additional effective potentials.
Journal ArticleDOI
VMD: Visual molecular dynamics
TL;DR: VMD is a molecular graphics program designed for the display and analysis of molecular assemblies, in particular biopolymers such as proteins and nucleic acids, which can simultaneously display any number of structures using a wide variety of rendering styles and coloring methods.
Journal ArticleDOI
Density-functional exchange-energy approximation with correct asymptotic behavior.
TL;DR: This work reports a gradient-corrected exchange-energy functional, containing only one parameter, that fits the exact Hartree-Fock exchange energies of a wide variety of atomic systems with remarkable accuracy, surpassing the performance of previous functionals containing two parameters or more.
Fast parallel algorithms for short-range molecular dynamics
TL;DR: Comparing the results to the fastest reported vectorized Cray Y-MP and C90 algorithm shows that the current generation of parallel machines is competitive with conventional vector supercomputers even for small problems.
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