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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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Four-scale description of membrane sculpting by BAR domains.
TL;DR: A computational study of membrane bending by BAR domains at four levels of resolution, described by 1), all-atom molecular dynamics; 2), residue-based coarse-graining (resolving single amino acids and lipid molecules); 3), shape- based coarse- graining (Resolving overall protein and membrane shapes); and 4), a continuum elastic membrane model.
Journal ArticleDOI
Identification of Transmembrane Domain 5 as a Critical Molecular Determinant of Menthol Sensitivity in Mammalian TRPA1 Channels
Bailong Xiao,Adrienne E. Dubin,Badry Bursulaya,Veena Viswanath,Timothy Jegla,Ardem Patapoutian,Ardem Patapoutian +6 more
TL;DR: Mouse-human TRPA1 chimeras reveal the pore region [including transmembrane domain 5 (TM5) and TM6] as the critical domain determining whether menthol can act as an inhibitor, and Chimeras between Drosophila melanogaster and mammalian TRP1 highlight specific residues within TM5 critical for menthol responsiveness, suggesting separable structural requirements for modulation of TRPA 1 by covalent and nonreactive molecules.
Journal ArticleDOI
Imaging the migration pathways for O2, CO, NO, and Xe inside myoglobin
TL;DR: This work presents a complete map of all the gas migration pathways inside Mb for small gas ligands (O2, NO, CO, and Xe), and introduces a computational approach for studying gas migration, which is called implicit ligand sampling.
Journal ArticleDOI
Structure of the immature HIV-1 capsid in intact virus particles at 8.8 Å resolution
Florian K. M. Schur,Wim J. H. Hagen,Michaela Rumlová,Tomáš Ruml,Barbara Müller,Hans-Georg Kräusslich,John A. G. Briggs +6 more
TL;DR: Cryo-electron tomography and sub-tomogram averaging methods are applied to resolve the structure of the capsid lattice within intact immature HIV-1 particles at subnanometre resolution, allowing unambiguous positioning of all α-helices.
Journal ArticleDOI
Chiral Graphene Quantum Dots.
Nozomu Suzuki,Yichun Wang,Paolo Elvati,Zhibei Qu,Kyoungwon Kim,Shuang Jiang,Elizabeth Baumeister,Jaewook Lee,Bongjun Yeom,Bongjun Yeom,Joong Hwan Bahng,Jaebeom Lee,Angela Violi,Nicholas A. Kotov +13 more
TL;DR: It is reported that covalent attachment of l/d-cysteine moieties to the edges of graphene quantum dots (GQDs) leads to their helical buckling due to chiral interactions at the "crowded" edges.
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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