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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
Citations
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Journal ArticleDOI
Liquid state DNP using a 260 GHz high power gyrotron.
Vasyl Denysenkov,Mark J. Prandolini,Marat Gafurov,Deniz Sezer,Burkhard Endeward,Thomas F. Prisner +5 more
TL;DR: These experimentally observed DNP enhancements, which by far exceed the predicted values extrapolated from low-field DNP experiments, demonstrate experimentally that DNP is possible in the liquid state also at high magnetic fields.
Journal ArticleDOI
In situ structural analysis of the Yersinia enterocolitica injectisome
Mikhail Kudryashev,Marco Stenta,Stefan Schmelz,Marlise Amstutz,Ulrich Wiesand,Daniel Castaño-Díez,Matteo T. Degiacomi,Stefan Münnich,Christopher Ke Bleck,Julia Kowal,Andreas Diepold,Dirk W. Heinz,Matteo Dal Peraro,Matteo Dal Peraro,Guy R. Cornelis,Henning Stahlberg +15 more
TL;DR: The first three-dimensional structure of Yersinia enterocolitica and Shigella flexneri injectisomes in situ and the first structural analysis of the Yerinia injectisome are presented.
Journal ArticleDOI
Three-dimensional modeling of single stranded DNA hairpins for aptamer-based biosensors
Iman Jeddi,Leonor Saiz +1 more
TL;DR: This work presents the first approach to predict from sequence the three-dimensional structures of single stranded DNA required for aptamer applications, focusing explicitly on ssDNA hairpins, and opens up a much-needed avenue for integrating DNA in the computational analysis and design of aptamer-based biosensors.
Journal ArticleDOI
Comparison of force fields for Alzheimer's A β42: A case study for intrinsically disordered proteins.
TL;DR: In this article, replica exchange molecular dynamics simulations were used to test five modern force fields, OPLS, AMBER99SB, AMber99SB*, AMBER 99SB*ILDN, AMB99SBILDN-NMR and CHARMM22*, in their ability to model Aβ42, an intrinsically disordered peptide associated with Alzheimer's disease, and compare their results to nuclear magnetic resonance (NMR) experimental data.
Journal ArticleDOI
Recognition of methylated DNA through methyl-CpG binding domain proteins
TL;DR: It is demonstrated that the methyl-CpG dinucleotides are recognized at the MBD–mDNA interface by two MBD arginines through an interplay of hydrogen bonding and cation-π interaction and that methylation enhances MBD-mDNA binding by increasing the hydrophobic interfacial area and by strengthening the interaction between mDNA and MBD proteins.
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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