Scalable Molecular Dynamics with NAMD

TL;DR: 4 angstrom resolution cryogenic electron microscopy reconstruction of a one-start, double-stranded helical copolymer composed of two different human ESCRT-III subunits, charged multivesicular body protein 1B (CHMP1B) and increased sodium tolerance 1 (IST1) suggests how common ESC RT-III filament architectures could stabilize different degrees and directions of membrane curvature.

...read moreread less

Posted Content

Multi-step nucleation of nanocrystals in aqueous solution

Duane Loh, +8 more

- 16 May 2016 -

arXiv: Mesoscale and Nanoscale Physics

TL;DR: In situ electron microscopy is used to show how gold and silver nanocrystals nucleate from supersaturated aqueous solutions in three distinct steps: spinodal decomposition into solute-rich andsolute-poor liquid phases, nucleation of amorphous nanoclusters within the metal-rich liquid phase, followed by crystallization of theseAmorphous clusters.

...read moreread less

Journal ArticleDOI

Lipid-Sorting Specificity Encoded in K-Ras Membrane Anchor Regulates Signal Output

Yong Zhou, +5 more

- 12 Jan 2017 -

Cell

TL;DR: In this paper, the authors used quantitative spatial imaging and atomistic molecular dynamics simulations to examine molecular details of K-Ras plasma membrane binding, and found that the anchor binds selected plasma membrane anionic lipids with defined head groups and lipid side chains.

...read moreread less

Journal ArticleDOI

Ribosome assembly factors prevent premature translation initiation by 40S assembly intermediates.

Bethany S. Strunk, +9 more

- 09 Sep 2011 -

Science

TL;DR: The electron cryo-microscopy structure of a late cytoplasmic 40S ribosome assembly intermediate from Saccharomyces cerevisiae at 18 angstrom resolution is presented and it is shown that redundant mechanisms probably ensure that pre-40S particles do not enter the translation pathway, which would result in their rapid degradation.

...read moreread less

Collapse

References

PDF

Open Access

More filters

Journal ArticleDOI

Generalized Gradient Approximation Made Simple

John P. Perdew, +2 more

- 28 Oct 1996 -

Physical Review Letters

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.

...read moreread less

Journal ArticleDOI

Self-Consistent Equations Including Exchange and Correlation Effects

Walter Kohn, +1 more

- 15 Nov 1965 -

Physical Review

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.

...read moreread less

Journal ArticleDOI

VMD: Visual molecular dynamics

William Humphrey, +2 more

- 01 Feb 1996 -

Journal of Molecular Graphics

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.

...read moreread less

Journal ArticleDOI

Density-functional exchange-energy approximation with correct asymptotic behavior.

Axel D. Becke

- 15 Sep 1988 -

Physical Review A

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.

...read moreread less

Fast parallel algorithms for short-range molecular dynamics

Steven J. Plimpton

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.

...read moreread less