- Full text PDF available (8)
- This year (0)
- Last 5 years (8)
- Last 10 years (13)
Journals and Conferences
Molecular dynamics (MD) allows the study of biological and chemical systems at the atomistic level on timescales from femtoseconds to milliseconds. It complements experiment while also offering a way to follow processes difficult to discern with experimental techniques. Numerous software packages exist for conducting MD simulations of which one of the… (More)
In this work, we critically assess the ability of the all-atom enhanced sampling method accelerated molecular dynamics (aMD) to investigate conformational changes in proteins that typically occur on the millisecond time scale. We combine aMD with the inherent power of graphics processor units (GPUs) and apply the implementation to the bovine pancreatic… (More)
G-protein-coupled receptors (GPCRs) are transmembrane receptors involved in diverse biological functions. Despite the diversity in their amino acid sequences, class A GPCRs exhibit a conserved structural topology and possibly a common mechanism of receptor activation. To understand how this high sequence diversity translates to a conserved functional… (More)
The effect of using the transcorrelated variational Monte Carlo (TC-VMC) approach to construct a trial function for fixed node diffusion Monte Carlo (DMC) energy calculations has been investigated for the first-row atoms, Li to Ne. The computed energies are compared with fixed node DMC energies obtained using trial functions constructed from Hartree-Fock… (More)
We present an implementation of explicit solvent all atom classical molecular dynamics (MD) within the AMBER program package that runs entirely on CUDA-enabled GPUs. First released publicly in April 2010 as part of version 11 of the AMBER MD package and further improved and optimized over the last two years, this implementation supports the three most… (More)
We use quantized molecular dynamics simulations to characterize the role of enzyme vibrations in facilitating dihydrofolate reductase hydride transfer. By sampling the full ensemble of reactive trajectories, we are able to quantify and distinguish between statistical and dynamical correlations in the enzyme motion. We demonstrate the existence of… (More)
The expulsion of water from surfaces upon molecular recognition and nonspecific association makes a major contribution to the free energy changes of these processes. In order to facilitate the characterization of water structure and thermodynamics on surfaces, we have incorporated Grid Inhomogeneous Solvation Theory (GIST) into the CPPTRAJ toolset of… (More)
The Zori 1.0 package for electronic structure computations is described. Zori performs variational and diffusion Monte Carlo computations as well as correlated wave function optimization. This article presents an overview of the implemented methods and code capabilities.
Rappture is a new GUI development kit that enables developers to build I/O interfaces for specific applications. In this article,, the authors describe the Rappture toolkit's use in generating a GUI for the Zori computer code.
Reaction pathways are presented for hydrogen-mediated isomerization of a five- and six-member carbon ring complex on the zigzag edge of a graphene layer. A new reaction sequence that reverses the orientation of the ring complex, or "flips" it, was identified. Competition between the flip reaction and the "ring separation" was examined. Ring separation is… (More)