Water models for biomolecular simulations
Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …
function rely heavily on a variety of methods—water models—to approximate the influence …
Progress in the prediction of pKa values in proteins
The pKa‐cooperative aims to provide a forum for experimental and theoretical researchers
interested in protein pKa values and protein electrostatics in general. The first round of the …
interested in protein pKa values and protein electrostatics in general. The first round of the …
A simplified and accurate model of power-performance efficiency on emergent GPU architectures
Emergent heterogeneous systems must be optimized for both power and performance at
exascale. Massive parallelism combined with complex memory hierarchies form a barrier to …
exascale. Massive parallelism combined with complex memory hierarchies form a barrier to …
Understanding GPU power: A survey of profiling, modeling, and simulation methods
RA Bridges, N Imam, TM Mintz - ACM Computing Surveys (CSUR), 2016 - dl.acm.org
Modern graphics processing units (GPUs) have complex architectures that admit
exceptional performance and energy efficiency for high-throughput applications. Although …
exceptional performance and energy efficiency for high-throughput applications. Although …
General purpose water model can improve atomistic simulations of intrinsically disordered proteins
Unconstrained atomistic simulations of intrinsically disordered proteins and peptides (IDP)
remain a challenge: widely used,“general purpose” water models tend to favor overly …
remain a challenge: widely used,“general purpose” water models tend to favor overly …
On the energy efficiency of graphics processing units for scientific computing
S Huang, S ** mitigate the efficiency obstacles given by the downsizing …
Why double-stranded RNA resists condensation
The addition of small amounts of multivalent cations to solutions containing double-stranded
DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the …
DNA leads to inter-DNA attraction and eventual condensation. Surprisingly, the …
Heterogeneous task scheduling for accelerated openmp
Heterogeneous systems with CPUs and computational accelerators such as GPUs, FPGAs
or the upcoming Intel MIC are becoming mainstream. In these systems, peak performance …
or the upcoming Intel MIC are becoming mainstream. In these systems, peak performance …
A fast and robust Poisson–Boltzmann solver based on adaptive Cartesian grids
AH Boschitsch, MO Fenley - Journal of chemical theory and …, 2011 - ACS Publications
An adaptive Cartesian grid (ACG) concept is presented for the fast and robust numerical
solution of the 3D Poisson–Boltzmann equation (PBE) governing the electrostatic …
solution of the 3D Poisson–Boltzmann equation (PBE) governing the electrostatic …