421 research outputs found
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
A Continuum Poisson-Boltzmann Model for Membrane Channel Proteins
Membrane proteins constitute a large portion of the human proteome and
perform a variety of important functions as membrane receptors, transport
proteins, enzymes, signaling proteins, and more. The computational studies of
membrane proteins are usually much more complicated than those of globular
proteins. Here we propose a new continuum model for Poisson-Boltzmann
calculations of membrane channel proteins. Major improvements over the existing
continuum slab model are as follows: 1) The location and thickness of the slab
model are fine-tuned based on explicit-solvent MD simulations. 2) The highly
different accessibility in the membrane and water regions are addressed with a
two-step, two-probe grid labeling procedure, and 3) The water pores/channels
are automatically identified. The new continuum membrane model is optimized (by
adjusting the membrane probe, as well as the slab thickness and center) to best
reproduce the distributions of buried water molecules in the membrane region as
sampled in explicit water simulations. Our optimization also shows that the
widely adopted water probe of 1.4 {\AA} for globular proteins is a very
reasonable default value for membrane protein simulations. It gives an overall
minimum number of inconsistencies between the continuum and explicit
representations of water distributions in membrane channel proteins, at least
in the water accessible pore/channel regions that we focus on. Finally, we
validate the new membrane model by carrying out binding affinity calculations
for a potassium channel, and we observe a good agreement with experiment
results.Comment: 40 pages, 6 figures, 5 table
Real-Space Mesh Techniques in Density Functional Theory
This review discusses progress in efficient solvers which have as their
foundation a representation in real space, either through finite-difference or
finite-element formulations. The relationship of real-space approaches to
linear-scaling electrostatics and electronic structure methods is first
discussed. Then the basic aspects of real-space representations are presented.
Multigrid techniques for solving the discretized problems are covered; these
numerical schemes allow for highly efficient solution of the grid-based
equations. Applications to problems in electrostatics are discussed, in
particular numerical solutions of Poisson and Poisson-Boltzmann equations.
Next, methods for solving self-consistent eigenvalue problems in real space are
presented; these techniques have been extensively applied to solutions of the
Hartree-Fock and Kohn-Sham equations of electronic structure, and to eigenvalue
problems arising in semiconductor and polymer physics. Finally, real-space
methods have found recent application in computations of optical response and
excited states in time-dependent density functional theory, and these
computational developments are summarized. Multiscale solvers are competitive
with the most efficient available plane-wave techniques in terms of the number
of self-consistency steps required to reach the ground state, and they require
less work in each self-consistency update on a uniform grid. Besides excellent
efficiencies, the decided advantages of the real-space multiscale approach are
1) the near-locality of each function update, 2) the ability to handle global
eigenfunction constraints and potential updates on coarse levels, and 3) the
ability to incorporate adaptive local mesh refinements without loss of optimal
multigrid efficiencies.Comment: 70 pages, 11 figures. To be published in Reviews of Modern Physic
Parallel software tool for decomposing and meshing of 3d structures
An algorithm for automatic parallel generation of three-dimensional unstructured computational meshes based on geometrical domain decomposition is proposed in this paper. Software package build upon proposed algorithm is described. Several practical examples of mesh generation on multiprocessor computational systems are given. It is shown that developed parallel algorithm enables us to reduce mesh generation time significantly (dozens of times). Moreover, it easily produces meshes with number of elements of order 5 · 107, construction of those on a single CPU is problematic. Questions of time consumption, efficiency of computations and quality of generated meshes are also considered
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