NDLI: A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Content Provider	IEEE Xplore Digital Library
Author	Bardhan, J.P. Hildebrandt, A.
Copyright Year	2011
Description	Author affiliation: Dept. of Molecular Biophysics and Physiology, Rush University Medical Center, Chicago, IL 60607, USA (Bardhan, J.P.) \|\| Institut für Informatik, Johannes Gutenberg Universität Mainz, Germany (Hildebrandt, A.)
Abstract	Biological molecules perform their functions surrounded by water and mobile ions, which strongly influence molecular structure and behavior. The electrostatic interactions between a molecule and solvent are particularly difficult to model theoretically, due to the forces' long range and the collective response of many thousands of solvent molecules. The dominant modeling approaches represent the two extremes of the trade-off between molecular realism and computational efficiency: all-atom molecular dynamics in explicit solvent, and macroscopic continuum theory (the Poisson or Poisson-Boltzmann equation). We present the first fast-solver implementation of an advanced nonlocal continuum theory that combines key advantages of both approaches. In particular, molecular realism is included by limiting solvent dielectric response on short length scales, using a model for nonlocal dielectric response allows the resulting problem (a linear integro-differential Poisson equation) to be reformulated as a system of coupled boundary-integral equations using double reciprocity. Whereas previous studies using the nonlocal theory had been limited to small model problems, owing to computational cost, our work opens the door to studying much larger problems including rational drug design, protein engineering, and nanofluidics
Starting Page	801
Ending Page	805
File Size	366067
Page Count	5
File Format	PDF
ISBN	9781450306362
ISSN	85644924
e-ISBN	9781450306362
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-06-05
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Association for Computing Machinery, Inc. (ACM)
Subject Keyword	Electrostatics Mathematical model Biological system modeling Computational modeling Equations Solvents Electric potential
Content Type	Text
Resource Type	Article

Sl.	Authority	Responsibilities	Communication Details
1	Ministry of Education (GoI), Department of Higher Education	Sanctioning Authority	https://www.education.gov.in/ict-initiatives
2	Indian Institute of Technology Kharagpur	Host Institute of the Project: The host institute of the project is responsible for providing infrastructure support and hosting the project	https://www.iitkgp.ac.in
3	National Digital Library of India Office, Indian Institute of Technology Kharagpur	The administrative and infrastructural headquarters of the project	Dr. B. Sutradhar bsutra@ndl.gov.in
4	Project PI / Joint PI	Principal Investigator and Joint Principal Investigators of the project	Dr. B. Sutradhar bsutra@ndl.gov.in Prof. Saswat Chakrabarti will be added soon
5	Website/Portal (Helpdesk)	Queries regarding NDLI and its services	support@ndl.gov.in
6	Contents and Copyright Issues	Queries related to content curation and copyright issues	content@ndl.gov.in
7	National Digital Library of India Club (NDLI Club)	Queries related to NDLI Club formation, support, user awareness program, seminar/symposium, collaboration, social media, promotion, and outreach	clubsupport@ndl.gov.in
8	Digital Preservation Centre (DPC)	Assistance with digitizing and archiving copyright-free printed books	dpc@ndl.gov.in
9	IDR Setup or Support	Queries related to establishment and support of Institutional Digital Repository (IDR) and IDR workshops	idr@ndl.gov.in

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Fast Solvers for Molecular Science and Engineering

Numerical Modeling of Biomolecular Electrostatic Properties by the Element-Free Galerkin Method

An effective method of electrostatic potential calculation on protein binding site

Calculation of elongated carbon structures with Density Functional Theory and fast Poisson solver

The electrostatic quadrupole lens mathematical modeling

A fast method for the computation of biomolecular electric potential using parallel computers

Enhancement of seed germination by applying electrostatic field

FEM-DBCI for efficient computation of electrostatic capacitance

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Similar Documents

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering

Fast Solvers for Molecular Science and Engineering

Numerical Modeling of Biomolecular Electrostatic Properties by the Element-Free Galerkin Method

An effective method of electrostatic potential calculation on protein binding site

Calculation of elongated carbon structures with Density Functional Theory and fast Poisson solver

The electrostatic quadrupole lens mathematical modeling

A fast method for the computation of biomolecular electric potential using parallel computers

Enhancement of seed germination by applying electrostatic field

FEM-DBCI for efficient computation of electrostatic capacitance

A fast solver for nonlocal electrostatic theory in biomolecular science and engineering