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Highly efficient and exact method for parallelization of grid-based algorithms and its implementation in DelPhi

Chuan Li, Lin Li, Jie Zhang, Emil Alexov
2012 Journal of Computational Chemistry  
However, standard implementation of the Gauss-Seidel method restricts its utilization in parallel computing due to its requirement of using updated neighboring values (i.e., in current iteration) as soon  ...  Here we report an efficient and exact (not requiring assumptions) method to parallelize iterations and to reduce the computational time as a linear/nearly linear function of the number of CPUs.  ...  Acknowledgments We thank Shawn Witham for reading the manuscript prior to submission. This work is supported by a grant from NIGMS, NIH with grant number R01 GM093937.  ... 
doi:10.1002/jcc.23033 pmid:22674480 pmcid:PMC3412928 fatcat:5anjdt4exncptnwis6x7ludnfi

Progress in developing Poisson-Boltzmann equation solvers

Chuan Li, Lin Li, Marharyta Petukh, Emil Alexov
2013 Molecular Based Mathematical Biology  
This review outlines the recent progress made in developing more accurate and efficient solutions to model electrostatics in systems comprised of bio-macromolecules and nano-objects, the last one referring  ...  In addition, specific attention is paid to methods to extend the capabilities of the existing solvers to model large systems toward applications of calculations of the electrostatic potential and energies  ...  Acknowledgments We thank Ray Luo and Guowei Wei for useful discussions and Shannon Stefl for proofreading the manuscript. The work was supported by a grant from NIH, NIGMS, grant number R01GM093937.  ... 
doi:10.2478/mlbmb-2013-0002 pmid:24199185 pmcid:PMC3816640 fatcat:3v7q5ehr3faqpmkcokrgr5lhne

A general and Robust Ray-Casting-Based Algorithm for Triangulating Surfaces at the Nanoscale

Sergio Decherchi, Walter Rocchia, Chris Lorenz
2013 PLoS ONE  
We present a general, robust, and efficient ray-casting-based approach to triangulating complex manifold surfaces arising in the nano-bioscience field.  ...  NanoShaper was integrated with the DelPhi Poisson-Boltzmann equation solver. Its SES grid coloring outperformed the DelPhi counterpart.  ...  Acknowledgments The Authors thank Nico Kruithof for useful discussions on CGAL Skin implementation, Marco Attene at IMATI for providing the loader of.ply files, and the referees for their stimulating suggestions  ... 
doi:10.1371/journal.pone.0059744 pmid:23577073 pmcid:PMC3618509 fatcat:rtjudccymnhg7kmm2czzkpb2sm

Acceleration of Linear Finite-Difference Poisson-Boltzmann Methods on Graphics Processing Units [article]

Ruxi Qi, Wesley M. Botello-Smith, Ray Luo
2017 arXiv   pre-print
Further efficiency may be possible with matrix-free operations and integrated grid stencil setup specifically tailored for the banded matrices in PBE-specific linear systems.  ...  In this study, we implemented and analyzed commonly used linear PBE solvers for the ever-improving graphics processing units (GPU) for biomolecular simulations, including both standard and preconditioned  ...  To date only the relatively simple successive over-relaxation (SOR) method was implemented on GPUs. 14 However, our prior algorithm analysis of SOR and other algorithms have shown its convergence rate  ... 
arXiv:1704.02745v1 fatcat:fmm7nih2frbojfgcgoktkej6ju

Exploring a coarse-grained distributive strategy for finite-difference Poisson–Boltzmann calculations

Meng-Juei Hsieh, Ray Luo
2010 Journal of Molecular Modeling  
A parallel version of thedistributive focusing method was also implemented.  ...  space is set to be 16 grid points and the block dimension is set to be at least (1/6) 3 of the fine-grid dimension, as in the one-block focusing method.  ...  Acknowledgments This work is supported in part by the National  ... 
doi:10.1007/s00894-010-0904-4 pmid:21127924 pmcid:PMC3143316 fatcat:ijsknbjylbegvlhak6czogegce

A taxonomy of peer-to-peer desktop grid paradigms

Han Zhao, Xinxin Liu, Xiaolin Li
2010 Cluster Computing  
This paper presents a taxonomy for classifying P2P desktop grid implementation paradigms, aiming to summarize the state-of-the-art technologies and explore the current and potential solution space.  ...  The emerging convergence of grid and peer-to-peer (P2P) computing technologies further opens new opportunities for enabling P2P Desktop Grid systems.  ...  Acknowledgement The authors would like to thank the editors and referees for their valuable suggestions, which have significantly helped improve the quality and presentation of this paper.  ... 
doi:10.1007/s10586-010-0138-3 fatcat:ena6nwlb7bcwzobygzo456g6lq

DelEnsembleElec: Computing Ensemble-Averaged Electrostatics Using DelPhi

Lane W. Votapka, Luke Czapla, Maxim Zhenirovskyy, Rommie E. Amaro
2013 Communications in Computational Physics  
The differences between the ensemble-averaged electrostatics and those obtained from a single structure are examined in detail for these examples, revealing how the plugin can be a powerful tool in facilitating  ...  The general theory and context of this approach are discussed, and examples of the plugin interface and calculations are presented.  ...  Acknowledgments This work was funded in part by the National Institutes of Health through the NIH Director's New Innovator Award Program 1-DP2-OD007237 and through the NSF TeraGrid Supercomputer resources  ... 
doi:10.4208/cicp.170711.111111s fatcat:j67ur35zhvd25mr4l5vmo7aqjy

Hybrid boundary element and finite difference method for solving the nonlinear Poisson-Boltzmann equation

Alexander H. Boschitsch, Marcia O. Fenley
2004 Journal of Computational Chemistry  
Because the correction potential contains no singularities (in particular, it is smooth at charge sites) it can be accurately and efficiently solved using a finite difference method.  ...  The motivation for and formulation of such a decomposition are presented together with the numerical method for calculating the linear and correction potentials.  ...  Xiang-Jun Lu and Wilma Olson for making available their 3DNA program. The authors are grateful to Drs.  ... 
doi:10.1002/jcc.20000 pmid:15027106 fatcat:wkt2mzbmdzaazc43resw3t6awm

Modeling and simulation for enterprise decision-making: Successful projects and approaches

Noha Ramadan, Racha Ajami, Nader Mohamed, Sanja Lazarova-Molnar
2015 2015 International Conference on Industrial Engineering and Operations Management (IEOM)  
Decision-making in enterprises holds different possibilities for profits and risks.  ...  In addition, we show some techniques that helped enterprises in reaching effective and efficient decisions by adopting modeling and simulation tools.  ...  Delphi Method in Decision Making Delphi technique is a useful method in allocating previous probabilities in a decision to be made under uncertainty condition.  ... 
doi:10.1109/ieom.2015.7093873 fatcat:bmwndo5zlzdddhyfw5dp34sesu

UK smart grid development: An expert assessment of the benefits, pitfalls and functions

Dimitrios Xenias, Colin J. Axon, Lorraine Whitmarsh, Peter M. Connor, Nazmiye Balta-Ozkan, Alexa Spence
2015 Renewable Energy  
Different methods for implementing smarter grid functions were considered, all thought to be more likely in urban settings. Implications for policy and future research are considered.  ...  It consists of many possible transitions and involves many actors relevant to existing and potential functions of the grid.  ...  The funder had no involvement in study design, data collection and analysis, or writing up this paper. We would like to thank Sophie Poulain for her help with data management.  ... 
doi:10.1016/j.renene.2015.03.016 fatcat:mcfdlzn6grhelnsxbn4sji2wmm

Algorithms for using a DEM for mapping catchment areas of stream sediment samples

Richard Jones
2002 Computers & Geosciences  
This algorithm is based on the priority-first-search weighted-graph algorithm. Relatively simple methods for defining internal basins and incorporating digitized stream data are also discussed.  ...  All of the selected methods are robust, computationally efficient, and avoid many of the problems associated with other methods.  ...  Acknowledgements I thank my wife, Laura McKerrow, Mark Mihalasky, Graeme Bonham-Carter, and two C&G reviewers for making numerous suggestions to improve the paper.  ... 
doi:10.1016/s0098-3004(02)00022-5 fatcat:4mprrmsanrfu5omw6togknw4c4

Accurate, robust and reliable calculations of Poisson-Boltzmann solvation energies [article]

Bao Wang, Guowei Wei
2016 arXiv   pre-print
In this work, we explore the accurate coarse grid PB solver based on the Green's function treatment of the singular charges, matched interface and boundary (MIB) method for treating the geometric singularities  ...  Reducing the grid size influence on the performance of the solver benefits to increasing the speed of solver and providing accurate electrostatics analysis for solvated molecules.  ...  A comparison of the GFM, IIM and MIB methods can be found in in Refs. 66, 67 Besides the accuracy of the PB solver, another important issue in the practical usage of the PB solver is its efficiency,  ... 
arXiv:1607.04594v1 fatcat:4t5tdopbofgmffcykqx4g7ygyu

Numerical solution of the nonlinear Poisson-Boltzmann equation: Developing more robust and efficient methods

Michael J. Holst, Faisal Saied
1995 Journal of Computational Chemistry  
We present a robust and efficient numerical method for solution of the nonlinear Poisson-Boltzmann equation arising in molecular biophysics.  ...  In addition, for problems which the other methods are able to solve, numerical experiments show that the new method is substantially more efficient, and the superiority of this method grows with the problem  ...  Figure 5 compares the methods in Table 1 for the crambin problem. Again, all of the methods converge, and the two multilevel-based algorithms are superior.  ... 
doi:10.1002/jcc.540160308 fatcat:pg22ajrz3nb4tcrx5dlpa5e4gq

Automotive-Radar-Based 50-cm Urban Positioning [article]

Lakshay Narula, Peter A. Iannucci, Todd E. Humphreys
2020 arXiv   pre-print
Deployment of automated ground vehicles (AGVs) beyond the confines of sunny and dry climes will require sub-lane-level positioning techniques based on radio waves rather than near-visible-light radiation  ...  This paper develops and demonstrates a novel technique for robust 50-cm-accurate urban ground positioning based on commercially-available low-cost automotive radars.  ...  It first details the statistical motivation behind the method, and then develops an efficient approximation to the exact solution. A.  ... 
arXiv:2005.00704v1 fatcat:rrsszrissnbcrftc3vkkwaxgxa

An analytical approach to computing biomolecular electrostatic potential. II. Validation and applications

John C. Gordon, Andrew T. Fenley, Alexey Onufriev
2008 Journal of Chemical Physics  
The dimensions of these pockets of locally highly negative curvature are comparable to the size of a water molecule; the applicability of a continuum dielectric models in these regions is discussed.  ...  The accuracy of the approximation, averaged over all test points in each structure, is within 0.6 kcal/ mol/ ͉e͉ϳkT per unit charge for all structures in the test set.  ...  The authors thank Grigori Sigalov, Jack Johnson, and Dave Bevan for reading the manuscript and providing valuable feedback. This work was supported by NIH Grant No.  ... 
doi:10.1063/1.2956499 pmid:19044803 pmcid:PMC2671192 fatcat:gnzxvx4fuvdtrf2fecr6o2alxe
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