Literature DB >> 18591998

Correcting Mesh-Based Force Calculations to Conserve Both Energy and Momentum in Molecular Dynamics Simulations.

Robert D Skeel1, David J Hardy, James C Phillips.   

Abstract

Year:  2007        PMID： 18591998      PMCID： PMC2346486          DOI： 10.1016/j.jcp.2007.03.010

Source DB:  PubMed          Journal:  J Comput Phys        ISSN： 0021-9991            Impact factor:   3.553


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  2 in total

1.  Multiple grid methods for classical molecular dynamics.

Authors:  Robert D Skeel; Ismail Tezcan; David J Hardy
Journal:  J Comput Chem       Date:  2002-04-30       Impact factor: 3.376

2.  Scalable molecular dynamics with NAMD.

Authors:  James C Phillips; Rosemary Braun; Wei Wang; James Gumbart; Emad Tajkhorshid; Elizabeth Villa; Christophe Chipot; Robert D Skeel; Laxmikant Kalé; Klaus Schulten
Journal:  J Comput Chem       Date:  2005-12       Impact factor: 3.376
  2 in total
  11 in total

1.  Modeling thermophoretic effects in solid-state nanopores.

Authors:  Maxim Belkin; Shu-Han Chao; Gino Giannetti; Aleksei Aksimentiev
Journal:  J Comput Electron       Date:  2014-12-01       Impact factor: 1.807

2.  Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations.

Authors:  David J Hardy; Matthew A Wolff; Jianlin Xia; Klaus Schulten; Robert D Skeel
Journal:  J Chem Phys       Date:  2016-03-21       Impact factor: 3.488

3.  Slowing down DNA translocation through a nanopore in lithium chloride.

Authors:  Stefan W Kowalczyk; David B Wells; Aleksei Aksimentiev; Cees Dekker
Journal:  Nano Lett       Date:  2012-01-27       Impact factor: 11.189

4.  Stretching and controlled motion of single-stranded DNA in locally heated solid-state nanopores.

Authors:  Maxim Belkin; Christopher Maffeo; David B Wells; Aleksei Aksimentiev
Journal:  ACS Nano       Date:  2013-07-26       Impact factor: 15.881

5.  Ionic conductivity, structural deformation, and programmable anisotropy of DNA origami in electric field.

Authors:  Chen-Yu Li; Elisa A Hemmig; Jinglin Kong; Jejoong Yoo; Silvia Hernández-Ainsa; Ulrich F Keyser; Aleksei Aksimentiev
Journal:  ACS Nano       Date:  2015-01-30       Impact factor: 15.881

6.  Multilevel summation for periodic electrostatics using B-splines.

Authors:  Hüseyin Kaya; David J Hardy; Robert D Skeel
Journal:  J Chem Phys       Date:  2021-04-14       Impact factor: 3.488

7.  A compression strategy for particle mesh Ewald theory.

Authors:  Andrew C Simmonett; Bernard R Brooks
Journal:  J Chem Phys       Date:  2021-02-07       Impact factor: 3.488

8.  Discovery of Klotho peptide antagonists against Wnt3 and Wnt3a target proteins using combination of protein engineering, protein-protein docking, peptide docking and molecular dynamics simulations.

Authors:  Shaher Bano Mirza; Ramin Ekhteiari Salmas; M Qaiser Fatmi; Serdar Durdagi
Journal:  J Enzyme Inhib Med Chem       Date:  2016-10-21       Impact factor: 5.051

9.  Structure-Based Virtual Screening of Tumor Necrosis Factor-α Inhibitors by Cheminformatics Approaches and Bio-Molecular Simulation.

Authors:  Sobia Ahsan Halim; Almas Gul Sikandari; Ajmal Khan; Abdul Wadood; Muhammad Qaiser Fatmi; René Csuk; Ahmed Al-Harrasi
Journal:  Biomolecules       Date:  2021-02-22

10.  Large-Conductance Transmembrane Porin Made from DNA Origami.

Authors:  Kerstin Göpfrich; Chen-Yu Li; Maria Ricci; Satya Prathyusha Bhamidimarri; Jejoong Yoo; Bertalan Gyenes; Alexander Ohmann; Mathias Winterhalter; Aleksei Aksimentiev; Ulrich F Keyser
Journal:  ACS Nano       Date:  2016-08-23       Impact factor: 15.881
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