Journal of Computational Chemistry

Cover image for Vol. 36 Issue 20

July 30, 2015

Volume 36, Issue 20

Pages i–ii, 1489–1572

  1. Cover Image

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      Cover Image, Volume 36, Issue 20 (pages i–ii)

      Article first published online: 26 JUN 2015 | DOI: 10.1002/jcc.23997

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      Application of density functional theory to molecules containing thousands of atoms is hindered by significant memory demands of the density fitting approximation. On page 1521 (DOI: 10.1002/jcc.23961), Lukáš Grajciar introduces a new low-memory iterative density fitting formulation that circumvents this problem using a combination of a continuous fast multipole method and a preconditioned conjugate gradient solver. The potential of the method implemented within the TURBOMOLE program package is demonstrated by performing density functional theory calculations for pure-silica zeolite chabazite fragment with 2592 atoms, 37 632 basis, and 121 248 auxiliary basis functions on a single processor workstation.

  2. Full Papers

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    1. Virtual-system-coupled adaptive umbrella sampling to compute free-energy landscape for flexible molecular docking (pages 1489–1501)

      Junichi Higo, Bhaskar Dasgupta, Tadaaki Mashimo, Kota Kasahara, Yoshifumi Fukunishi and Haruki Nakamura

      Article first published online: 4 JUN 2015 | DOI: 10.1002/jcc.23948

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      A two-dimensional free-energy landscape of dimerization for two peptide (Aβ30–35) chains is computed by a virtual-system-coupled adaptive umbrella sampling. The peptides are put in a periodic boundary box filled with explicit solvent. The x- and y-axes are the mutual molecular distance and the relative molecular orientation. Parallel and antiparallel β-sheets, cross-contact complexes, and α-helices are sampled as well as completely dissociated forms. Complex-labeled “N” is the parallel β-sheet observed in crystal.

    2. Multidimensional persistence in biomolecular data (pages 1502–1520)

      Kelin Xia and Guo-Wei Wei

      Article first published online: 30 MAY 2015 | DOI: 10.1002/jcc.23953

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      Persistent homology has emerged as a popular technique for the topological simplification of massive biomolecular data. Resolution-based multidimensional persistent homology is introduced to bridge the gap between traditional topology and geometry. The utility, robustness, and efficiency of the proposed topological methods for protein folding, protein flexibility analysis, the topological denoising of cryo-electron microscopy data, and the scale dependence of nanoparticles are demonstrated.

    3. Low-memory iterative density fitting (pages 1521–1535)

      Lukáš Grajciar

      Article first published online: 8 JUN 2015 | DOI: 10.1002/jcc.23961

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      Density fitting (DF) approximation within the density functional theory (DFT) leads to more than a tenfold increase of computational efficiency for systems containing few hundreds of atoms. However, application of the DF approximation to even larger systems is hindered by its significant memory demands. This article introduces a new DF formulation that circumvents this problem, enabling one to perform DFT calculations on molecules with thousands of atoms on single (multicore) processor work stations.

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      Accelerated molecular dynamics simulations of protein folding (pages 1536–1549)

      Yinglong Miao, Ferran Feixas, Changsun Eun and J. Andrew McCammon

      Article first published online: 12 JUN 2015 | DOI: 10.1002/jcc.23964

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      Folding of four fast-folding proteins, including chignolin, Trp-cage, villin headpiece, and WW domain, was simulated via accelerated molecular dynamics (aMD). Free energy profiles calculated through improved reweighting of the aMD simulations using cumulant expansion to the second-order are in good agreement with those obtained from long-timescale conventional molecular dynamics simulations. This work demonstrates the enhanced sampling power of aMD on protein folding and will provide basic references in using aMD for further studies.

    5. Efficient global optimization of reactive force-field parameters (pages 1550–1561)

      Mark Dittner, Julian Müller, Hasan Metin Aktulga and Bernd Hartke

      Article first published online: 17 JUN 2015 | DOI: 10.1002/jcc.23966

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      Fitting reactive force fields to reference data is a highly complex, global optimization problem. Significant implementation advances are presented, making the task highly efficient and scalable.

    6. A potential with low point charges for pure siliceous zeolites (pages 1562–1567)

      Sudhir K. Sahoo and Nisanth N. Nair

      Article first published online: 15 JUN 2015 | DOI: 10.1002/jcc.23968

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      A new potential with low point charges is proposed here for modeling siliceous zeolites.

  3. Software News and Updates

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    4. Software News and Updates
    1. Accounting for observed small angle X-ray scattering profile in the protein–protein docking server cluspro (pages 1568–1572)

      Bing Xia, Artem Mamonov, Seppe Leysen, Karen N. Allen, Sergei V. Strelkov, Ioannis Ch. Paschalidis, Sandor Vajda and Dima Kozakov

      Article first published online: 10 JUN 2015 | DOI: 10.1002/jcc.23952

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      SAXS is a high throughput experimental technique for obtaining low resolution structural data for macromolecules in solution. While it cannot be used on its own to solve the structure of complex structures, utilizing SAXS data during automated docking improves the ranking of predicted models. The option of using SAXS data as an experimental restraint has been added to the ClusPro server.

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