Jesus Izaguirre

New York, New York, United States Contact Info
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Volunteer Experience

  • Secretary and Director

    Thomas International

    - Present 18 years

    Education

    Sharing the Thomistic tradition with general public and scholars alike

Publications

  • Parallel multigrid summation for the N-body problem

    J. Parallel Distrib. Comput 01/2005; 65:949-962.

    An Θ(n) parallel multigrid summation method (MG) for the N-body problem is presented. The method was originally devised for vacuum boundary conditions. Here, it is extended to periodic boundary conditions and implemented in parallel using force decomposition and MPI. MG is based on a hierarchical decomposition of computational kernels on multiple grids. For low accuracy calculations, appropriate for molecular dynamics, a sequential implementation is as fast or faster than particle mesh Ewald…

    An Θ(n) parallel multigrid summation method (MG) for the N-body problem is presented. The method was originally devised for vacuum boundary conditions. Here, it is extended to periodic boundary conditions and implemented in parallel using force decomposition and MPI. MG is based on a hierarchical decomposition of computational kernels on multiple grids. For low accuracy calculations, appropriate for molecular dynamics, a sequential implementation is as fast or faster than particle mesh Ewald (PME). Our parallel implementation is more scalable than PME. The method can be combined with multiple time stepping integrators to produce a powerful simulation protocol for simulation of biological molecules and other materials. The parallel implementation is tested on both a Linux cluster with Myrinet interconnect and a shared memory computer. It is available as open-source at http://protomol.sourceforge.net. An auxiliary tool allows the automatic selection of optimal parameters for MG, and is available at http://mdsimaid.cse.nd.edu.

    See publication

  • http://www.ncbi.nlm.nih.gov/sites/myncbi/jesus.izaguirre.1/bibliography/43033532/public/?sort=date&direction=descending

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    Partial list of my bibliography in MyNCBI

Patents

  • Accelerated molecular dynamics of proteins and other biomolecules

    Issued US WO 2009151696 A3

    Embodiments herein relate to the field of computational biochemistry, in particular to accelerated molecular dynamics of proteins and other biomolecules. Various embodiments disclosed herein include methods, systems, and apparatus for determining the state, for example the kinetics or thermodynamics, of a biomolecule system. In some embodiments, the methods include partitioning the system's degrees of freedom into a subspace and a subspace complement according to frequency using Normal Mode…

    Embodiments herein relate to the field of computational biochemistry, in particular to accelerated molecular dynamics of proteins and other biomolecules. Various embodiments disclosed herein include methods, systems, and apparatus for determining the state, for example the kinetics or thermodynamics, of a biomolecule system. In some embodiments, the methods include partitioning the system's degrees of freedom into a subspace and a subspace complement according to frequency using Normal Mode Analysis (NMA), determining a harmonic approximation to the system around an initial equilibrium structure using a Mass Reweighted Hessian (MRH) of a biomolecular force field, using the partitioning to construct a damping matrix for the Langevin equation that overdamps and propagates high frequency modes using Brownian dynamics, propagating the low frequency modes using full Langevin dynamics, and accelerating the Brownian dynamics on the high frequency modes using an energy minimization. A coarse-grained normal mode analysis (CNMA) is also presented that enables application of this approach to very large proteins and long timescales.

    Other inventors
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Languages

  • Spanish

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