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Subject: search.filters.subject.530Institute: search.filters.UBSInstitut.Institut für ComputerphysikStart date: 2010End date: 2019Author: search.filters.author.Kesselheim, Stefan

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Now showing 1 - 2 of 2
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    Efficient algorithms for electrostatic interactions including dielectric contrasts
    (2013) Arnold, Axel; Breitsprecher, Konrad; Fahrenberger, Florian; Kesselheim, Stefan; Lenz, Olaf; Holm, Christian
    Coarse grained models of soft matter are usually combined with implicit solvent models that take the electrostatic polarizability into account via a dielectric background. In biophysical or nanoscale simulations that include water, this constant can vary greatly within the system. Performing molecular dynamics or other simulations that need compute exact electrostatic interactions between charges in those systems is computationally demanding. We review here several algorithms developped by us that perform exactly this task. For planar dielectric surfaces in partial periodic boundary conditions, the arising image charges can be either treated with the MMM2D algorithm in a very efficient and accurate way, or with the ELC term that enables the user to use his favorite 3D periodic Coulomb solver . Arbitrarily shaped interfaces can be dealt with using induced surface charges with the ICC algorithm. Finally, the local electrostatics algorithm MEMD (Maxwell Equations Molecular Dynamics) allows even to employ a smoothly varying dielectric constant in the systems. We introduce the concepts of these three algorithms, and an extension for the inclusion of boundaries that are to be held fixed at constant potential (metal conditions). For each method, we present a showcase application to highlight the importance of dielectric interfaces.
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    ItemOpen Access
    Simulations of DNA translocation through nanopores
    (2015) Kesselheim, Stefan; Holm, Christian (Prof. Dr.)
    In the past two decades, experiments addressing the transport of single molecules, especially DNA, has attracted great attention. This technology is considered promising for the next generation of rapid in cheap DNA sequencing methods. In this theses, physical models and computer simulation methods for the simulation of DNA transport through these so-called nanopores are investigated. Modelling techniques with different result ions are compared and evaluated with special focus on their predictions regarding the current modulation caused by DNA molecules that are transported through these pores.