Adam Kells

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Linda Martini, Adam Kells, Roberto Covino, Gerhard Hummer, Nicolae-Viorel Buchete, and Edina Rosta Department of Chemistry, King’s College London, SE1 1DB London, United Kingdom Department of Theoretical Biophysics, Max Planck Institute of Biophysics, 60438 Frankfurt am Main, Germany Institute of Biophysics, Goethe University Frankfurt, 60438 Frankfurt am(More)
We present an algorithm to calculate free energies and rates from molecular simulations on biased potential energy surfaces. As input, it uses the accumulated times spent in each state or bin of a histogram and counts of transitions between them. Optimal unbiased equilibrium free energies for each of the states/bins are then obtained by maximizing the(More)
We show how accurate rates of formation and dissociation of peptide dimers can be calculated using direct transition counting (DTC) from replica-exchange molecular dynamics (REMD) simulations. First, continuous trajectories corresponding to system replicas evolving at different temperatures are used to assign conformational states. Second, we analyze the(More)
We present a new method that enables the identification and analysis of both transition and metastable conformational states from atomistic or coarse-grained molecular dynamics (MD) trajectories. Our algorithm is presented and studied by using both analytical and actual examples from MD simulations of the helix-forming peptide Ala5, and of a larger system,(More)
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