Titlebook: Computer Simulations in Condensed Matter: From Materials to Chemical Biology. Volume 1; Mauro Ferrario,Giovanni Ciccotti,Kurt Binder Book

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Sampling Kinetic Protein Folding Pathways using All-Atom Models,e background of two state folding using energy landscapes I introduce common protein models and computational tools to study folding thermodynamics and kinetics. Free energy landscapes are able to capture the thermodynamics of two-state protein folding, and several methods for efficient sampling of

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GOUGE

Transition Path Theory,lived states. For over 70 years, transition state theory (TST) has provided the main theoretical framework for the description of these events [17,33,34]. Yet, while TST and evolutions thereof based on the reactive flux formalism [1, 5] (see also [30,31]) give an accurate estimate of the transition

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Multiscale Modelling in Molecular Dynamics: Biomolecular Conformations as Metastable States,oachis based on a hierarchical concept of metastability: metastable statesare understood as subsets of state or configuration space from which the dynamicsexits only very rarely; subsets with the smallest exit probabilities areof most interest, their further decomposition then may reveal subsets fro

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Hippocampus

Linearized Path Integral Methods for Quantum Time Correlation Functions,l expressions in the difference between paths representing the forward and backward propagators. Our focus here will be on problems that can be partitioned into two subsystems: One that is best described by a few discrete quantum states such as the high frequency vibrations or electronic states of m

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ANNUL

Large Scale Condensed Matter Calculations using the Gaussian and Augmented Plane Waves Method, of the KS method makes it also the favorite framework for new developments to improve both, accuracy and efficiency. Better accuracy in this context can be achieved along two lines. On one hand the numerical limit of a given model should be reached and on the other hand more accurate models should

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Transition Path Theory, trajectories may again be rather uninformative about the mechanism of the reaction. This may sound paradoxical at first: what more than actual reactive trajectories could one need to understand a reaction? The problem, however, is that the reactive trajectories by themselves give only a very indire