60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX)
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Institute
Some connections between importance sampling and enhanced sampling methods in molecular dynamics
(2017)
Enhanced sampling methods play an important role in molecular dynamics, because they enable the collection of better statistics of rare events that are important in many physical phenomena. We show that many enhanced sampling methods can be viewed as methods for performing importance sampling, by identifying important correspondences between the language of molecular dynamics and the language of probability theory. We illustrate these connections by highlighting the similarities between the rare event simulation method of Hartmann and Schütte (J. Stat. Mech. Theor. Exp., 2012), and the enhanced sampling method of Valsson and Parrinello (Phys. Rev. Lett. 113, 090601). We show that the idea of changing a probability measure is fundamental to both enhanced sampling and importance sampling.
The topic of this thesis is the examination of an optimization model
which stems from the clustering process of non-reversible markov processes.
We introduce the cycle clustering problem und formulate it as a mixed
integer program (MIP).
We prove that this problem is N P-hard and discuss polytopal aspects
such as facets and dimension. The focus of this thesis is the development of
solving methods for this clustering problem. We develop problem specific
primal heuristics, as well as separation methods and an approximation
algorithm. These techniques are implemented in practice as an application
for the MIP solver SCIP.
Our computational experiments show that these solving methods result
in an average speedup of ×4 compared to generic solvers and that our
application is able to solve more instances to optimality within the given
time limit of one hour.
An automatic adaptive importance sampling algorithm for molecular dynamics in reaction coordinates
(2017)
In this article we propose an adaptive importance sampling scheme for dynamical quantities of high dimensional complex systems which are metastable. The main idea of this article is to combine a method coming from Molecular Dynamics Simulation, Metadynamics, with a theorem from stochastic analysis, Girsanov's theorem. The proposed algorithm has two advantages compared to a standard estimator of dynamic quantities: firstly, it is possible to produce estimators with a lower variance and, secondly, we can speed up the sampling. One of the main problems for building importance sampling schemes for metastable systems is to find the metastable region in order to manipulate the potential accordingly. Our method circumvents this problem by using an assimilated version of the Metadynamics algorithm and thus creates a non-equilibrium dynamics which is used to sample the equilibrium quantities.