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- W99184483 abstract "Molecular simulation is an essential tool in understanding complex chemical and biochemical processes as real-life experiments prove increasingly costly or infeasible in practice . This thesis is devoted to methodological aspects of molecular simulation, with a particular focus on computing transition paths and their associated free energy profiles. The first part is dedicated to computational methods for reaction path and transition state searches on a potential energy surface. In Chapter 3 we propose an improvement to a widely-used transition state search method, the Activation Relaxation Technique (ART). We also present a local convergence study of a prototypical algorithm. The second part is dedicated to free energy computations. We focus in particular on an adaptive importance sampling technique, the Adaptive Biasing Force (ABF) method. The first contribution to this field, presented in Chapter 5, consists in showing the applicability to a large molecular system of a new parallel implementation, named multiple-walker ABF (MW-ABF). Numerical experiments demonstrated the robustness of MW-ABF against artefacts arising due to poorly chosen or oversimplified reaction coordinates. These numerical findings inspired a new study of the longtime convergence of the ABF method, as presented in Chapter 6. By studying a slightly modified model, we back our numerical results by showing a faster theoretical rate of convergence of ABF than was previously shown" @default.
- W99184483 created "2016-06-24" @default.
- W99184483 creator A5037351952 @default.
- W99184483 date "2010-11-24" @default.
- W99184483 modified "2023-09-24" @default.
- W99184483 title "Deterministic and stochastic methods for molecular simulation" @default.
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- W99184483 hasPublicationYear "2010" @default.
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