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Lecture

Sampling Algorithms for Constrained Systems

Description

This lecture covers sampling algorithms for constrained systems, focusing on the work of Benedict Leimkuhler from the University of Edinburgh. The presentation discusses the sampling problem, MCMC algorithms, and geodesic integrators, highlighting the challenges and applications in molecular modeling and statistics.

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Related concepts (32)

Molecular modelling

Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system.

Molecular design software

Molecular design software is notable software for molecular modeling, that provides special support for developing molecular models de novo. In contrast to the usual molecular modeling programs, such as for molecular dynamics and quantum chemistry, such software directly supports the aspects related to constructing molecular models, including: Molecular graphics interactive molecular drawing and conformational editing building polymeric molecules, crystals, and solvated systems partial charges development g

Post-transition metal

The metallic elements in the periodic table located between the transition metals to their left and the chemically weak nonmetallic metalloids to their right have received many names in the literature, such as post-transition metals, poor metals, other metals, p-block metals and chemically weak metals. The most common name, post-transition metals, is generally used in this article. Physically, these metals are soft (or brittle), have poor mechanical strength, and usually have melting points lower than those of the transition metals.

Docking (molecular)

In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction.

Molecular dynamics

Molecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.

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