Special Issue "Statistical Mechanics and Molecular Simulation"
Deadline for manuscript submissions: 30 September 2020.
2. Precision Oncology Center, Lausanne University Hospital, Lausanne, Switzerland
3. Molecular Modeling Group, Swiss Institute of Bioinformatics, Lausanne, Switzerland
Interests: molecular modeling; statistical mechanics; machine learning; allostery in proteins; T cell antigen recognition; membrane transporters
2. Department of Physiology and Biophysics, Weill Cornell Medical College, New York, NY 10065, USA
Interests: molecular modeling; statistical mechanics; machine learning; allostery in proteins; G protein-coupled receptors; membrane transporters
While hardware developments have continuously pushed the reach of molecular simulations, approaching realistic chemical and biological time scales remains a major bottleneck. To overcome this, many enhanced sampling methods that aim to accelerate the estimation of free energies, transition rates, and other ensemble averages are being developed, putting statistical mechanics at the forefront of molecular simulation. Of particular interest are distributed sampling methods, which combine sampling from independent simulations running in parallel, and methods that sample from statistically efficient alternative distributions.
A complementary challenge is to extract functionally relevant information from the increasingly vast amounts of raw simulation data generated in order to determine the physical mechanisms that control the relative stability of states or the transitions between them. Of particular interest in biological systems are allosteric mechanisms, where two or more molecular processes, sometimes separated by large distances, are dynamically or thermodynamically coupled. New rigorous physics-based approaches are needed to establish the relationship between qualitative descriptions of allostery in biochemistry and quantitative concepts from statistical mechanics and information theory.
For this Special Issue, we call for contributions at the crossroads of rigorous statistical mechanics and molecular simulation, focusing on i) enhanced sampling methods and ii) novel approaches to describe complex phenomena, such as macromolecular complex association and allostery.
Dr. Michel Alain Cuendet
Dr. Michael V. LeVine
Manuscript Submission Information
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- molecular simulation
- statistical mechanics
- enhanced sampling
- free energy