This week’s seminar will be jointly given by Dmitry Nerukh, Aston University and Gennady Chuev, visiting from the Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia.
It will be in INB 3305 at 1pm on Wednesday Jan 31st.
Dmitry will talk about ‘ Hybrid Molecular Dynamics – Hydrodynamics Modelling of Liquid Solutions: Whole Virus at Atomistic Resolution’ while Gennady will give an introduction to ‘Integral Equations Theory for Molecular Liquids: From toy models to self-assembled nanosolutes. Abstracts below.
Our novel methodology for modelling liquid molecular systems at very different space and time scales simultaneously with consistent transition between the scales is described. Regions of atomistic representation of the liquid of arbitrary shape and time evolution coexist with fluctuating hydrodynamics environment which in turn is coupled to macroscopic hydrodynamics at larger scales. The approach is implemented in a popular Molecular Dynamics package GROMACS. As an example, a virus PCV2 is modelled at all-atom resolution for the protein shell of the virus, surrounded by a layer of atomistic water (any model of water such as TIP3P, SPC, etc can be used) that gradually changes to hydrodynamic continuum away from the virus. We analyse the connection between the number of ions inside an empty capsid of PCV2 virus and its stability which helps clarify the details of the viral life cycle that is ultimately connected to the role of packaged viral genome inside the capsid.
The lecture outlines basics, current status, and perspectives of integral equation theory (IET) for molecular liquids. A special attention is given for models improving accuracy of the calculations.
1. Introduction to Solvation Phenomena.
Why is so difficult to treat solvation? Molecular simulations of solvation effects. Molecular dynamics: Challenges and problems of its application to solvation phenomena.
2. Key concepts of Integral Equations Theory for Molecular Liquids.
Density functional theory (DFT) in classical and quantum domains. Correlation functions. DFT and IET. Ornstein-Zernike (OZ) equation. IET for simple liquids.
3. IET for molecular liquids.
Molecular OZ equation. Interaction site formalism. 1D & 3D Reference interaction site models (RISM). Numerical algorithms for solution of RISM equations. Current status of the theory: accuracy and speed of calculations. Applications to biomolecules and nanosolutes.
4. Beyond conventional schemes.
Closures and bridge functions. Empirical bridge functions and the problem of accuracy of IET calculations. Reconstruction of bridge functions from simulations.
5. Conclusions & perspectives.