20022021

Research activity per year

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Personal profile

Research Interests

• Hybrid hydrodynamics/molecular dynamics multiscale, multiphysics modelling. Modelling bio-molecular systems where fully atomistic and purely hydrodynamic representations coexist and smoothly transform into each other at different spatial locations.
• All-atom molecular dynamics simulation of entire viruses. Modelling whole viruses including surrounding water at atomistic resolution. High performance molecular dynamics is used for systems of 3-5 million atoms.
• Kinetics of ligand binding. Obtaining the rates of binding of small molecules to proteins from realistic full-atom molecular dynamics simulations. Developing approaches for calculating correct bio-molecular transformation rates, taking into account non-Markvoian behaviour of states.
• Self-organising molecular systems. Adapting and evolving chemical systems. Applications to self-organising materials.
• Complexity of dynamical systems. Quantitative approaches to computing the complexity of physical systems. Informational contents of classical dynamics of molecular systems. Molecules as non-linear dynamical systems.
• Protein folding. Molecular Dynamics simulation of protein folding. Complexity of the dynamics of folding. “Controlled MD” a correct methods for accelerated folding simulations.
• Bohmian quantum dynamics. Application of Bohmian mechanics to realistic molecular systems. Developing methods for effective propagation of Bohmian quantum trajectories for multidimensional systems.

Membership of Professional Bodies

Chartered Chemist, Fellow of the Royal Society of Chemistry

Research Projects/Collaborations

Most important projects:

Current:

Horizon2020 RISE project “Theoretical and computational investigation of tuberculosis antimicrobial resistance development based on extensive experimental library of mycobacterium strains”, the consortium includes 11 partners in UK, Spain, Italy, Russia, Ukraine, Equador, Japan; 58 secondments are planned for 159 personmonths work, total budget 730k EUR.

Previous:

1.2M EUR project “Using next generation computers and algorithms for modelling the dynamics of large biomolecular systems” funded by G8 Research Councils Initiative on Multilateral Research Funding in 2011. The UK teams received e697K of funding (e415K in Aston University and e282K in Cambridge University).

2.1M EUR EU Framework 6 (NEST-2003-Path-1) project “Emergent organisation in complex biomolecular systems”, EMBIO, one of 13 EU funded large scale initiatives. The consortium consisted of 8 research groups from 6 European countries. Three major meetings have been organised (∼40 participants is a typical scale). The project resulted in 77 publications and over 60 conference presentations.

Funding Applications and Awards

• total number of grants: 21
• overall funding: ~£4.4M

Teaching Activity

Current:

Undergraduate module AM20VR “Vector Calculus”.

Undergraduate module AM30AT “Approximation Theory”.

Postgraduate module AM40AC “Algorithms and Computational Mathematics

Postgraduate module DS40AC for Rolls-Royce Digital Academy “Algorithms and Computational Mathematics

Previous:

Undergraduate module AM12EM “Mathematics for first year engineers

 

Contact Details

Phone number: +44 (0)121 204 3533
Email: D.Nerukh@aston.ac.uk
Room number: MB310M

External positions

Visiting Scientist

2005 → …

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