Photo of Dmitry Nerukh
    • School of Engineering and Applied Science, Aston University

      B4 7ET Birmingham

      United Kingdom

    20022019
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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 → …

    Fingerprint Dive into the research topics where Dmitry Nerukh is active. These topic labels come from the works of this person. Together they form a unique fingerprint.

    Molecular dynamics Chemical Compounds
    molecular dynamics Physics & Astronomy
    peptides Physics & Astronomy
    Water Chemical Compounds
    water Physics & Astronomy
    Peptides Chemical Compounds
    computational mechanics Physics & Astronomy
    Atoms Chemical Compounds

    Network Recent external collaboration on country level. Dive into details by clicking on the dots.

    Research Output 2002 2019

    In search of an optimal acid-base indicator for examining surfactant micelles: Spectrophotometric studies and molecular dynamics simulations

    Mchedlov-Petrossyan, N. O., Farafonov, V. S., Cheipesh, T. A., Shekhovtsov, S. V., Nerukh, D. A. & Lebed, A. V., 20 Mar 2019, In : Colloids and Surfaces A: Physicochemical and Engineering Aspects. 565, p. 97-107 11 p.

    Research output: Contribution to journalArticle

    Micelles
    Surface-Active Agents
    Molecular dynamics
    micelles
    Surface active agents

    Investigation of an Idealized Virus Capsid Model by the Dynamic Elasticity Apparatus

    Zhuravlova, Z., Nerukh, D., Reut, V. & Vaysfel’d, N., 1 Nov 2019, In : Journal of Mathematical Sciences (United States). 243, 1, p. 111–127 17 p.

    Research output: Contribution to journalArticle

    Open Access
    Viruses
    Virus
    Elasticity
    Boundary value problems
    Acoustics

    MS2 bacteriophage capsid studied using all-atom molecular dynamics

    Farafonov, V. S. & Nerukh, D., 6 Jun 2019, In : Interface Focus. 9, 3, 20180081.

    Research output: Contribution to journalArticle

    Open Access
    File
    Levivirus
    Bacteriophages
    Capsid
    Molecular Dynamics Simulation
    Molecular dynamics

    All-Atom Molecular Dynamics Simulations of Whole Viruses

    Tarasova, E. & Nerukh, D., 19 Sep 2018, In : Journal of Physical Chemistry Letters. 9, p. 5805-5809

    Research output: Contribution to journalArticle

    Open Access
    File
    viruses
    Viruses
    Molecular dynamics
    molecular dynamics
    Atoms

    Details of charge distribution in stable viral capsid

    Tarasova, E., Farafonov, V., Taiji, M. & Nerukh, D., 1 Sep 2018, In : Journal of Molecular Liquids. 265, p. 585-591

    Research output: Contribution to journalArticle

    Open Access
    File
    Charge distribution
    charge distribution
    ion distribution
    Ions
    ions

    Thesis

    Bridging large and small scales of water models using hybrid Molecular Dynamics/Fluctuating Hydrodynamics framework

    Author: Scukins, A., 11 Nov 2014

    Supervisor: Nerukh, D. (Supervisor) & Lowe, D. (Supervisor)

    Student thesis: Doctoral ThesisDoctor of Philosophy

    File

    Computational mechanics analysis of the hidden conformational dynamics within a molecular trajectory

    Author: Godwin, L., Oct 2013

    Supervisor: Chattopadhyay, A. K. (Supervisor) & Nerukh, D. (Supervisor)

    Student thesis: Master's ThesisMaster of Science (by Research)

    Statistical properties of liquid protein-water molecular system dynamics

    Author: Voraprateep, J., 20 Jun 2017

    Supervisor: Nerukh, D. (Supervisor)

    Student thesis: Doctoral ThesisDoctor of Philosophy

    File

    Activities 2011 2011

    • 1 Participation in conference

    9th Triennial Congress of the World Association of Theoretical and Computational Chemists

    Dmitry Nerukh (Speaker)
    2011

    Activity: Participating in or organising an event typesParticipation in conference