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Projects / Programmes source: ARIS

Computer Algorithms Development for Macromolecular Simulation

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Research activity

Code Science Field Subfield
1.07.00  Natural sciences and mathematics  Computer intensive methods and applications   

Code Science Field
P170  Natural sciences and mathematics  Computer science, numerical analysis, systems, control 
P190  Natural sciences and mathematics  Mathematical and general theoretical physics, classical mechanics, quantum mechanics, relativity, gravitation, statistical physics, thermodynamics 
Keywords
Computer simulations, Algorithms, Molecular Dynamics Simulations, DFT, Symplectic Methods, Normal Mode Analysis, Hamiltonian Systems, Potential Enery Functions, Macromolecule
Evaluation (rules)
source: COBISS
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (5)
no. Code Name and surname Research area Role Period No. of publications
1.  23422  PhD Urban Borštnik  Natural sciences and mathematics  Junior researcher  2004 - 2007  36 
2.  02287  PhD Milan Hodošček  Natural sciences and mathematics  Researcher  2004 - 2007  279 
3.  06734  PhD Dušanka Janežič  Natural sciences and mathematics  Head  2004 - 2007  495 
4.  13627  PhD Franci Merzel  Natural sciences and mathematics  Researcher  2004 - 2007  199 
5.  19037  PhD Matej Praprotnik  Natural sciences and mathematics  Researcher  2004 - 2007  317 
Organisations (1)
no. Code Research organisation City Registration number No. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  20,965 
Abstract
The goal of the proposed research is to introduce new improvements in molecular dynamics simulation of macromolecules that increase the accuracy and efficiency of present-day simulation approaches. We primarily aim to: i) improve algorithms for integration of classical and quantum equations of motion by further developing symplectic algorithms based on analytical treatment of high frequency motions, ii) take into account the quantum effects in dynamics of light particles via wave-packet propagation methods and a newly developed density functional theory approach, and iii) improve the treatment of the solvent in molecular dynamics simulation by developing explicit/implicit solvent methods in which the hydration water is represented explicitly while the surrounding bulk water is represented implicitly. The proposed methodological improvements should significantly extend the scope of presently used algorithms in terms of length- and time-scales and thus contribute to the general applicability of molecular dynamics simulation algorithms. The simulation results of selected examples will facilitate the understanding of some fundamental problems in molecular biology.
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