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Projects / Programmes source: ARIS

Computer simulations and analysis of collective motions of biomolecules

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Research activity

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

Code Science Field
P170  Natural sciences and mathematics  Computer science, numerical analysis, systems, control 
P230  Natural sciences and mathematics  Atomic and molecular physics 
B120  Biomedical sciences  Molecular biophysics 
Keywords
computer simulations, molecular dynamics, biomolecules, collective motions, phonons, neutron scattering, DNA molecules, principal component analysis, seered dynamics, oligomerization, amyloids
Evaluation (rules)
source: COBISS
Evaluation of bibliographic research performance indicators according to ARIS methodology
Citations Citations for bibliographic records in COBIB.SI that are linked to records in citation databases
source: WoS source: Scopus source: COBISS
Researchers (10)
no. Code Name and surname Research area Role Period No. of publications
1.  23422  PhD Urban Borštnik  Computer intensive methods and applications  Researcher  2007 - 2009  36 
2.  28560  PhD Nejc Carl  Computer intensive methods and applications  Junior researcher  2009  23 
3.  02287  PhD Milan Hodošček  Chemistry  Researcher  2007 - 2009  281 
4.  06734  PhD Dušanka Janežič  Computer intensive methods and applications  Researcher  2007 - 2009  500 
5.  17255  Tatjana Karba    Technical associate  2007  0 
6.  25435  PhD Janez Konc  Computer intensive methods and applications  Researcher  2007 - 2009  233 
7.  13627  PhD Franci Merzel  Computer intensive methods and applications  Head  2007 - 2009  209 
8.  19037  PhD Matej Praprotnik  Computer intensive methods and applications  Researcher  2007 - 2009  323 
9.  30286  PhD Blaž Vehar  Computer intensive methods and applications  Technical associate  2009  17 
10.  26516  PhD Jernej Zidar  Computer intensive methods and applications  Junior researcher  2007 - 2009  26 
Organisations (1)
no. Code Research organisation City Registration number No. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  20,982 
Abstract
The main goal of the proposed research project is to provide a new computational tools for simulating and analysing low frequency collective motions of biomolecules including: i) lattice- and internal-vibrations of molecular crystals, and ii) large-scale motions involved during configurational changes such as domain motions, aggregation and oligomerization, structural phase transitions... The developed methods and computer packages will allow inelastic neutron and X-ray scattering observables to be calculated from atomic detail models, allowing comparison with- and interpretation of- experimental data produced at large scale experimental facilities (DNA). Various simplification schemes will be presented for analysing displacement vectors, which are otherwise too complicated to recognize characteristic motions in very large systems. Using »principal component analysis« we aim to identify the form and tendency of configurational changes during the oligomerization process (i.e. during amyloid formation) and construct the molecular dynamics simulation method based on additional steering forces acting along selected principal components in order to speed up the detected configurational change. The proposed approaches will open the door to a general understanding of many dynamically- driven processes involved in biomolecular systems.
Significance for science
The developed methods present new efficient solutions of problems in the field of biomolecular simulations. The methods are built-in into existing simulation program packages, providing the availability of the moetgods to the wider range of researchers. Our methods present contribution to in improving the prediction power of biomolecular simulations.
Significance for the country
Within the project we collaborate with the leading institutions in the field, like institute ILL in Grenoble and University of Heidelberg, which strengthens our international connections. Besides, we get a chance to access the instruments for neutron scattering in ILL. The developed methods are made available to the users, in particular to Phd studens studying at different natural-science faculties.
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