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Projects / Programmes source: ARRS

COMPUTER SIMULATION OF MOLECULAR STRUCTURE AND DYNAMICS

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Periods
January 1, 2004 - December 31, 2008
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 
Keywords
Molecular Modeling, Computer Simulations, Algorithms, Molecular Dynamics, Symplectic Methods, Normal Mode Analysis, Integral Equation Theory, QM/MM methods, DFT methods, Hamiltonian Systems, Force Fields, Electronic Structure, Density Functionals, Multicomponent Reactions, Reaction Mechanisms, Parallel Computers
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 (12)
no. Code Name and surname Research area Role Period No. of publications
1.  23422  PhD Urban Borštnik  Natural sciences and mathematics  Researcher  2004 - 2008  36 
2.  28560  PhD Nejc Carl  Natural sciences and mathematics  Junior researcher  2007 - 2008  23 
3.  02287  PhD Milan Hodošček  Natural sciences and mathematics  Researcher  2004 - 2008  279 
4.  06734  PhD Dušanka Janežič  Natural sciences and mathematics  Principal Researcher  2004 - 2008  493 
5.  17255  Tatjana Karba    Technician  2004 - 2007  0 
6.  25435  PhD Janez Konc  Natural sciences and mathematics  Junior researcher  2005 - 2008  225 
7.  13627  PhD Franci Merzel  Natural sciences and mathematics  Researcher  2004 - 2008  192 
8.  03455  PhD Matej Penca  Natural sciences and mathematics  Researcher  2004 - 2008  66 
9.  06431  PhD Ksenija Poljanec  Natural sciences and mathematics  Researcher  2004 - 2008  26 
10.  19037  PhD Matej Praprotnik  Natural sciences and mathematics  Researcher  2004 - 2008  315 
11.  30286  PhD Blaž Vehar  Natural sciences and mathematics  Technician  2008  17 
12.  26516  PhD Jernej Zidar  Natural sciences and mathematics  Junior researcher  2006 - 2008  26 
Organisations (1)
no. Code Research organisation City Registration number No. of publications
1.  0104  National Institute of Chemistry  Ljubljana  5051592000  21,129 
Abstract
Computer simulation methods have been developing primarily in the areas of increasing the simulation lengths and the size of modeled systems, which allows a greater understanding of the relationship between the structure and function in biological macromolecules. Due to the heterogeneous nature of these macromolecules, an average of several simulations of the same system must be performed. Including a solvent in simulations greatly increases the scope of the simulated system. The length of simulations has to be greater than on the nanosecond scale to study chemically and biologically interesting processes, which occur on the microsecond scale. We expect that the development of new methods for molecular modeling and their implementation on parallel computers will increase the speed of computer simulations for several orders of magnitude. This will allow a more detailed examination of known problems as well as allow the examination of new problems. The program has the following goals: a) Further development and use of the SISM (Split Integration Symplectic Method) and HANA (Hydrogens ANAlytically) symplectic methods for molecular dynamics simulations of macromolecules that will allow integrating equations of motion with a long time step while remaining stable, computationally economical and being efficiently parallelizable. The methods are based on the factorization of the Liouville operator and differ from other methods using a split scheme in their analytical treatment of high frequency oscillations. Their benefit will be demonstrated on some biologically interesting examples, especially proteins. b) Further development and use of the combination of molecular dynamics methods, normal mode vibrational analysis, and quasiharmonic analysis of proteins in solutions for studying protein hydration. c) Further development and use of QM/MM methods, which allow computer simulations using a combination of a classical and quantum potential, allowing for more accurate simulations of large biological molecules at the ab initio level. d) Further development of computationally efficient methods for determining the time-dependent electronic structure of molecules based on the Kohn-Sham formulation of the density functional theory in which the electron density is calculated using single-electron Green's functions. Since the most computationally demanding operations are only computed locally, the speed of calculating the electronic structure of molecules is significantly increased. e) Further development and application of quantum chemical and classical approaches for calculating reaction mechanisms, especially calculating the ionic reactions of isocyanides. We will determine whether it is generally true that ionic reactions of isocyanides proceed as multicomponent chemical reactions. No such studies have been performed using computational methods and it is not possible to study this problem experimentally. f) Further development and use of the RISM formalism, which is based on the theory of integral equations, which will, in combination with Monte Carlo simulations, enable a deeper understanding of the relationship between the properties of molecules and the macroscopic properties of the matter they form. These relationships are given by distribution functions that are obtained by using the theory of integral equations. g) Further development of new and effective network topologies for connecting personal computers into clusters and that will enable fast parallel performance for molecular dynamics programs and allow for an effective implementation of the newly developed methods on parallel computers.
Significance for science
New developments in molecular dynamics integration methods can find wide applications in computer simulations of the structure and dynamics of biological macromolecules in contributing to higher precision and economy of computation. The proposed methods use less computer time and therefore extend the applicability of simulation strategies to larger systems and enable higher precision calculations. A particularly promising consequence of the enhanced possibilities offered by the proposed methods is the inclusion of solvent effects. This requires a major computational effort in present schemes, thus strongly limiting the number of solvent molecules that can be included in the simulation. The new methods should therefore highly improve on this important aspect of molecular simulations. From the practical point of view, protein engineering should benefit from the predicting capacity of the molecular dynamics simulation methods that would become more economical. Since protein engineering is a promising area of development in at least two institutes in Slovenia, the benefit of this research is obvious. The development of molecular dynamics algorithms as presented could be included as a software module in computer programs commonly used for molecular modeling of biological systems. The ability to improve the predicting power of methods used in the simulation of proteins is of paramount importance for protein engineering and is sealing the relation between the higher order structure of proteins and their biological function. With the prospects offered by the Human Genome Project, the need for predictions of the higher order structure of proteins from the primary structures, which will become available in large numbers, will sharply increase. The research carried out following this proposal is of great importance to the development of modern simulation techniques which hold the promise to greatly increase our ability to simulate large macromolecular systems with a reasonable amount of computational effort. It is expected that the product of this research effort will be added to the CHARMM (Chemistry at HARvard for Macromolecular Mechanics) program and distributed for use by others throughout the world.
Significance for the country
The purpose of the program is to develop, improve, and apply the computational methods for molecular dynamics simulations in the study of the structure and dynamics of biological macromolecules, such as proteins. The project will focus on specific problems of molecular biology, on code development and application, and also on its parallel implementation. An important component of the project will involve close collaboration with the leading laboratories in this research field. For the studies that we perform as part of our research, we develop and use molecular modeling methods, which have lead to many good results. We have also developed and built several computer systems call CROW (Columns and Rows of Workstations; VRANA in Slovenian). These systems are clusters of personal computers connected with high-speed networking. Besides the members of our program group, collaborators from other program groups and laboratories at the National Institute of Chemistry and from other institutions, such as the Jožef Stefan Institute, Faculty of Medicine, Faculty of Mathematics and Physics, Biotechnical Faculty, Faculty of Pharmacy, Faculty for Computer and Information Science, and others, also use these clusters. We also use these computer systems for computer modeling and other computations for satisfying obligations under contracts with the industry, e.g., Lek, Krka, and others. In addition to all of the above, we offer assistance to users with the installation and use of molecular modeling programs, as well as the installation and maintenance of computers and networks used for molecular modeling. The National Institute of Chemistry, Center for Molecular Modeling and the RIKEN Yokohama Institute, Japan signed a three-year agreement on scientific collaboration on 6.nov. 2006. With our scientific quality and other international activity (editor of an international scientific journal, participating and lecturing at international conferences, universities, and institutions) we increase our country's international recognition as well as sustain and enhance its national identity.
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