As a complex systems simulation research group, our work continues in line with two goals. Our main goal is to develop innovative algorithms using statistical mechanics. Our second goal is to understand the results obtained by simulation techniques with big data analysis techniques.
Molecular dynamic simulation is one of the most popular computational tools that has been widely applied to biological macromolecules such as proteins to understanding of folding and aggregation mechanism. Determination of such properties of macromolecules will be an important contribution especially for drug design. The aggregation, self-assembly such as the formation of amyloid fibers from the monomer has an important role in the understanding the causes of today's most important neurological diseases such as Alzheimer's, Huntington's disease.
In terms of statistical mechanics, the numerical calculations of physical quantities are based on how the phase space of the system is examined. In order to create correct statistics, the phase space of the sample such as protein must be sampled as accurately. This is indeed difficult task when the degrees of freedom of protein are increased. Creating or sampling of phase space of the system, two basic approaches can be considered in simulation studies. The first is to create an effective algorithm that will accurately describe the system by making a completely new approach, and the second is to increase the effectiveness of the current method by creating the large parts of the phase space in the large time scale simulation using supercomputer, GPU systems.
• Server with 8 Nodes x 4 Cores
* Server with GPU
,
• Prof. Dr. Fatih Yaşar
• Assoc. Prof. Dr. Mehmet Dilaver
• Res.Asist.. Özgür Güven
• Recep Kesin
• Protein-Ligand Interactions with Quantum Mechanical/Molecular Mechanical Simulation Techniques
• Macromolecules with Hybrid Simulation Techniques
• 2015 - 2018 Replica Exchange Tunneling Method and Applications, Project Supported by Higher Education Institutions, YAŞAR F. (Executive)
• 2015 - 2017 Organizing the International Workshop, called From Computational Biophysics to System Biology CBSB2016, Project Supported by Higher Education Institutions, DİLAVER M. (Executive) , YAŞAR F.
• 2015 - 2015 Hybrid MC/MD simulation of implicit Trpcage mini-protein, Higher Education Institutions Supported Project, YAŞAR F. (Executive)
• 2018 - 2019 Diagnosis of Irradiated Sugar and Sugar Containing Dry Foods by Electron Spin Resonance ESR Technique and Characterization of Radical Intermediate Products Formed by Irradiation in These Foods. Project Supported by Higher Education Institutions, POLAT M. (Executive), DİLAVER M.
• 2015 - 2017 Organizing the International Workshop called From Computational Biophysics to System Biology CBSB2016. Project Supported by Higher Education Institutions, DİLAVER M. (Executive), YAŞAR F.
Response to "Comment on 'Replica-exchange-with-tunneling for fast exploration of protein landscapes"' [J. Chem. Phys. 145, 057101 (2016)]. YAŞAR F. , Bernhardt N. A. , Hansmann U. H. E., JOURNAL OF CHEMICAL PHYSICS, cilt.145, 2016
Replica-exchange-with-tunneling for fast exploration of protein landscapes. YAŞAR F. , Bernhardt N. A. , Hansmann U. H. E., JOURNAL OF CHEMICAL PHYSICS, cilt.143, 2015
ESR investigation on the potential use of potassium citrate as a dosimeter material. KORKMAZ G. , DİLAVER M. , POLAT M., APPLIED RADIATION AND ISOTOPES, cilt.153, 2019.
Interconversion between Serum Amyloid A native and fibril conformations, F. Yasar, M.S. Sheridan and U.H.E. Hansmann, ,ACS Omega, 7 (2022), 12186,
Resolution Exchange with Tunneling for Enhanced Sampling of Protein Landscapes, F. Yasar, A.J. Ray and U.H.E. Hansmann,, Phys. Rev. E, 106 (2022), 015302.