About

This site is created only for teaching purposes. The site is maintained by H Kamberaj. If you have any remarks/comments, please contact me at km.ude.ubi|jarebmakh#km.ude.ubi|jarebmakh

I am an Associate Professor at International Balkan University, Skopje. My teaching interests include Information Theory, Electromagnetic Theory, General Physics, Algorithms, Discrete Mathematics, and Computer Programming. In addition, I work as an Adjunct Associate Professor at the State University of Tetovo, where I teach these modules: Theoretical Physics, Statistical Physics, Electrodynamics, and Medical Physics. I am also involved in research activities in the area such as Biophysics, Bioinformatics, Machine Learning, and Bio-inspired optimization.

Teaching Philosophy Statement: here

Research Projects Statement: here

Books:

  1. H. Kamberaj, Foundations of General Physics. Mechanics, Springer Nature, (To be Submitted), 2019. (Download the Table of Contents here)
  2. H. Kamberaj, Molecular Dynamics Simulations in Statistical Physics. Theory and Applications, Springer (Series in Scientific Computation), 2019. https://www.springer.com/gp/book/9783030357016
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A list of selected peer-reviewed publications:

2019-Present

  1. H. Kamberaj, Nanoparticle clusters using grand canonical and grand isothermal-isobaric ensemble molecular dynamics simulations, to be submitted, 2019.
  2. Dh. Nebiu and H. Kamberaj, Symbolic Information Flow Measurement (SIFM): A Software for Measurement of Information Flow Using Symbolic Analysis, bioRxiv 785782; doi: https://doi.org/10.1101/785782, September 2019.
  3. B. Rahmani and H. Kamberaj, Automation of (Macro)molecular Properties Using a Bootstrapping Swarm Artificial Neural Network Method: Databases for Machine Learning, bioRxiv 779496; doi: https://doi.org/10.1101/779496, September 2019.
  4. H.Kamberaj, Advanced Methods Used in Molecular Dynamics Simulation of Macromolecules, in Mechanical Design, Materials and Manufacturing, Nova Science Publishers, Inc., pages 57-133, 2019 (ISBN: 978-1-53614-791-9) PDF file. (https://novapublishers.com/shop/mechanical-design-materials-and-manufacturing/)

2014-2018

  1. H. Kamberaj, Faster Protein Folding Using Enhanced Conformational Sampling of Molecular Dynamics Simulation, Journal of Molecular Graphics and Modelling, 81, 32-49, 2018 (https://www.sciencedirect.com/science/article/pii/S109332631730654X).
  2. R.Izairi and H. Kamberaj, Comparison Study of Polar and Nonpolar Contributions to Solvation Free Energy, Journal of Chemical Information and Modeling, 57 (10), 2539-2553, 2017, http://dx.doi.org/10.1021/acs.jcim.7b00368
  3. H. Kamberaj, Sampling Convergence of Collective Motions in Proteins, Journal of Applied Physical Science International, 8(3), 101-112, 2017.[Abstract]
  4. H. Kamberaj, Replica Exchange Using q-Gaussian Swarm Quantum Particle Intelligence Method, Engineering and Applied Sciences, 1(2), 20-25, 2016.
  5. H. Kamberaj, Conformational Sampling Enhancement of Replica Exchange Molecular Dynamics Simulations Using Swarm Particle Intelligence, The Journal of Chemical Physics, 143, 124105, 2015.[pdf]
  6. H. Kamberaj, Q-Gaussian Swarm Quantum Particle Intelligence on Predicting Global Minimum of Potential Energy Function, Applied Mathematics and Computation, 229, 94-106, 2014.

2009-2013

  1. J. Spiriti, H. Kamberaj, A. de Graff, M. F. Thorpe and A. van der Vaart, DNA bending through large angles is aided by ionic screening, Journal of Chemical Theory and Computation, 8 (6), 2145–2156, 2012.
  2. J. Spiriti, H. Kamberaj, and A. van der Vaart, Development and application of enhanced sampling techniques to simulate the long-time scale dynamics of biomolecular systems, International Journal of Quantum Chemistry, 112, 33-43, 2012.
  3. H. Kamberaj, A Theoretical Model for the Collective Motion of Proteins by Means of Principal Component Analysis, Open Physics (former Central European Journal of Physics), 9(1), 96-109, 2011.
  4. H. Kamberaj and A. van der Vaart, Extracting the causality of correlated motions from molecular dynamics simulations, Biophysical Journal, 97(6), 1747-1755, 2009.
  5. H. Kamberaj and A. van der Vaart, An optimized replica exchange method for molecular dynamics simulations, The Journal of Chemical Physics, 130, 074904 2009.
  6. H. Kamberaj and A. van der Vaart, Correlated Motions and Interactions at the Onset of the DNA-Induced Partial Unfolding of Ets-1, Biophysical Journal, 96, 1307-1317, 2009.

2004-2008

  1. H. Kamberaj and A. van der Vaart, Multiple scaling replica exchange method for the efficient sampling of biomolecular systems, The Journal of Chemical Physics, 127, 234102-7, 2007.
  2. H. Kamberaj, R.J. Low and M.P. Neal, “Correlation between molecular chirality and helical twisting power. A computer simulation study”, Molecular Physics, 104(3), 335-357, 2006.
  3. M.P. Neal, H. Kamberaj and R.J. Low, “Some calculations of molecular chirality”, Mol. Cryst. Liq. Cryst., 439, 1937-1943, 2005.
  4. H. Kamberaj, R.J. Low and M.P. Neal, “Molecular structure and helical twisting power”, Ferroelectrics, 315, 183-196, 2005.
  5. H. Kamberaj, R.J. Low and M.P. Neal, “Symplectic and time reversible integrators for molecular dynamics simulations of rigid molecules”, The Journal of Chemical Physics, 122(22), 224114, 2005.
  6. H. Kamberaj, M. A. Osipov, R.J. Low and M.P. Neal, “Helical twisting power and chirality indices”, Molecular Physics, 102(5), 431-446, 2004.

2001-2003

  1. H. Kamberaj, R.J. Low and M.P. Neal, “Symplectic and time reversible integrators for rigid bodies”, System Science, 29(2), 31-45, 2003.
  2. H. Kamberaj and V. Helms, “Monte Carlo simulation of biomolecular systems with BIOMCSIM”, Computer Physics Communications, Vol. 141 (3), 375-402, 2001.

Master Thesis:

  1. Blerta Rahmani (2018-Present), Dynamics and their time scales in complex macromolecular systems, State University of Tetovo.
  2. Festim Kamberi (2018-2019), Development of a Web-Based University Career Network Center, International Balkan University.
  3. Dhurata Nebiu (2017-2018), Local and Average Transfer Entropy as an Information Flow Measure, International Balkan University.
  4. Granit Nebiu (2017-2018), The Semantics of Web Design and Development, International Balkan University.
  5. Redona Izairi (2016-2018), Study of Protein-Protein Interactions Using Molecular Dynamics Simulation Methods, State University of Tetovo.

Undergraduate Thesis:

  1. Yusuf Furkan Gurler, Nerves and Muscle Cells, International Balkan University, R. of North Macedonia, 2019.
  2. Berkay Karadeniz, Student Information System Using HTML/PHP, International Balkan University, R. of North Macedonia, 2019.
  3. Harun Shaban, File sharing system, International Balkan University, R. of North Macedonia, 2019.
  4. Lirim Dauti, Developing Mobile Applications Using Xamarin, International Balkan University, Skopje, R. of Macedonia, 2018.
  5. Merjem Hoxha, Website design and development using C#, International Balkan University, Skopje, R. of Macedonia, 2018.
  6. Ridvan Suleyman, Study of parallel processing in distributed environment machines using C++ programming language, International Balkan University, Skopje, R. of Macedonia, 2018.
  7. Edon Selimi, Application of a web-based service for analyzing the performance of the IBU academic staff, International Balkan University, Skopje, R. of Macedonia, 2018.
  8. Amina Kofrc, Online Database Management System, International Balkan University, Skopje, R. of Macedonia, 2018.
  9. Gazmend Rexhepi, IBU Study Curricula - Web Based Application, International Balkan University, Skopje, R. of Macedonia, 2018.
  10. Izudin Mamudi, Library Database Management System, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2018.
  11. Donika Rexhepi, Fundamental Concepts of Classical Cryptosystems, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2017.
  12. Haris Zenovic, Design and development of a web-based platform for teaching and learning, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2017.
  13. Festim Kamberi, Optimized University Students and Courses Information System, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2017.
  14. Argjent Haliti, Graphical User Interface for Data Analysis with Visual Molecular Dynamics Program Using Tcl/Tk, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2016.
  15. Skofiar Kamberi, Design and Application of a Database for Students, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2015.
  16. Redona Izairi, Calculations of the Electronic Properties of Molecules using Computational Quantum Mechanics Models, Department of Physics, State University of Tetovo, Tetovo, R. of Macedonia, 2014.

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