Publications

Books

7. H. Kamberaj, Optics in Physics, 2023/2024.

6. H. Kamberaj, Computer Simulations in Molecular Biology. From Quantum Mechanics to Molecular Mechanics, Springer Nature, Scientific Computation Series, ISBN-10: ‎ 3031348389, ISBN-13: ‎ 978-3031348389, 1st ed. 2023 edition (October 19, 2023).

5. H. Kamberaj, Introduction to Algorithms: Learning Algorithms by Examples, Lambert Academic Publishing, 978-620-6-15263-7, March 29, 2023.

4. H. Kamberaj, Relativistic theory of mechanics and electromagnetism, Lambert Academic Publishing, 978-620-5-50898-5, October 6, 2022. https://www.morebooks.shop/shop-ui/shop/product/9786205508985

3. H. Kamberaj, Electromagnetism: With Solved Problems, Springer Physics, Undergraduate Texts in Physics Series, 2022. https://link.springer.com/book/9783030967796

2. H. Kamberaj, Classical Mechanics, De Gruyter, 2021. https://www.degruyter.com/document/isbn/9783110755824/html

1. H. Kamberaj, Molecular Dynamics Simulations in Statistical Physics. Theory and Applications, Springer Nature (Series in Scientific Computation), April 2020. https://www.springer.com/gp/book/9783030357016

Peer-reviewed articles

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2019-Present

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1. Hiqmet Kamberaj, Viewpoint: The Physics in the New Era of Computing. European Scientific Journal, ESJ, 19(15), 1, 2023. https://doi.org/10.19044/esj.2023.v19n15p1
2. Rabie A. Ramadan, Ahmed Y. Khedr, Kusum Yadav, Eissa Jaber Alreshidi, Md Haidar Sharif, Ahmad Taher Azar & Hiqmet Kamberaj, Convolution neural network based automatic localization of landmarks on lateral x-ray images. Multimed Tools Appl (2022). https://doi.org/10.1007/s11042-021-11596-3
3. H. Kamberaj, Random Walks in a Free Energy Landscape Combining Augmented Molecular Dynamics Simulations with a Dynamic Graph Neural Network Model, Journal of Molecular Graphics and Modelling, 114, 108199, 2022, https://doi.org/10.1016/j.jmgm.2022.108199.(https://www.sciencedirect.com/science/article/pii/S109332632200078X)
4. Ramadan, Rabie A. and Sharif, Md. Haidar and Alreshidi, Eissa Jaber and Sharif, Md. Haris Uddin and Ince, Ibrahim Furkan and Kamberaj, Hiqmet and Khedr, Ahmed Y., Energy Coherent Fog Networks using Multi-Sink Wireless Sensor Networks, in IEEE Access, do: 10.1109/ACCESS.2021.3135311.
5. D. Rahmani and H. Kamberaj, The Capsule – An Artificial Intelligence Powered Chatbot in Human Resources Management Systems, IBU International Journal of Technical and Natural Sciences, 2, 53-69, 2021.
6. M. Gurboga, G. Kugu, H. Kamberaj and O. Mutlu, Identification of Benzamide Inhibitors for Histone Deacetylase 1 from Babesia and Theileria Species by High-Throughput Virtual Screening and Molecular Dynamics Simulations, Parasitology Research, 120, 2175, 2021.
7. M. Hoxha and H. Kamberaj, Automation of Some Macromolecular Properties Using a Machine Learning Approach, Machine Learning: Science and Technology, 2, 035016, 2021.
8. H. Kamberaj, Heat Flow Random Walks in Biomolecular Systems Using Symbolic Transfer Entropy and Graph Theory, Journal of Molecular Graphics and Modelling, 104, 107838, 2021.
9. Dh. Nebiu and H. Kamberaj, Symbolic Information Flow Measurement (SIFM): A Software for Measurement of Information Flow Using Symbolic Analysis, SoftwareX, 11, 100470, 2020.
10. M. Hoxha, B. Rahmani, H. Kamberaj, A database used for automation of molecular properties using machine deep-learning approach, Bulletin of Natural Sciences, 28, 62-80, 2019.
11. 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/)

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2014-2018

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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.

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2009-2013

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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.

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2004-2008

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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.

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2001-2003

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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. Hixhrete Demiri (2021-2023), Mathematical Interpretation of Some Physical Concepts, State University of Tetovo.
2. Sara Ismail (2021-2022), Computational methods for analyzing Next Generation Sequencing Data, International Balkan University.
3. Xheneta Veseli (2022-2022), Inventory Management System, International Balkan University.
4. Muhammed Shabani (2021-2022), Deep Learning, Machine Learning and Artificial Intelligence – General Assessment and their Relationships, International Balkan University.
5. Damir Rahmani (2020-2021), The Capsule- An Artificial Intelligence Job Interviewer, International Balkan University.
6. Blerta Rahmani (2018-2020), Dynamics and their time scales in complex macromolecular systems, State University of Tetovo.
7. Festim Kamberi (2018-2019), Development of a Web-Based University Career Network Center, International Balkan University.
8. Dhurata Nebiu (2017-2018), Local and Average Transfer Entropy as an Information Flow Measure, International Balkan University.
9. Granit Nebiu (2017-2018), The Semantics of Web Design and Development, International Balkan University.
10. Redona Izairi (2016-2018), Study of Protein-Protein Interactions Using Molecular Dynamics Simulation Methods, State University of Tetovo.

Undergraduate Thesis

1. Besir Amet, A modern web application structure, International Balkan University, North Macedonia, 2023.
2. Jetmir Bediu, The art of computer graphics, International Balkan University, North Macedonia, 2023.
3. Kebir Asim, Web 3.0 Applications and Metaverse, International Balkan University, North Macedonia, 2022.
4. Ajsha Hodovic, Web Application Security, International Balkan University, North Macedonia, 2022.
5. Jon Imeri, Cryptocurrency, International Balkan University, North Macedonia, 2022.
6. Eren Ahmed, Building Modern Apps in Android Development, International Balkan University, Skopje, North Macedonia, 2022.
7. Doruntina Ismaili (Project II), Website Design, International Balkan University, Skopje, North Macedonia, 2022.
8. Buen Ibish, Advanced Minesweeper Program, International Balkan University, Skopje, North Macedonia, 2022.
9. Ibrahim Etem, Design and Simulation of Circuits using LTspice Software, International Balkan University, Skopje, North Macedonia, 2022.
10. Metin Sirri Aksoy, Smart home system in arduino/Car Rental System with Html-Css-PHP, International Balkan University, Skopje, North Macedonia, 2022.
11. Vigan Ibrahimi, Online quiz application, International Balkan University, R. of North Macedonia, 2021.
12. Agon Junuzi, Development of a web-based database for the employees of an institution, International Balkan University, R. of North Macedonia, 2021.
13. Rasim Ramadani, Structure of a modern web application, International Balkan University, R. of North Macedonia, 2021.
14. Enes Ozer, Data Filtering and Text Cleaning, International Balkan University, R. of North Macedonia, 2021.
15. Munur Ceyhun Yaman, Stock Tracking Automation Website, International Balkan University, R. of North Macedonia, 2021.
16. Burhan Ismani,Recipe mobile app, International Balkan University, R. of North Macedonia, 2021.
17. Avni Thaci, Restaurant Management System, International Balkan University, R. of North Macedonia, 2021.
18. Abdil Cilafi, Banking System, International Balkan University, R. of North Macedonia, 2021.
19. Emine Halili, Security Issues of Cloud-Based Storage, International Balkan University, R. of North Macedonia, 2020.
20. Haris Jakupi, Power Electronics used in Renewable Energy Resources, International Balkan University, R. of North Macedonia, 2020.
21. Brajan Emini, The Impact of Frameworks in Building E-commerce Sites, International Balkan University, R. of North Macedonia, 2020.
22. Yll Xheladini, A Virtual Tour Guide, International Balkan University, R. of North Macedonia, 2020.
23. Gentrit Mehmeti, Social Network Application, International Balkan University, R. of North Macedonia, 2020.
24. Klei Aliaj, University Management System, International Balkan University, R. of North Macedonia, 2020.
25. Xheneta Veseli, A blog for internet-based laboratories, International Balkan University, R. of North Macedonia, 2020.
26. Vedat Shabani, Food Billing System, International Balkan University, R. of North Macedonia, 2020.
27. Vullnet Alija, Accessible Website for Robot Building, International Balkan University, R. of North Macedonia, 2020.
28. Ugur Degirmenci, A database for thermodynamics, International Balkan University, R. of North Macedonia, 2020.
29. Yusuf Furkan Gurler, Nerves and Muscle Cells, International Balkan University, R. of North Macedonia, 2019.
30. Berkay Karadeniz, Student Information System Using HTML/PHP, International Balkan University, R. of North Macedonia, 2019.
31. Harun Shaban, File sharing system, International Balkan University, R. of North Macedonia, 2019.
32. Lirim Dauti, Developing Mobile Applications Using Xamarin, International Balkan University, Skopje, R. of Macedonia, 2018.
33. Merjem Hoxha, Website design and development using C#, International Balkan University, Skopje, R. of Macedonia, 2018.
34. Ridvan Suleyman, Study of parallel processing in distributed environment machines using C++ programming language, International Balkan University, Skopje, R. of Macedonia, 2018.
35. 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.
36. Amina Kofrc, Online Database Management System, International Balkan University, Skopje, R. of Macedonia, 2018.
37. Gazmend Rexhepi, IBU Study Curricula - Web Based Application, International Balkan University, Skopje, R. of Macedonia, 2018.
38. Izudin Mamudi, Library Database Management System, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2018.
39. Donika Rexhepi, Fundamental Concepts of Classical Cryptosystems, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2017.
40. 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.
41. Festim Kamberi, Optimized University Students and Courses Information System, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2017.
42. 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.
43. Skofiar Kamberi, Design and Application of a Database for Students, Department of Information Technology, International Balkan University, Skopje, R. of Macedonia, 2015.
44. 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.