Research Interests
- Force-field parametrization for ultra–coarse-grained (UCG) biomolecular models
- Generative backmapping of proteins from coarse resolutions
- Computational modeling of fibrinogen/fibrin and thrombogenesis; polymerization and surface effects
- Scientific software, HPC/GPU acceleration, and distributed simulation workflows
Publications
Journal Papers
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Learning coarse-grained force fields for fibrinogenesis modeling
Computer Physics Communications 295, 108964, 2024 • cites: 5
Z. Zhang, G. Kementzidis, P. Zhang, L. Zhang, J. Kozloski, A. Hansen, M. Rafailovich, M. Simon, Y. Deng -
Modelling of SARS-CoV-2 spike protein structures at varying pH values
Molecular Simulation 50(17–18), 1540–1552, 2024 • cites: 3
Z. Niu, G. Kementzidis, P. Zhang, Z. Zhang, B. Essuman, K. Hasegawa, M. Rafailovich, M. Simon, B. Aktas, E. Papadopoulos, Y. Deng -
Simulations of pH and Thermal Effects on SARS-CoV-2 Spike Glycoprotein
Frontiers in Molecular Biosciences 12, 1545041, 2025 • cites: 2
Z. Niu, G. Kementzidis, M. Rafailovich, M. Simon, E. Papadopoulos, B. Aktas, Y. Deng -
Unraveling the molecular mechanism of in-situ surface-initiated thrombogenesis
Journal of Thrombosis and Haemostasis, 2025
A. Hansen, G. Kementzidis, B. Essuman, Z. Niu, J. Sheriff, V. Chernyshenko, Y. Deng, M. Rafailovich, D. Galanakis
Conference & Workshop Papers
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An Iterative Framework for Generative Backmapping of Coarse Grained Proteins
ICML 2025 Workshop on Generative AI and Biology, 2025 — Workshop
G. Kementzidis, E. Wong, J. Nicholson, R. Xu, Y. Deng -
APOD: Adaptive PDE-Observation Diffusion for Physics-Constrained Sampling
ICML 2025 Workshop on Assessing World Models, 2025 • cites: 2 — Workshop · ICML page
R. Xu, H. Wang, G. Kementzidis, C. Si, Y. Deng
Preprints
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An AI-Driven Framework for Discovery of BACE1 Inhibitors for Alzheimer’s Disease
bioRxiv: 2024.05.15.594361, 2024 • cites: 5
E. Xie, K. Hasegawa, G. Kementzidis, E. Papadopoulos, B. H. Aktas, Y. Deng
Talks
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Multiscale Modeling of the Structure and Dynamics of Soluble Fibrin
28th Workshop of the International Fibrinogen Research Society (IFRS), Corfu, Greece -
In silico Studies of Fibrinogen-PLA Interactions and Implications for Thrombosis
27th Workshop of the International Fibrinogen Research Society (IFRS), Esbjerg, Denmark