Theses#
PhD#
Elham Kianiharchegani, Data-Driven Exploration of Coarse-Grained Equations: Harnessing Machine Learning, PhD thesis, August 2023. Department of Mathematics, Collaborative Graduate Program in Scientific Computing.
Mahmood Mazarei, Modelling cell population growth, PhD thesis, April 2023. Department of Physics and Astronomy.
Sepideh Soltani, Computational modeling of melanin aggregation, PhD thesis, April 2023. Department of Physics and Astronomy.
Cecilia Chávez-García, A computational study on a globular protein and an intrinsically disordered protein, PhD thesis, Dec 2021. Department of Chemistry, Collaborative Graduate Program in Scientific Computing.
Pranav Madhikar, Molecular dynamics modeling of the mechanics of cells, PhD thesis, May 2019. Department of Mathematics and Computer Science.
Yuriy Khalak, Model Development: Reproducing Properties of Water, PhD thesis, February 2019. Department of Mathematics and Computer Science.
Behnaz Bagheri, Multiscale modeling of excitations in polymeric systems, PhD thesis, Jan 2017. Department of Mathematics and Computer Science
Bin Liu, Molecular Dynamics Studies of Lipid and Bilayer Systems, PhD thesis, July 2016. Department of Chemistry.
Mona Habibi, A Molecular Simulations Study on Micelle Fragmentation and Wetting in Nano-confined Channels, PhD thesis, January 2014. Department of Applied Mathematics.
Anna Mkrtchyan, A Single Cell Based Model for Cell Divisions with Spontaneous Topology Changes, PhD thesis, December 2013. Department of Applied Mathematics.
Elio A. Cino, Experimental and computational analysis of the structure and dynamics of intrinsically disordered proteins, PhD thesis, Nov 2012. Department of Biochemistry.
Susanna Hug, Molecular Dynamics Simulations of Peptide-Mineral Interactions, PhD thesis, April 2012. Department of Applied Mathematics.
Niloufar Faghihi, Phase Field Crystal Approach to the Solidification of Ferromagnetic Materials, PhD thesis, July 2012. Department of Applied Mathematics.
Amir Mohsen Pourmousa, Molecular Dynamics Studies of Interactions of Phospholipid membranes with Dehydroergosterol and Penetrating Peptides, PhD thesis, December 2011. Department of Applied Mathematics.
Markus S. Miettinen, Computational Modeling of Cationic Lipid Bilayers in Saline Solutions, PhD thesis, June 2010. Department of Physics.
Lei Dong, Dielectric properties of colloidal suspensions, PhD thesis, Jan. 2009. Department of Physics.
Wei Zhao, Molecular modeling of charged membrane systems, PhD thesis, Nov. 2006. Department of Electrical and Communications Engineering, Laboratory of Computational Engineering.
Petri Nikunen, Studies of surface diffusion and dissipative particle dynamics, Mar. 2006, PhD thesis. Department of Electrical and Communications Engineering, Laboratory of Computational Engineering.
Teemu Leppänen, Computational studies of pattern formation in Turing systems, PhD thesis, Nov. 2004. Department of Electrical and Communications Engineering, Laboratory of Computational Engineering.
MSc#
Carter J. Wilson, A Highly Charged Topic: intrinsically disordered proteins and protein \(\text{p}K_\text{a}\) calculations, April 2023. Department of Mathematics.
Megan Chang, Elucidating the Structural and Dynamical Properties of the Intrinsically Disordered Protein Nrf2 Using Molecular Dynamics Simulations, MSc thesis, Dec 2021. Department of Biohemistry.
Kalle Tuomi, Puhtaiden ja vettä sisältävien polymeerien faasimuutoslämpötilojen ja vetysitoutumisen määrittäminen molekyylidynamiikkasimulaatioilla, MSc thesis, Dec 2021. Tampere University (Finland), Department of Chemistry.
Steven Silber, SymPhas: A modular API for phase-field modeling using compile-time symbolic algebra, MSc thesis, Jul 2021. Department of Applied Mathematics.
Sarai Guerrero, Saponin Penetration and Interactions with Membranes, MSc thesis, Nov 2019. Department of Chemistry.
Mirko Bagnarol, Simulation of radiation in cells with CellSim3D, MSc thesis, Oct 2019. Department of Physics.
Pranav Madhikar, Studying the Properties of Cellular Materials with GPU Acceleration, MSc thesis, May 2015. Department of Chemistry.
Ali Madani, Modeling and Analysis of the Buckling Phenomena in the Homogeneous and Heterogeneous Biomembranes, MASc thesis, July 2013. Department of Mechanical and Mechatronics Engineering.
Alex Marshall, Molecular Dynamics Studies of Water Flow in Carbon Nanotubes, MSc thesis, Aug 2012. Department of Applied Mathematics.
Sepideh Soltani, Molecular Dynamics Analysis of the Behaviour of Prolyl Oligopeptidase (POP) in the Presence of Z-Pro-Prolinal Inhibitor, MSc thesis, December 2011. Department of Applied Mathematics.
Jason O’Young, Molecular dynamics and FRAP analysis of protein-crystal interactions, MSc thesis 2008. Department of Biochemistry.
Markus S. Miettinen, From molten globule to swollen coil: Simulations of a lone polymer chain in an explicit solvent, MSc thesis, Nov. 2004. Department of Electrical and Communications Engineering, Laboratory of Computational Engineering.
Teemu Leppänen, Spatial pattern formation in Turing systems, Dec. 2001, MSc thesis. Department of Electrical and Communications Engineering, Laboratory of Computational Engineering.