Following his Trial Lecture on “Non-equilibrium molecular dynamics simulations and derivation of kinetics”, Dr. Samiran Sen defended his PhD thesis physically before a public audience at the Faculty of Mathematics and Natural Sciences at the University of Oslo. The defence was live streamed for everyone else.
The evaluation committee consisted of Professor Stefano Vanni, Department of Biology, University of Fribourg, Switzerland (1. Opponent), Associate Professor Zoe Cournia, Biomedical Research Foundation, Academy of Athens, Greece (2. Opponent), and Researcher Erik Ingemar Tellgren, Department of Chemistry, University of Oslo, Norway (internal member). Dr. Sen’s work was supervised by Professor Michele Cascella, Department of Chemistry, University of Oslo (main supervisor) and Researcher Irep Gözen, Centre for Molecular
Medicine Norway, University of Oslo (co-supervisor). The Chair of Defence was Professor Harald Walderhaug, Department of Chemistry, University of Oslo.
Conferral Summary:
Complex molecular motion can be investigated to reveal valuable information about their nature using the laws of physics with the strategy of molecular dynamics. To understand the dynamics of mesoscale systems like membranes, proteins, and other large biological molecules, Sen and others employ a Hamiltonian hybrid particle-field approach. The work establishes this method in a rigorously energy-conserving scheme.
By accounting for interactions between molecules by a slowly varying density field instead of particle-particle interactions, a computationally cost-effective method is obtained. Ergo, larger and more biologically relevant systems can be simulated. This method operates at scales of micrometers and milliseconds without losing molecular resolution. With the new features by Sen, it is now possible to simulate soft matter
systems under physiological conditions of constant external pressure.
The current work focuses on the recent theoretical and computational developments, largely in the direction of pressure controlled simulations, as well as in establishing a stronger foundation of the underlying theory.
The dissertation proffers important developments that bridge scientific and life-sustaining interests, entering into a realm of simulating more realistic biological soft matter systems, thereby facilitating a reality of newer and better design of materials and drug-delivery mechanisms.
The thesis can be found at: https://hdl.handle.net/10852/102382
