Biophysics

Coarse-grained model of archaeal division
Coarse-grained model of archaeal division

I am currently an IST-BRIDGE postdoctoral fellow, a part of Marie Curie-Sklodowska Action, in the group of Anđela Šarić at the Institute of Science and Technology Austria (ISTA).

The Šarić group uses coarse-grained modelling to understand a large variety of processes in biological cells, including protein aggregation, filament treadmilling, constriction of the actomyosin ring and microtubule growth in cell division. My project focuses on membrane remodelling and cell division via the action of elastic filament. These filaments represent proteins from the ESCRT-III family and their homologues, which are involved, e.g. in the division of Sulfolobus acidocaldarius or the scission of the eukaryotic cytokinetic bridge.

Quantum chemical dynamics

Water octamer
Water octamer

As a PhD Student in the Althorpe group at the Department of Chemistry, University of Cambridge, I carried out research in the field of quantum chemical dynamics — we investigate the motion of atomic nuclei.

The Althorpe group is a theoretical and a computational group interested in the development of new computational methods for chemical dynamics and physical theories underlying them. The most recent theory originating in our group is the theory of Matsubara dynamics, due to Hele, Willatt, Muolo and Althorpe.1 It combines exact quantum statistics with classical dynamics making it one of the best descriptions for calculation of quantum time correlation functions. However, the complex phase present in this theory makes it impractical as method, when implemented naively. Nevertheless, Matsubara dynamics is a rigorous theory underpinning most other path integral based chemical dynamics methods, like Ring Polymer Molecular Dynamics (RPMD) and Centroid Molecular Dynamics (CMD). It has already proved useful in the development of new practical methods with the recent introduction of Quasi-Centroid Molecular Dynamics (QCMD) by Trenins and Althorpe.2 For more information see our group website

In my PhD I focused on the chemical dynamics of systems attached to baths. Baths are used as simplified models of the environment of the calculated system. In the first year of my PhD I worked on the Hierarchical Equations of Motion (HEOM), which is a method that allows numerically exact time propagation of a system attached to a harmonic bath. Some of my results can be found in my first-year report. In the rest of my PhD I developed a novel way of simulating Matsubara dynamics of a system coupled to a harmonic bath. This not only allowed the inclusion of a vast number of the harmonic bath degrees of freedom, but also solved the complex phase problem for sufficiently damped systems. This allowed, among others, the very first Matsubara calculation involving non-linear position operators.3,4

  1. T. J. H. Hele, M. J. Willatt, A. Muolo and S. C. Althorpe, J. Chem. Phys., 2015, 142, 134103, doi: 10.1063/1.4916311 ↩

  2. G. Trenins, M. J. Willatt and S. C. Althorpe, J. Chem. Phys., 2019, 151, 054109, doi: 10.1063/1.5100587 ↩

  3. Adam Prada, Eszter S. Pós, Stuart C. Althorpe; J. Chem. Phys. 21 March 2023; 158 (11): 114106. doi: 10.1063/5.0138250 ↩

  4. Adam Přáda, “Dissipative Matsubara Dynamics”, PhD Thesis, University of Cambridge, 2023, doi: 10.17863/CAM.95949 ↩