Project

Development of computational algorithms to predict the kinetics of biophysical molecular processes at the molecular scale

Code
DOCT/002041
Duration
30 November 2023 → 21 September 2025 (Ongoing)
Doctoral researcher
Research disciplines
  • Engineering and technology
    • Molecular and cellular biomechanics
    • High performance computing
    • Modelling and simulation
Keywords
Molecular Dynamics path sampling rare events Kinetic Monte-Carlo simulations Computational chemistry
 
Project description

My research involves the improvement and development of molecular dynamics simulation strategies to perform computational experiments on biophysical processes. This allows to achieve insights with atomic resolution on these processes, such as membrane permeation or a drug molecule binding to a protein. The processes we focus on are those of (cancer) drug molecules that reach a target, such as a protein binding site or the interior of a cell, where we usually want to compute the drug residence time or the permeation rate constant. 

A significant challenge of these processes is the vast difference between timescales, which makes our computational experiments extremely demanding. My simulations are therefore based on the path sampling methodology, as it makes use of Metropolis Monte Carlo sampling in path space to discover and analyze rare events in these complex biological systems. Moreover, path sampling allows studying the exact kinetics of the processes we are simulating. 

The central goal of my research is further developing the path sampling methodology to evaluate the kinetics and efficacy of certain drug molecules using molecular dynamics simulations and contribute to the field of (cancer) drug discovery in this way.