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Post-Doctoral Researcher
Research
Kasia graduated and received the PhD degree (in Physical and Theoretical Chemistry) from the Chemistry Department of the University of Gdansk, Poland. Her PhD project was concentrated on the development of physics-based functional forms of the side chain - side chain interaction potential for the UNRES united-residue force field for protein-structure prediction. She used large-scale umbrella-sampling molecular dynamics simulations and weighted-histogram analysis method (WHAM) to determine the respective potentials of mean force.
She is a researcher with strong computational skills in modeling, programming, scripting, with analytical skills in planning and designing projects by using statistics and data analysis software. She has an extensive postgraduate experience, having worked in the laboratories of Prof. Jooyoung Lee (Korea Institute for Advanced Studies, South Korea), Prof. Michael Feig (Michigan State University, USA), and Dr Willie Taylor (MRC National Institute for Medical Research, UK). She is fully conversant with all major computational tools and techniques required to conduct research mainly in the area of protein structure prediction, refinement and dynamics, protein/drug design, parameter optimization of potential energy function and protein-DNA interaction.
She joined to the Centre for Natural Inspired Engineering in March 2015. The main objective of her current work are (i) to understand the mechanisms behind the nano-confinement effects witnessed experimentally in biological and bio-inspired materials and (ii) to design bio-inspired catalysts and separation systems for chemical, pharmaceutical and medical applications. These goals will be achieved by carrying out molecular dynamics simulations with explicit solvent by examining the structure and behaviour between entrapped enzyme molecules ( more than one) and mesoporous silica. The knowledge of the interplay between the adsorbed proteins and mesoporous materials will allow us to assess whether the process is effected by kinetics or thermodynamics.
Research interests
鈥⒙犅犅� Enzyme confinement
鈥⒙犅犅� Protein/drug design
鈥⒙犅犅� Protein structure prediction
鈥⒙犅犅� Quantitative Structure Activity Relationships ( QSAR)
鈥⒙犅犅� Protein-ligand docking
鈥⒙犅犅� Protein-DNA interactions
鈥⒙犅犅� Potential parameter optimization
鈥⒙犅犅� Protein folding mechanisms: MD, MC simulations
鈥⒙犅犅� Cluster analysis
鈥⒙犅犅� Scoring functions
Education
PhD in Physical and Theoretical Chemistry, University of Gdansk, Poland
MSc in Chemistry, University of Gdansk, Poland
Postgraduate Certificate in Mathematics and Computer Sciences, University of Gdansk, Poland
