• Machine learned interatomic potentials for
solvated drug-like molecules (current work).
• Behaviour of simulated water at interfaces
and in mixtures.
• Production and use of open source, accessible
scientific software.
Publications📚
9. Total Free Energy Analysis of Fully Hydrated
Proteins,
Jas Kalayan, Arghya Chakravorty, Jim Warwicker
and Richard H. Henchman,
PROTEINS: Structure, Function, and Bioinformatics,
2022
(Paper,
Code,
)
We calculate the energy and entropy of globular proteins and
surrounding water molecules using multiscale cell correlation.
We focus on per-residue analysis of thermodynamic properties and
compare with other works.
8. Machine learning of atomic forces from quantum mechanics: An approach based on pairwise interatomic forces,
Ismaeel Ramzan, Jas Kalayan, Linghan Kong, Richard A. Bryce and Neil A. Burton,
International Journal of Quantum Chemistry, 2022
(Paper,
)
We decompose quantum chemistry derived atomic forces into invariant pairwise terms,
these are learned using artificial neural networks and predicted to perform molecular
dynamics simulations.
7. (THESIS) Computational Studies of Protein-Excipient Interactions - Thermodynamic Theory Development and Application to Solutions,
Jas Kalayan, 2021
(Paper,
)
I develop and apply new computational methods using statistical mechanics
and bioinformatics to understand the effects of small molecules
on the solubility and structural stability of biomolecules.
6. Energy–entropy method using multiscale cell correlation to calculate binding free energies in the SAMPL8 host–guest challenge,
Hafiz Saqib Ali, Arghya Chakravorty, Jas Kalayan, Samuel P. de Visser and Richard H. Henchman,
Journal of Computer-Aided Molecular Design, 2021
(Paper,
Code,
)
We calculate binding free energies from multiscale cell correlation energy-entropy calculations
and compare with experiment.
5. Energy-entropy prediction of octanol–water logP of SAMPL7 N-acyl sulfonamide bioisosters,
Fabio Falcioni, Jas Kalayan and Richard H. Henchman,
Journal of Computer-Aided Molecular Design, 2021
(Paper,
Code,
)
We calculate logP values from multiscale cell correlation energy-entropy calculations
and compare with experiment.
4. Thermodynamic Origin of Differential Excipient-Lysozyme Interactions,
Jas Kalayan, Robin Curtis, Jim Warwicker, Richard H. Henchman,
Frontiers in Molecular Biosciences, 2021
(Paper,
Code,
)
We apply metadynamics to increase sampling of protein-protein and protein-solvent
interactions, then analyse the energy-entropy of our simulations with
multiscale cell correlation.
3. Convergence Behaviour of Solvation Shells in Simulated Liquids,
Jas Kalayan and Richard H. Henchman,
Physical Chemistry Chemical Physics, 2021
(Paper,
)
2. The Attraction of Water for Itself at Hydrophobic Quartz Interfaces,
Quinn A. Besford*, Andrew J. Christofferson*, Jas Kalayan, Jens-Uwe Sommer, and Richard H. Henchman,
The Journal of Physical Chemistry B, 2020
(Paper,
)
We analyse the long range properties of simulated water molecules between
two quartz surfaces.
1. Model for Counterion Binding and Charge Reversal on Protein Surfaces,
Jas Kalayan, Richard H. Henchman and Jim Warwicker,
Molecular Pharmaceutics, 2020
(Paper,
Code,
)
We represent proteins and small molecules as point charges
to model experimental ζ-potentials of protein-buffer solutions.
Acknowledgements🙏🏽
• Postdoc funding from The Leverhulme Trust grant code RPG-2020-059.
• Postgrad funding from Engineering and Physical Sciences Research Council (EPSRC) grant codes EP/L015218/1 and
EP/N025105/1.
• Previous supervisors: Jim Warwicker,
Richard H. Henchman.