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ABOUT ME

I am a scientist at the interface of the physics of life, structural biology and artificial intelligence.  I apply theoretical and computational physics approaches to develop mechanistic models of how structural biological systems self-organise across scales of space and time.  By combining such models with AI-based frameworks, I seek to provide insight into emergent and universal principles that govern and regulate living matter. 

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EXPERIENCE

European Molecular Biology Laboratory, Heidelberg 

Data Scientist in Computational Biology, Genome Biology Unit

Heidelberg Institute for Theoretical Studies 

Senior Research Fellow

Universitat Pompeu Fabra

Research Fellow

EDUCATION

University College London, Department of Chemistry

PhD Theoretical & Computational Biophysics

Advisor: Prof. Peter Coveney, Centre for Computational Science

University of Cambridge, St. John's College

BA MSci Natural Sciences  (Theoretical Physics) 

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1997 - 2001

2004 - 2008

  • Part  IA Courses:

    • Physics, Chemistry, Materials and Minerals Science, Mathematics

  • Part IB & II Courses:

    • Experimental and Theoretical Physics

  • Part III Courses: 

    • Particle Physics, Relativistic Astrophysics and Cosmology, Quantum Computing

  • Master's Thesis Title (Advisor:  Prof. Andrew Fabian):

    • Effects of plasma ejection from magnetic flares on the X-ray spectra of black hole candidates

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  • Thesis Title:

    • Molecular dynamics simulation studies of drug resistance in HIV-1 protease

  • Gained expertise in statistical physics, all-atom molecular dynamics (MD) simulations and theoretical formalisms for reaction kinetics approaches in systems biology

  • Developed the Binding Affinity Calculator, a molecular dynamics-based software to compute accurate drug binding affinities for ligands binding to HIV-1 protease as part of the EU-funded Virolab project (http://www.virolab.org).

  • Created a computational framework for patient-specific decision support for anti-HIV therapy

  • Development on and use of high-performance computing resources and GRID architectures

2009 - 2015

2016 - 2020

2020 -

  • Marie Curie Postdoctoral Fellow:

    • Wrote and won a Marie Curie Intra-European Fellowship Award for research into the molecular dynamics of HIV-1 protease autocatalysis

    • Developed additional research lines in:

      • Conformational changes in metamorphic and disordered proteins

      • High-throughput MD methods for protein folding kinetics

      • Advanced sampling methods for binding affinity calculations

      • Molecular kinetics using Markov State Models

    • Gained expertise in volunteer distributed GPU computing (GPUGRID.net)

    • Responsibilities: project design, planning, implementing and data interpreting

  • American Foundation for AIDS Research (amfAR) Mathilde Krim Fellow:

    • Wrote and won amfAR grant as principal investigator for research into "Enhanced premature self-activation of HIV-1 protease to induce apoptosis"

    • Developed a computational drug-discovery pipeline including high-throughput virtual screening, all-atom MD and coarse-grained reaction diffusion.

    • Led collaboration with experimental virologists, biochemists and medicinal chemists exploring novel HIV interference pathways for AIDS eradication

    • Responsibilities: Budget planning, GPU cluster assembly and maintenance, student supervision, developing collaboration, full project delivery

  • Kinetics for Drug Discovery Fellow:

    • Developed enhanced sampling methods in all-atom molecular dynamics (MD) and Brownian dynamics (BD) for drug-protein binding kinetics.

    • Responsibilities: Project planning, implementing, delivery, reporting, disseminating, supervising

  • Volkswagen Foundation Fellow:

    • Wrote and won VW "Experiment!" grant as a principal investgator on RNA Epicatalysis and modulation of enzyme kinetics in phase-separated bio-condensates

    • Developed multiscale biophysics models of sub-cellular polymer-protein condensates, capsid assembly and reaction-diffusion modelling of retroviral infectivity

    • Responsibilities: Project lead, planning, implementing, interpreting, disseminating and supervising

  • Redevelopment of flagship software Mosaicatcher for data analysis of single cell strand-seq

  • Wrote and won VW "Experiment!" extension grant for investigating the theoretical biophysics of phase-separated bio-condensates induced by SARS CoV-2

  • Research into reaction-diffusion approaches for chromatin structure and dynamics and linkage to epigenetic expression

  • Development of protein structure prediction approaches for protein design

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