Introduction

I work as an independent software consultant, passionate about improving the velocity of software development. "Movement is life" and the faster you can navigate the software landscape the better. High-velocity can include some unexpected results: decisions can be refined quickly and engineers remain happy (because there is no "velocity" without "quality").

In particular, my current areas of interest include cloud engineering (Terraform, Pulumi) and build systems (CMake, Bazel).

Biography

From 2017 to 2020, I have been a co-founder and CTO at Labstep. Labstep set out to make scientists more productive and creative, by providing a best-in-class electronic notebook experience www.labstep.com.

Under the supervision of simulation masterminds, Mark Sansom (Oxford University) and Robert Best (NIH), I'm working on membrane protein folding.

While at D. E. Shaw Research, New York City, I used ultra-long molecular dynamics simulations to identify cryptic binding pockets in previously undruggable phosphatases.

I did my undergraduate work in Oxford, studying Biochemistry, earning an MBioch with honors and a medal from the Queen and Mick Jagger. My graduate project was in Groningen, Netherlands working on protein-lipid interactions, using coarse-grained molecular dynamics simulations and the Martini model.

Software projects

Labstep

A powerful web-tool helping scientists be more creative

Plumed

An extension to molecular dynamics codes for running enhanced sampling simulations

Link to contributions

Ligandbook

A public repository for OPLS-AA ligand parameters.

Lipidbook

Older brother to ligandbook.

Technical blog

A "Sargasso Sea" of assorted notes, unfinished projects.

Publications

Full list of publications can be found on my Google Scholar profile

  • Paulo CT Souza, Riccardo Alessandri, Jonathan Barnoud, Sebastian Thallmair, Ignacio Faustino, Fabian Grünewald, Ilias Patmanidis, Haleh Abdizadeh, Bart MH Bruininks, Tsjerk A Wassenaar, Peter C Kroon, Josef Melcr, Vincent Nieto, Valentina Corradi, Hanif M Khan, Jan Domański, Matti Javanainen, Hector Martinez-Seara, Nathalie Reuter, Robert B Best, Ilpo Vattulainen, Luca Monticelli, Xavier Periole, D Peter Tieleman, Alex H de Vries, Siewert J Marrink Martini 3: a general purpose force field for coarse-grained molecular dynamics Nature Methods https://www.nature.com/articles/s41592-021-01098-3
  • E Yamamoto, J Domański, FB Naughton, RB Best, AC Kalli, PJ Stansfeld, MSP Sansom, Multiple Lipid Binding Sites Determine the Affinity of PH Domains for Phosphoinositide-Containing Membranes Science advances https://advances.sciencemag.org/content/advances/6/8/eaay5736.full.pdf
  • Richard J Gowers, Max Linke, Jonathan Barnoud, Tyler John Edward Reddy, Manuel N Melo, Sean L Seyler, Jan Domanski, David L Dotson, Sébastien Buchoux, Ian M Kenney, Oliver Beckstein, MDAnalysis: a Python package for the rapid analysis of molecular dynamics simulations https://permalink.lanl.gov/object/tr?what=info:lanl-repo/lareport/LA-UR-19-29136
  • J. Domański, M.S.P. Sansom, P.J. Stansfeld, R.B. Best, Balancing Force Field Protein–Lipid Interactions To Capture Transmembrane Helix–Helix Association https://pubs.acs.org/doi/abs/10.1021/acs.jctc.7b00983
  • J. Domański, G. Hedger, R. Best, P.J. Stansfeld, M.S.P. Sansom, Convergence and Sampling in Determining Free Energy Landscapes for Membrane Protein Association DOI: 10.1021/acs.jpcb.6b08445