Our team needed an email ticket support system that fit within our workflow on GitHub. Unable to find an ideal commercial or open-source solution, I wrote my own. Read More ›
I presented a talk about campaign-scale simulations at a conference in Lausanne, combining my experiences with OpenPathSampling and Open Free Energy. Read More ›
I've started a new job as a Senior Software Scientist at the Open Molecular Software Foundation, where I'll be working on the Open Free Energy project. Read More ›
I wanted to get a better sense of what contributions I've made to various open-source projects, so I wrote a library to query GitHub and analyze the results. Read More ›
I've written and published a GitHub action that makes it easy to run a workflow (such as a test suite) when a conda-installed package publishes a release candidate. Read More ›
Peter Bolhuis and I have written a review article on transition path sampling, focusing on the analogies between sampling in configuration space and in trajectory space. Read More ›
Just before France went into its second lockdown, I dropped by a favorite liquor store in Lyon so I could use the time experimenting. Here's what I ended up with. Read More ›
There's a desire to compare the way the COVID-19 pandemic is evolving in different countries, to see which strategies are and aren't working. Here I analyze the exponential growth rates for several countries. Read More ›
Asked to predict how many COVID-19 cases the US would have a week later, experts vastly underestimated. If their estimates of the number of deaths are equally wrong, what are we in for? Read More ›
In addition to the well-known Watson-Crick base pairing motif, DNA can transiently take on the Hoogsteen conformation. My colleagues and I investigated the mechanism and rate of the conformational change between Watson-Crick and Hoogsteen DNA. Read More ›
I'm honored to be a co-author of a paper by the PLUMED consortium, focused on how to promote transparency and reproducibility in our subdomain of enhanced molecular simulations. Here are my thoughts on the paper. Read More ›
The two papers introducing OpenPathSampling, the software I've been developing for several years, have been published in the Journal of Chemical Theory and Computation. Read More ›
Poster I presented at the Recent Advances in Rare Events (RARE) conference, held in Agra, India, in December 2017. Includes both an introduction to OpenPathSampling and several applications. Read More ›
Poster I presented at the E-CAM General Assembly. Includes an introduction to OpenPathSampling as well as some other work in progress for the E-CAM project. Read More ›
What is the interplay between isotropic interactions and decoy anisotropic interactions during simple assembly processes? I explored this in a paper with Arthur Newton, Ramses Kools, and Peter Bolhuis. Read More ›
How does OpenPathSampling's Gromacs engine scale? And how does path sampling scale in general? I gave a talk on these topics at a conference on extreme scale computing. Read More ›
The quanum Zeno effect is one of the most fascinating and counter-intuitive results of quantum mechanics. In this talk, I present a paper that has used the quantum Zeno effect for quantum communication purposes. Read More ›
The generalized ensembles in OPS enable powerful tools for analysis and simulation. This talk at a CECAM workshop in Leiden describes some of those tools. Read More ›
