Blog Archive

Paper published on Kartograf, a novel atom-mapping framework

My colleagues and I recently published a paper on Kartograf, a novel atom-mapping framework for alchemical free energy calculations. We hope this combination of software and scientific advances will be useful for the computational chemistry community. Read More ›

ticgithub: A GitHub-based email ticketing system

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 ›

Talk at Electronic Structure Software Development meeting

I presented a talk about campaign-scale simulations at a conference in Lausanne, combining my experiences with OpenPathSampling and Open Free Energy. Read More ›

Talk about OpenPathSampling at ACS National Meeting

TODO Read More ›

New job at Open Molecular Software Foundation

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 ›

ghcontribs: A tool for looking at user contributions to GitHub

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 ›

A GitHub action to check for release candidates on conda

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 ›

American Physical Society March Meeting talk

I presented a (virtual) talk about channel switching in path sampling for the 2021 APS March Meeting. Read More ›

Review article on transition path sampling published

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 ›

Le Deuxième Confinement: My lockdown cocktail creation

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 ›

COVID-19: Trends in exponential growth rates

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 ›

COVID-19 death trends (26 March)

How do the death rates of COVID-19 evolve differently in different countries? Can we see evidence that lockdown strategies work? Read More ›

Analysis of expert estimates COVID-19 deaths in the USA

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 ›

Article on Watson-Crick to Hoogsteen transition in DNA published

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 ›

PLUMED Consortium article published

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 ›

OpenPathSampling 1.0 released!

We have (finally!) released OpenPathSampling 1.0! Read More ›

Articles about OpenPathSampling published

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 ›

Talk in Vienna about path sampling of medically relevant biomolecular systems

I was invited to give a talk at a CECAM workshop on large-scale activated event simulations. Read More ›

Poster of path sampling and OpenPathSampling at Machine Learning School

Poster I presented at a school on machine learning held in Nierstein, Germany. Read More ›

Talk about parallelization of RETIS

An invited talk about efforts to parallelize replica exchange transition interface sampling in OpenPathSampling. Read More ›

Talk about the LAMMPS engine in OpenPathSampling

A talk I was invited to give about OpenPathSampling and LAMMPS. Read More ›

Talk in Genoa about path sampling of medically relevant biomolecules

I was invited to give a talk at a meeting connecting academic computational scientists to their industrial counterparts. Read More ›

Poster on path sampling and OpenPathSampling at RARE 2017

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 on path sampling and OpenPathSampling at E-CAM General Assembly

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 ›

Article on effects of isotropic and anisotropic interaction on assembly processes

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 ›

Literature talk: Adding water to Scotch whisky

Two of my favorite things in the world: Molecular dynamics and Scotch whisky. How did someone else write this paper before I did? Read More ›

Talk at the Vrij Universiteit Amsterdam about OpenPathSampling

A talk I gave on path sampling, OpenPathSampling, and the application of both to problems in biomolecular simulation. Read More ›

Talk on Scalability of Path Sampling Simulations

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 ›

Literature talk: Using the quantum Zeno effect for counterfactual communication

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 ›

Invited talk on DNA "baserolling" at CHAINS

A talk at the Dutch national chemistry conference about my work on the transition from the Watson-Crick to Hoogsteen base pairing motifs. Read More ›

Workshop on OpenPathSampling in Traunkirchen, Austria

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 ›

Invited talk at Brown

Invited talk at Brown University, focusing on semiclassical approaches. Read More ›

Talk about OpenPathSampling at Dutch MD Day

A talk introducing OpenPathSampling to the Dutch MD Day audience. Read More ›

Paper on multiple interface set transition interface sampling

The paper introducing my MISTIS method has been published in the Journal of Chemical Physics. Read More ›

Talk at Monte Carlo/Quasi-Monte Carlo methods conference about MISTIS

I was invited to give a talk about MISTIS at the MC/QMC conference in Leuven, Belgium. Read More ›

Poster on MISTIS at CECAM workshop on long time dynamics

Poster about my preliminary work on MISTIS; presented at a CECAM workshop in Lugano Read More ›

Talk on multiple interface set TIS at Dutch Molecular Dynamics Day

Talk at Dutch MD day about mutliple interface set TIS. Read More ›

Poster at ACS academic employment initiative

Poster I presented at the Fall 2013 ACS National Meeting. Read More ›

ACS talk on multiple interface set TIS

A talk I gave at the 2013 Fall National Meeting of the ACS about developments in transition interface sampling. Read More ›

ACS talk on the important initial phase space distribution

Slides from a talk I gave at the ACS National Meeting, introducing some of my work on the "important initial phase space distribution." Read More ›

Paper on classical mapping of fermions for Anderson model

We published a paper comparing my DCMF approach to a new quaterion approach for classical mappings of fermion dynamics. Read More ›

Literature Talk: 'Ode to Steered Transition Path Sampling'

A paper I found interesting, presented as a series of limericks. Read More ›

Invited talk on classical mappings at ACMM symposium

As an invited talk for the Amsterdam Center for Multiscale Modelling, I presented my DCMF method to study dynamics of fermions. Read More ›

Talk at Dutch MD day on classical fermion mappings

I presented my DCMF method at the Dutch Molecular Dynamics Day in March 2012, held in Groningen. Read More ›

Paper on classical mapping of fermions for Holstein model

The second paper on the DCMF method, this shows that it can work on a more complicated model. Read More ›

ACS talk on classical fermion mappings

A talk about my DCMF method, presented at the 2011 ACS National Meeting in Denver. Read More ›

Paper on classical mapping of fermions for Landauer model

Paper introducting my "dynamics of classically mapped fermions", with an application to molecular electronics Read More ›

Poster about "TPS for semiclassical IVRs" at Mini Stat Mech

Poster on time-dependent sampling for semiclassical IVRs, which is essentially a generalization of transition path sampling. Read More ›

ACS poster on precision finite difference monodromy matrix

Poster on a method I developed to calculate the monodromy matrix. Read More ›

The large c limit of det(A+cB) where B is singular

Solution to a litte math problem my PhD advisor asked about. Read More ›

Tracking the Maslov index

A little trick to track the Maslov index in semiclassical calculations. Read More ›

Poster on grid-based Poisson solver at Mini Stat Mech Meeting

Poster on a Poisson solver presented at the 2007 Mini Stat Mech Meeting. Read More ›

Feature article on quadrupolar interactions

A feature article I wrote, discussing quadrupolar interactions and my work on hydrogen and benzene Read More ›

Paper on hydrogen clustering around benzene

The first paper I submitted, developing a potential energy surface for hydrogen clustering around benzene. Read More ›

Precision in the computation of polynomials

A little note on accuracy in single vs. double precision for calculating polynomials. Read More ›

About old posts

A little retroactive continuity for the site Read More ›