Bill spoke about his work on Stochastically Organizing the Early Embryo. Here is a link to the talk: http://www.birs.ca/events/2019/5-day-workshops/19w5080/videos/watch/201906192010-Holmes.html . Also, here’s a link to the great list of all the talks from this conference: http://www.birs.ca/events/2019/5-day-workshops/19w5080/videos .
Two students graduated this year from Bill’s lab. Linghui Feng, an undergraduate in mathematics and economics, has graduated and is moving to the University of Chicago to pursue graduate school. Linghui researched how the detailed stochastic dynamics of gene expression influence the ‘so called’ epigenetic landscape associated with those genes.
Payton O’Daniels, an undergraduate in computer science, used a joint modeling and experimental approach to investigate how pathologists make medical image based decisions. He is moving into industry after graduation and beginning a position with FAST Enterprises.
Thanks to both for all their hard work!
Bill published a new paper (https://www.sciencedirect.com/science/article/pii/S0006349519301481) at the Biophysical Journal. It has long been known that many intracellular particles exhibit sub-diffusive dynamics. One prominent hypothesis for the source of this anomalousness is that they are undergoing Fractional Brownian Motion or Generalized Langevin Dynamics. This article demonstrates that these types of dynamics necessarily lead to the presence of boundary layers. If such boundary layers are present, it would have profound implications biologically. If they do not, it would provide strong evidence that these models of anomalous dynamics are not an appropriate description of intracellular particle dynamics.
A new article with Yi-Shin Lin and Andrew Heathcote has been accepted for publication at Behavioral Research Methods. This article demonstrates a GPU based implementation of a relatively recent Bayesian parameter estimation algorithm I have helped refine. This implementation dramatically improves the efficiency of this simulation based methodology by using a mix of R, Armadillo C++, and CUDA. Here is a link to an OSF (osf.io/p4pdh/) that Yi-Shin has put together to house some of the code for this project. A pre-print of this article is provided below.
I’ve just submitted a new article for review (see the biorxiv link for preprint). This article investigates the consequences of sub-diffusive dynamics (Fractional Brownian or Generalized Langevin to be more specific) on the spatial localization of particles near cellular borders. The main finding here is that the fundamental statistical and physical assumptions encoded in these models of anomalous diffusive dynamics give rise to the formation of substantial boundary layers near any reflecting boundary (e.g. cell membrane). The question that remains is, do these boundary layers actually exist? Happy reading.
https://www.biorxiv.org/content/early/2018/10/31/458224
Thanks for visiting my new website.
Theoretical Biophysics Lab 