Scientific Research, Modeling, and Writing

Here are some examples of my scientific writing and research. With the exception of my undergraduate thesis (the first selection), all these works were written spontaneously, driven by my personal interests in these fields. Since starting my MD-PhD, I have only had time to write one spontaneous paper. It’s a mathematical model of the stochastic accrual of genetic mutations as a function of age, which I will post as soon as I have time to retool the math—I originally wrote it using tensors, but I’ve since decided that wasn’t the most elegant way to approach it. I’ll also post my thesis work when it’s completed. In the meantime, what’s here gives a good sense of the breadth of my interests.

A New Visualization Tool for the Analysis of Labeled Cell Position In-Situ Applied to the Study of Amphioxus Somites

Developmental Biology, Systems Biology, Bioinformatics, Information Theory

My undergraduate thesis.  Working at the Mansfield lab in Barnard, at which the work focuses on investigating the cell fates of somites in embryonic amphioxus, I innovated a method by which labeled expression patterns of specimens of varying morphologies can be super positioned to enable quantitative analysis. 

Modeling Genomic Fixation Probabilities of Tautomeric Mutations as a Function of Characteristic Fluctuations in Earth’s Magnetic Field

Theoretical Biophysics, Evo Devo, Molecular Genetics, Statistical Physics, Chaos Theory, EM Theory

This is the first part of a two part investigation I undertook to explore a possible connection between characteristic fluctuations in the Earth's magnetic field associated with a given region at the Earth's surface, and particular mutations occurring in the region within a short period of time (geologically speaking). The work was motivated by a fascination with the communication between selective genetic preferences manifested at the molecular level, and corresponding macro-conditions of the external environment. The objective was to create a model that would reconcile punctuated equilibrium theory with natural selection by establishing the possibility of a pathway by which local geomagnetic phenomena could promote certain mutations (in this case, tautomeric mutations) at certain loci in a given population of some species, such that concordance with external selective pressures could permit these mutations to fix in the genome substantially more rapidly than natural selection alone.  The arguments are set forth in the form of a proof.

Modeling Fluctuations in the Geomagnetic Field 

Astrophysics, EM Theory, Evo Devo

This investigation is an exploration of the nature of fluctuations of the Earth's magnetic field as they relate to the geo-specific field fluctuation characteristics proposed in "Modeling Genomic Fixation Probabilities of Tautomeric Mutations as a Function of Characteristic Fluctuations in Earth’s Magnetic Field."

An Exploration of Dynamic Force Modeling in Cells Applied to Unexplained Results in the Nagayama Cell Traction Investigation

Membrane Biomechanics, Biopolymer Chemistry, Biased Diffusion Theory, Theoretical Biophysics

On occasions when I come across results labeled "unexplained" in a journal article, I am frequently moved to attempt to explain them myself. In this instance, the article was "Heterogeneous response of traction force at focal adhesions of vascular smooth muscle cells subjected to macroscopic stretch on a micro pillar substrate," by Nagayama, et. al., at Nagoya Institute of Technology in Japan, published in the Journal of Biomechanics, in 2011.  Nagayama reported that in experiments analyzing cellular traction forces in which specimen cells were stretched on a micropillar substrate, about half of the cells performed active recovery in the first cycle, while all the cells underwent passive recovery in the second cycle.  Here, I introduce some topics in Biopolymer Chemistry and Biased Diffusion Theory, then attempt to use these to model possible explanations for Magayama's results.