Thumbnail figure for Edelmaier et al. 2019 Chromosome paper

Mechanisms of chromosome biorientation and bipolar spindle assembly analyzed by computational modeling

June 4, 2019

We develop a computational model of fission-yeast mitosis using a course-grained Brownian Dynamic framework in conjunction with a force-dependent kinetic Monte Carlo algorithm to replicate the biorientation and segregation of chromosomes.

Model overview

Theory of cytoskeletal reorganization during crosslinker-mediated mitotic spindle assembly

May 7, 2019

We develop a torque-balance model that describes spindle assembly due to dynamic microtubule bundles, spindle-pole bodies, the nuclear envelope, and crosslinkers to predict spindle-assembly dynamics.

Thumbnail image for Wall and Hough 2018 BiophysJ

In-Cell NMR within Budding Yeast Reveals Cytoplasmic Masking of Hydrophobic Residues of FG Repeats

April 19, 2019

In-cell NMR in S. cerevisiae is a novel way of looking at disordered proteins in a crowded cellular environment. The methodology has been developed here, which could be broadly applicable to other protein systems. In an example, the non-specific interactions of the FG Nup construct, FSFG-K, with the cytoplasm is similar to previously found bacterial interactions using NMR relaxation techniques. This work was recently published in Biophysical Journal.

Ants image

Collective clog control: Optimizing traffic flow in confined biological and robophysical excavation

Aug. 16, 2018

Groups of interacting active particles, insects, or humans can form clusters that hinder the goals of the collective. We find that digging performance can be robustly optimized within the constraints of narrow tunnels by individual idleness and retreating.

Model schematic for sticky and slippery obstacles.

Effects of soft interactions and bound mobility on diffusion in crowded environments: a model of sticky and slippery obstacles

June 12, 2017

There are many biological systems in which tracer particles diffuse in a crowded environment. We implemented a lattice Monte Carlo model to analyze the effects of binding kinetics, bound motion, and obstacle size on tracer diffusive in the presence of soft obstacles.

Model cartoon

Kinesin-5-independent mitotic spindle assembly requires the antiparallel microtubule crosslinker Ase1 in fission yeast

May 17, 2017

Pushing forces generated by microtubule polymerization are sufficient to promote spindle pole separation and the assembly of bipolar spindle in the absence of molecular motors.

Model schematic.

Analytical structure, dynamics, and coarse-graining of a kinetic model of an active fluid

March 6, 2017

One of the simplest active suspensions with complex dynamics is a suspension of immotile "Extensor" particles that exert active extensile dipolar stresses on the fluid in which they are immersed.

Spindle images.

Physical determinants of bipolar mitotic spindle assembly and stability in fission yeast

Jan. 20, 2017

Microtubules, motors, and cross-linkers are important for bipolarity, but the mechanisms necessary and sufficient for spindle assembly remain unknown. We describe a physical model that exhibits de novo bipolar spindle formation.

Molecular determinants of tubulin's C-terminal tail conformational ensemble

Aug. 19, 2016

The disordered C-terminal tails of tubulin are biologically important but difficult to study. We describe a method to isotopically label tubulin for structural studies by NMR of the C-terminal tails.

Model cartoon

Contributions of microtubule dynamic instability and rotational diffusion to kinetochore capture

June 24, 2016

Recent work has found that microtubule rotational diffusion about minus-end attachment points contributes to kinetochore capture in fission yeast, but the relative contributions of dynamic instability and rotational diffusion are not well understood.