Computational tools for cellular scale biophysics
Mathematical models are indispensable for disentangling the interactions through which biological components work together to generate the forces and flows…
Current Opinion in Cell BiologyBiophysical Modeling
The Biophysical Modeling group focuses on the modeling and simulation of complex systems that arise in biology and soft condensed matter physics. Areas of interest include the dynamics of complex and active materials, as well as aspects of collective behavior and self-organization in both natural systems (e.g., inside the cell) and synthetic ones.
Examples are the organization and dynamics of the nucleus, the structure and assembly of spindles, the positioning and transport of cellular organelles, and fluid-structure problems in biology. To address these, often in close collaboration with experimental collaborators, we build numerical and theoretical models from the ground up, revealing how the known mechanics of individual components give rise to collective behavior. Many such phenomena occur only within dense, highly interacting systems, inaccessible to standard techniques. To probe such regimes requires the development of fast and scalable algorithms for many-component systems, and of coarse-grained models that can be analyzed and simulated.
Research Highlights
E. coli do not count single molecules
H. Mattingly, Keita Kamino, Jude Ong, et al.
Organisms must perform sensory-motor behaviors to survive. What bounds or constraints limit behavioral performance? Previously, we found that the gradient-climbing…
ArXivYardangs sculpted by erosion of heterogeneous material
Samuel Boury, S. Weady, Leif Ristroph, et. al.
The recognizable shapes of landforms arise from processes such as erosion by wind or water currents. However, explaining the physical…
Applied Physical SciencesSoftware
STKFMM
This is a numerical computation package for various single- and double-layer kernels for Laplace and Stokes operators in boundary integral methods, implemented on top of the highly-optimized kernel independent fast-multipole method package PVFMM.
aLENS
This is the simulation tool for tracking assemblies of microtubules driven by motor proteins.
