Category Archives: Biopolymers

New NSF grant – mixing in active matter

The Hirst Lab has been awarded a new three-year NSF grant along with collaborator UC Merced’s Kevin Mitchell.

The grant, combining experiment and theory is titled “Self-mixing Active Fluids”


Active matter is one of the most exciting frontiers in soft matter science. Unlike typical fluids, active fluids are not in equilibrium. Instead, they consume energy locally, translating this energy into internal flows and spontaneous mixing. In this project, mass transport and chaotic mixing in active fluids will be investigated using a fluid consisting of microtubules and kinesin, biological molecules found in the cell. Densely packed microtubules slide antiparallel to each other at a controlled rate due to coupled kinesin molecular motors. An exciting outcome of this work could be the development of a new class of self-mixing active solvents. Such a solvent could revolutionize our understanding of the kinetics of mass transport and chemical reactions. The present proposal concerns much larger length scales than that of standard solvents and will thus serve as an experimental model for these new ideas, helping to establish fundamental laws that govern the behavior of active matter. Since the contents of biological cells are highly complex active materials, far from equilibrium, this work is expected to yield new insights into the role of active materials in biology. A proposed Telluride workshop on transport in active fluids will help to bring together the relatively disparate fields of liquid crystals, biological fluids and nonlinear dynamics. This work will have a significant educational impact at UC Merced, a new university in one of California’s most socio-economically disadvantaged areas. This research will provide the basis for several undergraduate theses and the PIs will use insights from this work to introduce cutting edge materials to their graduate and undergraduate teaching.

This project focuses on transport and mixing in a biologically inspired extensile active nematic. Densely packed microtubules slide antiparallel to each other at a controlled rate due to kinesin molecular motors and the resulting chaotic advection will be measured on different length scales, using the experimental tools of particle tracking, particle image velocimetry, and fluorescence imaging of labeled tracers. Experimental data will be theoretically interpreted using the tools of nonlinear and topological dynamics, thereby merging the fields of chaotic advection and liquid crystals in a unique collaborative effort. Topological entropy will play a central, unifying role in this study. Topological entropy is well known in studies of chaotic advection, but has been thus far overlooked in studies of active nematics. Specific aims are to: 1) use bead tracking and velocity reconstruction, together with tools from nonlinear dynamics, to measure the topological entropy of active nematic mixing; 2) measure the effective diffusivity, enhanced by chaotic advection, of the active nematic on the macroscale; and 3) investigate correlations between molecular-scale dynamics, mesoscale mixing, and macroscale diffusion by varying system parameters.

Congratulations Joe Lopes – CREST fellow 2017

Congratulations go to Joe, who was selected to receive funding for the Spring  and Fall semesters as a CREST fellow.


The CREST center (Center for cellular and biomolecular machines) is funded by the National Science Foundation and you can read more about their work and opportunities here.

Joe is working on kinesin – based  microtubule transport and active matter.

Microtubules gliding on kinesin motors





Studying microtubule spools

Understanding the role of transport velocity in biomotor-powered microtubule spool assembly

Amanda J. Tan, Dail E. Chapman, Linda S. Hirst and Jing Xu

In this new paper we examined the sensitivity of microtubule spools to transport velocity.
Perhaps surprisingly, we determined that the steady-state
number and size of spools remained constant over a seven-fold
range of velocities. Our data on the kinetics of spool assembly
further suggest that the main mechanisms underlying spool growth
vary during assembly.
Read the paper in RSC Advances here

Amanda Tan – winner 2016 faculty mentor fellowship

Congratulations to physics graduate student Amanda Tan for winning a UC Merced “faculty mentor” fellowship.  This prestigious fellowship is awarded to prepare future faculty and provides a year’s funding plus a travel stipend.

Amanda’s research project focuses on active biological materials, in particular microtubules and molecular motors. She is collaborating with the Xu lab at UC Merced and will have her first paper with the group out soon.

The award assists recipients in acquiring and developing advanced research skills under faculty mentorship and is aimed at increasing the number of students who complete their Ph.D. degree and successfully acquire a faculty appointment.



Congratulations Dr Pandolfi!

Congratulations go to Ron Pandolfi, the latest PhD graduate from the Hirst group. Ron’s PhD defense was on Monday Dec 8th, where he presented his thesis on “Self-assembly and Design of Tunable Soft Materials”

During his time in the lab Ron’s work has included molecular dynamics simulations of semi-flexible polymers and x-ray characterization of different soft systems.

Ron was recently hired at the Advanced Light Source, Lawrence Berkeley National Lab in Berkeley, CA where he’ll be working with soft matter x-ray team.




Designing highly tunable semi-flexible filament networks

“Designing highly tunable semi-flexible filament networks”

R. Pandolfi, L. Edwards, D. Johnston, P. Becich and L.S. Hirst, PHYS. REV. E. 89, 062602(2013) Link

Semiflexible polymers can generate a range of filamentous networks significantly different in structure from those seen in conventional polymer solutions. Our coarse-grained simulations with an implicit cross-linker potential show that networks of branching bundles, knotted morphologies, and structural chirality can be generated by a generalized approach independent of specific cross-linkers. Network structure depends primarily on filament flexibility and separation, with significant connectivity increase after percolation. Results should guide the design of engineered semiflexible polymers