All posts by Linda Hirst

Current Biology – Chitin in cartilaginous fishes

Our new work in collaboration with Chris Amemiya’s lab at UC Merced demonstrates the presence of Chitin in an unexpected place – the electro sensory organs of cartilaginous fishes.

Molly Phillips, W. Joyce Tang, Matthew Robinson, Daniel Ocampo Daza, Khan Hassan, Valerie Leppert, Linda S. Hirst, Chris T. Amemiya,
“Evidence of chitin in the ampullae of Lorenzini of chondrichthyan fishes”, Current Biology, Volume 30, Issue 20, 2020, Pages R1254-R1255,

Read a news article here

Abstract,We previously reported that the polysaccharide chitin, a key component of arthropod exoskeletons and fungal cell walls, is endogenously produced by fishes and amphibians in spite of the widely held view that it was not synthesized by vertebrates [1]. Genes encoding chitin synthase enzymes were found in the genomes of a number of fishes and amphibians and shown to be correspondingly expressed at the sites where chitin was localized [1,2]. In this report, we present evidence suggesting that chitin is prevalent within the specialized electrosensory organs of cartilaginous fishes (Chondrichthyes). These organs, the Ampullae of Lorenzini (AoL), are widely distributed and comprise a series of gel-filled canals emanating from pores in the skin ( Figure 1A). The canals extend into bulbous structures called alveoli that contain sensory cells capable of detecting subtle changes in electric fields ( Figure 1B) [3,4]. The findings described here extend the number of vertebrate taxa where endogenous chitin production has been detected and raise questions regarding chitin’s potential function in chondrichthyan fishes and other aquatic vertebrates.

FUndamentals of Soft matter science 2nd Ed – out now!


This revised edition continues to provide the most approachable introduction to the structure, characteristics, and everyday applications of soft matter. It begins with a substantially revised overview of the underlying physics and chemistry common to soft materials. Subsequent chapters comprehensively address the different classes of soft materials, from liquid crystals to surfactants, polymers, colloids, and biomaterials, with vivid, full-color illustrations throughout. There are new worked examples throughout, new problems, some deeper mathematical treatment, and new sections on key topics such as diffusion, active matter, liquid crystal defects, surfactant phases and more.

• Introduces the science of soft materials, experimental methods used in their study, and wide-ranging applications in everyday life.

• Provides brand new worked examples throughout, in addition to expanded chapter problem sets and an updated glossary.

• Includes expanded mathematical content and substantially revised introductory chapters. 

This book will provide a comprehensive introductory resource to both undergraduate and graduate students discovering soft materials for the first time and is aimed at students with an introductory college background in physics, chemistry or materials science. 

Topological Chaos in active nematics

Topological chaos in active nematics, Amanda J. Tan, Eric Roberts, Spencer Smith, Ulyses Alvarado, Jorge Arteaga, Sam Fortini, Kevin Mitchell, and Linda S. Hirst, Aug 5th, NATURE PHYSICS (2019) Link

Abstract: Active nematics are out-of-equilibrium fluids composed of rod-like subunits, which can generate large-scale, self-driven flows. We examine a microtubule-kinesin-based active nematic confined to two dimensions, exhibiting chaotic flows with moving topological defects. Applying tools from chaos theory, we investigate self-driven advection and mixing on different length scales. Local fluid stretching is quantified by the Lyapunov exponent. Global mixing is quantified by the topological entropy, calculated from both defect braiding and curve extension rates. We find excellent agreement between these independent mea-sures of chaos, demonstrating that the extensile stretching between microtubules directly translates into macroscopic braiding of positive defects. Remarkably, increasing extensile activity (through ATP concentration) does not increase the dimensionless topological entropy. This study represents an application of chaotic advection to the emerging field of active nematics and quantification of the collective motion of an ensemble of defects (through topological entropy) in a liquid crystal.

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Fluorescence microscope image of the active nematic phase

The full text of the paper can be found here

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E-tec braiding algorithm used on experimentally collected defect trajectory data

Nanofoams – Nature communications

Nanoparticle-based hollow microstructures formed by two-stage nematic nucleation and phase separation

Sheida T. Riahinasab, Amir Keshavarz, Charles N. Melton, Ahmed Elbaradei, Gabrielle I. Warren, Robin L. B. Selinger, Benjamin J. Stokes & Linda S. Hirst 

Nature Communications volume 10, Article number: 894 (2019)

read the paper here

Rapid bulk assembly of nanoparticles into microstructures is challenging, but highly desirable for applications in controlled release, catalysis, and sensing. We report a method to form hollow microstructures via a two-stage nematic nucleation process, generating size-tunable closed-cell foams, spherical shells, and tubular networks composed of closely packed nanoparticles. Mesogen-modified nanoparticles are dispersed in liquid crystal above the nematic-isotropic transition temperature (TNI). On cooling through TNI, nanoparticles first segregate into shrinking isotropic domains where they locally depress the transition temperature. On further cooling, nematic domains nucleate inside the nanoparticle-rich isotropic domains, driving formation of hollow nanoparticle assemblies. Structural differentiation is controlled by nanoparticle density and cooling rate. Cahn-Hilliard simulations of phase separation in liquid crystal demonstrate qualitatively that partitioning of nanoparticles into isolated domains is strongly affected by cooling rate, supporting experimental observations that cooling rate controls aggregate size. Microscopy suggests the number and size of internal voids is controlled by second-stage nucleation.

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 Dr Melton!

Nathan Melton, our most recent graduate walked at UC Merced commencement this month. Nathan’s recent work, focused on topological defects in liquid crystals with a new paper just out last month in the journal Nanomaterials.

“Phase-transition-driven nanoparticle assembly in liquid crystal droplets” Charles N. Melton, Sheida T. Riahinasab, Amir Keshavarz, Benjamin J. Stokes and Linda S. Hirst, Nanomaterials, 8, 146 (2018). Link

Dr Melton and Dr Hirst

Nathan has already started work as a postdoctoral scientist at Lawrence Berkeley National Lab at the Advanced Light Source!

Active Matter in Biology:Nature News and Views

Recently Prof Hirst authored a News and Views in Nature focussed on two exciting articles about the cell epithelium as active matter.

“Evidence has been found that a biological tissue might behave like a liquid crystal. Even more remarkably, topological defects in this liquid-crystal system seem to influence cell behaviour. A materials physicist and a biologist discuss what the findings mean for researchers in their fields”.

Read the full article here

Biological physics: Liquid crystals in living tissue