Dogic Lab Wins Andor Insight Award

The ‘Insight Awards‘  is a video contest showcasing research imagery from the physical and life sciences which utilize Andor technology to capture data.  This year, the Dogic Lab submitted a research video to the competition and garnered first prize in the Physical Sciences division for their video of Oscillating Microtubule Bundles.

From the competition notes:

Microtubules are a bio-polymer composed of the protein tubulin and are used extensively in the cell for cellular division, cell motility, and transportation of cargo within the cell. Here, we investigate the material properties of mixtures of microtubules, a depletion agent, and the molecular motor Kinesin. The microtubules, driven by Kinesin motors, spontaneously organize into bundles of microtubules that oscillate in a manner reminiscent of flagella and cilia found in biology. This engineered system will allow us to studying systems of self-propelled and self-organized matter that exist far from equilibrium in the field known as Active Matter.

We use standard fluorescent microscopy to image labeled microtubules in a thin, flow cell microscope chamber. An Andor Clara camera was used in conjunction with a Nikon Ti Eclipse microscope to capture this video.

Video and Entry by Stephen DeCamp.

For this, and more videos from the Dogic Lab, visit their YouTube page or their website at Brandeis University.

Materials in Motion: Engineering Bio-Inspired Motile Matter

Life is on the move! Motion is ubiquitous in biology. From the gargantuan steps of an elephant to the tiniest single celled amoeba, movement in biology is a complex phenomenon that originates at the cellular level and involves the organization and regulation of thousands of proteins. These proteins do everything from mixing the cytoplasm to driving cell motility and cell division. Deciphering the origins of motion is no easy feat and scientists have been studying such complex behavior for quite some time. With biology as an inspiration, studying these complex behaviors provides insight into engineering principals which will allow researchers to develop an entirely new category of far-from-equilibrium materials that spontaneously move, flow or swim.

In a recent report in the journal Nature, a team of researchers from Brandeis University consisting of Tim Sanchez, Daniel T. N. Chen, Stephen J. DeCamp, Michael Heymann, and Zvonimir Dogic have constructed a minimal experimental system for studying far-from-equilibrium materials. This system demonstrates the assembly of a simple mixture of proteins that results in a hierarchy of phenomena. This hierarchy begins with extending bundles of bio-filaments, produces networks that mix themselves, and finally culminates in active liquid crystals that impart self-motility to large emulsion droplets.

Their system consists of three basic components: 1) microtubule filaments, 2) kinesin motor proteins which exert forces between microtubule filaments, and 3) a depletion agent which bundles microtubule filaments together. When put together under well-defined conditions, these components form bundled active networks (BANs) that exhibit large-scale spontaneous motion driven by internally generated active stresses. These motions, in turn, drive coherent fluid flows. These features bear a striking resemblance to a biological process called cytoplasmic streaming, in which the cellular cytoskeleton spontaneously mixes its content. Additionally, the system has great potential for testing active matter theories because the researchers can precisely tune the relevant system parameters, such as ATP and protein concentration.


The researchers also demonstrate the utility of this biologically-inspired synthetic system by studying materials science topics that have no direct biological analog. Under dense confinement to an oil-water interface, microtubule bundles undergo a spontaneous transition to an aligned state. Soft matter physics describes such materials as liquid crystals, which are the materials used to make liquid crystal displays (LCDs). These active liquid crystals show a rich variety of dynamical behavior that is totally inaccessible to their equilibrium analogs and opens an avenue for studying an entirely new class of materials with highly desirable properties.

Lastly, inspired by streaming flows that occur in cells, the researchers encapsulate the bundled active networks into spherical emulsion droplets. Within the droplet, microtubules again formed a self-organized nematic liquid crystal at the oil-water interface. When the droplets were partially squished between glass plates, the streaming flows generated by the dynamic liquid crystals lead to the emergence of spontaneous self-motility.

This research constitutes several important advances in the studies of the cytoskeleton, non-equilibrium statistical mechanics, soft-condensed matter, active matter, and the hydrodynamics of fluid mixing. The researchers have demonstrated the use of biological materials to produce biomimetic functions ranging from self-motility to spontaneous fluid flows using fundamentally new mechanisms. Additionally, the experimental system of bundled active microtubules is poised to be a model for exploring the physics of gels, liquid crystals, and emulsions under far-from-equilibrium conditions.

To see more videos from the Dogic lab at Brandeis University, check out their YouTube page.

Baskaran Wins NSF-CAREER award to pursue research on active fluids

Dr. Aparna Baskaran of the Physics Department has been awarded the prestigious CAREER grant from the National Science Foundation that is a highly competitive development grant for early career tenure track faculty members. This grant will fund the research ongoing in Dr. Baskaran’s group on dynamics in active materials. Active materials are a novel class of complex fluids that are driven out of equilibrium at the level of individual entities. Examples of such systems include bacterial suspensions, cytoskeletal filaments interacting with motor proteins and inanimate systems such as self-propelled phoretic colloidal particles. The theoretical challenge in understanding these systems lies in the fact that, unlike traditional materials, we no longer have the scaffold of equilibrium on which to base the theoretical framework.  At the practical front, these materials exhibit novel properties not seen in regular materials.  Further, they form the physical framework of biological systems  in that regulatory mechanisms modulate the mechanical properties of this material in response to environmental stimuli.  Dr. Baskaran’s research in this field will be done in collaboration with the groups of Dr. Michael Hagan, Dr. Zvonimir Dogic and Dr. Bulbul Chakraborty. It will enhance and complement the MRSEC research activities in the active materials thrust.

Figure Caption : Videos of example systems for active materials. A) A fish school exhibiting complex collective swimming. B) Swarming at the edge of an E. Coli Bacterial Colony. C) Cytoplasmic streaming inside the yolk of a fertilized cell.

Barry awarded Joseph Katz Fellowship from Argonne Natl Lab

Edward Francis Barry (PhD ’11) has recently been awarded the prestigious Argonne Scholar-Joseph Katz Postdoctoral Fellowship at Argonne National Laboratory. Ed began his scientific career studying the self-assembly of fd virus with Zvonimir Dogic, during the latter’s Junior Fellowship at the Rowland Institute at Harvard University. When Dogic joined the physics faculty at Brandeis, Ed also came to Brandeis as a Ph.D. student and helped to start the Dogic lab. Ed published seven papers describing various novel assemblages found in the fd system. Most notably, his 2010 Proceedings of the National Academy of Sciences paper describing the physical properties of colloidal membranes won the 2010 Cozzarelli Prize for scientific excellence. As the Katz fellow, Ed will be working between Argonne National Laboratory and the University of Chicago, where he is working with Experimental Condensed Matter Professor Heinrich Jaeger studying the self-assembly of monolayers composed of nanoparticles.

A new twist on interfacial tension

In a mixture of two molecular components, the surface tension is defined as the energetic cost per unit area of moving molecules from the bulk and bringing them to the interface. The higher the magnitude of the surface tension, the greater the tendency of two components to demix. Surface tension allows trees to carry nutrients from the roots out to the branches, and water striders to walk on the surface of water.

The interface between hydrophobic and hydrophilic components has very high interfacial tension. A common way to adjust the magnitude of surface tension is to add amphiphilic molecules (like soaps), which contain both hydrophilic and hydrophobic components. These amphiphilic molecules prefer to be at the interface between the two components, and effectively lower the interfacial tension, allowing the components to mix more easily. This is how detergent causes oily stains to dissolve in water.

In a recently published article in Nature, an interdisciplinary team of researchers at Brandeis headed by Zvonimir Dogic, and consisting of experimental, theoretical, and computational physicists as well as biologists, has demonstrated a new way of controlling interfacial tension using a molecular property called chirality, or lack of mirror symmetry. The study was performed on a model system of two-dimensional colloidal membranes composed of the rod-like bacteriophage virus fd, which are about one micrometer in length and 7 nanometers in diameter. The electrostatically repulsive virus particles are condensed into membranes through the depletion mechanism by adding non-adsorbing polymer to a virus suspension. Because the fd rods are chiral, they tend to twist by a small angle with respect to neighboring rods. However, the geometry of the membrane prevents twisting in the structure’s interior; only along the perimeter can the rods twist. Thus, increasing the strength of chirality of the rods both lowers the energy of the rods along the membrane’s edge and increases the frustration of untwisted rods in the bulk, lowering the interfacial tension. This contrasts the standard method of controlling interfacial tension using amphiphilic molecules, since the rod-like particles are completely homogenous, and do not contain any hydrophilic components.

The strength of chiral interactions in fd is temperature sensitive; the rods are achiral at 60o C, and the strength of chirality increases with decreasing temperature. By increasing the strength of chiral interactions in-situ, the team of researchers was able to dynamically vary the membrane’s interfacial tension in order to drive a dramatic transition from a membrane to several twisted ribbon structures (Movie 1). The twisted ribbons have much more interfacial area than the membranes, but are much “twistier” structures, and are therefore favored when the strength of chirality is relatively high. Additionally, the team was able to drive the same membrane-to-ribbon transition using optical tweezers, as shown in Movie 2. Membranes and ribbons are only two of a myriad of structures that were observed in the fd system. This work presents a powerful new method to control the assembly of materials by tuning interfacial tension with chirality.

Microtubules and Molecular Motors Do The Wave

Most people are familiar with audiences in crowded arenas performing “the wave,” raising their hands in sync to produce a pattern that propagates around the whole stadium.  This self-organized motion appears seemingly out of nowhere.  It is not produced by any external control, but is rather emerges from thousands of individuals interacting only with their neighbors.  A similar principle of self-organization might also be relevant on length scales that are billion times smaller.  On this scale, nanometer-sized proteins interact with each other to produce dynamical structures and patterns that are essential for life—and some of these processes are reminiscent of waves in crowded stadiums.  For example, thousands of nano-sized molecular motors located within a single eukaryotic flagellum or cilium coordinate their activity to produce wave-like beating patterns.  Furthermore, dense arrays of cilia spontaneously synchronize their beating to produce metachronal waves.

Proper functioning of cilia is essential for health; for example, cilia determine the correct polarity and location of our organs during development.  Defective cilia can cause a serious condition called situs inversus, in which the positions of the heart and lungs are mirrored from the normal state.  In another example, thousands of cilia in our lungs function to clear airways of microscopic debris such as dust or smoke by organizing their beating into coordinated, wave-like patterns.  Despite the importance of ciliar function, the exact mechanisms that lead to spontaneous wave-like patterns within isolated cilia, as well as in dense ciliary fields, is not well understood.

In a paper published in the journal Science this week, an interdisciplinary team consisting of physics graduate student Timothy Sanchez and biochemistry graduate student David Welch working with biophysicist Zvonimir Dogic and biologist Daniela Nicastro present a striking finding: the first example of a simple microscopic system that self-organizes to produce cilia-like beating patterns.  Their experimental system consists of three main components: 1) microtubule filaments; 2) motor proteins called kinesin, which consume chemical fuel to move along microtubules; and (3) a bundling agent that induces assembly of filaments into bundles.  Sanchez et al. found that under a certain set of conditions, these very simple components are able to self-organize into active bundles that spontaneously beat in a periodic manner.  One large spontaneously beating bundle is featured below:

In addition to observing the beating of isolated bundles, the researchers were also able to assemble a dense field of bundles that spontaneously synchronized their beating patterns into traveling waves.  An example of this higher-level organization is shown here:

The significance of these observations is several-fold. First, due to the importance of ciliar function for health, there is great interest in elucidating the mechanism that controls the beating patterns of isolated cilia as well as dense ciliary fields.  However, the complexity of these structures presents a major challenge.  Each eukaryotic flagellum and cilium contains more than 600 different proteins.  For this reason, most previous studies of cilia and flagella have employed a top-down approach; they have attempted to elucidate the beating mechanism by deconstructing the fully functioning organelles through the systematic elimination ­­­of constituent proteins. In this study, the researchers utilize an alternative bottom-up approach and demonstrate for the first time that it is possible to construct artificial cilia-like structures from a “minimal system,” comprised of only three components.  These observations suggest that emergent properties, spontaneously arising when microscopic molecular motors interact with each other, might play a role in formation of ciliary beating patterns.

Second, self-organizing processes in general have recently become the focus of considerable interest in the physics community.  These processes range in scale from microscopic cellular functions and swarms of bacteria to macroscopic phenomena such as flocking of birds and manmade traffic jams. Theoretical models indicate that these vastly different phenomena can be described using similar theoretical formalisms.  However, controllable experiments with flocks of birds or crowds at football stadiums are virtually impossible to conduct.  The experiments described by Sanchez et al. could serve as a model system to test a broad range of theoretical predictions. Third, the reproduction of such an essential biological functionality in a simple in vitro system will be of great interest to the fields of cellular and evolutionary biology. Finally, these findings open the door for the development of one of the major goals of nanotechnology: to design motile nano-scale objects.

These encouraging results are only the first from this very new model system.  The Dogic lab is currently planning refinements to the system to study these topics in greater depth.

UPDATE: Today, this publication was additionally featured on NPR Science Friday as the video pick of the week:


Physics students present research at 20th Annual Berko Symposium on May 16

On Monday, May 16, the Physics Department will hold the Twentieth Annual Student Research Symposium in Memory of Professor Stephan Berko in Abelson 131. The symposium will end with talks by the two Berko Prize winning students, undergraduate Netta Engelhardt and graduate student Tim Sanchez. The whole department then gathers for a lunch of cold cuts, cookies and conversation. “It’s a great way to close out the academic year,” said Professor of Astrophysics and Department Chair John Wardle. “We come together to celebrate our students’ research and hear what the different research groups are doing.”

The undergraduate speakers will describe their senior thesis honors research. This is the final step in gaining an honors degree in physics, and most of them will also be co-authors on a paper published in a mainline science journal. The graduate student speakers are in the middle of their PhD research, and will disucss their progress and their goals.

The prize winners are nominated and chosen by the faculty for making particularly noteworthy progress in their research. Graduate student winner Sanchez’ talk is titled “Reconstructing cilia beating from the ground up.” He works in Professor Zvonimir Dogic’s lab studying soft condensed matter. Undergraduate winner Engelhardt’s talk is titled “A New Approach to Solving the Hermitian Yang-Mills Equations”. She works with Professors Matt Headrick and Bong Lian (Math) on problems in theoretical physics and string theory. The schedule for Monday morning and abstracts of all the talks can be found on the Physics Department website.

Sanchez’ research very much represents the growing interdisciplinary nature of science at Brandeis. Here, a physicist’s approach is used to study a biological organism. Professor Zvonimir Dogic says of his work “He has made a whole series of important discoveries that are going to have a measurable impact on a number of diverse fields ranging from cell biology, biophysics, soft matter physics and non-equilibrium statistical mechanics.  His discoveries have fundamentally transformed the direction of my laboratory and probably of many other laboratories as well.”

Engelhardt’s research is much more abstract and mathematical, and concerns fundamental problems in string theory, not usually an area tackled by undergraduates. Professor Headrick says “Netta really, really wants to be a theoretical physicist, preferably a string theorist. She has a passion for mathematics, physics, and the connections between them.” He adds that she is utterly fearless in tackling hard problems. Netta has been awarded an NSF Graduate Research Fellowship based on her undergraduate work here.  Next year she will enter graduate school at UC Santa Barbara and will likely work with eminent string theorist Gary Horowitz, who has already supervised the PhD research of two other Brandeis physics alumni, Matthew Roberts ’05, and Benson Way ’08.

This Student Research Symposium is now in its 20th year. The “First Annual…..” (two words which are always unwise to put next to each other) was initiated in 1992 by Wardle to honor Professor Stephan Berko, who had died suddenly the previous year. Family, friends and colleagues contributed to a fund to support and celebrate student research in his memory. This provides the prize money which Netta and Tim will share.

Stephan Berko was a brilliant and volatile experimental physicist who was one of the founding members of the physics department. He was born in Romania in 1924 and was a survivor of both the Auschwitz and Dachau concentration camps. He came to the United States under a Hillel Foundation scholarship and obtained his PhD at the University of Virginia. He came to Brandeis in 1961 to establish a program in experimental physics and worked tirelessly to build up the department. Together with Professors Karl Canter (dec. 2006) and Alan Mills (now at UC Riverside) he established Brandeis as a world center for research into positrons (the anti-matter mirror image of ordinary electrons). In a series of brilliant experiments they achieved many “firsts,” culminating in election to the National Academy of Sciences for Steve, and, it has been rumored, in a Nobel Prize nomination for the three of them. Steve was as passionate about teaching as he was about research, and when he died, it seemed most appropriate to honor his memory by celebrating the research of our graduate and undergraduate students. During the coffee break on Monday, we will show a movie of Steve lecturing on “cold fusion,” a headline-grabbing but phony claim for producing cheap energy from 1989.

Keith Cheveralls ’09, Daniel Beller ’10, and Netta Engelhardt ’11 awarded NSF Graduate Research Fellowships

Former physics majors Keith Cheveralls ’09 and Daniel Beller ’10 and current physics major Netta Engelhardt ’11 have been awarded the prestigious National Science Foundation Graduate Research Fellowship. The fellowship recognizes and supports outstanding graduate students in the US who have demonstrated exceptional promise in science research. Keith is currently a first year graduate student at UC Berkeley; while at Brandeis he did his senior thesis with Professor Jane Kondev and was a co-author on a paper that appeared last year in the Proceedings of the National Academy of Sciences. Dan, a first year graduate student at the University of Pennsylvania, completed his senior thesis at Brandeis with Professor Zvonimir Dogic and Professor Robert Meyer.  Currently, Dan is conducting research on liquid crystals in the group of Professor Randall Kamien at UPenn. Netta is currently doing her senior thesis with Professor Matthew Headrick, and is planning to attend graduate school in physics next year.

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