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.

Applications open for HHMI Interfaces Scholar Award Lecturer

The Quantitative Biology Program at Brandeis University, supported by a grant from Howard Hughes Medical Institute, is now accepting applications for an award for preparing an outstanding set of three pedagogical lectures on a subject at the interface of the physical and biomedical sciences.  These lectures will be given at the Quantitative Biology Bootcamp, January 26, through January 27, 2013.  The award consists of a cash prize of $2,000.

Any graduate student or postdoctoral research associate currently at Brandeis is eligible to apply.  The application packet should consist of short  curriculum vitae and a one page outline of the three lectures.  QB faculty will work with the successful applicant in preparing the lectures.  Applications should be submitted to Jen Scappini, (jscappin at brandeis dot edu). Due date will be discussed at meeting.

An information session for potential applicants will be held on Friday, October 26th, 9:30-10:00 in Kosow 207

A list of past winners and links to their lecture presentations can be found at http://www.brandeis.edu/programs/quantbio/interdisciplinary.html

 

Quantitative Biology Bootcamp 2012

What do dinosaur DNA, calculating the global amount of carbon dioxide consumed in photosynthesis, and cooperation and cheating between yeast cells have in common?  They were all topics discussed at the sixth annual Quantitative Biology Bootcamp, held on the Brandeis campus January 12 and 13.

At the bootcamp, more than 40 Ph.D. students and faculty participated in lectures, discussions, and computational projects using both computers and pencil-on-paper approaches.  The Brandeis Quantitative Biology Program is a unique “add-on” graduate program open to students in all six of the natural sciences Ph.D. programs at Brandeis.  The main goal of the program is to train students to work effectively as a part of research teams that span the boundaries of traditional scientific disciplines.  To this end, Quantitative Biology students participate in both courses and out-of-classroom activities, like the Bootcamp, that highlight the diverse approaches to scientific problems taken by scientists from different disciplines.

A central feature of this year’s Bootcamp were the lectures and computer laboratory exercise presented by Jeffrey Boucher, a student in the Biochemistry Ph.D. program and the winner of Quantitative Biology Program’s 2012 HHMI Interfaces Scholar Award.  Boucher’s presentations described mathematical techniques and experimental methods that can be used to understand the processes of biological evolution by reconstructing genes and proteins present in the long-extinct progenitors of present animal, plant and microbial species. Prospective graduate students and others interested in learning more about Brandeis Quantitative Biology can consult the program’s web site at http://www.brandeis.edu/programs/quantbio/index.html

Quantitative Biology Lecture Prize

The Quantitative Biology Program at Brandeis University, supported by a grant from Howard Huges Medical Institute, is now soliciting applications for an award for preparing an outstanding set of three pedagogical lectures on a subject at the interface of the physical and biomedical sciences.  These lectures will be given at the Quantitative Biology Boot camp, January 12, through Friday, January 13, 2012.  The award consists of a cash prize of $2,000.

Any graduate student or postdoctoral research associate currently at Brandeis is eligible to apply.  The application packet should consist of short/ curriculum vitae/ and a one page outline of the three lectures.  QB faculty will work with the successful applicant in preparing the lectures.  Applications should be submitted  to Jen Scappini either by campus mail (MS009), or e-mail (jscappin@brandeis.edu). (Due date will be discussed at the Wednesday, 10.19.11 Meeting).

An information session for potential applicants will be held on Wednesday, October 19th, 2:30-3:00 in Kosow 207.

Summer course on building a microscope from simple components

This past June the MRSEC Center offered a condensed summer course based on the popular graduate course QB120: Quantitative Biology Instrumentation Laboratory.

Professor Dogic

The course was taught by Zvonimir Dogic of the Physics Department (pictured).   Prof. Dogic has extensive experience with several forms of microscopy and his Lab features several home-built or heavily modified optical setups.

The course is designed to offer students hands on experience with building their own optical setups from basic components as well as learning how to optimally acquire imaging data from commercial microscopes.  The focus was on understanding the physics behind microscope function and leveraging that knowledge towards improving data acquisition in the lab.

Initially, students used basic lenses, apertures, an objective, a camera and a light source to build the simplest possible light microscope.  This initial setup was quickly extended to include Köhler illumination, a core principle in microscopy which allows even illumination of the sample as well as access to the conjugate image plane for image filtering.

The next project required students to build a fluorescence microscope, a highly relevant and ubiquitous technique in biological imaging.  To image a slide with fluorescently labeled beads students used a dichroic mirror to separate excitation light at one wavelength from emission light at another wavelength.  A schematic diagram, a photo of this setup with the light path superimposed and actual data acquired with one of these microscopes can be seen in the video below.

Next, a more advanced technique in microscopy, total internal reflection microscopy (TIRF), was introduced and an imaging setup using this technique was built.  TIRF microscopes excel at imaging small molecules that are immobilized in a small area.  A laser beam was pointed to shine through a prism at an angle sufficient to cause total internal reflection and the resulting evanescent wave caused fluorescent excitation of the sample.  The video below shows a schematic and imaging data of a TIRF microscope built by students.

Finally, students used commercial microscopes to understand the principles behind phase contrast and difference interference contrast microscopy, both techniques well suited for imaging samples that are nearly transparent.

Overall the Course provided an excellent introduction to the physical principles behind microscope function.  I highly recommend it to anyone interested in using microscopes in their research!

MRSEC summer course in Optical Microscopy (June 20-24, 2011)

Optical microscopy has become a powerful experimental tool capable of simultaneously visualizing large scale structures such as entire cells, and fluorescently labeled single molecules within these complex structures. It has found important applications in diverse scientific fields.  The Brandeis Materials Science Research and Enginering Center will offer a one-week intense summer course in optical microscopy from June 20 – June 24, 2011, “Introduction to Optical Microscopy.“  The primary goal of the course is to train students in the fundamentals of microscopy and optics. The students will start by constructing a bright field and fluorescence microscope from simple optical components before learning how to use research grade optical microscopes. After completing the course, students will acquire knowledge necessary for using optical microscopes at limits of their capabilities and critically evaluating their performance.

This summer course is a condensed version of a popular graduate level course in  Quantitative Biology (Quantitative Biology Instrumentation Laboratory QB 120 b).  Our goal is to make this course accessible to students with all scientific backgrounds.  The course will be taught by Zvonimir Dogic, who is a faculty member in the Physics Department at Brandeis University.

More information and application procedures are available at the following website: http://www.brandeis.edu/mrsec/summercourses.html.

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