Seth Fraden Group

Research Overview:

Our group studies a broad range of topics in Soft Matter. We utilize a variety of methods and approaches covering experiment, theory, and simulation. Our research interests lie squarely in the intersection of physics, chemistry, biology and materials science. Our lab is interdisciplinary, but we are also involved in several multi-investigator projects. Areas of interest are described below:

Testing Turing
After 60 years Turing's theory of morphogenesis has finally been tested directly in the lab. We've recently published a paper testing Turing's hypothesis and demonstrated chemophysical morphogenesis in chemical cells. Click on the image for more.

Active Matter
The material properties of living matter include a number of desirable qualities that have yet to be incorporated into inanimate materials. Examples are the self-healing ability of living materials and the ability to adapt to stress by self-strengthening mechanisms, as exhibited by tree limbs exposed to persistent wind or snow drifts. Another example is the ability for individual biological units to dynamically self-organize into larger ensembles as in the flocking behavior in birds, schooling of fish, and swarming of bacteria. At the sub-cellular level, active behavior is exhibited in cytoskeletal reorganization during replication and in the various forms of cellular motility, such as crawling (amoebae, macrophages) and flagellar driven propulsion (bacteria, protozoan). The opposite case, in which the flagellae propel fluid while the organism remains at rest also produces desirable material properties such as the self-cleansing mechanisms of ciliary fields on the lining of trachea.

The category of materials to which all these systems belong, as well as the field of inquiry devoted to their study is called Active Matter. Active matter consists of an assembly of objects, each of which consumes energy to generate continuous dynamics either propagating in space or oscillating in time.

Active matter is an active field. In the last decade, numerous exciting theoretical developments spanning approaches ranging from non-equilibrium statistical mechanics to hydrodynamics have produced a solid framework for which to base understanding and future inquiry of the disparate phenomena. The theories are based on the recognition that active matter exists far from equilibrium, that energy is consumed to generate stress and motion, and that the symmetry of the system dictates the nature of the collective behavior. Currently, experiments are lagging theory. This is because systems far from equilibrium choose many different paths to dissipate energy. So while the objective is to create materials in which the consumption of energy results in coordinated motion or self-strengthening, there are numerous other intervening chemical reactions that don't produce the desired action, but only generate heat and waste products.

The Fraden lab is involved in two collaborative projects in experimental Active Matter. Our goal is to develop robust systems that will serve as paradigms for investigations of active matter across different length scales ranging from the micro to macroscopic. One system will be of biological origin, but will contain the minimal biological components needed to exhibit active matter behavior. A second system focuses on building non-biologic materials that communicate, compute and actuate based on heterogeneous hydrogels containing the Belousov-Zhabotinsky oscillating chemical reaction.
Active Matter: Understanding and Building Cilia (Funded by the Keck Foundation)
Joint research with Zvonimir Dogic (physics) and Dany Nicastro (biology).
The goal of this project is to elucidate the behavior of active matter at lengthscales ranging from microscopic to macroscopic, using an interdisciplinary approach involving both physics and biology. The materials which unify all of our experiments are filamentous microtubules and kinesins, which are molecular motors that use ATP hydrolysis to propel themselves along the microtubule tracks and thus drive the assembly toward non-equilibrium active states. Specifically we will develop three model systems of active matter. First, using a “bottom up” approach we will determine the minimal system, consisting of microtubules, active motors and passive cross-linkers, required to create a self-oscillating active bundle. Second, using a complimentary “top down” approach we will deconstruct a fully functional axoneme and determine the minimal set of structural components required for its active beating. This effort will involve a combination of genetic, ultrastructural and biophysical methods. Third, we will assemble active nematic liquid crystals and characterize both its microscopic dynamics and behavior at continuum lengthscales.

The three aims of this project are related to each other in several important ways. First, all the materials we will study share the central motif of molecular motors that continuously hydrolyze ATP in order to actively push filamentous microtubules against each other, thus driving the system to non-equilibrium states. Second, they require similar experimental techniques and technologies with special emphasis being placed on advanced optical and electron microscopy to directly image materials at all relevant lengthscales. Third, they involve two complimentary methodologies. In a “bottom-up” approach we take isolated components, such as microtubule filaments and kinesin motors and assemble structures and materials of ever increasing complexity. In a “top-down” approach we systematically deconstruct a fully functioning biological assembly, the axoneme, in order to elucidate how its unique active properties arise from interactions among its individual components. Finally, and most importantly, all the investigations explore the central theme of hierarchical assembly of microtubules and molecular motors, with each specific aim focusing on a different level of hierarchy ranging from an isolated pair of microtubules, to axonemes containing dozens of microtubules and hundreds of motors, to macroscopic materials containing thousands of microtubules. Understanding these materials at each level of hierarchy represents a significant advance in the field. However, only the combined understanding of structure and dynamics at all relevant length scales will result in development of general design principles required for bottom-up engineering of novel active materials.
Active Matter: Interacting Nonlinear Chemical Oscillators (Funded by the Brandeis MRSEC) Joint research with Bing Xu (chem), Irv Epstein (chem), Bulbul Chakraborty (physics).
Living matter possesses remarkable material properties, such as the ability to sense the environment, make decisions based on sensory input, and through self-propulsion, move in the direction of choice. The simplest single cellular organism, the bacterium, possesses these properties, as do many multi-cellular organisms. Some bacteria and amoeba, such as Dictyostelium exhibit chemotaxis – or navigate along chemical gradients to forage for food. In other circumstances, such as starvation, individual Dictyostelium communicate with each other through a chemical reaction-diffusion mechanism and self-organize into a kind of tissue where the single cells aggregate into a fruiting body for survival. Some bacteria aggregate and then protect themselves by enveloping themselves in a starch coat called a bio-film. These materials have the ability to heal themselves. The goal of this project is to create a new class of materials, which have properties heretofore only associated with living matter. Like living matter, these materials will be active in the sense that they must consume energy in order to function, but will be entirely synthetic with no biological components at all. Combining methods of experiment, simulation and theory and personnel spanning the disciplines of neuroscience, computer science, physics and chemistry we will lay the scientific framework to create materials that have properties like trees that grow thicker and stronger in response to stress imposed by wind or snow, or muscle tissue, which increases in response to exercise.
The materials we will study are based on the Belousov-Zhabotinsky chemical reaction. The BZ system produces an oscillating redox reaction of a metal ion . In thermodynamically closed systems the BZ oscillations can occur 100 times, but will last forever in an open system in which the BZ reactants are continuously fed into the solution. In analogy with living matter, we produce “cells” by isolating the aqueous BZ reagents in either gels or in emulsion droplets where oil forms the continuous phase. We combine individual cells to create a “tissue” composed of many cells separated by a matrix or fluid.

A limited subset of the aqueous BZ chemicals permeates through the hydrophobic intercellular medium giving rise to intercellular communication. We also introduce light sensitive catalysts that allow external control of the reaction. We fabricate cells between 10 microns and 200 microns in diameter. Using a computer programmable illumination system we can individually “address” each cell and control the phase of the chemical oscillator using light. When confined to a two dimensional layer we can simultaneously image and control about 1000 cells.

The BZ chemistry is complex and can be understood semi-quantitatively at a detailed level of 80 chemical reactions. Focusing on the rate limiting reactions allows a simplified description in terms of two species; an activator and an inhibitor, which interact in three distinct steps. First, the metal ion is in the reduced state. The inhibitor suppresses oxidation of the metal ion while a slow process consumes the inhibitor. Second, once the inhibitor falls below a critical threshold, the activator is unleashed and an autocatylic reaction leads to a rapid oxidation transition consuming all the reduced metal ion. Third, once the oxidation is complete a slow process reduces the oxidized metal ion while simultaneously producing the inhibitor, thus restarting the oscillation.

Protein Crystallization. The goal of the human genome project was to sequence the genes that code the approximately 30,000 proteins that comprise the human body. While much valuable information is contained in a protein's genetic code, it is often desirable to obtain the three-dimensional structure of the protein in order to elucidate its function. The first step in structure determination is obtaining purified protein, either directly through biochemical separation processes, or if the DNA sequence is known, from expression of the protein using genetically modified organisms. The next step is crystallizing the protein, and the final step is solving the protein structure from x-ray diffraction measurements. However, the structures of only 4,000 of the 30,000 human proteins have been solved, and these represent fewer than 300 of the estimated 1,000 unique protein folds. Most of these structures belong to compact, water soluble, single proteins. More problematic is the lack of human membrane protein structures. Only a handful of the 10,000 human membrane proteins have been solved! Another category for which there are only a few structures are protein complexes. On average, each protein strongly interacts with several other proteins. Some important protein structures, such as the ribosome and slicesome are composed of over 100 individual proteins.

The rate-limiting step is the crystallization process. Crystallographers follow a set of recipes, which are the result of years of experience, and although intuition gleaned from colloidal chemistry aids in improvisation the crystallization process is poorly understood. A typical crystallography lab contains cold rooms stacked floor-to-ceiling with racks upon racks of suspensions of proteins in a range of solvent conditions. A theoretical framework for protein crystallization is needed in order to restrict the parameter space and eliminate crystallization as a bottleneck in structural determination of proteins. The current paradigm is that crystallization proceeds through nucleation and growth, but the microscopic details remain unclear.

The theme running through our technology and methodology development research is the long recognized fact that the key to optimizing crystallization is the separation of nucleation and growth. By squarely confronting the fundamental kinetic nature of crystallization, we are developing complementary, portable, scalable and economical high-throughput technologies designed to exploit the kinetics of crystallization. One consequence of the particulars of our approach is that the crystals produced will be small. Independently of our technology, it turns out that for the other popular methods of crystallization, i.e. vapor diffusion and microbatch, small crystals appear more frequently than large ones. Our strategy is to exploit the relative abundance of small crystals over large ones by developing a technology to obtain structures from microcrystals.

Microfluidics and the Phase Chip. Protein crystals are necessary in order to determine protein structure using x-ray diffraction. Typically the number of crystallization trials are limited by the availability of protein, hence the drive to minimize sample volume. To address this problem a high-throughput, low volume microfluidic device denoted the Phase Chip is being developed. On this device different microfluidic components have been designed, fabricated, and interconnected in order to precisely meter, mix, and store sub-nanoliter amounts of sample, solvent, and other reagents. The Phase Chip can store thousands of sub-nanoliter drops of protein solution in individual wells and a total of 10³ crystallization trials can be accomplished with 1 - 10 microgram of protein thereby enabling high-throughput crystallization of mammalian proteins expressed in tissue culture. Additionally each sample well is in contact with a reservoir through a dialysis membrane through which only water and other low molecular weight organic solvents can pass. Thus the concentration of all solutes in an aqueous solution can be reversibly, rapidly, and precisely varied in contrast to current microfluidic crystallization methods, which are irreversible. Rapid reversible dialysis solves a major problem in protein crystallization, the decoupling of nucleation from growth. Using the phase chip we will screen crystallization conditions using proteins that are not available in sufficient quantities for current techniques. The protein targets are bacterially-expressed recombinant channel proteins, G protein-coupled receptors heterologously expressed in a mammalian cell culture system, and enzymes which produce crystals too small for diffraction.

We study entropy driven phase transitions in colloidal liquid crystals of rod-like virus particles. The virus particles are very interesting because Nature has engineered them to be monodisperse -- which has not been achieved in the laboratory. Because of the simplicity of interparticle interactions there is hope that a microscopic theory of the phase behavior and bulk properties can be undertaken. These viral colloidal systems offer the possibility of serving as model systems for understanding all liquids composed of anisotropic particles. We have studied phase behavior of nematic, cholesteric, smectic, and colloidal crystals of virus particles. Currently we are modifying the viruses using a combination of genetic engineering to make viruses of different lengths, and chemistry to modify the diameter of the particles by either coating them with metal or bonding water soluble polymers, such as PEO to the surface of the virus.

Macromolecular Crowding is a project of direct biological relevance. Macromolecules occupy 30% of the volume of the cell, strongly influencing inter-molecular interactions. Even in the absence of any direct interactions between particles, such as electrostatic, hydrophobic, or van der Waals forces, the macromolecules feel each others presence simply because two molecules cannot occupy the same place at the same time. This crowding of molecules causes like species to phase separate into different regions of the cell, leading to macromolecular compartmentalization without the need for any intracellular membranes. Strong partitioning and bundling is observed for rodlike biopolymers such as actin or microtubules when mixed with globular proteins or polymers.

The biochemistry of the cell has evolved in this crowded, thermodynamically non-ideal environment, and it may be that the cell has exploited this fact. Prof. Herzfeld [Accounts of Chemical Research 29, 31-37 (1996)] has proposed that that bundling of filaments is driven by macromolecular crowding and that the role of specific bundling proteins is to fine tune certain aspects of the bundling, like the relative alignment of the biopolymers in a bundle. There are a number of questions we are seeking to answer. How crowded do suspensions have to be in order to partition? How strong is the degree of partitioning of the species? What is the organization of the macromolecules in the partitioned phases? How different do the species have to be from each other for this to occur? How does the interparticle potential affect the phenomena? To what extent is all this relevant to cellular biology?

We are studying the partitioning of mixtures of globular and filamentous proteins in vitro using suspensions of the biopolymer fd bacteriophage and Tobacco Mosaic Virus mixed with polymers such as polyethylene glycol and dextran or globular proteins like BSA. Genetic engineering methods are used to systematically alter the length of the biopolymers, an important thermodynamic variable. The viruses are labeled with fluorescent dyes and equilibrated samples are observed in the light microscope. Electron microscopy, light and x-ray scattering, and optical microscopy are used to determine the structure of the macromolecular suspension. We compare our experimental measurements of the phase behavior of these mixtures with several theoretical statistical mechanical models developed by ourselves, by Prof. J. Herzfeld of the Brandeis University Chemistry department and others, as well as with Monte Carlo computer simulations.

Rodlike Granular Matter The vast majority of studies of granular matter focus on frictional spherical particles. While the simplicity of the fricitonless sphere is appealing, in Nature the majority of grains are non-spherical and frictional. We experimentally study the coordination number and compactification of rods, as well as the formation of vortices in vibrated granular rods and obtain beautiful and counter-intuitive results.
Electro-rheological fluids are composed of dielectric spheres suspended in a solvent to which an electric field is applied. Under certain conditions the suspension rapidly solidifies. These materials are being developed for applications in the automotive industry. The microscopic structure is being studied using digital video optical microscopy, confocal laser scanning microscopy and light scattering.