The Fraden lab is engaged in “lab-on-a-chip” development. We are reducing the size chemistry and biology labs to the micron scale by using the same manufacturing methods that has allowed the semiconductor industry to produce computers whose power double every two years. This technology, known as “soft lithography” is transforming the way chemistry, biology, and the physics of soft condensed matter are practiced.
The project involves design, construction and testing of microfluidic chips, simulation of the physics of the devices using finite element computer simulations, interfacing chips with computers and automating data acquisition based on LabView. The current focus of the lab is building chips for protein crystallization, chemical communication and determining the properties of biological materials such as viruses, DNA and collagen. See movies of the chips in action.
Bob Pelcovits is engaged in numerical simulation studies of liquid crystal systems including confined and chiral systems. These systems include ones composed of biomolecules, and thus are model systems for exploring questions of self-assembly in biological systems. Undergraduates with some programming experience can easily learn the basics of liquid crystal physics and Monte Carlo simulations and begin carrying out an original research project in short order. Pelcovits works closely with the experimental groups of Dogic and Fraden, allowing for direct comparison of the numerical simulation results with experimental data.
The Hagan lab is applying computational and theoretical models to understand dynamical assembly processes, with an emphasis on understanding how molecular scale interactions and constraints, such as chirality, drive the emergence of particular large-scale structures. Projects include the assembly of proteins and nucleic acids to form a virus, as well as the super-assembly of complete viruses to form membranes, twisted ribbons, and other phenomena observed in the Dogic lab. Undergraduates with some programming experience can easily gain a practical understanding of molecular dynamics or Monte Carlo simulations in order to perform original research. The student will gain experience in computational modeling, learn how to develop coarse-grained descriptions of biomolecules, and be introduced to the application of statistical mechanics to understand biological and biomimetic systems.
We are a structural and cell biological lab (Biology Dept.) looking to hire an undergraduate student to help with the computer analysis of electron microscopic data. The job will include using software to reconstruct, model and visualize electron microscopic tomograms (three-dimensional images) of cells. This is also an excellent opportunity to get acquainted with the research in our lab, leading to the possibility of obtaining an undergrad research position/senior thesis. Student must be comfortable in using computers and problem solving, and must be dependable and organized. Find out more about what the lab is doing.
The Goode lab is combining biochemistry, genetics, and total internal reflection fluorescence (TIRF) light microscopy to understand in vitro and in vivo actin polymer dynamics and their regulation by key actin-associated proteins (e.g. formins, Arp2/3 complex, and ADF/cofilin). These projects address the fundamental mechanisms governing catalyzed actin polymer formation, spatial organization, and disassembly, studied on multiple levels: single molecule, single filament, and in living cells. Many of the projects are performed in collaboration with the Dogic, Gelles, and Kondev labs, and thus, there is the opportunity to gain valuable working experience at the interface of Physics and Biology. Undergraduates can easily gain a practical understanding of actin dynamics and contribute to this research, and in the process learn modern methods for biochemical purification of proteins and state-of-the-art light microscope technology. In addition, there are opportunities for students interested in theory and computation to rigorously analyze data and make quantitative models of these processes.
Pattern formation is a key phenomenon in many living systems, particularly in the processes of development and morphogenesis. We have been studying pattern formation in reaction-diffusion systems: simpler, often inorganic, chemical reactions, in which the interplay between nonlinear chemical kinetics and diffusive transport leads to the appearance of traveling waves (typically spirals or concentric circles), stationary Turing patterns (typically stripes or hexagonal arrays of spots) or more complex patterns such as superlattices or spatiotemporal chaos. Most prior studies have looked at pattern formation in simple, homogeneous aqueous solution. We are interested in exploring pattern formation in more complex media, such as emulsions (mixtures of oil, water and surfactant) and hydrogels. Such systems can give rise to more complex pattern formation and have the potential to lead to new materials with novel functional properties. The project involves preparation of new pattern-forming systems and investigation of their behavior.
Our research focuses on the interdisciplinary frontier of materials chemistry. We integrate knowledge and techniques from organic chemistry, materials science, surface chemistry, biochemistry, and nanotechnology to design new biofunctional materials, including nanomaterials, for the exploration in biomedicine (e.g., molecular drug delivery, cancer therapy, biomedical diagnostics, and biomimetics), and other fundamental problems in nanoscience and biological science. We are particularly interested enzyme catalyzed self-assembly of small molecule to create nanostructures inside cells, which offers a unique means for scientists to integrate molecular self-assembly with intrinsic enzymatic reactions inside cells for developing new biomaterials and therapeutics at the supramolecular level, and improving the basic understanding of dynamic molecular self-assembly in water.
The Gelles lab uses optical techniques to study the bending and looping of single DNA molecules by DNA-binding proteins. These mechanical deformations of DNA are essential to mechanisms by which cells switch individual genes on and off. By studying these dynamical processes at the level of single molecules, we hope to understand how fundamental physical phenomena, such as polymer mechanics, elctorstatics, and the scaling properties of one- and three-dimensional diffusion dictate the properties and functioning of the protein and nucleic acid macromolecules that comprise the machinery of life.
The Samadani lab utilizes a multidisciplinary approach, to understand the repair mechanism of the broken chromosomes. By tagging different parts of the chromosome with fluorescent proteins, we are able to visualize the dynamics of these chromosomes before and after induction of a double-strand break. These quantitative measurements are used to formulate a predictive mathematical model of the repair process, based on polymer models of chromosomes. We use microfluidic devices to enable rapid exchange of different media over the cells, thereby allowing precise regulation of the cells microenvironment. These experiments are performed in collaboration with Haber, Kondev, chakraborty and Fraden groups from Biology and Physics departments. During this REU program, undergraduate students will have the opportunity to genetically manipulate the yeast genome, use a research-grade fluorescent microscope to take quantitative images, work with microfluidic devices and write image analysis code.
The Chakraborty group develops mathematical models of complex behavior observed in a wide variety of systems.. The group uses a combination of computational modeling and theory to analyze collective behavior of biologically relevant materials. Projects include (a) the dynamics of polymers under confinement and crowding, (b) the polymerization process of active molecules such as actin and microtubules, and (c) pattern formation in active emulsions. Undergraduates with some programming experience can easily gain a practical understanding of Monte Carlo simulations in order to perform original research. The student will gain experience in numerical simulations, model building and the theoretical tools necessary to understand collective properties of interacting systems.
The Kondev group uses physics models to obtain a quantitative understanding of biological macromolecules, DNA and proteins, and the processes they engage in. Current problems of interest include repair of DNA breaks inside cells, regulation of gene expression, and assembly of cyroskeletal filaments. The work in the group is theoretical with close ties to Biology labs at Brandeis, MIT and Caltech.
Students in the group gain experience in developing theoretical and computational models of biological problems in close collaboration with experimental groups. There are also opportunities for combined experimental and theoretical projects.