Crocker Lab University of Pennsylvania
Department of Chemical and Biomolecular Engineering

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Research Overview:  Self-Assembly, Soft Devices, Active Matter, Cells and Soft Glasess

Our research interests are in soft matter physics and engineering and their border with cell biology. Our expertise lies in figuring out how to make careful mechanical measurements on very small objects, from colloidal particles and cells all the way down to single macromolecules. On the one hand, we can use biochemistry to construct novel and interesting soft-matter experiments and materials and perhaps ultimately to engineer useful devices. On the other hand, we can use methods originally developed for studying soft matter to probe interesting biological systems, such as the cytoskeleton of eukaryotic cells.
Directed Self-Assembly and Active Micro-devices by Molecular Recognition

The term self-assembly describes the spontaneous organization of component parts, for example, atoms arranging themselves into an ordered crystal. Much attention has been placed on the idea of 'directed self-assembly' to ‘grow’ useful devices from nanoscopic synthetic parts (also called ‘bottom up’ assembly) rather than current nanofabrication techniques based on photolithography (‘top down’ assembly). Ideally, we would like to have a technology platform that allows us to self-assemble arbitrary, complicated structures from a large number of different parts, and to do so rapidly and with a low probability of forming defective assemblies. In principle, this would seem to require parts that exclusively stick to each other in a user specified way. In practice, one of the most successful approaches is due originally to Ned Seeman. This approach, called DNA nanotechnology, uses DNA to stick structural components together by exploiting the tendency of single stranded DNA to form a double helix preferentially with strands having a complementary base sequence. While this method has been used by a number of researchers to form an ever increasing array of complicated structures, the details of why some designed structures form while others do not remain poorly understood.

In our lab, we apply DNA nanotechnology to self-assemble novel structures from micron-sized objects, specifically micron-sized polymer spheres called colloids. We chose colloids because the formation of ordered colloidal crystals is a comparatively well understood and prototypical example of self-assembly, and colloids are large enough to be imaged using an optical microscope, making it relatively easy both to watch the dynamics assembly process as it occurs, and to see what you made in the end. We were the first group to successfully form colloidal crystals using interactions due to DNA (or any molecular recognition system). In the end, we found issues of colloidal stability, reversible binding, equilibrium growth and annealing to be critically important. Along the way we developed a novel method for modifying the surface of colloids with a polymer brush and functional groups.

Our current efforts are directed at forming novel two and three dimensional alloy structures. This exploratory research receives input from detailed simulations by Talid Sinno’s group.  In our original approach, we prepare a mixture of different particles, A, B and C, having specific interactions (e.g. A sticks to B but not to C, etc.) which we describe by an interaction matrix.  By adjusting the number of species, their size, and the interaction matrix a variety of different crystal and cluster symmetries can be self-assembled.  In a second newer approach, we are investigating the role that particle shape plays in defining the final structure.  We currently produce non-spherical building blocks using a nano-molding method we call 'crystal templating' that uses a colloidal crystal as a general-purpose mold for building other shapes.

McGinley JT, Jenkins I, Sinno T and Crocker JC Assembling Colloidal Clusters using Crystalline Templates and Reprogrammable DNA Interactions Soft Matter, 9, 9119-9128, 2013

In a separate project with Daeyeon Lee and David Chenoweth, we are using a technique called Layer by Layer deposition to create thin, flexible films of DNA-grafted gold nanoparticles.  By placing DNA nano-actuators in these films, we can create films that reversibly fold themselves into new shapes, driven by DNA fuel strands.  Current efforts are directed at patterning these new active materials, and building novel micro-origami structures and simple micro-robotic devices.

Binding in the Single- and Few-Molecule Limit

As a spin-off of our self-assembly work, we have performed direct measurements of the effective pair potential of mean force prevailing between two colloidal particles bearing complimentary DNA. This effort required the refinement of an extended optical tweezer measurement system to achieve resolution at the few nanometer level. Direct measurements of the DNA induced interaction were well described by a semi-analytic model we developed based on polymer physics, chemical equilibrium and a generalized mass action principle. While our first measurements were at high DNA density (up to ~100 molecules could sterically reach between the colloids), we soon realized that our instrument was equally well suited to studying binding in the single or few molecule limit as well. That work confirmed what many have begun to suspect—that the kinetics of DNA hybridization near the melting temperature are non-exponential.

Cell Mechanics and Soft Glasses

It is increasingly clear that mechanical stress and deformation play a significant role in the behavior of eukaryotic cells. It also appears likely that cells are mechanically sophisticated, having an array of mechanical senses whose outputs are integrated together and used during differentiation decisions, tissue remodeling and, of course, motility. Understanding these aspects of cell mechanics would seem to be a prerequisite both for understanding tissue growth and morphology at the cellular scale and realizing the ultimate potential of tissue engineering. Despite this potential impact, the mechanical response (e.g. rheology) of cells and its physical and biochemical determinants remain largely mysterious. In our previous work, we applied a variety of different microrheology techniques to understand cell mechanics and rheology. The challenge of understanding cell mechanics is a consequence of their mechanical complexity. In a series of studies applying different microrheological methods to the same cells, we demonstrated that cells' different compartments and discrete structural elements each had their own distinct mechanical response. In general, different measurement techniques  measure different components, or different combinations of components, and can do so in a cell type dependent manner.

In our current research, we use a a unique tool for quantifying the stress fluctuations within a soft material, which we call stress fluctuation spectroscopy, developed with our collaborators Andy Lau and Tom Lubensky. A major current area of soft-matter research relates to understanding materials containing active elements that cause internal deformation, sliding or stress, for example, molecular motors. While cells are obviously an example of such materials, how quantities such as motor activity and intracellular stress relate in general to the mechanical response and function remain unclear. Given the array of different motors and stress generation mechanisms in cells, it seems likely that the observed basal stress and stress fluctuations will be a superposition of many different sources, some of which may be intimately related to the mechanics and others that are not. Current efforts are directed at understanding the molecular mechanisms and biophysics of neutrophil spreading with Dan Hammer and endothelial cell crawling and chemokinesis with Dan Reich at Johns Hopkins.

Henry SJ, Crocker JC, Hammer DA Ligand density elicits a phenotypic switch in human neutrophils Integrative Biology, 6 (3), 348-356, 2014

The mechanics of cell structures have distinctive, viscoelastic mechanical properties that closely resemble Soft Glassy Materials, a class of non-biological materials including foams, dense emulsions (like mayonnaise) and slurries (like ketchup), that are neither completely liquid nor solid.   The physical origin of these materials distinctive mechanics remains mysterious despite long study.  In a collaboration with Rob Riggleman, we are building novel computational models of such materials and relating their rheology to the nature of the unusual relaxation pathways the system takes when particles rearrange.