Project description:When a crystal melts into a liquid both long-ranged positional and orientational order are lost, and long-time translational and rotational self-diffusion appear. Sometimes, these properties do not change at once, but in stages, allowing states of matter such as liquid crystals or plastic crystals with unique combinations of properties. Plastic crystals/glasses are characterized by long-ranged positional order/frozen-in-disorder but short-ranged orientational order, which is dynamic. Here we show by quantitative three-dimensional studies that charged rod-like colloidal particles form three-dimensional plastic crystals and glasses if their repulsions extend significantly beyond their length. These plastic phases can be reversibly switched to full crystals by an electric field. These new phases provide insight into the role of rotations in phase behaviour and could be useful for photonic applications.
Project description:The capacity of proteins to interact specifically with one another underlies our conceptual understanding of how living systems function. Systems-level study of specificity in protein-protein interactions is complicated by the fact that the cellular environment is crowded and heterogeneous; interaction pairs may exist at low relative concentrations and thus be presented with many more opportunities for promiscuous interactions compared with specific interaction possibilities. Here we address these questions by using a simple computational model that includes specifically designed interacting model proteins immersed in a mixture containing hundreds of different unrelated ones; all of them undergo simulated diffusion and interaction. We find that specific complexes are quite robust to interference from promiscuous interaction partners only in the range of temperatures T(design) > T > T(rand). At T > T(design), specific complexes become unstable, whereas at T < T(rand), formation of specific complexes is suppressed by promiscuous interactions. Specific interactions can form only if T(design) > T(rand). This condition requires an energy gap between binding energy in a specific complex and set of binding energies between randomly associating proteins, providing a general physical constraint on evolutionary selection or design of specific interacting protein interfaces. This work has implications for our understanding of how the protein repertoire functions and evolves within the context of cellular systems.
Project description:We present the first approach to integrative structural modeling of the biological mesoscale within an interactive visual environment. These complex models can comprise up to millions of molecules with defined atomic structures, locations, and interactions. Their construction has previously been attempted only within a non-visual and non-interactive environment. Our solution unites the modeling and visualization aspect, enabling interactive construction of atomic resolution mesoscale models of large portions of a cell. We present a novel set of GPU algorithms that build the basis for the rapid construction of complex biological structures. These structures consist of multiple membrane-enclosed compartments including both soluble molecules and fibrous structures. The compartments are defined using volume voxelization of triangulated meshes. For membranes, we present an extension of the Wang Tile concept that populates the bilayer with individual lipids. Soluble molecules are populated within compartments distributed according to a Halton sequence. Fibrous structures, such as RNA or actin filaments, are created by self-avoiding random walks. Resulting overlaps of molecules are resolved by a forced-based system. Our approach opens new possibilities to the world of interactive construction of cellular compartments. We demonstrate its effectiveness by showcasing scenes of different scale and complexity that comprise blood plasma, mycoplasma, and HIV.
Project description:The design and assembly of novel colloidal particles are of both academic and technological interest. We developed a wet-chemical route to synthesize monodisperse bent rigid silica rods by controlled perturbation of emulsion-templated growth. The bending angle of the rods can be tuned in a range of 0-50° by varying the strength of perturbation in the reaction temperature or pH in the course of rod growth. The length of each arm of the bent rods can be individually controlled by adjusting the reaction time. For the first time we demonstrated that the bent silica rods resemble banana-shaped liquid-crystal molecules and assemble into ordered structures with a typical smectic B2 phase. The bent silica rods could serve as a visualizable mesoscopic model for exploiting the phase behaviors of bent molecules which represent a typical class of liquid-crystal molecules.
Project description:When a colloidal probe is forced through a viscoelastic fluid which is characterized by a long stress-relaxation time, the fluid is excited out of equilibrium. This is leading to a number of interesting effects including a non-trivial recoil of the probe when the driving force is removed. Here, we experimentally and theoretically investigate the transient recoil dynamics of non-spherical particles, i.e., colloidal dumbbells. In addition to a translational recoil of the dumbbells, we also find a pronounced angular reorientation which results from the relaxation of the surrounding fluid. Our findings are in good agreement with a Langevin description based on the symmetries of a director (dumbbell) as well as a microscopic bath-rod model. Remarkably, we find an instability with amplified fluctuations when the dumbbell is oriented perpendicular to the direction of driving. Our results demonstrate the complex behavior of non-spherical objects within a relaxing environment which are of immediate interest for the motion of externally but also self-driven asymmetric objects in viscoelastic fluids.
Project description:Optical tweezers provide a powerful tool to trap and manipulate living cells, which is expected to help people gain physiological insights at single-cell level. However, trapping and manipulating single cells under crowded environments, such as blood vessels and lymph nodes, is still a challenging task. To overcome this issue, an annular beam formed by the far-field Bessel beam is introduced to serve as an optical shield to isolate the target cells from being disturbed. With this scheme, we successfully trapped and manipulated single blood cells in a crowded environment. Furthermore, we demonstrated manipulation of two lymphocytes ejected from a lymph node independently with dual-trap optical tweezers, which paves the way for exploring cell interactions under living conditions. Such technique might be helpful in the study of how natural killer cells response to virus-infected cells or cancer cells.
Project description:Intracellular transport of cargo particles is performed by multiple motors working in concert. However, the mechanism of motor association to cargos is unknown. It is also unknown how long individual motors stay attached, how many are active, and how multimotor cargos would navigate a densely crowded filament with many other motors. Prior theoretical and experimental biophysical model systems of intracellular cargo have assumed fixed teams of motors transporting along bare microtubules or microtubules with fixed obstacles. Here, we investigate a regime of cargos transporting along microtubules crowded with free motors. Furthermore, we use cargos that are able to associate or dissociate motors as it translocates. We perform in vitro motility reconstitution experiments with high-resolution particle tracking. Our model system consists of a quantum dot cargo attached to kinesin motors, and additional free kinesin motors that act as traffic along the microtubule. Although high densities of kinesin motors hinder forward motion, resulting in a lower velocity, the ability to associate motors appears to enhance the run length and attachment time of the quantum dot, improving overall cargo transport. These results suggest that cargos that can associate new motors as they transport could overcome traffic jams.
Project description:Molecular crowding is a critical feature distinguishing intracellular environments from idealized solution-based environments and is essential to understanding numerous biochemical reactions, from protein folding to signal transduction. Many biochemical reactions are dramatically altered by crowding, yet it is extremely difficult to predict how crowding will quantitatively affect any particular reaction systems. We previously developed a novel stochastic off-lattice model to efficiently simulate binding reactions across wide parameter ranges in various crowded conditions. We now show that a polynomial regression model can incorporate several interrelated parameters influencing chemistry under crowded conditions. The unified model of binding equilibria accurately reproduces the results of particle simulations over a broad range of variation of six physical parameters that collectively yield a complicated, non-linear crowding effect. The work represents an important step toward the long-term goal of computationally tractable predictive models of reaction chemistry in the cellular environment.
Project description:Tracking single molecules inside cells reveals the dynamics of biological processes, including receptor trafficking, signalling and cargo transport. However, individual molecules often cannot be resolved inside cells due to their high density. Here we develop the PhotoGate technique that controls the number of fluorescent particles in a region of interest by repeatedly photobleaching its boundary. PhotoGate bypasses the requirement of photoactivation to track single particles at surface densities two orders of magnitude greater than the single-molecule detection limit. Using this method, we observe ligand-induced dimerization of a receptor tyrosine kinase at the cell surface and directly measure binding and dissociation of signalling molecules from early endosomes in a dense cytoplasm with single-molecule resolution. We additionally develop a numerical simulation suite for rapid quantitative optimization of Photogate experimental conditions. PhotoGate yields longer tracking times and more accurate measurements of complex stoichiometry than existing single-molecule imaging methods.
Project description:Here, we demonstrate the novel double-component liquid crystalline colloids composed of mesogenic inorganic nanosheets and the rods with dynamically variable length controlled by temperature. As the length-controllable rod, stiff biopolymer microtubule is used, which was successfully polymerized/depolymerized from tubulin proteins through a biochemical process even in the presence of the nanosheets. The mesoscopic structure of the liquid crystal phase was reversibly modifiable as caused by the change of the rod length.