Subscribe to the gold package and get unlimited access to Shamra Academy
Register a new userMolecular Assembly Lines in Active Droplets
308
0
0.0
(
0
)
Ask ChatGPT about the research
No Arabic abstract
Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific sequence of assembly steps. Using droplet interfaces to position compartment boundaries, we show that an assembly line can be self organized by active droplets. As a consequence, assembly steps can be arranged spatially so that a specific order of assembly is achieved and incorrect assembly is strongly suppressed.
rate research
Read More
Myosin motor proteins drive vigorous steady-state fluctuations in the actin cytoskeleton of cells. Endogenous embedded semiflexible filaments such as microtubules, or added filaments such as single-walled carbon nanotubes are used as novel tools to non-invasively track equilibrium and non-equilibrium fluctuations in such biopolymer networks. Here we analytically calculate shape fluctuations of semiflexible probe filaments in a viscoelastic environment, driven out of equilibrium by motor activity. Transverse bending fluctuations of the probe filaments can be decomposed into dynamic normal modes. We find that these modes no longer evolve independently under non-equilibrium driving. This effective mode coupling results in non-zero circulatory currents in a conformational phase space, reflecting a violation of detailed balance. We present predictions for the characteristic frequencies associated with these currents and investigate how the temporal signatures of motor activity determine mode correlations, which we find to be consistent with recent experiments on microtubules embedded in cytoskeletal networks.
We study collections of self-propelled rods (SPR) moving in two dimensions for packing fractions less than or equal to 0.3. We find that in the thermodynamical limit the SPR undergo a phase transition between a disordered gas and a novel phase-separated system state. Interestingly, (global) orientational order patterns -- contrary to what has been suggested -- vanish in this limit. In the found novel state, the SPR self-organize into a highly dynamical, high-density, compact region - which we call aggregate - which is surrounded by a disordered gas. Active stresses build inside aggregates as result of the combined effect of local orientational order and active forces. This leads to the most distinctive feature of these aggregates: constant ejection of polar clusters of SPR. This novel phase-separated state represents a novel state of matter characterized by large fluctuations in volume and shape, related to mass ejection, and exhibits positional as well as orientational local order. SPR systems display new physics unseen in other active matter systems due to the coupling between density, active stresses, and orientational order (such coupling cannot be reduced simply to a coupling between speed and density).
A stochastic version of the Barkai-Leibler model of chemotaxis receptors in {it E. coli} is studied here to elucidate the effects of intrinsic network noise in their conformational dynamics. It was originally proposed to explain the robust and near-perfect adaptation of {it E. coli} observed across a wide range of spatially uniform attractant/repellent (ligand) concentrations. A receptor is either active or inactive and can stochastically switch between the two states. Enzyme CheR methylates inactive receptors while CheB demethylates active ones and the probability for it to be active depends on its level of methylation and ligandation. A simple version of the model with two methylation sites per receptor (M=2) shows zero-order ultrasensitivity (ZOU) akin to the classical 2-state model of covalent modification studied by Goldbeter and Koshland (GK). For extremely small and large ligand concentrations, the system reduces to two 2-state GK modules. A quantitative measure of the spontaneous fluctuations in activity (variance) estimated mathematically under linear noise approximation (LNA) is found to peak near the ZOU transition. The variance is a weak, non-monotonic and decreasing functions of ligand and receptor concentrations. Gillespie simulations for M=2 show excellent agreement with analytical results obtained under LNA. Numerical results for M=2, 3 and 4 show ZOU in mean activity; the variance is found to be smaller for larger M. The magnitude of receptor noise deduced from available experimental data is consistent with our predictions. A simple analysis of the downstream signaling pathway shows that this noise is large enough to have a beneficial effect on the motility of the organism. The response of mean receptor activity to small time-dependent changes in the external ligand concentration, computed within linear response theory, is found to have a bilobe form.
Bacterial processes ranging from gene expression to motility and biofilm formation are constantly challenged by internal and external noise. While the importance of stochastic fluctuations has been appreciated for chemotaxis, it is currently believed that deterministic long-range fluid dynamical effects govern cell-cell and cell-surface scattering - the elementary events that lead to swarming and collective swimming in active suspensions and to the formation of biofilms. Here, we report the first direct measurements of the bacterial flow field generated by individual swimming Escherichia coli both far from and near to a solid surface. These experiments allowed us to examine the relative importance of fluid dynamics and rotational diffusion for bacteria. For cell-cell interactions it is shown that thermal and intrinsic stochasticity drown the effects of long-range fluid dynamics, implying that physical interactions between bacteria are determined by steric collisions and near-field lubrication forces. This dominance of short-range forces closely links collective motion in bacterial suspensions to self-organization in driven granular systems, assemblages of biofilaments, and animal flocks. For the scattering of bacteria with surfaces, long-range fluid dynamical interactions are also shown to be negligible before collisions; however, once the bacterium swims along the surface within a few microns after an aligning collision, hydrodynamic effects can contribute to the experimentally observed, long residence times. As these results are based on purely mechanical properties, they apply to a wide range of microorganisms.
By embedding inert tracer particles (TPs) in a growing multicellular spheroid the local stresses on the cancer cells (CCs) can be measured. In order for this technique to be effective the unknown effect of the dynamics of the TPs on the CCs has to be elucidated to ensure that the TPs do not greatly alter the local stresses on the CCs. We show, using theory and simulations, that the self-generated (active) forces arising from proliferation and apoptosis of the CCs drive the dynamics of the TPs far from equilibrium. On time scales less than the division times of the CCs, the TPs exhibit sub-diffusive dynamics (the mean square displacement, $Delta_{TP}(t) sim t^{beta_{TP}}$ with $beta_{TP}<1$), similar to glass-forming systems. Surprisingly, in the long-time limit, the motion of the TPs is hyper-diffusive ($Delta_{TP}(t) sim t^{alpha_{TP}}$ with $alpha_{TP}>2$) due to persistent directed motion for long times. In comparison, proliferation of the CCs randomizes their motion leading to superdiffusive behavior with $alpha_{CC}$ exceeding unity. Most importantly, $alpha_{CC}$ is not significantly affected by the TPs. Our predictions could be tested using textit{in vitro} imaging methods where the motion of the TPs and the CCs can be tracked.
Log in to be able to interact and post comments
comments
Fetching comments
Sign in to be able to follow your search criteria
