Related papers: Enhanced diffusion and chemotaxis at the nanoscale
Classical descriptions of enzyme kinetics ignore the physical nature of the intracellular environment. Main implicit assumptions behind such approaches are that reactions occur in compartment volumes which are large enough so that molecular…
Epitaxial growth on a surface vicinal to a high-symmetry crystallographic plane occurs through the propagation of atomic steps, a process called step-flow growth. In some instances, the steps tend to form close groups (or bunches), a…
Push-pull networks are ubiquitous in signal transduction pathways in both prokaryotic and eukaryotic cells. They allow cells to strongly amplify signals via the mechanism of zero-order ultrasensitivity. In a push-pull network, two…
A protein undergoes conformational dynamics with multiple time scales, which results in fluctuating enzyme activities. Recent studies in single molecule enzymology have observe this "age-old" dynamic disorder phenomenon directly. However,…
Multicellular chemotaxis can occur via individually chemotaxing cells that are mechanically coupled. Alternatively, it can emerge collectively, from cells chemotaxing differently in a group than they would individually. Here we consider…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Enzyme-catalysed reactions involve two distinct timescales. There is a short timescale on which enzymes bind to substrate molecules to produce bound complexes, and a comparatively long timescale on which the complex is transformed into a…
Chemotaxis and haptotaxis have been a main theme in the macroscopic study of bacterial and cellular motility. In this work we investigate the influence these processes have on the shape and motility of fast migrating cells. We note that…
In this work we investigate the convergence to equilibrium for mass action reaction-diffusion systems which model irreversible enzyme reactions. Using the standard entropy method in this situation is not feasible as the irreversibility of…
Directed cell motion in response to an external chemical gradient occurs in many biological phenomena such as wound healing, angiogenesis, and cancer metastasis. Chemotaxis is often characterized by the accuracy, persistence, and speed of…
The self-sustained motion of fluids on gradient substrates is a spectacular phenomenon, which can be employed and controlled in applications by carefully engineering the substrate properties. Here, we report on a design of a gel substrate…
This paper introduces a reaction-diffusion-chemotaxis model for bacterial aggregation patterns on the surface of thin agar plates. It is based on the non-linear degenerate cross diffusion model proposed by Kawasaki et al. (J. of Theor.…
Selected theoretical developments in modeling of deposition of submicrometer size (submicron) particles on solid surfaces, with and without surface diffusion, of interest in colloid, polymer, and certain biological systems, are surveyed. We…
Diffusiophoresis, a ubiquitous phenomenon that induces particle transport whenever solute concentration gradients are present, was recently observed in the context of microsystems and shown to strongly impact colloidal transport (patterning…
Most of our understanding of bacterial chemotaxis comes from studies of Escherichia coli. However, recent evidence suggests significant departures from the E. coli paradigm in other bacterial species. This variation may stem from different…
Biomolecular condensates help organize the cell cytoplasm and nucleoplasm into spatial compartments with different chemical compositions. A key feature of such compositional patterning is the local enrichment of enzymatically active…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
Chemotaxis plays a crucial role in a variety of processes in biology and ecology. Quite often it acts to improve efficiency of biological reactions; one example is the immune system signalling, where infected tissues release chemokines…
One of simplest examples of navigation found in nature is run-and-tumble chemotaxis. Tumbles reorient cells randomly, and cells can drift toward attractants or away from repellents by biasing the frequency of these events. The post-tumble…