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Thermophilic enzymes can operate at higher temperatures but show reduced activities at room temperature. They are in general more stable during preparation and, accordingly, are considered to be more rigid in structure. Crystallization is…
We study a synthetic system of motile Escherichia coli bacteria encapsulated inside giant lipid vesicles. Forces exerted by the bacteria on the inner side of the membrane are sufficient to extrude membrane tubes filled with one or several…
The transport of molecules through biological and synthetic nanopores is governed by multiple stochastic processes that lead to noisy, fluctuating currents. Disentangling the characteristics of different noise-generating mechanisms is…
We use molecular dynamics simulations to study the behavior of supercooled water subject to different stimuli from a diluted azobenzene hydrophobic probe. When the molecular motor does not fold, it acts as a passive probe, modifying the…
Numerous natural systems depend on the sedimentation of passive particles in presence of swimming microorganisms. Here, we investigate the dynamics of the sedimentation of spherical colloids at various E. coli concentration within the…
Motivated by the aim of understanding the effect of media heterogeneity on the swimming dynamics of flagellated bacteria, we study the rotation and swimming of rigid helices in dilute suspensions experimentally and theoretically. We first…
In bacterial chemotaxis, E. coli cells drift up chemical gradients by a series of runs and tumbles. Runs are periods of directed swimming, and tumbles are abrupt changes in swimming direction. Near the beginning of each run, the rotating…
Helical propulsion is used by many microorganisms to swim in viscous-dominated environments. Their swimming dynamics are relatively well understood, but detailed study of the flow fields and actuation mechanisms are still needed to realize…
Run-and-tumble is a basic model of persistent motion and a motility strategy widespread in micro-organisms and individual cells. In many natural settings, movement occurs in the presence of confinement. While accumulation at the surface has…
The presence of a nearby boundary is likely to be important in the life cycle and evolution of motile flagellate bacteria. This has led many authors to employ numerical simulations to model near-surface bacterial motion and compute…
As a paradigmatic model of active fluids, bacterial suspensions show intriguing rheological responses drastically different from their counterpart colloidal suspensions. Although the flow of bulk bacterial suspensions has been extensively…
The transport of an infinitely thin, hard rod in a random, dense array of point obstacles is investigated by molecular dynamics simulations. Our model mimics the sterically hindered dynamics in dense needle liquids. The center-of-mass…
We consider a heat conduction model introduced in \cite{Collet-Eckmann 2009}. This is an open system in which particles exchange momentum with a row of (fixed) scatterers. We assume simplified bath conditions throughout, and give a…
We show that the flagellar beat of bull spermatozoa and Chlamydomonas Reinhardtii can be modelled by a minimal, geometrically nonlinear reaction-diffusion system. Model solutions are spatio-temporally animated patterns describing flagellar…
Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active…
We study diffusion properties of an inertial Brownian motor moving on a ratchet substrate, i.e. a periodic structure with broken reflection symmetry. The motor is driven by an unbiased time-periodic symmetric force which takes the system…
Single-molecule experiments have found near-perfect thermodynamic efficiency in the rotary motor F1-ATP synthase. To help elucidate the principles underlying nonequilibrium energetic efficiency in such stochastic machines, we investigate…
In the present work we simulate the basic two-dimensional dynamics of swarming E. coli bacteria on the surface of a moderately soft agar plate. Individual bacteria are modelled by self-propelled ridged bodies (agents), which interact with…
We investigate the dynamics of a pair of rigid rotating helices in a viscous fluid, as a model for bacterial flagellar bundle and a prototype of microfluidic pumps. Combining experiments with hydrodynamic modeling, we examine how spacing…
Peritrichous bacteria such as Escherichia coli swim in viscous fluids by forming a helical bundle of flagellar filaments. The filaments are spatially distributed around the cell body to which they are connected via a flexible hook. To…