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The control over DNA elongation in nanofluidic devices holds great potential for large-scale genomic analysis. So far, the manipulation of DNA in nanochannels has been mostly carried out with electrophoresis and seldom with hydrodynamics,…
We introduce and theoretically investigate a minimal particle-based model for a new class of active matter where particles exhibit directional, volume-conserving division in confinement while interacting sterically, mimicking cells in early…
In this work, we present a novel approach to process the DIC measurements of multiple biaxial stretching protocols. In particular, we develop a optimization-based approach, which calculates the smoothed nodal displacements using a moving…
Brownian motion provides access to hydrodynamic properties of nanoscale objects independent of their optical resolvability. Here, we present a diffusion-based approach to infer effective particle size distributions of DNA-functionalized…
Recent experiments on active materials, such as dense bacterial suspensions and microtubule-kinesin motor mixtures, show a promising potential for achieving self-sustained flows. However, to develop active microfluidics it is necessary to…
Bacterial biofilms play a significant role in various fields that impact our daily lives, from detrimental public health hazards to beneficial applications in bioremediation, biodegradation, and wastewater treatment. However,…
Cells and other soft particles are often forced to flow in confined geometries in both laboratory and natural environments, where the elastic deformation induces an additional drag and pressure drop across the particle. In contrast with…
The coarse-grained molecular dynamics (MD) or Brownian dynamics (BD) simulation is a particle-based approach that has been applied to a wide range of biological problems that involve interactions with surrounding fluid molecules or the…
In molecular dynamics simulations, nanochannel flows are usually driven by a constant force, that aims to represent a pressure difference between inlet and outlet, and periodic boundary conditions are applied in the streamwise direction…
We introduce a simulation strategy to consistently couple continuum biomembrane dynamics to the motion of discrete biological macromolecules residing within or on the membrane. The methodology is used to study the diffusion of integral…
Biological microswimmers often encounter deformable boundaries in physiological conditions; for instance, the viscoelastic walls of reproductive tract during migration of spermatozoa, or host tissue during early bacterial biofilm formation.…
Trajectory tracking for microswimmers remains a key challenge in microrobotics, where low-Reynolds-number dynamics make control design particularly complex. In this work, we formulate the trajectory tracking problem as an optimal control…
Trajectories of endosomes inside living eukaryotic cells are highly heterogeneous in space and time and diffuse anomalously due to a combination of viscoelasticity, caging, aggregation and active transport. Some of the trajectories display…
The motion of self-propelled particles is modeled as a persistent random walk. An analytical framework is developed that allows the derivation of exact expressions for the time evolution of arbitrary moments of the persistent walk's…
Using scaling arguments and extensive numerical simulations, we study dynamics of a tracer particle in a corrugated channel represented by a periodic sequence of broad chambers and narrow funnel-like bottlenecks enclosed by a hard-wall…
Devising optimal interventions for constraining stochastic systems is a challenging endeavour that has to confront the interplay between randomness and nonlinearity. Existing methods for identifying the necessary dynamical adjustments…
Many aquatic organisms are able to track ambient flow disturbances and locate their source. These tasks are particularly challenging because they require the organism to sense local flow information and respond accordingly. Details of how…
We study the stochastic motion of active particles that undergo spontaneous transitions between two distinct modes of motion. Each mode is characterized by a velocity distribution and an arbitrary (anti-)persistence. We present an…
The transport of motile entities across modulated energy landscapes plays an important role in a range of phenomena in biology, colloidal science and solid-state physics. Here, an easily implementable strategy that allows for the collective…
The manipulation of a collection of fluid particles in a low Reynolds number environment has several important applications. As we demonstrate in this paper, this manipulation problem is related to the scientific question of how fluid flow…