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The acoustofluidic method holds great promise for manipulating microorganisms. When exposed to the steady vortex structures of acoustic streaming flow, these microorganisms exhibit intriguing dynamic behaviors, such as hydrodynamic trapping…
Bacterial biofilms are among the oldest and most prevalent multicellular life forms on Earth and are increasingly relevant in research areas related to industrial fouling, medicine and biotechnology. The main hurdles to obtaining definitive…
The controlled transport of colloids in dead-end structures is a key capability that can enable a wide range of applications, such as bio-chemical analysis, drug delivery and underground oil recovery. This letter presents a new trapping…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
Generative models on discrete state-spaces have a wide range of potential applications, particularly in the domain of natural sciences. In continuous state-spaces, controllable and flexible generation of samples with desired properties has…
Colloid or nanoparticle mobility under confinement is of central importance to a wide range of physical and biological processes. Here, we introduce a minimal model of particles in a hydrodynamic continuum to examine how particle shape and…
Hypothesis:Diffusion in confinement is an important fundamental problem with significant implications for applications of supported liquid phases. However, resolving the spatially dependent diffusion coefficient, parallel and perpendicular…
Viscosity is a fundamental property of liquids and determines the diffusivity of suspended particles. A gradient in viscosity leads to a gradient in diffusivity, yet it is unknown whether such a gradient can lead to directed transport of…
We propose a new scheme to infer the metabolic fluxes of cell cultures in a chemostat. Our approach is based on the Maximum Entropy Principle and exploits the understanding of the chemostat dynamics and its connection with the actual…
Metabolic substrates, such as oxygen and glucose, are rapidly delivered to the cell through filtration across microvessels walls. Modelling this important process is complicated by the coupling between flow and transport equations, which…
We introduce a model for ionic electrodiffusion and osmotic water flow through cells and tissues. The model consists of a system of partial differential equations for ionic concentration and fluid flow with interface conditions at deforming…
We investigate the margination of microparticles/platelets in blood flow through complex geometries typical for in vivo vessel networks: a vessel confluence and a bifurcation. Using 3D Lattice-Boltzmann simulations, we confirm that behind…
We introduce an in silico model for the initial spread of an aberrant phenotype with Warburg-like overflow metabolism within a healthy homeostatic tissue in contact with a nutrient reservoir (the blood), aimed at characterizing the role of…
Cells coexist together in colonies or as tissues. Their behaviour is controlled by an interplay between intercellular forces and biochemical regulation. We develop a simple model of the cell cycle, the fundamental regulatory network…
The biotransport of the intravascular nanoparticle (NP) is influenced by both the complex cellular flow environment and the NP characteristics. Being able to computationally simulate such intricate transport phenomenon with high efficiency…
The essence of a chemical reaction lies in the redistribution and reorganization of electrons, which is often manifested through electron transfer or the migration of electron pairs. These changes are inherently discrete and abrupt in the…
Living cells display a remarkable capacity to compartmentalize their functional biochemistry. A particularly fascinating example is the cell nucleus. Exchange of macromolecules between the nucleus and the surrounding cytoplasm does not…
In a recent paper, Michael J. Saxton proposes to interpret as anomalous diffusion the occurrence of apparent transient sub-diffusive regimes in mean-squared displacements (MSD) plots, calculated from experimental trajectories of molecules…
Driven by fundamental thermodynamic efficiency considerations, an emerging trend in the energy and propulsion systems is that the working fluid operates at a pressure above the critical pressure. Energy transport is thus accompanied by…
We study the transport and deposition dynamics of colloids in saturated porous media under unfavorable filtering conditions. As an alternative to traditional convection-diffusion or more detailed numerical models, we consider a mean-field…