Related papers: A generalized kinetic framework applied to whole-c…
System dynamics is a popular approach in many fields of science and technology, but it has not been investigated for cell signaling pathways yet. It is a well formulated methodology used to analyze the components of a system considering the…
To ensure homogeneous conditions within the complete area of perfused microfluidic bio-reactors, we develop a general design of a continuously feed bio-reactor with uniform perfusion flow. This is achieved by introducing a specific type of…
The Betz limit expresses the maximum proportion of the kinetic energy flux incident on an energy conversion device that can be extracted from an unbounded flow. The derivation of the Betz limit requires an assumption of steady flow through…
We experimentally study the emergence of collective bacterial swimming, a phenomenon often referred to as bacterial turbulence. A phase diagram of the flow of 3D E. coli suspensions spanned by bacterial concentration, the swimming speed of…
Transformers are central to advances in artificial intelligence (AI), excelling in fields ranging from computer vision to natural language processing. Despite their success, their large parameter count and computational demands challenge…
To advance understanding of cellular metabolism and reduce batch-to-batch variability in cell culture processes, this study introduces a multi-scale hybrid modeling framework designed to simulate and predict the dynamic behavior of CHO cell…
Two kinetic models are proposed for high-temperature rarefied (or non-equilibrium) gas flows with radiation. One of the models uses the Boltzmann collision operator to model the translational motion of gas molecules, which has the ability…
We develop a semi-analytical model for transport in structured catalytic microreactors, where both reactant and product are compressible fluids. Making use of the lubrication and Fick-Jacobs approximations, we reduce the three-dimensional…
Understanding the system level adaptive changes taking place in an organism in response to variations in the environment is a key issue of contemporary biology. Current modeling approaches such as the constraint-based flux balance analyses…
We present a numerical method to model the dynamics of inextensible biomembranes in a quasi-Newtonian incompressible flow, which better describes hemorheology in the small vasculature. We consider a level set model for the fluid-membrane…
In biochemical systems the Michaelis-Menten (MM) scheme is one of the best-known models of the enzyme- catalyzed kinetics. In the academic literature the MM approximation has been thoroughly studied in the context of differential equation…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Particle-based simulations are an essential tool for the study of biochemical systems for scales between molecular/Brownian dynamics and the reaction-diffusion master equation. These simulations utilise proximity-based reaction conditions…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
The finite element simulation of dynamic wetting phenomena, requiring the computation of flow in a domain confined by intersecting a liquid-fluid free surface and a liquid-solid interface, with the three-phase contact line moving across the…
An alternative step in understanding the flows of near wall drag-reducing turbulence can be examining the flow in a well-organized streamwise vortex with a laminar background. Herein, we studied the flow behaviors of the Giesekus…
We report on electrically-induced rotations in water films, which can function at many length scales. The device consists of a two-dimensional cell used for electrolysis of water films, as simple as an insulator frame with two electrodes on…
The dynamics of cellular aggregates is driven by the interplay of mechanochemical processes and cellular activity. Although deterministic models may capture mechanical features, local chemical fluctuations trigger random cell responses,…
Metal-organic frameworks (MOFs) provide a versatile and tailorable material platform that embody many desirable attributes for photocatalytic water-splitting. The approach taken in this study was to use Density Functional Theory (DFT) to…
This is the first report, to our knowledge, on a systematic method for constructing a large scale kinetic metabolic model with incomplete information on kinetic parametersr, and its initial application to the modeling of central metabolism…