Related papers: Flux cost functions and optimal metabolic states
Despite major environmental and genetic differences, microbial metabolic networks are known to generate consistent physiological outcomes across vastly different organisms. This remarkable robustness suggests that, at least in bacteria,…
The driving force for active physical and biological systems is determined by both the underlying landscape and the non-equilibrium curl flux. While landscape can be quantified in the experiments by the histograms of the collecting…
We present a new kinetic equation for cell migration driven by mechanical interactions with the substrate, an effect not previously captured in kinetic models, and essential for explaining observed collective behaviors such as those in…
We revisit optimal execution of an active portfolio in the presence of slippage (aka linear, proportional, or absolute-value) costs. Market efficiency implies a close balance between active alphas and trading costs, so even small changes to…
We develop an empirical Bayes procedure for estimating the cell means in an unbalanced, two-way additive model with fixed effects. We employ a hierarchical model, which reflects exchangeability of the effects within treatment and within…
Active nematic models explain the topological defects and flow patterns observed in epithelial tissues, but the nature of active stress-whether it is extensile or contractile, a key parameter of the theory-is not well established…
Cost volumes are used in every modern optical flow estimator, but due to their computational and space complexity, they are often a limiting factor regarding both processing speed and the resolution of input frames. Motivated by our…
Biological systems are governed by coupled interactions between intracellular metabolism and bioreactor operation that span multiple time scales. Constraint-based metabolic models are widely used to describe intracellular metabolism, but…
The present paper deals with the problem of improving the efficiency of large scale turbulent flow simulations. The high-fidelity methods for modelling turbulent flows become available for a wider range of applications thanks to the…
We investigate fusing several unreliable computational units that perform the same task. We model an unreliable computational outcome as an additive perturbation to its error-free result in terms of its fidelity and cost. We analyze…
The higher-order gas-kinetic scheme for solving the Navier-Stokes equations has been studied in recent years. In addition to the use of higher-order reconstruction techniques, many terms are used in the Taylor expansion of the gas…
We present a model for continuous cell culture coupling intra-cellular metabolism to extracellular variables describing the state of the bioreactor, taking into account the growth capacity of the cell and the impact of toxic byproduct…
In this paper, we study the following batch scheduling model: find a schedule that minimizes total flow time for $n$ uniform length jobs, with release times and deadlines, where the machine is only actively processing jobs in at most $k$…
The biomechanics of the human body allow humans a range of possible ways of executing movements to attain specific goals. Nevertheless, humans exhibit significant patterns in how they execute movements. We propose that the observed patterns…
We study the force generation by a set of parallel actin filaments growing against an elastic membrane. The elastic membrane tries to stay flat and any deformation from this flat state, either caused by thermal fluctuations or due to…
Several enzymes exhibit enhanced diffusion in the presence of a substrate. One explanation of this enhancement arises from fluctuating dimer models, which suggest that enzymes have a higher diffusion constant when interacting with…
We describe modeling approaches to a "network" of connected enzyme-catalyzed reactions, with added (bio)chemical processes that introduce biochemical filtering steps into the functioning of such a biocatalytic cascade. Theoretical…
All cells must sustain ionic motive forces (IMFs) -- the electrochemical gradients of permeant ions, together with the membrane potential they produce -- to regulate intracellular pH, drive secondary transport, and power ATP synthesis.…
An extended range of energy stable flux reconstruction schemes, developed using a summation-by-parts approach, is presented on quadrilateral elements for various sets of polynomial bases. For the maximal order bases, a new set of correction…
We study the current rectification of particles moving in a pulsating channel under the in uence of an applied force. We have shown the existence of diferent rectification scenarios in which entropic and energetic effects compete. The…