Related papers: Flux cost functions and optimal metabolic states
Modeling to generate alternatives (MGA) is an increasingly popular method in energy system optimization. MGA explores the near-optimal space, namely, system alternatives whose costs are within a certain fraction of the globally optimal…
Flux of rigid or soft particles (such as drops, vesicles, red blood cells, etc.) in a channel is a complex function of particle concentration, which depends on the details of induced dissipation and suspension structure due to hydrodynamic…
Various biological system models have been proposed in systems biology, which are based on the complex biological reactions kinetic of various components. These models are not practical because we lack of kinetic information. In this paper,…
Mathematical and statistical models underlie many of the world's most important fisheries management decisions. Since the 19th century, difficulty calibrating and fitting such models has been used to justify the selection of simple,…
Empirical force fields employed in molecular dynamics simulations of complex systems can be optimised to reproduce experimentally determined structural and thermodynamic properties. In contrast, experimental knowledge about the rates of…
We analyse the efficiency of several simulation methods which we have recently proposed for calculating rate constants for rare events in stochastic dynamical systems, in or out of equilibrium. We derive analytical expressions for the…
Soft biological tissues demonstrate strong time-dependent and strain-rate mechanical behavior, arising from their intrinsic visco-elasticity and fluid-solid interactions (especially at sufficiently large time scales). The time-dependent…
We present a specialized network simplex algorithm for the budget-constrained minimum cost flow problem, which is an extension of the traditional minimum cost flow problem by a second kind of costs associated with each edge, whose total…
Returning a system to a desired state under a force field involves a thermodynamic cost, i.e., {\it work}. This cost fluctuates for a small-scale system from one experimental realization to another. We introduce a general framework to…
We study the optimal provision of information for two natural performance measures of queuing systems: throughput and makespan. A set of parallel links is equipped with deterministic capacities and stochastic travel times where the latter…
Cell blebs are protrusions of the cell membrane and can be instrumental for cell migration. We derive a continuum model for the mechanical and geometrical aspects of the onset of blebbing in terms of a force balance. It is abstract and…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
There is increasing interest in the analysis of biological tissue, its organization and its dynamics with the help of mathematical models. In the ideal case emergent properties on the tissue scale can be derived from the cellular scale.…
We study the surface fluctuations of a tissue with a dynamics dictated by cell-rearrangement, cell-division, and cell-death processes. Surface fluctuations are calculated in the homeostatic state, where cell division and cell death…
Recent work on particle-based models of tissues has suggested that any finite rate of cell division and cell death is sufficient to fluidize an epithelial tissue. At the same time, experimental evidence has indicated the existence of glassy…
In this paper, we investigate the network utility maximization problem in FDMA systems. We summarize with a suite of criteria on designing utility functions so as to achieve the global optimization convex. After proposing the general form…
Metagenomics has revealed hundreds of bacterial species in almost all microbiota. In a few well-studied cases, bacterial communities have been observed to coordinate their metabolic fluxes. In principle, bacteria can divide tasks to reap…
In this paper, a system architecture is proposed that approximately models the functionality of metabolic networks. The AND/OR graph model is used to represent the metabolic network and each processing element in the system emulates the…
Flux reconstruction provides a framework for solving partial differential equations in which functions are discontinuously approximated within elements. Typically, this is done by using polynomials. Here, the use of radial basis functions…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…