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We propose an efficient threshold dynamics method for topology optimization for fluids modeled with the Stokes equation. The proposed algorithm is based on minimization of an objective energy function that consists of the dissipation power…
Flows are essential to transport resources over large distances. As soon as diffusion becomes time-limiting, flows are needed. Flows are key for the function of multiple human organs, from the blood vasculature to the lungs, the digestive…
In wet-lab experiments, the slime mold Physarum polycephalum has demonstrated its ability to solve shortest path problems and to design efficient networks. For the shortest path problem, a mathematical model for the evolution of the slime…
A fundamental question in the conjunction of information theory, biophysics, bioinformatics and thermodynamics relates to the principles and processes that guide the development of natural intelligence in natural environments where…
Model reduction of biochemical networks relies on the knowledge of slow and fast variables. We provide a geometric method, based on the Newton polytope, to identify slow variables of a biochemical network with polynomial rate functions. The…
This article demonstrates how an understanding of the geometry of a family of cost functions can be used to develop efficient numerical algorithms for real-time optimisation. Crucially, it is not the geometry of the individual functions…
Numerous problems of both theoretical and practical interest are related to finding shortest (or otherwise optimal) paths in networks, frequently in the presence of some obstacles or constraints. A somewhat related class of problems focuses…
Dynamic flux balance analysis uses a quasi-steady state assumption to calculate an organism's metabolic activity at each time-step of a dynamic simulation, using the well-known technique of flux balance analysis. For microbial communities,…
Many real-world systems are characterized by stochastic dynamical rules where a complex network of interactions among individual elements probabilistically determines their state. Even with full knowledge of the network structure and of the…
We address the problem of identifying the dynamical law governing the evolution of a population of indistinguishable particles, when only aggregate distributions at successive times are observed. Assuming a Markovian evolution on a discrete…
The aim of this paper is a short survey of models and methods that developed by the authors. These models and methods are used to optimize general networks with nonlinear non-convex restrictions and objectives possessing mixed…
Complex networks characterized by global transport processes rely on the presence of directed paths from input to output nodes and edges, which organize in characteristic linked components. The analysis of such network-spanning structures…
The rapid proliferation of food delivery platforms has reshaped urban mobility but has also contributed significantly to environmental degradation through increased greenhouse gas emissions. Existing optimization mechanisms produce…
An important challenge in theoretical ecology is to find good, coarse-grained representations of complex food webs. Here we use the approach of generalized modeling to show that it may be possible to formulate a coarse-graining algorithm…
This paper presents a convex optimization framework for eco-driving and vehicle energy management problems. We will first show that several types of eco-driving and vehicle energy management problems can be modelled using the same notions…
Predicting the fate of ecologies is a daunting, albeit extremely important, task. As part of this task one needs to develop an understanding of the organization, hierarchies, and correlations among the species forming the ecology. Focusing…
The paper focuses on a multidimensional optimization problem, which is formulated in terms of tropical mathematics and consists in minimizing a nonlinear objective function subject to linear inequality constraints. To solve the problem, we…
We examine the dynamic network flow problem under the assumption that the flow consists of discrete units. The dynamic network flow problem is commonly addressed in the context of developing evacuation plans, where the flow is typically…
Optimal Experiment Design for parameter estimation in water networks has been traditionally formulated to maximize either hydraulic model accuracy or spatial coverage. Because a unique sensor configuration that optimizes both objectives may…
Many applications of computational fluid dynamics require multiple simulations of a flow under different input conditions. In this paper, a numerical algorithm is developed to efficiently determine a set of such simulations in which the…