Related papers: A biologically inspired model for transshipment pr…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
The growth of world population, limitation of resources, economic problems and environmental issues force engineers to develop increasingly efficient solutions for logistic systems. Pure optimization for efficiency, however, has often led…
We introduce a modified and simplified version of the pre-existing fully parallelized three-dimensional Navier--Stokes flow solver known as TPLS. We demonstrate how the simplified version can be used as a pedagogical tool for the study of…
Using machine learning in solving constraint optimization and combinatorial problems is becoming an active research area in both computer science and operations research communities. This paper aims to predict a good solution for constraint…
In today's day and time solving real-world complex problems has become fundamentally vital and critical task. Many of these are combinatorial problems, where optimal solutions are sought rather than exact solutions. Traditional optimization…
We introduce a natural language interface for building stochastic pi calculus models of biological systems. In this language, complex constructs describing biochemical events are built from basic primitives of association, dissociation and…
Accurate representation of large-scale flow patterns in low-resolution ocean simulations is one of the most challenging problems in ocean modelling. The main difficulty is to correctly reproduce effects of unresolved small scales on the…
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,…
We study the connections between Physarum Dynamics and Dynamic Monge Kantorovich (DMK) Optimal Transport algorithms for the solution of Basis Pursuit problems. We show the equivalence between these two models and unveil their dynamic…
In this paper we present a novel transshipment problem for a large apparel retailer that operates an extensive retail network. Our problem is inspired by the logistics operations of a very large fast fashion retailer in Turkey, LC Waikiki,…
The design of control systems for the spatial self-organization of mobile agents is an open challenge across several engineering domains, including swarm robotics and synthetic biology. Here, we propose a bio-inspired leader-follower…
Active fluid transport is a hallmark of many biological transport networks. While animal circulatory systems generally rely on a single heart to drive flows, other organisms employ decentralized local pumps to distribute fluids and…
Nonlinear constrained optimization problems are encountered in many scientific fields. To utilize the huge calculation power of current computers, many mathematic models are also rebuilt as optimization problems. Most of them have…
Spacecraft trajectory design is a global search problem, where previous work has revealed specific solution structures that can be captured with data-driven methods. This paper explores two global search problems in the circular restricted…
This paper aims to introduce a concept of an equilibrium point of a dynamical system which will call it almost global asymptotically stable. A biological prey-predator model is also analyzed with a modification function growth in prey…
In this paper, a thermodynamically consistent phase-field model is proposed to describe the mass transport and reaction processes of multiple species in a fluid. A key feature of this model is that reactions between different species occur…
The dynamics of biological systems, from proteins to cells to organisms, is complex and stochastic. To decipher their physical laws, we need to bridge between experimental observations and theoretical modeling. Thanks to progress in…
Mode-based model-reduction is used to reduce the degrees of freedom of high dimensional systems, often by describing the system state by a linear combination of spatial modes. Transport dominated phenomena, ubiquitous in technical and…
The trade-off between model fidelity and computational cost remains a central challenge in the computational modeling of extrusion-based 3D printing, particularly for real time optimization and control. Although high fidelity simulations…
Many important chemical and biochemical processes in the condensed phase are notoriously difficult to simulate numerically. Often this difficulty arises from the complexity of simulating dynamics resulting from coupling to structured,…