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A problem studied in Systems Biology is how to find shortest paths in metabolic networks. Unfortunately, simple (i.e., graph theoretic) shortest paths do not properly reflect biochemical facts. An approach to overcome this issue is to use…
Quite generally, constraint-based metabolic flux analysis describes the space of viable flux configurations for a metabolic network as a high-dimensional polytope defined by the linear constraints that enforce the balancing of production…
We introduce the notion of a network's conduciveness, a probabilistically interpretable measure of how the network's structure allows it to be conducive to roaming agents, in certain conditions, from one portion of the network to another.…
Locally broken symmetries are used across fields to transport matter, particles and information in preferential directions. Beyond local mechanisms, spatially distributed nonlinearities in crystalline media have enabled non-reciprocal…
Modern biological tools have made it possible to unequivocally demonstrate the deep relationship among species in terms of genes and basic molecular mechanisms. In addition, results from genetic, physical and physiological approaches…
Transport networks are crucial to the functioning of natural and technological systems. Nature features transport networks that are adaptive over a vast range of parameters, thus providing an impressive level of robustness in supply.…
The structure and dynamics of a typical biological system are complex due to strong and inhomogeneous interactions between its constituents. The investigation of such systems with classical mathematical tools, such as differential equations…
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…
In this paper, we study the application of GIST SVM in disease prediction (detection of cancer). Pattern classification problems can be effectively solved by Support vector machines. Here we propose a classifier which can differentiate…
Branched Optimal Transport (BOT) is a generalization of optimal transport in which transportation costs along an edge are subadditive. This subadditivity models an increase in transport efficiency when shipping mass along the same route,…
Molecular motors are macromolecular complexes which use some form of input energy to perform mechanical work. The filamentary tracks, on which these motors move, are made of either proteins (e.g., microtubules) or nucleic acids (DNA or…
Transport networks are crucial for the functioning of natural and technological systems. We study a mathematical model of vascular network adaptation, where the network structure dynamically adjusts to changes in blood flow and pressure.…
We present a novel framework for understanding node target search in systems organized as hierarchical networks-within-networks. Our work generalizes traditional search models on complex networks, where the mean-first passage time is…
Molecular motion through pores plays a crucial role in various natural and industrial processes. One of the most fascinating features of biological channel-facilitated transport is a stochastic gating process, when the channels dynamically…
Internet, social media, neuronal or blood vessel are organized in complex networks. These networks are characterized by several quantities such as the underlying graph connectivity (topology), how they grow in time, scaling laws or by the…
We present an algorithm for finding optimal paths for multiple stochastic agents in a graph to reach their destinations with a user-specified maximum pairwise collision probability. Our algorithm, called STT-CBS, uses Conflict-Based Search…
We show that graphs, networks and other related discrete model systems carry a natural supersymmetric structure, which, apart from its conceptual importance as to possible physical applications, allows to derive a series of spectral…
Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and…
One common feature of a vehicle, an ant and a kinesin motor is that they all convert chemical energy, derived from fuel or food, into mechanical energy required for their forward movement; such objects have been modelled in recent years as…
We propose a solution of the multiple target tracking (MTT) problem based on sets of trajectories and the random finite set framework. A full Bayesian approach to MTT should characterise the distribution of the trajectories given the…