Related papers: SMT Solving for Vesicle Traffic Systems in Cells
A model of communication that is able to cope simultaneously with the problems of search and congestion is presented. We investigate the communication dynamics in model networks and introduce a general framework that enables a search of…
Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and…
Traffic-like collective movements are observed at almost all levels of biological systems. Molecular motor proteins like, for example, kinesin and dynein, which are the vehicles of almost all intra-cellular transport in eukayotic cells,…
Single-particle tracking (SPT) has become a popular tool to study the intracellular transport of molecules in living cells. Inferring the character of their dynamics is important, because it determines the organization and functions of the…
To address the limitations of traffic prediction from location-bound detectors, we present Geographical Cellular Traffic (GCT) flow, a novel data source that leverages the extensive coverage of cellular traffic to capture mobility patterns.…
Recent advances in microscopy and 3D reconstruction methods have allowed for characterization of cellular morphology in unprecedented detail, including the irregular geometries of intracellular subcompartments such as membrane-bound…
It was hypothesized that the structures of biological transport networks are the result of either energy consumption or adaptation dynamics. Although approaches based on these hypotheses can produce optimal network and form loop structures,…
Biological processes, including cell differentiation, organism development, and disease progression, can be interpreted as attractors (fixed points or limit cycles) of an underlying networked dynamical system. In this paper, we study the…
Life and functioning of higher organisms depends on the continuous supply of metabolites to tissues and organs. What are the requirements on the transport network pervading a tissue to provide a uniform supply of nutrients, minerals, or…
This paper addresses a variant of multi-agent path finding (MAPF) in continuous space and time. We present a new solving approach based on satisfiability modulo theories (SMT) to obtain makespan optimal solutions. The standard MAPF is a…
High-throughput techniques are leading to an explosive growth in the size of biological databases and creating the opportunity to revolutionize our understanding of life and disease. Interpretation of these data remains, however, a major…
The Sinkhorn algorithm has emerged as a powerful tool for solving optimal transport problems, finding applications in various domains such as machine learning, image processing, and computational biology. Despite its widespread use, the…
Generating a novel and optimized molecule with desired chemical properties is an essential part of the drug discovery process. Failure to meet one of the required properties can frequently lead to failure in a clinical test which is costly.…
Understanding the mechanisms of interactions within cells, tissues, and organisms is crucial to driving developments across biology and medicine. Mathematical modeling is an essential tool for simulating biological systems and revealing…
Single-cell genomics has significantly advanced our understanding of cellular behavior, catalyzing innovations in treatments and precision medicine. However, single-cell sequencing technologies are inherently destructive and can only…
Metabolism is a fascinating cell machinery underlying life and disease and genome-scale reconstructions provide us with a captivating view of its complexity. However, deciphering the relationship between metabolic structure and function…
Mathematical and computational models can assist in gaining an understanding of cell behavior at many levels of organization. Here, we review models in the literature that focus on eukaryotic cell motility at 3 size scales: intracellular…
Vehicular sensor network (VSN) is an emerging technology, which combines wireless communication offered by vehicular ad hoc networks (VANET) with sensing devices installed in vehicles. VSN creates a huge opportunity to extend the road-side…
Deciphering the control principles of metabolism and its interaction with other cellular functions is central to biomedicine and biotechnology. Yet, understanding the efficient control of metabolic fluxes remains elusive for large-scale…
Metabolic networks, formed by a series of metabolic pathways, are made of intracellular and extracellular reactions that determine the biochemical properties of a cell, and by a set of interactions that guide and regulate the activity of…