Related papers: SMT Solving for Vesicle Traffic Systems in Cells
Vesicle Traffic Systems (VTSs) are the material transport mechanisms among the compartments inside the biological cells. The compartments are viewed as nodes that are labeled with the containing chemicals and the transport channels are…
Accurately determining and classifying the structure of complex networks is the focus of much current research. One class of network of particular interest are metabolic pathways, which have previously been studied from a graph theoretical…
We propose an alternative mechanism for intracellular cargo transport which results from motor induced longitudinal fluctuations of cytoskeletal microtubules (MT). The longitudinal fluctuations combined with transient cargo binding to the…
Biological systems and processes are networks of complex nonlinear regulatory interactions between nucleic acids, proteins, and metabolites. A natural way in which to represent these interaction networks is through the use of a graph. In…
Biological transport networks are highly optimized structures that ensure power-efficient distribution of fluids across various domains, including animal vasculature and plant venation. Theoretically, these networks can be described as…
Many foraging microorganisms rely upon cellular transport networks to deliver nutrients, fluid and organelles between different parts of the organism. Networked organisms ranging from filamentous fungi to slime molds demonstrate a…
Networks are widely used in the biological, physical, and social sciences as a concise mathematical representation of the topology of systems of interacting components. Understanding the structure of these networks is one of the outstanding…
Data-driven approaches have been proven effective in solving combinatorial optimization problems over graphs such as the traveling salesman problems and the vehicle routing problem. The rationale behind such methods is that the input…
The metabolic networks are very well characterized for a large set of organisms, a unique case in within the large-scale biological networks. For this reason they provide a a very interesting framework for the construction of analytically…
Complex systems are successfully reduced to interacting elements via the network concept. Transport plays a key role in the survival of networks. For example the specialized signaling cascades of cellular networks filter noise 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,…
This paper addresses the path-planning challenge for very large-scale robotic systems (VLSR) operating in complex and cluttered environments. VLSR systems consist of numerous cooperative agents or robots working together autonomously.…
Many cellular networks rely on the regulated transport of their components to transduce extracellular information into precise intracellular signals. The dynamics of these networks is typically described in terms of compartmentalized…
Many living and physical systems such as cell aggregates, tissues or bacterial colonies behave as unconventional systems of particles that are strongly constrained by volume exclusion and shape interactions. Understanding how these…
Single-molecule tracking (SMT) methods are under considerable expansion in many fields of cell biology, as the dynamics of cellular components in biological mechanisms becomes increasingly relevant. Despite the development of SMT…
Inrecent time a rapid increase in the number of smart devices and user applications have generated an intensity volume of data traffic from/to a cellular network. So the Long Term Evaluation(LTE)network is facing some issuesdifficulties…
Cells are regulated by networks of controllers having many targets, and targets affected by many controllers, but these "many-to-many" combinatorial control systems are poorly understood. Here we analyze distinct cellular networks…
Modern transportation network modeling increasingly involves the integration of diverse methodologies including sensor-based forecasting, reinforcement learning, classical flow optimization, and demand modeling that have traditionally been…
Scientists have long sought to understand how vascular networks supply blood and oxygen to cells throughout the body. Recent work focuses on principles that constrain how vessel size changes through branching generations from the aorta to…
Recent advances in machine learning (ML) have expedited materials discovery and design. One significant challenge faced in ML for materials is the expansive combinatorial space of potential materials formed by diverse constituents and their…