Related papers: SMT Solving for Vesicle Traffic Systems in Cells
One of the most important concepts in biological network analysis is that of network motifs, which are patterns of interconnections that occur in a given network at a frequency higher than expected in a random network. In this work we are…
A model for traffic flow in street networks or material flows in supply networks is presented, that takes into account the conservation of cars or materials and other significant features of traffic flows such as jam formation, spillovers,…
Biological organisms are composed of numerous interconnected biochemical processes. Diseases occur when normal functionality of these processes is disrupted. Thus, understanding these biochemical processes and their interrelationships is a…
In this thesis, we have studied the large scale structure and system level dynamics of certain biological networks using tools from graph theory, computational biology and dynamical systems. We study the structure and dynamics of large…
Processive molecular motors which drive the traffic of organelles in cells move in a directed way along cytoskeletal filaments. On large time scales, they perform motor walks, i.e., peculiar random walks which arise from the repeated…
Although recent scientific output focuses on multiple shortest-path problem definitions for road networks, none of the existing solutions does efficiently answer all different types of SP queries. This work proposes SALT, a novel framework…
Semiconductor superlattices are interesting for two distinct reasons: the possibility to design their structure (band-width(s),doping, etc.) gives access to a large parameter space where different physical phenomena can be explored.…
Despite the wide existence of vesicles in living cells as well as their important applications like drug-delivery, the underlying mechanism of vesicle fusion/fission remains under debate. Here, we develop a constrained self-consistent field…
In this Doctoral Dissertation we propose new variational principles for traffic assignment problems. So to find equillibrium we have to solve large-scale convex optimization problem of special (multilevel) type. We propose different…
Facing the congestion challenges of mixed road networks comprising expressways and arterial road networks, traditional control solutions fall short. To effectively alleviate traffic congestion in mixed road networks, it is crucial to clear…
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks in living systems, understanding their…
Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…
Pathway enrichment analysis has become a key tool for biomedical researchers to gain insight into the underlying biology of differentially expressed genes, proteins and metabolites. It reduces complexity and provides a system-level view of…
A common feature of biological networks is the geometric property of self-similarity. Molecular regulatory networks through to circulatory systems, nervous systems, social systems and ecological trophic networks, show self-similar…
In this work, we present the development of a neuro-inspired approach for characterizing sensorimotor relations in robotic systems. The proposed method has self-organizing and associative properties that enable it to autonomously obtain…
This paper proposes a simplified version of classical models for urban transportation networks, and studies the problem of controlling intersections with the goal of optimizing network-wide congestion. Differently from traditional…
A classic network tomography problem is estimation of properties of the distribution of route traffic volumes based on counts taken on the network links. We consider inference for a general class of models for integer-valued traffic. Model…
We propose new variational principles for traffic assignment problems. So to find equillibrium we have to solve large-scale convex optimization problem of special type. We propose some kind of "algebra" on different models and corresponding…
Genetic regulatory networks enable cells to respond to the changes in internal and external conditions by dynamically coordinating their gene expression profiles. Our ability to make quantitative measurements in these biochemical circuits…
Molecular communication (MC) enables information exchange through the transmission of signaling molecules (SMs) and holds promise for many innovative applications. However, most existing works in MC rely on simplified transmitter (TX)…