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Advanced control strategies for delivering heat to users in a district heating network have the potential to improve performance and reduce wasted energy. To enable the design of such controllers, this paper proposes an automated plant…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
A complete thermodynamical analysis for a blood model, based on mixture theory, is performed. The model is developed considering the blood as a suspension of red blood cells (solid component) in the plasma (fluid component), and taking into…
Binding and unbinding of ligands to specific sites of a macromolecule are one of the most elementary molecular interactions inside the cell that embody the computational processes of biological regulations. The interaction between…
A method for reconstructing the energy landscape of simple polypeptidic chains is described. We show that we can construct an equivalent representation of the energy landscape by a suitable directed graph. Its topological and dynamical…
We present the bond-calculus, a process algebra for modelling biological and chemical systems featuring nonlinear dynamics, multiway interactions, and dynamic bonding of agents. Mathematical models based on differential equations have been…
The quest for ever higher information capacities has brought about a renaissance in multimode optical waveguide systems. This resurgence of interest has recently initiated a flurry of activities in nonlinear multimode fiber optics. The…
Information thermodynamics relates the rate of change of mutual information between two interacting subsystems to their thermodynamics when the joined system is described by a bipartite stochastic dynamics satisfying local detailed balance.…
The recent discovery of universal principles underlying many complex networks occurring across a wide range of length scales in the biological world has spurred physicists in trying to understand such features using techniques from…
Chemical reaction networks (CRNs) exhibit complex dynamics governed by their underlying network structure. In this paper, we propose a novel approach to study the dynamics of CRNs by representing them on species graphs (S-graphs). By…
We present a systematic mathematical analysis of the qualitative steady-state response to rate perturbations in large classes of reaction networks. This includes multimolecular reactions and allows for catalysis, enzymatic reactions,…
The behavior of complex systems is determined not only by the topological organization of their interconnections but also by the dynamical processes taking place among their constituents. A faithful modeling of the dynamics is essential…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
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…
Constraint-based stoichiometric models are ubiquitous in metabolic research, with Flux Balance Analysis (FBA) being the most widely used method to describe metabolic phenotypes of cells growing in steady-state. Of the many variants of…
Predicting missing links between entities in a knowledge graph is a fundamental task to deal with the incompleteness of data on the Web. Knowledge graph embeddings map nodes into a vector space to predict new links, scoring them according…
We introduce the idea of weakly coherent collisional models, where the elements of an environment interacting with a system of interest are prepared in states that are approximately thermal, but have an amount of coherence proportional to a…
Waste production, carbon dioxide atmospheric accumulation, and dependence on finite natural resources are expressions of the unsustainability of the current industrial networks that supply fuels, energy, and manufacturing products. In…
Tethered particle motion experiments are versatile single-molecule techniques enabling one to address in vitro the molecular properties of DNA and its interactions with various partners involved in genetic regulations. These techniques…
Cellular signaling is essential in information processing and decision making. Therefore, a variety of experimental approaches have been developed to study signaling on bulk and single-cell level. Single-cell measurements of signaling…