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The computational treatment of many-electron systems capable of exchanging {electrons and nuclei} with the environment represents one of the outermost frontiers in simulation methodology. The exchanging process occurs in a large variety of…
Cell signaling, gene expression, and metabolism are affected by cell-cell heterogeneity and random changes in the environment. The effects of such fluctuations on cell signaling and gene expression have recently been studied intensively…
In this paper homogenization of a mathematical model for plant tissue biomechanics is presented. The microscopic model constitutes a strongly coupled system of reaction-diffusion-convection equations for chemical processes in plant cells,…
The dynamic interplay between collective cell movement and the various molecules involved in the accompanying cell signalling mechanisms plays a crucial role in many biological processes including normal tissue development and pathological…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
Electrochemical communication is a mechanism that enables intercellular interaction among bacteria within communities. Bacteria achieves synchronization and coordinates collective actions at the population level through the utilization of…
Cell spreading is investigated at various scales in order to understand motility of living cells which is essential for a range of physiological activities in higher organisms as well as in microbes. At a microscopic scale, it has been seen…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
Molecular communication is a biologically-inspired method of communication with attractive properties for microscale and nanoscale devices. In molecular communication, messages are transmitted by releasing a pattern of molecules at a…
Many biological, physical, and social interactions have a particular dependence on where they take place. In living cells, protein movement between the nucleus and cytoplasm affects cellular response (i.e., proteins must be present in the…
This paper provides synchronization conditions for networks of nonlinear systems. The components of the network (referred to as "compartments'' in this paper) are made up of an identical interconnection of subsystems, each represented as an…
Cells can utilize chemical communication to exchange information and coordinate their behavior in the presence of noise. Communication can reduce noise to shape a collective response, or amplify noise to generate distinct phenotypic…
Biological signaling is imagined as a combination of activation and transport. The former is triggered by local molecular interactions and the latter is the result of molecular diffusion. However, other fundamental physical principles of…
Cells can be considered as systems that utilize changes in thermodynamic entropy as information. Therefore, they serve as useful models for investigating the relationships between entropy production and information transmission, i.e.,…
In this paper, we propose adding enzymes to the propagation environment of a diffusive molecular communication system as a strategy for mitigating intersymbol interference. The enzymes form reaction intermediates with information molecules…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such…
Living cells presumably employ optimized information transfer methods, enabling efficient communication even in noisy environments. As expected, the efficiency of chemical communications between cells depends on the properties of the…
In this paper, we apply dimensional analysis to study a diffusive molecular communication system that uses diffusing enzymes in the propagation environment to mitigate intersymbol interference. The enzymes bind to information molecules and…
Intracellular transport processes are essential to the healthy development of many organisms as well as more generally to healthy cellular function. The complex dynamics and interactions between protein molecules and filaments on different…