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Unlike macroscopic engines, the molecular machinery of living cells is strongly affected by fluctuations. Stochastic Thermodynamics uses Markovian jump processes to model the random transitions between the chemical and configurational…
In order to respond to environmental signals, cells often use small molecular circuits to transmit information about their surroundings. Recently, motivated by concrete examples in signaling and gene regulation, a body of work has focused…
We explore the critical behaviors in the dynamics of information transfer of a biologically-inspired system by an individual-based model. "Quorum response", a type of social interaction which has been recognized taxonomically in animal…
Bacterial quorum sensing can be engineered with a view to the design of biotechnological applications based on their intrinsic role as a means of communication. We propose the creation of a positive feedback loop that will promote the…
In this paper we study an important global regulation mechanism of transcription of biological cells using specific macro-molecules, 6S RNAs. The functional property of 6S RNAs is of blocking the transcription of RNAs when the environment…
A diffusion-based molecular communication system has two major components: the diffusion in the medium, and the ligand-reception. Information bits, encoded in the time variations of the concentration of molecules, are conveyed to the…
Electric circuits manipulate electric charge and magnetic flux via a small set of discrete components to implement useful functionality over continuous time-varying signals represented by currents and voltages. Much of the same…
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…
Recent molecular communication (MC) research has integrated more detailed computational models to capture the dynamics of practical biophysical systems. This research focuses on developing realistic models for MC transceivers inspired by…
Charge transfer can take place along double helical DNA over distances as long as 30 nanometers. However, given the active role of the thermal environment surrounding charge carriers in DNA, physical mechanisms driving the transfer process…
Immotile microbes inhabit nearly every environment on Earth, from soils and sediments to food matrices -- yet how they disperse through these physically confining environments is poorly understood. Here, we show that immotile microbial…
Molecular communication in nature can incorporate a large number of nano-things in nanonetworks as well as demonstrate how nano-things communicate. This paper presents molecular communication where transmit nanomachines deliver information…
The propagation of signalling molecules within cellular networks is affected by network topology, but also by the spatial arrangement of cells in the networks. Understanding the collective reaction--diffusion behaviour in space of signals…
Bacterial chemotaxis in Escherichia coli is a canonical system for the study of signal transduction. A remarkable feature of this system is the coexistence of precise adaptation in population with large fluctuating cellular behavior in…
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…
Photosynthesis transfers energy efficiently through a series of antenna complexes to the reaction center where charge separation occurs. Energy transfer in vivo is primarily monitored by measuring fluorescence signals from the small…
While it is commonly observed that the shape dynamics of mammalian cells can undergo large random fluctuations, theoretical models aiming at capturing cell mechanics often focus on the deterministic part of the motion. In this paper, we…
A theory of electrical transport through molecular wires is used to estimate the electronic factor in the intramolecular electron transfer (ET) in porphyrin-nitrobenzene supermolecules, and to analyze its structure. The chosen molecules…
Elastic confinements are an important component of many biological systems and dictate the transport properties of suspended particles under flow. In this chapter, we review the Brownian motion of a particle moving in the vicinity of a…
We propose a general parametrizable model to capture the dynamic interaction among bacteria in the formation of micro-colonies. micro-colonies represent the first social step towards the formation of structured multicellular communities…