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Receptor-induced apoptosis is a complex signal transduction pathway involving numerous protein/protein interactions and post-transcriptional modifications. The response to death receptor stimulation varies significantly from one cell line…
In a stochastic reaction network setting we consider the problem of tracking the fate of individual molecules. We show that using the classical large volume limit results, we may approximate the dynamics of a single tracked molecule in a…
Cells produce RNA and proteins via molecular templating networks. We show that information transmission in such networks is bounded by functions of a simple thermodynamic property of the network, regardless of complexity. Surprisingly,…
The network of biochemical reactions inside living organisms is characterized by an overwhelming complexity which stems from the sheer number of reactions and from the complicated topology of biochemical cycles. However the high speed of…
While Landauer's Principle sets a lower bound for the work required for a computation, that work is recoverable for efficient computations. However, practical physical computers, such as modern digital computers or biochemical systems, are…
Producing useful electrical work in consuming chemical energy, the fuel cell have to reject heat to its surrounding. However, as it occurs for any other type of engine, this thermal energy cannot be exchanged in an isothermal way in finite…
Life is a nonequilibrium phenomenon: metabolism provides a continuous supply of energy that drives nearly all cellular processes. However, very little is known about how much energy different cellular processes use, i.e. their energetic…
We introduce thermodynamic networks, a general framework for autonomous, physics-based computation using non-equilibrium steady states. These networks are modeled as a collection of finite-size reservoirs that exchange conserved…
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…
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…
Operando calorimetry has previously been utilized to study degradation, side reactions, and other electrochemical effects in electrochemical cells such as batteries at or near room temperature. Calorimetric data can provide important…
The ability of a cell to communicate with its environment is essential for key cellular functions like replication, metabolism, or cell fate decisions. The involved molecular mechanisms are highly dynamic and difficult to capture…
Biological systems sense and extract information from fluctuating signals while operating under energetic constraints and limited resolution. We introduce a general chemical model in which a sensor, coupled to a signaling pathway activated…
Living organisms survive and multiply even though they have uncertain and incomplete information about their environment and imperfect models to predict the consequences of their actions. Bayesian models have been proposed to face this…
Modularity dissipation identifies how locally-implemented computation entails costs beyond those required by Landauer's bound on thermodynamic computing. We establish a general theorem for efficient local computation, giving the necessary…
The chemotactic network of Escherichia coli has been studied extensively both biophysically and information-theoretically. Nevertheless, the connection between these two aspects is still elusive. In this work, we report such a connection by…
Cells are often considered input-output devices that maximize the transmission of information by converting extracellular stimuli (input) via signaling pathways (communication channel) to cell behavior (output). However, in biological…
Chemical modelling serves two purposes in dynamical models: accounting for the effect of microphysics on the dynamics and providing observable signatures. Ideally, the former must be done as part of the hydrodynamic simulation but this…
The increasing interest in understanding the behavior of the biological neural networks, and the increasing utilization of artificial neural networks in different fields and scales, both require a thorough understanding of how neuromorphic…
Cells often perform computations in response to environmental cues. A simple example is the classic problem, first considered by Berg and Purcell, of determining the concentration of a chemical ligand in the surrounding media. On general…