Related papers: Energy dissipation in an adaptive molecular circui…
Living systems operate far from thermal equilibrium by converting the chemical potential of ATP into mechanical work to achieve growth, replication or locomotion. Given time series observations of intra-, inter- or multicellular processes,…
The long-term temperature response to a given change in CO2 forcing, or Earth-system sensitivity (ESS), is a key parameter quantifying our understanding about the relationship between changes in Earth's radiative forcing and the resulting…
The responsivity of perturbation sensing can be effectively enhanced by using higher-order exceptional points (HOEPs) due to their nonlinear response to frequency perturbations. However, experimental realization can be difficult due to the…
This paper studies adaptive sensing for estimating the nonzero amplitudes of a sparse signal with the aim of providing analytical guarantees on the performance gain due to adaptive resource allocation. We consider a previously proposed…
This review describes recent advances by the authors and others on the topic of incorporating experimental data into molecular simulations through maximum entropy methods. Methods which incorporate experimental data improve accuracy in…
Sensing is the process of deriving signals from the environment that allows artificial systems to interact with the physical world. The Shannon theorem specifies the maximum rate at which information can be acquired. However, this upper…
This paper is concerned with a mathematical model of competition for resource where species consume noninteracting resources. This system of differential equations is formally obtained by renormalizing the MacArthur's competition model at…
Beta decay is a fundamental process that governs nuclear stability and serves as a sensitive probe of the weak interaction and possible physics beyond the Standard Model of particle physics. However, precise measurements of complete $\beta$…
The notion of entropy is shared between statistics and thermodynamics, and is fundamental to both disciplines. This makes statistical problems particularly suitable for reaction network implementations. In this paper we show how to perform…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
Detecting and quantifying non-equilibrium activity is essential for studying internally driven assemblies, including synthetic active matter and complex living systems such as cells or tissue. We discuss a non-invasive approach of measuring…
Exact-exchange energy density and energy density of a semilocal density functional approximation are two key ingredients for modeling the static correlation, a strongly nonlocal functional of the density, through a local hybrid functional.…
We study a stochastic system of interacting neurons and its metastable properties. The system consists of $N$ neurons, each spiking randomly with rate depending on its membrane potential. At its spiking time, the neuron potential is reset…
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…
This paper is about nonequilibrium steady states (NESS) of a class of stochastic models in which particles exchange energy with their "local environments" rather than directly with one another. The physical domain of the system can be a…
Understanding the organization of reaction fluxes in cellular metabolism from the stoichiometry and the topology of the underlying biochemical network is a central issue in systems biology. In this task, it is important to devise reasonable…
Non-Hermitian systems associated with exceptional points (EPs) are expected to demonstrate a giant response enhancement for various sensors. The widely investigated enhancement mechanism based on diverging from an EP should destroy the EP…
Stochastic thermodynamics has largely succeeded in characterizing both equilibrium and far-from-equilibrium phenomena. Yet many opportunities remain for application to mesoscopic complex systems -- especially biological ones -- whose…
When simulators are energetically coupled in a co-simulation, residual energies alter the total energy of the full coupled system. This distorts the system dynamics, lowers the quality of the results, and can lead to instability. By using…
We describe a mechanism for biological learning and adaptation based on two simple principles: (I) Neuronal activity propagates only through the network's strongest synaptic connections (extremal dynamics), and (II) The strengths of active…