Related papers: Improved estimation for energy dissipation in bioc…
Thermodynamic uncertainty relation (TUR) bounds coherence in stochastic oscillatory systems. In this paper, we show that both dynamical and thermodynamic bounds play important roles for the excitable oscillators, e.g. neurons. Firstly, we…
Free energy calculations based on atomistic Hamiltonians and sampling are key to a first principles understanding of biomolecular processes, material properties, and macromolecular chemistry. Here, we generalize the Free Energy Perturbation…
The fundamental insight into Brownian motion by Einstein is that all substances exhibit continual fluctuations due to thermal agitation balancing with the frictional resistance. However, even at thermal equilibrium, biological activity can…
We investigate how the kinetic energy acquired by a dense granular system driven by an external vibration depends on the input energy. Our focus is on the dependence of the granular behavior on two main parameters: frequency and vibration…
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 study the effects of a probabilistic refractory period in the collective behavior of coupled discrete-time excitable cells (SIRS-like cellular automata). Using mean-field analysis and simulations, we show that a synchronized phase with…
Energy efficiency is closely related to the evolution of biological systems and is important to their information processing. In this paper, we calculated the excitation probability of a simple model of a bistable biological unit in…
Stochastic density functional theory (sDFT) is becoming a valuable tool for studying ground state properties of extended materials. The computational complexity of describing the Kohn-Sham orbitals is replaced by introducing a set of random…
Double excitations are crucial to understanding numerous chemical, physical, and biological processes, but accurately predicting them remains a challenge. In this work, we explore the particle-particle random phase approximation (ppRPA) as…
We present the first quantified measure of the rate of energy dissipated per unit volume by high frequency electromagnetic waves in the transition region of the Earth's collisionless bow shock using data from the THEMIS spacecraft. Every…
We develop an effective description of noise-induced oscillations based on deterministic phase dynamics. The phase equation is constructed to exhibit correct frequency and distribution density of noise-induced oscillations. In the simplest…
We use an effective Markovian description to study the long-time behaviour of a nonlinear second order Langevin equation with Gaussian noise. When dissipation is neglected, the energy of the system grows as with time a power-law with an…
In the present work we investigate phase correlations by recourse to the Shannon entropy. Using theoretical arguments we show that the entropy provides an accurate measure of phase correlations in any dynamical system, in particular when…
We investigate the macroscopic behavior of the disordered harmonic chain of oscillators, through energy diffusion. The Hamiltonian dynamics of the system is perturbed by a degenerate conservative noise. After rescaling space and time…
Sensory adaptation enables organisms to adjust their perception in a changing environment. A paradigm is bacterial chemotaxis, where the output activity of chemoreceptors is adapted to different baseline concentrations via receptor…
We introduce a tempering approach with stochastic density functional theory (sDFT), labeled t-sDFT, which reduces the statistical errors in the estimates of observable expectation values. This is achieved by rewriting the electronic density…
We investigate the problem of estimating the tunneling frequency of a two-level atomic system embedded in a dissipative environment by employing a numerically rigorous hierarchical equations of motion method. The effect of…
In this article, we propose a generalized model for nonequilibrium vibrational energy distribution functions. The model can be used, in place of equilibrium (Boltzmann) distribution functions, when deriving reaction rate constants for…
Circadian clocks play a pivotal role in orchestrating numerous physiological and developmental events. Waveform shapes of the oscillations of protein abundances can be informative about the underlying biochemical processes of circadian…
The dynamics and structure of nonequilibrium liquids, driven by non-conservative forces which can be either external or internal, generically hold the signature of the net dissipation of energy in the thermostat. Yet, disentangling…