Related papers: Thermodynamically Driven Signal Amplification
Posttranslational modification of proteins is key in transmission of signals in cells. Many signaling pathways contain several layers of modification cycles that mediate and change the signal through the pathway. Here, we study a simple…
Under natural conditions, excitation of biological molecules, which display non-unitary open system dynamics, occurs via incoherent processes such as temperature changes or irradiation by sunlight/moonlight. The dynamics of such processes…
Boolean control networks (BCNs) are discrete-time dynamical systems with Boolean state-variables and inputs that are interconnected via Boolean functions. BCNs are recently attracting considerable interest as computational models for…
Understanding mechanosensitivity, i.e. how cells sense the stiffness of their environment is very important, yet there is a fundamental difficulty in understanding its mechanism: to measure an elastic modulus one requires two points of…
Quantum systems strongly coupled to many-body systems equilibrate to the reduced state of a global thermal state, deviating from the local thermal state of the system as it occurs in the weak-coupling limit. Taking this insight as a…
Modern laboratory techniques like ultrafast laser excitation and shock compression can bring matter into highly nonequilibrium states with complex structural transformation, metallization and dissociation dynamics. To understand and model…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
The Thermodynamic Formalism provides a rigorous mathematical framework to study quantitative and qualitative aspects of dynamical systems. At its core there is a variational principle corresponding, in its simplest form, to the Maximum…
Here we investigate how local properties of particles in a thermal bath influence the thermodynamics of the bath. We utilize nanothermodynamics, based on two postulates: that small systems can be treated self-consistently by coupling to an…
For multilayer structures, interfacial failure is one of the most important elements related to device reliability. For cohesive zone modelling, traction-separation relations represent the adhesive interactions across interfaces. However,…
Control of a dynamical system without the knowledge of dynamics is an important and challenging task. Modern machine learning approaches, such as deep neural networks (DNNs), allow for the estimation of a dynamics model from control inputs…
An empirical $s_cp^3_a$ tight-binding (TB) model is applied to the investigation of electronic states in semiconductor quantum dots. A basis set of three $p$-orbitals at the anions and one $s$-orbital at the cations is chosen. Matrix…
Proper characterization of quantum correlations in a multimode optical state is critical for applications in quantum information science; however, the most common entanglement measurements can lead to an incomplete state reconstruction.…
We introduce a general numerical method to compute dynamics and multi-time correlations of chains of quantum systems, where each system may couple strongly to a structured environment. The method combines the process tensor formalism for…
The idea of signal amplification is ubiquitous in the control of physical systems, and the ultimate performance limit of amplifiers is set by quantum physics. Increasing the amplitude of an unknown quantum optical field, or more generally…
Active Brownian particles (ABPs) function as self-driving agents that display non-equilibrium behavior through their pairwise interactions which lead to phase separation and vortex patterns in both soft matter and living systems. A…
This paper presents an algebraic framework to study sign-sensitivities for reaction networks modeled by means of systems of ordinary differential equations. Specifically, we study the sign of the derivative of the concentrations of the…
Hybrid molecular dynamics/Monte Carlo simulations used to study melts of unentangled, thermoreversibly associating supramolecular polymers. In this first of a series of papers, we describe and validate a model that is effective in…
We have investigated thermodynamic and dynamic properties as well as the dielectric constant of water-metha\-nol model mixtures in the entire range of composition by using constant pressure molecular dynamics simulations at ambient…
In systems with detailed balance, the stationary distribution and the equilibrium distribution are identical, creating a clear connection between energetic and entropic quantities. Many driven systems violate detailed balance and still pose…