Related papers: Modeling nanoconfined reaction kinetics: Alternati…
Equilibrium Constant Differential Equations (ECDE) are derived for several nanoconfined elemental bimolecular reactions in the frameworks of statistical mechanics and the ideal gas model. The ECDEs complement the well-known…
The Chemical Master Equation (CME) provides a highly accurate, yet extremely resource-intensive representation of a stochastic chemical reaction network and its kinetics due to the exponential scaling of its possible states with the number…
A partial differential equation (PDE) was developed to describe time-dependent ligand-receptor interactions for applications in biosensing using field effect transistors (FET). The model describes biochemical interactions at the sensor…
In this paper, we provide a detailed theoretical analysis of the numerical scheme introduced in J. Comput. Phys. 436 (2021) 110253 for the reaction kinetics of a class of chemical reaction networks that satisfies detailed balance condition.…
The convergence of stochastic interacting particle systems in the mean-field limit to solutions of conservative stochastic partial differential equations is established, with optimal rate of convergence. As a second main result, a…
Physical kinetic roughening processes are well known to exhibit universal scaling of observables that fluctuate in space and time. Are there analogous dynamic scaling laws that are unique to the chemical reaction mechanisms available…
We propose a novel Skew Gradient Embedding (SGE) framework for systematically reformulating thermodynamically consistent partial differential equation (PDE) models-capturing both reversible and irreversible processes-as generalized gradient…
A discretization scheme is introduced for a set of convection-diffusion equations with a non-linear reaction term, where the convection velocity is constant for each reactant. This constancy allows a transformation to new spatial variables,…
In an experimental study of single enzyme reactions, it has been proposed that the rate constants of the enzymatic reactions fluctuate randomly, according to a given distribution. To quantify the uncertainty arising from random rate…
Stochastic reaction networks are a fundamental model to describe interactions between species where random fluctuations are relevant. The master equation provides the evolution of the probability distribution across the discrete state space…
We present two approaches for describing chemical reactions taking place in fluid phase. The first method mirrors the usual derivation of the hydrodynamic equations of motion by relating conserved---or to account for chemical reactions,…
We report a new scanning nanomechanical noise microscopy platform enabling to both heat and acquire the fluctuations of mechanical nanostructures with nanometric resolution. We use this platform to image the thermally activated…
We present a method, based on characterizing efficiency fluctuations, to asses the performance of nanoscale thermoelectric junctions. This method accounts for effects typically arising in small junctions, namely, stochasticity in the…
We numerically and analytically investigate the behavior of a non-equilibrium phase transition in the second Schl\"ogl autocatalytic reaction scheme. Our model incorporates both an interaction-induced phase separation and a bifurcation in…
Stochastic partial differential equations (SPDEs) represent a very active research field with numerous recent developments and breakthrough results. There are several well-established approaches and methods used to construct solutions for…
According to contemporary views, equilibrium constant is relevant only to true thermodynamic equilibria in isolated systems with one chemical reaction. The paper presents a novel formula that ties-up equilibrium constant and chemical system…
We develop numerical methods for reaction-diffusion systems based on the equations of fluctuating hydrodynamics (FHD). While the FHD formulation is formally described by stochastic partial differential equations (SPDEs), it becomes similar…
In this work, we study the nonequilibrium statistical properties of the relaxation dynamics of a nanoparticle trapped in a harmonic potential. We report an exact time-dependent analytical solution to the Langevin dynamics that arises from…
We introduce EChemDID, a model to describe electrochemical driving force in reactive molecular dynamics simulations. The method describes the equilibration of external electrochemical potentials (voltage) within metallic structures and…
Stochastic differential equations (SDEs) are established tools to model physical phenomena whose dynamics are affected by random noise. By estimating parameters of an SDE intrinsic randomness of a system around its drift can be identified…