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While linear response theory, manifested by the fluctuation dissipation theorem, can be applied at any level of coarse graining, nonlinear response theory is fundamentally of microscopic nature. For perturbations of equilibrium systems, we…
In this paper, the inherent gradient flow structures of thermo-poro-visco-elastic processes in porous media are examined for the first time. In the first part, a modelling framework is introduced aiming for describing such processes as…
Using elementary methods, we prove that for a countable Markov chain $P$ of ergodic degree $d > 0$ the rate of convergence towards the stationary distribution is subgeometric of order $n^{-d}$, provided the initial distribution satisfies…
We derive a class of multi-species aggregation-diffusion systems from stochastic interacting particle systems via relative entropy method with quantitative bounds. We show an algebraic $L^1$-convergence result using moderately interacting…
Atomistic or ab-initio molecular dynamics simulations are widely used to predict thermodynamics and kinetics and relate them to molecular structure. A common approach to go beyond the time- and length-scales accessible with such…
We formulate thermodynamically consistent coarse-graining procedures for molecular systems undergoing thermally and photo-induced transitions: starting from elementary vibronic transitions, we derive effective photo-isomerization reactions…
Interacting-Particle Reaction Dynamics (iPRD) simulates the spatiotemporal evolution of particles that experience interaction forces and can react with one another. The combination of interaction forces and reactions enable a wide range of…
We study partially segregated elliptic systems through the use of penalized energy functionals. These systems arise from the minimization of Gross-Pitaevskii-type energies that capture the behavior of multi-component ultracold gas mixtures…
In this paper we study the rate of convergence to the complex balanced equilibrium for some chemical reaction-diffusion systems with boundary equilibria. We first analyze a three-species system with boundary equilibria in some…
Decarbonizing the energy supply is essential and urgent to mitigate the increasingly visible climate change. Its basis is identifying emission responsibility during power allocation by the carbon emission flow (CEF) model. However, the main…
We review some recent coarse-graining and multi-scale methods, but also put forward some new ideas for addressing such issues. We find that, if one is guided by nonequilibrium statistical mechanics and thermodynamics, it is possible to…
A novel global energy model for multi-class semantic image segmentation is proposed that admits very efficient exact inference and derivative calculations for learning. Inference in this model is equivalent to MAP inference in a particular…
Concentration gradients of signaling molecules are essential for patterning during development and they have been observed in both unicellular and multicellular systems. In subcellular systems, clustering of the signaling molecule has been…
By identifying potential composite states that occur in the Sel'kov-Gray-Scott (GS) model, we show that it can be considered as an effective theory at large spatio-temporal scales, arising from a more \textit{fundamental} theory (which…
Under the condition of detailed balance and some additional restrictions on the size of the coefficients, we identify the equilibrium distribution to which solutions of the discrete coagulation-fragmentation system of equations converge for…
Dynamical systems theory provides powerful methods to extract effective macroscopic dynamics from complex systems with slow modes and fast modes. Here we derive and theoretically support a macroscopic, spatially discrete, model for a class…
The computer-assisted modeling of re-entrant production lines, and, in particular, simulation scalability, is attracting a lot of attention due to the importance of such lines in semiconductor manufacturing. Re-entrant flows lead to…
Using a coarse molecular-dynamics (CMD) approach with an appropriate choice of coarse variable (order parameter), we map the underlying effective free-energy landscape for the melting of a crystalline solid. Implementation of this approach…
We provide a condition for f-ergodicity of strong Markov processes at a subgeometric rate. This condition is couched in terms of a supermartingale property for a functional of the Markov process. Equivalent formulations in terms of a drift…
We investigate a Poisson-Nernst-Planck type system in three spatial dimensions where the strength of the electric drift depends on a possibly small parameter and the particles are assumed to diffuse quadratically. On grounds of the global…