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The minimal set of thermodynamic control parameters consists of a statistical (thermal) and a mechanical one. These suffice to introduce all the pertinent thermodynamic variables; thermodynamic processes can then be defined as paths on this…
Non-equilibrium processes which convert chemical energy into mechanical motion enable the motility of organisms. Bundles of inextensible filaments driven by energy transduction of molecular motors form essential components of micron-scale…
As one increases the concentration of a colloidal suspension, the system exhibits a dramatic increase in viscosity. Structurally, the system resembles a liquid, yet motions within the suspension are slow enough that it can be considered…
Complex biochemical pathways or regulatory enzyme kinetics can be reduced to chains of elementary reactions, which can be described in terms of chemical kinetics. This discipline provides a set of tools for quantifying and understanding the…
Chemical kinetics and reaction engineering consists of the phenomenological framework for the disentanglement of reaction mechanisms, optimization of reaction performance and the rational design of chemical processes. Here, we utilize…
The problem of the insensitivity of the macroscopic behavior of any thermodynamical system to partitioning generates a bias between the reproducibility of its macroscopic behavior viewed as the simplest form of causality and its long-term…
The stability properties of models of spontaneous mirror symmetry breaking in chemistry are characterized algebraically. The models considered here all derive either from the Frank model or from autocatalysis with limited…
Single enzyme chemotaxis is a phenomenon by which a non-equilibrium spatial distribution of an enzyme is created and maintained by concentration gradients of the substrate and product of the catalyzed reaction. These gradients can arise…
Oscillating chemical reactions result from complex periodic changes in the concentration of the reactants. In spatially ordered ensembles of candle flame oscillators the fluctuations in the ratio of oxygen atoms with respect to that of…
Simulations of chemical dynamics are a powerful means for understanding chemistry. However, classical computers struggle to simulate many chemical processes, especially non-adiabatic ones, where the Born-Oppenheimer approximation breaks…
The excitation-chain theory of the glass transition, proposed in an earlier publication, predicts diverging, super-Arrhenius relaxation times and, {\it via} a similarly diverging length scale, suggests a way of understanding the relations…
Understanding the oscillating behaviors that govern organisms' internal biological processes requires interdisciplinary efforts combining both biological and computer experiments, as the latter can complement the former by simulating…
Despite the long history of electrochemistry, there is a lack of quantitative algorithms that rigorously correlate experiment with theory. Electrochemical modeling has had advanced across empirical, analytical, numerical, and data-driven…
Embedding sequential computations in biochemical environments is challenging because the computations are carried out by chemical reactions, which are inherently disordered. In this paper we apply modular design to specific calculations…
A central aim of physics is to describe the dynamics of physical systems. Schrodinger's equation does this for isolated quantum systems. Describing the time evolution of a quantum system that interacts with its environment, in its most…
The paper is devoted to recent advances in stochastic modeling of anomalous kinetic processes observed in dielectric materials which are prominent examples of disordered (complex) systems. Theoretical studies of dynamical properties of…
Ordinary differential equation models have become a standard tool for the mechanistic description of biochemical processes. If parameters are inferred from experimental data, such mechanistic models can provide accurate predictions about…
The dynamics of excitonic energy transfer in molecular complexes triggered by interaction with laser pulses offers a unique window into the underlying physical processes. The absorbed energy moves through the network of interlinked pigments…
Quantum thermodynamics with open systems is often based on the quantum optical weak-coupling master equation or on operational repeated interaction models, whereas early works on thermalisation and on decoherence theory were mostly…
In this article we propose and numerically implement a mathematical model for the simulation of three-dimensional semiconductor devices characterized by an heterogeneous material structure. The model consists of a system of nonlinearly…