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This study modifies the Covariance Matrix Adaptation Evolution Strategy (CMA-ES) algorithm for multi-modal optimization problems. The enhancements focus on addressing the challenges of multiple global minima, improving the algorithm's…
We study a nonlinear recombination model from population genetics as a combinatorial version of the Kac-Boltzmann equation from kinetic theory. Following Kac's approach, the nonlinear model is approximated by a mean field linear evolution…
A non-equilibrium steady state is characterized by a non-zero steady dissipation rate. Chemical reaction systems under suitable conditions may generate such states. We propose here a method that is able to distinguish states with identical…
Enzymes are nano-scale machines that have evolved to drive chemical reactions out of equilibrium in the right place at the right time. Given the complexity and specificity of enzymatic function, bottom-up design of enzymes presents a…
Many have speculated whether nonequilibrium systems obey principles of maximum or minimum entropy production. In this work, we use stochastic thermodynamics to derive the condition for the minimum entropy production state (MEPS) for…
The Metropolis Monte Carlo (MC) method is used to extract reaction kinetics from a given equilibrium distribution of states of a complex system. The approach is illustrated by the folding/unfolding reaction for two proteins - a model…
All current formulations of nonequilibrium thermodynamics of open chemical reaction networks rely on the assumption of non-interacting species. We develop a general theory which accounts for interactions between chemical species within a…
The molecular motor protein kinesin plays a key role in fundamental cellular processes such as intracellular transport, mitotic spindle formation, and cytokinesis, with important implications for neurodegenerative and cancer disease…
Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscles contraction. It is known that these biological molecular…
The single-particle and collective dynamics of systems comprising Janus motors, solvent and reactive solute species maintained in nonequilibrium states are investigated. Reversible catalytic reactions with the solute species take place on…
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…
Allosteric regulation is often viewed as thermodynamic in nature. However protein internal motions during an enzymatic reaction cycle can be slow hopping processes over numerous potential barriers. We propose that regulating molecules may…
The mechanics of cells is strongly affected by molecular motors that generate forces in the cellular cytoskeleton. We develop a model for cytoskeletal networks driven out of equilibrium by molecular motors exerting transient contractile…
This work describes a novel simulation approach that combines machine learning and device modelling simulations. The device simulations are based on the quantum mechanical non-equilibrium Greens function (NEGF) approach and the machine…
Based on our experience in kinetic modeling of coupled multiple metabolic pathways we propose a generic rate equation for the dynamical modeling of metabolic kinetics. Its symmetric form makes the kinetic parameters (or functions) easy to…
A general theory is developed for describing the nonlinear relaxation of spin systems from a strongly nonequilibrium initial state, when, in addition, the sample is coupled to a resonator. Such processes are characterized by nonlinear…
It has been recently observed that the dynamical properties of mass action systems arising from many models of biochemical reaction networks can be derived by considering the corresponding properties of a related generalized mass action…
The enzyme turnover rate is a fundamental parameter in enzyme kinetics, reflecting the catalytic efficiency of enzymes. However, enzyme turnover rates remain scarce across most organisms due to the high cost and complexity of experimental…
Synchronization is a fundamental component of computational models of human behavior, at both intra-personal and inter-personal level. Event synchronization analysis was originally conceived with the aim of providing a simple and robust…
Describing the kinetics of polymer reactions, such as the formation of loops and hairpins in nucleic acids or polypeptides, is complicated by the structural dynamics of their chains. Although both intramolecular reactions, such as…