Related papers: Conformational Nonequilibrium Enzyme Kinetics: Gen…
This research addresses two fundamental challenges in Marketing Mix Modeling: the tendency of models to over-attribute influence to high-investment channels and the difficulty in quantifying cross-channel effects. We propose integrating the…
Chemotaxis describes the movement of an organism, such as single or multi-cellular organisms and bacteria, in response to a chemical stimulus. Two widely used models to describe the phenomenon are the celebrated Keller-Segel equation and a…
Neural population activity exhibits complex, nonlinear dynamics, varying in time, over trials, and across experimental conditions. Here, we develop Conditionally Linear Dynamical System (CLDS) models as a general-purpose method to…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…
Motor enzymes are remarkable molecular machines that use the energy derived from the hydrolysis of a nucleoside triphosphate to generate mechanical movement, achieved through different steps that constitute their kinetic cycle. These…
Biochemical reactions inside living cells often occur in the presence of crowders -- molecules that do not participate in the reactions but influence the reaction rates through excluded volume effects. However the standard approach to…
The convergence to equilibrium of mass action reaction-diffusion systems arising from networks of chemical reactions is studied. The considered reaction networks are assumed to satisfy the detailed balance condition and have no boundary…
Recent experiments indicate that electromagnetic hysteresis behavior can be exhibited at the molecular level.A MD simulation using 2-body potentials and switches to form and break bonds is implemented to determine whether chemical reaction…
Understanding the emergent behavior of chemical reaction networks (CRNs) is a fundamental aspect of biology and its origin from inanimate matter. A closed CRN monotonically tends to thermal equilibrium, but when it is opened to external…
Metropolis Monte Carlo simulation is a powerful tool for studying the equilibrium properties of matter. In complex condensed-phase systems, however, it is difficult to design Monte Carlo moves with high acceptance probabilities that also…
Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal…
We develop a theory of enzyme catalysis within biological cells where the substrate concentration [S](t) is time dependent, in contrast to the Michaelis-Menten theory that assumes a steady state. We find that the time varying concentration…
The rigorous stability analysis of high-order implicit-explicit multistep (IEMS) methods for nonlinear parabolic equations by using discrete energy arguments is a long standing open issue due to their non-A-stable property. A novel…
Direct simulation of biomolecular dynamics in thermal equilibrium is challenging due to the metastable nature of conformation dynamics and the computational cost of molecular dynamics. Biased or enhanced sampling methods may improve the…
A rigorous mathematical framework for analyzing the chemical master equation (CME) with bistability, based on the theory of large deviation, is proposed. Using a simple phosphorylation-dephosphorylation cycle with feedback as an example, we…
Neuronal ensemble activity, including coordinated and oscillatory patterns, exhibits hallmarks of nonequilibrium systems with time-asymmetric trajectories to maintain their organization. However, assessing time asymmetry from neuronal…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
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…
We propose a nonequilibrium Monte Carlo (MC) approach to explore nonequilibrium dynamical ferromagnetism of interacting single molecule magnets (SMMs). Both quantum spin tunneling and thermally activated spin reversal are successfully…
Living systems are forced away from thermodynamic equilibrium by exchange of mass and energy with their environment. In order to model a biochemical reaction network in a non-equilibrium state one requires a mathematical formulation to…