Related papers: Conformational Nonequilibrium Enzyme Kinetics: Gen…
Enzymes show two distinct transport behaviors in the presence of their substrates in solution. First, their diffusivity enhances with increasing substrate concentration. In addition, enzymes perform directional motion toward regions with…
We analyze the standard model of enzyme-catalyzed reactions at various substrate-enzyme ratios to identify the regions of validity of the quasi-steady-state approximation. Certain prevalent conditions are checked and compared against the…
We study the nonequilibrium stationary state (NESS) induced by quantum resetting of a system of $N$ noninteracting bosons in a harmonic trap. Our protocol consists of preparing initially the system in the ground state of a harmonic…
Determining the work statistics of quantum engines is challenging due to measurement backaction. We here show that a dynamic Bayesian network-based measurement scheme, which preserves quantum coherence within an engine cycle, is minimally…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
The regulation of metabolic activity by tuning enzyme expression levels is crucial to sustain cellular growth in changing environments. Metabolic networks are often studied at steady state using constraint-based models and optimization…
Kinetic parameters such as the turnover number ($k_{cat}$) and Michaelis constant ($K_{\mathrm{M}}$) are essential for modelling enzymatic activity but experimental data remains limited in scale and diversity. Previous methods for…
Statistical mechanics provides an effective framework to investigate information processing in biochemical reactions. Within such framework far-reaching analogies are established among (anti-) cooperative collective behaviors in chemical…
Complex chemical reaction networks, which underlie many industrial and biological processes, often exhibit non-monotonic changes in chemical species concentrations, typically described using nonlinear models. Such non-monotonic dynamics are…
We show how to evaluate mobility profiles, characterizing the transport of confined fluids under a perturbation, from equilibrium molecular simulations. The correlation functions derived with the Green-Kubo formalism are difficult to sample…
Black-box coevolution in mixed-motive games is often undermined by opponent-drift non-stationarity and noisy rollouts, which distort progress signals and can induce cycling, Red-Queen dynamics, and detachment. We propose the \emph{Marker…
In this paper we prove that the well-known quasi-steady state approximations, commonly used in enzyme kinetics, which can be interpreted as the reduced system of a differential system depending on a perturbative parameter, according to…
The weighted ensemble (WE) simulation strategy provides unbiased sampling of non-equilibrium processes, such as molecular folding or binding, but the extraction of rate constants relies on characterizing steady state behavior.…
A brief derivation of a specific regularization for the magnetic gas dynamic system of equations is given in the case of general equations of gas state (in presence of a body force and a heat source). The entropy balance equation in two…
[Background] Several studies have mentioned network modularity -- that a network can easily be decomposed into subgraphs that are densely connected within and weakly connected between each other -- as a factor affecting metabolic…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Expectation-Maximization (EM) algorithm is a widely used iterative algorithm for computing (local) maximum likelihood estimate (MLE). It can be used in an extensive range of problems, including the clustering of data based on the Gaussian…
Quasi-elastic neutron scattering (QENS) probes atomic and molecular motion on length and time scales central to catalysis, energy materials, and gas adsorption. However, conventional analytical fitting of QENS spectra often fails to…
Simulations of biophysical systems inevitably include steps that correspond to time integrations of ordinary differential equations. These equations are often related to enzyme action in the synthesis and destruction of molecular species,…
We demonstrate that the Michaelis-Menten reaction mechanism can be accurately approximated by a linear system when the initial substrate concentration is low. This leads to pseudo-first-order kinetics, simplifying mathematical calculations…