Related papers: Field theory of enzyme-substrate systems with rest…
Characterization of protein energy landscape and conformational ensembles is important for understanding mechanisms of protein folding and function. We studied ensembles of bound and unbound conformations of six proteins to explore their…
The effect of conformational fluctuations of modular macromolecules, such as enzymes, on their diffusion properties is addressed using a simple generic model of an asymmetric dumbbell made of two hydrodynamically coupled subunits. It is…
Biocatalysis is a promising approach to sustainably synthesize pharmaceuticals, complex natural products, and commodity chemicals at scale. However, the adoption of biocatalysis is limited by our ability to select enzymes that will catalyze…
We provide a short historic of the early development of kinetic theory in plasma physics and synthesize the basic kinetic equations describing the evolution of systems with long-range interactions derived in Paper I. We describe the…
We develop tools from computational algebraic geometry for the study of steady state features of autonomous polynomial dynamical systems via elimination of variables. In particular, we obtain nontrivial bounds for the steady state…
Lying-standing transitions in the first molecular monolayer at organic-inorganic interfaces strongly influence interface dipoles, energy-level alignment, and growth modes, yet their collective kinetics remain difficult to predict. Here, we…
Living systems contain intricate biochemical networks whose structure is closely related to their function and allows them to exhibit robust behavior in the presence of external stimuli. Such networks typically involve catalytic enzymes,…
We present a numerical study of dynamical correlations (structure factors) of the long-range generalization of the Fermi-Pasta-Ulam oscillator chain, where the strength of the interaction between two lattice sites decays as a power $\alpha$…
The quantitative characterization of mutational landscapes is a task of outstanding importance in evolutionary and medical biology: It is, e.g., of central importance for our understanding of the phenotypic effect of mutations related to…
We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…
The classical theory of enzymatic inhibition aims to quantitatively describe the effect of certain molecules -- called inhibitors -- on the progression of enzymatic reactions, but growing signs indicate that it must be revised to keep pace…
We examine the applicability of the extended law of corresponding states (ELCS) to equilibrium and non equilibrium features of the state diagram of the globular protein lysozyme. We provide compelling evidence that the ELCS correctly…
Energetic correlations due to polymeric constraints and the locality of interactions, in conjunction with the apriori specification of the existence of a particularly low energy state, provides a method of introducing the aspect of minimal…
Ligand receptor interactions are commonly assessed through equilibrium occupancy and pharmacodynamic measures that describe binding and saturation by means of bounded response curves. Thermodynamic approaches relate binding affinity to…
An overarching question in strongly correlated electron systems is how the landscape of quantum phases emerges from electron correlations. The method of extended dynamical mean field theory (EDMFT) has been developed for clean lattice…
Enzyme-based systems have been shown to undergo directional motion in response to their substrate gradient. Here, we formulate a kinetic model to analyze the directional movement of an ensemble of protein molecules in response to a gradient…
The dynamics of linear stochastic growth equations on growing substrates is studied. The substrate is assumed to grow in time following the power law $t^\gamma$, where the growth index $\gamma$ is an arbitrary positive number. Two different…
We derive a widely-applicable first principles approach for determining two-body, static effective interactions for low-energy Hamiltonians with quantitative accuracy. The algebraic construction rigorously conserves all instantaneous…
Different graphical plots involving the catalytic rate with the (initial) substrate concentration exist in the enzyme kinetics literature to estimate the reaction constants. But, none of these standard plots can unambiguously distinguish…
Many experiments in recent years have reported that, when exposed to their corresponding substrate, catalytic enzymes undergo enhanced diffusion as well as chemotaxis (biased motion in the direction of a substrate gradient). Among other…