Theoretical Improvements in Enzyme Efficiency Associated with Noisy Rate Constants and Increased Dissipation.

Previous studies have revealed the extraordinarily large catalytic efficiency of some enzymes. High catalytic proficiency is an essential accomplishment of biological evolution. Natural selection led to the increased turnover number, k, and enzyme efficiency, k/K, of uni-uni enzymes, which convert a single substrate into a single product.

Maximum Entropy Production Theorem for Transitions between Enzyme Functional States and Its Applications.

Transitions between enzyme functional states are often connected to conformational changes involving electron or proton transport and directional movements of a group of atoms. These microscopic fluxes, resulting in entropy production, are driven by non-equilibrium concentrations of substrates and products. Maximal entropy production exists for any chosen transition, but such a maximal transitional entropy production (MTEP) requirement does not ensure an increase of total entropy production, nor an increase in catalytic performance.

The coupling effects of surface plasmons and Fermi arc plasmons in Weyl semimetals.

We study the effects of coupling between surface plasmon and Fermi arc plasmon modes on a planar surface of the Weyl semimetal. A model Hamiltonian is proposed in the second quantization representation for the system of coupled surface plasmon and Fermi arc plasmon modes. We obtain the dispersion relations of coupled modes using the Bogoliubov transformation technique.

The maximum entropy production requirement for proton transfers enhances catalytic efficiency for β-lactamases.

Movement of charges during enzyme catalytic cycle may be due to conformational changes, or to fast electron or proton transfer, or to both events. In each case, entropy production can be calculated using Terrel L. Hill's method, if relevant microscopic rate constants are known.

Surface plasmons in Weyl semimetals.

The surface plasmon excitation spectrum is calculated for the Weyl semimetal within the random phase approximation. Recently, a surface plasmon mode has been predicted to exist at the three-dimensional Dirac semimetal surface due to the Dirac plasmon mode in the bulk. In addition, Weyl semimetals possess Fermi arc electron states on their surfaces resulting in an anisotropic Fermi arc plasmon mode.

Surface plasmon of three-dimensional Dirac semimetals.

The surface plasmon excitation spectrum is calculated for the semi-infinite 3D Dirac semimetal. We used the random phase approximation for the calculation of the surface dielectric function, from which we derived the dynamical structure factor. The surface excitation spectrum shows a well-defined strong surface plasmon peak due to the plasmon mode in the bulk, with a noticeable influence of electron-hole excitations at large wave vectors parallel to the surface.

Is the catalytic activity of triosephosphate isomerase fully optimized? An investigation based on maximization of entropy production.

Triosephosphate isomerase (TIM) is often described as a fully evolved housekeeping enzyme with near-maximal possible reaction rate. The assumption that an enzyme is perfectly evolved has not been easy to confirm or refute. In this paper, we use maximization of entropy production within known constraints to examine this assumption by calculating steady-state cyclic flux, corresponding entropy production, and catalytic activity in a reversible four-state scheme of TIM functional states.

Enzyme kinetics and the maximum entropy production principle.

A general proof is derived that entropy production can be maximized with respect to rate constants in any enzymatic transition. This result is used to test the assumption that biological evolution of enzyme is accompanied with an increase of entropy production in its internal transitions and that such increase can serve to quantify the progress of enzyme evolution. The state of maximum entropy production would correspond to fully evolved enzyme.