Related papers: Dynamical contribution into enzyme catalytic effic…
A mechanism for relationship of solvent viscosity with reaction rate constant at enzyme action is suggested. It is based on fluctuations of electric field in enzyme active site produced by thermally equilibrium rocking (cranckshaft motion)…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
The Empirical Valence Bond (EVB) method offers a suitable framework to obtain reactive potentials through the coupling of non-reactive force fields. However, most of the implemented functional forms for the coupling terms depend on complex…
Understanding how the effectiveness of natural photosynthetic energy harvesting systems arises from the interplay between quantum coherence and environmental noise represents a significant challenge for quantum theory. Recently it has begun…
This paper describes a method to do ab initio molecular dynamics in electronically excited systems within the random phase approximation (RPA). Using a dynamical variational treatment of the RPA frequency, which corresponds to the…
Statistics of the 1d dynamics of a single particle in a box of length L is studied under different conditions of periodic excitation: vibrated container, or 1 wall moving periodically or two walls vibrating in opposite phases. Theoretical…
In the present paper we address the general problem of selective electrodynamic interactions between DNA and protein, which is motivated by decades of theoretical study and our very recent experimental findings (M. Lechelon et al,…
Cells generally convert nutrient resources to useful products via energy transduction. Accordingly, the thermodynamic efficiency of this conversion process is one of the most essential characteristics of living organisms. However, although…
Energy efficiency is a crucial issue towards longterm deployment of compliant robots in the real world. In the context of variable impedance actuators (VIAs), one of the main focuses has been on improving energy efficiency through reduction…
Enzymes speed up biochemical reactions at the core of life by as much as 15 orders of magnitude. Yet, despite considerable advances, the fine dynamical determinants at the microscopic level of their catalytic proficiency are still elusive.…
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…
We consider an electronic spin, such as a nitrogen-vacancy (NV) center in diamond, weakly coupled to a large number (bath) of nuclear spins, and subjected to the Rabi driving with a periodically alternating phase (multiple rotary echo). We…
Novel mechanisms of defect annealing in solids are discussed, which are based on the large amplitude anharmonic lattice vibrations, a.k.a. intrinsic localized modes or discrete breathers (DBs). A model for amplification of defect annealing…
A growing amount of evidence points to the fact that many enzymes exhibit fluctuations in their catalytic activity, which are associated with conformational changes on a broad range of timescales. The experimental study of this phenomenon,…
Quantum resonant activation is investigated for the archetype setup of an externally driven two-state (spin-boson) system subjected to strong dissipation by means of both analytical and extensive numerical calculations. The phenomenon of…
In this work we study, at the single molecular level, the thermodynamic and dynamic characteristics of an enzymatic reaction comprising a rate limiting step. We investigate how the stability of the enzyme-state stationary probability…
Macromolecular crowding in living biological cells effects subdiffusion of larger biomolecules such as proteins and enzymes. Mimicking this subdiffusion in terms of random walks on a critical percolation cluster, we here present a case…
This study introduces a novel computational approach based on ratchet-and-pawl molecular dynamics (rMD) for accurately estimating ligand dissociation kinetics in protein-ligand complexes. By integrating Kramers' theory with Bell's equation,…
Understanding protein conformational dynamics is essential for elucidating biological function but remains challenging due to the wide range of timescales and the complexity of collective motions. Enhanced sampling methods overcome…
The bottleneck in enhanced sampling lies in finding collective variables (CVs) that can effectively accelerate protein conformational changes. True reaction coordinates (tRCs) that can predict the committor are considered the optimal CVs,…