Related papers: Energy Transfer in molecular devices
We show how to localize and quantify the functional evolutionary constraints on natural proteins. The method compares the perturbations caused by local sequence variants to the energetics of the protein folding process and to the…
Determining the different conformational states of a protein and the transition paths between them is key to fully understanding the relationship between biomolecular structure and function. This can be accomplished by sampling protein…
The dynamical characterization of proteins is crucial to understand protein function. From a microscopic point of view, protein dynamics is governed by the local atomic interactions that, in turn, trigger the functional conformational…
Intrinsically nonlinear coupled systems present different oscillating components that exchange energy among themselves. We present a new approach to deal with such energy exchanges and to investigate how it depends on the system control…
Under physiological conditions, ballistic long-range transfer of electronic excitations in molecular aggregates is generally expected to be suppressed by noise and dissipative processes. Hence, quantum phenomena are not considered to be…
Recent experimental findings on a protein showed the diffusion of vibrational energy does not occur along the backbone interaction,as it might be expected, but prevalently on non-bonded contacts. These results are explained presenting a…
In quantum targeted energy transfer, bosons are transferred from a certain crystal site to an alternative one, utilizing a nonlinear resonance configuration similar to the classical targeted energy transfer. We use a novel computational…
Molecular machines composed of coupled subsystems transduce free energy between different external reservoirs, in the process internally transducing energy and information. While subsystem efficiencies of these molecular machines have been…
We consider the dependence of the electron transfer in photosynthetic complexes on correlation properties of random fluctuations of the protein environment. The electron subsystem is modeled by a finite network of connected electron…
Topological defects in low-dimensional non-linear systems feature a sliding-to-pinning transition of relevance for a variety of research fields, ranging from biophysics to nano- and solid-state physics. We find that the dynamics after a…
At molecular scales, fluctuations play a significant role and prevent biomolecular processes from always proceeding in a preferred direction, raising the question of how limited amounts of free energy can be dissipated to obtain directed…
Biological molecular machines are bifunctional enzymes that catalyze two processes: one donating free energy and the other accepting it. Recent studies show that most protein enzymes have rich stochastic dynamics of transitions between the…
Molecular motor proteins serve as an essential component of intracellular transport by generating forces to haul cargoes along cytoskeletal filaments. Two species of motors that are directed oppositely (e.g. kinesin, dynein) can be attached…
We consider the reduced dynamics of a molecular chain weakly coupled to a phonon bath. With a small and constant inhomogeneity in the coupling, the excitation relaxation rates are obtained in closed form. They are dominated by transitions…
Using an Ising-like model of protein mechanical unfolding, we introduce a diffusive dynamics on its exactly known free energy profile, reducing the nonequilibrium dynamics of the model to a biased random walk. As an illustration, the model…
We present a detailed study of the performance and reliability of design procedures based on energy minimization. The analysis is carried out for model proteins where exact results can be obtained through exhaustive enumeration. The…
Microscopic machines utilize free energy to create and maintain out-of-equilibrium organization in virtually all living things. Often this takes the form of converting the free energy stored in nonequilibrium chemical potential differences…
We report on the energy transport between two coupled probes in contact with granular thermostats at different temperatures. In our experiment, two identical blades, which are electromechanically coupled, are immersed in two granular gases…
Quantifying the flow of energy within and through fluctuating nanoscale systems poses a significant challenge to understanding microscopic biological machines. A common approach involves coarse-graining, which allows a simplified…
Intercellular signaling has an important role in organism development, but not all communication occurs using the same mechanism. Here, we analyze the energy efficiency of intercellular signaling by two canonical mechanisms: diffusion of…