相关论文: How superlocalization affects Vibrational Energy E…

We analyze various limits of vibrationally coupled resonant electron transport in single-molecule junctions. Based on a master equation approach, we discuss analytic and numerical results for junctions under a high bias voltage or weak…

In this paper, using multiple scale analysis we derive a generalized mathematical model for amplitude evolution, and for calculating the energy exchange in resonant and near-resonant global triads consisting of weakly nonlinear internal…

We consider the propagation of a single particle in a random chain, assisted by the coupling to dispersive bosons. Time evolution treated with rate equations for hopping between localized states reveals a qualitative difference between…

We investigate theoretically the behavior of proteins as well as other large macromolecules which are incorporated into amphiphilic monolayers at the air-water interface. We assume the monolayer to be in the coexistence region of the…

Protein dynamics form a critical bridge between protein structure and function, yet the impact of evolution on ultrafast processes inside proteins remains enigmatic. This study delves deep into nanosecond-scale protein dynamics of a…

Proteins created by combinatorial methods in vitro are an important source of information for understanding sequence-structure-function relationships. Alignments of folded proteins from combinatorial libraries can be analyzed using methods…

When a self-localized quasiparticle excitation propagates along a discrete one dimensional lattice, it becomes subject to a dissipation that converts the kinetic energy into lattice vibrations. Eventually the kinetic energy does no longer…

In structure-based models of proteins, one often assumes that folding is accomplished when all contacts are established. This assumption may frequently lead to a conceptual problem that folding takes place in a temperature region of very…

We investigate cooperative phenomena and superradiance for vibrational transitions in polar molecule spectroscopy when a high optical-depth (OD) sample is studied. Such cooperativity comes from the build-up of inter-particle coherence…

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…

Proteins are minimally frustrated polymers. However, for realistic protein models non-native interactions must be taken into account. In this paper we analyze the effect of non-native interactions on the folding rate and on the folding free…

Previous studies of the flexibilities of ancestral proteins suggests that proteins evolve their function by altering their native state ensemble. Here we propose a more direct method of visualizing this by measuring the changes in the…

We study the spreading of initially localized excitations in 1D disordered granular crystals. We thereby investigate localization phenomena in strongly nonlinear systems, which we demonstrate to be fundamentally different from localization…

We show that the efficient excitation energy transfer in the Fenna-Matthews-Olson molecular aggregate under realistic physiological conditions is fueled by underdamped vibrations of the embedding proteins. For this, we present numerically…

Although ligand-binding sites in many proteins contain a high number density of charged side chains that can polarize small organic molecules and influence binding, the magnitude of this effect has not been studied in many systems. Here, we…

Focusing on a small set of proteins that i) fold in a concerted, all-or-none fashion and ii) do not contain knots or slipknots, we show that the Gauss linking integral, the torsion and the number of sequence-distant contacts provide…

Protein folding is a universal process, very fast and accurate, which works consistently (as it should be) in a wide range of physiological conditions. The present work is based on three premises, namely: ($i$) folding reaction is a process…

We propose a novel approach to calculate dynamical processes at ultrafast time scale in molecules in which vibrational and electronic motions are strongly mixed. The relevant electronic orbitals and their interactions are described by a…

We recently proposed effective normal modes for excitonically coupled aggregates which exactly transform the energy transfer Hamiltonian into a sum of one-dimensional Hamiltonians along the effective normal modes. Identifying physically…

A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…