Related papers: Correlated fluctuations in the exciton dynamics an…
We consider continuum dielectric models as minimal models to understand the effect of a surrounding globular protein and solvent on the quantum dynamics of electronic excitations in a biological chromophore. We derive expressions for the…
Experiments have revealed correlation-driven behavior of DNA in charged solutions, including charge inversion and condensation. This paper presents calculations of a lattice-gas model of charge inversion for the adsorption of charged dimers…
We study a pair of quantum dot exciton qubits interacting with a number of fluctuating charges that can induce a Stark shift of both exciton transition energies. We do this by solving the optical master equation using a numerical transfer…
To date X-ray spectroscopy has become a routine tool that can reveal highly local and element-specific information on the electronic structure of atoms in complex environments. Here, we focus on nuclear dynamical effects in X-ray spectra…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA, and how those effects are modified by noise. Starting from previous results on soliton dynamics on lattices defined by aperiodic…
Exciton transfer dynamics between chromophores depends on excitonic coupling, which is governed by relative orientation between the chromophores. While the excitonic coupling is treated as a static parameter in many cases, structural…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
By assuming that not only counter-ions but DNA molecules as well are thermally distributed according to a Boltzmann law, we propose a modified Poisson-Boltzmann equation at the classical level as starting point to compute the effects of…
The role of thermal pressure fluctuations in the ejection of tightly packaged DNA from protein capsid shells is discussed in a model calculation. At equilibrium before ejection we assume the DNA is folded many times into a bundle of…
Biomolecules couple to their aqueous environment through a variety of noncovalent interactions. Local structures at the surface of DNA and RNA are frequently determined by hydrogen bonds with water molecules, complemented by non-specific…
Motivated by recent experiments we have studied the optical conductivity of DNA in its natural environment containing water molecules and counter ions. Our density functional theory calculations (using SIESTA) for four base pair B-DNA with…
DNA regulation and repair processes require direct interactions between proteins and DNA at specific sites. Local fluctuations of the sugar-phosphate backbones and bases of DNA (a form of DNA "breathing") play a central role in such…
The interplay between exctions and vibrations is considered to be a key factor in determining the exciton transfer properties in light-harvesting exciton transfer complexes. Here we study this interplay theoretically in a model for exciton…
Protein evolution involves mutations occurring across a wide range of time scales. In analogy with disordered systems in statistical physics, this dynamical heterogeneity suggests strong correlations between mutations happening at distinct…
The observed relation between the X-ray radiation from AGNs, originating in the corona, and the optical/UV radiation from the disk is usually described by the anticorrelation between the UV to X-ray slope alpha_ox and the UV luminosity.…
One of the major functions of RecA protein in the cell is to bind single-stranded DNA exposed upon damage, thereby triggering the SOS repair response.We present fluorescence anisotropy measurements at the binding onset, showing enhanced DNA…
We study the ultrafast dynamics initiated by a coherent superposition of core-excited states of nitrous oxide molecule. Using high-level \textit{ab-initio} methods, we show that the decoherence caused by the electronic decay and the nuclear…
Recently, nuclear vibrational contribution signatures in 2D electronic spectroscopy have attracted considerable interest, in particular as regards interpretation of the oscillatory transients observed in light-harvesting complexes. These…
Many physical and natural systems, including the population of species, evolve in habitats with spatial stochastic variations of the individuals' motility. We study here the effect of those fluctuations on invasion and genetic loss. A…
We study color fluctuations in the quark-gluon plasma produced at the early stage of nucleus-nucleus collision at RHIC or LHC. The fluctuating color current, which flows along the beam, can be very {\it large} due to the strong anisotropy…