Theoretical study of collective modes in DNA at ambient temperature

The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal modes are not plane waves with a single wave number q but have a finite and frequency dependent damping width. The density of modes rho(nu), the average dispersion relation nu(q) as well as the coherence length xi(nu) are analytically calculated. The Gibbs averaged resolvent is computed using a replicated transfer matrix formalism and variational wave functions for the ground and first excited state. Our results for the density of modes are compared to Raman spectroscopy measurements of the collective modes for DNA in solution and show a good agreement with experimental data in the low frequency regime nu < 150 cm^{-1}. Radial modes extend over frequencies ranging from 50 cm^{-1} to 110 cm^{-1}. Angular modes, related to helical axis vibrations are limited to nu < 25 cm^{-1}. Normal modes are highly disordered and coherent over a few base pairs only (xi < 2 nm) in good agreement with neutron scattering experiments.Comment: 20 pages + 13 ps figure

Energy Localization in the Peyrard-Bishop DNA model

We study energy localization on the oscillator-chain proposed by Peyrard and Bishop to model the DNA. We search numerically for conditions with initial energy in a small subgroup of consecutive oscillators of a finite chain and such that the oscillation amplitude is small outside this subgroup for a long timescale. We use a localization criterion based on the information entropy and we verify numerically that such localized excitations exist when the nonlinear dynamics of the subgroup oscillates with a frequency inside the reactive band of the linear chain. We predict a mimium value for the Morse parameter $(\mu >2.25)$ (the only parameter of our normalized model), in agreement with the numerical calculations (an estimate for the biological value is $\mu =6.3$). For supercritical masses, we use canonical perturbation theory to expand the frequencies of the subgroup and we calculate an energy threshold in agreement with the numerical calculations

Functional modes of proteins are among the most robust ones

It is shown that a small subset of modes which are likely to be involved in protein functional motions of large amplitude can be determined by retaining the most robust normal modes obtained using different protein models. This result should prove helpful in the context of several applications proposed recently, like for solving difficult molecular replacement problems or for fitting atomic structures into low-resolution electron density maps. Moreover, it may also pave the way for the development of methods allowing to predict such motions accurately.Comment: 4 pages, 5 figure

The dynamical transition in proteins and non-Gaussian behavior of low frequency modes in Self Consistent Normal Mode Analysis

Self Consistent Normal Mode Analysis (SCNMA) is applied to heme c type cytochrome f to study temperature dependent protein motion. Classical Normal Mode Analysis (NMA) assumes harmonic behavior and the protein Mean Square Displacement (MSD) has a linear dependence on temperature. This is only consistent with low temperature experimental results. To connect the protein vibrational motions between low temperature and physiological temperature, we have incorporated a fitted set of anharmonic potentials into SCNMA. In addition, Quantum Harmonic Oscillator (QHO) theory has been used to calculate the displacement distribution for individual vibrational modes. We find that the modes involving soft bonds exhibit significant non-Gaussian dynamics at physiological temperature, which suggests it may be the cause of the non-Gaussian behavior of the protein motions probed by Elastic Incoherent Neutron Scattering (EINS). The combined theory displays a dynamical transition caused by the softening of few "torsional" modes in the low frequency regime (< 50cm-1or 0.6ps). These modes change from Gaussian to a classical distribution upon heating. Our theory provides an alternative way to understand the microscopic origin of the protein dynamical transition.Comment: 17 pages, 6 figures, 1 tabl

Complex-k modes of plasmonic chain waveguides

Nanoparticle chain waveguide based on negative-epsilon material is investigated through a generic 3D finite-element Bloch-mode solver which derives complex propagation constant ($k$). Our study starts from waveguides made of non-dispersive material, which not only singles out "waveguide dispersion" but also motivates search of new materials to achieve guidance at unconventional wavelengths. Performances of gold or silver chain waveguides are then evaluated; a concise comparison of these two types of chain waveguides has been previously missing. Beyond these singly-plasmonic chain waveguides, we examine a hetero-plasmonic chain system with interlacing gold and silver particles, inspired by a recent proposal; the claimed enhanced energy transfer between gold particles appears to be a one-sided view of its hybridized waveguiding behavior --- energy transfer between silver particles worsens. Enabled by the versatile numerical method, we also discuss effects of inter-particle spacing, background medium, and presence of a substrate. Our extensive analyses show that the general route for reducing propagation loss of e.g. a gold chain waveguide is to lower chain-mode frequency with a proper geometry (e.g. smaller particle spacing) and background material setting (e.g. high-permittivity background or even foreign nanoparticles). In addition, the possibility of building mid-infrared chain waveguides using doped silicon is commented based on numerical simulation.Comment: 26 pages, many figures, now including "Supplementary Data". Accepted, Journal of Physics Communicatio

Coherent electronic and nuclear dynamics in a rhodamine heterodimer-DNA supramolecular complex

Elucidating the role of quantum coherences in energy migration within biological and artificial multichromophoric antenna systems is the subject of an intense debate. It is also a practical matter because of the decisive implications for understanding the biological processes and engineering artificial materials for solar energy harvesting. A supramolecular rhodamine heterodimer on a DNA scaffold was suitably engineered to mimic the basic donor-acceptor unit of light-harvesting antennas. Ultrafast 2D electronic spectroscopic measurements allowed identifying clear features attributable to a coherent superposition of dimer electronic and vibrational states contributing to the coherent electronic charge beating between the donor and the acceptor. The frequency of electronic charge beating is found to be 970 cm-1 (34 fs) and can be observed for 150 fs. Through the support of high level ab initio TD-DFT computations of the entire dimer, we established that the vibrational modes preferentially optically accessed do not drive subsequent coupling between the electronic states on the 600 fs of the experiment. It was thereby possible to characterize the time scales of the early time femtosecond dynamics of the electronic coherence built by the optical excitation in a large rigid supramolecular system at a room temperature in solution. © 2017 the Owner Societies.Multi valued and parallel molecular logi

Dynamics of Metal Centers Monitored by Nuclear Inelastic Scattering

Nuclear inelastic scattering of synchrotron radiation has been used now since 10 years as a tool for vibrational spectroscopy. This method has turned out especially useful in case of large molecules that contain a M\"ossbauer active metal center. Recent applications to iron-sulfur proteins, to iron(II) spin crossover complexes and to tin-DNA complexes are discussed. Special emphasis is given to the combination of nuclear inelastic scattering and density functional calculations