R. A. Caetano

Charge transport through biomolecular wires in a solvent: bridging molecular dynamics and model Hamiltonian approaches.

We present a hybrid method based on a combination of classical molecular dynamics simulations, quantum-chemical calculations, and a model Hamiltonian approach to describe charge transport through biomolecular wires with variable lengths in presence of a solvent. The core of our approach consists in a mapping of the biomolecular electronic structure, as obtained from density-functional based tight-binding calculations of molecular structures along molecular dynamics trajectories, onto a low-dimensional model Hamiltonian including the coupling to a dissipative bosonic environment. The latter encodes fluctuation effects arising from the solvent and from the molecular conformational dynamics. We apply this approach to the case of pG-pC and pA-pT DNA oligomers as paradigmatic cases and show that the DNA conformational fluctuations are essential in determining and supporting charge transport.

Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories

We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.

Structural fluctuations and quantum transport through DNA molecular wires: a combined molecular dynamics and model Hamiltonian approach

Charge transport through a short DNA oligomer (Dickerson dodecamer (DD)) in the presence of structural fluctuations is investigated using a hybrid computational methodology based on a combination of quantum mechanical electronic structure calculations and classical molecular dynamics (MD) simulations with a model Hamiltonian approach. Based on a fragment orbital description, the DNA electronic structure can be coarse-grained in a very efficient way. The influence of dynamical fluctuations, arising either from the solvent fluctuations or from base-pair vibrational modes, can be taken into account in a straightforward way through the time series of the effective DNA electronic parameters, evaluated at snapshots along the MD trajectory. We show that charge transport can be promoted through the coupling to solvent fluctuations, which gate the on-site energies along the DNA wire.

Dynamics of one electron in a nonlinear disordered chain

In this paper we report new numerical results on the disordered Schrödinger equation with nonlinear hopping. By using a classical harmonic Hamiltonian and the Su-Schrieffer-Heeger approximation we write an effective Schrödinger equation. This model with off-diagonal nonlinearity allows us to study the interaction of one electron and acoustical phonons. We solve the effective Schrödinger equation with nonlinear hopping for an initially localized wavepacket by using a predictor-corrector Adams-Bashforth-Moulton method. Our results indicate that the nonlinear off-diagonal term can promote a long-time subdiffusive regime similar to that observed in models with diagonal nonlinearity.

Surface-enhanced Raman scattering using bismuth nanoparticles: a study with amino acids

Bismuth nanoparticles produced by laser ablation synthesis in solution (LASiS) show localized surface plasmon resonances (LSPRs). The nanoparticles show surface-enhanced Raman scattering (SERS) activity for several tested amino acids. Optical absorption, dynamic light scattering (DLS), and transmission electron microscopy (TEM) as well as Raman scattering were used to characterize the samples. The search for new biocompatible nanoparticles for diagnostic purposes is important, and the demonstration that a semimetal is capable to act as a SERS active system opens new possibilities for molecular detection.

Spin-Current and Spin-Splitting in Helicoidal Molecules Due to Spin-Orbit Coupling.

The use of organic materials in spintronic devices has been seriously considered after recent experimental works have shown unexpected spin-dependent electrical properties. The basis for the confection of any spintronic device is ability of selecting the appropriated spin polarization. In this direction, DNA has been pointed out as a potential candidate for spin selection due to the spin-orbit coupling originating from the electric field generated by accumulated electrical charges along the helix. Here, we demonstrate that spin-orbit coupling is the minimum ingredient necessary to promote a spatial spin separation and the generation of spin-current. We show that the up and down spin components have different velocities that give rise to a spin-current. By using a simple situation where spin-orbit coupling is present, we provide qualitative justifications to our results that clearly point to helicoidal molecules as serious candidates to integrate spintronic devices.

Suppression of Bose-Einstein condensation in one-dimensional scale-free random potentials

A perfect Bose gas can condensate in one dimension in the presence of a random potential due to the presence of Lifshitz tails in the one-particle density of states. Here, we show that scale-free correlations in the random potential suppress the disorder induced Bose-Einstein condensation BEC. Within a tight-binding approach, we consider free Bosons moving in a scale-free correlated random potential with spectral density decaying as 1 /k. The critical temperature for BEC is shown to vanish in chains with a binary nonstationary potential 1. On the other hand, a weaker suppression of BEC takes place in nonbinarized scale-free potentials. After a slightly increase in the stationary regime, the BEC transition temperature continuously decays as the spectral exponent →.

Localization length enhancement in two-dimensional self-assembled systems

Disorder correlations lead to important effects on the localization of states in one-dimensional systems, as shown for a large number of correlation models in the context of polymers and macromolecules. The extension of the problem to two-dimensional systems has been less frequently discussed due to the lack, until recently, of realistic systems with properties that could be addressed to the effects of correlations in disorder. The advent of self-assembled quantum dots, which may show short-range ordering, has changed this scenario. In the present work we investigate the properties of a two-dimensional disordered lattice with short-range correlations in the disorder that reveals itself as a minimal model for self-assembled quantum dots. The short-range correlations in disorder may lead to significant enhancement of the localization length for wide energy windows.

Delocalized states in damaged DNA

Recent studies suggest that base pairing is an efficient electronic delocalization mechanism. However, defects may break down such effect. In the present work we show how a simple model of defects suppresses the delocalization, which survives only for low defect concentrations.