Charge transport in DNA: dependence of diffusion coefficient on temperature and electron-phonon coupling constant

Bubble Relaxation Dynamics in Homopolymer DNA Sequences

Understanding the inherent timescales of large bubbles in DNA is critical to a thorough comprehension of its physicochemical characteristics, as well as their potential role on helix opening and biological function. In this work, we employ the coarse-grained Peyrard-Bishop-Dauxois model of DNA to study relaxation dynamics of large bubbles in homopolymer DNA, using simulations up to the microsecond time scale. By studying energy autocorrelation functions of relatively large bubbles inserted into thermalised DNA molecules, we extract characteristic relaxation times from the equilibration process for both adenine-thymine (AT) and guanine-cytosine (GC) homopolymers. Bubbles of different amplitudes and widths are investigated through extensive statistics and appropriate fittings of their relaxation. Characteristic relaxation times increase with bubble amplitude and width. We show that, within the model, relaxation times are two orders of magnitude longer in GC sequences than in AT sequences. Overall, our results confirm that large bubbles leave a lasting impact on the molecule's dynamics, for times between 0.5-500 ns depending on the homopolymer type and bubble shape, thus clearly affecting long-time evolutions of the molecule.

Charge transfer mechanisms in DNA at finite temperatures: From quasiballistic to anomalous subdiffusive charge transfer

We address various regimes of charge transfer in DNA within the framework of the Peyrard-Bishop-Holstein model and analyze them from the standpoint of the characteristic size and timescales of the electronic and vibrational subsystems. It is demonstrated that a polaron is an unstable configuration within a broad range of temperatures and therefore polaronic contribution to the charge transport is irrelevant. We put forward an alternative fluctuation-governed charge transfer mechanism and show that the charge transfer can be quasiballistic at low temperatures, diffusive or mixed at intermediate temperatures, and subdiffusive close to the DNA denaturation transition point. Dynamic fluctuations in the vibrational subsystem is the key ingredient of our proposed mechanism which allows for explanation of all charge transfer regimes at finite temperatures. In particular, we demonstrate that in the most relevant regime of high temperatures (above the aqueous environment freezing point), the electron dynamics is completely governed by relatively slow fluctuations of the mechanical subsystem. We argue also that our proposed analysis methods and mechanisms can be relevant for the charge transfer in other organic systems, such as conjugated polymers, molecular aggregates, α-helices, etc.

Distributions of bubble lifetimes and bubble lengths in DNA

We investigate the distribution of bubble lifetimes and bubble lengths in DNA at physiological temperature, by performing extensive molecular dynamics simulations with the Peyrard-Bishop-Dauxois (PBD) model, as well as an extended version (ePBD) having a sequence-dependent stacking interaction, emphasizing the effect of the sequences' guanine-cytosine (GC)/adenine-thymine (AT) content on these distributions. For both models we find that base pair-dependent (GC vs AT) thresholds for considering complementary nucleotides to be separated are able to reproduce the observed dependence of the melting temperature on the GC content of the DNA sequence. Using these thresholds for base pair openings, we obtain bubble lifetime distributions for bubbles of lengths up to ten base pairs as the GC content of the sequences is varied, which are accurately fitted with stretched exponential functions. We find that for both models the average bubble lifetime decreases with increasing either the bubble length or the GC content. In addition, the obtained bubble length distributions are also fitted by appropriate stretched exponential functions and our results show that short bubbles have similar likelihoods for any GC content, but longer ones are substantially more likely to occur in AT-rich sequences. We also show that the ePBD model permits more, longer-lived, bubbles than the PBD system.

Coherence preservation and electron-phonon interaction in electron transfer in DNA

We analyze the influence of electron-phonon (e-ph) interaction in a model for electron transfer (ET) processes in DNA in terms of the envelope function approach for spinless electrons. We are specifically concerned with the effect of e-ph interaction on the coherence of the ET process and how to model the interaction of DNA with phonon reservoirs of biological relevance. We assume that the electron bearing orbitals are half filled and derive the physics of e-ph coupling in the vicinity in reciprocal space. We find that at half filling, the acoustical modes are decoupled to ET at first order, while optical modes are predominant. The latter are associated with inter-strand vibrational modes in consistency with previous studies involving polaron models of ET. Coupling to acoustic modes depends on electron doping of DNA, while optical modes are always coupled within our model. Our results yield e-ph coupling consistent with estimates in the literature, and we conclude that large polarons are the main result of such e-ph interactions. This scenario will have strong consequences on decoherence of ET under physiological conditions due to relative isolation from thermal equilibration of the ET mechanism.

Discrete-breather-assisted charge transport along DNA-like molecular wires

Mobile discrete breathers (MDBs) are here suggested as localized excitations underlying the trapping and transport of charged particles (electron or hole) along a DNA-like molecular wire with anchored ends such as attached to two electrodes. For illustration the Peyrard-Bishop-Dauxois-Holstein (PBDH) model is used. MDBs are excited by imposing appropriate disturbances to velocities or space positions of adjacent nucleotide pairs or lattice units of the wire. They can be directed either towards or away from the wire hence transverse to it. Numerical computer simulations show that a rather stable quasiparticle MDB + electron is possible when just a few of the nucleotide pairs near one of the fixed ends of the wire are excited. For the process to be effective, the charge, e.g., the electron, must be initially placed around the disturbed region of the molecule. Once the MDB + electron quasiparticle is formed it may be transported to quite a long distance up to ca. 60-70 nm in real space. Our findings show that such process does not demand intervention of an externally applied electric field and hence it may be considered as alternative to the polaron transport process.

Heterogeneity and chaos in the Peyrard-Bishop-Dauxois DNA model

We discuss the effect of heterogeneity on the chaotic properties of the Peyrard-Bishop-Dauxois nonlinear model of DNA. Results are presented for the maximum Lyapunov exponent and the deviation vector distribution. Different compositions of adenine-thymine (AT) and guanine-cytosine (GC) base pairs are examined for various energies up to the melting point of the corresponding sequence. We also consider the effect of the alternation index, which measures the heterogeneity of the DNA chain through the number of alternations between different types (AT or GC) of base pairs, on the chaotic behavior of the system. Biological gene promoter sequences have been also investigated, showing no distinct behavior of the maximum Lyapunov exponent.

Charge transport in a DNA model with solvent interaction

The charge transport in the modified DNA model is studied by taking into account the factor of solvent and the effect of coupling motions of nucleotides. We report on the presence of the modulational instability (MI) of a plane wave for charge migration in DNA and the generation of soliton-like excitations in DNA nucleotides. By applying the continuum approximation, we show that the original differential-difference equation for the DNA dynamics can be reduced to a set of three coupled nonlinear equations. The linear stability analysis of wave solutions of the coupled systems is performed and the growth rate of instability is found numerically. We also investigate the impact of solvent interaction. The solvent factor introduces a new behavior to the wave patterns, modifying also the intrinsic properties of localized structures. In the numerical simulations, we show that the solitons exists when taking into account the effect of solvent and confirms an highest propagation of localized structures in the systems. The effect of solvent forces introduces a robustness behavior to the formed patterns, reinforcing the idea that the information in the DNA model is confined and concentrated to specific regions for efficiency. We also show that the localized structures can be disappeared with the highest value of solvent factor and thereafter the information within the molecule is not perceptible or not transmitted to another sites.

An asymmetric mesoscopic model for single bulges in RNA

Simple one-dimensional DNA or RNA mesoscopic models are of interest for their computational efficiency while retaining the key elements of the molecular interactions. However, they only deal with perfectly formed DNA or RNA double helices and consider the intra-strand interactions to be the same on both strands. This makes it difficult to describe highly asymmetric structures such as bulges and loops and, for instance, prevents the application of mesoscopic models to determine RNA secondary structures. Here we derived the conditions for the Peyrard-Bishop mesoscopic model to overcome these limitations and applied it to the calculation of single bulges, the smallest and simplest of these asymmetric structures. We found that these theoretical conditions can indeed be applied to any situation where stacking asymmetry needs to be considered. The full set of parameters for group I RNA bulges was determined from experimental melting temperatures using an optimization procedure, and we also calculated average opening profiles for several RNA sequences. We found that guanosine bulges show the strongest perturbation on their neighboring base pairs, considerably reducing the on-site interactions of their neighboring base pairs.

Geometrically nonlinear deformation and the emergent behavior of polarons in soft matter

Mechanical strain can alter the electronic structure of both bulk semiconductors as well as nanostructures such as quantum dots. This fact has been extensively researched and exploited for tailoring electronic properties. The strain mediated interaction between the charge carriers and the lattice is interpreted through the so-called deformation potential. In the case of soft materials or nanostructures, such as DNA, the deformation potential leads to the formation of polarons which largely determine the electronic characteristics of DNA and similar polymer entities. In addition, polarons are also speculated to be responsible for the mechanism of quantum actuation in carbon nanotubes. The deformation potential is usually taken to be a linear function of the lattice deformation (U ∼ αε) where α is the deformation potential "constant" that determines the coupling strength and ε is the mechanical strain. In this letter, by carefully accounting for nonlinear geometric deformation that has been hitherto ignored so far in this context, we show that the deformation potential constant is renormalized in a non-trivial manner and is hardly a constant. It varies spatially within the material and with the size of the material. This effect, while negligible for hard materials, is found to be important for soft materials and critically impacts the interpretation of quantities such as polaron size, binding energy, and accordingly, electronic behavior.