Tight-Binding Modeling of Nucleic Acid Sequences: Interplay between Various Types of Order or Disorder and Charge Transport

Ultrafast excitonic dynamics in DNA: Bridging correlated quantum dynamics and sequence dependence

After photoexcitation of DNA, the excited electron (in the LUMO) and the remaining hole (in the HOMO) localized on the same DNA base form a bound pair, called the Frenkel exciton, due to their mutual Coulomb interaction. In this study, we demonstrate that a tight-binding (TB) approach, using TB parameters for electrons and holes available in the literature, allows us to correlate relaxation properties, average charge separation, and dipole moments to a large ensemble of double-stranded DNA sequences (all 16384 possible sequences with 14 nucleobases). This way, we are able to identify a relatively small subensemble of sequences responsible for long-lived excited states, high average charge separation, and high dipole moment. Further analysis shows that these sequences are particularly T rich. By systematically screening the impact of electron-hole interaction (Coulomb forces), we verify that these correlations are relatively robust against finite-size variations of the interaction parameter, not directly accessible experimentally. This methodology combines simulation methods from quantum physics and physical chemistry with statistical analysis known from genetics and epigenetics, thus representing a powerful bridge to combine information from both fields.

Computation of the Spatial Distribution of Charge-Carrier Density in Disordered Media

The space- and temperature-dependent electron distribution n(r,T) determines optoelectronic properties of disordered semiconductors. It is a challenging task to get access to n(r,T) in random potentials, while avoiding the time-consuming numerical solution of the Schrödinger equation. We present several numerical techniques targeted to fulfill this task. For a degenerate system with Fermi statistics, a numerical approach based on a matrix inversion and one based on a system of linear equations are developed. For a non-degenerate system with Boltzmann statistics, a numerical technique based on a universal low-pass filter and one based on random wave functions are introduced. The high accuracy of the approximate calculations are checked by comparison with the exact quantum-mechanical solutions.

Quantum biology. π-π entanglement signatures in Protein-DNA interactions

DNA biological functions are carried out by individual proteins that interact with specific sequences along DNA to prime molecular processes required by cellular metabolism. Protein-DNA interactions include DNA replication, gene expression and its regulation, DNA repair, DNA restriction and modification by endonucleases, generally classified as enzymatic functions, or transcription factors functions. To find specific binding target sequences and finalize their activities, proteins must operate in symbiosis with cellular crowded environment identifying extremely small cognate sequences along the DNA chain, ranging from 15-20 bps for repressors to 4-6 bps for restriction enzymes in less than one second.

Synchronized Oscillations in Double-Helix B-DNA Molecules with Mirror-Symmetric Codons

A fully analytical treatment of the base-pair and codon dynamics in double-stranded DNA molecules is introduced, by means of a realistic treatment that considers different mass values for G, A, T, and C nucleotides and takes into account the intrinsic three-dimensional, helicoidal geometry of DNA in terms of a Hamitonian in cylindrical coordinates. Within the framework of the Peyrard–Dauxois–Bishop model, we consider the coupling between stretching and stacking radial oscillations as well as the twisting motion of each base pair around the helix axis. By comparing the linearized dynamical equations for the angular and radial variables corresponding to the bp local scale with those of the longer triplet codon scale, we report an underlying hierarchical symmetry. The existence of synchronized collective oscillations of the base-pairs and their related codon triplet units are disclosed from the study of their coupled dynamical equations. The possible biological role of these correlated, long-range oscillation effects in double standed DNA molecules containing mirror-symmetric codons of the form XXX, XX’X, X’XX’, YXY, and XYX is discussed in terms of the dynamical equations solutions and their related dispersion relations.

Protein-DNA target search relies on quantum walk

Protein-DNA interactions play a fundamental role in all life systems. A critical issue of such interactions is given by the strategy of protein search for specific targets on DNA. The mechanisms by which the protein are able to find relatively small cognate sequences, typically 15-20 base pairs (bps) for repressors, and 4-6 bps for restriction enzymes among the millions of bp of non-specific chromosomal DNA have hardly engaged researchers for decades. Recent experimental studies have generated new insights on the basic processes of protein-DNA interactions evidencing the underlying complex dynamic phenomena involved, which combine three-dimensional and one-dimensional motion along the DNA chain. It has been demonstrated that protein molecules have an extraordinary ability to find the target very quickly on the DNA chain, in some cases, with two orders of magnitude faster than the diffusion limit. This unique property of protein-DNA search mechanism is known as facilitated diffusion. Several theoretical mechanisms have been suggested to describe the origin of facilitated diffusion. However, none of such models currently has the ability to fully describe the protein search strategy. In this paper, we suggest that the ability of proteins to identify consensus sequences on DNA is based on the entanglement of π-π electrons between DNA nucleotides and protein amino acids. The π-π entanglement is based on Quantum Walk (QW), through Coin-position entanglement (CPE). First, the protein identifies a dimer belonging to the consensus sequence, and localize a π on such dimer, hence, the other π electron scans the DNA chain until the sequence is identified. Focusing on the example of recognition of consensus sequences of EcoRV or EcoRI, we will describe the quantum features of QW on protein-DNA complexes during the search strategy, such as walker quadratic spreading on a coherent superposition of different vertices and environment-supported long-time survival probability of the walker. We will employ both discrete- or continuous-time versions of QW. Biased and unbiased classical Random Walk (CRW) have been used for a long time to describe the Protein-DNA search strategy. QW, the quantum version of CRW, has been widely studied for its applications in quantum information applications. In our biological application, the walker (the protein) resides at a vertex in a graph (the DNA structural topology). Differently to CRW, where the walker moves randomly, the quantum walker can hop along the edges in the graph to reach other vertices entering coherently a superposition across different vertices spreading quadratically faster than CRW analogous evidencing the typical speed up features of the QW. When applied to a protein-DNA target search problem, QW gives the possibility to achieve the experimental diffusional motion of proteins over diffusion classical limits experienced along DNA chains exploiting quantum features such as CPE and long-time survival probability supported by the environment. In turn, we come to the conclusion that, under quantum picture, the protein search strategy does not distinguish between one-dimensional (1D) and three-dimensional (3D) cases.

Base-Pairs' Correlated Oscillation Effects on the Charge Transfer in Double-Helix B-DNA Molecules

By introducing a suitable renormalization process, the charge carrier and phonon dynamics of a double-stranded helical DNA molecule are expressed in terms of an effective Hamiltonian describing a linear chain, where the renormalized transfer integrals explicitly depend on the relative orientations of the Watson-Crick base pairs, and the renormalized on-site energies are related to the electronic parameters of consecutive base pairs along the helix axis, as well as to the low-frequency phonons' dispersion relation. The existence of synchronized collective oscillations enhancing the π-π orbital overlapping among different base pairs is disclosed from the study of the obtained analytical dynamical equations. The role of these phonon-correlated, long-range oscillation effects on the charge transfer properties of double-stranded DNA homopolymers is discussed in terms of the resulting band structure.

Quantum walks with sequential aperiodic jumps

We analyze a set of discrete-time quantum walks for which the displacements on a chain follow binary aperiodic jumps according to three paradigmatic sequences: Fibonacci, Thue-Morse, and Rudin-Shapiro. We use a generalized Hadamard coin, C[over ̂]_{H}, as well as a generalized Fourier coin, C[over ̂]_{K}. We verify the QW experiences a slowdown of the wave packet spreading, σ^{2}(t)∼t^{α}, by the aperiodic jumps whose exponent, α, depends on the type of aperiodicity. Additional aperiodicity-induced effects also emerge, namely, (1) while the superdiffusive regime (1<α<2) is predominant, α displays an unusual sensibility with the type of coin operator where the more pronounced differences emerge for the Rudin-Shapiro and random protocols and (2) even though the angle θ of the coin operator is homogeneous in space and time, there is a nonmonotonic dependence of α with θ. Fingerprints of the aperiodicity in the hoppings are also found when distributional measures such as the Shannon and von Neumann entropies, the Inverse Participation Ratio, the Jensen-Shannon dissimilarity, and the kurtosis are computed, which allow assessing informational and delocalization features arising from these protocols and understanding the impact of linear and nonlinear correlations of the jump sequence in a quantum walk as well. Finally, we argue the spin-lattice entanglement is enhanced by aperiodic jumps.

Real Space Theory for Electron and Phonon Transport in Aperiodic Lattices via Renormalization

Structural defects are inherent in solids at a finite temperature, because they diminish free energies by growing entropy. The arrangement of these defects may display long-range orders, as occurring in quasicrystals, whose hidden structural symmetry could greatly modify the transport of excitations. Moreover, the presence of such defects breaks the translational symmetry and collapses the reciprocal lattice, which has been a standard technique in solid-state physics. An alternative to address such a structural disorder is the real space theory. Nonetheless, solving 1023 coupled Schrödinger equations requires unavailable yottabytes (YB) of memory just for recording the atomic positions. In contrast, the real-space renormalization method (RSRM) uses an iterative procedure with a small number of effective sites in each step, and exponentially lessens the degrees of freedom, but keeps their participation in the final results. In this article, we review aperiodic atomic arrangements with hierarchical symmetry investigated by means of RSRM, as well as their consequences in measurable physical properties, such as electrical and thermal conductivities.

Localization Properties of Non-Periodic Electrical Transmission Lines

The properties of localization of the I ω electric current function in non-periodic electrical transmission lines have been intensively studied in the last decade. The electric components have been distributed in several forms: (a) aperiodic, including self-similar sequences (Fibonacci and m-tuplingtupling Thue–Morse), (b) incommensurate sequences (Aubry–André and Soukoulis–Economou), and (c) long-range correlated sequences (binary discrete and continuous). The localization properties of the transmission lines were measured using typical diagnostic tools of quantum mechanics like normalized localization length, transmission coefficient, average overlap amplitude, etc. As a result, it has been shown that the localization properties of the classic electric transmission lines are similar to the one-dimensional tight-binding quantum model, but also features some differences. Hence, it is worthwhile to continue investigating disordered transmission lines. To explore new localization behaviors, we are now studying two different problems, namely the model of interacting hanging cells (consisting of a finite number of dual or direct cells hanging in random positions in the transmission line), and the parity-time symmetry problem ( PT -symmetry), where resistances R n are distributed according to gain-loss sequence ( R 2 n = + R , R 2 n − 1 = − R ). This review presents some of the most important results on the localization behavior of the I ω electric current function, in dual, direct, and mixed classic transmission lines, when the electrical components are distributed non-periodically.