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.

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.

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.

Sequencing-independent delocalization in a DNA-like double chain with base pairing

The question of whether or not DNA is intrinsically conducting is still a challenge. The ongoing debate on DNA molecules as an electronic material has so far underestimated a key distinction of the system: the role of base pairing in opposition to correlations along each chain. We show that a disordered base paired double chain presents truly or, at least, effectively delocalized states. This effect is irrespective to the sequencing along each chain.

Diversity patterns and speciation processes in a two-island system with continuous migration

Geographic isolation is a central mechanism of speciation, but perfect isolation of populations is rare. Although speciation can be hindered if gene flow is large, intermediate levels of migration can enhance speciation by introducing genetic novelty in the semi-isolated populations or founding small communities of migrants. Here, we consider a two-island neutral model of speciation with continuous migration and study diversity patterns as a function of the migration probability, population size, and number of genes involved in reproductive isolation (dubbed as genome size). For small genomes, low levels of migration induce speciation on the islands that otherwise would not occur. Diversity, however, drops sharply to a single species inhabiting both islands as the migration probability increases. For large genomes, sympatric speciation occurs even when the islands are strictly isolated. Then species richness per island increases with the probability of migration, but the total number of species decreases as they become cosmopolitan. For each genome size, there is an optimal migration intensity for each population size that maximizes the number of species. We discuss the observed modes of speciation induced by migration and how they increase species richness in the insular system while promoting asymmetry between the islands and hindering endemism.

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.

Deficient cell-cell cohesion is linked with lobular localization in simplified models of lobular carcinoma in situ (LCIS)

Lobular carcinoma in situ (LCIS) is a precursor of invasive lobular carcinoma of the breast. LCIS cells lack cell-cell cohesion due to the loss of E-cadherin. LCIS cells grow in mammary lobules rather than in ducts. The etiology of this pattern, especially its dependence on cellular cohesion, is incompletely understood. We simulated passive intra-glandular scattering of carcinoma in situ (CIS) cells in an ultra-simplified hollow mold tissue replica (HMTR) and a discrete-time mathematical model featuring particles of variable sizes representing single cells (LCIS-like particles) or groups of cohesive carcinoma cells (DCIS-like particles). The HMTR features structures reminiscent of a mammary duct with associated lobules. The discrete mathematical model characterizes spatial redistribution over time and includes transition probabilities between ductal or lobular localizations. Redistribution of particles converged toward an equilibrium depending on particle size. Strikingly, equilibrium proportions depended on particle properties, which we also confirm in a continuous-time mathematical model that considers controlling lobular properties such as crowding. Particles of increasing size, representing CIS cells with proficient cohesion, showed increasingly higher equilibrium ductal proportions. Our investigations represent two conceptual abstractions implying a link between loss of cell-cell cohesion and lobular localization of LCIS, which provide a much-needed logical foundation for studying the connections between collective cell behavior and cancer development in breast tissues. In light of the findings from our simplified modeling approach, we discuss multiple avenues for near-future research that can address and evaluate the redistribution hypothesis mathematically and empirically.

Intermittent migration can induce pulses of speciation in a two-island system

Geographic barriers can come and go depending on natural conditions. These fluctuations cause population cycles of expansion and contraction, introducing intermittent migrations that may not hinder speciation but rather promote diversification. Here, we study a neutral 2-island speciation model with intermittent migration driven by sea-level fluctuations. Seabed depth modulates isolation and connection periods between the islands, with migration occurring during connection periods with a certain probability. Mating is restricted to genetically compatible individuals on the same island and offspring inherit genomes from both parents through recombination. We observe speciation pulses that would not occur under strict isolation or continuous migration, with infrequent, temporary increases in species richness happening at different times depending on the combination of geographic settings and migration probability. The resulting dynamic patterns of richness exhibit contrasting behavior between connected and isolated scenarios, often including species that do not persist. Prolonged isolation can reduce richness to 1 species per island, resembling patterns commonly associated with archipelagos under sea-level fluctuations. Together with other studies, our results in out-of-equilibrium populations support the relevance of investigating the impact of variable migration on diversification, particularly in regions of high diversity.