Claudette Cordeiro | Searcharxiv

arXiv2015

The Electronic Behavior of Zinc-Finger Protein Binding Sites in the Context of the DNA Extended Ladder Model

The eukaryotic Cys2His2 zinc finger proteins bind to DNA ubiquitously at highly conserved domains, responsible for gene regulation and the spatial organization of DNA. To study and understand the zinc finger DNA-protein interaction, we use the extended ladder in the DNA model proposed by Zhu, Rasmussen, Balatsky \& Bishop (2007) \cite{Zhu-2007}. Considering one single spinless electron in each nucleotide $π$-orbital along a double DNA chain (dDNA), we find a typical pattern for the {\color{black} bottom of the occupied molecular orbital (BOMO)}, highest occupied molecular orbital (HOMO) and lowest unoccupied orbital (LUMO) along the binding sites. We specifically looked at two members of zinc finger protein family: specificity protein 1 (SP1) and early grown response 1 transcription factors (EGR1). When the valence band is filled, we find electrons in the purines along the nucleotide sequence, compatible with the electric charges of the binding amino acids in SP1 and EGR1 zinc finger.

q-bio.BM↗

arXiv2004

Effects of anisotropy on a quantum Heisenberg spin glass in a three-dimensional hierarchical lattice

We study the anisotropic Heisenberg spin-glass model in a three-dimensional hierarchical lattice (designed to approximate the cubic lattice), within a real-space renormalization-group approach. Two different initial probability distributions for the exchange interaction ($J_{ij}$), Gaussian and uniform, are used, with zero mean and width $\bar{J}$. The $(kT/\bar{J}) \times Δ_0$ phase diagram is obtained, where $T$ is the temperature, $Δ_0$ is the first moment of the probability distribution for the uniaxial anisotropy, and $k$ is the Boltzmann constant. For the Ising model ($Δ_0=1$), there is a spin-glass phase at low temperatures (high $\bar{J}$) and a paramagnetic phase at high temperatures (low $\bar{J}$). For the isotropic Heisenberg model ($Δ_0=0$), our results indicate no spin-glass phase at finite temperatures. The transition temperature between the spin-glass and paramagnetic phase decreases with $Δ_0$, as expected, but goes to zero at a finite value of the anisotropy parameter, namely $Δ_0 = Δ_c \sim 0.59$. Our results indicate that the whole transition line, between the paramagnetic and the spin-glass phases, for $Δ_c \leq Δ_0 < 1$, belongs to the same universality class as the transition for the Ising spin glass.

cond-mat.stat-mech↗