Related papers: Double chains with base pairing: delocalization ir…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
The mechanism of threshold elongation (overstretching) of DNA macromolecules under the action of external force is studied within the framework of phenomenological approach. When considering the task it is taken into account that…
We introduce and train distributed neural architectures (DNA) in vision and language domains. DNAs are initialized with a proto-architecture that consists of (transformer, MLP, attention, etc.) modules and routers. Any token (or patch) can…
Sequences of nucleotides (for DNA and RNA) or amino acids (for proteins) are central objects in biology. Among the most important computational problems is that of sequence alignment, i.e. arranging sequences from different organisms in…
We consider long-range correlated disorder and mutual interacting particles according to a dipole-dipole coupling as modifications to the one-dimensional Anderson model. Technically we rely on the (numerical) exact diagonalization of the…
DNA bending is biologically important for genome regulation and is relevant to a range of nanotechnological systems. Recent results suggest that sharp bending is much easier than implied by the widely-used worm-like chain model; many of…
We investigate how robust is the modified XX spin-1/2 chain of [R. Vieira and G. Rigolin, Phys. Lett. A 382, 2586 (2018)] in transmitting entanglement when several types of disorder and noise are present. First, we consider how deviations…
The study of energy transport properties in heterogeneous materials has attracted scientific interest for more than a century, and it continues to offer fundamental and rich questions. One of the unanswered challenges is to extend Anderson…
RNA forms elaborate secondary structures through intramolecular base pairing. These structures perform critical biological functions within each cell. Due to the availability of a polynomial algorithm to calculate the partition function…
We theoretically show how two impurity defects in a crystalline structure can be entangled through coupling with the crystal. We demonstrate this with a harmonic chain of trapped ions in which two ions of a different species are embedded.…
We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous…
We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA…
We consider different classes of quenched disordered quantum XY spin chains, including quantum XY spin glass and quantum XY model with a random transverse field, and investigate the behavior of genuine multiparty entanglement in the ground…
We consider a model for strand separation in negatively supercoiled dna, and study the effect of supercoiling on the localization of denaturation, using notions from statistical mechanics. The model is based on on mean field Ising system,…
We consider the evolution of an initially localized wave packet after a sudden change in the Hamiltonian, i.e.\ a quench. When both bound and scattering eigenstates exist in the post-quench Hamiltonian, one might expect partial…
We report measurements of a tunable double quantum dot, operating in the quantum regime, with integrated local charge sensors. The spatial resolution of the sensors is sufficient to allow the charge distribution within the double dot system…
We investigate the electron (hole) transport through short double-stranded DNA wires in which the electrons are strongly coupled to the specific vibrational modes (vibrons) of the DNA. We analyze the problem starting from a tight-binding…
Charge diffusion through desoxyribonucleic acid (DNA) is a physico-chemical phenomenon that on the one hand is being explored for technological purposes, on the other hand is applied by nature for various informational processes in life.…
DNA nanotechnology uses predictable interactions of nucleic acids to precisely engineer complex nanostructures. Characterizing these self-assembled structures at the single-structure level is crucial for validating their design and…
Molecular recognition between two double stranded (ds) DNA with homologous sequences may not seem compatible with the B-DNA structure because the sequence information is hidden when it is used for joining the two strands. Nevertheless, it…