Related papers: Reparametrizing loop entropy weights: Effect on DN…
When the DNA double helix is subjected to external forces it can stretch elastically to elongations reaching 100% of its natural length. These distortions, imposed at the mesoscopic or macroscopic scales, have a dramatic effect on…
DNA loop formation is one of several mechanisms used by organisms to regulate genes. The free energy of forming a loop is an important factor in determining whether the associated gene is switched on or off. In this paper we use an elastic…
We compute the entanglement entropy in a composite system separated by a finitely ramified boundary with the structure of a self-similar lattice graph. We derive the entropy as a function of the decimation factor which determines the…
Defects in two-dimensional conformal field theories (CFTs) contain signatures of their characteristics. In this work, we compute the entanglement entropy (EE) and the entanglement negativity (EN) of subsystems in the presence of energy and…
Recently, the reflected entropy is proposed in holographic approach to describe the entanglement of a bipartite quantum system in a mixed state, which is identified as the area of the reflected minimal surface inside the entanglement wedge.…
Entropy is a quantity for counting physical degrees of freedom in a system. At a finite temperature, one can use thermal entropy to study thermodynamical properties. At zero temperature, entanglement entropy is expected to provide a…
We describe an algorithm for studying the entanglement entropy and spectrum of 2D systems, as a coupled array of $N$ one dimensional chains in their continuum limit. Using the algorithm to study the quantum Ising model in 2D, (both in its…
Products of truncated unitary matrices, independently and uniformly drawn from the unitary group, can be used to study universal aspects of monitored quantum circuits. The von Neumann entropy of the corresponding density matrix decreases…
We propose a model that can account for the experimentally observed phase behavior of DNA-nanoparticle assemblies (R. Jin et al., JACS 125, 1643 (2003); T. A. Taton et al., Science 289, 1757 (2000)). The binding of DNA-coated nano-particles…
Foundation models in genomics have shown mixed success compared to their counterparts in natural language processing. Yet, the reasons for their limited effectiveness remain poorly understood. In this work, we investigate the role of…
Experimental data of the DNA cyclization (J-factor) at short length scales, as a way to study the elastic behavior of tightly bent DNA, exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to…
The DNA storage channel is considered, in which a codeword is comprised of $M$ unordered DNA molecules. At reading time, $N$ molecules are sampled with replacement, and then each molecule is sequenced. A coded-index concatenated-coding…
Loop extrusion convincingly describes how certain Structural Maintenance of Chromosome (SMC) proteins mediate the formation of large DNA loops. Yet, most of the existing computational models cannot reconcile recent in vitro observations…
Building on a general variational framework for multi-fluid dynamics, we discuss finite temperature effects in superfluids. The main aim is to provide insight into the modelling of more complex finite temperature superfluid systems, like…
Current biophysical models for transcriptionally active chromatin view this as a polymer with sticky sites, mimicking transcription units such as promoters and enhancers which interact via the binding of multivalent complexes of…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
DNA is increasingly employed for bio and nanotechnology thanks to its exquisite versatility and designability. Most of its use is limited to linearised and torsionally relaxed DNA but non-trivial architectures and torsionally constrained --…
A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base…