Related papers: A quantum spin approach to histone dynamics
Epigenetic modifications of histones crucially affect the eukaryotic gene activity, while the epigenetic histone state is largely determined by the binding of specific factors such as the transcription factors (TFs) to DNA. Here, the way…
Epigenetic histone modifications play an important role in the maintenance of different cell phenotypes. The exact molecular mechanism for inheritance of the modification patterns over cell generations remains elusive. We construct a…
Epigenetic modifications to histones may promote either activation or repression of the transcription of nearby genes. Recent experimental studies show that the promoters of many lineage-control genes in stem cells have "bivalent domains"…
Histone modification is a vital epigenetic mechanism for transcriptional control in eukaryotes. High-throughput techniques have enabled whole-genome analysis of histone modifications in recent years. However, most studies assume one…
Following on from our recent work, we investigate a stochastic approach to non-equilibrium quantum spin systems. We show how the method can be applied to a variety of physical observables and for different initial conditions. We provide…
A quantum mechanical model on histone modification is proposed. Along with the methyl / acetate or other groups bound to the modified residues the torsion angles of the nearby histone chain are supposed to participate in the quantum…
Reprogramming is a process of transforming differentiated cells into pluripotent stem cells by inducing specific modifying factors in the cells. Reprogramming is a non-equilibrium process involving a collaboration at levels separated by…
Nucleosomes are the fundamental building blocks of chromatin that not only help in the folding of chromatin but also in carrying epigenetic information. It is known that nucleosome sliding is responsible for dynamically organizing chromatin…
We investigate a stochastic approach to non-equilibrium quantum spin systems based on recent insights linking quantum and classical dynamics. Exploiting a sequence of exact transformations, quantum expectation values can be recast as…
We investigate the non-equilibrium dynamics of isolated quantum spin systems via an exact mapping to classical stochastic differential equations. We show that one can address significantly larger system sizes than recently obtained,…
We study the quantum dynamics generated by a non-Hermitian Hamiltonian subject to stochastic perturbations in its anti-Hermitian part, describing fluctuating gains and losses. The dynamics averaged over the noise is described by an…
We study in detail the properties of the quantum East model, an interacting quantum spin chain inspired by simple kinetically-constrained models of classical glasses. Through a combination of analytics, exact diagonalization and…
Designing a good transfer channel for arbitrary quantum states in spin chains implies optimizing a cost function, usually the averaged fidelity of transmission. The fidelity of transmission measures how much the transferred state resembles…
Beyond the genetic code, there is another layer of information encoded as chemical modifications on histone proteins positioned along the DNA. Maintaining these modifications is crucial for survival and identity of cells. How the…
We investigate dynamics of semi-quantal spin systems in which quantum bits are attached to classically and possibly stochastically moving classical particles. The interaction between the quantum bits takes place when the respective…
We investigate a specific limit of the one-dimensional non-Hermitian Hubbard Hamiltonian with complex interactions. In this framework, fermions with different spin quantum numbers are mapped onto two distinct spin species, resulting in two…
We study a chain of non-linear, interacting spins driven by a static and a time-dependent magnetic field. The aim is to identify the conditions for the locally and temporally controlled spin switching. Analytical and full numerical…
In the framework of simple spin-boson Hamiltonian we study an interplay between dynamic and spectral roots to stochastic-like behavior. The Hamiltonian describes an initial vibrational state coupled to discrete dense spectrum reservoir. The…
This thesis, explores the quantum entanglement and evolution through both a geometric and dynamical perspective. The first part focuses on classical phase space and its central role in Hamiltonian mechanics, emphasizing the importance of…
The quantum dynamics of open many-body systems poses a challenge for computational approaches. Here we develop a stochastic scheme based on the positive P phase-space representation to study the nonequilibrium dynamics of coupled spin-boson…