Related papers: Intermediate State Formation of Topologically Asso…
One of the most important problems in development is how epigenetic domains can be first established, and then maintained, within cells. To address this question, we propose a framework which couples 3D chromatin folding dynamics, to a…
Recent chromosome conformation capture experiments have led to the discovery of dense, contiguous, megabase-sized topological domains that are similar across cell types and conserved across species. These domains are strongly correlated…
The rotational and fine structure of open-shell molecules in a $\Sigma$ electronic state gives rise to crossings between Zeeman states of different parity. These crossings become avoided in the presence of an electric field. We propose an…
Chromatin is a polymer complex of DNA and proteins that regulates gene expression. The three-dimensional structure and organization of chromatin controls DNA transcription and replication. High-throughput chromatin conformation capture…
Graph states are versatile resources for quantum computation and quantum-enhanced measurement. Their generation illustrates a high level of control over entanglement. We report on the generation of continuous-variable graph states of atomic…
Topological electronic phases exist in a variety of naturally occurring materials but can also be created artificially. We used a cryogenic scanning tunneling microscope to create dimerized chains of identical quantum dots on a…
Quantum annealing is a novel type of analog computation that aims to use quantum mechanical fluctuations to search for optimal solutions of Ising problems. Quantum annealing in the transverse field Ising model, implemented on D-Wave…
Quantum entanglement and classical topology are two distinct phenomena that are difficult to be connected together. Here we discover that an open bosonic quadratic chain exhibits topology-induced entanglement effect. When the system is in…
Characterizing thermally activated transitions in high-dimensional rugged energy surfaces is a very challenging task for classical computers. Here, we develop a quantum annealing scheme to solve this problem. First, the task of finding the…
Constrained quantum annealing (CQA) is a quantum annealing approach that is designed so that constraints are satisfied without penalty terms. There is an analogy between the model for the CQA of graph coloring and a set of disordered spin…
In applications where multiple optimal solutions are needed, transverse-field quantum annealing (QA) is known to sample degenerate ground states in a strongly biased manner. Despite extensive empirical observations, it remains unclear which…
The 3D folding of a mammalian gene can be studied by a polymer model, where the chromatin fibre is represented by a semiflexible polymer which interacts with multivalent proteins, representing complexes of DNA-binding transcription factors…
Recent high resolution experiments have provided a quantitative description of the statistical properties of interphase chromatin at large scales. These findings have stimulated a search for generic physical interactions that give rise to…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
Topological phases of matter possess intricate correlation patterns typically probed by entanglement entropies or entanglement spectra. In this work, we propose an alternative approach to assessing topologically induced edge states in free…
Column chromatography is an important process in downstream biopharmaceutical manufacturing that enables high-selectivity separation of proteins through various modalities, such as affinity, ion exchange, hydrophobic interactions, or a…
Three-dimensional (3D) chromatin structure is closely related to genome function, in particular transcription. However, the folding path of the chromatin fiber in the interphase nucleus is unknown. Here, we systematically measured the 3D…
The three dimensional structure of DNA in the nucleus (chromatin) plays an important role in many cellular processes. Recent experimental advances have led to high-throughput methods of capturing information about chromatin conformation on…
A dilutely filled $N$-site optical lattice near zero temperature within a high-$Q$ multimode cavity can be mapped to a spin ensemble with tailorable interactions at all length scales. The effective full site to site interaction matrix can…
We develop a heuristic graph coloring approximation algorithm that uses the D-Wave 2X as an independent set sampler and evaluate its performance against a fully classical implementation. A randomly generated set of small but hard graph…