Related papers: A contact map method to capture the features of kn…
We use machine learning algorithms to detect the crystalline phase in undercooled melts in molecular dynamics simulations. Our classification method is based on local conformation and environmental fingerprints of individual monomers. In…
We consider a generalized Jaynes-Cummings model of a two-level atom interacting with a multimode nondegenerate coherent field. The sum of the mode frequencies is equal to the two-level transition frequency, creating the resonance condition.…
The thermodynamic properties of systems with long-range interactions is still an ongoing challenge, both from the point of view of theory as well as computer simulation. In this work we study a model system, a Coulomb gas confined inside a…
Several experiments show that the three dimensional (3D) organization of chromosomes affects genetic processes such as transcription and gene regulation. To better understand this connection, researchers developed the Hi-C method that is…
The topological framework of circuit topology has recently been introduced to complement knot theory and to help in understanding the physics of molecular folding. Naturally evolved linear molecular chains, such as proteins and nucleic…
We report a numerical study of self-avoiding polymers on the square lattice, including an attractive potential between nonconsecutive monomers. Using Wang-Landau sampling (WLS) with adaptive windows, we obtain the density of states for…
Rapidly growing capabilities of quantum simulators to probe quantum many-body phenomena require new methods to characterize increasingly complex states. We present a protocol that constrains quantum states by experimentally measured…
We examine the effect of interactions between the electrons on the conductances of some systems of quantum wires with different geometries. The systems include a wire with a stub in the middle, a wire containing a ring which can enclose a…
While the structure of chromatin has been studied in great detail on length scales below 30 nm, amazingly little is known about the higher-order folding motifs of chromatin in interphase. Recent experiments give evidence that the folding…
We propose tabular two-dimensional correlation analysis for extracting features from multifaceted characterization data, essential for understanding material properties. This method visualizes similarities and phase lags in structural…
Under high cylindrical confinement, segments of ring polymers can be localized along the long axis of the cylinder by introducing internal loops within the ring polymer. The emergent organization of the polymer segments occurs because of…
Entanglement detection is an important problem in quantum information theory because quantum entanglement is a key resource in quantum information processing. Realignment criteria is a powerful tool for detection of entangled states in…
By means of contact-density chain-growth simulations, we investigate a simple lattice model of a flexible polymer interacting with an attractive substrate. The contact density is a function of the numbers of monomer-substrate and…
A contact map is a simple representation of the structure of proteins and other chain-like macromolecules. This representation is quite amenable to numerical studies of folding. We show that the number of contact maps corresponding to the…
In this work a new strategy is proposed in order to build analytic and microscopic models of fluctuating polymer rings subjected to topological constraints. The topological invariants used to fix these constraints belong to a wide class of…
We present a braided circuit topology framework for investigating topology and structural phase transitions in aggregates of semiflexible polymers. In the conventional approach to circuit topology, which specifically applies to single…
The conformational statistics of ring polymers in melts or dense solutions is strongly affected by their quenched microscopic topological state. The effect is particularly strong for non-concatenated unknotted rings, which are known to…
We review recently introduced numerical methods for the unbiased detection of the order parameter and/or dominant correlations, in many-body interacting systems, by using reduced density matrices. Most of the paper is devoted to the…
We describe a class of "bare bones" models of homopolymers which undergo coil-globule collapse and proteins which fold into their native states in free space or into denatured states when captured by an attractive substrate as the…
It has been shown that under high cylindrical confinement, two ring polymers with excluded volume interactions between monomers, segregate to two halves of the cylinder to maximize their entropy. In contrast, two ring polymers remain mixed…