Related papers: A contact map method to capture the features of kn…
Band structures of electrons in a periodic potential are well-known to host topologies that impact their behaviors at edges and interfaces. The concept however is more general than the single-electron setting. In this work, we consider…
Here we report on the translocation of folded polymers through nano-pores using molecular dynamic simulations. Two cases are studied; one in which a folded molecule unfolds upon passage and one in which the folding remains intact as the…
The interplay of topological constraints and Coulomb interactions in static and dynamic properties of charged polymers is investigated by numerical simulations and scaling arguments. In the absence of screening, the long-range interaction…
Chemical mapping is a widespread technique for structural analysis of nucleic acids in which a molecule's reactivity to different probes is quantified at single-nucleotide resolution and used to constrain structural modeling. This…
In the past couple of decades, there have been significant advances in measuring quantum properties of light, such as quadratures of squeezed light and single-photon counting. Here, we explore whether such tools can be leveraged to probe…
Cumulant mapping employs a statistical reconstruction of the whole by sampling its parts. The theory developed in this work formalises and extends ad hoc methods of `multi-fold' or `multi-dimensional' covariance mapping. Explicit formulae…
Successful scientific applications of large-scale molecular dynamics often rely on automated methods for identifying the local crystalline structure of condensed phases. Many existing methods for structural identification, such as Common…
Contact geometry allows to describe some thermodynamic and dissipative systems. In this paper we introduce a new geometric structure in order to describe time-dependent contact systems: cocontact manifolds. Within this setting we develop…
Two ring polymers close to each other in space may be either in a segregated phase if there is a strong repulsion between monomers in the polymers, or intermingle in a mixed phase if there is a strong attractive force between the monomers.…
Indentation is a common experimental technique to study the mechanics of polymeric materials. The main advantage of using indentation is because this provides a direct correlation between the microstructure and the small-scale mechanical…
Elucidating the physics of a concentrated suspension of ring polymers, or of an ensemble of ring polymers in a complex environment, is an important outstanding question in polymer physics. Many of the characteristic features of these…
The detection and classification of entanglement properties in a two-qubit and a multi-qubit system is a topic of great interest. This topic has been extensively studied, and as a result, we discovered various approaches for detecting and…
Quantum entanglement is a particularly useful characterization of topological orders which lack conventional order parameters. In this work, we study the entanglement in topologically ordered states between two arbitrary spatial regions,…
The detection of community structure is probably one of the hottest trends in complex network research as it reveals the internal organization of people, molecules or processes behind social, biological or computer networks\dots The issue…
Recent advances in Generalized Ensemble simulations and microcanonical analysis allowed the investigation of structural transitions in polymer models over a broad range of local bending and torsion strengths. It is reasonable to argue that…
Modern biological techniques such as Hi-C permit to measure probabilities that different chromosomal regions are close in space. These probabilities can be visualised as matrices called contact maps. In this paper, we introduce a…
Entanglement production in coupled chaotic systems is studied with the help of kicked tops. Deriving the correct classical map, we have used the reduced Husimi function, the Husimi function of the reduced density matrix, to visualize the…
Polymer models are used to describe chromatin, which can be folded at different spatial scales by binding molecules. By folding, chromatin generates loops of various sizes. We present here a randomly cross-linked (RCL) polymer model, where…
Stochastic simulations are used to characterize the knotting distributions of random ring polymers confined in spheres of various radii. The approach is based on the use of multiple Markov chains and reweighting techniques, combined with…
Polymers are an effective test-bed for studying topological constraints in condensed matter due to a wide array of synthetically-available chain topologies. When linear and ring polymers are blended together, emergent rheological properties…