Related papers: A contact map method to capture the features of kn…
The art of tying knots is exploited in nature and occurs in multiple applications ranging from being an essential part of scouting programs to engineering molecular knots. Biomolecular knots, such as knotted proteins, bear various cellular…
This paper presents a novel method for qualitative mapping of large scale spaces. The proposed framework makes use of a graphical representation of the world in order to build a map consisting of qualitative constraints on the geometric…
Light emitted from a source into a scene can undergo complex interactions with scene surfaces of different material types before being reflected. During this transport, every surface reflection is encoded in the properties of the photons…
Contact can be conceptualized as a set of constraints imposed on two bodies that are interacting with one another in some way. The nature of a contact, whether a point, line, or surface, dictates how these bodies are able to move with…
A ring polymer in a confining space may exhibit at least two phases, namely an expanded (or solvent-rich phase) if its concentration is small, or a collapsed (or polymer-rich phase) when it is concentrated and compressed. These phases are…
We propose an empirical method for identifying low damped modes and corresponding mode shapes using frequency measurements from a Wide Area Monitoring System. The method consists of two main steps: Firstly, Complex Principal Component…
Numerical studies of the reduced density matrix of a gapped spin-1/2 Heisenberg antiferromagnet on a two-leg ladder find that it has the same form as the Gibbs density matrix of a gapless spin-1/2 Heisenberg antiferromagnetic chain at a…
Coupled mode theory (CMT) is a powerful framework for decomposing interactions between electromagnetic waves and scattering bodies into resonances and their couplings with power-carrying channels. It has widespread use in few-resonance,…
The work in this article is inspired by a classical problem: the statistical physical properties of a closed polymer loop that is wound around a rod. Historically the preserved topology of this system has been addressed through…
We use a semi-supervised, neural-network based machine learning technique, the confusion method, to investigate structural transitions in magnetic polymers, which we model as chains of magnetic colloidal nanoparticles characterized by…
Temperature dependent conformations of linear polymer molecules adsorbed at carbon nanotube (CNT) interfaces are investigated through molecule dynamics simulations. Model polyethylene (PE) molecules are shown to have selective conformations…
Statistical models are widely used for the investigation of complex system's behavior. Most of the models considered in the literature are formulated on regular lattices with nearest-neighbor interactions. The models with non-local…
Understanding regional dynamical structures in the sea is fundamental to characterize energy transfer and transport properties, with implications in physical and biogeochemical modeling and characterization. In this work, we study the…
Crystal structure prediction is now playing an increasingly important role in discovery of new materials. Global optimization methods such as genetic algorithms (GA) and particle swarm optimization (PSO) have been combined with first…
Computing equilibrium concentrations of molecular complexes is generally analytically intractable and requires numerical approaches. In this work we focus on the polymer-monomer level, where indivisible molecules (monomers) combine to form…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
Physical mechanisms underlying the empirical correlation between relative contact order (CO) and folding rate among naturally-occurring small single-domain proteins are investigated by evaluating postulated interaction schemes for a set of…
The reaction-coordinate mapping is a useful technique to study complex quantum dissipative dynamics into structured environments. In essence, it aims to mimic the original problem by means of an 'augmented system', which includes a suitably…
We present a quantum information-inspired framework for analyzing complex systems through multivariate time series. In this approach the system's state is encoded into a density matrix, providing a compact representation of higher-order…
The field theory approach to the statistical mechanics of a system of N polymer rings linked together is generalized to the case of links that have a fixed number $2s$ of maxima and minima. Such kind of links are called plats and appear for…