Related papers: Topological Analysis of Linear Polymer Melts
A clustering algorithm partitions a set of data points into smaller sets (clusters) such that each subset is more tightly packed than the whole. Many approaches to clustering translate the vector data into a graph with edges reflecting a…
Network embedding methods aim at learning low-dimensional latent representation of nodes in a network. These representations can be used as features for a wide range of tasks on graphs such as classification, clustering, link prediction,…
We present a theoretical approach which maps polymer blends onto mixtures of soft-colloidal particles. The analytical mesoscale pair distribution functions reproduce well data from united atom molecular dynamics simulations of polyolefin…
Although the behavior of entangled polymers in startup shear flows with constant shear rates has been thoroughly investigated, the response under creep has not been frequently considered. In this study, primitive chain network simulations,…
In this thesis the formation and properties of a polymer gel on and at a surface are investigated. The gel under investigation is defined as a three-dimensional network of "phantom" macromolecules that form permanent links with one another…
Complex molecules and mesoscopic structures are naturally described by general networks of elementary building blocks and tight-binding is one of the simplest quantum model suitable for studying the physical properties arising from the…
Rapid advances in high-throughput technologies have led to considerable interest in analyzing genome-scale data in the context of biological pathways, with the goal of identifying functional systems that are involved in a given phenotype.…
Discrete mesoscale network models, in which explicitly modeled polymer chains are replaced by implicit pairwise potentials, are capable of predicting the macroscale mechanical response of polymeric materials such as elastomers and gels,…
Randomly branching polymers with {\em annealed} connectivity are model systems for ring polymers and chromosomes. In this context, the branched structure represents transient folding induced by topological constraints. Here we present…
A simple model for the formation of the polymer-enzyme conjugates has been proposed and described using corresponding extension of the Wertheim's first-order thermodynamic perturbation theory (TPT1) for the system of associating chain…
Topological data analysis offers a robust way to extract useful information from noisy, unstructured data by identifying its underlying structure. Recently, an efficient quantum algorithm was proposed [Lloyd, Garnerone, Zanardi, Nat.…
Equilibration of polymer melts containing highly entangled long polymer chains in confinement or with free surfaces is a challenge for computer simulations. We approach this problem by first studying polymer melts based on the soft-sphere…
Recently a distributed algorithm has been proposed for multi-agent networks to solve a system of linear algebraic equations, by assuming each agent only knows part of the system and is able to communicate with nearest neighbors to update…
Networks are important representations in computer science to communicate structural aspects of a given system of interacting components. The evolution of a network has several topological properties that can provide us information on the…
The large-scale properties of chemical reaction systems, such as the metabolism, can be studied with graph-based methods. To do this, one needs to reduce the information -- lists of chemical reactions -- available in databases. Even for the…
The Leibler theory [L. Leibler, Macromolecules, v.13, 1602 (1980)] for microphase separation in AB block copolymer melts is generalized for systems with arbitrary topology of molecules. A diagrammatic technique for calculation of the…
Social and biological contagions are influenced by the spatial embeddedness of networks. Historically, many epidemics spread as a wave across part of the Earth's surface; however, in modern contagions long-range edges -- for example, due to…
We develop topological methods for characterizing the relationship between polymer chain entanglement and bulk viscoelastic responses. We introduce generalized Linking Number and Writhe characteristics that are applicable to open linear…
We use Brownian dynamics simulations and advanced topological profiling methods to characterize the out-of-equilibrium evolution of self-entanglement in linear polymers confined into nano-channels and under periodic compression. We…
Characterization of transient intermediate or transition states is crucial for the description of biomolecular folding pathways, which is however difficult in both experiments and computer simulations. Such transient states are typically of…