Related papers: Polymer Dynamics via Cliques: New Conditions for A…
We consider the force on the end of a polymer chain being pulled through a network at velocity $v$, using computer simulations. We develop algorithms for measuring the force on the end of the chain using lattice models of polymers. Our…
Particle filters are a group of algorithms to solve inverse problems through statistical Bayesian methods when the model does not comply with the linear and Gaussian hypothesis. Particle filters are used in domains like data assimilation,…
In the first part of a series of two papers, we present in considerable detail a collision-driven molecular dynamics algorithm for a system of nonspherical particles, within a parallelepiped simulation domain, under both periodic or…
Field-theoretical method is efficient in predicting the assembling structures of polymeric systems. However, for the polymer/nanoparticle mixture, the continuous density description is not suitable to capture the realistic assembly of…
While modern physics and biology satisfactorily explain the passage from the Big Bang to the formation of Earth and the first cells to present-day life, respectively, the origins of biochemical life still remain an open question. Since…
Parametric Markov chains (pMCs) are Markov chains (MCs) with symbolic probabilities. A pMC encodes a family of MCs, where each member is obtained by replacing parameters with constants. The parameters allow encoding dependencies between…
The quasi--equilibrium or maximum entropy approximation is applied in order to derive constitutive equations from kinetic models of polymer dynamics. It is shown in general and illustrated for an example how canonical distribution functions…
Understanding the complex viscoelastic properties of polymeric liquids remains a challenge in materials science and soft matter physics. Here, we present a simple and computationally efficient criterion for the topological constraints in…
The tube model is a central concept in polymer physics, and allows to reduce the complex many-filament problem of an entangled polymer solution to a single filament description. We investigate the probability distribution function of…
The presence of nanoparticles in a diblock copolymer leads to changes in the morphology and properties of the matrix and can produce highly organized hybrid materials. The resulting material properties depend not only on the polymer…
Active polymeric systems exhibit a rich spectrum of non-equilibrium phenomena arising from stochastic forces that explicitly break detailed balance. Despite the rapid growth of experimental and numerical studies, analytical progress remains…
Many combinatorial optimization problems can be formulated as the search for a subgraph that satisfies certain properties and minimizes the total weight. We assume here that the vertices correspond to points in a metric space and can take…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Motivated by problems in data clustering, we establish general conditions under which families of nonparametric mixture models are identifiable, by introducing a novel framework involving clustering overfitted \emph{parametric} (i.e.…
Finding complete subgraphs in a graph, that is, cliques, is a key problem and has many real-world applications, e.g., finding communities in social networks, clustering gene expression data, modeling ecological niches in food webs, and…
We study a continuous-time, infinite-horizon dynamic bipartite matching problem. Suppliers arrive according to a Poisson process; while waiting, they may abandon the queue at a uniform rate. Customers on the other hand must be matched upon…
There are many proteins or protein complexes which have multiple DNA binding domains. This allows them to bind to multiple points on a DNA molecule (or chromatin fibre) at the same time. There are also many proteins which have been found to…
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…
The filtering distribution captures the statistics of the state of a dynamical system from partial and noisy observations. Classical particle filters provably approximate this distribution in quite general settings; however they behave…
Polymer electrolytes are promising candidates for the next generation lithium-ion battery technology. Large scale screening of polymer electrolytes is hindered by the significant cost of molecular dynamics (MD) simulation in amorphous…