Related papers: Factoring the Laplacian to understand topological …
Modeling of polymer chains has received a lot of attention in mathematics. In fact, probabilistic models that naturally arise in statistical mechanics have been widely studied by mathematicians for the very challenging and novel problems…
The statistical mechanics of a long knotted collapsed polymer is determined by a free-energy with a knot-dependent subleading term, which is linked to the length of the shortest polymer that can hold such knot. The only other parameter…
We present a comprehensive extension of the latent position network model known as the random dot product graph to accommodate multiple graphs -- both undirected and directed -- which share a common subset of nodes, and propose a method for…
We study the entanglement spectrum of a translationally-invariant lattice system under a random partition, implemented by choosing each site to be in one subsystem with probability $p\in[0, 1]$. We apply this random partitioning to a…
We present clustering methods for multivariate data exploiting the underlying geometry of the graphical structure between variables. As opposed to standard approaches that assume known graph structures, we first estimate the edge structure…
The step-growth polymerisation of a mixture of arbitrary-functional monomers is viewed as a time-continuos random graph process with degree bounds that are not necessarily the same for different vertices. The sequence of degree bounds acts…
A Hamiltonian cycle of a graph is a closed path that visits every vertex once and only once. It serves as a model of a compact polymer on a lattice. I study the number of Hamiltonian cycles, or equivalently the entropy of a compact polymer,…
Monte Carlo dynamics of the lattice 48 monomers toy protein is interpreted as a random walk in an abstract (discrete) space of conformations. To test the geometry of this space, we examine the return probability $P(T)$, which is the…
In this paper, we employ Molecular Dynamics computer simulations to study and compare the statics and dynamics of linear and circular (ring) polymer chains in entangled solutions of different densities. While we confirm that linear chain…
In the last twenty years network science has proven its strength in modelling many real-world interacting systems as generic agents, the nodes, connected by pairwise edges. Yet, in many relevant cases, interactions are not pairwise but…
Random walks on graphs are a fundamental concept in graph theory and play a crucial role in solving a wide range of theoretical and applied problems in discrete math, probability, theoretical computer science, network science, and machine…
The statistical mechanics of polymer loops entangled in the two-dimensional array of randomly distributed obstacles of infinite length is discussed. The area of the loop projected to the plane perpendicular to the obstacles is used as a…
The chapter presents mathematical models intended for creating a topological drawing of a non-separable non-planar graph based on the methods of G. Ringel's vertex rotation theory. The induced system of cycles generates a topological…
There is a wealth of applied problems that can be posed as a dynamical system defined on a network with both attractive and repulsive interactions. Some examples include: understanding synchronization properties of nonlinear oscillator;,…
Using a theoretical model we show that ideal ring polymers are stronger depletants than ideal linear polymers of equal radii of gyration, but not of equal hydrodynamic radii. The difference in the depletion-induced force profile is largely…
Extensive molecular simulations are applied to characterize the equilibrium dynamics, entanglement topology, and nonlinear extensional rheology of symmetric ring-linear polymer blends with systematically varied ring fraction $\phi_R$.…
We address the properties of continuous-time quantum walks with Hamiltonians of the form $\mathcal{H}= L + \lambda L^2$, being $L$ the Laplacian matrix of the underlying graph and being the perturbation $\lambda L^2$ motivated by its…
The notion of Laplacian of a graph can be generalized to simplicial complexes and hypergraphs, and contains information on the topology of these structures. Even for a graph, the consideration of associated simplicial complexes is…
For $\lambda>0$, we define a $\lambda$-damped random walk to be a random walk that is started from a random vertex of a graph and stopped at each step with probability $\frac{\lambda}{1+\lambda}$, otherwise continued with probability…
Several cycle lexicographical orders are found to describe the relative likelihood of elements of the random walks on the symmetric group generated by the conjugacy classes of transpositions, 3-cycles, and n-cycles. Spectral analysis finds…