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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…
Large language models achieve strong reasoning performance, yet existing decoding strategies either explore blindly (random sampling) or redundantly (independent multi-sampling). We propose Entropy-Tree, a tree-based decoding method that…
We introduce and implement a Monte Carlo scheme to study the equilibrium statistics of polymers in the globular phase. It is based on a model of "interacting elastic lattice polymers" and allows a sufficiently good sampling of long and…
Based on an estimate of the knot entropy of a worm-like chain we predict that the interplay of bending energy and confinement entropy will result in a compact metastable configuration of the knot that will diffuse, without spreading, along…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
We introduce an exactly solvable lattice model that reveals a universal finite-size scaling law for configurational entropy driven purely by geometry. Using exact enumeration via Burnside's lemma, we compute the entropy for diverse 1D, 2D,…
Compact polymers are self-avoiding random walks which visit every site on a lattice. This polymer model is used widely for studying statistical problems inspired by protein folding. One difficulty with using compact polymers to perform…
The strong bending of polymers is poorly understood. We propose a general quantitative framework of polymer bending that includes both the weak and strong bending regimes on the same footing, based on a single general physical principle. As…
The reptation Monte Carlo algorithm is a simple, physically motivated and efficient method for equilibrating semi-dilute solutions of linear polymers. Here we propose two simple generalizations for the analogue {\it Amoeba} algorithm for…
The definition of $k^{th}$-order empirical entropy of strings is extended to node labelled binary trees. A suitable binary encoding of tree straight-line programs (that have been used for grammar-based tree compression before) is shown to…
The number of allowed configurations of a polymer is reduced by the presence of a repulsive surface resulting in an entropic force between them. We develop a method to calculate the entropic force, and detailed pressure distribution, for…
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 $\phi_R$.…
In a recent paper, the authors proposed a general methodology for probabilistic learning on manifolds. The method was used to generate numerical samples that are statistically consistent with an existing dataset construed as a realization…
Confinement is a versatile and well-established tool to study the properties of polymers either to understand biological processes or to develop new nano-biomaterials. We investigate the conformations of a semiflexible polymer ring in weak…
A tanglegram consists of two binary rooted trees with the same number of leaves and a perfect matching between the leaves of the trees. We show that the two halves of a random tanglegram essentially look like two independently chosen random…
We derive a message passing method for computing the spectra of locally tree-like networks and an approximation to it that allows us to compute closed-form expressions or fast numerical approximates for the spectral density of random graphs…
Tree ensemble models such as random forests and boosted trees are among the most widely used and practically successful predictive models in applied machine learning and business analytics. Although such models have been used to make…
Understanding how topological constraints affect the dynamics of polymers in solution is at the basis of any polymer theory and it is particularly needed for melts of rings. These polymers fold as crumpled and space-filling objects and,…
We give new general formulas for the asymptotics of the number of spanning trees of a large graph. A special case answers a question of McKay (1983) for regular graphs. The general answer involves a quantity for infinite graphs that we call…
The range-minimum query (RMQ) problem is a fundamental data structuring task with numerous applications. Despite the fact that succinct solutions with worst-case optimal $2n+o(n)$ bits of space and constant query time are known, it has been…