Related papers: Discrete Folding
Many machine learning problems involve regressing variables on a non-Euclidean manifold -- e.g. a discrete probability distribution, or the 6D pose of an object. One way to tackle these problems through gradient-based learning is to use a…
We study the flat phase of nematic elastomer membranes with rotational symmetry spontaneously broken by in-plane nematic order. Such state is characterized by a vanishing elastic modulus for simple shear and soft transverse phonons. At…
We present a generic and systematic approach for constructing D-dimensional lattice models with exactly solvable d-dimensional boundary states localized to corners, edges, hinges and surfaces. These solvable models represent a class of…
Lattice models have been used extensively over the past thirty years to examine the principles of protein folding and design. These models can be used to determine the conformation of the lowest energy fold out of a large number of possible…
We study conformational transitions of simple coarse-grained models for protein-like heteropolymers on the simple cubic lattice and off-lattice, respectively, by means of multicanonical sampling algorithms. The effective hydrophobic/polar…
We study a discrete-space model of active matter with excluded volume. Particles are restricted to the sites of a triangular lattice, and can assume one of three orientations. Varying the density and noise intensity, Monte Carlo simulations…
A lattice model with soft repulsion followed by attraction is developed for a monolayer of hybrid core-shell particles self-assembling at an interface. The model is solved exactly in one dimension. One, two or three periodic structures and…
We present the crumpling transition in three-dimensional Euclidian space of dynamically triangulated random surfaces with edge extrinsic curvature and fixed topology of a sphere as well as simulations of a dynamically triangulated torus. We…
Monte Carlo simulations of a Miyazawa-Jernigan lattice-polymer model indicate that, depending on the native's structure geometry, the model exhibits two broad classes of folding mechanisms for two-state folders. Folding to native structures…
We investigate the convergence of solutions of a recently proposed diffuse interface/phase field model for cell blebbing by means of matched asymptotic expansions. It is a biological phenomenon that increasingly attracts attention by both…
We show that fluctuating tethered membranes with {\it any} intrinsic anisotropy unavoidably exhibit a new phase between the previously predicted ``flat'' and ``crumpled'' phases, in high spatial dimensions $d$ where the crumpled phase…
We consider a simple model consisting of particles with four bonding sites ("patches"), two of type A and two of type B, on the square lattice, and investigate its global phase behavior by simulations and theory. We set the interaction…
The original models of causal dynamical triangulations construct space-time by arranging a set of simplices in layers separated by a fixed time-like distance. The importance of the foliation structure in the 2+1 dimensional model is studied…
Our previous molecular dynamic simulation studies of simple two-dimensional (2D) systems \cite{matt_big} suggested that both geometrical defects (localized, large-amplitude deviations from hexagonal ordering) and topological defects…
We introduce a 2-dimensional lattice model of granular matter. We use a combination of proof and simulation to demonstrate an order/disorder phase transition in the model, to which we associate the granular phenomenon of random close…
We set up a harmonic lattice model for 2D defect melting which, in contrast to earlier simple-cubic models, lives on a triangular lattice. Integer-valued plastic defect gauge fields allow for the thermal generation of dislocations and…
We study dynamics of a membrane and its matrix regularisation. We present the matrix regularisation for a membrane propagating in a curved space-time geometry in the presence of an arbitrary 3-form field. In the matrix regularisation, we…
If the structure of spacetime is discrete, then Lorentz symmetry should only be an approximation, valid at long length scales. At finite lattice spacings there will be small corrections to the Dirac evolution that could in principle be…
Off-equilibrium dynamics of a three-dimensional lattice model with nearest- and next nearest-neighbors exclusions is studied. At equilibrium, the model undergoes a first-order fluid-solid transition. Non-equilibrium filling, through random…
We investigate a discrete model consisting of self-propelled particles that obey simple interaction rules. We show that this model can self-organize and exhibit coherent localized solutions in one- and in two-dimensions.In one-dimension,…