A caricature of a singular curvature flow in the plane

We study a singular parabolic equation of the total variation type in one dimension. The problem is a simplification of the singular curvature flow. We show existence and uniqueness of weak solutions. We also prove existence of weak solutions to the semi-discretization of the problem as well as convergence of the approximating sequences. The semi-discretization shows that facets must form. For a class of initial data we are able to study in details the facet formation and interactions and their asymptotic behavior. We notice that our qualitative results may be interpreted with the help of a special composition of multivalued operators

Partial Kekule Ordering of Adatoms on Graphene

Electronic and transport properties of Graphene, a one-atom thick crystalline material, are sensitive to the presence of atoms adsorbed on its surface. An ensemble of randomly positioned adatoms, each serving as a scattering center, leads to the Bolzmann-Drude diffusion of charge determining the resistivity of the material. An important question, however, is whether the distribution of adatoms is always genuinely random. In this Article we demonstrate that a dilute adatoms on graphene may have a tendency towards a spatially correlated state with a hidden Kekule mosaic order. This effect emerges from the interaction between the adatoms mediated by the Friedel oscillations of the electron density in graphene. The onset of the ordered state, as the system is cooled below the critical temperature, is accompanied by the opening of a gap in the electronic spectrum of the material, dramatically changing its transport properties

RecFinder – a new tool to find phage proteins responsible for host recognition

(Bacterio)phages are bacterial viruses that represent the most abundant and genetically diverse biological entities on the planet [1,2]. The largest virus group, the order Caudovirales (containing 96% of all known phages), has evolved recognition peptides for efficient virus-host interaction [3]. The peptides, usually located at the phage tail fiber, baseplate and other tail proteins mediate recognition and attachment specifically to bacterial cell wall receptors - lipopolysaccharides, teichoic acids, proteins and flagella. These proteins responsible for host recognition and binding (HBP) are macromolecular machines that make the process of infection highly efficient and finely regulated, and most likely play an important role in the evolutionary success of tailed phages. As a result of this specific binding affinity certain phages can only infect certain bacteria, determining in this manner the phage host range [4]. (...

Edge states of graphene bilayer strip

The electronic structure of the zig-zag bilayer strip is analyzed. The electronic spectra of the bilayer strip is computed. The dependence of the edge state band flatness on the bilayer width is found. The density of states at the Fermi level is analytically computed. It is shown that it has the singularity which depends on the width of the bilayer strip. There is also asymmetry in the density of states below and above the Fermi energy.Comment: 9 page

Adaptive Evolutionary Clustering

In many practical applications of clustering, the objects to be clustered evolve over time, and a clustering result is desired at each time step. In such applications, evolutionary clustering typically outperforms traditional static clustering by producing clustering results that reflect long-term trends while being robust to short-term variations. Several evolutionary clustering algorithms have recently been proposed, often by adding a temporal smoothness penalty to the cost function of a static clustering method. In this paper, we introduce a different approach to evolutionary clustering by accurately tracking the time-varying proximities between objects followed by static clustering. We present an evolutionary clustering framework that adaptively estimates the optimal smoothing parameter using shrinkage estimation, a statistical approach that improves a naive estimate using additional information. The proposed framework can be used to extend a variety of static clustering algorithms, including hierarchical, k-means, and spectral clustering, into evolutionary clustering algorithms. Experiments on synthetic and real data sets indicate that the proposed framework outperforms static clustering and existing evolutionary clustering algorithms in many scenarios.Comment: To appear in Data Mining and Knowledge Discovery, MATLAB toolbox available at http://tbayes.eecs.umich.edu/xukevin/affec

The electronic properties of bilayer graphene

We review the electronic properties of bilayer graphene, beginning with a description of the tight-binding model of bilayer graphene and the derivation of the effective Hamiltonian describing massive chiral quasiparticles in two parabolic bands at low energy. We take into account five tight-binding parameters of the Slonczewski-Weiss-McClure model of bulk graphite plus intra- and interlayer asymmetry between atomic sites which induce band gaps in the low-energy spectrum. The Hartree model of screening and band-gap opening due to interlayer asymmetry in the presence of external gates is presented. The tight-binding model is used to describe optical and transport properties including the integer quantum Hall effect, and we also discuss orbital magnetism, phonons and the influence of strain on electronic properties. We conclude with an overview of electronic interaction effects.Comment: review, 31 pages, 15 figure

Statistical Inference for Valued-Edge Networks: Generalized Exponential Random Graph Models

Across the sciences, the statistical analysis of networks is central to the production of knowledge on relational phenomena. Because of their ability to model the structural generation of networks, exponential random graph models are a ubiquitous means of analysis. However, they are limited by an inability to model networks with valued edges. We solve this problem by introducing a class of generalized exponential random graph models capable of modeling networks whose edges are valued, thus greatly expanding the scope of networks applied researchers can subject to statistical analysis

Approximation hardness of Travelling Salesman via weighted amplifiers

The expander graph constructions and their variants are the main tool used in gap preserving reductions to prove approximation lower bounds of combinatorial optimisation problems. In this paper we introduce the weighted amplifiers and weighted low occurrence of Constraint Satisfaction problems as intermediate steps in the NP-hard gap reductions. Allowing the weights in intermediate problems is rather natural for the edge-weighted problems as Travelling Salesman or Steiner Tree. We demonstrate the technique for Travelling Salesman and use the parametrised weighted amplifiers in the gap reductions to allow more flexibility in fine-tuning their expanding parameters. The purpose of this paper is to point out effectiveness of these ideas, rather than to optimise the expander’s parameters. Nevertheless, we show that already slight improvement of known expander values modestly improve the current best approximation hardness value for TSP from 123/122 ([9]) to 117/116 . This provides a new motivation for study of expanding properties of random graphs in order to improve approximation lower bounds of TSP and other edge-weighted optimisation problems

Singular Cucker-Smale Dynamics

The existing state of the art for singular models of flocking is overviewed, starting from microscopic model of Cucker and Smale with singular communication weight, through its mesoscopic mean-filed limit, up to the corresponding macroscopic regime. For the microscopic Cucker-Smale (CS) model, the collision-avoidance phenomenon is discussed, also in the presence of bonding forces and the decentralized control. For the kinetic mean-field model, the existence of global-in-time measure-valued solutions, with a special emphasis on a weak atomic uniqueness of solutions is sketched. Ultimately, for the macroscopic singular model, the summary of the existence results for the Euler-type alignment system is provided, including existence of strong solutions on one-dimensional torus, and the extension of this result to higher dimensions upon restriction on the smallness of initial data. Additionally, the pressureless Navier-Stokes-type system corresponding to particular choice of alignment kernel is presented, and compared - analytically and numerically - to the porous medium equation