The discretizable molecular distance geometry problem

Given a simple weighted undirected graph G=(V,E,d) with d:E???₊, the Molecular Distance Geometry Problem (MDGP) consists in finding an embedding x:V???³ such that ??x _u ?x _v ??=d _uv for each {u,v}??E. We show that under a few assumptions usually satisfied in proteins, the MDGP can be formulated as a search in a discrete space. We call this MDGP subclass the Discretizable MDGP (DMDGP). We show that the DMDGP is NP-hard and we propose a solution algorithm called Branch-and-Prune (BP). The BP algorithm performs remarkably well in practice in terms of speed and solution accuracy, and can be easily modified to find all incongruent solutions to a given DMDGP instance. We show computational results on several artificial and real-life instances.     

Asymptotic profiles for wave equations with strong damping

We consider the Cauchy problem in Rⁿ${\mathbf{R}}^n$ for strongly damped wave equations. We derive asymptotic profiles of these solutions with weighted L^1,1(Rⁿ)$L^{1,1}({\mathbf{R}}^n)$ data by using a method introduced in [9] and/or [10].     

The stationary Oseen equations in an exterior domain: An approach in weighted Sobolev spaces

In this work, we study the linearized Navier–Stokes equations in an exterior domain of R³${\mathbb{R}}^3$ at the steady state, that is, the Oseen equations. We are interested in the existence and the uniqueness of weak, strong and very weak solutions in L^p$L^p$-theory which makes our work more difficult. Our analysis is based on the principle that linear exterior problems can be solved by combining their properties in the whole space R³${\mathbb{R}}^3$ and the properties in bounded domains. Our approach rests on the use of weighted Sobolev spaces.     

A theorem on measures in dimension 2 and applications to vortex sheets

We find conditions under which measures belong to H⁻¹(R²)$H^{-1}({\mathbb{R}}^2)$. Next we show that measures generated by the Prandtl, Kaden as well as Pullin spirals, objects considered by physicists as incompressible flows generating vorticity, satisfy assumptions of our theorem, thus they are (locally) elements of H⁻¹(R²)$H^{-1}({\mathbb{R}}^2)$. Moreover, as a by-product, we prove an embedding of the space of Morrey type measures in H⁻¹$H^{-1}$.     

Remark on the stability of the large stationary solutions to the Navier–Stokes equations under the general flux condition

Consider stationary weak solutions of the Navier–Stokes equations in a bounded domain in R³${\mathbb{R}}^3$ under the nonhomogeneous boundary condition. We give a new approach for the stability of the stationary flow in the L²$L^2$-framework. Furthermore, we give some examples of stable solutions which may be large in L³(Ω)$L^3\left(\Omega \right)$ or W^1,3/2(Ω)$W^{1,3/2}\left(\Omega \right)$.     

On removable sets for convex functions

In the present article we provide a sufficient condition for a closed set F∈R^d$F\in {\mathbb{R}}^d$ to have the following property which we call c  -removability: Whenever a continuous function f:R^d→R$f:{\mathbb{R}}^d\to \mathbb{R}$ is locally convex on the complement of F  , it is convex on the whole R^d${\mathbb{R}}^d$. We also prove that no generalized rectangle of positive Lebesgue measure in R²${\mathbb{R}}^2$ is c-removable. Our results also answer the following question asked in an article by Jacek Tabor and Józef Tabor (2010) [5]: Assume the closed set F⊂R^d$F\subset {\mathbb{R}}^d$ is such that any locally convex function defined on R^d?F${\mathbb{R}}^d?F$ has a unique convex extension on R^d${\mathbb{R}}^d$. Is F   necessarily intervally thin (a notion of smallness of sets defined by their “essential transparency” in every direction)? We prove the answer is negative by finding a counterexample in R²${\mathbb{R}}^2$.     

Uncertainty principles in finitely generated shift-invariant spaces with additional invariance

We consider finitely generated shift-invariant spaces (SIS) with additional invariance in L²(R^d)$L^2({\mathbb{R}}^d)$. We prove that if the generators and their translates form a frame, then they must satisfy some stringent restrictions on their behavior at infinity. Part of this work (non-trivially) generalizes recent results obtained in the special case of a principal shift-invariant spaces in L²(R)$L^2(\mathbb{R})$ whose generator and its translates form a Riesz basis.     

The topological structure of fuzzy sets with sendograph metric

For a non-degenerate convex subset Y of the n  -dimensional Euclidean space Rⁿ${\mathbb{R}}^n$, let F(Y)$\mathbb{F}(Y)$ be the family of all fuzzy sets of Rⁿ${\mathbb{R}}^n$ which are upper semicontinuous, fuzzy convex and normal with compact supports contained in Y  . We show that the space F(Y)$\mathbb{F}(Y)$ with the topology of sendograph metric is homeomorphic to the separable Hilbert space ?²${?}^2$ if Y   is compact; and the space F(Rⁿ)$\mathbb{F}({\mathbb{R}}^n)$ is also homeomorphic to ?²${?}^2$.     

Tuning interval Branch-and-Prune for protein structure determination

The interval Branch and Prune (iBP) algorithm for obtaining solutions to the interval Discretizable Molecular Distance Geometry Problem (iDMDGP) has proven itself as a powerful method for molecular structure determination. However, substantial obstacles still must be overcome before iBP may be employed as a tractable general-purpose alternative to existing structure determination algorithms. This work introduces an iterative variant of the iBP algorithm that leverages existing knowledge of protein structures in order to reduce the size of the effective search space by many orders of magnitude. These improvements are included in a newly released implementation of the iBP software that aims to provide a solid platform for both research and application of the iDMDGP.     

A note on the zeros of Freud–Sobolev orthogonal polynomials

We prove that the zeros of a certain family of Sobolev orthogonal polynomials involving the Freud weight function e^-x4${\mathrm{e}}^{-x^4}$ on R$\mathbb{R}$ are real, simple, and interlace with the zeros of the Freud polynomials, i.e., those polynomials orthogonal with respect to the weight function e^-x4${\mathrm{e}}^{-x^4}$. Some numerical examples are shown.     

Compact imbeddings between variable exponent spaces with unbounded underlying domain

In this paper, we have established some compact imbedding theorems for some subspaces of W^1,p(x)(U)$W^{1,p\left(x\right)}\left(U\right)$ when the underlying domain U$U$ is unbounded. The domain we consider is mainly of type R^N(N≥2)$R^N(N\ge 2)$ or R^L×Ω(L≥2)$R^L\times \Omega (L\ge 2)$, where Ω⊂R^M$\Omega \subset R^M$ is a bounded domain with smooth boundary.     

Energy decay for the linear Klein–Gordon equation and boundary control

In this work we study the asymptotic behavior of the solutions of the linear Klein–Gordon equation in R^N${\mathbb{R}}^N$, N?1$N?1$. We prove that local energy of solutions to the Cauchy problem decays polynomially. Afterwards, we use the local decay of energy to study exact boundary controllability for the linear Klein–Gordon equation in general bounded domains of R^N${\mathbb{R}}^N$, N?1$N?1$.     

Pullback attractors of non-autonomous stochastic degenerate parabolic equations on unbounded domains

This paper is concerned with pullback attractors of the stochastic p  -Laplace equation defined on the entire space Rⁿ${\mathbb{R}}^n$. We first establish the asymptotic compactness of the equation in L²(Rⁿ)$L^2({\mathbb{R}}^n)$ and then prove the existence and uniqueness of non-autonomous random attractors. This attractor is pathwise periodic if the non-autonomous deterministic forcing is time periodic. The difficulty of non-compactness of Sobolev embeddings on Rⁿ${\mathbb{R}}^n$ is overcome by the uniform smallness of solutions outside a bounded domain.     

Higher order commutator estimates and local existence for the non-resistive MHD equations and related models

This paper establishes the local-in-time existence and uniqueness of strong solutions in H^s$H^s$ for s>n/2$s>n/2$ to the viscous, non-resistive magnetohydrodynamics (MHD) equations in Rⁿ${\mathbb{R}}^n$, n=2,3$n=2,3$, as well as for a related model where the advection terms are removed from the velocity equation. The uniform bounds required for proving existence are established by means of a new estimate, which is a partial generalisation of the commutator estimate of Kato and Ponce (1988) [13].     

Harness processes and harmonic crystals

In the Hammersley harness processes the R$\mathbb{R}$-valued height at each site i∈Z^d$i\in {\mathbb{Z}}^d$ is updated at rate 1 to an average of the neighboring heights plus a centered random variable (the noise). We construct the process “a la Harris” simultaneously for all times and boxes contained in Z^d${\mathbb{Z}}^d$. With this representation we compute covariances and show L²$L^2$ and almost sure time and space convergence of the process. In particular, the process started from the flat configuration and viewed from the height at the origin converges to an invariant measure. In dimension three and higher, the process itself converges to an invariant measure in L²$L^2$ at speed t^1−d/2$t^{1-d/2}$ (this extends the convergence established by Hsiao). When the noise is Gaussian the limiting measures are Gaussian fields (harmonic crystals) and are also reversible for the process.     

Soliton solutions for quasilinear Schrödinger equations: The critical exponential case

Quasilinear elliptic equations in R²${\mathbb{R}}^2$ of second order with critical exponential growth are considered. By using a change of variable, the quasilinear equations are reduced to semilinear equations, whose respective associated functionals are well defined in H¹(R²)$H^1\left({\mathbb{R}}^2\right)$ and satisfy the geometric hypotheses of the mountain pass theorem. Using this fact, we obtain a Cerami sequence converging weakly to a solution v$v$. In the proof that v$v$ is nontrivial, the main tool is the concentration–compactness principle [P.L. Lions, The concentration compactness principle in the calculus of variations. The locally compact case. Part I and II, Ann. Inst. H. Poincaré Anal. Non. Linéaire 1 (1984) 109–145, 223–283] combined with test functions connected with optimal Trudinger–Moser inequality.     

Multiplicity of layered solutions for Allen–Cahn systems with symmetric double well potential

We study the existence of solutions u:R³→R²$u:{\mathbb{R}}^3\to {\mathbb{R}}^2$ for the semilinear elliptic systems

equation(0.1)

−Δu(x,y,z)+∇W(u(x,y,z))=0,$-\mathrm{\Delta }u(x,y,z)+\mathrm{\nabla }W(u(x,y,z))=0,$

where W:R²→R$W:{\mathbb{R}}^2\to \mathbb{R}$ is a double well symmetric potential. We use variational methods to show, under generic non-degenerate properties of the set of one dimensional heteroclinic connections between the two minima _a±${\mathbf{a}}_{\pm }$ of W, that (0.1) has infinitely many geometrically distinct solutions u∈C²(R³,R²)$u\in C^2({\mathbb{R}}^3,{\mathbb{R}}^2)$ which satisfy u(x,y,z)→_a±$u(x,y,z)\to {\mathbf{a}}_{\pm }$ as x→±∞$x\to \pm \infty$ uniformly with respect to (y,z)∈R²$(y,z)\in {\mathbb{R}}^2$ and which exhibit dihedral symmetries with respect to the variables y and z  . We also characterize the asymptotic behavior of these solutions as |(y,z)|→+∞$|(y,z)|\to +\infty$.