Efficient algorithms for tensor scaling, quantum marginals and moment polytopes

We present a polynomial time algorithm to approximately scale tensors of any format to arbitrary prescribed marginals (whenever possible). This unifies and generalizes a sequence of past works on matrix, operator and tensor scaling. Our algorithm provides an efficient weak membership oracle for the associated moment polytopes, an important family of implicitly-defined convex polytopes with exponentially many facets and a wide range of applications. These include the entanglement polytopes from quantum information theory (in particular, we obtain an efficient solution to the notorious one-body quantum marginal problem) and the Kronecker polytopes from representation theory (which capture the asymptotic support of Kronecker coefficients). Our algorithm can be applied to succinct descriptions of the input tensor whenever the marginals can be efficiently computed, as in the important case of matrix product states or tensor-train decompositions, widely used in computational physics and numerical mathematics. We strengthen and generalize the alternating minimization approach of previous papers by introducing the theory of highest weight vectors from representation theory into the numerical optimization framework. We show that highest weight vectors are natural potential functions for scaling algorithms and prove new bounds on their evaluations to obtain polynomial-time convergence. Our techniques are general and we believe that they will be instrumental to obtain efficient algorithms for moment polytopes beyond the ones consider here, and more broadly, for other optimization problems possessing natural symmetries

Topological Entropy of Braids on the Torus

A fast method is presented for computing the topological entropy of braids on the torus. This work is motivated by the need to analyze large braids when studying two-dimensional flows via the braiding of a large number of particle trajectories. Our approach is a generalization of Moussafir's technique for braids on the sphere. Previous methods for computing topological entropies include the Bestvina--Handel train-track algorithm and matrix representations of the braid group. However, the Bestvina--Handel algorithm quickly becomes computationally intractable for large braid words, and matrix methods give only lower bounds, which are often poor for large braids. Our method is computationally fast and appears to give exponential convergence towards the exact entropy. As an illustration we apply our approach to the braiding of both periodic and aperiodic trajectories in the sine flow. The efficiency of the method allows us to explore how much extra information about flow entropy is encoded in the braid as the number of trajectories becomes large.Comment: 19 pages, 44 figures. SIAM journal styl

Strictly Toral Dynamics

This article deals with nonwandering (e.g. area-preserving) homeomorphisms of the torus $\mathbb{T}^2$ which are homotopic to the identity and strictly toral, in the sense that they exhibit dynamical properties that are not present in homeomorphisms of the annulus or the plane. This includes all homeomorphisms which have a rotation set with nonempty interior. We define two types of points: inessential and essential. The set of inessential points $ine(f)$ is shown to be a disjoint union of periodic topological disks ("elliptic islands"), while the set of essential points $ess(f)$ is an essential continuum, with typically rich dynamics (the "chaotic region"). This generalizes and improves a similar description by J\"ager. The key result is boundedness of these "elliptic islands", which allows, among other things, to obtain sharp (uniform) bounds of the diffusion rates. We also show that the dynamics in $ess(f)$ is as rich as in $\mathbb{T}^2$ from the rotational viewpoint, and we obtain results relating the existence of large invariant topological disks to the abundance of fixed points.Comment: Incorporates suggestions and corrections by the referees. To appear in Inv. Mat

Cooperative Origin of Low-Density Domains in Liquid Water

We study the size of clusters formed by water molecules possessing large enough tetrahedrality with respect to their nearest neighbors. Using Monte Carlo simulation of the SPC/E model of water, together with a geometric analysis based on Voronoi tessellation, we find that regions of lower density than the bulk are formed by accretion of molecules into clusters exceeding a minimum size. Clusters are predominantly linear objects and become less compact as they grow until they reach a size beyond which further accretion is not accompanied by a density decrease. The results suggest that the formation of "ice-like" regions in liquid water is cooperative.Comment: 16 pages, 6 figure

Aperiodic invariant continua for surface homeomorphisms

We prove that if a homeomorphism of a closed orientable surface S has no wandering points and leaves invariant a compact, connected set K which contains no periodic points, then either K=S and S is a torus, or $K$ is the intersection of a decreasing sequence of annuli. A version for non-orientable surfaces is given.Comment: 8 pages, to appear in Mathematische Zeitschrif

Thermodynamic behaviour and structural properties of an aqueous sodium chloride solution upon supercooling

We present the results of a molecular dynamics simulation study of thermodynamic and structural properties upon supercooling of a low concentration sodium chloride solution in TIP4P water and the comparison with the corresponding bulk quantities. We study the isotherms and the isochores for both the aqueous solution and bulk water. The comparison of the phase diagrams shows that thermodynamic properties of the solution are not merely shifted with respect to the bulk. Moreover, from the analysis of the thermodynamic curves, both the spinodal line and the temperatures of maximum density curve can be calculated. The spinodal line appears not to be influenced by the presence of ions at the chosen concentration, while the temperatures of maximum density curve displays both a mild shift in temperature and a shape modification with respect to bulk. Signatures of the presence of a liquid-liquid critical point are found in the aqueous solution. By analysing the water-ion radial distribution functions of the aqueous solution we observe that upon changing density, structural modifications appear close to the spinodal. For low temperatures additional modifications appear also for densities close to that corresponding to a low density configurational energy minimum.Comment: 10 pages, 13 figures, 2 tables. To be published in J. Chem. Phy

Depth dependent dynamics in the hydration shell of a protein

We study the dynamics of hydration water/protein association in folded proteins, using lysozyme and myoglobin as examples. Extensive molecular dynamics simulations are performed to identify underlying mechanisms of the dynamical transition that corresponds to the onset of amplified atomic fluctuations in proteins. The number of water molecules within a cutoff distance of each residue scales linearly with protein depth index and is not affected by the local dynamics of the backbone. Keeping track of the water molecules within the cutoff sphere, we observe an effective residence time, scaling inversely with depth index at physiological temperatures while the diffusive escape is highly reduced below the transition. A depth independent orientational memory loss is obtained for the average dipole vector of the water molecules within the sphere when the protein is functional. While below the transition temperature, the solvent is in a glassy state, acting as a solid crust around the protein, inhibiting any large scale conformational fluctuations. At the transition, most of the hydration shell unfreezes and water molecules collectively make the protein more flexible.Comment: Journal of Chemical Physics in pres

Mine Fire Detection in the Presence Of Diesel Emissions

A series of four coal combustion experiments was conducted at the National Institute for Occupational Safety and Health\u27s (NIOSH) Pittsburgh Research Laboratory (PRL) in the Safety Research Coal Mine (SRCM) to evaluate the response of fire sensors to a small 0.61 m square smoldering coal fire which transitions to flaming combustion in the presence of diesel emissions. An optical path smoke sensor alarmed earlier than a point type diffusion mode ionization smoke sensor, which alarmed prior to a co alert value of 5 PPM above ambient. The presence of steady state diesel emissions resulted in a decrease in the optical smoke sensor analog output voltage signal by less than 1.4 pet for the three coal fire experiments in which a diesel engine was operating, whereas the ionization smoke sensor output decreased between 10.8 and 26.7 pet after the initial surge of the diesel engine. A commercial diesel discriminating fire sensor did not alarm for a fire in the one experiment for which it was used. The results of the experiments demonstrated that an optical path smoke sensor might be used to detect a coal fire under the experimental conditions considered of starting a diesel engine followed by a slowly developing coal fire

A statistical method for revealing form-function relations in biological networks

Over the past decade, a number of researchers in systems biology have sought to relate the function of biological systems to their network-level descriptions -- lists of the most important players and the pairwise interactions between them. Both for large networks (in which statistical analysis is often framed in terms of the abundance of repeated small subgraphs) and for small networks which can be analyzed in greater detail (or even synthesized in vivo and subjected to experiment), revealing the relationship between the topology of small subgraphs and their biological function has been a central goal. We here seek to pose this revelation as a statistical task, illustrated using a particular setup which has been constructed experimentally and for which parameterized models of transcriptional regulation have been studied extensively. The question "how does function follow form" is here mathematized by identifying which topological attributes correlate with the diverse possible information-processing tasks which a transcriptional regulatory network can realize. The resulting method reveals one form-function relationship which had earlier been predicted based on analytic results, and reveals a second for which we can provide an analytic interpretation. Resulting source code is distributed via http://formfunction.sourceforge.net.Comment: To appear in Proc. Natl. Acad. Sci. USA. 17 pages, 9 figures, 2 table