Integrating Singular Functions on the Sphere

We obtain rigorous results concerning the evaluation of integrals on the two sphere using complex methods. It is shown that for regular as well as singular functions which admit poles, the integral can be reduced to the calculation of residues through a limiting procedure.Comment: 15 pages, revte

Complex-linear invariants of biochemical networks

The nonlinearities found in molecular networks usually prevent mathematical analysis of network behaviour, which has largely been studied by numerical simulation. This can lead to difficult problems of parameter determination. However, molecular networks give rise, through mass-action kinetics, to polynomial dynamical systems, whose steady states are zeros of a set of polynomial equations. These equations may be analysed by algebraic methods, in which parameters are treated as symbolic expressions whose numerical values do not have to be known in advance. For instance, an "invariant" of a network is a polynomial expression on selected state variables that vanishes in any steady state. Invariants have been found that encode key network properties and that discriminate between different network structures. Although invariants may be calculated by computational algebraic methods, such as Gr\"obner bases, these become computationally infeasible for biologically realistic networks. Here, we exploit Chemical Reaction Network Theory (CRNT) to develop an efficient procedure for calculating invariants that are linear combinations of "complexes", or the monomials coming from mass action. We show how this procedure can be used in proving earlier results of Horn and Jackson and of Shinar and Feinberg for networks of deficiency at most one. We then apply our method to enzyme bifunctionality, including the bacterial EnvZ/OmpR osmolarity regulator and the mammalian 6-phosphofructo-2-kinase/fructose-2,6-bisphosphatase glycolytic regulator, whose networks have deficiencies up to four. We show that bifunctionality leads to different forms of concentration control that are robust to changes in initial conditions or total amounts. Finally, we outline a systematic procedure for using complex-linear invariants to analyse molecular networks of any deficiency.Comment: 36 pages, 6 figure

Linear Toric Fibrations

These notes are based on three lectures given at the 2013 CIME/CIRM summer school. The purpose of this series of lectures is to introduce the notion of a toric fibration and to give its geometrical and combinatorial characterizations. Polarized toric varieties which are birationally equivalent to projective toric bundles are associated to a class of polytopes called Cayley polytopes. Their geometry and combinatorics have a fruitful interplay leading to fundamental insight in both directions. These notes will illustrate geometrical phenomena, in algebraic geometry and neighboring fields, which are characterized by a Cayley structure. Examples are projective duality of toric varieties and polyhedral adjunction theory

Tropical surface singularities

In this paper, we study tropicalisations of singular surfaces in toric threefolds. We completely classify singular tropical surfaces of maximal-dimensional type, show that they can generically have only finitely many singular points, and describe all possible locations of singular points. More precisely, we show that singular points must be either vertices, or generalized midpoints and baricenters of certain faces of singular tropical surfaces, and, in some cases, there may be additional metric restrictions to faces of singular tropical surfaces.Comment: A gap in the classification was closed. 37 pages, 29 figure

Singular Tropical Hypersurfaces

We study the notion of singular tropical hypersurfaces of any dimension. We characterize the singular points in terms of tropical Euler derivatives and we give an algorithm to compute all singular points. We also describe non-transversal intersection points of planar tropical curves

Weighted integral formulas on manifolds

We present a method of finding weighted Koppelman formulas for $(p,q)$-forms on $n$-dimensional complex manifolds $X$ which admit a vector bundle of rank $n$ over $X \times X$, such that the diagonal of $X \times X$ has a defining section. We apply the method to \Pn and find weighted Koppelman formulas for $(p,q)$-forms with values in a line bundle over \Pn. As an application, we look at the cohomology groups of $(p,q)$-forms over \Pn with values in various line bundles, and find explicit solutions to the \dbar-equation in some of the trivial groups. We also look at cohomology groups of $(0,q)$-forms over \Pn \times \Pm with values in various line bundles. Finally, we apply our method to developing weighted Koppelman formulas on Stein manifolds.Comment: 25 page

Residue currents associated with weakly holomorphic functions

We construct Coleff-Herrera products and Bochner-Martinelli type residue currents associated with a tuple $f$ of weakly holomorphic functions, and show that these currents satisfy basic properties from the (strongly) holomorphic case, as the transformation law, the Poincar\'e-Lelong formula and the equivalence of the Coleff-Herrera product and the Bochner-Martinelli type residue current associated with $f$ when $f$ defines a complete intersection.Comment: 28 pages. Updated with some corrections from the revision process. In particular, corrected and clarified some things in Section 5 and 6 regarding products of weakly holomorphic functions and currents, and the definition of the Bochner-Martinelli type current

Polynomial-Time Amoeba Neighborhood Membership and Faster Localized Solving

We derive efficient algorithms for coarse approximation of algebraic hypersurfaces, useful for estimating the distance between an input polynomial zero set and a given query point. Our methods work best on sparse polynomials of high degree (in any number of variables) but are nevertheless completely general. The underlying ideas, which we take the time to describe in an elementary way, come from tropical geometry. We thus reduce a hard algebraic problem to high-precision linear optimization, proving new upper and lower complexity estimates along the way.Comment: 15 pages, 9 figures. Submitted to a conference proceeding

A Linear Algebra Approach for Detecting Binomiality of Steady State Ideals of Reversible Chemical Reaction Networks

Motivated by problems from Chemical Reaction Network Theory, we investigate whether steady state ideals of reversible reaction networks are generated by binomials. We take an algebraic approach considering, besides concentrations of species, also rate constants as indeterminates. This leads us to the concept of unconditional binomiality, meaning binomiality for all values of the rate constants. This concept is different from conditional binomiality that applies when rate constant values or relations among rate constants are given. We start by representing the generators of a steady state ideal as sums of binomials, which yields a corresponding coefficient matrix. On these grounds we propose an efficient algorithm for detecting unconditional binomiality. That algorithm uses exclusively elementary column and row operations on the coefficient matrix. We prove asymptotic worst case upper bounds on the time complexity of our algorithm. Furthermore, we experimentally compare its performance with other existing methods

Statistical-Thermodynamic Model for Light Scattering from Eye Lens Protein Mixtures

We model light-scattering cross sections of concentrated aqueous mixtures of the bovine eye lens proteins γB- and α-crystallin by adapting a statistical-thermodynamic model of mixtures of spheres with short-range attractions. The model reproduces measured static light scattering cross sections, or Rayleigh ratios, of γB-α mixtures from dilute concentrations where light scattering intensity depends on molecular weights and virial coefficients, to realistically high concentration protein mixtures like those of the lens. The model relates γB-γB and γB-α attraction strengths and the γB-α size ratio to the free energy curvatures that set light scattering efficiency in tandem with protein refractive index increments. The model includes (i) hard-sphere α-α interactions, which create short-range order and transparency at high protein concentrations, (ii) short-range attractive plus hard-core γ-γ interactions, which produce intense light scattering and liquid-liquid phase separation in aqueous γ-crystallin solutions, and (iii) short-range attractive plus hard-core γ-α interactions, which strongly influence highly non-additive light scattering and phase separation in concentrated γ-α mixtures. The model reveals a new lens transparency mechanism, that prominent equilibrium composition fluctuations can be perpendicular to the refractive index gradient. The model reproduces the concave-up dependence of the Rayleigh ratio on α/γ composition at high concentrations, its concave-down nature at intermediate concentrations, non-monotonic dependence of light scattering on γ-α attraction strength, and more intricate, temperature-dependent features. We analytically compute the mixed virial series for light scattering efficiency through third order for the sticky-sphere mixture, and find that the full model represents the available light scattering data at concentrations several times those where the second and third mixed virial contributions fail. The model indicates that increased γ-γ attraction can raise γ-α mixture light scattering far more than it does for solutions of γ-crystallin alone, and can produce marked turbidity tens of degrees celsius above liquid-liquid separation