Matroids over a ring

We introduce the notion of a matroid M over a commutative ring R, assigning to every subset of the ground set an R-module according to some axioms. When R is a field, we recover matroids. When R D Z, and when R is a DVR, we get (structures which contain all the data of) quasi-arithmetic matroids, and valuated matroids, i.e. tropical linear spaces, respectively. More generally, whenever R is a Dedekind domain, we extend all the usual properties and operations holding for matroids (e.g., duality), and we explicitly describe the structure of the matroids over R. Furthermore, we compute the Tutte-Grothendieck ring of matroids over R. We also show that the Tutte quasi-polynomial of a matroid over Z can be obtained as an evaluation of the class of the matroid in the Tutte-Grothendieck ring

On Symbolic Ultrametrics, Cotree Representations, and Cograph Edge Decompositions and Partitions

Symbolic ultrametrics define edge-colored complete graphs K_n and yield a simple tree representation of K_n. We discuss, under which conditions this idea can be generalized to find a symbolic ultrametric that, in addition, distinguishes between edges and non-edges of arbitrary graphs G=(V,E) and thus, yielding a simple tree representation of G. We prove that such a symbolic ultrametric can only be defined for G if and only if G is a so-called cograph. A cograph is uniquely determined by a so-called cotree. As not all graphs are cographs, we ask, furthermore, what is the minimum number of cotrees needed to represent the topology of G. The latter problem is equivalent to find an optimal cograph edge k-decomposition {E_1,...,E_k} of E so that each subgraph (V,E_i) of G is a cograph. An upper bound for the integer k is derived and it is shown that determining whether a graph has a cograph 2-decomposition, resp., 2-partition is NP-complete

Pattern Avoidance in Poset Permutations

We extend the concept of pattern avoidance in permutations on a totally ordered set to pattern avoidance in permutations on partially ordered sets. The number of permutations on $P$ that avoid the pattern $\pi$ is denoted $Av_P(\pi)$. We extend a proof of Simion and Schmidt to show that $Av_P(132) \leq Av_P(123)$ for any poset $P$, and we exactly classify the posets for which equality holds.Comment: 13 pages, 1 figure; v2: corrected typos; v3: corrected typos and improved formatting; v4: to appear in Order; v5: corrected typos; v6: updated author email addresse

Polynomial-sized Semidefinite Representations of Derivative Relaxations of Spectrahedral Cones

We give explicit polynomial-sized (in $n$ and $k$) semidefinite representations of the hyperbolicity cones associated with the elementary symmetric polynomials of degree $k$ in $n$ variables. These convex cones form a family of non-polyhedral outer approximations of the non-negative orthant that preserve low-dimensional faces while successively discarding high-dimensional faces. More generally we construct explicit semidefinite representations (polynomial-sized in $k,m$, and $n$) of the hyperbolicity cones associated with $k$th directional derivatives of polynomials of the form $p(x) = \det(\sum_{i=1}^{n}A_i x_i)$ where the $A_i$ are $m\times m$ symmetric matrices. These convex cones form an analogous family of outer approximations to any spectrahedral cone. Our representations allow us to use semidefinite programming to solve the linear cone programs associated with these convex cones as well as their (less well understood) dual cones.Comment: 20 pages, 1 figure. Minor changes, expanded proof of Lemma

The Lee-Yang and P\'olya-Schur Programs. I. Linear Operators Preserving Stability

In 1952 Lee and Yang proposed the program of analyzing phase transitions in terms of zeros of partition functions. Linear operators preserving non-vanishing properties are essential in this program and various contexts in complex analysis, probability theory, combinatorics, and matrix theory. We characterize all linear operators on finite or infinite-dimensional spaces of multivariate polynomials preserving the property of being non-vanishing whenever the variables are in prescribed open circular domains. In particular, this solves the higher dimensional counterpart of a long-standing classification problem originating from classical works of Hermite, Laguerre, Hurwitz and P\'olya-Schur on univariate polynomials with such properties.Comment: Final version, to appear in Inventiones Mathematicae; 27 pages, no figures, LaTeX2

Structural Dynamic of a Self-Assembling Peptide d-EAK16 Made of Only D-Amino Acids

We here report systematic study of structural dynamics of a 16-residue self-assembling peptide d-EAK16 made of only D-amino acids. We compare these results with its chiral counterpart L-form, l-EAK16. Circular dichroism was used to follow the structural dynamics under various temperature and pH conditions. At 25°C the d-EAK16 peptide displayed a typical beta-sheet spectrum. Upon increasing the temperature above 70°C, there was a spectrum shift as the 218 nm valley widens toward 210 nm. Above 80°C, the d-EAK16 peptide transformed into a typical alpha-helix CD spectrum without going through a detectable random-coil intermediate. When increasing the temperature from 4°C to 110°C then cooling back from 110°C to 4°C, there was a hysteresis: the secondary structure from beta-sheet to alpha-helix and then from alpha-helix to beta-sheet occurred. d-EAK16 formed an alpha-helical conformation at pH0.76 and pH12 but formed a beta-sheet at neutral pH. The effects of various pH conditions, ionic strength and denaturing agents were also noted. Since D-form peptides are resistant to natural enzyme degradation, such drastic structural changes may be exploited for fabricating molecular sensors to detect minute environmental changes. This provides insight into the behaviors of self-assembling peptides made of D-amino acids and points the way to designing new peptide materials for biomedical engineering and nanobiotechnology

Peptide Bond Distortions from Planarity: New Insights from Quantum Mechanical Calculations and Peptide/Protein Crystal Structures

By combining quantum-mechanical analysis and statistical survey of peptide/protein structure databases we here report a thorough investigation of the conformational dependence of the geometry of peptide bond, the basic element of protein structures. Different peptide model systems have been studied by an integrated quantum mechanical approach, employing DFT, MP2 and CCSD(T) calculations, both in aqueous solution and in the gas phase. Also in absence of inter-residue interactions, small distortions from the planarity are more a rule than an exception, and they are mainly determined by the backbone ψ dihedral angle. These indications are fully corroborated by a statistical survey of accurate protein/peptide structures. Orbital analysis shows that orbital interactions between the σ system of Cα substituents and the π system of the amide bond are crucial for the modulation of peptide bond distortions. Our study thus indicates that, although long-range inter-molecular interactions can obviously affect the peptide planarity, their influence is statistically averaged. Therefore, the variability of peptide bond geometry in proteins is remarkably reproduced by extremely simplified systems since local factors are the main driving force of these observed trends. The implications of the present findings for protein structure determination, validation and prediction are also discussed