On Additive Combinatorics of Permutations of Z(n)

Let Z(n) denote the ring of integers modulo n. A permutation of Z(n) is a sequence of n distinct elements of Z(n). Addition and subtraction of two permutations is defined element-wise. In this paper we consider two extremal problems on permutations of Z(n), namely, the maximum size of a collection of permutations such that the sum of any two distinct permutations in the collection is again a permutation, and the maximum size of a collection of permutations such that no sum of two distinct permutations in the collection is a permutation. Let the sizes be denoted by s (n) and t (n) respectively. The case when n is even is trivial in both the cases, with s (n) = 1 and t (n) = n!. For n odd, we prove (n phi(n))/2(k) <= s(n) <= n!.2(-)(n-1)/2/((n-1)/2)! and 2 (n-1)/2 . (n-1/2)! <= t (n) <= 2(k) . (n-1)!/phi(n), where k is the number of distinct prime divisors of n and phi is the Euler's totient function.

The combinatorics of transcriptional regulation

The ability to regulate gene expression is of central importance for the adaptability of living organisms to changes in their internal and external environment. At the transcriptional level, binding of transcription factors (TFs) in the vicinity of promoters can modulate the rate at which transcripts are produced, and as such play an important role in gene regulation. TFs with regulatory action at multiple promoters is the rule rather than the exception, with examples ranging from TFs like the cAMP receptor protein (CRP) in E. coli that regulates hundreds of different genes, to situations involving multiple copies of the same gene, such as on plasmids, or viral DNA. When the number of TFs heavily exceeds the number of binding sites, TF binding to each promoter can be regarded as independent. However, when the number of TF molecules is comparable to the number of binding sites, TF titration will result in coupling ("entanglement") between transcription of different genes. The last few decades have seen rapid advances in our ability to quantitatively measure such effects, which calls for biophysical models to explain these data. Here we develop a statistical mechanical model which takes the TF titration effect into account and use it to predict both the level of gene expression and the resulting correlation in transcription rates for a general set of promoters. To test these predictions experimentally, we create genetic constructs with known TF copy number, binding site affinities, and gene copy number; hence avoiding the need to use free fit parameters. Our results clearly prove the TF titration effect and that the statistical mechanical model can accurately predict the fold change in gene expression for the studied cases. We also generalize these experimental efforts to cover systems with multiple different genes, using the method of mRNA fluorescence in situ hybridization (FISH). Interestingly, we can use the TF titration affect as a tool to measure the plasmid copy number at different points in the cell cycle, as well as the plasmid copy number variance. Finally, we investigate the strategies of transcriptional regulation used in a real organism by analyzing the thousands of known regulatory interactions in E. coli. We introduce a "random promoter architecture model" to identify overrepresented regulatory strategies, such as TF pairs which coregulate the same genes more frequently than would be expected by chance, indicating a related biological function. Furthermore, we investigate whether promoter architecture has a systematic effect on gene expression by linking the regulatory data of E. coli to genome-wide expression censuses.

Density profiles in the raise and peel model with and without a wall; physics and combinatorics

We consider the raise and peel model of a one-dimensional fluctuating interface in the presence of an attractive wall. The model can also describe a pair annihilation process in disordered unquenched media with a source at one end of the system. For the stationary states, several density profiles are studied using Monte Carlo simulations. We point out a deep connection between some profiles seen in the presence of the wall and in its absence. Our results are discussed in the context of conformal invariance ( c = 0 theory). We discover some unexpected values for the critical exponents, which are obtained using combinatorial methods. We have solved known ( Pascal`s hexagon) and new (split-hexagon) bilinear recurrence relations. The solutions of these equations are interesting in their own right since they give information on certain classes of alternating sign matrices.

Henon-like maps with arbitrary stationary combinatorics

We extend the renormalization operator introduced in [A. de Carvalho, M. Martens and M. Lyubich. Renormalization in the Henon family, I: universality but non-rigidity. J. Stat. Phys. 121(5/6) (2005), 611-669] from period-doubling Henon-like maps to Henon-like maps with arbitrary stationary combinatorics. We show that the renonnalization picture also holds in this case if the maps are taken to be strongly dissipative. We study infinitely renormalizable maps F and show that they have an invariant Cantor set O on which F acts like a p-adic adding machine for some p > 1. We then show, as for the period-doubling case in the work of de Carvalho, Martens and Lyubich [Renormalization in the Henon family, I: universality but non-rigidity. J. Stat. Phys. 121(5/6) (2005), 611-669], that the sequence of renormalizations has a universal form, but that the invariant Cantor set O is non-rigid. We also show that O cannot possess a continuous invariant line field.

Geometry and combinatorics of the cutting angle method

Lower approximation of Lipschitz functions plays an important role in deterministic global optimization. This article examines in detail the lower piecewise linear approximation which arises in the cutting angle method. All its local minima can be explicitly enumerated, and a special data structure was designed to process them very efficiently, improving previous results by several orders of magnitude. Further, some geometrical properties of the lower approximation have been studied, and regions on which this function is linear have been identified explicitly. Connection to a special distance function and Voronoi diagrams was established. An application of these results is a black-box multivariate random number generator, based on acceptance-rejection approach.

Polyhedral combinatorics of the cardinality constrained quadratic knapsack problem and the quadratic selective travelling salesman problem

This paper considers the Cardinality Constrained Quadratic Knapsack Problem (QKP) and the Quadratic Selective Travelling Salesman Problem (QSTSP). The QKP is a generalization of the Knapsack Problem and the QSTSP is a generalization of the Travelling Salesman Problem. Thus, both problems are NP hard. The QSTSP and the QKP can be solved using branch-and-cut methods. Good bounds can be obtained if strong constraints are used. Hence it is important to identify strong or even facet-defining constraints. This paper studies the polyhedral combinatorics of the QSTSP and the QKP, i.e. amongst others we identify facet-defining constraints for the QSTSP and the QKP, and provide mathematical proofs that they do indeed define facets.

Eits: Combinatorics, Potential and Genre

Eits is a work of fiction, a non-traditional novel whose structure is largely determined by an Oulipian-style constraint. The constraint in Eits is culled from the album names and song titles of the band Explosions in the Sky. Each album corresponds to a chapter in the novel, and the language of each album title must be used in some way as an introduction to each chapter. Within each chapter (album), song titles correspond to numbered sections where each title must appear as is in the first sentence of that section. This not only dictates, to some degree, the direction of the text that will follow, but, looking ahead, the title of the next section will dictate where this section must arrive. From this, a narrative naturally takes shape. Albums/chapters appear chronologically, according to each album's release date, and within each album/chapter, songs/sections appear in the order they do on the album. This is, perhaps, the most straightforward way of ordering the received language of the constraint, the possibilities beyond this exponential. Eits is a novel that shifts in form, providing a texture to the space and reading experience of the novel, all in hopes of creating a space in which content and form inform and push each other to new limits. Eits is never satisfied to settle on one form for too long, and it is in the movement between forms that the narrative develops in interesting ways. Eits demonstrates the combinatoric possibilities inherent in language, and this exploration of potential highlights the reciprocal relationship between writing and reading. As Eits builds upon a limited language set, it explores and exploits the combinatory possibilities that language allows for both writer and reader. It demonstrates that all combinatoric potentialities, visible or not, always co-exist in the same time and space, and in this infinite space, individuals are invited to be writers and readers in simultaneity.