An Analytical Approach to the Protein Designability Problem

We present an analytical method for determining the designability of protein structures. We apply our method to the case of two-dimensional lattice structures, and give a systematic solution for the spectrum of any structure. Using this spectrum, the designability of a structure can be estimated. We outline a heirarchy of structures, from most to least designable, and show that this heirarchy depends on the potential that is used.Comment: 16 pages 4 figure

Uniform generation in trace monoids

We consider the problem of random uniform generation of traces (the elements of a free partially commutative monoid) in light of the uniform measure on the boundary at infinity of the associated monoid. We obtain a product decomposition of the uniform measure at infinity if the trace monoid has several irreducible components-a case where other notions such as Parry measures, are not defined. Random generation algorithms are then examined.Comment: Full version of the paper in MFCS 2015 with the same titl

Lower Bounds on the Redundancy of Huffman Codes with Known and Unknown Probabilities

In this paper we provide a method to obtain tight lower bounds on the minimum redundancy achievable by a Huffman code when the probability distribution underlying an alphabet is only partially known. In particular, we address the case where the occurrence probabilities are unknown for some of the symbols in an alphabet. Bounds can be obtained for alphabets of a given size, for alphabets of up to a given size, and for alphabets of arbitrary size. The method operates on a Computer Algebra System, yielding closed-form numbers for all results. Finally, we show the potential of the proposed method to shed some light on the structure of the minimum redundancy achievable by the Huffman code

Efficient indexing of necklaces and irreducible polynomials over finite fields

We study the problem of indexing irreducible polynomials over finite fields, and give the first efficient algorithm for this problem. Specifically, we show the existence of poly(n, log q)-size circuits that compute a bijection between {1, ... , |S|} and the set S of all irreducible, monic, univariate polynomials of degree n over a finite field F_q. This has applications in pseudorandomness, and answers an open question of Alon, Goldreich, H{\aa}stad and Peralta[AGHP]. Our approach uses a connection between irreducible polynomials and necklaces ( equivalence classes of strings under cyclic rotation). Along the way, we give the first efficient algorithm for indexing necklaces of a given length over a given alphabet, which may be of independent interest