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In this paper, we present and analyze a fast algorithm that determines the possible molecular formulae corresponding to the resolved peaks in the spectral data obtained from a mass analyzer like an FT-ICR-MS. In contrast to our approach, most known algorithms and software that attempt to solve this important problem are brute-force in nature and consequently, highly prone to combinatorial explosion when dealing with the volume of real data. We also present an object-oriented implementation of our algorithm in a general-purpose, user-friendly, interactive, and easily extensible software tool PG C ompound M atch F inder. A run-time performance analysis of our software shows that even when dealing with several billion theoretical possibilities matched against tens of thousands of resolved peaks, a complete analysis using today’s standard desktop machines can take only a few minutes. [ABSTRACT FROM AUTHOR]

In this paper we establish a fundamental link between the search for weighing matrices constructed from two circulants and the operation of sorting strings, an operation that has been studied extensively in computer science. In particular, we demonstrate that the search for weighing matrices constructed from two circulants using the power spectral density criterion and exploiting structural patterns for the locations of the zeros in candidate solutions, can be viewed as a string sorting problem together with a linear time algorithm to locate common strings in two sorted arrays. This allows us to bring into bear efficient algorithms from the string sorting literature. We also state and prove some new enhancements to the power spectral density criterion, that allow us to treat successfully the rounding error effect and speed up the algorithm. Finally, we use these ideas to find new weighing matrices of order 2 n and weights 2 n – 13, 2 n – 17 constructed from two circulants. [ABSTRACT FROM AUTHOR]

In his famous book “Combinatory Analysis” MacMahon introduced Partition Analysis (“Omega Calculus”) as a computational method for solving problems in connection with linear diophantine inequalities and equations. The technique has recently been given a new life by G.E. Andrews and his coauthors, who had the idea of marrying it with the tools of to-day’s Computer Algebra. The theory consists of evaluating a certain type of rational function of the form A(λ)-1B(1/λ)-1 by the MacMahon Ω operator. So far, the case where the two polynomials A and B are factorized as products of polynomials with two terms has been studied in details. In this paper we study the case of arbitrary polynomials A and B. We obtain an algorithm for evaluating the Ω operator using the coefficients of those polynomials without knowing their roots. Since the program efficiency is a persisting problem in several-variable polynomial Calculus, we did our best to make the algorithm as fast as possible. As an application, we derive new combinatorial identities. [ABSTRACT FROM AUTHOR]