Group-theoretic models of the inversion process in bacterial genomes

The variation in genome arrangements among bacterial taxa is largely due to the process of inversion. Recent studies indicate that not all inversions are equally probable, suggesting, for instance, that shorter inversions are more frequent than longer, and those that move the terminus of replication are less probable than those that do not. Current methods for establishing the inversion distance between two bacterial genomes are unable to incorporate such information. In this paper we suggest a group-theoretic framework that in principle can take these constraints into account. In particular, we show that by lifting the problem from circular permutations to the affine symmetric group, the inversion distance can be found in polynomial time for a model in which inversions are restricted to acting on two regions. This requires the proof of new results in group theory, and suggests a vein of new combinatorial problems concerning permutation groups on which group theorists will be needed to collaborate with biologists. We apply the new method to inferring distances and phylogenies for published Yersinia pestis data.Comment: 19 pages, 7 figures, in Press, Journal of Mathematical Biolog

Combinatorics and geometry of finite and infinite squaregraphs

Squaregraphs were originally defined as finite plane graphs in which all inner faces are quadrilaterals (i.e., 4-cycles) and all inner vertices (i.e., the vertices not incident with the outer face) have degrees larger than three. The planar dual of a finite squaregraph is determined by a triangle-free chord diagram of the unit disk, which could alternatively be viewed as a triangle-free line arrangement in the hyperbolic plane. This representation carries over to infinite plane graphs with finite vertex degrees in which the balls are finite squaregraphs. Algebraically, finite squaregraphs are median graphs for which the duals are finite circular split systems. Hence squaregraphs are at the crosspoint of two dualities, an algebraic and a geometric one, and thus lend themselves to several combinatorial interpretations and structural characterizations. With these and the 5-colorability theorem for circle graphs at hand, we prove that every squaregraph can be isometrically embedded into the Cartesian product of five trees. This embedding result can also be extended to the infinite case without reference to an embedding in the plane and without any cardinality restriction when formulated for median graphs free of cubes and further finite obstructions. Further, we exhibit a class of squaregraphs that can be embedded into the product of three trees and we characterize those squaregraphs that are embeddable into the product of just two trees. Finally, finite squaregraphs enjoy a number of algorithmic features that do not extend to arbitrary median graphs. For instance, we show that median-generating sets of finite squaregraphs can be computed in polynomial time, whereas, not unexpectedly, the corresponding problem for median graphs turns out to be NP-hard.Comment: 46 pages, 14 figure

Active shielding of magnetic field with circular space-time characteristic

Aim. The synthesis of two degree of freedom robust two circuit system of active shielding of magnetic field with circular spacetime characteristic, generated by overhead power lines with "triangle" type of phase conductors arrangements for reducing the magnetic flux density to the sanitary standards level and to reducing the sensitivity of the system to plant parameters uncertainty. Methodology. The synthesis is based on the multi-criteria game decision, in which the payoff vector is calculated on the basis of the Maxwell equations quasi-stationary approximation solutions. The game decision is based on the stochastic particles multiswarm optimization algorithms. The initial parameters for the synthesis by system of active shielding are the location of the overhead power lines with respect to the shielding space, geometry and number of shielding coils, operating currents, as well as the size of the shielding space and magnetic flux density normative value, which should be achieved as a result of shielding. The objective of the synthesis is to determine their number, configuration, spatial arrangementand and shielding coils currents, setting algorithm of the control systems as well as the resulting of the magnetic flux density value at the shielding space. Results. Computer simulation and field experimental research results of two degree of freedom robust two circuit system of active shielding of magnetic field, generated by overhead power lines with «triangle» type of phase conductors arrangements are given. The possibility of initial magnetic flux density level reducing and system sensitivity reducing to the plant parameters uncertainty is shown. Originality. For the first time the synthesis, theoretical and experimental research of two degree of freedom robust two -circuit t system of active shielding of magnetic field generated by single-circuit overhead power line with phase conductors triangular arrangements carried out. Practical value. Practical recommendations from the point of view of the practical implementation on reasonable choice of the spatial arrangement of two shielding coils of robust two -circuit system of active shielding of the magnetic field with circular space-time characteristic generated by single-circuit overhead power line with phase conductors triangular arrangements are given.Цель. Синтез комбинированной робастной двухконтурной системы активного экранирования магнитного поля с круговой пространственно-временной характеристикой, генерируемого одноконтурной воздушной линией электропередачи с треугольным подвесом проводов для снижения индукции магнитного поля до уровня санитарных норм и для снижения чувствительности системы к неопределенности параметров объекта управления. Методология. Синтез основан на решении многокритериальной стохастической игры, в которой векторный выигрыш вычисляется на основании решений уравнений Максвелла в квазистационарном приближении. Решение игры находится на основе алгоритмов стохастической мультиагентной оптимизации мультироем частиц. Исходными параметрами для синтеза системы активного экранирования являются расположение высоковольтной линий электропередачи по отношению к экранируемому пространству, геометрические размеры, количество проводов и рабочие токи линии электропередачи, а также размеры экранируемого пространства и нормативное значение индукции магнитного поля, которое должно быть достигнуто в результате экранирования. Задачей синтеза является определение количества, конфигурации, пространственного расположения и токов экранирующих обмоток, алгоритма работы системы управления, а также результирующего значения индукции магнитного поля в экранируемом пространстве. Результаты. Приводятся результаты теоретических и полевых экспериментальных исследований комбинированной робастной двухконтурной системы активного экранирования магнитного поля, генерируемого воздушной линией электропередачи с треугольным подвесом проводов. Показана возможность снижения уровня индукции исходного магнитного поля внутри экранируемого пространства и снижения чувствительности системы к неопределенностям параметров объекта управления. Оригинальность. Впервые проведены синтез, теоретические и экспериментальные исследования комбинированной робастной двухконтурной системы активного экранирования магнитного поля, генерируемого одноконтурной воздушной линией электропередачи с треугольным подвесом проводов. Практическая ценность. Приводятся практические рекомендации по обоснованному выбору с точки зрения практической реализации пространственного расположения двух экранирующих обмоток двухконтурной робастной системы активного экранирования магнитного поля с круговой пространственно-временной характеристикой, создаваемого одноконтурной воздушной линией электропередачи с треугольным подвесом проводов

Quasi-Parallel Segments and Characterization of Unique Bichromatic Matchings

Given n red and n blue points in general position in the plane, it is well-known that there is a perfect matching formed by non-crossing line segments. We characterize the bichromatic point sets which admit exactly one non-crossing matching. We give several geometric descriptions of such sets, and find an O(nlogn) algorithm that checks whether a given bichromatic set has this property.Comment: 31 pages, 24 figure