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

On Maltsev digraphs

The original publication is available at www.springerlink.com Copyright SpringerWe study digraphs preserved by a Maltsev operation, Maltsev digraphs. We show that these digraphs retract either onto a directed path or to the disjoint union of directed cycles, showing that the constraint satisfaction problem for Maltsev digraphs is in logspace, L. (This was observed in [19] using an indirect argument.) We then generalize results in [19] to show that a Maltsev digraph is preserved not only by a majority operation, but by a class of other operations (e.g., minority, Pixley) and obtain a O(V G4)-time algorithm to recognize Maltsev digraphs. We also prove analogous results for digraphs preserved by conservative Maltsev operations which we use to establish that the list homomorphism problem for Maltsev digraphs is in L. We then give a polynomial time characterisation of Maltsev digraphs admitting a conservative 2-semilattice operation. Finally, we give a simple inductive construction of directed acyclic digraphs preserved by a Maltsev operation.Peer reviewe

Maximum likelihood estimates of pairwise rearrangement distances

Accurate estimation of evolutionary distances between taxa is important for many phylogenetic reconstruction methods. In the case of bacteria, distances can be estimated using a range of different evolutionary models, from single nucleotide polymorphisms to large-scale genome rearrangements. In the case of sequence evolution models (such as the Jukes-Cantor model and associated metric) have been used to correct pairwise distances. Similar correction methods for genome rearrangement processes are required to improve inference. Current attempts at correction fall into 3 categories: Empirical computational studies, Bayesian/MCMC approaches, and combinatorial approaches. Here we introduce a maximum likelihood estimator for the inversion distance between a pair of genomes, using the group-theoretic approach to modelling inversions introduced recently. This MLE functions as a corrected distance: in particular, we show that because of the way sequences of inversions interact with each other, it is quite possible for minimal distance and MLE distance to differently order the distances of two genomes from a third. This has obvious implications for the use of minimal distance in phylogeny reconstruction. The work also tackles the above problem allowing free rotation of the genome. Generally a frame of reference is locked, and all computation made accordingly. This work incorporates the action of the dihedral group so that distance estimates are free from any a priori frame of reference.Comment: 21 pages, 7 figures. To appear in the Journal of Theoretical Biolog

A philosophical approach to entrepreneurial education: a model based on Kantian and Aristotelian thought

In the field of entrepreneurship education, how to develop an effective program to teach entrepreneurship has been widely debated. However, an inductive approach based on analysis of educational program experiences and outcomes has led to mixed conclusions about the appropriate scope and structure of entrepreneurship education. In contrast, we take a deductive approach to develop a comprehensive entrepreneurship education model based on concepts from two schools of philosophical thought: the Kantian debate about freedom versus determinism, and the Aristotelian concepts of praxis and poïesis. These philosophical concepts are related to scope and structure dimensions that delineate the soft (art) and hard (science) of entrepreneurship education, their components and interrelationships. Pedagogies associated with each component as well as integrative pedagogies are identified to guide the development of entrepreneurship education programs and teaching. Theoretical propositions are presented for future research

Layer-by-layer biofunctionalization of nanostructured porous silicon for high-sensitivity and high-selectivity label-free affinity biosensing

Nanostructured materials premise to revolutionize the label-free biosensing of analytes for clinical applications, leveraging the deeper interaction between materials and analytes with comparable size. However, when the characteristic dimension of the materials reduces to the nanoscale, the surface functionalization for the binding of bioreceptors becomes a complex issue that can affect the performance of label-free biosensors. Here we report on an effective and robust route for surface biofunctionalization of nanostructured materials based on the layer-by-layer (LbL) electrostatic nano-assembly of oppositely-charged polyelectrolytes, which are engineered with bioreceptors to enable label-free detection of target analytes. LbL biofunctionalization is demonstrated using nanostructured porous silicon (PSi) interferometers for affinity detection of streptavidin in saliva, through LbL nano-assembly of a bi-layer of positively-charged poly(allylamine hydrochloride) (PAH) and negatively-charged biotinylated poly(methacrylic acid) (b-PMAA). High sensitivity in streptavidin detection is achieved, with high selectivity and stability, down to a detection limit of 600 fM

The Effective Particle-Hole Interaction and the Optical Response of Simple Metal Clusters

Following Sham and Rice [L. J. Sham, T. M. Rice, Phys. Rev. 144 (1966) 708] the correlated motion of particle-hole pairs is studied, starting from the general two-particle Greens function. In this way we derive a matrix equation for eigenvalues and wave functions, respectively, of the general type of collective excitation of a N-particle system. The interplay between excitons and plasmons is fully described by this new set of equations. As a by-product we obtain - at least a-posteriori - a justification for the use of the TDLDA for simple-metal clusters.Comment: RevTeX, 15 pages, 5 figures in uufiles format, 1 figure avaible from [email protected]

Absorption and wavepackets in optically excited semiconductor superlattices driven by dc-ac fields

Within the one-dimensional tight-binding minibands and on-site Coloumbic interaction approximation, the absorption spectrum and coherent wavepacket time evolution in an optically excited semiconductor superlattice driven by dc-ac electric fields are investigated using the semiconductor Bloch equations. The dominating roles of the ratios of dc-Stark to external ac frequency, as well as ac-Stark to external ac frequency, is emphasized. If the former is an integer ${\cal N}$, then also ${\cal N}$ harmonics are present within one Stark frequency, while the fractional case leads to the formation of excitonic fractional ladders. The later ratio determines the size and profile of the wavepacket. In the absence of excitonic interaction it controls the maximum size wavepackets reach within one cycle, while the interaction produces a strong anisotropy and tends to palliate the dynamic wavepacket localization.Comment: 14 pages, 7 postscript figure

Evolving absorptive capacity: the mediating role of systematic knowledge management

Absorptive capacity is mediated through knowledge management capacity on innovation output and performance in technology-oriented firms. While prior research has focused on the direct effect of absorptive capacity on innovation, our model posits that absorptive capacity is more efficient in promoting firms’ innovation provided that it is supported by systematic knowledge management practices. We tested this model that included all four components of absorptive capacity using a sample of 127 manufacturing and technology firms in Croatia. Structural equation modelling procedures were used to test hypotheses. Our findings confirm the significance of the relationship between absorptive capacity and knowledge management within firms. Further, we found that firms with higher acquisition and transformation dimensions of absorptive capacity can enhance and replenish their knowledge management practices, which in return results in higher innovation output. These findings extend previous research by explaining the sometimes contradictory findings concerning knowledge management practices, which firms may adopt to enhance their absorptive capacity

Diagrammatic Quantum Monte Carlo for Two-Body Problem: Exciton

We present a novel method for precise numerical solution of the irreducible two-body problem and apply it to excitons in solids. The approach is based on the Monte Carlo simulation of the two-body Green function specified by Feynman's diagrammatic expansion. Our method does not rely on the specific form of the electron and hole dispersion laws and is valid for any attractive electron-hole potential. We establish limits of validity of the Wannier (large radius) and Frenkel (small radius) approximations, present accurate data for the intermediate radius excitons, and give evidence for the charge transfer nature of the monopolar exciton in mixed valence materials.Comment: 4 pages, 5 figure