Bifurcation effects on the plasma edge of tokamaks with ergodic limiter.

In the present paper, we solve a twist symplectic map for the action of an ergodic magnetic limiter in a large aspect-ratio tokamak. In this model, we study the bifurcation scenarios that occur in the remnants regular islands that co-exist with chaotic magnetic surfaces. The onset of atypical local bifurcations created by secondary shearless tori are identified through numerical profiles of internal rotation number and we observe that their rupture can reduce the usual magnetic field line escape at the tokamak plasma edge.

Each one teaches one: characterizing active forms of proteins by single molecule force spectroscopy

This Ph.D. candidate thesis collects the research work I conducted under the supervision of Prof.Bruno Samor´ı in 2005,2006 and 2007. Some parts of this work included in the Part III have been begun by myself during my undergraduate thesis in the same laboratory and then completed during the initial part of my Ph.D. thesis: the whole results have been included for the sake of understanding and completeness. During my graduate studies I worked on two very different protein systems. The theorical trait d’union between these studies, at the biological level, is the acknowledgement that protein biophysical and structural studies must, in many cases, take into account the dynamical states of protein conformational equilibria and of local physico-chemical conditions where the system studied actually performs its function. This is introducted in the introductory part in Chapter 2. Two different examples of this are presented: the structural significance deriving from the action of mechanical forces in vivo (Chapter 3) and the complexity of conformational equilibria in intrinsically unstructured proteins and amyloid formation (Chapter 4). My experimental work investigated both these examples by using in both cases the single molecule force spectroscopy technique (described in Chapter 5 and Chapter 6). The work conducted on angiostatin focused on the characterization of the relationships between the mechanochemical properties and the mechanism of action of the angiostatin protein, and most importantly their intertwining with the further layer of complexity due to disulfide redox equilibria (Part III). These studies were accompanied concurrently by the elaboration of a theorical model for a novel signalling pathway that may be relevant in the extracellular space, detailed in Chapter 7.2. The work conducted on -synuclein (Part IV) instead brought a whole new twist to the single molecule force spectroscopy methodology, applying it as a structural technique to elucidate the conformational equilibria present in intrinsically unstructured proteins. These equilibria are of utmost interest from a biophysical point of view, but most importantly because of their direct relationship with amyloid aggregation and, consequently, the aetiology of relevant pathologies like Parkinson’s disease. The work characterized, for the first time, conformational equilibria in an intrinsically unstructured protein at the single molecule level and, again for the first time, identified a monomeric folded conformation that is correlated with conditions leading to -synuclein and, ultimately, Parkinson’s disease. Also, during the research work, I found myself in the need of a generalpurpose data analysis application for single molecule force spectroscopy data analysis that could solve some common logistic and data analysis problems that are common in this technique. I developed an application that addresses some of these problems, herein presented (Part V), and that aims to be publicly released soon.

Structural and elastic properties of DNA and chromatin

We investigate a chain consisting of two coupled worm-like chains withconstant distance between the strands. The effects due todouble-strandedness of the chain are studied. In a previous analyticalstudy of this system an intrinsic twist-stretch coupling and atendency of kinking is predicted. Even though a local twist structureis observed the predicted features are not recovered. A new model for DNA at the base-pair level is presented. Thebase-pairs are treated as flat rigid ellipsoids and thesugar-phosphate backbones are represented as stiff harmonic springs.The base-pair stacking interaction is modeled by a variant of theGay-Berne potential. It is shown by systematic coarse-graininghow the elastic constants of a worm-like chain are related to thelocal fluctuations of the base-pair step parameters. Even though a lotof microscopic details of the base-pair geometry is neglected themodel can be optimized to obtain a B-DNA conformation as ground stateand reasonable elastic properties. Moreover the model allows tosimulate much larger length scales than it is possible with atomisticsimulations due to the simplification of the force-field and inparticular due to the possibility of non-local Monte-Carlo moves. Asa first application the behavior under stretching is investigated. Inagreement with micromanipulation experiments on single DNA moleculesone observes a force-plateau in the force-extension curvescorresponding to an overstretching transition from B-DNA to aso-called S-DNA state. The model suggests a structure for S-DNA withhighly inclined base-pairs in order to enable at least partialbase-pair stacking. Finally a simple model for chromatin is introduced to study itsstructural and elastic properties. The underlying geometry of themodeled fiber is based on a crossed-linker model. The chromatosomesare treated as disk-like objects. Excluded volume and short rangenucleosomal interaction are taken into account by a variant of theGay-Berne potential. It is found that the bending rigidity and thestretching modulus of the fiber increase with more compact fibers. Fora reasonable parameterization of the fiber for physiologicalconditions and sufficiently high attraction between the nucleosomes aforce-extension curve is found similar to stretching experiments onsingle chromatin fibers. For very small stretching forces a kinkedfiber forming a loop is observed. If larger forces are applied theloop formation is stretched out and a decondensation of the fibertakes place.

Classificazione delle galassie: Caratteristiche morfologiche, fotometriche e cinematiche

In questa tesi si cercherà di passare in rassegna le caratteristiche fondamentali dei principali tipi galattici. Dopo un breve ex-cursus storico, si passerà al primo capitolo, nel quale si osserverà come le prime catalogazioni si siano basate sulla morfologia di questi oggetti. Si cercherà quindi di mostrare come molte grandezze fisiche siano strettamente legate all’aspetto che questi oggetti celesti mostrano. Nel secondo capitolo verranno trattate le principali caratteristiche fotometriche: si mostreranno isofote di galassie ellittiche, si accennerà al fenomeno dell’isophotal twist, si introdurranno diversi profili di brillanza, sia per galassie ellittiche che per galassie a spirale. Nel terzo ed ultimo capitolo si tratteranno le caratteristiche cinematiche dei due principali tipi galattici. Riusciremo, a questo punto, a trovare una relazione tra l’isophotal twist e le caratteristiche cinematiche delle galassie ellittiche. Dopo aver introdotto il concetto di dispersione di velocità, sarà possibile introdurre brevemente il piano fondamentale, importante relazione tra le caratteristiche principali delle galassie ellittiche. Si discuterà infine della particolare curva di rotazione delle galassie a spirale, la cui velocità si mantiene costante ben oltre i limiti di quanto si possa stimare osservando la materia visibile; questa peculiarità delle galassie a spirale ha portato direttamente all’idea che possa esserci della materia oscura in grado di esercitare una attrazione gravitazionale sulla materia ordinaria.

Simulations of amphiphilic peptides at the air-water interface

Amphiphile Peptide, Pro-Glu-(Phe-Glu)n-Pro, Pro-Asp-(Phe-Asp)n-Pro, und Phe-Glu-(Phe-Glu)n-Phe, können so aus n alternierenden Sequenzen von hydrophoben und hydrophilen Aminosäuren konstruiert werden, dass sie sich in Monolagen an der Luft-Wasser Grenzfläche anordnen. In biologischen Systemen können Strukturen an der organisch-wässrigen Grenzfläche als Matrix für die Kristallisation von Hydroxyapatit dienen, ein Vorgang der für die Behandlung von Osteoporose verwendet werden kann. In der vorliegenden Arbeit wurden Computersimulationenrneingesetzt, um die Strukturen und die zugrunde liegenden Wechselwirkungen welche die Aggregation der Peptide auf mikroskopischer Ebene steuern, zu untersuchen. Atomistische Molekulardynamik-Simulationen von einzelnen Peptidsträngen zeigen, dass sie sich leicht an der Luft-Wasser Grenzfläche anordnen und die Fähigkeit haben, sich in β-Schleifen zu falten, selbst für relativ kurze Peptidlängen (n = 2). Seltene Ereignisse wie diese (i.e. Konformationsänderungen) erfordern den Einsatz fortgeschrittener Sampling-Techniken. Hier wurde “Replica Exchange” Molekulardynamik verwendet um den Einfluss der Peptidsequenzen zu untersuchen. Die Simulationsergebnisse zeigten, dass Peptide mit kürzeren azidischen Seitenketten (Asp vs. Glu) gestrecktere Konformationen aufwiesen als die mit längeren Seitenketten, die in der Lage waren die Prolin-Termini zu erreichen. Darüber hinaus zeigte sich, dass die Prolin-Termini (Pro vs. Phe) notwendig sind, um eine 2D-Ordnung innerhalb derrnAggregate zu erhalten. Das Peptid Pro-Asp-(Phe-Asp)n-Pro, das beide dieser Eigenschaften enthält, zeigt das geordnetste Verhalten, eine geringe Verdrehung der Hauptkette, und ist in der Lage die gebildeten Aggregate durch Wasserstoffbrücken zwischen den sauren Seitenketten zu stabilisieren. Somit ist dieses Peptid am besten zur Aggregation geeignet. Dies wurde auch durch die Beurteilung der Stabilität von experimentnah-aufgesetzten Peptidaggregaten, sowie der Neigung einzelner Peptide zur Selbstorganisation von anfänglich ungeordneten Konfigurationen unterstützt. Da atomistische Simulationen nur auf kleine Systemgrößen und relativ kurze Zeitskalen begrenzt sind, wird ein vergröbertes Modell entwickelt damit die Selbstorganisation auf einem größeren Maßstab studiert werden kann. Da die Selbstorganisation an der Grenzfläche vonrnInteresse ist, wurden existierenden Vergröberungsmethoden erweitert, um nicht-gebundene Potentiale für inhomogene Systeme zu bestimmen. Die entwickelte Methode ist analog zur iterativen Boltzmann Inversion, bildet aber das Update für das Interaktionspotential basierend auf der radialen Verteilungsfunktion in einer Slab-Geometrie und den Breiten des Slabs und der Grenzfläche. Somit kann ein Kompromiss zwischen der lokalen Flüssigketsstruktur und den thermodynamischen Eigenschaften der Grenzfläche erreicht werden. Die neue Methode wurde für einen Wasser- und einen Methanol-Slab im Vakuum demonstriert, sowie für ein einzelnes Benzolmolekül an der Vakuum-Wasser Grenzfläche, eine Anwendung die von besonderer Bedeutung in der Biologie ist, in der oft das thermodynamische/Grenzflächenpolymerisations-Verhalten zusätzlich der strukturellen Eigenschaften des Systems erhalten werden müssen. Daraufrnbasierend wurde ein vergröbertes Modell über einen Fragment-Ansatz parametrisiert und die Affinität des Peptids zur Vakuum-Wasser Grenzfläche getestet. Obwohl die einzelnen Fragmente sowohl die Struktur als auch die Wahrscheinlichkeitsverteilungen an der Grenzfläche reproduzierten, diffundierte das Peptid als Ganzes von der Grenzfläche weg. Jedoch führte eine Reparametrisierung der nicht-gebundenen Wechselwirkungen für eines der Fragmente der Hauptkette in einem Trimer dazu, dass das Peptid an der Grenzfläche blieb. Dies deutet darauf hin, dass die Kettenkonnektivität eine wichtige Rolle im Verhalten des Petpids an der Grenzfläche spielt.

5a-Butyl-1,3,8,10-tetra-chloro-7,13-bis-(4-nitro-benzo-yl)-5a,6a,12a,12b-tetra-hydro-7H,13H-thieno[2,3-b:4,5-b']bis-(1,4-benzoxazine)

The title compound, C(34)H(24)Cl(4)N(4)O(8)S, is a linear penta-cyclic system formed of two substituted benzoxazinyl groups fused to 2-n-butyl-tetra-hydro-thio-phene. The oxazine ring, which is fused to the n-butyl-substituted side of the thio-phene ring, is in a boat conformation. The other fused oxazine ring and the tetra-hydro-thiene ring are each in an envelope conformation. The bridgehead C atom alpha to both the S and N atoms forms the flap of each envelope. This results in a twist of the penta-cyclic system such that the dihedral angle between the terminal dichloro-benzene rings is 82.92 (8)°. In the crystal, inversion-related mol-ecules form a weakly hydrogen-bonded dimer, with two C-H⋯O inter-actions between an H atom on the oxazine ring and an amide O atom. Additionally, C-H⋯O inter-actions occur between an H atom on a screw-related nitro-benzene ring and an O atom on the nitro-benzene ring of one mol-ecule. One of the Cl atoms and the butyl group are disordered over two sets of sites with occupancy ratios of 0.94 (2):0.06 (2) and 0.624 (4):0.376 (4), respectively.

Kalman Filter approaches on crane swing

The purpose of this study is to explore a Kalman Filter approach to estimating swing of crane-suspended loads. Measuring real-time swing is needed to implement swing damping control strategies where crane joints are used to remove energy from a swinging load. The typical solution to measuring swing uses an inertial sensor attached to the hook block. Measured hook block twist is used to resolve the other two sensed body rates into tangential and radial swing. Uncertainty in the twist measurement leads to inaccurate tangential and radial swing calculations and ineffective swing damping. A typical mitigation approach is to bandpass the inertial sensor readings to remove low frequency drift and high frequency noise. The center frequency of the bandpass filter is usually designed to track the load length and the pass band width set to trade off performance with damping loop gain. The Kalman Filter approach developed here allows all swing motions (radial, tangential and twist) to be measured without the use of a bandpass filter. This provides an alternate solution for swing damping control implementation. After developing a Kalman Filter solution for a two-dimensional swing scenario, the three-dimensional system is considered where simplifying assumptions, suggested by the two-dimensional study, are exploited. One of the interesting aspects of the three-dimensional study is the hook block twist model. Unlike the mass-independence of a pendulum's natural frequency, the twist natural frequency depends both on the pendulum length and the load’s mass distribution. The linear Kalman Filter is applied to experimental data demonstrating the ability to extract the individual swing components for complex motions. It should be noted that the three-dimensional simplifying assumptions preclude the ability to measure two "secondary" hook block rotations. The ability to segregate these motions from the primary swing degrees of freedom was illustrated in the two-dimensional study and could be included into the three-dimensional solution if they were found to be important for a particular application.

COMPUTATIONAL ANALYSIS OF THE AEROELASTIC DYNAMICS OF A WIND TURBINE BLADE WITH VARIABLE-SPEED STALL CONTROL

The accuracy of simulating the aerodynamics and structural properties of the blades is crucial in the wind-turbine technology. Hence the models used to implement these features need to be very precise and their level of detailing needs to be high. With the variety of blade designs being developed the models should be versatile enough to adapt to the changes required by every design. We are going to implement a combination of numerical models which are associated with the structural and the aerodynamic part of the simulation using the computational power of a parallel HPC cluster. The structural part models the heterogeneous internal structure of the beam based on a novel implementation of the Generalized Timoshenko Beam Model Technique.. Using this technique the 3-D structure of the blade is reduced into a 1-D beam which is asymptotically equivalent. This reduces the computational cost of the model without compromising its accuracy. This structural model interacts with the Flow model which is a modified version of the Blade Element Momentum Theory. The modified version of the BEM accounts for the large deflections of the blade and also considers the pre-defined structure of the blade. The coning, sweeping of the blade, tilt of the nacelle and the twist of the sections along the blade length are all computed by the model which aren’t considered in the classical BEM theory. Each of these two models provides feedback to the other and the interactive computations lead to more accurate outputs. We successfully implemented the computational models to analyze and simulate the structural and aerodynamic aspects of the blades. The interactive nature of these models and their ability to recompute data using the feedback from each other makes this code more efficient than the commercial codes available. In this thesis we start off with the verification of these models by testing it on the well-known benchmark blade for the NREL-5MW Reference Wind Turbine, an alternative fixed-speed stall-controlled blade design proposed by Delft University, and a novel alternative design that we proposed for a variable-speed stall-controlled turbine, which offers the potential for more uniform power control and improved annual energy production.. To optimize the power output of the stall-controlled blade we modify the existing designs and study their behavior using the aforementioned aero elastic model.

Iowa State Daily (March 30, 2012)

ContentsPutting a face to the causeAg pavilion receives $2 million donationSterle receives professorship in animal scienceSpangler wrestles with concussionsBleak future could await AmericaSustainability finds a new twist with feminism

Iowa State Daily (January 25, 2012)

ContentsPresident: U.S. is 'built to last'Silent voices no moreCity makes investment in remodel of areaHill: policies must be 'balanced'Wrestlers struggle through season with concussionsPlacement testing would benefit allGrilled cheese recipes offer grown-up twist

Quantification of Popliteal Artery Deformation During Leg Flexion in Subjects With Peripheral Artery Disease: A Pilot Study

Purpose: To quantify the in vivo deformations of the popliteal artery during leg flexion in subjects with clinically relevant peripheral artery disease (PAD). Methods: Five patients (4 men; mean age 69 years, range 56–79) with varying calcification levels of the popliteal artery undergoing endovascular revascularization underwent 3-dimensional (3D) rotational angiography. Image acquisition was performed with the leg straight and with a flexion of 70°/20° in the knee/hip joints. The arterial centerline and the corresponding branches in both positions were segmented to create 3D reconstructions of the arterial trees. Axial deformation, twisting, and curvatures were quantified. Furthermore, the relationships between the calcification levels and the deformations were investigated. Results: An average shortening of 5.9%±2.5% and twist rate of 3.8±2.2°/cm in the popliteal artery were observed. Maximal curvatures in the straight and flexed positions were 0.12±0.04 cm−1 and 0.24±0.09 cm−1, respectively. As the severity of calcification increased, the maximal curvature in the straight position increased from 0.08 to 0.17 cm−1, while an increase from 0.17 to 0.39 cm−1 was observed for the flexed position. Axial elongations and arterial twisting were not affected by the calcification levels. Conclusion: The popliteal artery of patients with symptomatic PAD is exposed to significant deformations during flexion of the knee joint. The severity of calcification directly affects curvature, but not arterial length or twisting angles. This pilot study also showed the ability of rotational angiography to quantify the 3D deformations of the popliteal artery in patients with various levels of calcification.

How fluids bend: the elastic expansion for higher-dimensional black holes

Hydrodynamics can be consistently formulated on surfaces of arbitrary co-dimension in a background space-time, providing the effective theory describing long-wavelength perturbations of black branes. When the co-dimension is non-zero, the system acquires fluid-elastic properties and constitutes what is called a fluid brane. Applying an effective action approach, the most general form of the free energy quadratic in the extrinsic curvature and extrinsic twist potential of stationary fluid brane configurations is constructed to second order in a derivative expansion. This construction generalizes the Helfrich-Canham bending energy for fluid membranes studied in theoretical biology to the case in which the fluid is rotating. It is found that stationary fluid brane configurations are characterized by a set of 3 elastic response coefficients, 3 hydrodynamic response coefficients and 1 spin response coefficient for co-dimension greater than one. Moreover, the elastic degrees of freedom present in the system are coupled to the hydrodynamic degrees of freedom. For co-dimension-1 surfaces we find a 8 independent parameter family of stationary fluid branes. It is further shown that elastic and spin corrections to (non)-extremal brane effective actions can be accounted for by a multipole expansion of the stress-energy tensor, therefore establishing a relation between the different formalisms of Carter, Capovilla-Guven and Vasilic-Vojinovic and between gravity and the effective description of stationary fluid branes. Finally, it is shown that the Young modulus found in the literature for black branes falls into the class predicted by this approach - a relation which is then used to make a proposal for the second order effective action of stationary blackfolds and to find the corrected horizon angular velocity of thin black rings.

ELUCIDATING THE ROLE OF CD44 EXPRESSION ON MESENCHYMAL STEM CELLS WITHIN THE TUMOR MICROENVIRONMENT

The tumor microenvironment is comprised of a vast array of heterogeneous cells including both normal and neoplastic cells. The tumor stroma recruitment process has been exploited for an effective gene delivery technique using bone marrow derived MSC. Targeted migration of the MSC toward the tumor microenvironment, while successful, is not yet fully understood. This study was designed to assess the role of CD44 in the migration of MSC toward the tumor microenvironment and to determine the implications of CD44-deficient MSC within the tumor stroma. Inhibition of MSC migration was evaluated through a variety of methods in vitro and in vivo including CD44 receptor knockdown, CD44 antagonists, CD44 neutralizing antibodies and small molecule inhibitor of matrix metalloproteinases. Blocking CD44 signaling through MMP inhibition was characterized by lack of intracellular domain cleavage and lead to the decrease in Twist gene expression. A functional relationship between CD44 and Twist expression was confirmed by chromatin immunoprecipitation. Next, a series of murine tumor models were used to examine the role of CD44 deficient stroma within the tumor microenvironment. Labeled transgenic CD44 knockout (KO) MSC or wild type (WT) C57/B6 MSC were used to analyze the stromal incorporation within murine breast carcinomas (EO771 and 4T1). Subsequent tumors were analyzed for vessel formation (CD31), and the presence of tumor associated fibroblast (TAF) markers, α-smooth muscle actin (α-SMA), fibroblast activation protein (FAP), and fibroblast specific protein (FSP). The tumors with CD44KO MSC cells had less vessel formation than the tumors with WT MSC. The lack of fibroblastic TAF population as defined by FAP/FSP expression by the CD44KO MSC admixed tumors suggest that the bone marrow derived population of MSC were unable to contribute to the fibroblastic stromal population. Subsequently, a bone marrow transplantation experiment confirmed the endogenous migratory deficiencies of the CD44KO bone marrow derived stromal cells toward the tumor microenvironment in vivo. WT mice with CD44KO bone marrow had less CD44KOderived tumor stroma compared to mice with WT bone marrow. These results indicate that CD44 is crucial to stromal cell migration and incorporation to the tumor microenvironment as TAF.

The Role of IL-6 in Adenosine-Mediated Pulmonary Fibrosis

Adenosine is a purinergic signaling molecule that regulates various aspects of inflammation and has been implicated in the pathogenesis of chronic lung diseases. Previous studies have demonstrated that adenosine up-regulates IL-6 production through the engagement of the A2B adenosine receptor in various cell types, including alveolar macrophages. IL-6 is elevated in mouse models and humans with chronic lung disease, suggesting a potential role in disease progression. Furthermore, chronic elevation of adenosine in the lungs of adenosine deaminase deficient (Ada-/-) mice leads to the development of pulmonary inflammation, alveolar destruction, and fibrosis, in conjunction with IL-6 elevation. Thus, it was hypothesized that IL-6 contributes to pulmonary inflammation and fibrosis in this model. To test this hypothesis, Ada/IL-6 double knockout mice (Ada/IL-6-/-) were generated to assess the consequences of genetically removing IL-6 on adenosine-dependent pulmonary injury. Ada/IL-6-/- mice exhibited a significant reduction in inflammation, alveolar destruction, and pulmonary fibrosis. Next, Ada-/- mice were treated systematically with IL-6 neutralizing antibodies to test the efficacy of blocking IL-6 on chronic lung disease. These treatments were associated with decreased pulmonary inflammation, alveolar destruction, and fibrosis. To determine the role of IL-6 in a second model of pulmonary fibrosis, wild type mice and IL-6-/- mice were subjected to intraperitoneal injections of bleomycin twice a week for four weeks. Results demonstrated that IL-6-/- mice developed reduced pulmonary fibrosis. To examine a therapeutic approach in this model, wild type mice exposed to bleomycin were treated with IL-6 neutralizing antibodies. Similar results were observed as with Ada-/- mice, namely diminished pulmonary inflammation and fibrosis. In both models, elevations in IL-6 were associated with increased phosphorylated STAT-3 in the nuclei of numerous cell types in the airways, including type II alveolar epithelial cells (AEC). Genetic removal and neutralization of IL-6 in both models was associated with decreased STAT-3 activation in type II AEC. The mechanism of activation in these cells that lack the membrane bound IL-6Ra suggests IL-6 trans-signaling may play a role in regulating fibrosis. Characterization of this mechanism demonstrated that the soluble IL-6Ra (sIL-6Ra) is upregulated in both models during chronic conditions. In vitro studies in MLE-12 alveolar epithelial cells confirmed that IL-6, in combination with the sIL-6Ra, activates STAT-3 and TWIST in association with enhancement of epithelial-to-mesenchymal transition, which can contribute to fibrosis. Similarly, patients with idiopathic pulmonary fibrosis demonstrated a similar pattern of increased IL-6 expression, STAT-3 activation, and sIL-6Ra increases. These findings demonstrate that adenosine-dependent elevations in IL-6 contribute to the development and progression of pulmonary inflammation and fibrosis. The implications from these studies are that adenosine and/or IL-6 neutralizing agents represent novel therapeutic targets for the treatment of pulmonary disorders where fibrosis is a detrimental component.

Hybridization and adaptive radiation

Whether interspecific hybridization is important as a mechanism that generates biological diversity is a matter of controversy. Whereas some authors focus on the potential of hybridization as a source of genetic variation, functional novelty and new species, others argue against any important role, because reduced fitness would typically render hybrids an evolutionary dead end. By drawing on recent developments in the genetics and ecology of hybridization and on principles of ecological speciation theory, I develop a concept that reconciles these views and adds a new twist to this debate. Because hybridization is common when populations invade new environments and potentially elevates rates of response to selection, it predisposes colonizing populations to rapid adaptive diversification under disruptive or divergent selection. I discuss predictions and suggest tests of this hybrid swarm theory of adaptive radiation and review published molecular phylogenies of adaptive radiations in light of the theory. Some of the confusion about the role of hybridization in evolutionary diversification stems from the contradiction between a perceived necessity for cessation of gene flow to enable adaptive population differentiation on the one hand [1], and the potential of hybridization for generating adaptive variation, functional novelty and new species 2, 3 and 4 on the other. Much progress in the genetics 5, 6, 7, 8 and 9 and ecology of hybridization 9, 10 and 11, and in our understanding of the role of ecology in speciation (see Glossary) 12, 13 and 14 make a re-evaluation timely. Whereas botanists traditionally stressed the diversity-generating potential of hybridization 2, 3 and 14, zoologists traditionally saw it as a process that limits diversification [1] and refer to it mainly in the contexts of hybrid zones (Box 1) and reinforcement of reproductive isolation [15]. Judging by the wide distribution of allopolyploidy among plants, many plant species might be of direct hybrid origin or descended from a hybrid species in the recent past [16]. The ability to reproduce asexually might explain why allopolyploid hybrid species are more common in plants than in animals. Allopolyploidy arises when meiotic mismatch of parental chromosomes or karyotypes causes hybrid sterility. Mitotic error, duplicating the karyotype, can restore an asexually maintained hybrid line to fertility. Although bisexual allopolyploid hybrid species are not uncommon in fish [17] and frogs [18], the difficulty with which allopolyploid animals reproduce, typically requiring gynogenesis[19], makes establishment and survival of allopolyploid animal species difficult.