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1Latest Papers from Table of Contents or Articles in PressE. Ruark ; K. Snape ; P. Humburg ; C. Loveday ; I. Bajrami ; R. Brough ; D. N. Rodrigues ; A. Renwick ; S. Seal ; E. Ramsay ; V. Duarte Sdel ; M. A. Rivas ; M. Warren-Perry ; A. Zachariou ; A. Campion-Flora ; S. Hanks ; A. Murray ; N. Ansari Pour ; J. Douglas ; L. Gregory ; A. Rimmer ; N. M. Walker ; T. P. Yang ; J. W. Adlard ; J. Barwell ; J. Berg ; A. F. Brady ; C. Brewer ; G. Brice ; C. Chapman ; J. Cook ; R. Davidson ; A. Donaldson ; F. Douglas ; D. Eccles ; D. G. Evans ; L. Greenhalgh ; A. Henderson ; L. Izatt ; A. Kumar ; F. Lalloo ; Z. Miedzybrodzka ; P. J. Morrison ; J. Paterson ; M. Porteous ; M. T. Rogers ; S. Shanley ; L. Walker ; M. Gore ; R. Houlston ; M. A. Brown ; M. J. Caufield ; P. Deloukas ; M. I. McCarthy ; J. A. Todd ; C. Turnbull ; J. S. Reis-Filho ; A. Ashworth ; A. C. Antoniou ; C. J. Lord ; P. Donnelly ; N. Rahman
Nature Publishing Group (NPG)
Published 2012Staff ViewPublication Date: 2012-12-18Publisher: Nature Publishing Group (NPG)Print ISSN: 0028-0836Electronic ISSN: 1476-4687Topics: BiologyChemistry and PharmacologyMedicineNatural Sciences in GeneralPhysicsKeywords: Alleles ; Breast Neoplasms/*genetics ; Cluster Analysis ; Exons ; Female ; Genetic Predisposition to Disease/*genetics ; Humans ; Isoenzymes/genetics ; Lymphocytes/metabolism ; *Mosaicism ; *Mutation ; Ovarian Neoplasms/*genetics ; Phosphoprotein Phosphatases/*genetics ; Sequence Analysis, DNA ; Tumor Suppressor Protein p53/metabolismPublished by: -
2Latest Papers from Table of Contents or Articles in PressStaff View
Publication Date: 2018-05-26Publisher: BMJ Publishing GroupPrint ISSN: 0022-2593Electronic ISSN: 1468-6244Topics: MedicineKeywords: Open access, Molecular geneticsPublished by: -
3Articles: DFG German National LicensesStaff View
ISSN: 1089-7674Source: AIP Digital ArchiveTopics: PhysicsNotes: In Part I of this work [Phys. Plasmas 2, 1926 (1995)], the behavior of linearly stable, integrable systems of waves in a simple plasma model was described using a Hamiltonian formulation. Explosive instability arose from nonlinear coupling between positive and negative energy modes, with well-defined threshold amplitudes depending on the physical parameters. In this concluding paper, the nonintegrable case is treated numerically. The time evolution is modeled with an explicit symplectic integrator derived using Lie algebraic methods. For amplitudes large enough to support two-wave decay interactions, strongly chaotic motion destroys the separatrix bounding the stable region in phase space. Diffusive growth then leads to explosive instability, effectively reducing the threshold amplitude. For initial amplitudes too small to drive decay instability, slow growth via Arnold diffusion might still lead to instability; however, this was not observed in numerical experiments. The diffusion rate is probably underestimated in this simple model. © 1995 American Institute of Physics.Type of Medium: Electronic ResourceURL: -
4Articles: DFG German National LicensesStaff View
ISSN: 1089-7674Source: AIP Digital ArchiveTopics: PhysicsNotes: The energy density expression Best presents is not (when integrated) equal to the energy of a linear perturbation in Vlasov theory. The exact expression is given by either Eq.(42) or Eq.(48) of Ref.2. The authors comment on this and other discrepancies. (AIP)Type of Medium: Electronic ResourceURL: -
5Articles: DFG German National LicensesStaff View
ISSN: 1089-7674Source: AIP Digital ArchiveTopics: PhysicsNotes: Magnetic field lines typically do not behave as described in the symmetrical situations treated in conventional physics textbooks. Instead, they behave in a chaotic manner; in fact, magnetic field lines are trajectories of Hamiltonian systems. Consequently the quest for fusion energy has interwoven, for 50 years, the study of magnetic field configurations and Hamiltonian systems theory. The manner in which invariant tori breakup in symplectic twist maps, maps that embody one and a half degree-of-freedom Hamiltonian systems in general and describe magnetic field lines in tokamaks in particular, will be reviewed, including symmetry methods for finding periodic orbits and Greene's residue criterion. In nontwist maps, which describe, e.g., reverse shear tokamaks and zonal flows in geophysical fluid dynamics, a new theory is required for describing tori breakup. The new theory is discussed and comments about renormalization are made. © 2000 American Institute of Physics.Type of Medium: Electronic ResourceURL: -
6Articles: DFG German National LicensesStaff View
ISSN: 1089-7674Source: AIP Digital ArchiveTopics: PhysicsNotes: Conventional linear stability analyses may fail for fluid systems with an indefinite free-energy functional. When such a system is linearly stable, it is said to possess negative energy modes. Instability may then occur either via dissipation of the negative energy modes, or nonlinearly via resonant wave–wave coupling, leading to explosive growth. In the dissipationless case, it is conjectured that intrinsic chaotic behavior may allow initially nonresonant systems to reach resonance by diffusion in phase space. In this and a companion paper (submitted to Phys. Plasmas), this phenomenon is demonstrated for a simple equilibrium involving cold counterstreaming ions. The system is described in the fluid approximation by a Hamiltonian functional and associated noncanonical Poisson bracket. By Fourier decomposition and appropriate coordinate transformations, the Hamiltonian for the perturbed energy is expressed in action-angle form. The normal modes correspond to Doppler-shifted ion-acoustic waves of positive and negative energy. Nonlinear coupling leads to decay instability via two-wave interactions, and to either decay or explosive instability via three-wave interactions. These instabilities are described for various integrable systems of waves interacting via single nonlinear terms. This discussion provides the foundation for the treatment of nonintegrable systems in the companion paper. © 1995 American Institute of Physics.Type of Medium: Electronic ResourceURL: -
7Articles: DFG German National LicensesStaff View
ISSN: 1089-7674Source: AIP Digital ArchiveTopics: PhysicsNotes: The energy content of electrostatic perturbations about homogeneous equilibria is discussed. The calculation leading to the well-known dielectric (or as it is sometimes called, the wave) energy is revisited and interpreted in light of Vlasov theory. It is argued that this quantity is deficient because resonant particles are not correctly handled. A linear integral transform is presented that solves the linear Vlasov–Poisson equation. This solution, together with the Kruskal–Oberman energy [Phys. Fluids 1, 275 (1958)], is used to obtain an energy expression in terms of the electric field [Phys. Fluids B 4, 3038 (1992)]. It is described how the integral transform amounts to a change to normal coordinates in an infinite-dimensional Hamiltonian system.Type of Medium: Electronic ResourceURL: -
8Articles: DFG German National LicensesSu, X. N. ; Horton, W. ; Morrison, P. J.
New York, NY : American Institute of Physics (AIP)
Published 1992Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: Nonlinear coherent structures governed by the coupled drift wave–ion-acoustic mode equations in nonuniform plasmas with sheared magnetic fields are studied analytically and numerically. A solitary vortex equation that includes the effects of density and temperature gradients and magnetic shear is derived and analyzed. The analytic and numerical studies show that for a plasma in a sheared magnetic field, even without the temperature and drift velocity gradients, solitary vortex solutions are possible; however, these solutions are not exponentially localized due to the presence of a nonstructurally stable perturbative tail that connects to the core of the vortex. The new coherent vortex structures are dipolelike in their symmetry, but are not the modons of Larichev and Reznik. In the presence of a small temperature or drift velocity gradient, the new shear-induced dipole cannot survive and will separate into monopoles, like the case of the modon in a sheared drift velocity as studied in Su et al. [Phys. Fluids B 3, 921 (1991)]. The solitary solutions are found from the nonlinear eigenvalue problem for the effective potential in a quasi-one-dimensional approximation. The numerical simulations are performed in two dimensions with the coupled vorticity and parallel mass flow equations.Type of Medium: Electronic ResourceURL: -
9Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: The interaction of two near-marginal tearing modes in the presence of shear flow is studied. To find the time asymptotic states, the resistive magnetohydrodynamic (MHD) equations are reduced to four amplitude equations, using center manifold reduction. These amplitude equations are subject to the constraints due to the symmetries of the physical problem. For the case without flow, the model that is adopted has translation and reflection symmetries. Presence of flow breaks the reflection symmetry, while the translation symmetry is preserved, and hence flow allows the coefficients of the amplitude equations to be complex. Bifurcation analysis is employed to find various possible time asymptotic states. In particular, the oscillating magnetic island states discovered numerically by Persson and Bondeson [Phys. Fluids 29, 2997 (1986)] are discussed. It is found that the flow-introduced parameters (imaginary part of the coefficients) play an important role in driving these oscillating islands.Type of Medium: Electronic ResourceURL: -
10Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: A previously derived expression [Phys. Rev. A 40, 3898 (1989)] for the energy of arbitrary perturbations about arbitrary Vlasov–Maxwell equilibria is transformed into a very compact form. The new form is also obtained by a canonical transformation method for solving Vlasov's equation, which is based on Lie group theory. This method is simpler than the one used before and provides better physical insight. Finally, a procedure is presented for determining the existence of negative-energy modes. In this context the question of why there is an accessibility constraint for the particles, but not for the fields, is discussed.Type of Medium: Electronic ResourceURL: -
11Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: The effect of equilibrium velocity shear on the resistive tearing instability has been systematically studied, using the boundary layer approach. Both the "constant-ψ'' tearing mode, which has a growth rate that scales as S−3/5, and the "nonconstant-ψ'' tearing mode [Δ'(αS)−1/3(very-much-greater-than)1], which has a growth rate that scales as S−1/3, are analyzed in the presence of flow. Here S is the usual ratio of the resistive diffusion and Alfvén times. It is found that the shear flow has a significant influence on both the external ideal region and the internal resistive region. In the external ideal region, the shear flow can dramatically change the value of the matching quantity Δ'. In the internal resistive region, the tearing mode is sensitive to the flow shear at the magnetic null plane: G'(0). When G'(0) is comparable to the magnetic field shear, F'(0), the scalings of the constant-ψ tearing mode are changed and the Δ'〉0 instability criterion is removed, provided G'(0)G‘(0)−F'(0)F‘(0)≠0. The scalings of the nonconstant-ψ tearing mode remain unchanged. When the flow shear is larger than the magnetic field shear at the magnetic null plane, both tearing modes are stabilized. Finally, the transition to ideal instability is discussed.Type of Medium: Electronic ResourceURL: -
12Articles: DFG German National LicensesKull, H. J. ; Berk, H. L. ; Morrison, P. J.
New York, NY : American Institute of Physics (AIP)
Published 1989Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: Wave energy flow conservation is demonstrated for Hermitian differential operators that arise in the Vlasov–Maxwell theory for propagation perpendicular to a magnetic field. The energy flow can be related to the bilinear concomitant, for a solution and its complex conjugate, by using the Lagrange identity of the operator. This bilinear form obeys a conservation law and is shown to describe the usual Wentzel–Kramers–Brillouin (WKB) energy flow for asymptotically homogeneous regions. The additivity and lack of uniqueness of the energy flow expression is discussed for a general superposition of waves with real and complex wave-numbers. Furthermore, a global energy conservation theorem is demonstrated for an inhomogeneity in one dimension and generalized reflection and transmission coefficients are thereby obtained.Type of Medium: Electronic ResourceURL: -
13Articles: DFG German National LicensesHastings, D. E. ; Hazeltine, R. D. ; Morrison, P. J.
[S.l.] : American Institute of Physics (AIP)
Published 1986Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: The ambipolar radial electric field in a nonaxisymmetric plasma can be described by a nonlinear diffusion equation. This equation is shown to possess solitary wave solutions. A model nonlinear diffusion equation with a cubic nonlinearity is studied. An explicit analytic step-like form for the solitary wave is found. It is shown that the solitary wave solutions are linearly stable against all but translational perturbations. Collisions of these solitary waves are studied and three possible final states are found: two diverging solitary waves, two stationary solitary waves, or two converging solitary waves leading to annihilation.Type of Medium: Electronic ResourceURL: -
14Articles: DFG German National Licensesdel-Castillo-Negrete, Diego ; Morrison, P. J.
New York, NY : American Institute of Physics (AIP)
Published 1993Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: Transport and mixing properties of Rossby waves in shear flow are studied using tools from Hamiltonian chaos theory. The destruction of barriers to transport is studied analytically, by using the resonance overlap criterion and the concept of separatrix reconnection, and numerically by using Poincaré sections. Attention is restricted to the case of symmetric velocity profiles with a single maximum; the Bickley jet with velocity profile sech2 is considered in detail. Motivated by linear stability analysis and experimental results, a simple Hamiltonian model is proposed to study transport by waves in these shear flows. Chaotic transport, both for the general case and for the sech2 profile, is investigated. The resonance overlap criterion and the concept of separatrix reconnection are used to obtain an estimate for the destruction of barriers to transport and the notion of banded chaos is introduced to characterize the transport that typically occurs in symmetric shear flows. Comparison between the analytical estimates for barrier destruction and the numerical results is given. The role of potential vorticity conservation in chaotic transport is discussed. An area preserving map, termed standard nontwist map, is obtained from the Hamiltonian model. It is shown that the map reproduces the transport properties and the separatrix reconnection observed in the Hamiltonian model. The conclusions reached are used to explain experimental results on transport and mixing by Rossby waves in rotating fluids.Type of Medium: Electronic ResourceURL: -
15Articles: DFG German National LicensesOfman, L. ; Morrison, P. J. ; Steinolfson, R. S.
New York, NY : American Institute of Physics (AIP)
Published 1993Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: The nonlinear evolution of the tearing mode instability with equilibrium shear flow is investigated via numerical solutions of the resistive magnetohydrodynamic (MHD) equations. The two-dimensional simulations are in slab geometry, are periodic in the x direction, and are initiated with solutions of the linearized MHD equations. The magnetic Reynolds number S was varied from 102 to 105, a parameter V that measures the strength of the flow in units of the average Alfvén speed was varied from 0 to 0.5, and the viscosity as measured by the Reynolds number Sν satisfied Sν≥103. When the shear flow is small (V≤0.3) the tearing mode saturates within one resistive time, while for larger flows the nonlinear saturation develops on a longer time scale. The two-dimensional spatial structure of both the flux function and the streamfunction distort in the direction of the equilibrium flow. The magnetic energy release decreases and the saturation time increases with V for both small and large resistivity. Shear flow decreases the saturated magnetic island width, and generates currents far from the tearing layer. The validity of the numerical solutions was tested by verifying that the total energy and the magnetic helicity are conserved. The results of the present study suggest that equilibrium shear flow may improve the confinment of tokamak plasma.Type of Medium: Electronic ResourceURL: -
16Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: Five action principles for the Vlasov–Poisson and Vlasov–Maxwell equations, which differ by the variables incorporated to describe the distribution of particles in phase space, are presented. Three action principles previously known for the Vlasov–Maxwell equations are altered so as to produce the Vlasov–Poisson equation upon variation with respect to only the particle variables, and one action principle previously known for the Vlasov–Poisson equation is altered to produce the Vlasov–Maxwell equations upon variations with respect to particle and field variables independently. Also, a new action principle for both systems, which is called the leaf action, is presented. This new action has the desirable features of using only a single generating function as the dynamical variable for describing the particle distribution, and manifestly preserving invariants of the system known as Casimir invariants. The relationships between the various actions are described, and it is shown that the leaf action is a link between actions written in terms of Lagrangian and Eulerian variables.Type of Medium: Electronic ResourceURL: -
17Articles: DFG German National LicensesPrahovic, M. G. ; Hazeltine, R. D. ; Morrison, P. J.
New York, NY : American Institute of Physics (AIP)
Published 1992Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: A method is presented for constructing exact solutions to a system of nonlinear plasma fluid equations that combines the physics of reduced magnetohydrodynamics and the electrostatic drift-wave description of the Charney–Hasegawa–Mima equation. The system has nonlinearities that take the form of Poisson brackets involving the fluid field variables. The method relies on modifying a class of simple equilibrium solutions, but no approximations are made. A distinguishing feature is that the original nonlinear problem is reduced to the solution of two linear partial differential equations, one fourth order and the other first order. The first-order equation has Hamiltonian characteristics and is easily integrated, supplying information about the propagation of solutions.Type of Medium: Electronic ResourceURL: -
18Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: Expressions for the energy content of one-dimensional electrostatic perturbations about homogeneous equilibria are revisited. The well-known dielectric energy, ED, is compared with the exact plasma free energy expression, δ2F, that is conserved by the Vlasov–Poisson system [Phys. Rev. A 40, 3898 (1989) and Phys. Fluids B 2, 1105 (1990)]. The former is an expression in terms of the perturbed electric field amplitude, while the latter is determined by a generating function, which describes perturbations of the distribution function that respect the important constraint of dynamical accessibility of the system. Thus the comparison requires solving the Vlasov equation for such a perturbation of the distribution function in terms of the electric field. This is done for neutral modes of oscillation that occur for equilibria with stationary inflection points, and it is seen that for these special modes δ2F=ED. In the case of unstable and corresponding damped modes it is seen that δ2F≠ED; in fact δ2F≡0. This failure of the dielectric energy expression persists even for arbitrarily small growth and damping rates since ED is nonzero in this limit, whereas δ2F remains zero. In the case of general perturbations about stable equilibria, the two expressions are not equivalent; the exact energy density is given by an expression proportional to ω||E(k,ω)||2||ε(k,ω)||2/εI(k,ω), where E(k,ω) is the Fourier transform in space and time of the perturbed electric field (or equivalently the electric field associated with a single Van Kampen mode) and ε(k,ω) is the dielectric function with ω and k real and independent. The connection between the new exact energy expression and the at-best approximate ED is described. The new expression motivates natural definitions of Hamiltonian action variables and signature. A general linear integral transform (or equivalently a coordinate transformation) is introduced that maps the linear version of the noncanonical Hamiltonian structure, which describes the Vlasov equation, to action-angle (diagonal) form.Type of Medium: Electronic ResourceURL: -
19Articles: DFG German National LicensesStaff View
ISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: A simple sufficient condition is given for the linear ideal instability of plane parallel equilibria with antisymmetric shear flow and symmetric or antisymmetric magnetic field. Application of this condition shows that plane Couette flow, which is stable in the absence of a magnetic field, can be driven unstable by a symmetric magnetic field. Also, although strong magnetic shear can stabilize shear flow with a hyperbolic tangent profile, there exists a range of magnetic shear that causes destabilization.Type of Medium: Electronic ResourceURL: -
20Articles: DFG German National LicensesSu, X. N. ; Horton, W. ; Morrison, P. J.
New York, NY : American Institute of Physics (AIP)
Published 1991Staff ViewISSN: 1089-7666Source: AIP Digital ArchiveTopics: PhysicsNotes: The effects of density and temperature gradients on drift wave vortex dynamics are studied using a fully nonlinear model with the Boltzmann density distribution. The equation based on the full Boltzmann relation, in the short wavelength (∼ρs) region, possesses no localized monopole solution, while in the longer wavelength [∼(ρsrn)1/2] region the density profile governs the existence of monopolelike solutions. In the longer wavelength regime, however, the results of analysis show that due to the inhomogeneity of the plasma the monopoles cannot be localized sufficiently to avoid coupling to propagating drift waves. Thus, the monopole drift wave vortex is a long-lived coherent structure, but it is not precisely a stationary structure since the coupling results in a "flapping'' tail. The flapping tail causes energy of the vortex to leak out, but the effect of the temperature gradient-induced nonlinearity is to reduce the leaking of this energy.Type of Medium: Electronic ResourceURL: