Dynein structure and power stroke

Dynein ATPases are microtubule motors that are critical to diverse processes such as vesicle transport and the beating of sperm tails; however, their mechanism of force generation is unknown. Each dynein comprises a head, from which a stalk and a stem emerge. Here we use electron microscopy and image processing to reveal new structural details of dynein c, an isoform from Chlamydomonas reinhardtii flagella, at the start and end of its power stroke. Both stem and stalk are flexible, and the stem connects to the head by means of a linker approximately 10 nm long that we propose lies across the head. With both ADP and vanadate bound, the stem and stalk emerge from the head 10 nm apart. However, without nucleotide they emerge much closer together owing to a change in linker orientation, and the coiled-coil stalk becomes stiffer. The net result is a shortening of the molecule coupled to an approximately 15-nm displacement of the tip of the stalk. These changes indicate a mechanism for the dynein power stroke

D3-brane Potentials from Fluxes in AdS/CFT

We give a comprehensive treatment of the scalar potential for a D3-brane in a warped conifold region of a compactification with stabilized moduli. By studying general ultraviolet perturbations in supergravity, we systematically incorporate `compactification effects' sourced by supersymmetry breaking in the compact space. Significant contributions to the D3-brane potential, including the leading term in the infrared, arise from imaginary anti-self-dual (IASD) fluxes. For an arbitrary Calabi-Yau cone, we determine the most general IASD fluxes in terms of scalar harmonics, then compute the resulting D3-brane potential. Specializing to the conifold, we identify the operator dual to each mode of flux, and for chiral operators we confirm that the potential computed in the gauge theory matches the gravity result. The effects of four-dimensional curvature, including the leading D3-brane mass term, arise directly from the ten-dimensional equations of motion. Furthermore, we show that gaugino condensation on D7-branes provides a local source for IASD flux. This flux precisely encodes the nonperturbative contributions to the D3-brane potential, yielding a promising ten-dimensional representation of four-dimensional nonperturbative effects. Our result encompasses all significant contributions to the D3-brane potential discussed in the literature, and does so in the single coherent framework of ten-dimensional supergravity. Moreover, we identify new terms with irrational scaling dimensions that were inaccessible in prior works. By decoupling gravity in a noncompact configuration, then systematically reincorporating compactification effects as ultraviolet perturbations, we have provided an approach in which Planck-suppressed contributions to the D3-brane effective action can be computed.Comment: 70 page

Fractional branes, warped compactifications and backreacted orientifold planes

The standard extremal p-brane solutions in supergravity are known to allow for a generalisation which consists of adding a linear dependence on the world-volume coordinates to the usual harmonic function. In this note we demonstrate that remarkably this generalisation goes through in exactly the same way for p-branes with fluxes added to it that correspond to fractional p-branes. We relate this to warped orientifold compactifications by trading the Dp-branes for Op-planes that solve the RR tadpole condition. This allows us to interpret the worldvolume dependence as due to lower-dimensional scalars that flow along the massless directions in the no-scale potential. Depending on the details of the fluxes these flows can be supersymmetric domain wall flows. Our solutions provide explicit examples of backreacted orientifold planes in compactifications with non-constant moduli.Comment: 20 pages, incl. references. v2: small changes required for JHEP publication. v3: few equation typos correcte

Scalar and vector mesons of flavor chiral symmetry breaking in the Klebanov-Strassler background

Recently, Dymarsky, Kuperstein and Sonnenschein constructed an embedding of flavor D7- and anti-D7-branes in the Klebanov-Strassler geometry that breaks the supersymmetry of the background, yet is stable. In this article, we study in detail the spectrum of vector mesons in this new model of flavor chiral symmetry breaking and commence an analytical analysis of the scalar mesons in this setup.Comment: v1: 35 pages, 5 figures, 4 tables, includes self-contained review of DKS construction; v2: corrected signs in eqs. (2.22) and (2.23), improved discussion of scalar mesons in section 3.2; v3: major revision of the results on scalar mesons, version submitted to JHEP; v4: version accepted by JHE

On Supersymmetric D7-branes in the Warped Deformed Conifold

We study the supersymmetric properties of D7-branes in the warped deformed conifold. We consider the $\kappa$-symmetry conditions on D7-branes in this specific warped background, taking into account the background NS-NS 2-form flux. While any holomorphic embedding defines a supersymmetric D7-brane in the absence of background H-flux, most of the D7-brane embeddings considered in the literature do not preserve supersymmetry for the warped deformed conifold without also including brane worldvolume flux. For the simplest such embedding, we construct numerically the worldvolume fluxnecessary to restore supersymmetry. We also comment on the dual field theory descriptions in terms of cascading N=1 supersymmetric gauge theories with flavors. Finally, we discuss some possible applications of our results to moduli stabilization and vacuum energy uplifting, gauge/gravity duality, and string inflationary model building.Comment: 37 pages, 2 figures, v3:many clarifications and improvements to susy restoring flu

On thermodynamics of N=6 superconformal Chern-Simons theory

We study thermodynamics of N=6 superconformal Chern-Simons theory by computing quantum corrections to the free energy. We find that in weakly coupled ABJM theory on R(2) x S(1), the leading correction is non-analytic in the 't Hooft coupling lambda, and is approximately of order lambda^2 log(lambda)^3. The free energy is expressed in terms of the scalar thermal mass m, which is generated by screening effects. We show that this mass vanishes to 1-loop order. We then go on to 2-loop order where we find a finite and positive mass squared m^2. We discuss differences in the calculation between Coulomb and Lorentz gauge. Our results indicate that the free energy is a monotonic function in lambda which interpolates smoothly to the N^(3/2) behaviour at strong coupling.Comment: 29 pages. v2: references added. v3: minor changes, references added, published versio

Spinflation with Angular Potentials

We investigate in detail the cosmological consequences of realistic angular dependent potentials in the brane inflation scenario. Embedding a warped throat into a compact Calabi-Yau space with all moduli stabilized breaks the no-scale structure and induces angular dependence in the potential of the probe D3-brane. We solve the equations of motion from the DBI action in the warped deformed conifold including linearized perturbations around the imaginary self-dual solution. Our numerical solutions show that angular dependence is a next to leading order correction to the dominant radial motion of the brane, however, just as angular motion typically increases the amount of inflation (spinflation), having additional angular dependence also increases the amount of inflation. We also derive an analytic approximation for the number of e-foldings along the DBI trajectory in terms of the compactification parameters.Comment: 20 pages, 10 figures. Revised to published version: minor errors corrected, references and discussion adde

Correlation Functions of Large N Chern-Simons-Matter Theories and Bosonization in Three Dimensions

We consider the conformal field theory of N complex massless scalars in 2+1 dimensions, coupled to a U(N) Chern-Simons theory at level k. This theory has a 't Hooft large N limit, keeping fixed \lambda = N/k. We compute some correlation functions in this theory exactly as a function of \lambda, in the large N (planar) limit. We show that the results match with the general predictions of Maldacena and Zhiboedov for the correlators of theories that have high-spin symmetries in the large N limit. It has been suggested in the past that this theory is dual (in the large N limit) to the Legendre transform of the theory of fermions coupled to a Chern-Simons gauge field, and our results allow us to find the precise mapping between the two theories. We find that in the large N limit the theory of N scalars coupled to a U(N)_k Chern-Simons theory is equivalent to the Legendre transform of the theory of k fermions coupled to a U(k)_N Chern-Simons theory, thus providing a bosonization of the latter theory. We conjecture that perhaps this duality is valid also for finite values of N and k, where on the fermionic side we should now have (for N_f flavors) a U(k)_{N-N_f/2} theory. Similar results hold for real scalars (fermions) coupled to the O(N)_k Chern-Simons theory.Comment: 49 pages, 16 figures. v2: added reference

Soft branes in supersymmetry-breaking backgrounds

We revisit the analysis of effective field theories resulting from non-supersymmetric perturbations to supersymmetric flux compactifications of the type-IIB superstring with an eye towards those resulting from the backreaction of a small number of anti-D3-branes. Independently of the background, we show that the low-energy Lagrangian describing the fluctuations of a stack of probe D3-branes exhibits soft supersymmetry breaking, despite perturbations to marginal operators that were not fully considered in some previous treatments. We take this as an indication that the breaking of supersymmetry by anti-D3-branes or other sources may be spontaneous rather than explicit. In support of this, we consider the action of an anti-D3-brane probing an otherwise supersymmetric configuration and identify a candidate for the corresponding goldstino.Comment: 36+5 pages. References added, minor typos correcte