Phylogeny of Prokaryotes and Chloroplasts Revealed by a Simple Composition Approach on All Protein Sequences from Complete Genomes Without Sequence Alignment

The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of chloroplasts have helped to resolve the evolution of this organelle in photosynthetic eukaryotes. In this paper we propose an alternative method of phylogenetic analysis using compositional statistics for all protein sequences from complete genomes. This new method is conceptually simpler than and computationally as fast as the one proposed by Qi et al. (2004b) and Chu et al. (2004). The same data sets used in Qi et al. (2004b) and Chu et al. (2004) are analyzed using the new method. Our distance-based phylogenic tree of the 109 prokaryotes and eukaryotes agrees with the biologists tree of life based on 16S rRNA comparison in a predominant majority of basic branching and most lower taxa. Our phylogenetic analysis also shows that the chloroplast genomes are separated to two major clades corresponding to chlorophytes s.l. and rhodophytes s.l. The interrelationships among the chloroplasts are largely in agreement with the current understanding on chloroplast evolution

BPS Monopole Equation in Omega-background

We study deformed supersymmetries in N=2 super Yang-Mills theory in the Omega-backgrounds characterized by two complex parameters $\epsilon_1, \epsilon_2$. When one of the $\epsilon$-parameters vanishes, the theory has extended supersymmetries. We compute the central charge of the algebra and obtain the deformed BPS monopole equation. We examine supersymmetries preserved by the equation.Comment: 14 pages, typos corrected, published version in JHE

Non-abelian Action for Multiple Five-Branes with Self-Dual Tensors

We construct an action for non-abelian 2-form in 6-dimensions. Our action consists of a non-abelian generalization of the abelian action of Perry and Schwarz for a single five-brane. It admits a self-duality equation on the field strength as the equation of motion. It has a modified 6d Lorentz symmetry. On dimensional reduction on a circle, our action gives the standard 5d Yang-Mills action plus higher order corrections. Based on these properties, we propose that our theory describes the gauge sector of multiple M5-branes in flat space.Comment: LaTeX, 26 pages. v2: improved discussion of Lorentz symmetry. ref added. v3: add comments in the discussion section on the inclusion of scalar fields and supersymmetry; title changed to a more suitable one; version published in JHE

Boundary Conditions for Interacting Membranes

We investigate supersymmetric boundary conditions in both the Bagger-Lambert and the ABJM theories of interacting membranes. We find boundary conditions associated to the fivebrane, the ninebrane and the M-theory wave. For the ABJM theory we are able to understand the enhancement of supersymmetry to produce the (4,4) supersymmetry of the self-dual string. We also include supersymmetric boundary conditions on the gauge fields that cancel the classical gauge anomaly of the Chern-Simons terms.Comment: 36 pages, latex, v2 minor typos correcte

More on the Nambu-Poisson M5-brane Theory: Scaling limit, background independence and an all order solution to the Seiberg-Witten map

We continue our investigation on the Nambu-Poisson description of M5-brane in a large constant C-field background (NP M5-brane theory) constructed in Refs.[1, 2]. In this paper, the low energy limit where the NP M5-brane theory is applicable is clarified. The background independence of the NP M5-brane theory is made manifest using the variables in the BLG model of multiple M2-branes. An all order solution to the Seiberg-Witten map is also constructed.Comment: expanded explanations, minor corrections and typos correcte

Critical solutions in topologically gauged N=8 CFTs in three dimensions

In this paper we discuss some special (critical) background solutions that arise in topological gauged ${\mathcal N}=8$ three-dimensional CFTs with SO(N) gauge group. These solutions solve the TMG equations (containing the parameters $\mu$ and $l$) for a certain set of values of $\mu l$ obtained by varying the number of scalar fields with a VEV. Apart from Minkowski, chiral round $AdS_3$ and null-warped $AdS_3$ (or Schr\"odinger(z=2)) we identify also a more exotic solution recently found in $TMG$ by Ertl, Grumiller and Johansson. We also discuss the spectrum, symmetry breaking pattern and the supermultiplet structure in the various backgrounds and argue that some properties are due to their common origin in a conformal phase. Some of the scalar fields, including all higgsed ones, turn out to satisfy three-dimensional singleton field equations. Finally, we note that topologically gauged ${\mathcal N}=6$ ABJ(M) theories have a similar, but more restricted, set of background solutions.Comment: 34 pages, v2: minor corrections, note about a new solution added in final section, v3: two footnotes adde

N=2 Instanton Effective Action in Omega-background and D3/D(-1)-brane System in R-R Background

We study the relation between the ADHM construction of instantons in the Omega-background and the fractional D3/D(-1)-branes at the orbifold singularity of C \times C^2/Z_2 in Ramond-Ramond (R-R) 3-form field strength background. We calculate disk amplitudes of open strings connecting the D3/D(-1)-branes in certain R-R background to obtain the D(-1)-brane effective action deformed by the R-R background. We show that the deformed D(-1)-brane effective action agrees with the instanton effective action in the Omega-background.Comment: 35 pages, no figures, references adde

Supersymmetric Intersecting Branes on the Waves

We construct a general family of supersymmetric solutions in time- and space-dependent wave backgrounds in general supergravity theories describing single and intersecting p-branes embedded into time-dependent dilaton-gravity plane waves of an arbitrary (isotropic) profile, with the brane world-volume aligned parallel to the propagation direction of the wave. We discuss how many degrees of freedom we have in the solutions. We also propose that these solutions can be used to describe higher-dimensional time-dependent "black holes", and discuss their property briefly.Comment: 12 pages, LaTe

Worldvolume Superalgebra Of BLG Theory With Nambu-Poisson Structure

Recently it was proposed that the Bagger-Lambert-Gustavsson theory with Nambu-Poisson structure describes an M5-brane in a three-form flux background. In this paper we investigate the superalgebra associated with this theory. We derive the central charges corresponding to M5-brane solitons in 3-form backgrounds. We also show that double dimensional reduction of the superalgebra gives rise to the Poisson bracket terms of a non-commutative D4-brane superalgebra. We provide interpretations of the D4-brane charges in terms of spacetime intersections.Comment: 23 pages; references added, section 4 clarification