Measures of epitope binding degeneracy from T cell receptor repertoires

Adaptive immunity is driven by specific binding of hypervariable receptors to diverse molecular targets. The sequence diversity of receptors and targets are both individually known but because multiple receptors can recognize the same target, a measure of the effective "functional" diversity of the human immune system has remained elusive. Here, we show that sequence near-coincidences within T cell receptors that bind specific epitopes provide a new window into this problem and allow the quantification of how binding probability covaries with sequence. We find that near-coincidence statistics within epitope-specific repertoires imply a measure of binding degeneracy to amino acid changes in receptor sequence that is consistent across disparate experiments. Paired data on both chains of the heterodimeric receptor are particularly revealing since simultaneous near-coincidences are rare and we show how they can be exploited to estimate the number of epitope responses that created the memory compartment. In addition, we find that paired-chain coincidences are strongly suppressed across donors with different human leukocyte antigens, evidence for a central role of antigen-driven selection in making paired chain receptors public. These results demonstrate the power of coincidence analysis to reveal the sequence determinants of epitope binding in receptor repertoires

Low-Lying Dirac Eigenmodes, Topological Charge Fluctuations and the Instanton Liquid Model

The local structure of low-lying eigenmodes of the overlap Dirac operator is studied. It is found that these modes cannot be described as linear combinations of 't Hooft "would-be" zeromodes associated with instanton excitations that underly the Instanton Liquid Model. This implies that the instanton liquid scenario for spontaneous chiral symmetry breaking in QCD is not accurate. More generally, our data suggests that the vacuum fluctuations of topological charge are not effectively dominated by localized lumps of unit charge with which the topological "would-be" zeromodes could be associated.Comment: Presented by I. Horvath at the NATO Advanced Research Workshop "Confinement, Topology, and other Non-Perturbative Aspects of QCD", January 21-27, 2002, Stara Lesna, Slovakia. 12 pages, 6 figures, uses crckapb.st

Holographic Anyons in the ABJM Theory

We consider the holographic anyons in the ABJM theory from three different aspects of AdS/CFT correspondence. First, we identify the holographic anyons by using the field equations of supergravity, including the Chern-Simons terms of the probe branes. We find that the composite of Dp-branes wrapped over CP3 with the worldvolume magnetic fields can be the anyons. Next, we discuss the possible candidates of the dual anyonic operators on the CFT side, and find the agreement of their anyonic phases with the supergravity analysis. Finally, we try to construct the brane profile for the holographic anyons by solving the equations of motion and Killing spinor equations for the embedding profile of the wrapped branes. As a by product, we find a BPS spiky brane for the dual baryons in the ABJM theory.Comment: 1+33 pages, 3 figures; v2 discussion for D4-D6 case added, references added; v3 comments adde

Moving Branes with Background Massless and Tachyon Fields in the Compact Spacetime

In this article we shall obtain the boundary state associated with a moving $Dp$-brane in the presence of the Kalb-Ramond field $B_{\mu\nu}$, an internal U(1) gauge field $A_{\alpha}$ and a tachyon field, in the compact spacetime. According to this state, properties of the brane and a closed string, with mixed boundary conditions emitted from it, will be obtained. Using this boundary state we calculate the interaction amplitude of two moving $Dp_{1}$ and $Dp_{2}$-branes with above background fields in a partially compact spacetime. They are parallel or perpendicular to each other. Properties of the interaction amplitude will be analyzed and contribution of the massless states to the interaction will be extracted.Comment: 13 pages, Latex, no figur

Holographic Penta and Hepta Quark State in Confining Gauge Theories

We study a new embedding solutions of D5 brane in an asymptotic AdS${}_5\times S^5$ space-time, which is dual to a confining $SU(N_c)$ gauge theory. The D5 brane is wrapped on $S^5$ as in the case of the vertex of holographic baryon. However, the solution given here is different from the usual baryon vertex in the point that it couples to $k$-anti-quarks and $N_c+k$ quarks on the opposite two points of $S^5$, the north and south poles, respectively. The total quark number of this state is preserved as $N_c$ when minus one is assigned to anti-quark, then it forms a color singlet like the baryon. However, this includes anti-quarks and quarks, whose number is larger than that of the baryon. When we set as $N_c=3$, we find the so called penta and hepta-quark states. We study the dynamical properties of these states by solving the vertex and string configurations for such states. The mass spectra of these states and the tension of the stretched vertex are estimated, and they are compared with that of the baryon.Comment: 24 pages, 6 figure

Four-Dimensional String/String Duality

We present supersymmetric soliton solutions of the four-dimensional heterotic string corresponding to monopoles, strings and domain walls. These solutions admit the $D=10$ interpretation of a fivebrane wrapped around $5$, $4$ or $3$ of the $6$ toroidally compactified dimensions and are arguably exact to all orders in $\alpha'$. The solitonic string solution exhibits an $SL(2,Z)$ {\it strong/weak coupling} duality which however corresponds to an $SL(2,Z)$ {\it target space} duality of the fundamental string.Comment: 14 page

M-Branes and Metastable States

We study a supersymmetry breaking deformation of the M-theory background found in arXiv:hep-th/0012011. The supersymmetric solution is a warped product of R^{2,1} and the 8-dimensional Stenzel space, which is a higher dimensional generalization of the deformed conifold. At the bottom of the warped throat there is a 4-sphere threaded by \tilde{M} units of 4-form flux. The dual (2+1)-dimensional theory has a discrete spectrum of bound states. We add p anti-M2 branes at a point on the 4-sphere, and show that they blow up into an M5-brane wrapping a 3-sphere at a fixed azimuthal angle on the 4-sphere. This supersymmetry breaking state turns out to be metastable for p / \tilde{M} < 0.054. We find a smooth O(3)-symmetric Euclidean bounce solution in the M5-brane world volume theory that describes the decay of the false vacuum. Calculation of the Euclidean action shows that the metastable state is extremely long-lived. We also describe the corresponding metastable states and their decay in the type IIA background obtained by reduction along one of the spatial directions of R^{2,1}.Comment: 33 pages, 5 figures; v2 note adde

Quantum Cosmology for the General Bianchi Type II, VI(Class A) and VII(Class A) vacuum geometries

The canonical quantization of the most general minisuperspace actions --i.e. with all six scale factor as well as the lapse function and the shift vector present-- describing the vacuum type II, VI and VII geometries, is considered. The reduction to the corresponding physical degrees of freedom is achieved through the usage of the linear constraints as well as the quantum version of the entire set of classical integrals of motion.Comment: 23 pages, LaTeX2e, No figure

A note on wavemap-tensor cosmologies

We examine theories of gravity which include finitely many coupled scalar fields with arbitrary couplings to the curvature (wavemaps). We show that the most general scalar-tensor $\sigma$-model action is conformally equivalent to general relativity with a minimally coupled wavemap with a particular target metric. Inflation on the source manifold is then shown to occur in a novel way due to the combined effect of arbitrary curvature couplings and wavemap self-interactions. A new interpretation of the conformal equivalence theorem proved for such `wavemap-tensor' theories through brane-bulk dynamics is also discussed.Comment: 8 pages, LaTeX, to appear in the Proceedings of the 2nd Hellenic Cosmology Workshop, National Observatory of Athens, April 21-22, 2001, (Kluwer 2001

Geometry of open strings ending on backreacting D3-branes

We investigate open string theory on backreacting D3-branes using a spacetime approach. We study in detail the half-BPS supergravity solutions describing open strings ending on D3-branes, in the near horizon of the D3-branes. We recover quantitatively several non-trivial features of open string physics including the appearance of D3-brane spikes, the polarization of fundamental strings into D5-branes, and the Hanany-Witten effect. Finally we detail the computation of the gravitational potential between two open strings, and contrast it with the holographic computation of Wilson lines. We argue that the D-brane backreaction has a large influence on the low-energy gravity, which may lead to experimental tests for string theory brane-world scenarios.Comment: 64 pages, 20 figure