A Three-Flavor AdS/QCD Model with a Back-Reacted Geometry

A fully back-reaction geometry model of AdS/QCD including the strange quark is described. We find that with the inclusion of the strange quark the impact on the metric is very small and the final predictions are changed only negligibly.Comment: 10 pages, 2 figures; references revised, minor change for caption of fig

Canonical Coordinates and Meson Spectra for Scalar Deformed N=4 SYM from the AdS/CFT Correspondence

Five supersymmetric scalar deformations of the AdS_5xS^5 geometry are investigated. By switching on condensates for the scalars in the N=4 multiplet with a form which preserves a subgroup of the original R-symmetry, disk and sphere configurations of D3-branes are formed in the dual supergravity background. The analytic, canonical metric for each geometry is formulated and the singularity structure is studied. Quarks are introduced into two of the corresponding field theories using D7-brane probes and the pseudoscalar meson spectrum is calculated. For one of the condensate configurations, a mass gap is found and shown analytically to be present in the massless limit. It is also found that there is a stepped spectrum with eigenstate degeneracy in the limit of small quark masses. In the case of a second, similar deformation, it is necessary to understand the full D3-D7 brane interaction to study the limit of small quark masses. It is seen that simple solutions to the equations of motion for the other three geometries are unlikely to exist.Comment: 16 pages, 7 figures, references added, typos correcte

A note on conductivity and charge diffusion in holographic flavour systems

We analyze the charge diffusion and conductivity in a Dp/Dq holographic setup that is dual to a supersymmetric Yang-Mills theory in p+1 dimensions with N_f<< N_c flavour degrees of freedom at finite temperature and nonvanishing U(1) baryon number chemical potential. We provide a new derivation of the results that generalize the membrane paradigm to the present context. We perform a numerical analysis in the particular case of the D3/D7 flavor system. The results obtained support the validity of the Einstein relation at finite chemical potential.Comment: 15 pages, 3 figures, v2 with minor correction

A metastable equilibrium model for the relative abundances of microbial phyla in a hot spring

Many studies link the compositions of microbial communities to their environments, but the energetics of organism-specific biomass synthesis as a function of geochemical variables has rarely been assessed. We describe a thermodynamic model that integrates geochemical and metagenomic data for biofilms sampled at five sites along a thermal and chemical gradient in the outflow channel of the hot spring known as ‘‘Bison Pool’’ in Yellowstone National Park. The relative abundances of major phyla in individual communities sampled along the outflow channel are modeled by computing metastable equilibrium among model proteins with amino acid compositions derived from metagenomic sequences. Geochemical conditions are represented by temperature and activities of basis species, including pH and oxidation-reduction potential quantified as the activity of dissolved hydrogen. By adjusting the activity of hydrogen, the model can be tuned to closely approximate the relative abundances of the phyla observed in the community profiles generated from BLAST assignments. The findings reveal an inverse relationship between the energy demand to form the proteins at equal thermodynamic activities and the abundance of phyla in the community.Although the metabolisms used by many members of these communities are driven by chemical disequilibria, the results support the possibility that higher-level patterns of chemotrophic microbial ecosystems are shaped by metastable equilibrium states that depend on both the composition of biomass and the environmental conditions

Linear square-mass trajectories of radially and orbitally excited hadrons in holographic QCD

We consider a new approach towards constructing approximate holographic duals of QCD from experimental hadron properties. This framework allows us to derive a gravity dual which reproduces the empirically found linear square-mass trajectories of universal slope for radially and orbitally excited hadrons. Conformal symmetry breaking in the bulk is exclusively due to infrared deformations of the anti-de Sitter metric and governed by one free mass scale proportional to Lambda_QCD. The resulting background geometry exhibits dual signatures of confinement and provides the first examples of holographically generated linear trajectories in the baryon sector. The predictions for the light hadron spectrum include new relations between trajectory slopes and ground state masses and are in good overall agreement with experiment.Comment: 33 pages, 5 figures, updated to the extended version published in JHEP, vector meson bulk potential and metric corrected, comments and references added, phenomenology and conclusions unchange

AdS/CFT with Flavour in Electric and Magnetic Kalb-Ramond Fields

We investigate gauge/gravity duals with flavour for which pure-gauge Kalb-Ramond B fields are turned on in the background, into which a D7 brane probe is embedded. First we consider the case of a magnetic field in two of the spatial boundary directions. We show that at finite temperature, i.e. in the AdS-Schwarzschild background, the B field has a stabilizing effect on the mesons and chiral symmetry breaking occurs for a sufficiently large value of the B field. Then we turn to the electric case of a B field in the temporal direction and one spatial boundary direction. In this case, there is a singular region in which it is necessary to turn on a gauge field on the brane in order to ensure reality of the brane action. We find that the brane embeddings are attracted towards this region. Far away from this region, in the weak field case at zero temperature, we investigate the meson spectrum and find a mass shift similar to the Stark effect.Comment: 34 pages, 18 figures, v2: added references and comments on mode decoupling, on thermodynamics and holographic renormalisation, JHEP style, v3: Final published versio

Drip vs. furrow irrigation in the delivery of Escherichia coli to onions

Surface irrigation systems that reuse water may deliver bacteria to produce destined for fresh consumption. Four irrigation systems delivered (1) well water free of Escherichia coli via subsurface drip irrigation, (2) canal water with moderate levels of E. coli via subsurface drip irrigation, (3) canal water with moderate levels of E. coli via furrow irrigation, and (4) canal water with enhanced levels of E. coli via furrow irrigation. The four irrigation systems (replicated five times) applied water to onion on silt loam. Water was sampled hourly for E. coli, and the lateral movement of E. coli in the soil solution was tracked by soil samples following irrigations. Onion bulbs were sampled for E. coli contamination. The most probable numbers of E. coli in water and soil water were determined using IDEXX Colilert® and Colisure®, respectively, and Quanti-Tray/2000®. Under both furrow and subsurface drip irrigation, a fraction of the E. coli was delivered to the soil immediately adjacent to the onion bulbs. The silt loam retained most of the E. coli content away from the onion bulbs and close to where the water entered the soil. No E. coli was detected inside of the onion bulbs from any irrigation treatment. Current subsurface drip or furrow (flood) irrigation practices do not appear to pose a significant risk for bacterial contamination of dry bulb onion grown on silt loam

Calculation of the relative metastabilities of proteins using the CHNOSZ software package

<p>Abstract</p> <p>Background</p> <p>Proteins of various compositions are required by organisms inhabiting different environments. The energetic demands for protein formation are a function of the compositions of proteins as well as geochemical variables including temperature, pressure, oxygen fugacity and pH. The purpose of this study was to explore the dependence of metastable equilibrium states of protein systems on changes in the geochemical variables.</p> <p>Results</p> <p>A software package called CHNOSZ implementing the revised Helgeson-Kirkham-Flowers (HKF) equations of state and group additivity for ionized unfolded aqueous proteins was developed. The program can be used to calculate standard molal Gibbs energies and other thermodynamic properties of reactions and to make chemical speciation and predominance diagrams that represent the metastable equilibrium distributions of proteins. The approach takes account of the chemical affinities of reactions in open systems characterized by the chemical potentials of basis species. The thermodynamic database included with the package permits application of the software to mineral and other inorganic systems as well as systems of proteins or other biomolecules.</p> <p>Conclusion</p> <p>Metastable equilibrium activity diagrams were generated for model cell-surface proteins from archaea and bacteria adapted to growth in environments that differ in temperature and chemical conditions. The predicted metastable equilibrium distributions of the proteins can be compared with the optimal growth temperatures of the organisms and with geochemical variables. The results suggest that a thermodynamic assessment of protein metastability may be useful for integrating bio- and geochemical observations.</p

Localized Backreacted Flavor Branes in Holographic QCD

We investigate the perturbative (in $g_s N_{D8}$) backreaction of localized D8 branes in D4-D8 systems including in particular the Sakai Sugimoto model. We write down the explicit expressions of the backreacted metric, dilaton and RR form. We find that the backreaction remains small up to a radial value of $u \ll \ell_s/(g_s N_{D8})$, and that the background functions are smooth except at the D8 sources. In this perturbative window, the original embedding remains a solution to the equations of motion. Furthermore, the fluctuations around the original embedding, describing scalar mesons, do not become tachyonic due to the backreaction in the perturbative regime. This is is due to a cancelation between the DBI and CS parts of the D8 brane action in the perturbed background.Comment: 1+48 pages (7 figures) + 15 pages, citations added & minor correction

Experimental investigation of single carbon compounds under hydrothermal conditions

Author Posting. © The Authors, 2005. This is the author's version of the work. It is posted here by permission of Elsevier B.V. for personal use, not for redistribution. The definitive version was published in Geochimica et Cosmochimica Acta 70 (2006): 446-460, doi:10.1016/j.gca.2005.09.002.The speciation of carbon in subseafloor hydrothermal systems has direct implications for the maintenance of life in present day vent ecosystems and possibly the origin of life on early Earth. Carbon monoxide is of particular interest because it represents a key reactant during the abiotic synthesis of reduced carbon compounds via Fischer-Tropsch-type processes. Laboratory experiments were conducted to constrain reactions that regulate the speciation of aqueous single carbon species under hydrothermal conditions and determine kinetic parameters for the oxidation of CO according to the water water-gas shift reaction (CO2 + H2 = CO + H2O). Aqueous fluids containing added CO2, CO, HCOOH, NaHCO3, NaHCOO, and H2 were heated at 150, 200, and 300°C and 350 bar in flexible cell hydrothermal apparatus, and the abundance of carbon compounds were monitored as a function of time. Variations in fluid chemistry suggest that the reduction of CO2 to CH3OH under aqueous conditions occurs via a stepwise process that involves the formation of HCOOH, CO, and possibly CH2O, as reaction intermediaries. Kinetic barriers that inhibit the reduction of CH3OH to CH4 allow the accumulation of reaction intermediaries in solution at high concentrations regulated by metastable equilibrium. Reaction of CO2 to form CO involves a two-step process in which CO2 initially undergoes a reduction step to HCOOH which subsequently dehydrates to form CO. Both reactions proceed readily in either direction. A preexponential factor of 1.35 x 106 s-1 and an activation energy of 102 KJ mol-1 were retrieved from the experimental results for the oxidation of CO to CO2. Reactions rates amongst single carbon compounds during the experiments suggests SCO2 (CO2 + HCO3- + CO3=), CO, SHCOOH (HCOOH + HCOO-), and CH3OH may reach states of redox-dependent metastable thermodynamic equilibrium in subseafloor and other hydrothermal systems. The abundance of CO under equilibrium conditions, which in turn may influence the likelihood for abiotic synthesis via Fischer-Tropsch-type processes, is strongly dependent on temperature, the total carbon content of the fluid, and host-rock lithology. If crustal residence times following the mixing of high-temperature hydrothermal fluids with cool seawater are sufficiently long, reequilibration of aqueous carbon can result in the generation of additional reduced carbon species such as HCOOH and CH3OH and the consumption of H2. The present study suggests that abiotic reactions involving aqueous carbon compounds in hydrothermal systems are sufficiently rapid to influence metabolic pathways utilized by organisms that inhabit vent environments.This study was supported by the National Science Foundation grant #OCE-0136954, the Office of Basic Energy Sciences, U.S. Department of Energy grant #DEFG0297ER14746, and by NASA Exobiology grant #NAG5-7696 and Origins grant #NNG04GG23G