Improvements of rolling circle amplification (RCA) efficiency and accuracy using Thermus thermophilus SSB mutant protein

Rolling circle amplification (RCA) of plasmid or genomic DNA using random hexamers and bacteriophage phi29 DNA polymerase has become increasingly popular in the amplification of template DNA in DNA sequencing. We have found that the mutant protein of single-stranded DNA binding protein (SSB) from Thermus thermophilus (Tth) HB8 enhances the efficiency of amplification of DNA templates. In addition, the TthSSB mutant protein increased the specificity of phi29 DNA polymerase. We have overexpressed the native and mutant forms of TthSSB protein in Escherichia coli and purified them to homogeneity. In vitro, these proteins were found to bind specifically to single-stranded DNA. Addition of TthSSB mutant protein to RCA halved the elongation time required for phi29 DNA polymerase to synthesize DNA fragments in RCA. Furthermore, the presence of the TthSSB mutant protein essentially eliminates nonspecific DNA products in RCA reactions

Brownian motion in AdS/CFT

We study Brownian motion and the associated Langevin equation in AdS/CFT. The Brownian particle is realized in the bulk spacetime as a probe fundamental string in an asymptotically AdS black hole background, stretching between the AdS boundary and the horizon. The modes on the string are excited by the thermal black hole environment and consequently the string endpoint at the boundary undergoes an erratic motion, which is identified with an external quark in the boundary CFT exhibiting Brownian motion. Semiclassically, the modes on the string are thermally excited due to Hawking radiation, which translates into the random force appearing in the boundary Langevin equation, while the friction in the Langevin equation corresponds to the excitation on the string being absorbed by the black hole. We give a bulk proof of the fluctuation-dissipation theorem relating the random force and friction. This work can be regarded as a step toward understanding the quantum microphysics underlying the fluid-gravity correspondence. We also initiate a study of the properties of the effective membrane or stretched horizon picture of black holes using our bulk description of Brownian motion.Comment: 54 pages (38 pages + 5 appendices), 5 figures. v2: references added, clarifications in 6.2. v3: clarifications, version submitted to JHE

Perturbative instabilities in Horava gravity

We investigate the scalar and tensor perturbations in Horava gravity, with and without detailed balance, around a flat background. Once both types of perturbations are taken into account, it is revealed that the theory is plagued by ghost-like scalar instabilities in the range of parameters which would render it power-counting renormalizable, that cannot be overcome by simple tricks such as analytic continuation. Implementing a consistent flow between the UV and IR limits seems thus more challenging than initially presumed, regardless of whether the theory approaches General Relativity at low energies or not. Even in the phenomenologically viable parameter space, the tensor sector leads to additional potential problems, such as fine-tunings and super-luminal propagation.Comment: 21 pages, version published at Class. Quant. Gra

Development of an experimental platform for the investigation of laser-plasma interaction in conditions relevant to shock ignition regime

The shock ignition (SI) approach to inertial confinement fusion is a promising scheme for achieving energy production by nuclear fusion. SI relies on using a high intensity laser pulse (≈1016 W/cm2, with a duration of several hundred ps) at the end of the fuel compression stage. However, during laser-plasma interaction (LPI), several parametric instabilities, such as stimulated Raman scattering and two plasmon decay, nonlinearly generate hot electrons (HEs). The whole behavior of HE under SI conditions, including their generation, transport, and final absorption, is still unclear and needs further experimental investigation. This paper focuses on the development of an experimental platform for SI-related experiments, which simultaneously makes use of multiple diagnostics to characterize LPI and HE generation, transport, and energy deposition. Such diagnostics include optical spectrometers, streaked optical shadowgraph, an x-ray pinhole camera, a two-dimensional x-ray imager, a Cu Kα line spectrometer, two hot-electron spectrometers, a hard x-ray (bremsstrahlung) detector, and a streaked optical pyrometer. Diagnostics successfully operated simultaneously in single-shot mode, revealing the features of HEs under SI-relevant conditions.T. Tamagawa, Y. Hironaka, K. Kawasaki, D. Tanaka, T. Idesaka, N. Ozaki, R. Kodama, R. Takizawa, S. Fujioka, A. Yogo, D. Batani, Ph. Nicolai, G. Cristoforetti, P. Koester, L. A. Gizzi, and K. Shigemori, "Development of an experimental platform for the investigation of laser–plasma interaction in conditions relevant to shock ignition regime", Review of Scientific Instruments 93, 063505 (2022) https://doi.org/10.1063/5.008996

Massless black holes and black rings as effective geometries of the D1-D5 system

We compute correlation functions in the AdS/CFT correspondence to study the emergence of effective spacetime geometries describing complex underlying microstates. The basic argument is that almost all microstates of fixed charges lie close to certain "typical" configurations. These give a universal response to generic probes, which is captured by an emergent geometry. The details of the microstates can only be observed by atypical probes. We compute two point functions in typical ground states of the Ramond sector of the D1-D5 CFT, and compare with bulk two-point functions computed in asymptotically AdS_3 geometries. For large central charge (which leads to a good semiclassical limit), and sufficiently small time separation, a typical Ramond ground state of vanishing R-charge has the M=0 BTZ black hole as its effective description. At large time separation this effective description breaks down. The CFT correlators we compute take over, and give a response whose details depend on the microstate. We also discuss typical states with nonzero R-charge, and argue that the effective geometry should be a singular black ring. Our results support the argument that a black hole geometry should be understood as an effective coarse-grained description that accurately describes the results of certain typical measurements, but breaks down in general.Comment: 47 pages, 4 figures. v2: references added. v3: minor corrections to Appendix A, references adde

Laser-Shock Compression and Hugoniot Measurements of Liquid Hydrogen to 55 GPa

The principal Hugoniot for liquid hydrogen was obtained up to 55 GPa under laser-driven shock loading. Pressure and density of compressed hydrogen were determined by impedance-matching to a quartz standard. The shock temperature was independently measured from the brightness of the shock front. Hugoniot data of hydrogen provide a good benchmark to modern theories of condensed matter. The initial number density of liquid hydrogen is lower than that for liquid deuterium, and this results in shock compressed hydrogen having a higher compression and higher temperature than deuterium at the same shock pressure.Comment: 8 pages, 7 figures, 2 tables, accepted for publication in Physical Review

Development and evaluation of 10-inch Photo-Multiplier Tubes for the Double Chooz experiment

The goal of Double Chooz experiment is a precise measurement of the last unknown mixing angle theta_13 using two identical detectors placed at far and near sites from Chooz reactor cores. The detector is optimized for reactor-neutrino detection using specially developed 10-inch PMTs. We developed two types of measurement systems and evaluated 400 PMTs before the installation. Those PMTs fulfill our requirements, and a half of those have been installed to the far detector in 2009. The character and performance data of the PMTs are stored in a database and will be referenced in analysis and MC simulation.Comment: Submitted to Nuclear Instruments and Methods

Shock Hugoniot data for water up to 5 Mbar obtained with quartz standard at high-energy laser facilities

In this work, we present experimental results on the behavior of liquid water at megabar pressure. The experiment was performed using the HIPER (High-Intensity Plasma Experimental Research) laser facility, a uniaxial irradiation chamber of GEKKO XII (GXII) at the Institute of Laser Engineering (ILE), and the PHELIX at GSI (GSI Helmholtz Centre for Heavy Ion Research), a single-beam high-power laser facility, to launch a planar shock into solid multilayered water samples. Equation-of-state data of water (H2O) are obtained in the pressure range 0.50–4.6 Mbar by tuning the laser-drive parameters. The Hugoniot parameters (pressure, density, etc.) and the shock temperature were simultaneously determined by using VISAR and SOP as diagnostic tools and quartz as the standard material for impedance mismatch experiments. Finally, our experimental results are compared with hydrodynamic simulations tested with different equations of state, showing good compatibility with tabulated SESAME tables for water.The authors would like to acknowledge the support of the laser technical team at GEKKO XII (ILE) and PHELIX (GSI). This work received funding from the Euratom Research and Training Program 2014–2018 and 2019-2020 (Grant agreement no. 633053). The involved teams were operated within the framework of the Enabling Research Project ENR-IFE19.CEA-01, Study of Direct Drive and Shock Ignition for IFE: Theory, Simulations, Experiments, Diagnostics Development. JIHT RAS team members were supported by the Ministry of Science and Higher Education of the Russian Federation (State Assignment no. 075-00460-21-00).Peer reviewe

Genotoxicity and mutagenicity of Echinodorus macrophyllus (chapéu-de-couro) extracts

Echinodorus macrophyllus, commonly known as chapéu-de-couro, is a medicinal plant used in folk medicine to treat inflammation and rheumatic diseases. In this work, we used short-term bacterial assays based on the induction of SOS functions to examine the genotoxicity and mutagenicity of an aqueous extract of E. macrophyllus leaves. Whole extract and an ethyl acetate fraction showed similar genotoxicity and caused an ~70-fold increase in lysogenic induction. The extract also gave a positive result in the SOS chromotest with an increase of 12-fold in β-Galactosidase enzymatic units. There was a strong trend towards base substitutions and frameshifts at purine sites in the mutations induced by the extract in Escherichia coli (CC103 and CC104 strains) and Salmonella typhimurium test strains (22-fold increase in histidine revertants in TA98 strain). Since reactive oxygen species may be implicated in aging process and in degenerative diseases, we used antioxidant compounds as catalase, thiourea and dipyridyl in the lysogenic induction test. All this compounds were able to reduce the induction factor observed in the treatment with chapéu-de-couro, thus suggesting that the genotoxicity and mutagenicity were attributable to the production of reactive oxygen species that targeted DNA purines