Google's 2019 "Quantum Supremacy'' Claims: Data, Documentation, and Discussion

In October 2019, "Nature" published a paper describing an experimental work that took place at Google. The paper claims to demonstrate quantum (computational) supremacy on a 53-qubit quantum computer. Since September 2019 the authors have been involved in a long-term project to study various statistical aspects of the Google experiment. In particular, we have been trying to gather the relevant data and information, to reconstruct and verify those parts of the Google 2019 supremacy experiments that are based on classical computations (unless they require too heavy computation), and to put the data under statistical analysis. We have now (August 2022) almost concluded the part relating to the gathering of data and information needed for our study of the 2019 Google experiment, and this document describes the available data and information for the Google 2019 experiment and some of our results and plans.Comment: v2. 34 pages, 2 figures; contains a few more details regarding the calibration process, a reference to a major new confirmation, a couple additional concerns (17,18) that were omitted in the first version, and a few minor correction

Questions and Concerns About Google's Quantum Supremacy Claim

In October 2019, Nature published a paper [6] describing an experimental work that was performed at Google. The paper claims to demonstrate quantum (computational) supremacy on a 53-qubit quantum computer. Since then we have been involved in a long-term project to study various statistical aspects of the Google experiment. In [30] we studied Google's statistical framework that we found to be very sound and offered some technical improvements. This document describes three main concerns (based on statistical analysis) about the Google 2019 experiment. The first concern is that the data do not agree with Google's noise model (or any other specific model). The second concern is that a crucial simple formula for a priori estimation of the fidelity seems to involve an unexpected independence assumption, and yet it gives very accurate predictions. The third concern is about statistical properties of the calibration process.Comment: 49 pages, 13 Figures, 7 Table

TLR9 activation dampens the early inflammatory response to paracoccidioides brasiliensis, Impacting host survival

Background: Paracoccidioides brasiliensis causes paracoccidioidomycosis, one of the most prevalent systemic mycosis in Latin America. Thus, understanding the characteristics of the protective immune response to P. brasiliensis is of interest, as it may reveal targets for disease control. The initiation of the immune response relies on the activation of pattern recognition receptors, among which are TLRs. Both TLR2 and TLR4 have been implicated in the recognition of P. brasiliensis and regulation of the immune response. However, the role of TLR9 during the infection by this fungus remains unclear.J.F. Menino was supported by a grant from Fundacao para a Ciencia e Tecnologia (FCT), Portugal (SFRH/BD/33446/2008). This work was supported by a grant from FCT (PTDC/BIA-MIC/108309/2008). M. Saraiva is a Ciencia 2007 fellow and M. Sturme is a Ciencia 2008 fellow. We would also like to thank FAPESP (Fundacao para Amparo a Pesquisa do Estado de Sao Paulo) and CNPq (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico) for financial support. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Effect of Dimer Dissociation on Activity and Thermostability of the α-Glucuronidase from Geobacillus stearothermophilus: Dissecting the Different Oligomeric Forms of Family 67 Glycoside Hydrolases

The oligomeric organization of enzymes plays an important role in many biological processes, such as allosteric regulation, conformational stability and thermal stability. α-Glucuronidases are family 67 glycosidases that cleave the α-1,2-glycosidic bond between 4-O-methyl-d-glucuronic acid and xylose units as part of an array of hemicellulose-hydrolyzing enzymes. Currently, two crystal structures of α-glucuronidases are available, those from Geobacillus stearothermophilus (AguA) and from Cellvibrio japonicus (GlcA67A). Both enzymes are homodimeric, but surprisingly their dimeric organization is different, raising questions regarding the significance of dimerization for the enzymes' activity and stability. Structural comparison of the two enzymes suggests several elements that are responsible for the different dimerization organization. Phylogenetic analysis shows that the α-glucuronidases AguA and GlcA67A can be classified into two distinct subfamilies of bacterial α-glucuronidases, where the dimer-forming residues of each enzyme are conserved only within its own subfamily. It seems that the different dimeric forms of AguA and GlcA67A represent the two alternative dimeric organizations of these subfamilies. To study the biological significance of the dimerization in α-glucuronidases, we have constructed a monomeric form of AguA by mutating three of its interface residues (W328E, R329T, and R665N). The activity of the monomer was significantly lower than the activity of the wild-type dimeric AguA, and the optimal temperature for activity of the monomer was around 35°C, compared to 65°C of the wild-type enzyme. Nevertheless, the melting temperature of the monomeric protein, 72.9°C, was almost identical to that of the wild-type, 73.4°C. It appears that the dimerization of AguA is essential for efficient catalysis and that the dissociation into monomers results in subtle conformational changes in the structure which indirectly influence the active site region and reduce the activity. Structural and mechanistic explanations for these effects are discussed

Crystal structure and snapshots along the reaction pathway of a family 51 α-l-arabinofuranosidase

High-resolution crystal structures of α-l-arabinofuranosidase from Geobacillus stearothermophilus T-6, a family 51 glycosidase, are described. The enzyme is a hexamer, and each monomer is organized into two domains: a (β/α)(8)-barrel and a 12-stranded β sandwich with jelly-roll topology. The structures of the Michaelis complexes with natural and synthetic substrates, and of the transient covalent arabinofuranosyl– enzyme intermediate represent two stable states in the double displacement mechanism, and allow thorough examination of the catalytic mechanism. The arabinofuranose sugar is tightly bound and distorted by an extensive network of hydrogen bonds. The two catalytic residues are 4.7 Å apart, and together with other conserved residues contribute to the stabilization of the oxocarbenium ion-like transition state via charge delocalization and specific protein–substrate interactions. The enzyme is an anti-protonator, and a 1.7 Å electrophilic migration of the anomeric carbon takes place during the hydrolysis

Crystallization and preliminary crystallographic analysis of a family 43 β-d-xylosidase from Geobacillus stearothermophilus T-6

The crystallization and preliminary X-ray analysis of a β-d-xylosidase from G. stearothermophilus T-6, a family 43 glycoside hydrolase, is described. Native and catalytic inactive mutants of the enzymes were crystallized in two different space groups, orthorhombic P21212 and tetragonal P41212 (or the enantiomorphic space group P43212), using a sensitive cryoprotocol. The latter crystal form diffracted X-rays to a resolution of 2.2 Å