Few-qubit quantum-classical simulation of strongly correlated lattice fermions

We study a proof-of-principle example of the recently proposed hybrid quantum-classical simulation of strongly correlated fermion models in the thermodynamic limit. In a "two-site" dynamical mean-field theory (DMFT) approach we reduce the Hubbard model to an effective impurity model subject to self-consistency conditions. The resulting minimal two-site representation of the non-linear hybrid setup involves four qubits implementing the impurity problem, plus an ancilla qubit on which all measurements are performed. We outline a possible implementation with superconducting circuits feasible with near-future technology.Comment: 20 pages, 10 figure

Non-linear quantum-classical scheme to simulate non-equilibrium strongly correlated fermionic many-body dynamics

We propose a non-linear, hybrid quantum-classical scheme for simulating non-equilibrium dynamics of strongly correlated fermions described by the Hubbard model in a Bethe lattice in the thermodynamic limit. Our scheme implements non-equilibrium dynamical mean field theory (DMFT) and uses a digital quantum simulator to solve a quantum impurity problem whose parameters are iterated to self-consistency via a classically computed feedback loop where quantum gate errors can be partly accounted for. We analyse the performance of the scheme in an example case.Comment: 15 pages, 5 figure

Finding novel relationships with integrated gene-gene association network analysis of Synechocystis sp. PCC 6803 using species-independent text-mining

The increasing move towards open access full-text scientific literature enhances our ability to utilize advanced text-mining methods to construct information-rich networks that no human will be able to grasp simply from 'reading the literature'. The utility of text-mining for well-studied species is obvious though the utility for less studied species, or those with no prior track-record at all, is not clear. Here we present a concept for how advanced text-mining can be used to create information-rich networks even for less well studied species and apply it to generate an open-access gene-gene association network resource for Synechocystis sp. PCC 6803, a representative model organism for cyanobacteria and first case-study for the methodology. By merging the text-mining network with networks generated from species-specific experimental data, network integration was used to enhance the accuracy of predicting novel interactions that are biologically relevant. A rule-based algorithm (filter) was constructed in order to automate the search for novel candidate genes with a high degree of likely association to known target genes by (1) ignoring established relationships from the existing literature, as they are already 'known', and (2) demanding multiple independent evidences for every novel and potentially relevant relationship. Using selected case studies, we demonstrate the utility of the network resource and filter to (i) discover novel candidate associations between different genes or proteins in the network, and (ii) rapidly evaluate the potential role of any one particular gene or protein. The full network is provided as an open-source resource.</p

A novel transport mechanism for MOMP in Chlamydophila pneumoniae and its putative role in immune-therapy

Major outer membrane proteins (MOMPs) of Gram negative bacteria are one of the most intensively studied membrane proteins. MOMPs are essential for maintaining the structural integrity of bacterial outer membranes and in adaptation of parasites to their hosts. There is evidence to suggest a role for purified MOMP from Chlamydophila pneumoniae and corresponding MOMP-derived peptides in immune-modulation, leading to a reduced atherosclerotic phenotype in apoE−/− mice via a characteristic dampening of MHC class II activity. The work reported herein tests this hypothesis by employing a combination of homology modelling and docking to examine the detailed molecular interactions that may be responsible. A three-dimensional homology model of the C. pneumoniae MOMP was constructed based on the 14 transmembrane β-barrel crystal structure of the fatty acid transporter from Escherichia coli, which provides a plausible transport mechanism for MOMP. Ligand docking experiments were used to provide details of the possible molecular interactions driving the binding of MOMP-derived peptides to MHC class II alleles known to be strongly associated with inflammation. The docking experiments were corroborated by predictions from conventional immuno-informatic algorithms. This work supports further the use of MOMP in C. pneumoniae as a possible vaccine target and the role of MOMP-derived peptides as vaccine candidates for immune-therapy in chronic inflammation that can result in cardiovascular events

Lypsylehmien rehujen sulavuudet ja typpitaseet urean ollessa ainoana tai osittaisena typenlähteenä

The digestibility and nitrogen balance tests were performed both with cows on purified protein-free feed (0-feed) with urea as the sole source of nitrogen, and with cows on a urea-rich, low-protein diet (ULP-feed). In addition to ordinary low-protein fodders, ULP-feed contained also as the source of energy so-called hemicellulose and 0-fibre, which are waste products of the cellulose industry. The determinations were made either with chromic oxide as an indicator, or by collecting the faeces and urine separately. The average digestibility percentage of the nitrogen (= urea-N) with 0-cows was 67.0±5.2, that of the dry matter 73.9±5.1 and that of the organic matter 76.6±5.1. With ULP-cows the average digestibility percentage of the total nitrogen was 71.2±4.9 and that of the urea nitrogen varied between 70 and 86. The average digestibility percentage of hemicellulose was 83 and that of the 0-fibre of the sulphite cellulose industry (0-fibre 2) 80. The nitrogen balance was positive in all experiments, + 20.4 ± 20.6 g with 0-cows and + 39,4 ± 16.4 g with ULP-cows per day.Sulavuus- ja typpitasekokeita on tehty sekä puhdistetulla, proteiinittomalla ruokinnalla olleilla lehmillä (0-ruokinta ja 0-lehmät), joilla urea on ollut ainoana typenlähteenä että lehmillä, joiden rehut ovat sisältäneet vähän proteiinia ja runsaasti ureaa (ULP-ruokinta ja ULP-lehmät). Tavanomaisten vähän proteiinia sisältävien rehujen lisäksi on ULP-ruokinnassa ollut energialähteenä puunjalostusteollisuuden jätteitä ns. hemiselluloosaa ja ns. 0-kuitua. Lannan määrän toteamiseksi on käytetty indikaattorina kromioksidia tai kerätty kaikki lanta talteen. Typpitaseenselville saamiseksi on kerätty joko lanta ja virtsa yhdessä talteen, jolloin kromioksidilla on määritetty lannan määrä tai lanta ja virtsa on kerätty erikseen talteen. 0-lehmillä on typen (= urea-N) keskimääräinen sulavuus ollut 67.0 ± 5.2 %, kuiva-aineen 73.9±5.1 % ja orgaanisen aineen 76.6±5.1 %. ULP-lehmillä kokonaistypen sulavuus on ollut keskimäärin 71.2±4.9 % ja ureatypen vaihdellut välillä 70—86 %. Hemiselluloosan keskimääräiseksi sulavuudeksi on saatu 83 % ja sulfiittiselluloosateollisuuden jätekuidun (0-kuitu 2) 80 %. Typpitase on ollut kaikissa kokeissa positiivinen, 0-lehmillä +20.4±20.6 g ja ULP-lehmillä +39.4±16.4 g päivässä

On The metabolism of benzoic acid by cows on purified protein-free and low-protein feed

vokKirjasto Aj-KBentsoehapon metaboliasta proteiinittomilla puhdistetuilla rehuilla ja vähän proteiinia sisältävillä rehulla ruokituilla koelehmill

The composition of the faecal microbial flora of milking cows on feeds containing urea as the sole or partial source of nitrogen

Using a variety of culture media, counts of live bacteria in the faeces of milking cows on purified, protein-free feed in which urea was the only source of nitrogen (0-cows) and on urea-rich, low-protein feed (ULP-cows) were made. Samples were taken from 3 0-cows and 3 ULP-cows weekly. Counts of lactobacilli, micrococci, propionic acid bacteria and lactate-utilising butyric acid bacteria were made during a period of 41 weeks, and counts of anaerobic and aerobic bacteria, enterococci and coliform bacteria for 26 weeks. Counts are given as log10 number/g fresh faeces. In the 0 cows anaerobic bacteria counts were 5—9, ULP cows 6—9; aerobic bacteria were 5—7 and 5—8 respectively. »Propionic acid bacteria» counts were 4—7 with both 0- and ULP-cows, lactobacilli 3—8 in 0 cows and 4—8 in ULP cows, and micrococci 2—7 in both groups. Enterococci were 2—6 in 0 cows and 37 in ULP cows, and coliforms 3—6 and 2—6respectively. Lactate utilising butyric acid bacteria were 0—4600/g fresh faeces, being fewer in 0-cows than in ULP cows. There was large variation in the counts of all bacteria from one week to the next. In a single cow almost all the bacterial counts could be low at the same time and the following week they could all be high. In different animals the timing of these variations was not the same. The counts of bacteria growing under anaerobic conditions were the main exception to the above variations. The ratio between gram-negative and gram-positive bacteria in faeces was measured and it was found that with both types of test feed the gram-negative were more numerous. In addition the occurrence of bacterial spores was studied; their counts, as a proportion of the total number of bacteria reacting to stain, averaged 6.5 and 26.7 % respectively in 0- and ULP-cows