Measuring surface-area-to-volume ratios in soft porous materials using laser-polarized xenon interphase exchange NMR

We demonstrate a minimally invasive nuclear magnetic resonance (NMR) technique that enables determination of the surface-area-to-volume ratio (S/V) of soft porous materials from measurements of the diffusive exchange of laser-polarized 129Xe between gas in the pore space and 129Xe dissolved in the solid phase. We apply this NMR technique to porous polymer samples and find approximate agreement with destructive stereological measurements of S/V obtained with optical confocal microscopy. Potential applications of laser-polarized xenon interphase exchange NMR include measurements of in vivo lung function in humans and characterization of gas chromatography columns.Comment: 14 pages of text, 4 figure

Artificial intelligence methods enhance the discovery of RNA interactions

Understanding how RNAs interact with proteins, RNAs, or other molecules remains a challenge of main interest in biology, given the importance of these complexes in both normal and pathological cellular processes. Since experimental datasets are starting to be available for hundreds of functional interactions between RNAs and other biomolecules, several machine learning and deep learning algorithms have been proposed for predicting RNA-RNA or RNA-protein interactions. However, most of these approaches were evaluated on a single dataset, making performance comparisons difficult. With this review, we aim to summarize recent computational methods, developed in this broad research area, highlighting feature encoding and machine learning strategies adopted. Given the magnitude of the effect that dataset size and quality have on performance, we explored the characteristics of these datasets. Additionally, we discuss multiple approaches to generate datasets of negative examples for training. Finally, we describe the best-performing methods to predict interactions between proteins and specific classes of RNA molecules, such as circular RNAs (circRNAs) and long non-coding RNAs (lncRNAs), and methods to predict RNA-RNA or RNA-RBP interactions independently of the RNA type

Single-artificial-atom lasing using a voltage-biased superconducting charge qubit

We consider a system composed of a single artificial atom coupled to a cavity mode. The artificial atom is biased such that the most dominant relaxation process in the system takes the atom from its ground state to its excited state, thus ensuring population inversion. A recent experimental manifestation of this situation was achieved using a voltage-biased superconducting charge qubit. Even under the condition of `inverted relaxation', lasing action can be suppressed if the `relaxation' rate is larger than a certain threshold value. Using simple transition-rate arguments and a semiclassical calculation, we derive analytic expressions for the lasing suppression condition and the state of the cavity in both the lasing and suppressed-lasing regimes. The results of numerical calculations agree very well with the analytically derived results. We start by analyzing a simplified two-level-atom model, and we then analyze a three-level-atom model that should describe accurately the recently realized superconducting artificial-atom laser.Comment: 21 pages in preprint format, 6 figure

Preface: BITS2014, the annual meeting of the Italian Society of Bioinformatics

This Preface introduces the content of the BioMed Central journal Supplements related to BITS2014 meeting, held in Rome, Italy, from the 26th to the 28th of February, 2014

Bonn Potential and Shell-Model Calculations for 206,205,204Pb

The structure of the nuclei 206,205,204Pb is studied interms of shell model employing a realistic effective interaction derived from the Bonn A nucleon-nucleon potential. The energy spectra, binding energies and electromagnetic properties are calculated and compared with experiment. A very good overall agreement is obtained. This evidences the reliability of our realistic effective interaction and encourages use of modern realistic potentials in shell-model calculations for heavy-mass nuclei.Comment: 4 pages, 4 figures, submitted to Physical Review

COVID-19 and genetic variants of protein involved in the SARS-CoV-2 entry into the host cells

The recent global COVID-19 public health emergency is caused by SARS-CoV-2 infections and can manifest extremely variable clinical symptoms. Host human genetic variability could influence susceptibility and response to infection. It is known that ACE2 acts as a receptor for this pathogen, but the viral entry into the target cell also depends on other proteins. The aim of this study was to investigate the variability of genes coding for these proteins involved in the SARS-CoV-2 entry into the cells. We analyzed 131 COVID-19 patients by exome sequencing and examined the genetic variants of TMPRSS2, PCSK3, DPP4, and BSG genes. In total we identified seventeen variants. In PCSK3 gene, we observed a missense variant (c.893G>A) statistically more frequent compared to the EUR GnomAD reference population and a missense mutation (c.1906A>G) not found in the GnomAD database. In TMPRSS2 gene, we observed a significant difference in the frequency of c.331G>A, c.23G>T, and c.589G>A variant alleles in COVID-19 patients, compared to the corresponding allelic frequency in GnomAD. Genetic variants in these genes could influence the entry of the SARS-CoV-2. These data also support the hypothesis that host genetic variability may contribute to the variability in infection susceptibility and severity

Time-optimal CNOT between indirectly coupled qubits in a linear Ising chain

We give analytical solutions for the time-optimal synthesis of entangling gates between indirectly coupled qubits 1 and 3 in a linear spin chain of three qubits subject to an Ising Hamiltonian interaction with equal coupling $J$ plus a local magnetic field acting on the intermediate qubit. The energy available is fixed, but we relax the standard assumption of instantaneous unitary operations acting on single qubits. The time required for performing an entangling gate which is equivalent, modulo local unitary operations, to the $\mathrm{CNOT}(1, 3)$ between the indirectly coupled qubits 1 and 3 is $T=\sqrt{3/2} J^{-1}$, i.e. faster than a previous estimate based on a similar Hamiltonian and the assumption of local unitaries with zero time cost. Furthermore, performing a simple Walsh-Hadamard rotation in the Hlibert space of qubit 3 shows that the time-optimal synthesis of the $\mathrm{CNOT}^{\pm}(1, 3)$ (which acts as the identity when the control qubit 1 is in the state $\ket{0}$, while if the control qubit is in the state $\ket{1}$ the target qubit 3 is flipped as $\ket{\pm}\rightarrow \ket{\mp}$) also requires the same time $T$.Comment: 9 pages; minor modification

Ground-γ\gamma band coupling in heavy deformed nuclei and SU(3) contraction limit

We derive analytic expressions for the energies and $B(E2)$-transition probabilities in the states of the ground and $\gamma$ bands of heavy deformed nuclei within a collective Vector-Boson Model with SU(3) dynamical symmetry. On this basis we examine the analytic behavior of the SU(3) energy splitting and the B(E2) interband transition ratios in the SU(3) contraction limits of the model. The theoretical analyses outline physically reasonable ways in which the ground-$\gamma$ band coupling vanishes. The experimental data on the lowest collective states of even-even rare earth nuclei and actinides strongly support the theoretical results. They suggest that a transition from the ground-$\gamma$ band coupling scheme to a scheme in which the ground band is situated in a separate irreducible representation of SU(3) should be realized towards the midshell regions. We propose that generally the SU(3) group contraction process should play an important role for such a kind of transitions in any collective band coupling scheme in heavy deformed nuclei.Comment: 24 pages (LaTeX), 7 figures (12 postscript files

Photodetection of propagating quantum microwaves in circuit QED

We develop the theory of a metamaterial composed of an array of discrete quantum absorbers inside a one-dimensional waveguide that implements a high-efficiency microwave photon detector. A basic design consists of a few metastable superconducting nanocircuits spread inside and coupled to a one-dimensional waveguide in a circuit QED setup. The arrival of a {\it propagating} quantum microwave field induces an irreversible change in the population of the internal levels of the absorbers, due to a selective absorption of photon excitations. This design is studied using a formal but simple quantum field theory, which allows us to evaluate the single-photon absorption efficiency for one and many absorber setups. As an example, we consider a particular design that combines a coplanar coaxial waveguide with superconducting phase qubits, a natural but not exclusive playground for experimental implementations. This work and a possible experimental realization may stimulate the possible arrival of "all-optical" quantum information processing with propagating quantum microwaves, where a microwave photodetector could play a key role.Comment: 27 pages, submitted to Physica Scripta for Nobel Symposium on "Qubits for Quantum Information", 200