On the quantum origin of few response properties.

In modern physics, the entanglement between quantum states is a well-established phenomenon. Going one step forward, one can conjecture the likely existence of an entanglement between excitations of one-particle quantum states. Working with a density matrix that is well defined within the polarization propagator formalism, together with information theory, we found that the quantum origin of, at least, few molecular response properties can be described by the entanglement between two pairs of virtual excitations of molecular orbitals (MOs).

Calibration methods of charge sensitive amplifiers at the Colorado dust accelerator.

Charge sensitive amplifiers (CSAs) are electronic integrating circuits frequently used for detecting quick charge pulses such as those produced in semiconductor detector devices and electron multipliers. One of the limitations of highly sensitive CSA circuits is the accuracy with which they can be calibrated due to the necessity of using injection capacitors on the order of a few pF, which are difficult to calibrate and to disentangle from other stray capacitance in calibration circuits. This paper presents an alternate method for calibrating the electronics for CSAs with conductive detectors, referred to as the "external conductor" method, using the detector itself to form the injection circuit.

Short-wavelength-sensitive 2 (Sws2) visual photopigment models combined with atomistic molecular simulations to predict spectral peaks of absorbance.

For many species, vision is one of the most important sensory modalities for mediating essential tasks that include navigation, predation and foraging, predator avoidance, and numerous social behaviors. The vertebrate visual process begins when photons of the light interact with rod and cone photoreceptors that are present in the neural retina. Vertebrate visual photopigments are housed within these photoreceptor cells and are sensitive to a wide range of wavelengths that peak within the light spectrum, the latter of which is a function of the type of chromophore used and how it interacts with specific amino acid residues found within the opsin protein sequence.

ΦX174 Attenuation by Whole-Genome Codon Deoptimization.

Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live-attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion.

Bacterial Populations in International Artisanal Kefirs.

Artisanal kefir is a traditional fermented dairy product made using kefir grains. Kefir has documented natural antimicrobial activity and health benefits. A typical kefir microbial community includes lactic acid bacteria (LAB), acetic acid bacteria, and yeast among other species in a symbiotic matrix.

Antimicrobial Activity of Six International Artisanal Kefirs Against serovar Enteritidis, and .

Kefir, a fermented dairy beverage, exhibits antimicrobial activity due to many metabolic products, including bacteriocins, generated by lactic acid bacteria. In this study, the antimicrobial activities of artisanal kefir products from Fusion Tea (A), Britain (B), Ireland (I), Lithuania (L), the Caucuses region (C), and South Korea (K) were investigated against select foodborne pathogens. CWD 1198, serovar Enteritidis ATCC 13076, ATCC 25923, and ATCC 14579 were inhibited by artisanal kefirs made with kefir grains from diverse origins.

Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness.

One of the long-standing holy grails of molecular evolution has been the ability to predict an organism's fitness directly from its genotype. With such predictive abilities in hand, researchers would be able to more accurately forecast how organisms will evolve and how proteins with novel functions could be engineered, leading to revolutionary advances in medicine and biotechnology. In this work, we assemble the largest reported set of experimental TEM-1 β-lactamase folding free energies and use this data in conjunction with previously acquired fitness data and computational free energy predictions to determine how much of the fitness of β-lactamase can be directly predicted by thermodynamic folding and binding free energies.

Imputation of single-cell gene expression with an autoencoder neural network.

Background: Single-cell RNA-sequencing (scRNA-seq) is a rapidly evolving technology that enables measurement of gene expression levels at an unprecedented resolution. Despite the explosive growth in the number of cells that can be assayed by a single experiment, scRNA-seq still has several limitations, including high rates of dropouts, which result in a large number of genes having zero read count in the scRNA-seq data, and complicate downstream analyses.

Methods: To overcome this problem, we treat zeros as missing values and develop nonparametric deep learning methods for imputation.

Calibration of polyvinylidene fluoride based dust detectors in response to varying grain density and incidence angle.

Permanently polarized Polyvinylidene Fluoride (PVDF) films have been used on a variety of spacecraft as in situ dust detectors to measure the size and spatial distributions of micron and sub-micron dust particles. The detectors produce a short electric pulse when impacted by a hypervelocity dust particle. The pulse amplitude depends on the mass and relative speed of the dust grain.

Saturation Mutagenesis Genome Engineering of Infective ΦX174 Bacteriophage Unamplified Oligo Pools and Golden Gate Assembly.

Here we present a novel protocol for the construction of saturation single-site-and massive multisite-mutant libraries of a bacteriophage. We segmented the ΦX174 genome into 14 nontoxic and nonreplicative fragments compatible with Golden Gate assembly. We next used nicking mutagenesis with oligonucleotides prepared from unamplified oligo pools with individual segments as templates to prepare near-comprehensive single-site mutagenesis libraries of genes encoding the F capsid protein (421 amino acids scanned) and G spike protein (172 amino acids scanned).

Protein Stability in Titan's Subsurface Water Ocean.

Models of Titan predict that there is a subsurface ocean of water and ammonia under a layer of ice. Such an ocean would be important in the search for extraterrestrial life since it provides a potentially habitable environment. To evaluate how Earth-based proteins would behave in Titan's subsurface ocean environment, we used molecular dynamics simulations to calculate the properties of proteins with the most common secondary structure types (alpha helix and beta sheet) in both Earth and Titan-like conditions.

Building a Weakly Outgassing Comet from a Generalized Ohm's Law.

When a weakly outgassing comet is sufficiently close to the Sun, the formation of an ionized coma results in solar wind mass loading and magnetic field draping around its nucleus. Using a 3D fully kinetic approach, we distill the components of a generalized Ohm's law and the effective electron equation of state directly from the self-consistently simulated electron dynamics and identify the driving physics in the various regions of the cometary plasma environment. Using the example of space plasmas, in particular multispecies cometary plasmas, we show how the description for the complex kinetic electron dynamics can be simplified through a simple effective closure, and identify where an isotropic single-electron fluid Ohm's law approximation can be used, and where it fails.

Experimental Methods of Dust Charging and Mobilization on Surfaces with Exposure to Ultraviolet Radiation or Plasmas.

Electrostatic dust transport has been hypothesized to explain a number of observations of unusual planetary phenomena. Here, it is demonstrated using three recently developed experiments in which dust particles are exposed to thermal plasma with beam electrons, beam electrons only, or ultraviolet (UV) radiation only. The UV light source has a narrow bandwidth in wavelength centered at 172 nm.

Activity of the 2013 Geminid meteoroid stream at the Moon.

The Lunar Dust Experiment (LDEX) onboard the mission orbited the Moon from 2013 October to 2014 April and detected impact ejecta generated by the continual bombardment of meteoroids to the lunar surface. While the Moon transited the Geminid meteoroid stream, LDEX observed a large enhancement in the lunar impact ejecta cloud, particularly above the portion of lunar surface normal to the Geminids radiant. Here, we present the LDEX measurements during the Geminids, using the surface density of impact ejecta at the Moon as a proxy for meteoroid activity.

A large ion beam device for laboratory solar wind studies.

The Colorado Solar Wind Experiment is a new device constructed at the Institute for Modeling Plasma, Atmospheres, and Cosmic Dust at the University of Colorado. A large cross-sectional Kaufman ion source is used to create steady state plasma flow to model the solar wind in an experimental vacuum chamber. The plasma beam has a diameter of 12 cm at the source, ion energies of up to 1 keV, and ion flows of up to 0.

Electron and Ion Dynamics of the Solar Wind Interaction with a Weakly Outgassing Comet.

Using a 3D fully kinetic approach, we disentangle and explain the ion and electron dynamics of the solar wind interaction with a weakly outgassing comet. We show that, to first order, the dynamical interaction is representative of a four-fluid coupled system. We self-consistently simulate and identify the origin of the warm and suprathermal electron distributions observed by ESA's Rosetta mission to comet 67P/Churyumov-Gerasimenko and conclude that a detailed kinetic treatment of the electron dynamics is critical to fully capture the complex physics of mass-loading plasmas.

New experimental capability to investigate the hypervelocity micrometeoroid bombardment of cryogenic surfaces.

Ice is prevalent throughout the solar system and beyond. Though the evolution of many of these icy surfaces is highly dependent on associated micrometeoroid impact phenomena, experimental investigation of these impacts has been extremely limited, especially at the impactor speeds encountered in space. The dust accelerator facility at the Institute for Modeling Plasmas, Atmospheres, and Cosmic Dust (IMPACT) of NASA's Solar System Exploration Research Virtual Institute has developed a novel cryogenic system that will facilitate future study of hypervelocity impacts into ice and icy regolith.

A permanent, asymmetric dust cloud around the Moon.

Interplanetary dust particles hit the surfaces of airless bodies in the Solar System, generating charged and neutral gas clouds, as well as secondary ejecta dust particles. Gravitationally bound ejecta clouds that form dust exospheres were recognized by in situ dust instruments around the icy moons of Jupiter and Saturn, but have hitherto not been observed near bodies with refractory regolith surfaces. High-altitude Apollo 15 and 17 observations of a 'horizon glow' indicated a putative population of high-density small dust particles near the lunar terminators, although later orbital observations yielded upper limits on the abundance of such particles that were a factor of about 10(4) lower than that necessary to produce the Apollo results.

Theoretical study of the relativistic molecular rotational g-tensor.

An original formulation of the relativistic molecular rotational g-tensor valid for heavy atom containing compounds is presented. In such formulation, the relevant terms of a molecular Hamiltonian for non-relativistic nuclei and relativistic electrons in the laboratory system are considered. Terms linear and bilinear in the nuclear rotation angular momentum and an external uniform magnetic field are considered within first and second order (relativistic) perturbation theory to obtain the rotational g-tensor.

Toward a QFT-based theory of atomic and molecular properties.

The search for a QED-based (and then QFT-based) formalism that brings solid grounds to the whole area of relativistic quantum chemistry was just implicit in the first decades of the quantum theory. During the last few years it was shown that it is still unclear how to derive a well-defined N-electron relativistic Hamiltonian, and also the way negative-energy states may contribute to electron correlation. Furthermore, the relationship among electron correlation and radiative QED corrections is even more difficult to guess.

Breit interaction effects in relativistic theory of the nuclear spin-rotation tensor.

In this work, relativistic effects on the nuclear spin-rotation (SR) tensor originated in the electron-nucleus and electron-electron Breit interactions are analysed. To this end, four-component numerical calculations were carried out in model systems HX (X=H,F,Cl,Br,I). The electron-nucleus Breit interaction couples the electrons and nuclei dynamics giving rise to a purely relativistic contribution to the SR tensor.

Relativistic effects on the nuclear magnetic resonance shielding of FX (X = F, Cl, Br, I, and At) molecular systems.

We present ab inito full four-component and spin-free calculations of the NMR shielding parameter, σ, in the FX (X = F, Cl, Br, I and At) molecular systems. A different expression that overcomes the traditional non-relativistic (NR) approximation used to calculate the relationship between spin-rotation constants and the paramagnetic terms of σ(p) are given. Large deviations from NR results are obtained for σ(X; X = I and At) and for σ(F; FAt).