Joint Institute for Computational Sciences

Correlation consistent basis sets for accurately describing core–core and core–valence correlation effects in atoms and molecules have been developed for the second row atoms Al–Ar. Two different optimization strategies were investigated, which led to two families of core–valence basis sets when the optimized functions were added to the standard correlation consistent basis sets (cc-pVnZ). In the first case, the exponents of the augmenting primitive Gaussian functions were optimized with respect to the difference between all-electron and valence–electron correlated calculations, i.e., for the core–core plus core–valence correlation energy. This yielded the cc-pCVnZ family of basis sets, which are analogous to the sets developed previously for the first row atoms [D. E. Woon and T. H. Dunning, Jr., J. Chem. Phys. 103, 4572 (1995)]. Although the cc-pCVnZ sets exhibit systematic convergence to the all-electron correlation energy at the complete basis set limit, the intershell (core–valence) correlation energy converges more slowly than the intrashell (core–core) correlation energy. Since the effect of including the core electrons on the calculation of molecular properties tends to be dominated by core–valence correlation effects, a second scheme for determining the augmenting functions was investigated. In this approach, the exponents of the functions to be added to the cc-pVnZ sets were optimized with respect to just the core–valence (intershell) correlation energy, except that a small amount of core–core correlation energy was included in order to ensure systematic convergence to the complete basis set limit. These new sets, denoted weighted core–valence basis sets (cc-pwCVnZ), significantly improve the convergence of many molecular properties with n. Optimum cc-pwCVnZ sets for the first-row atoms were also developed and show similar advantages. Both the cc-pCVnZ and cc-pwCVnZ basis sets were benchmarked in coupled cluster [CCSD(T)] calculations on a series of second row homonuclear diatomic molecules (Al2, Si2, P2, S2, and Cl2), as well as on selected diatomic molecules involving first row atoms (CO, SiO, PN, and BCl). For the calculation of core correlation effects on energetic and spectroscopic properties, the cc-pwCVnZ basis sets are recommended over the cc-pCVnZ ones.

The last eight years (2009-2017) have seen an explosive growth of interest in organic-inorganic halide perovskites in the research communities of photovoltaics and light-emitting diodes. In addition, recent advancements have demonstrated that this type of perovskite has a great potential in the technology of light-signal detection with a comparable performance to commercially available crystalline Si and III-V photodetectors. The contemporary growth of state-of-the-art multifunctional perovskites in the field of light-signal detection has benefited from its outstanding intrinsic optoelectronic properties, including photoinduced polarization, high drift mobilities, and effective charge collection, which are excellent for this application. Photoactive perovskite semiconductors combine effective light absorption, allowing detection of a wide range of electromagnetic waves from ultraviolet and visible, to the near-infrared region, with low-cost solution processability and good photon yield. This class of semiconductor might empower breakthrough photodetector technology in the field of imaging, optical communications, and biomedical sensing. Therefore, here, the focus is specifically on the critical understanding of materials synthesis, design, and engineering for the next-stage development of perovskite photodetectors and highlighting the current challenges in the field, which need to be further studied in the future.

Since the first two complete bacterial genome sequences were published in 1995, the science of bacteria has dramatically changed. Using third-generation DNA sequencing, it is possible to completely sequence a bacterial genome in a few hours and identify some types of methylation sites along the genome as well. Sequencing of bacterial genome sequences is now a standard procedure, and the information from tens of thousands of bacterial genomes has had a major impact on our views of the bacterial world. In this review, we explore a series of questions to highlight some insights that comparative genomics has produced. To date, there are genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. However, the distribution is quite skewed towards a few phyla that contain model organisms. But the breadth is continuing to improve, with projects dedicated to filling in less characterized taxonomic groups. The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system provides bacteria with immunity against viruses, which outnumber bacteria by tenfold. How fast can we go? Second-generation sequencing has produced a large number of draft genomes (close to 90 % of bacterial genomes in GenBank are currently not complete); third-generation sequencing can potentially produce a finished genome in a few hours, and at the same time provide methlylation sites along the entire chromosome. The diversity of bacterial communities is extensive as is evident from the genome sequences available from 50 different bacterial phyla and 11 different archaeal phyla. Genome sequencing can help in classifying an organism, and in the case where multiple genomes of the same species are available, it is possible to calculate the pan- and core genomes; comparison of more than 2000 Escherichia coli genomes finds an E. coli core genome of about 3100 gene families and a total of about 89,000 different gene families. Why do we care about bacterial genome sequencing? There are many practical applications, such as genome-scale metabolic modeling, biosurveillance, bioforensics, and infectious disease epidemiology. In the near future, high-throughput sequencing of patient metagenomic samples could revolutionize medicine in terms of speed and accuracy of finding pathogens and knowing how to treat them.

Ground-state properties of exotic even-even nuclei with extreme neutron-to-proton ratios are described in the framework of self-consistent mean-field theory with pairing formulated in coordinate space. This theory properly accounts for the influence of the particle continuum, which is particularly important for weakly bound systems. The pairing properties of nuclei far from stability are studied with several interactions emphasizing different aspects, such as the range and density dependence of the effective interaction. Measurable consequences of spatially extended pairing fields are presented, and the sensitivity of the theoretical predictions to model details is discussed. \textcopyright{} 1996 The American Physical Society.

Abstract The Joint Automated Repository for Various Integrated Simulations (JARVIS) is an integrated infrastructure to accelerate materials discovery and design using density functional theory (DFT), classical force-fields (FF), and machine learning (ML) techniques. JARVIS is motivated by the Materials Genome Initiative (MGI) principles of developing open-access databases and tools to reduce the cost and development time of materials discovery, optimization, and deployment. The major features of JARVIS are: JARVIS-DFT, JARVIS-FF, JARVIS-ML, and JARVIS-tools. To date, JARVIS consists of ≈40,000 materials and ≈1 million calculated properties in JARVIS-DFT, ≈500 materials and ≈110 force-fields in JARVIS-FF, and ≈25 ML models for material-property predictions in JARVIS-ML, all of which are continuously expanding. JARVIS-tools provides scripts and workflows for running and analyzing various simulations. We compare our computational data to experiments or high-fidelity computational methods wherever applicable to evaluate error/uncertainty in predictions. In addition to the existing workflows, the infrastructure can support a wide variety of other technologically important applications as part of the data-driven materials design paradigm. The JARVIS datasets and tools are publicly available at the website: https://jarvis.nist.gov .

In the past few decades, it has become apparent that most of the microbial diversity on Earth has never been characterized in laboratory cultures. We show that these unknown microbes, sometimes called “microbial dark matter,” are numerically dominant in all major environments on Earth, with the exception of the human body, where most of the microbes have been cultured. We also estimate that about one-quarter of the population of microbial cells on Earth belong to phyla with no cultured relatives, suggesting that these never-before-studied organisms may be important for ecosystem functions.

Abstract Single-atom catalysts (SACs) have attracted considerable attention in the catalysis community. However, fabricating intrinsically stable SACs on traditional supports (N-doped carbon, metal oxides, etc.) remains a formidable challenge, especially under high-temperature conditions. Here, we report a novel entropy-driven strategy to stabilize Pd single-atom on the high-entropy fluorite oxides (CeZrHfTiLa)O x (HEFO) as the support by a combination of mechanical milling with calcination at 900 °C. Characterization results reveal that single Pd atoms are incorporated into HEFO (Pd 1 @HEFO) sublattice by forming stable Pd–O–M bonds (M = Ce/Zr/La). Compared to the traditional support stabilized catalysts such as Pd@CeO 2 , Pd 1 @HEFO affords the improved reducibility of lattice oxygen and the existence of stable Pd–O–M species, thus exhibiting not only higher low-temperature CO oxidation activity but also outstanding resistance to thermal and hydrothermal degradation. This work therefore exemplifies the superiority of high-entropy materials for the preparation of SACs.

Bacterioplankton of the marine Roseobacter clade have genomes that reflect a dynamic environment and diverse interactions with marine plankton. Comparative genome sequence analysis of three cultured representatives suggests that cellular requirements for nitrogen are largely provided by regenerated ammonium and organic compounds (polyamines, allophanate, and urea), while typical sources of carbon include amino acids, glyoxylate, and aromatic metabolites. An unexpectedly large number of genes are predicted to encode proteins involved in the production, degradation, and efflux of toxins and metabolites. A mechanism likely involved in cell-to-cell DNA or protein transfer was also discovered: vir-related genes encoding a type IV secretion system typical of bacterial pathogens. These suggest a potential for interacting with neighboring cells and impacting the routing of organic matter into the microbial loop. Genes shared among the three roseobacters and also common in nine draft Roseobacter genomes include those for carbon monoxide oxidation, dimethylsulfoniopropionate demethylation, and aromatic compound degradation. Genes shared with other cultured marine bacteria include those for utilizing sodium gradients, transport and metabolism of sulfate, and osmoregulation.

Burkholderia xenovorans LB400 (LB400), a well studied, effective polychlorinated biphenyl-degrader, has one of the two largest known bacterial genomes and is the first nonpathogenic Burkholderia isolate sequenced. From an evolutionary perspective, we find significant differences in functional specialization between the three replicons of LB400, as well as a more relaxed selective pressure for genes located on the two smaller vs. the largest replicon. High genomic plasticity, diversity, and specialization within the Burkholderia genus are exemplified by the conservation of only 44% of the genes between LB400 and Burkholderia cepacia complex strain 383. Even among four B. xenovorans strains, genome size varies from 7.4 to 9.73 Mbp. The latter is largely explained by our findings that >20% of the LB400 sequence was recently acquired by means of lateral gene transfer. Although a range of genetic factors associated with in vivo survival and intercellular interactions are present, these genetic factors are likely related to niche breadth rather than determinants of pathogenicity. The presence of at least eleven "central aromatic" and twenty "peripheral aromatic" pathways in LB400, among the highest in any sequenced bacterial genome, supports this hypothesis. Finally, in addition to the experimentally observed redundancy in benzoate degradation and formaldehyde oxidation pathways, the fact that 17.6% of proteins have a better LB400 paralog than an ortholog in a different genome highlights the importance of gene duplication and repeated acquirement, which, coupled with their divergence, raises questions regarding the role of paralogs and potential functional redundancies in large-genome microbes.

An improved prescription for choosing a transformed harmonic-oscillator (THO) basis for use in configuration-space Hartree-Fock-Bogoliubov (HFB) calculations is presented. The new $\text{HFB}+\text{THO}$ framework that follows accurately reproduces the results of coordinate-space HFB calculations for spherical nuclei, including those that are weakly bound. Furthermore, it is fully automated, facilitating its use in systematic investigations of large sets of nuclei throughout the periodic table. As a first application, we have carried out calculations using the Skyrme force SLy4 and volume pairing, with exact particle-number projection following application of the Lipkin-Nogami prescription. Calculations were performed for all even-even nuclei from the proton drip line to the neutron drip line having proton numbers $Z=2,4,\dots{},108$ and neutron numbers $N=2,4,\dots{},188$. We focus on nuclei near the neutron drip line and find that there exist numerous particle-bound even-even nuclei (i.e., nuclei with negative Fermi energies) that have at the same time negative two-neutron separation energies. This phenomenon, which was earlier noted for light nuclei, is attributed to bound shape isomers beyond the drip line.

The production of kaons at subthreshold energies from heavy-ion collisions is sensitive to the nuclear equation of state. In the Boltzmann-Uehling-Uhlenbeck model, the number of produced kaons from central collisions between heavy nuclei at incident energies around 700 MeV/nucleon can vary by a factor of \ensuremath{\sim} 3, depending on the equation of state.

Quantitative and well-targeted design of modern alloys is extremely challenging due to their immense compositional space. When considering only 50 elements for compositional blending the number of possible alloys is practically infinite, as is the associated unexplored property realm. In this paper, we present a simple property-targeted quantitative design approach for atomic-level complexity in complex concentrated and high-entropy alloys, based on quantum-mechanically derived atomic-level pressure approximation. It allows identification of the best suited element mix for high solid-solution strengthening using the simple electronegativity difference among the constituent elements. This approach can be used for designing alloys with customized properties, such as a simple binary NiV solid solution whose yield strength exceeds that of the Cantor high-entropy alloy by nearly a factor of two. This study provides general design rules that enable effective utilization of atomic level information to reduce the immense degrees of freedom in compositional space without sacrificing physics-related plausibility.

ABSTRACT We have performed ab initio neutrino radiation hydrodynamics simulations in three and two spatial dimensions (3D and 2D) of core-collapse supernovae from the same 15 M ☉ progenitor through 440 ms after core bounce. Both 3D and 2D models achieve explosions; however, the onset of explosion (shock revival) is delayed by ∼100 ms in 3D relative to the 2D counterpart and the growth of the diagnostic explosion energy is slower. This is consistent with previously reported 3D simulations utilizing iron-core progenitors with dense mantles. In the ∼100 ms before the onset of explosion, diagnostics of neutrino heating and turbulent kinetic energy favor earlier explosion in 2D. During the delay, the angular scale of convective plumes reaching the shock surface grows and explosion in 3D is ultimately lead by a single, large-angle plume, giving the expanding shock a directional orientation not dissimilar from those imposed by axial symmetry in 2D simulations. We posit that shock revival and explosion in the 3D simulation may be delayed until sufficiently large plumes form, whereas such plumes form more rapidly in 2D, permitting earlier explosions.

Supernova simulations to date have assumed that during core collapse electron captures occur dominantly on free protons, while captures on heavy nuclei are Pauli blocked and are ignored. We have calculated rates for electron capture on nuclei with mass numbers A=65-112 for the temperatures and densities appropriate for core collapse. We find that these rates are large enough so that, in contrast to previous assumptions, electron capture on nuclei dominates over capture on free protons. This leads to significant changes in core collapse simulations.

As an important model for transmembrane signaling, methyl-accepting chemotaxis proteins (MCPs) have been extensively studied by using genetic, biochemical, and structural techniques. However, details of the molecular mechanism of signaling are still not well understood. The availability of genomic information for hundreds of species enables the identification of features in protein sequences that are conserved over long evolutionary distances and thus are critically important for function. We carried out a large-scale comparative genomic analysis of the MCP signaling and adaptation domain family and identified features that appear to be critical for receptor structure and function. Based on domain length and sequence conservation, we identified seven major MCP classes and three distinct structural regions within the cytoplasmic domain: signaling, methylation, and flexible bundle subdomains. The flexible bundle subdomain, not previously recognized in MCPs, is a conserved element that appears to be important for signal transduction. Remarkably, the N- and C-terminal helical arms of the cytoplasmic domain maintain symmetry in length and register despite dramatic variation, from 24 to 64 7-aa heptads in overall domain length. Loss of symmetry is observed in some MCPs, where it is concomitant with specific changes in the sensory module. Each major MCP class has a distinct pattern of predicted methylation sites that is well supported by experimental data. Our findings indicate that signaling and adaptation functions within the MCP cytoplasmic domain are tightly coupled, and that their coevolution has contributed to the significant diversity in chemotaxis mechanisms among different organisms.

The odd-even staggering of nuclear masses was recognized in the early days of nuclear physics. Recently, a similar effect was discovered in other finite fermion systems, such as ultrasmall metallic grains and metal clusters. It is believed that the staggering in nuclei and grains is primarily due to pairing correlations (superconductivity), while in clusters it is caused by the Jahn-Teller effect. We find that, for light- and medium-mass nuclei, the staggering has two components. The first originates from pairing while the second, comparable in magnitude, has its roots in the deformed mean field.

Real-time personalized motion monitoring and analysis are important for human health. Thus, to satisfy the needs in this area and the ever-increasing demand for wearable electronics, we design and develop a wireless piezoelectric device consisting of a piezoelectric pressure sensor based on electrospun PVDF/BaTiO3 nanowire (NW) nanocomposite fibers and a wireless circuit system integrated with a data conversion control module, a signal acquisition and amplification module, and a Bluetooth module. Finally, real-time piezoelectric signals of human motion can be displayed by an App on an Android mobile phone for wireless monitoring and analysis. This wireless piezoelectric device is proven to be sensitive to human motion such as squatting up and down, walking, and running. The results indicate that our wireless piezoelectric device has potential applications in wearable medical electronics, particularly in the fields of rehabilitation and sports medicine.

Structure of the odd- $N$ superheavy elements with $Z\ensuremath{\lesssim}118$ and $N\ensuremath{\lesssim}175$ is investigated using the self-consistent Skyrme-Hartree-Fock-Bogoliubov method with pairing. Microscopic analysis of one-quasiparticle neutron states, alpha-decay energies, and deformations is performed. Good agreement was obtained with the recently reported $\ensuremath{\alpha}$-decay chains of ${}^{289}114$ and ${}^{293}118$.

Additive manufacturing, commonly known as 3D printing, is an advancement over traditional formative manufacturing methods. It can increase efficiency in manufacturing operations highlighting advantages such as rapid prototyping, reduction of waste, reduction of manufacturing time and cost, and increased flexibility in a production setting. The additive manufacturing (AM) process consists of five steps: (1) preparation of 3D models for printing (designing the part/object), (2) conversion to STL file, (3) slicing and setting of 3D printing parameters, (4) actual printing, and (5) finishing/post-processing methods. Very often, the 3D printed part is sufficient by itself without further post-printing processing. However, many applications still require some forms of post-processing, especially those for industrial applications. This review focuses on the importance of different finishing/post-processing methods for 3D-printed polymers. Different 3D printing technologies and materials are considered in presenting the authors’ perspective. The advantages and disadvantages of using these methods are also discussed together with the cost and time in doing the post-processing activities. Lastly, this review also includes discussions on the enhancement of properties such as electrical, mechanical, and chemical, and other characteristics such as geometrical precision, durability, surface properties, and aesthetic value with post-printing processing. Future perspectives is also provided towards the end of this review.

The elementary excitations of vibration in solids are phonons. But in liquids phonons are extremely short lived and marginalized. In this Letter through classical and ab initio molecular dynamics simulations of the liquid state of various metallic systems we show that different excitations, the local configurational excitations in the atomic connectivity network, are the elementary excitations in high temperature metallic liquids. We also demonstrate that the competition between the configurational excitations and phonons determines the so-called crossover phenomenon in liquids. These discoveries open the way to the explanation of various complex phenomena in liquids, such as fragility and the rapid increase in viscosity toward the glass transition, in terms of these excitations.