Efficient calculation of electronic structure using O(N) density functional theory

We propose an efficient way to calculate the electronic structure of large systems by combining a large-scale first-principles density functional theory code, Conquest, and an efficient interior eigenproblem solver, the Sakurai-Sugiura method. The electronic Hamiltonian and charge density of large systems are obtained by \conquest and the eigenstates of the Hamiltonians are then obtained by the Sakurai-Sugiura method. Applications to a hydrated DNA system, and adsorbed P2 molecules and Ge hut clusters on large Si substrates demonstrate the applicability of this combination on systems with 10,000+ atoms with high accuracy and efficiency.Comment: Submitted to J. Chem. Theor. Compu

Optimized multi-site local orbitals in the large-scale DFT program CONQUEST

We introduce numerical optimization of multi-site support functions in the linear-scaling DFT code CONQUEST. Multi-site support functions, which are linear combinations of pseudo-atomic orbitals on a target atom and those neighbours within a cutoff, have been recently proposed to reduce the number of support functions to the minimal basis while keeping the accuracy of a large basis [J. Chem. Theory Comput., 2014, 10, 4813]. The coefficients were determined by using the local filter diagonalization (LFD) method [Phys. Rev. B, 2009, 80, 205104]. We analyse the effect of numerical optimization of the coefficients produced by the LFD method. Tests on crystalline silicon, a benzene molecule and hydrated DNA systems show that the optimization improves the accuracy of the multi-site support functions with small cutoffs. It is also confirmed that the optimization guarantees the variational energy minimizations with multi-site support functions.Comment: 25 pages, 3 figures, submitted to Phys. Chem. Chem. Phy

Large-Scale DFT Methods for Calculations of Materials with Complex Structures

Large-scale density functional theory (DFT) calculations provide a powerful tool to investigate the atomic and electronic structure of materials with complex structures. This article reviews a large-scale DFT calculation method, the multi-site support function (MSSF) method, in the CONQUEST code. MSSFs are linear combinations of the basis functions which belong to a group of atoms in a local region. The method can reduce the computational time while preserving accuracy. The accuracy of MSSFs has been assessed for bulk Si, Al, Fe and NiO and hydrated DNA, which demonstrate the applicability of the MSSFs for varied materials. The applications of MSSFs on large systems with several thousand atoms, which have complex interfaces and non-periodic structures, indicate that the MSSF method is promising for precise investigations of materials with complex structures

GESI: Gammachirp Envelope Similarity Index for Predicting Intelligibility of Simulated Hearing Loss Sounds

We propose an objective intelligibility measure (OIM), called the Gammachirp Envelope Similarity Index (GESI), which can predict the speech intelligibility (SI) of simulated hearing loss (HL) sounds for normal hearing (NH) listeners. GESI is an intrusive method that computes the SI metric using the gammachirp filterbank (GCFB), the modulation filterbank, and the extended cosine similarity measure. The unique features of GESI are that i) it reflects the hearing impaired (HI) listener's HL that appears in the audiogram and is caused by active and passive cochlear dysfunction, ii) it provides a single goodness metric, as in the widely used STOI and ESTOI, that can be used immediately to evaluate SE algorithms, and iii) it provides a simple control parameter to accept the level asymmetry of the reference and test sounds and to deal with individual listening conditions and environments. We evaluated GESI and the conventional OIMs, STOI, ESTOI, MBSTOI, and HASPI versions 1 and 2 by using four SI experiments on words of male and female speech sounds in both laboratory and remote environments. GESI was shown to outperform the other OIMs in the evaluations. GESI could be used to improve SE algorithms in assistive listening devices for individual HI listeners.Comment: This paper was submitted to JASA on March 14, 202

Genetic diversity of group A rotaviruses associated with repeated outbreaks of diarrhea in a farrow-to-finish farm: identification of a porcine rotavirus strain bearing a novel VP7 genotype, G26

Group A rotaviruses (GARs) are one of the most common causes of diarrhea in suckling pigs. Although a number of G and P genotypes have been identified in porcine GARs, few attempts have been made to study the molecular epidemiology of these viruses associated with diarrhea outbreaks within a farm over an extended period of time. Here, we investigated the molecular characteristics of GARs that caused four outbreaks of diarrhea among suckling pigs in a farrow-to-finish farm over the course of a year. G and P genotyping of GARs detected at each outbreak demonstrated genetic diversity in this farm as follows: G9P[23] was detected at the first outbreak, G9P[13]/[22] and G9P[23] at the second, G3P[7] at the third, and G9P[23], G5P[13]/[22], and P[7] combined with an untypeable G genotype at the fourth. Sequence analysis of the detected GARs revealed that such genetic diversity could have resulted not only from the introduction of new GAR strains, but also from gene reassortment between GAR strains within the farm. Further, the GAR strain carrying the untypeable G genotype was shown to be a novel porcine GAR bearing a new G26 genotype, as confirmed by the Rotavirus Classification Working Group

High-accuracy large-scale DFT calculations using localized orbitals in complex electronic systems: The case of graphene-metal interfaces

Over many years, computational simulations based on Density Functional Theory (DFT) have been used extensively to study many different materials at the atomic scale. However, its application is restricted by system size, leaving a number of interesting systems without a high-accuracy quantum description. In this work, we calculate the electronic and structural properties of a graphene-metal system significantly larger than in previous plane-wave calculations with the same accuracy. For this task we use a localised basis set with the \textsc{Conquest} code, both in their primitive, pseudo-atomic orbital form, and using a recent multi-site approach. This multi-site scheme allows us to maintain accuracy while saving computational time and memory requirements, even in our exemplar complex system of graphene grown on Rh(111) with and without intercalated atomic oxygen. This system offers a rich scenario that will serve as a benchmark, demonstrating that highly accurate simulations in cells with over 3000 atoms are feasible with modest computational resources.Comment: 11 pages, 3 figures, submitted to J. Chem. Theor. Compu

Hepatocyte apoptosis is enhanced after ischemia/reperfusion in the steatotic liver

Liver steatosis is associated with organ dysfunction after hepatic resection and transplantation which may be caused by hepatic ischemia/reperfusion injury. The aim of the current study was to determine the precise mechanism leading to hepatocyte apoptosis after steatotic liver ischemia/reperfusion. Using a murine model of partial hepatic ischemia for 90 min, we examined the levels and pathway of apoptosis, and the peroxynitrite expression, serum alanine aminotransferase levels, and liver histology 1 and 4 h after reperfusion. In the steatotic liver, the peroxynitrite expression increased after ischemia/reperfusion. Significant hepatocyte apoptosis in the steatotic liver was seen after reperfusion, caused by upregulation of cleaved caspases 9 and 3, but not caspase 8. Serum alanine aminotransferase levels were elevated and histological examination revealed severe liver injury in the steatotic liver 4 h after reperfusion. In mice treated with aminoguanidine, ischemia/reperfusion-induced increases in serum alanine aminotransferase levels and apoptosis were significantly reduced in steatotic liver compared with mice treated with phosphate buffered saline. Survival of mice with steatotic livers significantly improved by treatment with aminoguanidine. Our data suggested that the steatotic liver is vulnerable to hepatic ischemia/reperfusion, leading to significant hepatocyte apoptosis by the mitochondrial permeability transition, and thereby resulting in organ dysfunction

Isolation and immortalization of macrophages derived from fetal porcine small intestine and their susceptibility to porcine viral pathogen infections

Macrophages are a heterogeneous population of cells that are present in all vertebrate tissues. They play a key role in the innate immune system, and thus, in vitro cultures of macrophages provide a valuable model for exploring their tissue-specific functions and interactions with pathogens. Porcine macrophage cultures are often used for the identification and characterization of porcine viral pathogens. Recently, we have developed a simple and efficient method for isolating primary macrophages from the kidneys and livers of swine. Here, we applied this protocol to fetal porcine intestinal tissues and demonstrated that porcine intestinal macrophages (PIM) can be isolated from mixed primary cultures of porcine small intestine-derived cells. Since the proliferative capacity of primary PIM is limited, we attempted to immortalize them by transferring the SV40 large T antigen and porcine telomerase reverse transcriptase genes using lentiviral vectors. Consequently, immortalized PIM (IPIM) were successfully generated and confirmed to retain various features of primary PIM. We further revealed that IPIM are susceptible to infection by the African swine fever virus and the porcine reproductive and respiratory syndrome virus and support their replication. These findings suggest that the IPIM cell line is a useful tool for developing in vitro models that mimic the intestinal mucosal microenvironments of swine, and for studying the interactions between porcine pathogens and host immune cells