Atomic cluster expansion force field based thermal property material design with density functional theory level accuracy in non-equilibrium molecular dynamics calculations over sub-million atoms

Non-equilibrium molecular dynamics (NEMD) techniques are widely used for investigating lattice thermal conductivity. Recently, machine learning force fields (MLFFs) have emerged as a promising approach to enhance the precision in NEMD simulations. This study is aimed at demonstrating the potential of MLFFs in realizing NEMD calculations for large-scale systems containing over 100,000 atoms with density functional theory (DFT)-level accuracy. Specifically, the atomic cluster expansion (ACE) force field is employed, using Si as an example. The ACE potential incorporates 4-body interactions and features a training dataset consisting of 1000 order structures from first-principles molecular dynamics calculations, resulting in a highly accurate vibrational spectrum. Moreover, the ACE potential can reproduce thermal conductivity values comparable with those derived from DFT calculations via the Boltzmann equation. To demonstrate the application of MLFFs to systems containing over 100,000 atoms, NEMD simulations are conducted on thin films ranging from 100 nm to 500 nm, with the 100 nm films exhibiting defect rates of up to 1.5%. The results show that the thermal conductivity deviates by less than 5% from DFT or theoretical results in both scenarios, which highlights the ability of the ACE potential in calculating the thermal conductivity on a large scale with DFT-level accuracy. The proposed approach is expected to promote the application of MLFFs in various fields and serve as a feasible alternative to virtual experiments. Furthermore, this work demonstrates the potential of MLFFs in enhancing the accuracy of NEMD simulations for investigating lattice thermal conductivity for systems with over 100,000 atoms.Comment: 24 pages including with supporting infomatio

An optical transition-edge sensor with high energy resolution

Optical transition-edge sensors have shown energy resolution for resolving the number of incident photons at the telecommunication wavelength. Higher energy resolution is required for biological imaging and microscope spectroscopy. In this paper, we report on a Au/Ti (10/20 nm) bilayer TES that showed high energy resolution. This was achieved by lowering the critical temperature Tc to 115 mK and the resultant energy resolution was 67 meV full width at half maximum (FWHM) at 0.8 eV. When Tc was lowered to 115 mK, the theoretical resolution would scaled up to 30 meV FWHM, considering that the typical energy resolution of optical TESs is 150 meV and Tc is 300 mK. To investigate the gap between the theoretical expectation (30 meV) and the measured value (67 meV), we measured its complex impedance and current noise. We found excess Johnson noise in the TES and an excess Johnson term M was 1.5 at a bias point where the resistance was 10% of normal resistance. For reference, the TES was compared with a TES showing typical energy resolution (156 meV FWHM). We will discuss what improved the energy resolution and what might have been the limiting factor on it

海洋酸性化による音波伝搬損失への影響

発表番号: 10-29 / 海洋音響学会2010年度研究発表会（2010年5月27日～28日, 東京工業大学） / 海洋音響学会2010年度研究発表会講演論文集から転

SDGs Education at Kibi International University

departmental bulletin pape

Molecular basis of virulence in clinical isolates of Escherichia coli and Salmonella species from a tertiary hospital in the Eastern Cape, South Africa

<p>Abstract</p> <p>Background</p> <p>Apart from localized gastrointestinal infections, <it>Escherichia coli </it>and <it>Salmonella </it>species are major causes of systemic disease in both humans and animals. <it>Salmonella </it>spp. cause invasive infections such as enteric fever, septicemia, osteomyelitis and meningitis while certain types of <it>E. coli </it>can cause systemic infections, including</p> <p>pyelonephritis, meningitis and septicemia. These characteristic requires the involvement of a myriad of virulence factors.</p> <p>Methods</p> <p>This study investigated the virulence factors of <it>Escherichia coli </it>and <it>Salmonella </it>species in clinical specimens from patients with diarrhoea presenting to health care centres in Oliver R. Tambo District Municipality, Eastern Cape Province, Republic of South Africa. Microbiology analysis involved the use of cultural and molecular techniques.</p> <p>Results</p> <p>Out of a total of 315 samples screened, <it>Salmonella </it>isolates were obtained in 119 (37.8%) of cases and these comprised: <it>S. choleraesuis </it>(6%), <it>S. enteritidis </it>(4%), <it>S. eppendorf </it>(1%), <it>S. hadar </it>(1%), <it>S. isangi </it>(8%), <it>S. panama </it>(1%), <it>S. typhi </it>(52%), <it>S. typhimurium </it>(25%) and untyped <it>Salmonella </it>spp. (2%). Among the <it>Salmonella </it>species 87 (73.1%) were invasive. Using molecular diagnostic methods, diarrheagenic <it>E. coli </it>were detected in 90 cases (28.6%): the greater proportion of this were enteroaggregative <it>E. coli </it>(EAEC) 37 (41.1%), enteropathogenic <it>E. coli </it>(EPEC) 21 (23.3%) and enterohemorrhagic <it>E. coli </it>(EHEC) 21 (23.3%). The predominant virulence gene among the diarrheagenic <it>E. coli </it>was EAEC heat-stable enterotoxin <it>astA </it>genes while the virulence genes identified in the <it>Salmonella </it>strains were 15 (12.6%) flic and 105 (88.2%) inv genes. The amino acid identity of the representative genes showed 95-100% similarity to corresponding blast searched sequence.</p> <p>Conclusions</p> <p>This study showed the diversity of virulence gene expression in two major enteric pathogens. <it>S. typhi </it>and enteroaggregative <it>E. coli </it>were the predominant enteropathogens in our study area with an indication that EAEC is endemic within our study population. It was observed among other things that some diarrheagenic <it>E. coli </it>isolated from apparently asymptomatic subjects expressed some virulence genes at frequency as high as seen in diarrheagenic cases. This study underlines the importance of understanding the virulence composition and diversity of pathogens for enhanced clinico-epidemiological monitoring and health care delivery.</p

Inhibition of infection of incoming HIV-1 virus by RNA-cleaving DNA enzyme

AbstractNine different DNA enzymes (DzV3-n, n=1–9) targeting the V3 loop region of HIV-1 HXB2 were synthesized. One of those, DzV3-9, efficiently cleaved the target in the conserved sequence in the RNA transcript in vitro. DzV3-9 was stable in the cells and inhibited replication of both NL432 and SF162 strains in U87 cells expressing CD4 and co-receptors. The inhibitory effect of DNAzyme on incoming HIV-1 was also demonstrated with pseudotype virions generated by NL432-based luciferase reporter genes. Thus, an efficient, stable DNAzyme against a functionally important region of HIV-1 was identified, and it may be useful for prevention of HIV-1 infection

Enhanced visualization of the portal vein system in superior mesenteric arterial portography using prostaglandin E1.

The portal vein system was clearly visualized in superior mesenteric arterial portography using prostaglandin E1. Angiographic examination was performed in 68 patients with various liver diseases during the 2 year period from 1980 to 1981. Twenty microgram of prostaglandin E1 was injected into the superior mesenteric artery 30 seconds before injection of 60 ml of contrast medium. The main portal vein was visualized in all of 68 cases. A high rate of success for visualization of the intrahepatic portal vein system by prostaglandin E1 was achieved. The first branches of the intrahepatic portal vein were visualized in 100% of the cases, the second branches in 82%, the third branches in 44%, and the fourth branches in 4% in the right portal vein system. In the left portal vein system, the first branches were visualized in 87%, the second branches in 41%, and the third branches in 3% of the cases. The intrahepatic portal vein system was more clearly visualized in females than in males (P less than 0.05). This procedure is simple, safe and useful for clear visualization of the portal vein system.</p

Up-regulation of hepatitis C virus replication by human T cell leukemia virus type I-encoded Tax protein

AbstractCo-infection of hepatitis C virus (HCV) with other blood-borne pathogens such as human T cell leukemia virus (HTLV) is common in highly endemic areas. Clinical evidence showing a correlation between HTLV-I co-infection and rapid progression of HCV-associated liver disease promoted us to investigate the effect of HTLV-I-encoded Tax protein on HCV replication. Reporter assay showed that HCV replicon-encoded luciferase expression was significantly augmented by co-transfection of the Tax-expressing plasmid. Further, HCV RNA replication in replicon cells was increased either by co-culture with cells stably expressing Tax protein (Huhtax) or by culture in the presence of Huhtax-conditioned medium, indicating that Tax could also modulate HCV replication of adjacent cells in a paracrine manner. Additionally, HCV replication in Huhtax exhibited a reduced responsiveness to interferon-α-induced antiviral activity. This study demonstrates the facilitation of HCV replication by Tax protein, which may partially account for severer clinical consequences of HCV-related disease in HCV/HTLV co-infected individuals