A Multiple-Precision Study on the Modified Collocation Trefftz Method

Recently, Liu (CMES 21(2007), 53) developed the modified collocation Trefftz method (MCTM) by setting a characteristic length slightly larger than the maximum radius of the computational domain. In this study, we find that the range of admissible characteristic length can be significantly enlarged if the LU decomposition is applied for solving the resulted dense unsymmetric matrix. Furthermore, we discover a range formula for admissible characteristic length, in which the number of the T-complete functions, the shape of the computation domain, and the exponent bits of the involved floating-point arithmetic have been taken into consideration. In order to validate the prescribed formula for different exponent bits, the multiple precision floating-point reliable (MPFR) library is used. In addition, we find that the MCTM is a numerical method of exponential convergence. In other words, increasing the numbers of the T-complete functions can reduce the logarithmic error proportionally till the precision limit, which can be set up for the MPFR library. Numerical experiments are carried out to demonstrate that the proposed MCTM with the LU decomposition can solve the Laplace equation stably and accurately, even for a Cauchy problem. A multiple-precision comparison between the MCTM and the method of fundamental solution is also preformed

Density Functional Theory Study of Pt_3M Alloy Surface Segregation with Adsorbed O/OH and Pt_3Os as Catalysts for Oxygen Reduction Reaction

Using quantum mechanics calculations, we have studied the segregation energy with adsorbed O and OH for 28 Pt_3M alloys, where M is a transition metal. The calculations found surface segregation to become energetically unfavorable for Pt_3Co and Pt_3Ni, as well as for the most other Pt binary alloys, in the presence of adsorbed O and OH. However, Pt_3Os and Pt_3Ir remain surface segregated and show the best energy preference among the alloys studied for both adsorbed species on the surface. Binding energies of various oxygen reduction reaction (ORR) intermediates on the Pt(111) and Pt_3Os(111) surfaces were calculated and analyzed. Energy barriers for different ORR steps were computed for Pt and Pt_3Os catalysts, and the rate-determining steps (RDS) were identified. It turns out that the RDS barrier for the Pt_3Os alloy catalyst is lower than the corresponding barrier for pure Pt. This result allows us to predict a better ORR performance of Pt_3Os compared to that of pure Pt

Quantum Mechanics Studies of Fuel Cell Catalysts and Proton Conducting Ceramics with Validation by Experiment

We carried out quantum mechanics (QM) studies aimed at improving the performance of hydrogen fuel cells. This led to predictions of improved materials, some of which were subsequently validated with experiments by our collaborators. In part I, the challenge was to find a replacement for the Pt cathode that would lead to improved performance for the Oxygen Reduction Reaction (ORR) while remaining stable under operational conditions and decreasing cost. Our design strategy was to find an alloy with composition Pt3M that would lead to surface segregation such that the top layer would be pure Pt, with the second and subsequent layers richer in M. Under operating conditions we expect the surface to have significant O and/or OH chemisorbed on the surface, and hence we searched for M that would remain segregated under these conditions. Using QM we examined surface segregation for 28 Pt3M alloys, where M is a transition metal. We found that only Pt3Os and Pt3Ir showed significant surface segregation when O and OH are chemisorbed on the catalyst surfaces. This result indicates that Pt3Os and Pt3Ir favor formation of a Pt-skin surface layer structure that would resist the acidic electrolyte corrosion during fuel cell operation environments. We chose to focus on Os because the phase diagram for Pt-Ir indicated that Pt-Ir could not form a homogeneous alloy at lower temperature. To determine the performance for ORR, we used QM to examine all intermediates, reaction pathways, and reaction barriers involved in the processes for which protons from the anode reactions react with O2 to form H2O. These QM calculations used our Poisson-Boltzmann implicit solvation model include the effects of the solvent (water with dielectric constant 78 with pH 7 at 298K). We found that the rate determination step (RDS) was the Oad hydration reaction (Oad + H2Oad -&#62; OHad + OHad) in both cases, but that the barrier for pure Pt of 0.50 eV is reduced to 0.48 eV for Pt3Os, which at 80 degrees C would increase the rate by 218%. We collaborated with the Pu-Wei Wu’s group to carry out experiments, where we found that the dealloying process-treated Pt2Os catalyst showed two-fold higher activity at 25 degrees C than pure Pt and that the alloy had 272% improved stability, validating our theoretical predictions. We also carried out similar QM studies followed by experimental validation for the Os/Pt core-shell catalyst fabricated by the underpotential deposition (UPD) method. The QM results indicated that the RDS for ORR is a compromise between the OOH formation step (0.37 eV for Pt, 0.23 eV for Pt2ML/Os core-shell) and H2O formation steps (0.32 eV for Pt, 0.22 eV for Pt2ML/Os core-shell). We found that Pt2ML/Os has the highest activity (compared to pure Pt and to the Pt3Os alloy) because the 0.37 eV barrier decreases to 0.23 eV. To understand what aspects of the core shell structure lead to this improved performance, we considered the effect on ORR of compressing the alloy slab to the dimensions of pure Pt. However this had little effect, with the same RDS barrier 0.37 eV. This shows that the ligand effect (the electronic structure modification resulting from the Os substrate) plays a more important role than the strain effect, and is responsible for the improved activity of the core- shell catalyst. Experimental materials characterization proves the core-shell feature of our catalyst. The electrochemical experiment for Pt2ML/Os/C showed 3.5 to 5 times better ORR activity at 0.9V (vs. NHE) in 0.1M HClO4 solution at 25 degrees C as compared to those of commercially available Pt/C. The excellent correlation between experimental half potential and the OH binding energies and RDS barriers validate the feasibility of predicting catalyst activity using QM calculation and a simple Langmuir–Hinshelwood model. In part II, we used QM calculations to study methane stream reforming on a Ni-alloy catalyst surfaces for solid oxide fuel cell (SOFC) application. SOFC has wide fuel adaptability but the coking and sulfur poisoning will reduce its stability. Experimental results suggested that the Ni4Fe alloy improves both its activity and stability compared to pure Ni. To understand the atomistic origin of this, we carried out QM calculations on surface segregation and found that the most stable configuration for Ni4Fe has a Fe atom distribution of (0%, 50%, 25%, 25%, 0%) starting at the bottom layer. We calculated that the binding of C atoms on the Ni4Fe surface is 142.9 Kcal/mol, which is about 10 Kcal/mol weaker compared to the pure Ni surface. This weaker C binding energy is expected to make coke formation less favorable, explaining why Ni4Fe has better coking resistance. This result confirms the experimental observation. The reaction energy barriers for CHx decomposition and C binding on various alloy surface, Ni4X (X=Fe, Co, Mn, and Mo), showed Ni4Fe, Ni4Co, and Fe4Mn all have better coking resistance than pure Ni, but that only Ni4Fe and Fe4Mn have (slightly) improved activity compared to pure Ni. In part III, we used QM to examine the proton transport in doped perovskite-ceramics. Here we used a 2x2x2 supercell of perovskite with composition Ba8X7M1(OH)1O23 where X=Ce or Zr and M=Y, Gd, or Dy. Thus in each case a 4+ X is replace by a 3+ M plus a proton on one O. Here we predicted the barriers for proton diffusion allowing both includes intra-octahedron and inter-octahedra proton transfer. Without any restriction, we only observed the inter-octahedra proton transfer with similar energy barrier as previous computational work but 0.2 eV higher than experimental result for Y doped zirconate. For one restriction in our calculations is that the Odonor-Oacceptor atoms were kept at fixed distances, we found that the barrier difference between cerates/zirconates with various dopants are only 0.02~0.03 eV. To fully address performance one would need to examine proton transfer at grain boundaries, which will require larger scale ReaxFF reactive dynamics for systems with millions of atoms. The QM calculations used here will be used to train the ReaxFF force field.</p

Cijepni soj virusa zaraznog bronhitisa patogeniji je za pileće zametke od divljeg soja 2575/98.

An avian infectious bronchitis virus (IBV) strain 2575/98 was attenuated using serial chicken embryo passage to become a vaccine in Taiwan. The aim of this study was to investigate the replication ability, pathogenicity, and tissue tropism of the wild and vaccine strains in chicken embryos. The embryos were inoculated with different titers of wild and vaccine strains. Quantification of virus in allantoic fluid was evaluated using real time RT-PCR. The results showed that the vaccine strain replicated in higher titers than the wild strain, and caused embryo death so quickly that only a few dwarfisms occurred. The embryos inoculated with wild and vaccine strains had similar lesions that were confined primarily to the chorionallantoic membrane (CAM), liver, and kidneys. The immunohistochemical data showed that IBV was present predominantly in the lungs, kidneys, and CAM. Although both strains caused hepatic damage, very few virus antigens were detected in the hepatic tissue. The pathogenicity of the vaccine becomes higher in embryos although it is lower in chickens than its wild strain. The vaccine strain could be used as a possible new vaccine candidate for IBV control.Virus zaraznog bronhitisa peradi soj 2575/98 bio je oslabljen uzastopnim pasažama u pilećim zametcima da bi poslužio kao cijepni soj u Tajvanu. Cilj je ovog rada bio istražiti mogućnost umnožavanja, patogenost i tropizam terenskog i cijepnog soja u pilećim zametcima. Zametci su bili inokulirani cijepnim sojem različitog titra. Količina virusa u alantoisnoj tekućini bila je određena RT-PCR-om u stvarnom vremenu. Rezultati su pokazali da se cijepni soj umnažao u višem titru od divljeg soja i prouzročio uginuće zametaka tako brzo da se uspjelo razviti svega nekoliko kržljavih. U inokuliranih zametaka, bez obzira na divlji ili cijepni soj, razvile su se slične promjene pretežito na korioalantoisnoj opni, jetrima i bubrezima. Imunohistokemijski je dokazano da se virus zaraznog bronhitisa prvenstveno nalazio u plućima, bubrezima i korioalantoisnoj opni. Iako su oba soja prouzročila oštećenja jetara, neznatna količina virusnog antigena bila je dokazana u jetrenom tkivu. Patogenost cijepnog soja bila je u zametcima jača, a u pilićima slabija od divljeg soja. Cijepni soj bi se mogao rabiti kao mogući kandidat za proizvodnju novog cjepiva protiv zaraznog bronhitisa

Exploring the Mechanism Responsible for Cellulase Thermostability by Structure-Guided Recombination

Cellulases from Bacillus and Geobacillus bacteria are potentially useful in the biofuel and animal feed industries. One of the unique characteristics of these enzymes is that they are usually quite thermostable. We previously identified a cellulase, GsCelA, from thermophilic Geobacillus sp. 70PC53, which is much more thermostable than its Bacillus homolog, BsCel5A. Thus, these two cellulases provide a pair of structures ideal for investigating the mechanism regarding how these cellulases can retain activity at high temperature. In the present study, we applied the SCHEMA non-contiguous recombination algorithm as a novel tool, which assigns protein sequences into blocks for domain swapping in a way that lessens structural disruption, to generate a set of chimeric proteins derived from the recombination of GsCelA and BsCel5A. Analyzing the activity and thermostability of this designed library set, which requires only a limited number of chimeras by SCHEMA calculations, revealed that one of the blocks may contribute to the higher thermostability of GsCelA. When tested against swollen Avicel, the highly thermostable chimeric cellulase C10 containing this block showed significantly higher activity (22%-43%) and higher thermostability compared to the parental enzymes. With further structural determinations and mutagenesis analyses, a 3_(10) helix was identified as being responsible for the improved thermostability of this block. Furthermore, in the presence of ionic calcium and crown ether (CR), the chimeric C10 was found to retain 40% residual activity even after heat treatment at 90°C. Combining crystal structure determinations and structure-guided SCHEMA recombination, we have determined the mechanism responsible for the high thermostability of GsCelA, and generated a novel recombinant enzyme with significantly higher activity

Acetylome of acinetobacter baumannii SK17 reveals a highly-conserved modification of histone-like protein HU

Lysine acetylation is a prevalent post-translational modification in both eukaryotes and prokaryotes. Whereas this modification is known to play pivotal roles in eukaryotes, the function and extent of this modification in prokaryotic cells remain largely unexplored. Here we report the acetylome of a pair of antibiotic-sensitive and -resistant nosocomial pathogen Acinetobacter baumannii SK17-S and SK17-R. A total of 145 lysine acetylation sites on 125 proteins was identified, and there are 23 acetylated proteins found in both strains, including histone-like protein HU which was found to be acetylated at Lys13. HU is a dimeric DNA-binding protein critical for maintaining chromosomal architecture and other DNA-dependent functions. To analyze the effects of site-specific acetylation, homogenously Lys13-acetylated HU protein, HU(K13ac) was prepared by genetic code expansion. Whilst not exerting an obvious effect on the oligomeric state, Lys13 acetylation alters both the thermal stability and DNA binding kinetics of HU. Accordingly, this modification likely destabilizes the chromosome structure and regulates bacterial gene transcription. This work indicates that acetyllysine plays an important role in bacterial epigenetics

The flow and turbulence structure at a rectangular bridge pier with a low angle of attack

River hydrodynamicsInteraction with structure

Diffusion-SS3D: Diffusion Model for Semi-supervised 3D Object Detection

Semi-supervised object detection is crucial for 3D scene understanding, efficiently addressing the limitation of acquiring large-scale 3D bounding box annotations. Existing methods typically employ a teacher-student framework with pseudo-labeling to leverage unlabeled point clouds. However, producing reliable pseudo-labels in a diverse 3D space still remains challenging. In this work, we propose Diffusion-SS3D, a new perspective of enhancing the quality of pseudo-labels via the diffusion model for semi-supervised 3D object detection. Specifically, we include noises to produce corrupted 3D object size and class label distributions, and then utilize the diffusion model as a denoising process to obtain bounding box outputs. Moreover, we integrate the diffusion model into the teacher-student framework, so that the denoised bounding boxes can be used to improve pseudo-label generation, as well as the entire semi-supervised learning process. We conduct experiments on the ScanNet and SUN RGB-D benchmark datasets to demonstrate that our approach achieves state-of-the-art performance against existing methods. We also present extensive analysis to understand how our diffusion model design affects performance in semi-supervised learning.Comment: Accepted in NeurIPS 2023. Code is available at https://github.com/luluho1208/Diffusion-SS3