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

Molecular Adsorption Behavior on an Au(111) Surface(STM-other surfaces)

Scanning tunneling microscopy (STM) was used to study molecular adsorption behavior on reconstructed Au(111) surface. The STM images of ethyl 4-[2-(2-pyrazyl)ethenyl]cinnamate (E25PC) molecules adsorbed on Au(111) revealed ordered nucleation of molecular islands at the initial growth stage. The islands grew with spacing 38 Å in rows 77 Å apart. The periodicity of 38 Å×77 Å corresponds to that of STM images of bare Au(111) reconstructed surface in air. The behavior of molecules adsorbed on Au(111) is discussed from a view point of Au(111) herringbone reconstruction

Accuracy assessment methods of tissue marker clip placement after 11-gauge vacuum-assisted stereotactic breast biopsy: comparison of measurements using direct and conventional methods

BACKGROUND:　 The objective of the study was to compare direct measurement with a conventional method for evaluation of clip placement in stereotactic vacuum-assisted breast biopsy (ST-VAB) and to evaluate the accuracy of clip placement using the direct method.　 METHODS:　 Accuracy of clip placement was assessed by measuring the distance from a residual calcification of a targeted calcification clustered to a clip on a mammogram after ST-VAB. Distances in the craniocaudal (CC) and mediolateral oblique (MLO) views were measured in 28 subjects with mammograms recorded twice or more after ST-VAB. The difference in the distance between the first and second measurements was defined as the reproducibility and was compared with that from a conventional method using a mask system with overlap of transparent film on the mammogram. The 3D clip-to-calcification distance was measured using the direct method in 71 subjects.　 RESULTS:　 The reproducibility of the direct method was higher than that of the conventional method in CC and MLO views (P = 0.002, P < 0.001). The median 3D clip-to-calcification distance was 2.8 mm, with an interquartile range of 2.0-4.8 mm and a range of 1.1-36.3 mm.　 CONCLUSION:　 The direct method used in this study was more accurate than the conventional method, and gave a median 3D distance of 2.8 mm between the calcification and clip

Single chain distributions at the interface in micro phase separated structures obtained by self consistent field calculations

この論文は国立情報学研究所の電子図書館事業により電子化されました。研究会報告昨年度、3次元透過型電子顕微鏡により得られた3次元ラメラ構造上で自己無撞着場計算を行い、実験で得られた構造に村してさらに詳細な鎖の情報が得られる事を示した。本発表では、ブロックポリマーによって得られる幾つかのミクロ相分離構造に村して上の方法を適用し、鎖の伸び等に関して解析を行ったので報告する

UV-Induced Ubiquitylation of XPC Protein Mediated by UV-DDB-Ubiquitin Ligase Complex

SummaryThe xeroderma pigmentosum group C (XPC) protein complex plays a key role in recognizing DNA damage throughout the genome for mammalian nucleotide excision repair (NER). Ultraviolet light (UV)-damaged DNA binding protein (UV-DDB) is another complex that appears to be involved in the recognition of NER-inducing damage, although the precise role it plays and its relationship to XPC remain to be elucidated. Here we show that XPC undergoes reversible ubiquitylation upon UV irradiation of cells and that this depends on the presence of functional UV-DDB activity. XPC and UV-DDB were demonstrated to interact physically, and both are polyubiquitylated by the recombinant UV-DDB-ubiquitin ligase complex. The polyubiquitylation altered the DNA binding properties of XPC and UV-DDB and appeared to be required for cell-free NER of UV-induced (6-4) photoproducts specifically when UV-DDB was bound to the lesion. Our results strongly suggest that ubiquitylation plays a critical role in the transfer of the UV-induced lesion from UV-DDB to XPC

Initial Stage of Molecular Adsorption on Si(100) and H-terminated Si(100) Investigated by UHV-STM(STM-Si(001))

We have investigated the initial stage of adsorption of a conjugated aromatic compound, 1, 4-bis[β-pyridyl-(2)-vinyl]benzene (P2VB), on the clean Si(100)-2×1 surface and the hydrogen terminated Si(100)-2×1-H surface by ultra-high-vacuum (UHV) scanning tunneling microscopy (STM). We found adsorbed molecules cannot migrate on the chemically active Si(100)-2×1 surface, while they can migrate on the chemically inactive hydrogen terminated Si(100)-2×1-H surface until they are trapped to hydrogen-missing dangling bonds. On the clean Si(100)-2×1, we observed four different adsorption directions. An individual molecule appears as two or three bright spots, the brightness and distance between bright spots varying for different cases. Through structural analysis and bias-voltage-dependent STM images, we conclude that the electronic states of Si dimers modulated by the adsorbed molecules are observed instead of the molecules themselves. A simple estimation by considering only the molecular size and shape reproduces the distribution of four different kinds of adsorption structures we observed

Functional regulation of the DNA damage-recognition factor DDB2 by ubiquitination and interaction with xeroderma pigmentosum group C protein

In mammalian nucleotide excision repair, the DDB1-DDB2 complex recognizes UV-induced DNA photolesions and facilitates recruitment of the XPC complex. Upon binding to damaged DNA, the Cullin 4 ubiquitin ligase associated with DDB1-DDB2 is activated and ubiquitinates DDB2 and XPC. The structurally disordered N-terminal tail of DDB2 contains seven lysines identified as major sites for ubiquitination that target the protein for proteasomal degradation; however, the precise biological functions of these modifications remained unknown. By exogenous expression of mutant DDB2 proteins in normal human fibroblasts, here we show that the N-terminal tail of DDB2 is involved in regulation of cellular responses to UV. By striking contrast with behaviors of exogenous DDB2, the endogenous DDB2 protein was stabilized even after UV irradiation as a function of the XPC expression level. Furthermore, XPC competitively suppressed ubiquitination of DDB2 in vitro, and this effect was significantly promoted by centrin-2, which augments the DNA damage-recognition activity of XPC. Based on these findings, we propose that in cells exposed to UV, DDB2 is protected by XPC from ubiquitination and degradation in a stochastic manner; thus XPC allows DDB2 to initiate multiple rounds of repair events, thereby contributing to the persistence of cellular DNA repair capacit

Effects of attentional bias modification on chronic low back pain in older outpatients

Objectives: In the present study, the effect of attentional bias modification (ABM) on older outpatients, with chronic low back pain, was examined.Design: This was a single-center, randomized, single-blinded, crossover trial and patients were randomly divided in a 1:1 allocation ratio into two groups: an ABM Leading group and an ABM Trailing group.Participants: Forty-three outpatients with chronic low back pain participated.Interventions: Patients were evaluated four times and the treatments were ABM + Normal intervention or Normal intervention only.Outcomes: Outcome measures included pain intensity on the Numerical Rating Scale, the Pain Catastrophizing Scale, Fear-Avoidance Beliefs Questionnaire, Hospital Anxiety and Depression Scale, Somatic Symptom Scale-8, and EuroQol 5 Dimension-3 levels questionnaire. In addition, we performed the 30-second Chair-Stand test and the Timed Up & Go test for physical function evaluations.Results: There was no change in pain intensity due to ABM. However, the total Pain Catastrophizing Scale score was significantly decreased, and the EuroQol 5 Dimension-3 levels questionnaire and 30-second chair-stand test were significantly improved (P <.05).Trial registration: The Health Science Ethics Committee, Graduate School of Biomedical Sciences, Nagasaki University (permit number: 17060861), and the clinical trial was registered with UMIN (UMIN000029424)

Primary placement technique of jejunostomy using the entristar™ skin-level gastrostomy tube in patients with esophageal cancer

<p>Abstract</p> <p>Background</p> <p>We developed a skin-level jejunostomy tube (SLJT) procedure for patients undergoing esophagectomy using a skin-level gastrostomy tube (G-tube) (Entristar™; Tyco Healthcare, Mansfield, Mass), in order to improve their nutrition status and quality of life (QOL). We describe the procedure and the adverse effects of SLJT in patients with esophageal cancer (EC).</p> <p>Methods</p> <p>Over a 24-month period (March 2008 to March 2010), there were 16 patients (mean age: 61.8 years; age range: 49-75 years; 15 men, 1 woman) who had Stage II or III EC. Primary jejunostomy was performed under general anesthesia during esophagectomy. The technical success and the immediate and delayed complications of the procedure were recorded.</p> <p>Jejunostomy techniques</p> <p>SLJT placement using the G-tube (20Fr) was performed 20 cm from the Treitz ligament on the side opposing the jejunal mesenterium. The internal retention bolster was exteriorized through an incision in the abdominal wall. A single purse string suture using a 4-0 absorbable suture was performed. The internal retention bolster was then inserted into the jejunal lumen via the small incision. The intestine adjacent to the tube was anchored to the peritoneum using a single stitch.</p> <p>Results</p> <p>The SLJT was successfully inserted in all 16 patients. No early complications were documented. Follow-up for a median of 107 days (range, 26-320 days) revealed leakage to the skin in four patients, including superficial wound infections in two patients. There were no cases of obstruction of the tube or procedure-related death.</p> <p>Conclusions</p> <p>This SLJT placement technique using the G-tube is a safe procedure in patients with EC and allows the creation of a long-term feeding jejunostomy.</p