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High-throughput predictions of metal-organic framework electronic properties:theoretical challenges,graph neural networks,and data exploration

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npj Computational Materials 2022年第1期8卷 1053-1062页

作者： Andrew S.Rosen Victor Fung Patrick Huck cody T.o’Donnell Matthew K.Horton Donald G.Truhlar Kristin A.Persson Justin M.Notestein Randall Q.Snurr Department of Materials Science and Engineering University of CaliforniaBerkeleyCA94720USA Miller Institute for Basic Research in Science University of CaliforniaBerkeleyBerkeleyCA94720USA Materials Science Division Lawrence Berkeley National LaboratoryBerkeleyCA94720USA Department of Chemical and Biological Engineering Northwestern UniversityEvanstonIL60208USA Center for Nanophase Materials Sciences Oak Ridge National LaboratoryOak RidgeTN37831USA Energy Technologies Area Lawrence Berkeley National LaboratoryBerkeleyCA94720USA Department of Chemistry Chemical Theory Centerand Minnesota Supercomputing InstituteUniversity of MinnesotaMinneapolisMN55455USA Molecular Foundry Lawrence Berkeley National LaboratoryBerkeleyCA94720USA

With the goal of accelerating the design and discovery of metal–organic frameworks(MoFs)for electronic,optoelectronic,and energy storage applications,we present a dataset of predicted electronic structure properties for thousands of MoFs carried out using multiple density functional *** to more accurate hybrid functionals,we find that the widely used PBE generalized gradient approximation(GGA)functional severely underpredicts MoF band gaps in a largely systematic manner for semi-conductors and insulators without magnetic ***,an even larger and less predictable disparity in the band gap prediction is present for MoFs with open-shell 3d transition metal *** regards to partial atomic charges,we find that different density functional approximations predict similar charges overall,although hybrid functionals tend to shift electron density away from the metal centers and onto the ligand environments compared to the GGA point of *** more significant differences in partial atomic charges are observed when comparing different charge partitioning *** conclude by using the dataset of computed MoF properties to train machine-learning models that can rapidly predict MoF band gaps for all four density functional approximations considered in this work,paving the way for future high-throughput screening *** encourage exploration and reuse of the theoretical calculations presented in this work,the curated data is made publicly available via an interactive and user-friendly web application on the Materials Project.

关键词： charges electronic centers

Blood metal concentrations and cardiac structure and function in total joint arthroplasty patients

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World Journal of orthopedics 2024年第8期15卷 773-782页

作者： Peter C Brennan Stephanie M Peterson Thomas J o'Byrne Mariana L Laporta cody C Wyles Paul J Jannetto Garvan C Kane Maria Vassilaki Hilal Maradit Kremers Department of orthopedic Surgery Mayo ClinicRochesterMN 55905United States Department of Quantitative Health Sciences Mayo ClinicRochesterMN 55905United States Department of Anesthesiology and Perioperative Medicine Mayo ClinicRochesterMN 55905United States Department of Laboratory Medicine and Pathology Mayo ClinicRochesterMN 55905United States Department of Cardiovascular Diseases Mayo ClinicRochesterMN 55905United States

BACKGRoUND There is concern regarding potential long-term cardiotoxicity with systemic distribution of metals in total joint arthroplasty(TJA)*** To determine the association of commonly used implant metals with echocardiographic measures in TJA *** The study comprised 110 TJA patients who had a recent history of high chromium,cobalt or titanium *** underwent two-dimensional,three-dimensional,Doppler and speckle-strain transthoracic echocardiography and a blood draw to measure metal *** and sex-adjusted linear and logistic regression models were used to examine the association of metal concentrations(exposure)with echocardiographic measures(outcome).RESULTS Higher cobalt concentrations were associated with increased left ventricular end-diastolic volume(estimate 5.09;95%CI:0.02-10.17)as well as left atrial and right ventricular dilation,particularly in men but no changes in cardiac *** titanium concentrations were associated with a reduction in left ventricle global longitudinal strain(estimate 0.38;95%CI:0.70 to 0.06)and cardiac index(estimate 0.08;95%CI,-0.15 to-0.01).CoNCLUSIoN Elevated cobalt and titanium concentrations may be associated with structural and functional cardiac changes in some *** studies are warranted to better understand the systemic effects of metals in TJA patients.

关键词： Total joint arthroplasty Metal-on-metal Cardiotoxicity Heart failure Echocardiography Cobalt

Swelling and Deswelling Kinetics of AT-o3S Polymer

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Journal of Energy and Power Engineering 2017年第3期11卷 164-172页

作者： Mahmoud Elsharafi cody Chancellor McCoy School of Engineering College of Science and Mathematics Midwestern State University Wichita Falls Texas 76310 United States

In the oil industry, techniques decreasing unwanted water production have drawn large amounts of interest from many companies. During water injection operations, water is injected into the oil reservoir to extract oil trapped in the formation. Due to the heterogeneity in the reservoir formation, oil production will decline and water production will increase as the injected water sweeps the high permeability zones. In order to flush out the oil remaining in the low permeability zones, many treatments have been used. one such treatment involves the injection of an SAP （superabsorbent polymer） into the high permeability zones. The swelled polymer will decrease the heterogeneity of reservoir permeability, thus forcing water injection into the oil rich, unswept zones/areas of the formation. Proper application of an SAP can have a dramatic impact on both the production and lifespan of mature oil wells. Successful treatment is reliant upon the reservoir salinity, temperature, and pH.

关键词： Water shutoff reservoir heterogeneity swelling and deswelling of polymer pH value chemical treatment enhanced oilrecovery.

Applying Virtual Reality to Molecular Graphics System

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Journal of Computer Science & Technology 1996年第5期11卷 507-511页

作者： Chang No Yoon Myung Hwan Chi Heedong Ko and Jongsei Park(Doping Control Centen , CAD/CAM Lab Korea Institute of Science and Technology P. o. Box 131, Cheongryang, Seoul 130-650, KoreaE-mail f cody@kistmail.kist.re.kr) Doping Control Center Korea Institute of Science and Technology Seoul Korea CAD/CAM Lab Korea Institute of Science and Technology Seoul Korea

Molecular graphics can be thought of as a window to the computer through which the chemist expresses ideas for computational evaluation and receives results in an understandable form. Furthermore, with beautiful graphic images it can give out the realistic molecular model like a real thing in real *** has various properties including volume, electronic, van der Waals forces, etc. These properties are very important to understand the molecular world. So if the virtual reality tools are used, then the imaginary world can be studied intuitively by touching and feeling a tremendous amount of *** chemistry generates such amount of molecular property data through supercomputing with molecular simulation experiment. one of the objects to investigate the molecular world is to understand the intermolecular interaction such as drug-receptor interaction. Another thing is to measure the geometrical data in molecular architecture. Virtual reality system provides the easiest way to meet these objects. This kind of simple system changes a numerical data set, which is very difficult to deal with, into a visible and understandable data set. Recently two functions of such a system were improved to get an insight into biomolecular interaction. The first one is a real time force generation during navigation in macromolecular environment. An cylindrical arrow shows the magnitude and direction of molecular force. The second one is to see a moIecular vibration such as a concerted motion of the binding site in protein molecule. So one can understand the molecular shape change for drugreceptor docking procedure. But some problems which are difficult to solve still remain.

关键词： Molecular graphics molecular docking virtual reality force vector real-time docking

Dominance network structure across reproductive contexts in the cooperatively breeding cichlid fish Neolamprologus pulcher

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Current Zoology 2015年第1期61卷 45-54页

作者： cody J. DEY Q.Y. Joanne TAN Constance M. o'CoNNoR Adam R. REDDoN J. Ryan CALDWELL Sigal BALSHINE Department of Biology McMaster University Hamilton Ontario ON L8S 4K1 Canada Department of Psychology Neuroscience and Behaviour McMaster University Hamilton Ontario L8S 4L8 Canada

While a large number of studies have described animal social networks, we have a poor understanding of how these networks vary with ecological and social conditions. For example, reproductive periods are an important life-history stage that may involve changes in dominance relationships among individuals, yet no study to date has compared social networks of do- minance interactions （i.e. dominance networks） across reproductive contexts. We first analyzed a long-term dataset on captive so- cial groups of the cooperatively breeding cichlid Neolamprologuspulcher, and found that eviction events were significantly more common around reproduction than expected by chance. Next, we compared the structure of dominance networks during early pa- rental care and non-reproductive periods, using one of the first applications of exponential random graph models in behavioral biology. Contrary to our predictions, we found that dominance networks showed few changes between early parental care and non-reproductive periods. We found no evidence that dominance interactions became more skewed towards larger individuals, became more frequent between similar-sized individuals, or became more biased towards a particular sex during parental care. However, we did find that there were relatively more dominance interactions between opposite-sex dyads in the early parental care period, which may be a by-product of increased sexual interactions during this time. This is the first study in behavioral ecology to compare social networks using exponential random graph modeling, and demonstrates a powerful analytical framework for future studies in the field [Current Zoology 61 （1）： 45-54, 2015].

关键词： Social network Aggression Submissive Hierarchy Parental care P* model

预期寿命估计对脊柱转移瘤手术选择与预后预测的临床意义

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癌症 2006年第11期25卷 1406-1410页

作者：邹学农 Anders Grejs 李海声 Kristian Hφy Ebbe S Hansen cody Bünger 丹麦奥胡斯大学医院骨科

背景与目的:目前,临床上对脊柱转移瘤患者是否采取手术治疗以及如何选择手术仍然存在较大的争议。预期寿命的估计是手术选择的决定因素之一。本研究旨在评价Tokuhashi和Tomita评分系统这两种常用的预期寿命估计方法对硬膜外脊柱转移瘤... 详细信息

背景与目的:目前,临床上对脊柱转移瘤患者是否采取手术治疗以及如何选择手术仍然存在较大的争议。预期寿命的估计是手术选择的决定因素之一。本研究旨在评价Tokuhashi和Tomita评分系统这两种常用的预期寿命估计方法对硬膜外脊柱转移瘤患者手术选择与预后预测的临床价值。方法:对2001年1月至2004年4月丹麦奥胡斯大学医院脊柱外科中心收治的169例硬膜外脊柱转移瘤入组患者,术前用Tokuhashi与Tomita评分系统进行评分以及估计预期寿命,并结合Tomita脊柱肿瘤分型,选择实施手术分级治疗。术后6个月、12个月以及24个月分别进行前瞻性随访观察。对在预期寿命为“3个月内死亡”、“6个月内死亡”以及“12个月内死亡”的患者通过Tokuhashi与Tomita评分系统绘制受试者作业特征曲线(receiveroperatingcharacteristiccurves,RoC曲线),比较两个评分系统对预期寿命估计的准确性。同时采用Kaplan-Meier生存曲线分析法,计算Tokuhashi和Tomita评分系统各分数段患者术后的实际平均生存时间。结果:预期寿命分别为“3个月内死亡”、“6个月内死亡”以及“12个月内死亡”的病例RoC曲线分析显示,Tomita评分系统与Tokuhashi评分系统之间的差异均无显著性(各组P值分别为0.16、0.47与0.38)。Kaplan-Meier生存曲线分析显示,Tomita评分系统在4～7分之间对预后估计过高,Tokuhashi评分系统在0～8分之间对预后估计过低。结论:Tokuhashi和Tomita评分系统均可成功地预测脊柱转移瘤患者术后预后的情况。Tokuhashi评分系统可较为准确地预测生存期较短的患者,从而避免对这类患者做不必要的大手术。

关键词：脊柱肿瘤/继发性手术疗法预期寿命预后

7.0T磁共振关节软骨T2弛豫时间图与量化分析的实验研究

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中国医学影像技术 2008年第2期24卷 171-175页

作者：周智洋单鸿邹学农 Steffen Ringgaard 邹立津李海声 Hans Stodkilde-Jorgensen cody Bunger 中山大学附属第三医院放射科与附属第一医院骨科广东广州510630 丹麦奥胡斯大学医院骨科与磁共振研究中心丹麦奥胡斯8000

目的建立超高场强磁共振关节软骨T2弛豫时间图成像技术和量化分析方法。方法用7.0T微磁共振机,采用多回波SE序列对琼脂糖凝胶体模和家猪髌骨扫描,获得T2加权图像,测定体模与髌骨软骨的信噪比。重构T2弛豫时间图,人工画感兴趣区测量T2值... 详细信息

目的建立超高场强磁共振关节软骨T2弛豫时间图成像技术和量化分析方法。方法用7.0T微磁共振机,采用多回波SE序列对琼脂糖凝胶体模和家猪髌骨扫描,获得T2加权图像,测定体模与髌骨软骨的信噪比。重构T2弛豫时间图,人工画感兴趣区测量T2值。结果琼脂糖凝胶体模和家猪髌骨T2加权图像清晰,对比度好,无异常伪影,信噪比高,重复性好。琼脂糖凝胶体模的T2值随浓度降低而增加。髌骨软骨呈分层状表现,软骨表层T2值高于中间层、深层、钙化层和软骨全层,差异具有统计学意义(P<0.05)。结论T2弛豫时间图可量化测定关节软骨,是可行的、敏感的、特异的软骨分子成像技术。

关键词：磁共振成像信噪比体模关节软骨

家猪体外胰蛋白酶消化关节软骨：7.0TMR T1ρ加权成像与量化分析

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中国组织工程研究与临床康复 2009年第37期13卷 7221-7225页

作者：周智洋单鸿李占军邹学农 Steffen Ringgaard 邹立津李海声 Hans Stodkilde-Jorgensen cody Bünger 中山大学附属第六医院放射科广东省广州市510655 中山大学附属第三医院放射科广东省广州市510630 中山大学附属第三医院放射科 519000 丹麦奥胡斯大学医院骨科与磁共振研究中心丹麦奥胡斯8000 中山大学附属第一医院骨科广东省广州市510080

背景:T1ρ驰豫时间是探测软骨生化改变的最具吸引力的新的磁共振参数。早期骨关节炎主要表现为蛋白多糖的丢失以及胶原的轻微改变。目的:应用T1ρ成像技术与弛豫时间图量化分析方法,评价体外胰蛋白酶消化与未消化家猪髌骨软骨T1ρ驰豫... 详细信息

背景:T1ρ驰豫时间是探测软骨生化改变的最具吸引力的新的磁共振参数。早期骨关节炎主要表现为蛋白多糖的丢失以及胶原的轻微改变。目的:应用T1ρ成像技术与弛豫时间图量化分析方法,评价体外胰蛋白酶消化与未消化家猪髌骨软骨T1ρ驰豫时间的改变。设计、时间及地点:同体对照观察,于2007-02/2008-01在丹麦奥胡斯大学医院骨科与磁共振研究中心完成。材料:丹麦雌性长白猪10头,左右侧髌骨共20个。方法:选择10头家猪,取右侧髌骨10个为对照组,浸泡于PBS中4h后取出。取左侧髌骨10个为消化组,浸泡于含有胰蛋白酶的PBS溶液中,4h后取出。利用7.0T磁共振机,分别采用自旋锁定自动补偿脉冲簇的三维SE序列进行扫描,获得关节软骨的T1ρ加权图像。重构T1ρ弛豫时间图,测定关节软骨T1ρ值。取两组髌骨软骨标本行番红o/固绿染色进行组织学观察。主要观察指标:①T1ρ弛豫时间图量化分析结果。②两组软骨标本组织学结果。结果:经酶诱导消化的体外家猪髌骨关节软骨T1ρ加权图像成像清晰,呈分层状表现,对比度好,无异常伪影。大体观察两组关节软骨T1ρ加权图像,见局部的信号异常改变。重构T1ρ弛豫时间图并量化测定分析显示,消化组软骨表层T1ρ值高于对照组,差异具有显著性意义(P0.05)。结论:经胰蛋白酶诱导消化可引起退变软骨T1ρ驰豫时间改变,特别是在软骨的表层变化明显,提示T1ρ驰豫时间是较敏感、特异性的检测指标,可进一步应用于关节软骨退变的早期诊断。

关键词：磁共振成像 T1ρ 酶诱导关节软骨退变量化分析

Morphological and optical Properties of Dimetallo-Phthalocyanine-Complex Thin Films

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Advances in Materials Physics and Chemistry 2014年第2期4卷 20-28页

作者： María Elena Sánchez-Vergara Jose R. álvarez-Bada Carlos o. Perez-Baeza Elías A. Loza-Neri Ricardo A. Torres-García Arturo Rodríguez-Gómez Juan C. Alonso-Huitron Facultad de Ingeniería Universidad Anáhuac (México Norte) Huixquilucan México Instituto de Física Universidad Nacional Autónoma de México México D.F. México Instituto de Investigaciones en Materiales Universidad Nacional Autónoma de México México D. F. México

In this work, the synthesis of semiconducting molecular materials formed from metallo-phthalocyanines (MPcs) and bidentate amines is reported. Powder and thin-film samples of the synthesized materials, deposited by vacuum thermal evaporation, show the same intra-molecular bonds in IR-spectroscopy studies. The morphology of the deposited films was studied using scanning electron microscopy and atomic force microscopy. The optical parameters have been investigated using spectrophotometric measurements of transmittance in the wavelength range 200 - 1100 nm. The absorption spectra in the UV-Vis region for the deposited samples showed two bands, namely the Q and Soret bands. The optical band gap values of the thin films were calculated from the absorption coefficient α in the absorption region and were found to be around 1.4 - 1.6 eV. The dependence of the Tauc and cody optical gaps on the thickness of the film was also determined.

关键词： Phthalocyanines organic Semiconductors Thin Films optical Gap