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通过单体作用控制生物高聚物中的纽结

通过单体作用控制生物高聚物中的纽结

中国化学会2016年软物质理论计算与模拟会议

作者：代亮 patrick s.doyle 麻省理工学院化工系

纽结（knot）在我们日常生活中以及聚合物中都很常见。在前期的研究中,我们推导并计算模拟了纽结形成的自由能与纽结大小的关系,从而得到了随机形成纽结的概率与纽结大小【1】。在这项工作中,我们研究了如何通过高分子链内部的单体相互... 详细信息

纽结（knot）在我们日常生活中以及聚合物中都很常见。在前期的研究中,我们推导并计算模拟了纽结形成的自由能与纽结大小的关系,从而得到了随机形成纽结的概率与纽结大小【1】。在这项工作中,我们研究了如何通过高分子链内部的单体相互作用来人为控制纽结概率与纽结大小。我们观察到一个反常现象。当单体相互作用的力程范围较大时,单体间相互排斥力使得纽结紧缩变小。我们对这个现象也给出了理论解释。通过考虑真实的参数,我们预测这个现象在DNA长链与肽链（蛋白质）中可以发生。我们的全原子模拟也证实肽链中的静电排斥力在低盐浓度下,会使得纽结紧缩。

关键词：高分子纽结分子模拟自由能计算

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高分子链中自发形成的拓扑纽结大小

高分子链中自发形成的拓扑纽结大小

Human endogenous retrovirus type-W and multiple sclerosis–related smoldering neuroinflammation

2015年全国高分子学术论文报告会

作者：代亮 C.Benjamin Renner patrick s.doyle 新加坡与麻省理工学院联合研究中心麻省理工学院化工系

溶液中线性高分子链的无规则热运动会导致纽结的形成,就像生活中耳机线打结一样。实验上,在DNA链和蛋白质结构中也观察到纽结的存在。这些纽结的存在,会影响生物功能和流变力学性质。我们的研究主要是定量分析无规则热运动下,这些纽结... 详细信息

溶液中线性高分子链的无规则热运动会导致纽结的形成,就像生活中耳机线打结一样。实验上,在DNA链和蛋白质结构中也观察到纽结的存在。这些纽结的存在,会影响生物功能和流变力学性质。我们的研究主要是定量分析无规则热运动下,这些纽结形成的概率,以及这些纽结的大小。我们发现纽结大小呈单峰分布,形成某个特定大小的纽结概率最高。或者说,在某个亚稳态纽结大小下,高分子链有一个自由能局域极小值。与直觉不同的是,这个亚稳态（最概然）纽结非常的紧致,其回转半径约等于半柔性链的持久长度,其线长约等于12倍的持久长度。这个与Grosberg和Rabin预言吻合。Grosberg-Rabin理论中没有考虑到体积排斥作用的影响。我们修正了Grosberg-Rabin理论,计算了在不同体积排斥作用下的亚稳态纽结大小,与蒙特卡洛模拟结果吻合。实验上,经常使用λ-DNA来研究单个高分子链的行为,以及纽结的性质。我们的计算预测出λ-DNA上亚稳态纽结的大小,在常用的盐浓度区间内,约为600到1800纳米。

关键词：高分子链拓扑结构蒙特卡洛模拟

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Neural Regeneration Research 2025年第3期20卷 813-814页

作者： Joel Gruchot Laura Reiche Andrew Chan Robert Hoepner patrick Küry Department of Neurology Medical Faculty and University Hospital DüsseldorfHeinrich Heine University DüsseldorfDüsseldorfGermany Department of Neurology InselspitalBern University Hospital and University of BernBernSwitzerland

Introduction to human endogenous retrovirus type-W(HERV-W): Genomic inheritance from the past includes retroviral sequences that have been stably incorporated into our genomes and account for up to 8% of human DNA.

关键词： endogenous inflammation Human

silk-based nerve guidance conduits with macroscopic holes modulate the vascularization of regenerating rat sciatic nerve

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Neural Regeneration Research 2025年第6期20卷 1789-1800页

作者： Carina Hromada patrick Heimel Markus Kerbl LászlóGál sylvia Nürnberger Barbara schaedl James Ferguson Nicole swiadek Xavier Monforte Johannes C.Heinzel Antal Nógrádi Andreas H.Teuschl-Woller David Hercher Department Life science Engineering University of Applied Sciences Technikum WienViennaAustria Austrian Cluster for Tissue Regeneration ViennaAustria Ludwig Boltzmann Institute for Traumatology The Research Center in Cooperation with AUVAViennaAustria University Clinic of Dentistry Medical University of ViennaViennaAustria Department of Plastic Reconstructive and Aesthetic SurgeryLandesklinikum Wiener Neustadt2700 Wiener NeustadtAustria Department of Anatomy Histology and EmbryologyAlbert Szent-Györgyi Medical SchoolUniversity of SzegedSzegedHungary Medical University of Vienna Department of Orthopedics and Trauma SurgeryDevision of Trauma SurgeryViennaAustria Department of Hand- PlasticReconstructive and Burn SurgeryBG Unfallklinik TuebingenUniversity of TuebingenTuebingenGermany

Peripheral nerve injuries induce a severe motor and sensory deficit. since the availability of autologous nerve transplants for nerve repair is very limited, alternative treatment strategies are sought, including the use of tubular nerve guidance conduits(tNGCs). However, the use of tNGCs results in poor functional recovery and central necrosis of the regenerating tissue, which limits their application to short nerve lesion defects(typically shorter than 3 cm). Given the importance of vascularization in nerve regeneration, we hypothesized that enabling the growth of blood vessels from the surrounding tissue into the regenerating nerve within the tNGC would help eliminate necrotic processes and lead to improved regeneration. In this study, we reported the application of macroscopic holes into the tubular walls of silk-based tNGCs and compared the various features of these improved silk^(+) tNGCs with the tubes without holes(silk^(–) tNGCs) and autologous nerve transplants in an 8-mm sciatic nerve defect in rats. Using a combination of micro-computed tomography and histological analyses, we were able to prove that the use of silk^(+) tNGCs induced the growth of blood vessels from the adjacent tissue to the intraluminal neovascular formation. A significantly higher number of blood vessels in the silk^(+) group was found compared with autologous nerve transplants and silk^(–), accompanied by improved axon regeneration at the distal coaptation point compared with the silk^(–) tNGCs at 7 weeks postoperatively. In the 15-mm(critical size) sciatic nerve defect model, we again observed a distinct ingrowth of blood vessels through the tubular walls of silk^(+) tNGCs, but without improved functional recovery at 12 weeks postoperatively. Our data proves that macroporous tNGCs increase the vascular supply of regenerating nerves and facilitate improved axonal regeneration in a short-defect model but not in a critical-size defect model. This study suggests that further optimizatio

关键词： axon regeneration blood vessel functional recovery macroporous nerve lesion peripheral nerve repair sciatic nerve silk-based nerve guidance conduit vascularization

Cogon grass biochar amendment and Panicum coloratum planting improve selected properties of sandy soil under humid lowland tropical climatic conditions

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Biochar 2020年第4期2卷 489-502页

作者： patrick s.Michael Department of Agriculture Papua New Guinea University of TechnologyPMBLae 411MPPapua New Guinea

Biochar amendment improves the physical,chemical and biological characteristics of different soil types under different climatic and environmental *** this study,effects of biochar or live pasture plants existing alone or co-existing on selected soil properties of sandy loam soil under humid lowland tropical climatic conditions were *** changes measured in the amended soil,with or without plants,were compared to the unamended and unplanted *** amendment with or without pasture improved moisture retention,lowered bulk density,increased pH and kept the electrical conductivity within ranges conducive for pasture ***,contents of all the nutrients increased following biochar amendment,however pasture establishment without amendment resulted in depletion of available potassium and *** all treatment conditions,soil organic carbon and soil organic matter were significantly *** grass is invasive under all land use systems and contributes to greenhouse gas emissions through *** biomass from the grass instead of burning would mitigate CO2 emissions from the tropics.

关键词： Biochar Effect Pasture sandy loam soil PNG

Management of non-variceal upper gastrointestinal tract hemorrhage:Controversies and areas of uncertainty

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World Journal of Gastroenterology 2012年第11期18卷 1159-1165页

作者： Eric P Trawick patrick s Yachimski Division of Gastroenterology Hepatology and NutritionVanderbilt University Medical Center

Upper gastrointestinal tract hemorrhage （UGIH） remains a common presentation requiring urgent evaluation and treatment. Accurate assessment, appropriate intervention and apt clinical skills are needed for proper management from time of presentation to discharge. The advent of pharmacologic acid suppression, endoscopic hemostatic techniques, and recognition of Helicobacter pylori as an etiologic agent in peptic ulcer disease （PUD） has revolutionized the treatment of UGIH. Despite this, acute UGIH still carries considerable rates of morbidity and mortality. This review aims to discuss current areas of uncertainty and controversy in the management of UGIH. Neoadjuvant proton pump inhibitor （PPI） therapy has become standard empiric treatment for UGIH given that PUD is the leading cause of non variceal UGIH, and PPIs are extremely effective at promoting ulcer healing. Howeve, neoadjuvant PPI administration has not been shown to affect hard clinical outcomes such as rebleeding or mortality. The optimal timing of upper endoscopy in UGIH is often debated. Upon completion of volume resuscitation and hemodynamic stabilization, upper endoscopy should be performed within 24 h in all patientswith evidence of UGIH for both diagnostic and therapeutic purposes. With rising healthcare cost paramount in today＇s medical landscape, the ability to appropriately triage UGIH patients is of increasing value. Upper en- doscopy in conjunction with the clinical scenario allows for accurate decision making concerning early discharge home in low risk lesions or admission for further moni toring and treatment in higher risk lesions. Concomitant pharmacotherapy with non steroidal antiinflammatory drugs （NsAIDs） and antiplatelet agents, such as clopidogrel, has a major impact on the etiology, severib/, and potential treatment of UGIH. Long term PPI use in patients taking chronic NsAIDs or clopidogrel is discussed thoroughly in this review.

关键词： Hemorrhage Proton pump inhibitors He/i-cobacter py/ori Prokinetic agents Hemostasis Thieno-pyridines

Adaptive optics in laser processing

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Light(science & Applications) 2019年第1期8卷 140-155页

作者： patrick s.salter Martin J.Booth Department of Engineering science University of OxfordParks RoadOxford OX13PJUK

Adaptive optics are becoming a valuable tool for laser processing,providing enhanced functionality and flexibility for a range of *** a single adaptive element,it is possible to correct for aberrations introduced when focusing inside the workpiece,tailor the focal intensity distribution for the particular fabrication task and/or provide parallelisation to reduce processing *** is particularly promising for applications using ultrafast lasers for threedimensional *** review recent developments in adaptive laser processing,including methods and applications,before discussing prospects for the future.

关键词： laser optics workpiece

Error Estimates for 1D Asymptotic Models in Coaxial Cables with Non-Homogeneous Cross-section

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Advances in Applied Mathematics and Mechanics 2012年第6期4卷 647-664页

作者： sébastien Imperiale patrick Joly Department of Applied Physics and Applied Mathematics Columbia UniversityNY 10027USA INRIA Rocquencourt POemsdomaine de Voluceau78153 Le ChesnayFrance

This paper is the first contribution towards the rigorous justification of asymptotic 1D models for the time-domain simulation of the propagation of electromagnetic waves in coaxial *** general objective is to derive error estimates between the"exact"solution of the full 3D model and the"approximate"solution of the 1D model known as the Telegraphist’s equation.

关键词： Coaxial cables Telegraphist’s equation error estimates non-homogeneous crosssection

High-Throughput Field Plant Phenotyping:A self-supervised sequential CNN Method to segment Overlapping Plants

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Plant Phenomics 2023年第2期5卷 285-294页

作者： Xingche Guo Yumou Qiu Dan Nettleton patrick s.schnable Department of statistics Iowa State UniversityAmesIAUSA Plant sciences Institute Iowa State UniversityAmesIAUSA Department of Agronomy Iowa State UniversityAmesIAUSA

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely *** first step in this process is typically plant segmentation,which requires a well-labeled training dataset to enable accurate segmentation of overlapping ***,preparing such training data is both time and labor *** solve this problem,we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping *** first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth *** proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are *** then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and *** show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision *** approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

关键词： computer preparing Plant