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Calculating pH-dependent free energy of proteins by using Monte Carlo protonation probabilities of ionizable residues

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Protein & Cell 2012年第3期3卷 230-238页

作者： Qiang Huang andreas Herrmann State Key Laboratory of Genetic Engineering School of Life SciencesFudan UniversityShanghai 200433China Department of Biology Molecular BiophysicsHumboldt University of Berlin10115 BerlinGermany

Protein folding,stability,and function are usually in-fluenced by *** free energy plays a fundamental role in analysis of such pH-dependent ***-trostatics-based theoretical framework using dielectric solvent continuum model and solving Poisson-Boltzm-ann equation numerically has been shown to be very successful in understanding the pH-dependent ***,in this approach the exact computation of pH-dependent free energy becomes impractical for proteins possessing more than several tens of ioni-zable sites(e.g.>30),because exact evaluation of the partition function requires a summation over a vast number of possible protonation *** we present a method which computes the free energy us-ing the average energy and the protonation probabili-ties of ionizable sites obtained by the well-established Monte Carlo sampling *** key feature is to calculate the entropy by using the protonation *** used this method to examine a well-studied protein(lysozyme)and produced results which agree very well with the exact *** to the optimum pH of maximal stability of proteins and pro-tein-DNA interactions have also resulted in good agreement with experimental *** examples recommend our method for application to the elucidation of the pH-dependent properties of proteins.

关键词： protein protonation protein electrostatics pH-dependent free energy Poisson-Boltzmann equation Monte Carlo simulation

A Comprehensive Numerical Investigation on the Mechanical Properties of Hetero-Junction Carbon Nanotubes

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Communications in Theoretical Physics 2015年第8期64卷 215-230页

作者： Ali Ghavamian andreas chsner School of Engineering Griffith University Gold Coast Campus

A set of forty-three hetero-junction CNTs, made of forty-four homogeneous carbon nanotubes of different chiralities and configurations with all possible hetero-connection types, were numerically simulated, based on the finite element method in a commercial finite element software and their Young's and shear moduli, and critical buckling loads were obtained and evaluated under the tensile, torsional and buckling loads with an assumption of linear elastic deformation and also compared with each other. The comparison of the linear elastic behavior of hetero-junction CNTs and their corresponding fundamental tubes revealed that the size, type of the connection, and the bending angle in the structure of hetero-junction CNTs considerably influences the mechanical properties of these hetero-structures. It was also discovered that the Stone-Wales defect leads to lower elastic and torsional strength of hetero-junction CNTs when compared to homogeneous CNTs. However, the buckling strength of the hetero-junction CNTs was found to lie in the range of the buckling strength of their corresponding fundamental tubes. It was also determined that the shear modulus of hetero-junction carbon nanotubes generally tends to be closer to the shear modulus of their wider fundamental tubes while critical buckling loads of these heterostructures seem to be closer to critical buckling loads of their thinner fundamental tubes. The evaluation of the elastic properties of hetero-junction carbon nanotubes showed that among the hetero-junction models, those with armchair-armchair and zigzag-zigzag kinks have the highest elastic modulus while the models with armchair-zigzag connections show the lowest elastic stiffness. The results from torsion tests also revealed the fact that zigzag-zigzag and armchair-zigzag hetero-junction carbon nanotubes have the highest and the lowest shear modulus, respectively. Finally, it was observed that the highest critical buckling loads belong to armchair-armchair heter

关键词： finite element method carbon nanotube hetero-junct

Is the Prform of phytochrome biologically active in the nucleus?

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Molecular Plant 2021年第4期14卷 535-537页

作者： Jigang Li andreas Hlitbrunner State Key Laboratory of Plant Physiology and Biochemistry College of Biological SciencesChina Agicultural UniversityBeijing 100193China Institute of Biology I Faculty of Biology and Signalling Research Centres BIOSS and CIBSSUniversity of Freiburg79104 FreiburgGermany

The sessile nature of plants has promoted the evolution of a wide range of mechanisms that enable plants to adapt to the changing *** particular,the light environment is highly dynamic and,therefore,plants have evolved several families of photoreceptors to detect almost all facets of light,such as quality,quantity,direction,and *** are red(R)and far-red(FR)light photoreceptors in plants that play fundamental roles in modulating adaptive growth of plants in response to their changing light environment(Li et al.,2011).In the model plant Arabidopsis thaliana there are five phytochrome photoreceptors,named phytochrome A(phyA)to *** is photolabile,whereas phyB to phyE are *** and phyB,the two most abundant phytochromes,account for-95% of total phytochrome proteins in etiolated Arabidopsis seedlings and play the most important role in regulating seedling photomorphogenesis(Li et al.,2011).

关键词： photoreceptor environment. Arabidopsis

Abandoned Altitudes? Decrease and Expansion of Grassland in the Hinterland of Popayán, Southern Colombian Andes

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Journal of Mountain Science 2015年第1期12卷 123-133页

作者： andreas Haller Oliver Bender Institute of Geography University of Innsbruck Institute for Interdisciplinary Mountain Research Austrian Academy of Sciences Technikerstrasse 21a 6020 InnsbruckAustria

Due to their ecological disadvantages, many mountain regions have experienced land-use abandonment and shrub encroachment on former grassland at higher altitudinal zones--especially during recent decades of urbanization. But does this trend also apply to the hinterland of urban settlements？ By using the Southern Colombian example of Popay^n, a medium-sized city located in the Northern Andes, we can show that the landscape changes observed between 1989 and 2010 can hardly be related to agricultural abandonment. Hypsometric variations of land-cover change indicate that, until 2001, woods or shrubland expanded faster at the lower altitudinal range adjacent to the city than at the more remote higher zones. In contrast, after 2001 grassland areas increased on former woods or shrnbland at all altitudinal belts. Both periods thus present developments that can be interpreted as the result of land-use expansion below 2000 m asl and land-use persistence in the tierrafrla of the mountain city＇s hinterland.

关键词： Land-cover change Land-use change Rural-urban linkages Northern Andes

Mapping Natural Hazard Impacts on Road Infrastructure——The Extreme Precipitation in Baden-Württemberg, Germany, June 2013

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International Journal of Disaster Risk Science 2014年第3期5卷 227-241页

作者： Sina Keller andreas Atzl Institute of Regional Science/Institute of Urban and Regional Planning Karlsruhe Institute of TechnologyKaiserstraße 1276131 KarlsruheGermany

Infrastructures in Europe have been affected by impacts of extreme natural events with increasing frequency over the past decades. One of the most recent examples is the flooding that affected parts of Germany in June 2013. Global warming is expected to change patterns of climate-related extreme events affecting *** article presents an explanatory approach. Based on an observational design, causal connections between the occurrence and patterns of extreme events and related road infrastructure impacts are analyzed. The hazard mapping case study in the state of Baden-Wrttemberg combines traffic information and data on the June 2013 extreme precipitation in Germany. It examines the precipitation occurrence and road infrastructure impact characteristics in Baden-Wu¨ rttemberg and identifies spatiotemporal hazard patterns. The article suggests further research needs and fields of application for risk mapping in climate change adaptation research in Germany.

关键词： Extreme precipitation Floods Germany Hazard patterns Landslides Road infrastructure

Morphology and electric potential-induced mechanical behavior of metallic porous nanostructures

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Friction 2020年第3期8卷 604-612页

作者： Sunghan KIM andreas APOLYCARPOU Hong LIANG School of Mechanical Engineering Chung Ang UniversinSeoul 06974Republic of Korea Department of Mechanical Engineering Texas A&M UniversiyCollege Sation 77843-3123USA

Understanding mechanical behaviors influenced by electric potential and tribological contacts is important for verifying the robustness and reliability of applications based on metallic porous nanostructures in electrical *** this work,nickel-based metallic porous nanostructures were studied to characterize their mechanical properties and morphologically dependent contact areas during application of an electric potential using a nanoindenter.W e observed that the indentation moduli of nickel-based metallic porous nanostructures were altered by pore size and application of electric *** addition,the structural aspects of the surface morphology of nickel-based porous nanostructures had a critical effect on the determination of contact area.W e suggest that the relation between electric potential and the mechanical behaviors of metallic porous nanostructures can be crucial for building mechanically robust functional devices,which are influenced by electric *** morphological shape characteristics of metallic porous nanostructures can be alternative decisive factors for manipulation of tribological performance through regulation of contact area.

关键词： mechanical properties nanoindentation metallic porous nanostructures contact area electric potentia

Roughness Measurements with Polychromatic Speckles on Tilted Surfaces

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Nanomanufacturing and Metrology 2021年第4期4卷 237-246页

作者： Johannes Stempin andreas Tausendfreund Dirk Stobener andreas Fischer Bremen Institute for Metrology Automation and Quality ScienceUniversity of BremenLinzer Str.1328359 BremenGermany

Surface light scattering enables contactless and fast measurements of surface roughness.A surface inclination alters the direction of the scattering beam and thus the measured surface roughness is calculated from the detected intensity ***,an accurate sensor-surface alignment is *** order to achieve tilt-independent roughness measurements,a model-based evaluation approach for polychromatic speckle patterns is *** evaluating the shape of the superposed speckles,which occur for polychromatic illumination,with regard to the distance to the scattering centre,surfaces with an Sa roughness value in the range of 0.8-3.2μm are *** investigations demonstrate that the influence of a surface tilt up to±1.25°on the roughness measurement is reduced by 90%.As a result,the robustness of the polychromatic speckle roughness measurement is improved,which allows to speed up the adjustment of the measurement system or the surface sample,respectively.

关键词： Surface roughness Polychromatic light scattering Surface tilting In-process measurement

Evaluating performance of lignite pillars with 2D approximation techniques and 3D numerical analyses

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International Journal of Mining Science and Technology 2017年第6期27卷 929-936页

作者： Deliveris Alexandros V. Benardos andreas Centre for Research and Technology Hellas (CERTH) Chemical Process & Energy Resources Institute (CPERI) Athens GR15 125 Greece National Technical University of Athens (NTUA) School of Mining and Metallurgical Engineering (SMME) Athens GR15 780 Greece

This paper attempts to investigate the use of approximate 2D numerical simulation techniques for the evaluation of lignite pillar geomechanical response, formed via the room and pillar mining *** and applicability of the developing methodology are assessed through benchmarking with a more direct and accurate 3D numerical model. This analysis utilizes an underground lignite mine which is being developed in soft rock environment. Through the decisions made for the optimum room and pillar layout, the design process highlights the strong points and the weaknesses of 2D finite element analysis, and provides useful recommendations for future reference. The interpretations of results demonstrate that 2D approximation techniques come near quite well to the actual 3D ***, external load approximation technique seems to fit even better with the respective outcomes from the 3D analyses.

关键词： Geomechanics Room and pillar Underground lignite mine Finite element method 3D numerical analysis Average pillar stress

Evolution and future of laparoscopic colorectal surgery

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World Journal of Gastroenterology 2014年第41期20卷 15119-15124页

作者： andreas M Kaiser Department of Colorectal Surgery Keck School of MedicineUniversity of Southern California

The advances of laparoscopic surgery since the early 1990 s have caused one of the largest technical revolutions in medicine since the detection of antibiotics(1922,Flemming),the discovery of DNA structure(1953,Watson and Crick),and solid organ transplantation(1954,Murray).Perseverance through a rocky start and increased familiarity with the chop-stick surgery in conjunction with technical refinements has resulted in a rapid expansion of the indications for minimally invasive ***-related factors initially contributed to this success and included the improved postoperative recovery and cosmesis,fewer wound complications,lower risk for incisional hernias and for subsequent adhesionrelated small bowel obstructions; the major breakthrough however came with favorable long-term outcomes data on oncological *** future will have to determine the specific role of various technical approaches,define prognostic factors of success and true progress,and consider directing further innovation while potentially limiting approaches that do not add to patient outcomes.

关键词： Laparoscopic Laparoscopy Open surgery Colorectal surgery Colectomy Robot