Free energy surface reconstruction from umbrella samples using Gaussian process regression

We demonstrate how the Gaussian process regression approach can be used to efficiently reconstruct free energy surfaces from umbrella sampling simulations. By making a prior assumption of smoothness and taking account of the sampling noise in a consistent fashion, we achieve a significant improvement in accuracy over the state of the art in two or more dimensions or, equivalently, a significant cost reduction to obtain the free energy surface within a prescribed tolerance in both regimes of spatially sparse data and short sampling trajectories. Stemming from its Bayesian interpretation the method provides meaningful error bars without significant additional computation. A software implementation is made available on www.libatoms.org.

Free energy surface reconstruction from umbrella samples using Gaussian process regression II: Multiple collective variables

We demonstrate how a prior assumption of smoothness can be used to enhance the reconstruction of free energy profiles from multiple umbrella sampling simulations using the Bayesian Gaussian process regression approach. The method we derive allows the concurrent use of histograms and free energy gradients and can easily be extended to include further data. In Part I we review the necessary theory and test the method for one collective variable. We demonstrate improved performance with respect to the weighted histogram analysis method and obtain meaningful error bars without any significant additional computation. In Part II we consider the case of multiple collective variables and compare to a reconstruction using least squares fitting of radial basis functions. We find substantial improvements in the regimes of spatially sparse data or short sampling trajectories. A software implementation is made available on www.libatoms.org.

A fracture criterion for the notch strength of high strength steels in the presence of hydrogen

High strength steels can suffer from a loss of ductility when exposed to hydrogen, and this may lead to sudden failure. The hydrogen is either accommodated in the lattice or is trapped at defects, such as dislocations, grain boundaries and carbides. The challenge is to identify the effect of hydrogen located at different sites upon the drop in tensile strength of a high strength steel. For this purpose, literature data on the failure stress of notched and un-notched steel bars are re-analysed; the bars were tested over a wide range of strain rates and hydrogen concentrations. The local stress state at failure has been determined by the finite element (FE) method, and the concentration of both lattice and trapped hydrogen is predicted using Oriani's theory along with the stress-driven diffusion equation. The experimental data are rationalised in terms of a postulated failure locus of peak maximum principal stress versus lattice hydrogen concentration. This failure locus is treated as a unique material property for the given steel and heat treatment condition. We conclude that the presence of lattice hydrogen increases the susceptibility to hydrogen embrittlement whereas trapped hydrogen has only a negligible effect. It is also found that the observed failure strength of hydrogen charged un-notched bars is less than the peak local stress within the notched geometries. Weakest link statistics are used to account for this stressed volume effect. © 2013 Elsevier Ltd.

Designing folding rings using polynomial continuation

© 2014 by ASME. Two types of foldable rings are designed using polynomial continuation. The first type of ring, when deployed, forms regular polygons with an even number of sides and is designed by specifying a sequence of orientations which each bar must attain at various stages throughout deployment. A design criterion is that these foldable rings must fold with all bars parallel in the stowed position. At first, all three Euler angles are used to specify bar orientations, but elimination is also used to reduce the number of specified Euler angles to two, allowing greater freedom in the design process. The second type of ring, when deployed, forms doubly plane-symmetric (irregular) polygons. The doubly symmetric rings are designed using polynomial continuation, but in this example a series of bar end locations (in the stowed position) is used as the design criterion with focus restricted to those rings possessing eight bars.

Acrossocheilus spinifer, a new species of barred cyprinid fish from south China (Pisces : Teleostei)

Acrossocheilus spinifer sp. nov. is described from the river basins in Fujian Province and the Han Jiang basin in Guangdong Province, south China. It is one of the barred Acrossocheihis species sharing five or six vertical bars on the flanks, with each bar being two scales in width. Acrossocheilus spinifer sp. nov. is morphologically most similar to Acrossocheilus wenchowensis. but distinguished from it by: a colour pattern of all vertical bars extending ventrally to the second scale row below the lateral line, and having the second bar placed posterior to the base of the last simple dorsal-fin ray, a blunt snout; and a stout, last simple dorsal-fin ray. Acrossocheilus spinifer sp. nov. resembles Acrossocheilus kreyenbergii and Acrossocheilus stenotaeniatus with which it shares a stout, last simple dorsal-fin ray with a serrated posterior edge, but is separated from both species by having a narrow median interruption in the lower lip, a lower jaw fully covered by the lower lip when viewed ventrally and the second vertical bar placed posterior to the base of the last simple dorsal-fin ray. The absence of a longitudinal stripe extending along the lateral line on the flanks in males readily distinguishes A. spinifer sp. nov. from Four other species, namely Acrossocheilus fasciatus, Acrossocheilus paradoxus, Acrossocheilus parallens, and Acrossocheilus jishouensis. (c) 2006 The Authors Journal compilation (c) 2006 The Fisheries Society of the British Isles.

Revision of the genus Niwaella in China (Pisces, Cobitidae), with description of two new species

Loaches of the genus Niwaella, family Cobitidae, are distributed only in East Asia. At present only in Japan and South Korea have fishes of the genus Niwaella been found. Herein we revise the genus Niwaella in China. Son and He ( 2001) transferred the species Cobitis laterimaculata to the genus Niwaella, but their specimens were not N. laterimaculata, but a new species, N. longibarba sp. n., collected from Cao'ejiang River, Huangzezhen, Chengxian County, Zhejiang Province. The new species is distinguished from N. laterimaculata by its colour pattern of a row of slightly large, and long, scattered dark brown vertical bars on the dorsolateral surface, two or three striations on the caudal fin, and long barbels and undeveloped mental lobes. In this paper we also describe another new species, N. xinjiangensis sp. n., collected from Xinjiang River, Guangfeng County, Jiangxi Province, May 1990, with diagnostic colour pattern of 17 - 20 large and long, dark brown vertical bars on the dorsolateral surface, a dark stripe or rounded black spots along the lateral midline and some blotches below the lateral midline; it is a large-sized species, with shorter barbels, and longer caudal peduncle. Thus five species of the genus Niwaella are known, three are endemic to eastern China and two are endemic to either Japan or South Korea.

The Yangtze River dolphin or baiji (Lipotes vexillifer): population status and conservation issues in the Yangtze River, China

1. Baiji were sighted 17 times during three recent simultaneous multi-vessel surveys in the Yangtze River, China (November 4-10, 1997; December 4-9, 1998; October 31-November 5, 1999). There were 11 sightings in 1997 (consisting of 17 animals), five in 1998 (seven animals), and two in 1999 (four animals). It was concluded that 13 individuals Could be considered as a minimum number of the baiji currently in the Yangtze River. 2. An annual rate of population decrease was roughly estimated as 10%. From the body sizes observed, the proportions of old, adult and immature individuals were approximately estimated at 57, 26, and 17% respectively. 3. Baiji showed a significant attraction to confluences and sand bars with large eddies. The present distribution range of the baiji is less than 1400 km in length in the Yangtze main river. Distances between the two nearest groups of baiji appear to be increasing. 4. Two typical sightings are described, in which surfacing and movements of baiji were recorded. Baiji were often found swimming together with finless porpoise. In the surveys they occurred in the same group in 63% of occurrences. Interactions between baiji and finless porpoise are described and discussed. 5. Human activities are the main threats to the baiji. Illegal electrical fishing accounted for 40% of known mortalities during the 1990s. Engineering explosions for maintaining navigation channels have become another main cause of baiji deaths. The last hope of saving the species may be to translocate the remaining baiji into a semi-captive reserve. known as the 'Baiji Semi-natural Reserve'. Copyright (C) 2003 John Wiley Sons, Ltd.

Advances in high power semiconductor diode lasers - art. no. 682402

High power semiconductor lasers have broad applications in the fields of military and industry. Recent advances in high power semiconductor lasers are reviewed mainly in two aspects: improvements of diode lasers performance and optimization of packaging architectures of diode laser bars. Factors which determine the performance of diode lasers, such as power conversion efficiency, temperature of operation, reliability, wavelength stabilization etc., result from a combination of new semiconductor materials, new diode structures, careful material processing of bars. the latest progress of today's high-power diode lasers at home and abroad is briefly discussed and typical data are presented. The packaging process is of decisive importance for the applicability of high-power diode laser bars, not only technically but also economically. The packaging techniques include the material choosing and the structure optimizing of heat-sinks, the bonding between the array and the heat-sink, the cooling and the fiber coupling, etc. The status of packaging techniques is stressed. There are basically three different diode package architectural options according to the integration grade. Since the package design is dominated by the cooling aspect,. different effective cooling techniques are promoted by different package architectures and specific demands. The benefit and utility of each package are strongly dependent upon the fundamental optoelectronic properties of the individual diode laser bars. Factors which influence these properties are outlined and comparisons of packaging approaches for these materials are made. Modularity of package for special application requirements is an important developing tendency for high power diode lasers.

808-nm fiber coupled module with a CW output power up to 130 W

A fiber coupled module is fabricated with integrating the emitting light from four laser diode bars into multimode fiber bundle. The continuous wave (CW) output power of the module is about 130 W with a coupling efficiency of around 80%. The output power is very stable after the temperature cycling and vibration test. No apparent power decrease has been observed as the device working continuously for 500 h.

AIN Monolithic Microchannel Cooled Heatsink for High Power Laser Diode Array

A novel AIN monolithic microchannel cooled heatsink for high power laser diode array is introduced.The high power stack laser diode array with an AIN monolithic microchannel heatsink is fabricated and tested.The thermal impedance of a 10 stack laser diode array is 0.121℃/W.The pitch between two adjacent bars is 1.17mm.The power level of 611W is achieved under the 20% duty factor condition at an emission wavelength around 808nm.

Applications of dielectric thin film by electron cyclotron resonance plasma chemical vapor deposition for semiconductor photoelectronic devices

The paper reports a method of depositing SiO2, SiNx, a:Si, Si3N4 and SiOxNy dielectric thin films by electron cyclotron resonance plasma chemical vapor deposition (ECR CVD) on InP, InGaAs and other compound semiconductor optoelectronic devices,and give a technology of depositing dielectric thin films and optical coatings by ECR CVD on Laser's Bars. The experiment results show the dielectric thin films and optical coatings are stable at thermomechanical property,optical properties and the other properties. In addition, the dielectric thin film deposition that there is low leakage current is reported for using as diffusion and ion implatation masks in the paper. In the finally, the dielectric film refractive index can be accurately controlled by the N-2/O-2/Ar gas flow rate.

Ag2S morphology controllable via simple template-free solution route

Different morphologies of Ag2S nano- and micro-materials, including spokewise micrometer bars, microfibers, nanowires, worm-like nanoparticles and nanopolyhedrons have been obtained controllably by a facile one-step method at room temperature. Powder X-ray diffraction (XRD), X-ray photo-electron spectroscopy (XPS) and scanning electron microscope (SEM) were employed to characterize the structure and compositions of those nanomaterials. Furthermore, ultraviolet visible (UV-vis) spectra of Ag2S with different morphologies show different spectral features.

Heinrich event imprints in the Okinawa Trough: evidence from oxygen isotope and planktonic foraminifera

Planktonic foraminiferal faunas, oxygen isotope and modern analog technique sea surface temperature records were obtained in piston core DGKS9603 (28degrees08.869'N, 127degrees16.238'E, water depth 1100 in) collected from the middle Okinawa Trough. During the last glaciation, four cold events were identified and correlate Heinrich events (HE) H2-5 of the last 45 ka. During the last deglaciation, core DGKS9603 has begun to be influenced by the Kuroshio since about 16 cal ka BP. Three weakenings of this warm current occurred at about 2.8-5.3, 11.4 and 15.5 cal ka BP respectively. Among the three fluctuations, the oldest one is synchronous with HE1 and could be a response to the strong cooling observed in the North Atlantic Ocean. The fluctuation occurring at about 11.4 cal ka ago corresponds to the Younger Dryas within the age error bars. Our observations provide new evidence that the HEs documented from Greenland and the northern North Atlantic had a global climatic impact. Changes in the intensity of the East Asian monsoon could be the main mechanism responsible for the paleoccanographic variations observed in the Okinawa Trough. (C) 2001 Elsevier Science B.V. All rights reserved.

三种海水经济鱼类早期发育生物学的研究

海水经济鱼类的养殖在我国已经形成第四次海水养殖浪潮，经济效益显著，有力地推动了我国海水养殖的产业结构调整和可持续发展。然而在海水养殖发展过程中也存在着诸多问题，尤其是早期发育阶段的高死亡率，严重制约了我国海水养殖产业的稳定和健康发展。 海水鱼类养殖的关键为高质量，高存活率苗种的生产和培育，由于鱼类种类繁多，生物多样性丰富，对应实际的繁育技术，尤其是新品种的开发，必须要做出相应的调整。这就要求我们必须对每一种鱼类早期发育有所了解，并将形态和组织上的数据用于指导生产。 本文通过显微观察和组织学研究，主要描述和研究了我国北方三种重要的海水经济鱼类(条斑星鲽、杂交鲆、条石鲷)的早期发育生物学，并结合实际生产进一步阐明关键期的产生原因，机理以及采用相应的对策。具体结果如下： 1.条斑星鲽：作为冷温性鲆鲽鱼类，条斑星鲽早期发育过程的特征主要有： ① 条斑星鲽受精卵无油球，卵子呈半浮性；不同步卵裂现象提前，发生在第三次卵裂；卵裂期裂球大小差异大。孵化过程较长，在水温8 ± 0.3℃，盐度33的条件下，经9 d孵化。条斑星鲽胚胎发育的不同时期对温度的敏感性不同，其中原肠期对温度比较敏感。 ②在8-10℃，盐度33的条件下，8-9 dph开口摄食。且开口时，其吻前端出现有一点状黑褐色素，构成了条斑星鲽仔鱼“开口期”的重要标志。卵黄囊于消失。在后期仔鱼末期，背鳍和臀鳍上形成特有的黑褐色条斑带。 ③杯状细胞首先出现在咽腔后部和食道前段，胃腺和幽门盲囊出现于29 dph，变态期始于30dph。在条斑星鲽早期发育过程中，观察到其直肠粘膜层细胞质出现大量嗜伊红颗粒，为仔鱼肠道上皮吸收的蛋白质。 ④首先淋巴化的免疫器官是头肾，然后是胸腺和脾脏，这与大部分硬骨鱼类不同。条斑星鲽除头肾和脾脏外，胸腺实质也形成MMCs。其中以脾脏形成MMCs最为丰富，形态多样。 2. 杂交鲆：为同属的牙鲆和夏鲆间的远缘杂交种，其发育过程的特点为： ① 在温度为15.4～16.0℃，杂交鲆胚胎从受精到孵化所需的时间为76 h左右，胚孔关闭前期，胚胎先出现视囊及克氏囊，而后形成体节。孵出前胚体在卵膜内环绕不到1周。 ② 孵化后消失。杂交鲆群体变态间隔长(34-60 dph)，且变态高峰期出现的冠状幼鳍不明显(与母本牙鲆相比)，数量为7-8根。 ③组织学观察发现，其消化系统中胃腺出现较晚，且胃腺发育过程缓慢(与母本牙鲆相比)。甲状腺滤泡增生不明显，颜色较浅，数量较少。杂交鲆在早期发育过程中，并没有出现鳔原基。 3. 条石鲷作为岩礁性的暖水性鱼类，早期发育过程也较为特殊，包括外形以及内部的器官结构。主要特点有： ① 受精卵：受精卵卵黄上具有龟裂结构，为鱼卵的分类特征之一。 ② 初孵仔鱼：初孵仔鱼背鳍膜上的黑色素，从体背面向背鳍膜边缘移动，到3dph仔鱼基本消失，此为本种仔鱼发育所特有的特点。 ③ 后期仔鱼和稚鱼：肠道肌肉层加厚明显，仔稚鱼胃肠排空率急剧上升，死亡率增加，通过改善常规的投饵方式部分解决了这个死亡高峰的问题。在幼鱼初期，牙齿融合为骨喙，为石鲷科鱼类的特征。 ④胸腺上皮分泌细胞：类似的现象同样在虹鳟鱼中发现，但是虹鳟鱼胸腺上皮分泌细胞不如条石鲷的丰富，同样也不如条石鲷的排列整齐，而是零星分布在胸腺上皮与咽腔接触的表面。除了正常的造血器官—脾脏和头肾外，肝脏、胰腺和鳔等多种组织等也出现MMCs，此现象在硬骨鱼类不多见，一般发生在软骨鱼类。

中太平洋海区富钴结壳地球化学特征及成因机制

本文利用ICP-AES、EPMA、X-ray衍射等测试技术以及聚类分析和因子分析等多种数理统计方法，系统地对中太平洋海区富钴结壳的元素地球化学特征、矿物组成和微观组构进行了研究，并探讨了其成因机制，获得以下主要认识： 1中太平洋海区富钴结壳类型多样，均为水成成因，其矿物相主要由锰矿物相、铁矿物相和非金属矿物相组成；富钴结壳壳层发育多种原生和次生构造类型。 2磷酸盐化作用不仅强烈改变富钴结壳元素初始含量，而且造成富钴结壳某些元素间的相关性发生改变，这些敏感型元素对可用于指示富钴结壳是否发生磷酸盐化。在不同水深段内，未磷酸盐化型富钴结壳的主要元素随经向、纬向的变化趋势相似，表明其受水体化学障、表面生产力和物质来源等环境参数控制；而随水深的变化则具有区域一致性，表明水体化学具有区域成层性。 3未磷酸盐化富钴结壳稀土元素含量和轻重稀土分馏程度随水深发生规律变化，这种变化不仅与它们在海洋中的含量和行为有关，也与海洋背景颗粒的吸附有关；铈(Ce)在富钴结壳中基本上呈4价，且动力学因素控制了其富集过程，因此Ce异常不能用于指示富钴结壳形成环境的氧化程度。 4基于富钴结壳微层呈锯齿状且同一微层生长速率不同，提出了富钴结壳在各种基底表面生长以及后继发育过程受固液界面双电层控制的发育模式。在富钴结壳整个发育过程中，经历了从贫氧环境向富氧环境的转变，但微环境则呈富氧-低氧过程的交替。 关键词： 富钴结壳；中太平洋；元素地球化学；界面双电层