EMBOSS和EMBnet

笔者撰写的“EMBOSS软件包序列分析程序实例”一文,已经在《生物信息学》期刊2021年第19卷第1期发表。此文介绍欧洲分子生物学开放软件包(European Molecular Biology Open Software Suite,EMBOSS)。EMBOSS是欧洲分子生物学网络组织(European Molecular Biology Network,EMBnet)于上世纪九十年代末启动的以欧洲国家为主的国际合作项目,是生物信息学领域中较早投入使用的大型开源软件包。本文基于笔者亲身经历,回顾EMBOSS项目的来龙去脉,讲述EMBnet三十多年来的发展历程,及其对生物信息开发、服务和教育培训等方面的贡献,从某个侧面为读者特别是年轻读者展示生物信息学发展早期的一段历史。

EMBOSS软件包序列分析程序应用实例

本文介绍欧洲分子生物学开放软件包EMBOSS序列分析程序应用实例。第1节简单介绍EMBOSS软件包的概况和基本用法。第2节介绍格式转换、序列提取、序列变换和序列显示等常用序列处理程序。第3节介绍序列比对程序,包括双序列比对、多序列比对和点阵图程序。第4节介绍常用核酸序列分析程序,可用于核苷酸组分统计、开放读码框分析、CpG岛识别、密码子使用统计和重复序列寻找等。第5节介绍常用蛋白质序列分析程序,包括氨基酸组分统计、序列特征位点识别、二级结构分析等。文中结合教学实例,选择部分常用程序,给出具体运行方式,并扼要说明分析结果的生物学意义。文末对程序运行过程中需要注意的地方加以讨论,并用表格列出部分常用程序的名称和用途,以便读者查阅。

EXPERIMENTAL STUDY ON THE HOT EMBOSSING POLYMER MICROFLUIDIC CHIP

Experiments are used to study the fabrication of polymer microfluidic chip with hot embossing method. The pattern fidelity with respect to the process parameters is analyzed. Experiment results show that the relationship between the imprint temperature and the microchannel width is approximately exponential. However, the depth of micro channel isn＇t sensitive to the imprint temperature. When the imprint pressure is larger than 1 MPa and the imprint time is longer than 2 min, the increasing of imprint pressure and holding time has little impact on the microchannel width. So over long holding time is not needed in hot embossing. Based on the experiment analysis, a series of optimization process parameters is obtained and a fine microfluidic chip is fabricated. The electrophoresis separation experiment are used to verify the microfluidic chip performance after bonding. The results show that 100bp-ladder DNA sample can be separated in less than 5 min successfully.

HOT EMBOSSING METHODS FOR PLASTIC MICROCHANNEL FABRICATION

Fabrication of microchannels on polymethylmethacrylate （PMMA） substrates using novel microfabrication methods is demonstrated. The image of microchannels is transferred from a silicon master possessing the inverse image of the microchannel to a PMMA plate by using hot embossing methods. The silicon master is electrostatically bonded to a Pyrex 7740 glass wafer, which improves the device yield from about 20 devices to hundreds of devices per master. Effects of embossing temperature, pressure and time on the accuracy of replication are systematically studied using the orthogonal factorial design. According to the suggested experimental model, the time for the whole embossing procedure is shorten from about 20 min to 6 min, and the accuracy of replication is 99.3%. The reproducibility of the hot embossing method is evaluated using 10 channels on different microfluidic devices, with variations of 1.4 % in depth and 1.8% in width.

OPTIMUM DESIGN OF PROCESSING CONDITION AND EXPERIMENTAL INVESTIGATION OF GRATING FABRICATION WITH HOT EMBOSSING LITHOGRAPHY

The cross-section profiles of polymer deformation in the hot embossing lithography process were studied by finite element method for various temperature, time and pressure. In order to successfully fabricate high-frequency grating lines, an optimal imprint condition was selected and the related experiments were carried out. The fabricated gratings were illuminated by the SEM image and AFM analysis, which agree well with the simulated results. Therefore, the finite element methods are helpful for a better comprehension of the polymer flow phenomena governing the pattern definition and the design of optimum processing conditions for successful grating fabrication.

Hot embossing of micro energy director for micro polymer fusion ultrasonic bonding

In order to use micro ultrasonic bonding technique to package polymer microfluidic chips, an auxiliary microstructure named micro energy director is designed and fabricated. The hot embossing process for PMMA （ polymethyl methacrylate） substrates with both concave micro channel and convex micro energy director for ultrasonic bonding is studied. The embossing processes with different embossing temperatures are simulated using Finite Element Method （FEM）. The optimized parameters are： the embossing temperature of 135 ℃ , holding time of 200 s, and the embossing pressure of 1.65 MPa. The experimental results show that the replication error between experiments and simulations is less than 2% and the replication accuracy of the microstrueture is more than 96%. The study offers a method for quick optimizing parameters for hot embossing both concave and convex microstructures.

A Novel Extrusion Microns Embossing Method of Polymer Film

A continuous hot embossing method is reported in this paper. The continuous means that the extruder and the hot embossing equipment is used in series, the polymer film is embossed after extrusion immediately. The basic principle of this method, the key design point and the corresponding operate process of the embossing equipment is described in this paper. The polymer diffuser with micro-lens matrix on its surface is designed and the optical properties are simulated. Then, the diffuser is fabricated by the embossing equipment. The optical properties of the diffuser are tested and compared with the results of the simulation to verify the reproducibility of the equipment. By this method, the diffuser with large area can be fabricated with high precision of graphic replication, high efficiency and low cost.

PRESSURE FORCE CONTROL FOR FABRICATION OF PLASTIC MICROFLUIDIC CHIPS WITH HOT EMBOSSING METHOD

A pressure force control system for hot embossing of microfluidic chips is designed with a moment motor and a ball bearing lead screw. Based on the numeric PID technique, the algorithm of pulsant integral accelerated PID control is presented and the negative effects of nonlinearity from friction, clearance and saturation are eliminated. In order to improve the quick-resixmse characteristic, independent thread technique is adopted. The method of pressure force control based on pulsant integral accelerated PID control and independent thread technique is applied with satisfactory control performance.

Hot-embossing fabrication of chalcogenide glasses rib waveguide for mid-infrared molecular sensing

Chalcogenide glasses have shown promise in fabricating mid infrared（MIR） photonic sensing devices due to their excellent optical properties in MIR. In addition, the glass transition temperature of chalcogenide glasses are generally low,making them ideal to create the high-throughput patterns of micro-scale structures based on hot embossing that is alternative to the standard lithographic technology. In this paper, we outline the research progress in the chalcogenide waveguide based on the hot embossing method, and discuss the problems remaining to be solved and the possible solutions.

Finite Element Analysis (FEA) and Thermal Gradient of a Solid Rectangular Fin with Embossing’s for Aerospace Applications

Fins are the extended surfaces through which heat transfer takes place by conduction and convection to keep the base surface cool. Fins of various configurations are presently used ranging from automobile engines to cooling of chip in a computer. Fins used presently are solid with different shapes but in the present research such solid fins are compared with solid fins having maximum of 10 numbers of embossing’s that further increases the surface area for maximum heat transfer. Importance in this research is given to variation of temperature along the length of the fins which in turn gives rate of heat transfer. Thus this research is under taken to increase the efficiency of fins (by extracting heat from the base surface) which is highly demanded today for air cooled engines, compressors, refrigerators etc. In the present research, SOLID70 element and SURF152 elements are used for FE analysis. Methodology involves 3D rectangular fin modelling and meshing, creation of surf elements for the modeling, applying the boundary conditions and source temperature, applying the material property (aluminum) to obtain the steady state thermal contours. FEA results are finally compared with analytic and experimental values for validity. In the present research, a solid rectangular aluminum fin and the same rectangular fin with 2, 4, 8 and 10 embossing’s were compared through finite element analysis for its temperature distribution along the length. FEA analysis of the present research showed that fins having embossing’s were more efficient compared to that a simple solid fin. Hence it is concluded from the present research that embossing’s at preferred locations further increases the rate of heat transfer. From the present analysis it is concluded that the mathematical and FEA for a solid rectangular fin without embossing’s are converging within ±1.2°C and rectangular fin with 10 embossing’s is converging within ±1.4°C and hence the validity.

激光烧蚀压印制备疏水铝箔表面的耐久性

提出了一种激光烧蚀压印技术制备具有多级微结构的疏水铝箔表面。该技术利用激光直接辐照在工件表面,利用烧蚀诱导的冲击压印获得一级微结构,同时利用烧蚀诱导的融化材料的流动获得二级微结构。为了检验耐久性,对疏水铝箔工件进行了酸碱腐蚀实验和不同环境存储实验。实验结果表明,酸碱腐蚀会破坏工件表面的微观形貌和低表面能,因此工件接触角随着腐蚀时间增长而降低。其中碱腐蚀工件时反应比酸腐蚀剧烈得多,工件表面形貌受损也更大,工件表面在碱腐蚀16 h后就达到了超亲水状态(25°),而酸腐蚀24 h后也依然表现为疏水性(97°)。再次进行时效处理后,工件依然能在三周后达到稳定的疏水状态,但疏水性能比腐蚀前要差,且酸腐蚀工件的最终疏水性(120°)比碱腐蚀工件(105°)要好。不同存储环境对工件表面形貌几乎没有影响。存储在空气中的工件接触角无明显变化,存储在盐水中的工件丧失疏水性(87°),存储在纯水中的工件表现比盐水稍好(96°)。再次进行时效处理后,纯水存储的工件接触角可以恢复到135°左右,而盐水存储的工件仅能恢复到120°。激光烧蚀压印制备的疏水铝箔基本能够满足应对复杂环境的要求。

聚丙烯纤维混凝土力学性能试验

为了探究不同类型、不同掺量的聚丙烯纤维对混凝土力学性能的作用效果,在混凝土材料中加入3种不同类型的聚丙烯纤维(波浪型聚丙烯纤维、压花型聚丙烯纤维、单丝型聚丙烯纤维),并分别使用不同掺量(0、0.08%、0.11%、0.14%、0.17%、0.20%)作为水平变量,对聚丙烯纤维试块进行抗压强度试验、劈裂抗拉强度试验、轴心抗压强度试验.研究发现:波浪型聚丙烯纤维掺量为0.17%时,混凝土抗压强度最佳;单丝型聚丙烯纤维掺量为0.20%时,混凝土的劈裂抗拉强度最佳;单丝型聚丙烯纤维掺量为0.17%时,对于混凝土的抗折强度有较好作用效果.

聚乙烯油水分离膜的制备及表征

线型低密度聚乙烯(LLDPE)与聚氧乙烯(PEO)以不同质量比混合,通过热压成型技术制备了LLDPE/PEO膜,利用超声沥滤工艺除去PEO,实现多孔结构,再采用热压印技术在膜表面构筑微结构制备LLDPE高效油水分离膜。结果表明:LLDPE/PEO最佳质量比为40/60;超声沥滤的时间为6 h;LLDPE油水分离膜能快速选择性吸附二氯甲烷和环己烷等油剂,对环己烷、花生油和N,N-二甲基甲酰胺的饱和吸附量约为150%~180%;油水分离膜对二氯甲烷/水混合物的分离效率为99.9%。

材料表面微图案结构成型技术及其研究进展

表面微图案结构成型技术作为实现材料表面纹理化并促进材料先进化、功能化的一种手段已经广泛应用到实际生产制造中。根据材料应用领域的差异,表面微图案成型的主要方法包括热压花、化学蚀刻、电火花加工、光刻和3D打印。本文综述了不同表面微图案结构成型技术及制备表面纹理化功能材料的基本原理,并列举其在光伏、电子信息、智能制造、超精密制造等领域的实际应用。总结了不同表面微图案结构成型技术的特点及适用范围,提出了实现材料表面纹理化和功能化所面临的关键问题,为表面微图案结构的微加工技术提供了一定参考。

聚合物微针阵列热压印成型仿真与试验研究

【目的】针对聚合物微针阵列热压印成型过程中充型不完整、脱模后继续变形和应力集中等问题,将成型仿真与试验相结合,探究热压印成型参数对残余应力与平均填充深度的影响,以满足高精度批量制造聚合物微针阵列的需求。【方法】在聚合物材料热-机械性能研究的基础上,建立微针阵列的有限元模型,分析热压印温度、热压印速率和下压量等成型参数对残余应力及其分布的影响,进行热压印成型试验,探讨相关成型参数对微针成型的影响,对比分析了平均填充深度仿真与试验值。【结果】随热压印温度的升高,最大成型应力呈先降后升的趋势;随热压印速率与下压量的增加,最大成型应力均呈增大的趋势;除热压印温度高于125℃之外,平均填充深度的仿真值与试验值变化趋势一致,且仿真值均高于试验值。此外,还获得了适用于聚苯乙烯微针阵列的最佳热压印参数,即热压印温度125℃、热压印速率10μm/s、下压量2.6 mm。【结论】在一定温度范围内,该数值仿真结果具有较高的指导意义,聚苯乙烯微针阵列结构的残余应力与平均填充深度具有较为敏感的温度与时间相关性。

塑料压花辊模具的加工工艺研究

通过分析塑料压花辊模具的加工工艺和优化切削加工参数,选用五轴数控机床完成模具的数控加工实践,有效解决塑料压花辊模具凹模型高硬度难加工问题。经过塑料压花辊模具现场使用验收,尺寸精度与表面粗糙度均达到使用性能要求,验证了模具数控加工工艺的合理性。塑料压花辊模具的加工工艺对类似辊类模具的加工具有一定的借鉴指导意义。

热压印成型复合微透镜阵列的微光学照明特性

在LED照明中,光线分布不均产生的眩光及光线中的紫外光、蓝光成分容易造成视觉疲劳和眼睛损伤,目前主要是以调节光源为主,纳米级光波段调节的表面结构加工成本较高。因此,利用热压印快速成型技术开发了一种微米尺度的复合微透镜阵列导光板,探究健康照明的复合微透镜尺度效应。首先分析微棱镜表面小微透镜的深宽比与反射电场分布的关系,然后研究导光板的微结构参数对漫反射率、镜面反射率和透射率的影响。最后,对比市面上丝网印刷微点、微棱镜阵列等结构导光板,研究复合微透镜微米尺度对照度、均匀度等微光学性能的影响。分析表明:当小微透镜深宽比在0.6~1内时,紫外光和蓝光的反射面有更小的反射电场变异系数,说明其漫反射大。实验结果表明:热压印技术可以在4 s内将微透镜高5~30μm和微棱镜高10~80μm的复合微透镜阵列导光板加工成型;照度均匀度随着小微透镜深宽比的增大而增大,照度分别比微棱镜和丝网印刷微点阵列提高45%和83%;与微棱镜相比,紫外光和蓝光的漫反射率分别提高8%和18%,镜面反射率下降80%~83%。控制复合微透镜的深宽比可以减少照明眩光,抑制紫外光和蓝光。

微流控芯片非等温热压印微结构成型仿真分析

传统的热压印方法需要将模具和基片同时加热至一定温度后进行压印成型来生产微流控芯片,存在反复加热冷却、循环时间长、成型效率低的问题。课题组在模具和基片非等温条件下,采用有限元方法研究微流控芯片的非等温热压印成型规律。模拟分析可知:当模具温度高于基片温度时,通过热传递基片能在短时间内与模具温度平衡,延长压印时间可以减少基片应力集中;当模具温度低于基片温度,且都高于玻璃态转化温度时,微结构的压印过程能够达到边压印边冷却的效果,压印周期缩短。通过对微流道压印误差分析可知:在模具温度一定的情况下,微流道深度的相对误差最大;随着模具温度升高,微流道的整体成型质量先升后降,120℃时误差最小。

印纹陶的饰意对现代陶艺的启发

印纹陶是我国原始古代部落所遗留下来的民族财富,传统的印纹陶作为一种古老的艺术形式,承载了人类文明的记忆与情感。印纹陶纹饰也沉淀了人类的智慧和时代的变迁,现代的表现手法与创作形式为印纹陶纹饰提供了创新的途径,传统的印纹陶纹饰也为现代陶瓷设计提供了丰富素材,为现代陶艺家表达审美感受和思想观念提供了新的方式。

基于PLC的气流辅助热压印设备自动控制系统设计

微流控芯片、微透镜阵列等高附加值产品批量化生产依赖热压印设备,但传统热压印设备加热效率及控制精度较低,较难满足快速精密生产需求。提出采用气流和加热棒一起加热的方法提高加热效率,并基于PID级联控制原理设计气流辅助热压印设备的自动化控制系统。首先,采用SolidWorks建立气流辅助热压印设备三维模型;然后,采用TIA portal软件设计自动控制系统;最后,创建WinCC组态监控工程,搭建实物设备,研究气流辅助热压印设备及自动控制系统性能。实验结果表明:采用气、固双热源加热方法的加热效率比单一热源提高50%~70%;利用PID级联控制方式调控温度参数的响应速度快,抗干扰能力强;通过组态系统可以实时监控热压温度、热压压力、保压时间等工艺参数;在68 s内实现了微透镜阵列产品快速精密微成型。