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Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

《化学科学与工程前沿(英文)》 2017年 第11卷 第1期   页码 37-45 doi: 10.1007/s11705-017-1618-2

摘要: The ability to go from a digitized DNA sequence to a predictable biological function is central to synthetic biology. Genome engineering tools facilitate rewriting and implementation of engineered DNA sequences. Recent development of new programmable tools to reengineer genomes has spurred myriad advances in synthetic biology. Tools such as clustered regularly interspace short palindromic repeats enable RNA-guided rational redesign of organisms and implementation of synthetic gene systems. New directed evolution methods generate organisms with radically restructured genomes. These restructured organisms have useful new phenotypes for biotechnology, such as bacteriophage resistance and increased genetic stability. Advanced DNA synthesis and assembly methods have also enabled the construction of fully synthetic organisms, such as J. Craig Venter Institute (JCVI)-syn 3.0. Here we summarize the recent advances in programmable genome engineering tools.

关键词: CRISPR     genome engineering     synthetic biology     rational design    

Rational design on photoelectrodes and devices to boost photoelectrochemical performance of solar-driven

《化学科学与工程前沿(英文)》 2022年 第16卷 第6期   页码 777-798 doi: 10.1007/s11705-022-2148-0

摘要: As an eco-friendly, efficient, and low-cost technique, photoelectrochemical water splitting has attracted growing interest in the production of clean and sustainable hydrogen by the conversion of abundant solar energy. In the photoelectrochemical system, the photoelectrode plays a vital role in absorbing the energy of sunlight to trigger the water splitting process and the overall efficiency depends largely on the integration and design of photoelectrochemical devices. In recent years, the optimization of photoelectrodes and photoelectrochemical devices to achieve highly efficient hydrogen production has been extensively investigated. In this paper, a concise review of recent advances in the modification of nanostructured photoelectrodes and the design of photoelectrochemical devices is presented. Meanwhile, the general principles of structural and morphological factors in altering the photoelectrochemical performance of photoelectrodes are discussed. Furthermore, the performance indicators and first principles to describe the behaviors of charge carriers are analyzed, which will be of profound guiding significance to increasing the overall efficiency of the photoelectrochemical water splitting system. Finally, current challenges and prospects for an in-depth understanding of reaction mechanisms using advanced characterization technologies and potential strategies for developing novel photoelectrodes and advanced photoelectrochemical water splitting devices are demonstrated.

关键词: photoelectrochemical water splitting     photoelectrodes     hydrogen production     charge separation     catalytic mechanism    

Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

《工程(英文)》 doi: 10.1016/j.eng.2023.01.015

摘要: The development of effective antifreeze peptides to control ice growth has attracted a significant amount of attention yet still remains a great challenge. Here, we propose a novel design method based on an in-depth investigation of repetitive motifs in various ice-binding proteins (IBPs) with an evolution analysis. In this way, several peptides with notable antifreeze activity were developed. In particular, a designed antifreeze peptide named AVD exhibits ideal ice recrystallization inhibition (IRI), solubility, and biocompatibility, making it suitable for use as a cryoprotective agent (CPA). A mutation analysis and molecular dynamics (MD) simulations indicated that the Thr6 and Asn8 residues of the AVD peptide are fundamental to its ice-binding capacity, while the Ser18 residue can synergistically enhance their interaction with ice, revealing the antifreeze mechanism of AVD. Furthermore, to demonstrate the cryoprotection potential of AVD, the peptide was successfully employed for the cryopreservation of various cells, which demonstrated significant post-freezing cell recovery. This work opens up a new avenue for designing antifreeze materials and provides peptide-based functional modules for synthetic biology.

关键词: Antifreeze peptides     Evolution analysis     Ice recrystallization inhibition     Molecular dynamics simulation     Cryopreservation     Synthetic biology    

理性设计大幅提高一种丝孢堆黑粉菌来源脂肪酶催化活性——用于合成莫西沙星手性中间体 Article

蔡雪, 沈江伟, 强煜, 华婧, 马樟奇, 柳志强, 郑裕国

《工程(英文)》 2022年 第19卷 第12期   页码 207-216 doi: 10.1016/j.eng.2022.03.020

摘要:

通过脂肪酶不对称拆分外消旋N-乙酰基-哌啶-2,3-二甲酸二甲酯[cis-(±)-1],从而获得手性中间体 (S,S)-2,8-二氮杂双环壬烷,是合成氟喹诺酮类抗生素莫西沙星重要手性中间体的一条具有吸引力的工艺路线。在前期研究中,筛选得到了一株丝孢堆黑粉菌(SRL)来源的脂肪酶,该脂肪酶具有高热稳定性和pH值稳定性。但SRL来源的脂肪酶活性较低,无法满足工业化应用的需求。因此本研究依据前期南极假丝酵母来源脂肪酶B(CALB)改造策略,采用理性设计方法对SRL进行定点突变改造,获得一个双突变体SRLI194N/V195L。随后,确定了位于活性口袋外的环6 上两个关键氨基酸残基L145 和L154;获得四位点突变体SRL-I194N/V195L/L145V/L154G(V13),活性显著提高,达到87.8 U·mg−1,是野生型SRL的2195 倍(E > 200)。该突变体在50 ℃下的半衰期达到92.5 h。突变体V13(100 mg·L−1)能够高效拆分1 mol·L−1cis-(±)-1,2 h 内底物转化率达到49.9%,实现严格立体选择性(E > 200)。总体而言,研究发现了一株对cis-(±)-1 (S,S)-2,8-二氮杂双环壬烷具有高催化活性、严格立体选择性的脂肪酶,可应用于工业化生产,并为其他具有相似结构的脂肪酶和其他种类酶的活性提高提供了一种通用策略。

关键词: 脂肪酶     丝孢堆黑粉菌     定点突变     分子动力学模拟     理性设计     莫西沙星    

一种新型葡激酶分子的设计 基因构建 表达纯化及性质研究

宋钢,于敏,莫炜,宋后燕

《中国工程科学》 2000年 第2卷 第11期   页码 68-72

摘要:

在葡激酶构效关系的研究过程中发现,葡激酶易形成二聚体,甚至多聚体,不利于葡激酶的临床应用。为了探究聚合体的形成机制以研制不易聚合的新型葡激酶分子,在葡激酶X射线晶体衍射结构模型的基础上,采用分子对接软件GRAMM V1.03,以高分辨率整体对接方式预测了葡激酶二聚体可能的结合区。结合区主要有两种可能的形成方式,通过强疏水相互作用及氢键结合。根据模型设计了旨在降低聚合能力的葡激酶突变体RGD-Sak,将Fill置换为D111,并且改变K109为R109,恰好使分子中形成RGD结构,使新型分子还可能具有抑制血小板聚集作用。利用定点突变及DNA重组技术,构建了RGD-Sak基因,并利用大肠杆菌原核表达系统进行了高效表达。RGD-Sak以包涵体形式存在,包涵体经洗涤,8 mol/L尿素溶解,稀释复性,离子交换色谱一步分离得到电泳纯的RGD-Sak,纯度达95%以上,分子量与理论值相符,比活性5×10HU/mg。RGD-Sak与纤溶酶形成的复合物催化纤溶酶原的Km、Kcat值分别为12.40 μmol/L、0.81 s-1。RGD-Sak显示了很弱的聚合能力。此研究为研制防止二聚体形成的新型葡激酶分子打下了基础。

关键词: 葡激酶     二聚体     分子对接     分子设计     定点突变    

Implementation of an adaptive feed speed 3D NURBS interpolation algorithm

LIANG Hong-bin, WANG Yong-zhang, LI Xia

《机械工程前沿(英文)》 2006年 第1卷 第4期   页码 403-408 doi: 10.1007/s11465-006-0047-6

摘要: NURBS (non-uniform rational B-spline) interpolation algorithms have been provided in modern CNC (computer numerical control) systems. However, most of them focus on a constant feed speed without considering the contour accuracy. In order to deal with this problem, an adaptive feed speed interpolation algorithm for 3D NURBS parametric curves with confined chord errors is proposed. When the instantaneous radius of the curvature is small enough, the proposed interpolation algorithm automatically reduces the feed speed to meet the specified chord error. In the other situation it uses the second-order Taylor s expansions approximation interpolation algorithm to obtain a constant feed speed so that the contour accuracy in the CNC system is guaranteed. Experimental results were provided to verify the feasibility and precision of the proposed interpolation algorithm.

关键词: NURBS parametric     rational B-spline     second-order     non-uniform rational     precision    

矿井提升机绳系合理激励加速度反演分析与设计

彭佑多,刘德顺,朱萍玉,张永忠,郭迎福

《中国工程科学》 2002年 第4卷 第4期   页码 64-68

摘要:

提升绳系的激励加速度决定着提升容器的乘坐舒适性和提升钢绳中动张力的大小,过大的动张力将导致滑绳(摩擦提升)或断绳(缠绕式提升)。基于提升钢绳为连续弹性杆的条件,建立了绳系的偏微分方程,采用特性线数值分析方法,以满足提升容器的乘坐舒适性和提升钢丝绳产生较小动张力为目标,对矿井提升机绳系要求的合理激励加速度曲线进行了反演分析与设计。

关键词: 提升钢丝绳系     激励加速度     乘坐舒适性     动张力     反演设计    

高分子材料的智能制造平台——高分子材料基因工程 Perspective

高梁, 王立权, 林嘉平, 杜磊

《工程(英文)》 2023年 第27卷 第8期   页码 31-36 doi: 10.1016/j.eng.2023.01.018

摘要:

高性能高分子材料是高新科技和先进制造业的基石。高分子材料基因工程正在成为高分子材料智能制造的重要平台。然而,高分子材料基因工程的发展仍处于起步阶段,许多问题亟待解决。本文阐述了高分子材料基因工程的概念,总结了最新研究成果,并强调了该领域的重要挑战和发展前景。特别强调了高分子材料的性能预估方法,包括性能代理量预测和机器学习性能预测。最后,讨论了高分子材料基因工程在先进复合材料、通信和集成电路等领域所亟需的高性能高分子材料创制方面的潜在工程应用前景。

关键词: 高分子材料     材料基因组方法     机器学习     性能预测     理性设计    

Evolutionary Decision-Making and Planning for Autonomous Driving Based on Safe and Rational Exploration

Kang Yuan,Yanjun Huang,Shuo Yang,Zewei Zhou,Yulei Wang,Dongpu Cao,Hong Chen,

《工程(英文)》 doi: 10.1016/j.eng.2023.03.018

摘要: Decision-making and motion planning are extremely important in autonomous driving to ensure safe driving in a real-world environment. This study proposes an online evolutionary decision-making and motion planning framework for autonomous driving based on a hybrid data- and model-driven method. First, a data-driven decision-making module based on deep reinforcement learning (DRL) is developed to pursue a rational driving performance as much as possible. Then, model predictive control (MPC) is employed to execute both longitudinal and lateral motion planning tasks. Multiple constraints are defined according to the vehicle’s physical limit to meet the driving task requirements. Finally, two principles of safety and rationality for the self-evolution of autonomous driving are proposed. A motion envelope is established and embedded into a rational exploration and exploitation scheme, which filters out unreasonable experiences by masking unsafe actions so as to collect high-quality training data for the DRL agent. Experiments with a high-fidelity vehicle model and MATLAB/Simulink co-simulation environment are conducted, and the results show that the proposed online-evolution framework is able to generate safer, more rational, and more efficient driving action in a real-world environment.

关键词: Autonomous driving     Decision-making     Motion planning     Deep reinforcement learning     Model predictive control    

卫星物联网:挑战、方案和发展趋势 Review

荀远阳,李思琦,张飞宇,洪岩,许可,陈立刚,刘松,李斌

《信息与电子工程前沿(英文)》 2023年 第24卷 第7期   页码 945-963 doi: 10.1631/FITEE.2200552

摘要: 由于城市化和工业化的快速建设所带来的气体污染,气体传感器受到广泛关注。基于半导体金属氧化物(SMO)的气体传感器具有响应高、重复性好、稳定性好、性价比高等优点,已成为气体传感器领域极其重要的元器件。通常,具有规则结构和可控形态的材料表现出更稳定且可重复的性能。然而,由于微观世界的不可控性,在材料合成过程中纳米材料往往表现出不规则、不均匀等缺点。因此,具有规整结构的一维(1D)结构、二维(2D)结构和三维(3D)结构的气敏材料的合成受到广泛关注。为了定向获得具有理想形貌和尺寸的结构规整的纳米材料,低成本且操作简洁可控的模板辅助合成法是一种非常有效的策略。本文介绍了一维、二维和三维结构的SMO传感器的形貌和性能,讨论了各种形貌对气体传感器性能(响应和稳定性)的影响,为结构稳定、性能优异的气敏材料的合成提供了新的思路。

关键词: 气体传感器;化学式电阻器;模板法;纳米结构;维度    

用于生物医学的基于微藻的生物杂化材料的设计和开发 Review

张忠阳,  陈雨萌, Lasse Hyldgaard Klausen, Sebastian Amland Skaanvik, 王丹, 陈建峰, 董明东

《工程(英文)》 2023年 第24卷 第5期   页码 102-113 doi: 10.1016/j.eng.2022.09.016

摘要:

微藻是一种体积微小的真核生物,可通过叶绿素a 的光合作用将二氧化碳转化为多种生物活性物质。在过去的10 年中,有关活体微藻和由其他生物相容性成分组成的生物杂化材料在解决许多医学难题,如肿瘤治疗、组织重建和药物输送方面显示出巨大的潜力。固定在常规生物材料中的微藻可以长时间维持其光合活性,从而在局部提供氧气,同时也可作为调节细胞活性的生物相容性界面材料。微藻的运动性还激发了生物杂化机器人的发展,其中药物分子可通过非共价键吸附结合至微藻表面,并通过精确控制其运动轨迹将药物输送到目标区域。此外,微藻的自发荧光、趋光性和生物质生产特性可以被整合到具有多种功能的新型生物杂化材料的设计中;通过基因工程改造的微藻可以赋予生物杂化材料新的特性,如特异性细胞靶向能力和从藻类细胞中局部释放重组蛋白。这些技术有望促进微藻基生物杂化材料(MBBM)在多个生物医学领域的临床应用。本文总结了MBBM的制造、生理学和运动能力;然后,回顾了MBBM近年来在生物医学领域的典型应用报道;最后,对MBBM的挑战和未来前景进行了讨论。

关键词: 生物界面     微藻     生物杂化材料     微型机器人    

Application of cable-supported spatial grid in dry coal shed

XING Haidong, HAO Jiping, XU Guobin

《结构与土木工程前沿(英文)》 2008年 第2卷 第1期   页码 26-29 doi: 10.1007/s11709-008-0008-8

摘要: This paper presented a new structural style cable-supported spatial grid, which was applied in large span dry coal sheds. The influence of configuration of cable on the force of cable and beam, the ratio of beam force to cable force and the deflection of span was investigated, and a rational configuration of cable was obtained. The results show that the cable-supported spatial grid can maximize the use of material strength, and have the advantages of low usage of steel, large span and sufficient headroom.

关键词: dry     material strength     low     rational configuration     influence    

我国北方地区水资源合理配置与南水北调

潘家铮

《中国工程科学》 2000年 第2卷 第10期   页码 26-32

摘要:

根据我国的水资源状况及可持续发展的需要,从水量丰富的长江流域引水北上的南水北调工程是势在必行和可以做到的。南水北调的原则应是:建立节水型社会,以供定需;合理配置,注意挖潜;东线、中线相辅相成,并非有我无他;编制概算实事求是,力戒“上马概算”;局部利益服从整体利益,暂时利益服从长远利益;坚持水资源统一管理,科学调配,有偿使用;西南调水不现实,宜暂缓。

关键词: 水资源     可持续发展     南水北调    

有理包络线的蒙皮应用

Kinga KRUPPA1,2

《信息与电子工程前沿(英文)》 2021年 第22卷 第2期   页码 141-286 doi: 10.1631/FITEE.1900377

摘要: 闵可夫斯基空间中的特殊曲线如闵可夫斯基毕达哥拉斯矢端线,在计算机辅助几何设计中有着重要作用,其应用近年来得到深入研究。Bizzarri等人在2016年介绍了一类有理包络(RE)曲线;提出用于G1 Hermite数据的插值方法,其合成的RE曲线能对所表示的区域生成有理边界。本文提出RE曲线的一类新的应用领域——离散输入圆集的蒙皮。若未选择正确的Hermite数据进行插值,得到的RE曲线将不适合蒙皮。本文介绍一种新颖的方法,按此方法得到的包络曲线能够接触每个圆预定的接触点。因此,我们克服了因接触点位置导致不适合蒙皮的问题。本文所提方法的一个显著优点在于其边界偏移量修剪的效率,这在计算机数控方面非常有用。

关键词: 中轴变换;包络;插值;蒙皮;圆    

Rational Understanding about Renaissance Path of China's Road and Bridge Engineering

Mao-run Feng,Zheng-song Zhao

《工程管理前沿(英文)》 2014年 第1卷 第1期   页码 42-51 doi: 10.15302/J-FEM-2014013

摘要: At the turn of this century, China began the largest road and bridge development in the world, which has virtuously interacted with the social and economic development and has elevated the engineering technology to world-class level. Surveying the development of world transportation, and comparing the road and bridge construction efforts of Europe, U.S.A, Japan and China, general experiences of success can be derived as follows: It is greatly beneficial to give priority to transportation for economic development; it takes national strategy and social action to build up a transportation network; demand and innovation are the driving forces to upgrade road and bridge technology; management innovation and quality assurance can greatly improve development caliber. While rationally acknowledging China's transportation infrastructure achievements, we should reflect on issues with Chinese characteristics that have affected quality and efficiency, expose all construction practices that violate scientific law, overall management defects in road and bridge construction and maintenance, and search for new ways to strengthen social management and the creation of a healthy soft environment.

关键词: road network     expressway     bridge project     technological innovation     construction management     social management    

标题 作者 时间 类型 操作

Genome reprogramming for synthetic biology

Kylie Standage-Beier,Xiao Wang

期刊论文

Rational design on photoelectrodes and devices to boost photoelectrochemical performance of solar-driven

期刊论文

Rational Design of and Mechanism Insight into an Efficient Antifreeze Peptide for Cryopreservation

Haishan Qi,Yihang Gao,Lin Zhang,Zhongxin Cui,Xiaojie Sui,Jianfan Ma,Jing Yang,Zhiquan Shu,Lei Zhang,

期刊论文

理性设计大幅提高一种丝孢堆黑粉菌来源脂肪酶催化活性——用于合成莫西沙星手性中间体

蔡雪, 沈江伟, 强煜, 华婧, 马樟奇, 柳志强, 郑裕国

期刊论文

一种新型葡激酶分子的设计 基因构建 表达纯化及性质研究

宋钢,于敏,莫炜,宋后燕

期刊论文

Implementation of an adaptive feed speed 3D NURBS interpolation algorithm

LIANG Hong-bin, WANG Yong-zhang, LI Xia

期刊论文

矿井提升机绳系合理激励加速度反演分析与设计

彭佑多,刘德顺,朱萍玉,张永忠,郭迎福

期刊论文

高分子材料的智能制造平台——高分子材料基因工程

高梁, 王立权, 林嘉平, 杜磊

期刊论文

Evolutionary Decision-Making and Planning for Autonomous Driving Based on Safe and Rational Exploration

Kang Yuan,Yanjun Huang,Shuo Yang,Zewei Zhou,Yulei Wang,Dongpu Cao,Hong Chen,

期刊论文

卫星物联网:挑战、方案和发展趋势

荀远阳,李思琦,张飞宇,洪岩,许可,陈立刚,刘松,李斌

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