Rational surface charge engineering of haloalkane dehalogenase for boosting the enzymatic performance in organic solvent solutions

Biocatalysis in organic solvents(OSs)has numerous important applications,but native enzymes in OSs often exhibit limited catalytic performance.Herein,we proposed a computation-aided surface charge engineering strategy to improve the catalytic performance of haloalkane dehalogenase DhaA in OSs based on the energetic analysis of substrate binding to the DhaA surface.Several variants with enhanced OS resistance were obtained by replacing negative charged residues on the surface with positive charged residue(Arg).Particularly,a four-substitution variant E16R/E93R/E121R/E257R exhibited the best catalytic performance(five-fold improvement in OS resistance and seven-fold half-life increase in 40%(vol)dimethylsulfoxide).As a result,the overall catalytic performance of the variant could be at least 26 times higher than the wild-type DhaA.Fluorescence spectroscopy and molecular dynamics simulation studies revealed that the residue substitution mainly enhanced OS resistance from four aspects:(a)improved the overall structural stability,(b)increased the hydrophobicity of the local microenvironment around the catalytic triad,(c)enriched the hydrophobic substrate around the enzyme molecule,and(d)lowered the contact frequency between OS molecules and the catalytic triad.Our findings validate that computationaided surface charge engineering is an effective and ingenious rational strategy for tailoring enzyme performance in OSs.

Molecular Dynamics (MD) Applications in Materials Science and Engineering and Nanotechnology

Molecular dynamics (MD) is a computer simulation technique that helps to explore the behavior and properties of molecules and atoms. MD has been used in research and development in many spaces, including materials science and engineering and nanotechnology. MD has been proven useful in topics like the nano-engineering of construction materials, correcting graphene planar defects, studying self-assembling bio-materials, and the densification, consolidation, and sintering of nanocrystalline materials.

Expression of Transforming Growth Factor β_1 in Mesenchymal Stem Cells: Potential Utility in Molecular Tissue Engineering for Osteochondral Repair

Summary: The feasibility of using gene therapy to treat full-thickness articular cartilage defects was investigated with respect to the transfection and expression of exogenous transforming growth factor (TGF)-β 1 genes in bone marrow-derived mesenchymal stem cells (MSCs) in vitro. The full-length rat TGF-β 1 cDNA was transfected to MSCs mediated by lipofectamine and then selected with G418, a synthetic neomycin analog. The transient and stable expression of TGF-β 1 by MSCs was detected by using immunohistochemical staining. The lipofectamine-mediated gene therapy efficiently transfected MSCs in vitro with the TGF-β 1 gene causing a marked up-regulation in TGF-β 1 expression as compared with the vector-transfected control groups, and the increased expression persisted for at least 4 weeks after selected with G418. It was suggested that bone marrow-derived MSCs were susceptible to in vitro lipofectamine mediated TGF-β 1 gene transfer and that transgene expression persisted for at least 4 weeks. Having successfully combined the existing techniques of tissue engineering with the novel possibilities offered by modern gene transfer technology, an innovative concept, i.e. molecular tissue engineering, are put forward for the first time. As a new branch of tissue engineering, it represents both a new area and an important trend in research. Using this technique, we have a new powerful tool with which: (1) to modify the functional biology of articular tissue repair along defined pathways of growth and differentiation and (2) to affect a better repair of full-thickness articular cartilage defects that occur as a result of injury and osteoarthritis.

Molecular Tissue Engineering: Applications for Modulation of Mesenchymal Stem Cells Proliferation by Transforming Growth Factor β_1 Gene Transfer

The effect of transforming growth factor β 1 (TGF β 1 ) gene transfection on the proliferation of bone marrow derived mesenchymal stem cells (MSC S ) and the mechanism was investigated to provide basis for accelerating articular cartilage repairing using molecular tissue engineering technology. TGF β 1 gene at different doses was transduced into the rat bone marrow derived MSCs to examine the effects of TGF β 1 gene transfection on MSCs DNA synthesis, cell cycle kinetics and the expression of proliferating cell nuclear antigen (PCNA). The results showed that 3 μl lipofectamine mediated 1 μg TGF β 1 gene transfection could effectively promote the proliferation of MSCs best; Under this condition (DNA/Lipofectamine=1μg/3μl), flow cytometry and immunohistochemical analyses revealed a significant increase in the 3 H incorporation, DNA content in S phase and the expression of PCNA. Transfection of gene encoding TGF β 1 could induce the cells at G0/G1 phase to S1 phase, modulate the replication of DNA through the enhancement of the PCNA expression, increase the content of DNA at S1 phase and promote the proliferation of MSCs. This new molecular tissue engineering approach could be of potential benefit to enhance the repair of damaged articular cartilage, especially those caused by degenerative joint diseases.

Ultra-large Scale Molecular Dynamics Simulation for Nano-engineering

In light of the special need of nano-engineering, an ultra-large scale and high-performance molecular dynamics（MD） simulation program was implemented. In many nano-engineering processes, the free boundary condition should be adopted. To meet this particular requirement, a pointer link and dynamic array data structures were employed so that both reliability and accuracy of simulation could be ensured. Using this method, one could realize the MD simulation of the nano-engineering system consisting of several million atoms per single CPU.

Molecular Tissue Engineering:Concepts,Status and Challenge

Tissue engineering has confronted many difficulties mainly as follows:1)How to modulate the adherence,proliferation,and oriented differentiation of seed cells, especially that of stemcells. 2) Massive preparation and sustained controllable delivery of tissue inducing factors or plasmid DNA, such as growth factors, angiogenesis stimulators,and so on. 3) Development of 'intelligent biomimetic materials' as extracellular matrix with a good superficial and structural compatibility as well as biological activity to stimulate predictable, controllable and desirable responses under defined conditions.Molecular biology is currently one of the most exciting fields of research across life sciences,and the advances in it also bring a bright future for tissue engineering to overcome these difficulties.In recent years,tissue engineering benefits a lot from molecular biology.Only a comprehensive understanding of the involved ingredients of tissue engineering (cells,tissue inducing factors,genes,biomaterials) and the subtle relationships between them at molecular level can lead to a successful manipulation of reparative processes and a better biological substitute.Molecular tissue engineering,the offspring of the tissue engineering and molecular biology,has gained an increasing importance in recent years.It offers the promise of not simply replacing tissue,but improving the restoration.The studies presented in this article put forward this new concept for the first time and provide an insight into the basic principles,status and challenges of this emerging technology.

Molecular engineering and live-cell imaging in mechanobiology

Cells in the body are exposed to physiological and pathophysiological stimuli that encompass both chemical and mechanical factors,which coordinately modulate cellular functions. Compared to the large amount of information on cellular re-

Defect engineering: A versatile tool for tuning the activation of key molecules in photocatalytic reactions

Many photocatalytic reactions such as CO2 reduction and N2 fixation are often limited by the activation of some key molecules. Defects in solid materials can robustly introduce coordinately unsaturated sites to serve as highly active sites for molecular chemisorption and activation. As a result, rational defect engineering has endowed a versatile approach to further develop photocatalytic applications beyond water splitting. The subtly designed defects in photocatalysts can play critical and decisive roles in molecular activation as proven in recent years. The defects cannot only serve as active sites for molecular chemisorption, but also spatially supply channels for energy and electron transfer. In this review, we aim to summarize the diversiform photocatalytic applications using defects as active sites, including but not limited to CO2 reduction, O2 activation,H2O dissociation, N2 fixation as well as activation of other molecules. In particular, we emphatically outline how the parameters of defects (e.g.,concentration,location,geometric and electronic structures) can serve as the knobs for maneuvering molecular adsorption and activation as well as altering subsequent reaction pathway. Moreover, we underline the remaining challenges at the current stage and the potential development in the future.It is anticipated that this review consolidates the in-depth understanding towards the structure-activity relationship between defects and related reactions.

Review of deep learning algorithms in molecular simulations and perspective applications on petroleum engineering

In the last few decades,deep learning(DL)has afforded solutions to macroscopic problems in petroleum engineering,but mechanistic problems at the microscale have not benefited from it.Mechanism studies have been the strong demands for the emerging projects,such as the gas storage and hydrate production,and for some problems encountered in the storage process,which are common found as the chemical interaction between injected gas and mineral,and the formation of hydrate.Emerging advances in DL technology enable solving molecular dynamics(MD)with quantum accuracy.The conventional quantum chemical method is computational expensive,whereas the classical MD method cannot guarantee high accuracy because of its empirical force field parameters.With the help of the DL force field,precision at the quantum chemistry level can be achieved in MD.Moreover,the DL force field promotes the computational speed compared with first-principles calculations.In this review,the basic knowledge of the molecular force field and deep neural network(DNN)is first introduced.Then,three representative opensource packages relevant to the DL force field are introduced.As the most common components in the development of oil and gas reservoirs,water and methane are studied from the aspects of computational efficiency and chemical reaction respectively,providing the foundation of oil and gas researches.However,in the oil and gas problems,the complex molecular topo structures and various element types set a high challenge for the DL techniques in MD.Regarding the computational efficiency,it needs improvement via GPU and parallel accelerations to compete with classical MD.Even with such difficulties,the booming of this technique in the area of petroleum engineering can be predictable.

Microscale and Nanoscale Process Systems Engineering： Challenge and Progress

This is an overview of the development of process systems engineering (PSE) in a smaller world. Two different spatio-temporal scopes are identified for microscale and nanoscale process systems. The features and challenges for each scale are reviewed, and different methodologies used by them discussed. Comparison of these two new areas with traditional process systems engineering is described. If microscale PSE could be considered as an extension of traditional PSE, nanoscale PSE should be accepted as a new discipline which has looser connection with the extant core of chemical engineering. Since "molecular factories" is the next frontier of processing scale, nanoscale PSE will be the new theory to handle the design, simulation and operation of those active processing systems.

Control of surface wettability via strain engineering

Reversible control of surface wettability has wide applications in lab-on-chip systems, tunable optical lenses, and microfluidic tools. Using a graphene sheet as a sam- ple material and molecular dynamic simulations, we demon- strate that strain engineering can serve as an effective way to control the surface wettability. The contact angles 0 of water droplets on a graphene vary from 72.5° to 106° under biaxial strains ranging from -10% to 10% that are applied on the graphene layer. For an intrinsic hydrophilic surface （at zero strain）, the variation of 0 upon the applied strains is more sensitive, i.e., from 0° to 74.8°. Overall the cosines of the contact angles exhibit a linear relation with respect to the strains. In light of the inherent dependence of the contact an- gle on liquid-solid interfacial energy, we develop an analytic model to show the cos 0 as a linear function of the adsorption energy Eads of a single water molecule over the substrate sur- face. This model agrees with our molecular dynamic results very well. Together with the linear dependence of Eads on bi- axial strains, we can thus understand the effect of strains on the surface wettability. Thanks to the ease of reversibly ap- plying mechanical strains in micro/nano-electromechanical systems, we believe that strain engineering can be a promis- ing means to achieve the reversibly control of surface wetta- bility.

Intensification of chemical separation engineering by nanostructured channels and nanofluidics: From theories to applications

With the development of manufacturing technology on the nanoscale, the precision of nano-devices is rapidly increasing with lower cost. Different from macroscale or microscale fluids, many specific phenomena and advantages are observed in nanofluidics. Devices and process involving and utilizing these phenomena play an important role in many fields in chemical engineering including separation, chemical analysis and transmission.In this article, we summarize the state-of-the-art progress in theoretical studies and manufacturing technologies on nanofluidics. Then we discuss practical applications of nanofluidics in many chemical engineering fields,especially in separation and encountering problems. Finally, we are looking forward to the future of nanofluidics and believe it will be more important in the separation process and the modern chemical industry.

Genetic Engineering of Field, Industrial and Pharmaceutical Crops

Ability to modify plants at the genomic level by advanced molecular technology has enhanced the scope of improvements in plant traits attempted earlier through conventional breeding methods. Techniques such as genetic transformation have opened new vistas whereby functional genes, not commonly present in a particular species can be added from other species. The traits incorporated into the genetically engineered plants in the beginning were confined to those governed by dominant genes, e.g. insecticide resistance and herbicide tolerance but advancements with time now also permit the transfer of complexly inherited traits such as drought and cold tolerance. Transgenic technology is also useful in understanding gene expression and metabolic pathways which can then be used to harness the full genomic potential of the plant. This review presents a narrative on development of transgenics and their use for the improvement of field, industrial and pharmaceuticals crops. In addition, discussions are made on current status on genetically modified crops, hurdles to genetic engineering, overcoming strategies and future scope.

In Silico Disulfide Bond Engineering to Improve Human LEPTIN Stability

Enhancing the stability of biomolecules is one of the hot topics in industry.In this study,we enhanced the stability of an important protein called LEPTIN.LEPTIN is a hormone secreted by fat cells playing an essential role in body weight and composition,and its deficiency can result in several disorders.The treatment of related LEPTIN dysfunctions is often available in the form of injection.To decrease the cost and the frequency of its applications can be achieved by increasing its lifetime through engineering LEPTIN.In this study,to engineer LEPTIN,we have introduced disulfide bonds.Disulfide By Design server was used to predict the suitable nominate pairs,which suggested three pairs of amino acids to be mutated to cysteine for disulfide bond formation.Additionally,to further evaluate the effect of combined mutations,we combined these three nominated pairs to produce three more mutants.In order to assess the effect of introduced mutations,molecular dynamic(MD)simulation was performed.The result suggests that Mutant-1 is more stable in comparison to wild-type and the other mutants.Moreover,docking results showed that the introduced mutation does not affect the receptor binding performance;therefore,it can be considered a suitable choice for future protein engineering.

Surface Molecular Encapsulation with Cyclodextrin in Promoting the Activity and Stability of Fe Single-Atom Catalyst for Oxygen Reduction Reaction

Fe single-atom catalysts(Fe-SACs)have been extensively studied as a highly efficient electrocatalyst toward the oxygen reduction reaction(ORR).Nonetheless,they suffer from stability issue induced by dissolution of Fe metal center and the OH^(−)blocking.Herein,a surface molecular engineering strategy is developed by usingβ-cyclodextrins(CDs)as a localized molecular encapsulation.The CD-modified Fe-SAC(Fe-SNC-β-CD)shows obviously improved activity toward the ORR with 0.90 V,4.10 and 4.09 mA cm^(-2)for E_(1/2),J_(0)and Jk0.9,respectively.Meanwhile,the Fe-SNC-β-CD shows the excellent long-term stability against aggressive stress and the poisoning.It is confirmed through electrochemical investigation that modification ofβ-CD can,on one hand,regulate the atomic Fe coordination chemistry through the interaction between the CD and FeN_(x) moiety,while on the other mitigate the strong adsorption of OH^(−)and function as protective barrier against the poisoning molecules leading to enhanced ORR activity and stability for the Fe-SACs.The molecular encapsulation strategy demonstrates the uniqueness of post-pyrolysis surface molecular engineering for the design of single-atom catalyst.

不同老化方式下新旧沥青的扩散融合

分别制备了热氧老化沥青和热氧-紫外老化沥青,构建了新、旧沥青双层扩散模型,并且通过相对浓度与扩散系数的模拟计算、拉拔试验与荧光显微镜试验研究了新、旧沥青扩散融合程度与温度、沥青四组分的关系.结果表明:热氧-紫外老化沥青更不易与基质沥青扩散融合,与基质沥青的黏附性较差;在10~40℃内,新、旧沥青能够快速扩散融合,超过40℃后,升高温度对扩散融合的促进作用逐渐减小,且对热氧-紫外老化沥青与基质沥青的扩散融合促进作用的减小速率更大;沥青四组分扩散系数的大小顺序依次为:饱和分>芳香分≥胶质>沥青质,经紫外老化后,四组分的扩散系数均有所下降,沥青质的降幅最大.

脂肪酸捕收剂分子结构与性能的密度泛函理论研究

这是一篇矿物加工工程领域的论文。脂肪酸类捕收剂广泛应用于浮选氧化矿,其分子结构是影响浮选性能的重要因素,为了从微观角度揭示脂肪酸捕收剂结构变化对其反应活性的影响,采用密度泛函理论研究了脂肪酸电子结构与性能的关系。研究结果表明:油酸分子和油酸根离子中氧原子有很强的反应活性,氧原子是油酸与氧化矿物表面作用的键合原子;油酸根离子的两个氧原子具有相近的化学活性,且在费米能级处的态密度大于油酸分子,使得油酸根离子的活性明显强于油酸分子;碳链长度和烃基不饱和度几乎不影响脂肪酸中氧原子的态密度,其对脂肪酸性能的影响不是通过羧基作用的;脂肪酸与常见金属阳离子的相互作用能与其溶度积常数降低的规律一致,两者存在较好的对应关系;研究对了解脂肪酸捕收剂结构与性能的关系及开发新型脂肪酸类捕收剂有一定的理论意义和参考价值。

硫化氢气体在金属有机骨架中吸附机理的分子模拟研究

研究硫化氢(H_(2)S)气体在金属有机骨架(Metal Organic Frameworks, MOFs)材料中的吸附机理,对应用MOFs材料控制城市地下有限空间内的H_(2)S气体具有重要意义。以不同类型的MOFs材料作为研究对象,基于Materials Studio软件建立了MOFs-H_(2)S吸附体系,应用巨正则蒙特卡洛(Rand Canonical Monte Carlo, GCMC)方法及分子动力学(Molecular Dynamics, MD)理论研究了相互作用能、吸附热、金属位点、官能团等的影响,在分子层面讨论了H_(2)S气体在MOFs中的吸附特性及机理。应用等温吸附试验验证了所使用分子模型及力场的可靠性。结果表明:不同金属位点对于吸附量有较大影响,对H_(2)S气体的吸附作用由强到弱依次为Mg^(2+)、Ni^(2+)、Co^(2+)、Mn^(2+)、Zn^(2+);亲水性官能团的引入利于H_(2)S气体的吸附捕捉;UiO-66-Cu因其团簇为网状结构更利于H_(2)S气体的捕捉与吸附。同时,该研究建立了吸附热方程,提供了MOFs吸附效果评判标准,为MOFs材料应用于城市地下有限空间吸附H_(2)S气体提供了理论依据。

分子生物学与基因工程课程思政教学模式探索

专业课程是思政教育的重要载体。分子生物学与基因工程是生物工程专业的一门重要核心专业课程,课程思政元素丰富。该文筛选出五个课程相关的典型案例,从家国情怀、科学精神、国际视野、人文素养和生态文明等思政点切入,将“知识传授、能力培养与价值引领”融为一体,引导学生树立正确的世界观、人生观、价值观,拓展课程育人功能,提升教学育人质量。该课程思政模式受到学生的高度评价,课程教学质量、教学效果和用人单位反馈良好。

改性淀粉对垃圾焚烧飞灰中Pb和Cd稳定化研究

垃圾焚烧飞灰中Pb和Cd对人体及环境危害极大且浸出质量浓度严重超标。为稳定飞灰中的Pb和Cd,合成了一种以玉米淀粉为主体的有机螯合剂,用于处理飞灰中的Pb和Cd。通过改变螯合剂投加质量分数、养护时间、液固比(mL∶g)和pH值来研究螯合剂稳定效果并进行表征。X射线衍射(X-ray Diffraction,XRD)结果显示,改性处理未改变玉米淀粉的结晶结构类型。通过对结晶度计算,表明改性过程发生在淀粉结晶区。扫描电镜(Scanning Electron Microscope,SEM)结果显示,处理前飞灰比表面积较大,飞灰经过改性玉米淀粉处理后粒径明显增大,降低了飞灰比表面积。通过傅里叶变换红外(Fourier Transform Infrared,FT-IR)光谱表征,显示飞灰处理前后主要存在碳酸盐、硫酸盐和硅铝酸盐。采用单因素试验确定改性淀粉螯合飞灰Pb和Cd的最佳条件为:改性淀粉投加质量分数为3%、养护时间为24 h、液固比(mL∶g)为2∶5、pH值为7~9。该条件下,Pb和Cd浸出质量浓度最低分别为0.162 mg/L、0.087 mg/L,对Pb和Cd稳定化率均大于93%,浸出质量浓度远低于《生活垃圾填埋场控制标准》限值。淋溶试验显示,淋溶速率较慢及酸雨条件下,螯合体中Pb和Cd的溶解程度较高。