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Bioenergy Division
Applied Energy Technology Division
Biobased Materials Division
Location: Home>Research>Research System>Bioenergy Division>Modeling and Simulation-I
Modeling and Simulation




Group Leader: Prof. Dr. YAO LishanLU Xuefeng

Tel: 86-532-80662792

E-mail: yaols (AT) qibebt.ac.cn 


Education and working experiences:   

2010-present  Professor, Modeling and Simulation Group, Qingdao institute of Bioenergy & Bioprocess Technology, CAS 

2006-2010   Post Doc, Lab of Chemical Physics, National Institutes of Health, USA 

2001-2006 Department of Chemistry, Michigan State University, Ph.D., Physical Chemistry 

1996-2001 Department of Applied Chemistry, University of Science and Technology of China, B.S., Chemistry 

Research Focus  

General: Protein structure and function; protein engineering; computational biology, NMR 

Specifically: Computer aided protein design; Molecular dynamics simulation; NMR study of protein structure and dynamics. 

Research Progress  

1. T. Reesi CBHI catalyzed cellooligomer hydrolysis   

 Figure 1. Mutational effects on CBHI catalysis.
The wild type and D214N CBHI adopts a concerted mechanism whereas E212Q employs
a stepwise mechanism in the glycosylation of the

2. Improving the thermostability of T. Reesi EGI 

 Figure 2. Residual catalytic activity after thermal treatment.
The mutants show higher residual activity than the wild type, suggesting a better
The mutants were designed by a free energy based computational method. 

Selected Publications  

Year 2013  

·         Guan, J., Chen, X., Peng, G., Wang, X., Cao, Q., Lan, Z., & Mu, X. (2013). Role of ReOx in Re-modified Rh/ZrO2 and Ir/ZrO2 catalysts in glycerol hydrogenolysis: insights from first-principles study. Chinese Journal of Catalysis, 34(9), 1656-1666.  

·         Guo, X., Lan, Z., & Cao, Z. (2013). Ab initio insight into ultrafast nonadiabatic decay of hypoxanthine: keto-N7H and keto-N9H tautomers. [Research Support, Non-U.S. Gov't]. Phys Chem Chem Phys, 15(26), 10777-10782.  

·         Hong, J., Jing, Q., & Yao, L. (2013). The protein amide (1)H(N) chemical shift temperature coefficient reflects thermal expansion of the N-H...O=C hydrogen bond. [Research Support, Non-U.S. Gov't]. J Biomol NMR, 55(1), 71-78.  

·         Jiang, F., Wang, J., Li, J., Wang, N., Bao, X., Wang, T., . . . Yang, R. (2013). Supramolecular Assemblies with Symmetrical Octahedral Structures - Synthesis, Characterization, and Electrochemical Properties. European Journal of Inorganic Chemistry, 2013(3), 375-380.  

·         Wang, N., Bao, X., Yang, C., Wang, J., Woo, H. Y., Lan, Z., . . . Yang, R. (2013). Design and synthesis of indole-substituted fullerene derivatives with different side groups for organic photovoltaic devices. Organic Electronics, 14(2), 682-692.  

·         Yin, Z., Qian, H., Wang, Q., Dong, H., Yan, S., Zhang, C., & Li, J. (2013). Electrochemical Properties and Regioselectivity of Cyclopalladation of Chiral Ferrocenylimines Deriving from (S)-Ferrocenylethylamine. Australian Journal of Chemistry, 66(2), 218. 

·          Zhang, Y., Yan, S., & Yao, L. (2013). A mechanistic study of Trichoderma reesei Cel7B catalyzed glycosidic bond cleavage. [Research Support, Non-U.S. Gov't]. J Phys Chem B, 117(29), 8714-8722.  

·         Zhang, Y., Yan, S., & Yao, L. (2013). Mechanism of the Humicola insolens Cel7B E197S mutant catalyzed flavonoid glycosides synthesis: a QM/MM metadynamics simulation study. Theoretical Chemistry Accounts, 132(6), 1367. 

·          Zhuang, X., Wang, J., & Lan, Z. (2013). Photoinduced nonadiabatic decay and dissociation dynamics of dimethylnitramine. [Research Support, Non-U.S. Gov't]. J Phys Chem A, 117(23), 4785-4793. doi: 10.1021/jp402180p 

·         Song X, Wang Y, Shu Z, Hong J, Li T, et al. (2013) Engineering a More Thermostable Blue Light Photo Receptor Bacillus subtilis YtvA LOV Domain by a Computer Aided Rational Design Method. PLoS Comput Biol 9(7): e1003129.  

·         Dorit Shemesh, Zhenggang Lan, and R. Benny Gerber.(2013)Dynamics of Triplet-State Photochemistry of Pentanal: Mechanisms of Norrish I, Norrish II, and H Abstraction Reactions. J Phys Chem A, 117, 11711-11724.   

·         Xuhui Zhuang, Jun Wang, and Zhenggang Lan.(2013)Tracking of the Molecular Motion in the Primary Event of Photoinduced Reactions of a Phytochromobilin Model. J Phys Chem B, 11750,15976-15986.  

Year 2012   

·         J. Yang, H. Wei and V. Kadirkamanathan, X. Ling, System Identification from small data sets using an output jittering method with application to model estimation of bioethanol production, 2012 International Conference on Machine Learning and Cybernetics. 

·         J. Yang, X. Ling, L. Yao, H. Wei and V. Kadirkamanathan, System identification of the fermentation system of Thermoanaerobacter sp. X514,  6th IEEE conference on systems biology 2012. 

·         J. Yang, X. Ling and L. Yao, Analyzing Intracellular flux Distributions of Thermoanaerobacter sp. X514 under Various Substrate Conditions by Gibbs Sampling, Journal of Biometrics & Biostatistics 2012, S7:014 

·         Li, T., Yan, S., & Yao, L. (2012). The impact of Trichoderma reesei Cel7A carbohydrate binding domain mutations on its binding to a cellulose surface: a molecular dynamics free energy study. J Mol Model, 18(4), 1355-1364. doi: 10.1007/s00894-011-1167-4 

·         Lu, Y., Lan, Z., & Thiel, W. (2012). Monomeric adenine decay dynamics influenced by the DNA environment. J Comput Chem, 33, 1225-1235. doi: 10.1002/jcc.22952 

·         Huang,qs.,Yao,ls.,Liu,tz.,Yang,j.,Simulation of the light evolution in anannu larphotobioreactor for thecultivationof Porphyridium cruentum Chemical EngineeringScience84(2012)718–726 

·         S. Wang, G.Z. Cui, X.F. Song , Y. Feng (*) ,Q. Cui,Efficiency and Stability Enhancement of Cis-epoxysuccinic Acid Hydrolase by Fusion with a Carbohydrate Binding Module and Immobilization onto Cellulose Appl Biochem Biotechnol (2012) 168:708–717.DOI 10.1007/s12010-012-9811-8 

·         W. Zhang, Z. Lan, Z. Sun, K. J. Gaffney, Resolving Photo-induced Twisted Intramolecular Charge Transfer with Vibrational Anisotropy and TDDFT, J. Phys. Chem. B, Accepted.  

·         S. Wang, S. Dong, J. Wang, L. Zhang, P. Han, C. Zhang, X. Wang, K .Zhang, Z. Lan, G. Cui, Oxygen-enriched carbon material for 1 catalyzing oxygen reduction towards hybrid electrolyte Li-air battery, Journal of Materials Chemistry. Accepted. 

·         Q. Sun, Z. Li, Z. Lan, C. Pisterer, M. Doerr, S. Fischer, S. C. Smith and W. Thiel,Isomerization Mechanism of the HcRed Fluorescent Protein Chromophore. Accepted by Phys. Chem. Chem. Phys. [link] 

·         Fei Jiang, Ning Wang, Zhengkun Du, Jun Wang, Zhenggang Lan, and Renqiang Yang, Thiophene-Coated Functionalized M12L24 Spheres: Synthesis, Characterization, and Electrochemical Properties. Accepted by Chemistry-An Asian Journal. 

·         Z. Lan, J. Shao, Approximate Theoretical Methods for Nonadiabatic Dynamics of Polyatomic Molecules. Chem. Prog. (In Chinese), 24, 270-284 (2012). [link] 

·         T. S. Venkatesan, S. G. Ramesh, Z. Lan, and W. Domcke, Theoretical analysis of photoinduced H-atom elimination in thiophenol. J. Chem. Phys., 136, 174312 (2012). [link] 

·         B. Heggen, Z. Lan, and W. Thiel, Nonadiabatic decay dynamcis of 9H-Guanine in aqueous solutions. Phys. Chem. Chem. Phys., 14, 8137-8146 (2012). [link] 

·         Z. Lan, S. Nonell, M. Barbatti, Theoretical characterization of absorption and emission spectra of an asymmetric porphycene. J. Phys. Chem. A., 116, 3366-3376 (2012). [link] 

·         Z. Lan, Y. Lu, O. Weingart and W. Thiel, Nonadiabatic decay dynamics of a Benzylidene Malononitrile. J. Phys. Chem. A., 6, 1510-1518 (2012). [link] 

·         You Lu, Z. Lan, and W. Thiel, Monomeric adenine decay dynamics influenced by the DNA environment. J. Comput. Chem., 33, 1225-1235 (2012). [link] 

·         G. Cui Z. Lan, and W. Thiel, Intramolecular Hydrogen Bonding Plays a Crucial Role in the Photophysics and Photochemistry of the GFP Chromophore. J. Am. Chem. Soc., 3, 1662-1672 (2012). [link] 

·         Kuan-Wei Wu, Po-Chin Chen, Jun Wang,Ying-Chieh Sun Computation of relative binding free energy for an inhibitor and its analogs binding with Erk kinase using thermodynamic integration MD simulation J Comput Aided Mol Des. Accepted 

·         Jing Huang, Li Zhang, Ru-Ping Liang, Jian-Ding Qiu. “On-off” switchable electrochemical affinity nanobiosensor based on graphene oxide for ultrasensitive glucose sensing. Biosensors and Bioelectronics. DOI: 10.1016/j.bios.2012.09.007.  

Year 2011  

·         Tong Li, Qingqing Jing, and Lishan Yao.Dynamics of the GB3 Loop Regions from MD Simulation: How Much of It Is Real? J. Phys. Chem. B (2011) 115: 3488–3495. 

·         Li, T.; Yan, S. H.; Yao, L. S.  The impact of the T. Reesei Cel7A carbohydrate binding domain mutations on its binding to cellulose surface: a molecular dynamics simulation free energy study  J. Mol. Model. 2011, 18, 1355-1364.  

·         Zhou, X. H.; Duan, Y. L.; Yan, S. H.; Liu, Z. H.; Zhang, C. J.; Yao, L. S.; Cui, G. L.  Optical modulation of supramolecular assembly of amphiphilic photochromic diarylethene: from nanofiber to nanosphere  Chem. Comm. 2011, 47, 6876-6878. 

·         Kang, B. T.; Kang, S. W.; Yan, S. H.*; Lee, J. Y.  Curvature Effect on the Barrier from the Physisorption to the Chemisorption of H2 on Graphene  B. Korean Chem. Soc. 2011, 32, 934-938. 

·         Bai, L. L.; Yan, S. H.*; Ma, H. Q.; Bi, S. W.  Theoretical Investigation on Proton Transfer Mechanism of Hydrated Melamine  Comp. & Theo. Chem. 2011, 964, 218-233. 

·         Shihai Yan, Tong Li, and Lishan Yao .Mutational Effects on the Catalytic Mechanism of Cellobiohydrolase I from Trichoderma reesei. J. Phys. Chem. B (2011) 115: 4982–4989. 

·         Qingshan Huang, TianzhongLiu,JingYang,LishanYao,LiliGao.Evaluation of radiative transfer using the finite volume method in cylindrical photoreactors. Chemical Engineering Science (2011) 66: 3930–3940. 

·         J . YANG, K. KOHLER, D.M. DAVIS and N. J . BURROUGHS. An improved strip FRAP method for estimating diffusion coefficients: correcting for the degree of photobleaching. Journal ofMicroscopy (2010) 238: 240–253. 

·         E. Fabiano, Z. Lan, Y. Lu and W. Thiel, Nonadiabatic trajectory calculations with ab initio and semiempirical methods, in Book "Conical Intersections II ", edited by D. R. Yarkony, H. Koeppel, W. Domcke, World Scientic, Singapore, 2011 

·         A. Kazaryan Z. Lan, L. Schaefer, W. Thiel and M. Filatov, Surface Hopping Excited-state Dynamics Study of the Photoisomerization of a light-driven fluorene molecular rotary. J. Chem. Theo. Compt., 7, 2189-2199 (2011). [link] 

·         O. Weingart, Z. Lan, A. Koslowski, and W. Thiel, Chiral Pathways and Periodic Decay in cis-Azobenzene Photodynamics. J. Phys. Chem. Lett., 2, 1506-1509 (2011). [link] 

·         You Lu, Z. Lan, and W. Thiel, Hydrogen Bonding Regulates the Monomeric Nonradiative Decay of Adenine in DNA Strands. Angewandte Chemie International Edition, 50, 6864-6867, (2011). [link]  

·         Z. Lan, You Lu, E. Fabiano and W. Thiel, QM/MM Nonadiabatic Decay Dynamics of 9H-Adenine in Aqueous Solution. ChemPhysChem, 12, 1989-1998, (2011). [link]  

·         Song, X. F. and Xue, Y. M. Comparison of Three Thermostable beta-Glucosidases for Application in the Hydrolysis of Soybean Isoflavone Glycosides. J. Agr. Food Chem. 59,1954-1961 (2011). 

·         Jian-Ding Qiu, Jing Huang, Ru-Ping Liang. Nanocomposite film based on graphene oxide for high performance flexible glucose biosensor. Sensors and Actuators B: Chemistry. 2011, 160(1), 287-294.  

Year 2010  

·         Lishan Yao,† Alexander Grishaev,† Gabriel Cornilescu,‡ and Ad Bax*,† Site-Specific Backbone Amide 15N Chemical Shift Anisotropy Tensors in a Small Protein from Liquid Crystal and Cross-Correlated Relaxation Measurements J. AM. CHEM. SOC. 2010, 132, 4295–4309 

·         Lishan Yao, Alexander Grishaev, Gabriel Cornilescu, and Ad Bax. The Impact of Hydrogen Bonding on Amide 1H Chemical Shift Anisotropy Studied by Cross-Correlated Relaxation and Liquid Crystal NMR Spectroscopy. J. AM. CHEM. SOC. (2010) 132: 10866–10875. 

·         Shihai Yan, Do Hyun Ryu, and Jin Yong Lee. Origin of Exo/Endo Selectivity in the Intramolecular Diels-Alder Reaction. Bull. Korean Chem. Soc. (2010) 31: 2527-2530. 

·         Qingshan Huang a,b, ChaoYang a,n, GengzhiYu a, Zai-ShaMao. CFD simulation of hydrodynamics and mass transfer in an internal airlift loop reactor using a steady two-fluid model. Chemical Engineering Science (2010) 65:5527–5536. 

·         Wang, R. L, Xue, Y. M., Wu, X. X. And Song, X. F. Enhancement of engineered trifunctional enzyme by optimizing linker peptides for degradation of agricultural by-products. Enzyme Microb. Tech. 47:194-199 (2010). 

·         Yan, S. H.; Ryu, D. H.; Lee, J. Y.  Origin of Exo/Endo Selectivity in the Intramolecular Diels-Alder Reaction  B. Korean Chem. Soc. 2010, 31, 2527-2530.  

·         Yan, S. H.; Kang, S. W.; Hayashi, T.; Mukamel S.; Lee, J. Y.  Computational Studies on Electron and Proton Transfer in Phenol-Imidazole-Base Triads  J. Comput. Chem. 2010, 31, 393-402. 

·         Kang, S. W.; Lee, S. J.; Yan, S. H.; Nam, K. C.; Lee, J. Y. F- Preference of Polyamide Cryptand to Cl- J. Incl. Phenom. Macro. 2010, 66, 75-79.  

·         Kang, S. W.; Lee, S. J.; Yan, S. H.; Nam, K. C.; Lee, J. Y. Hydrogen Bonding Nature between Calix[6]arene and Piperidine/Triethylamine J. Incl. Phenom. Macro. 2010, 66, 67-73.  

·         Wang, Y. F. and Liu, C. B. Delocalization and electron transfer in polypeptides with different secondary structures. J. Mol. Struc-THEOCHEM 948, 78-82 (2010). 

·         Xiaomin Chen, Xiaoxue Sang, Shaohe Li, Shujun Zhang, Linhan Bai. Studies on a chlorogenic acid-producing endophytic fungi isolated from Eucommia ulmoides Oliver[J]. J Ind Microbiol Biotechnol (2010) 37: 447-454. 

Year 2009  

·         Lishan Yao . Jinfa Ying . Ad Bax. Improved accuracy of 15N–1H scalar and residual dipolar couplings from gradient-enhanced IPAP-HSQC experiments on protonated proteins J Biomol NMR (2009) 43:161–170 DOI 10.1007/s10858-009-9299-x 

·         Beat Vo¨ geli*,† and Lishan Yao‡ Correlated Dynamics between Protein HN and HC Bonds Observed by NMR Cross Relaxation J. AM. CHEM. SOC. 2009, 131, 3668–3678 

·         Alexander Grishaev,† Lishan Yao,† Jinfa Ying,† Arthur Pardi,‡ and Ad Bax*,† Chemical Shift Anisotropy of Imino 15N Nuclei in Watson-Crick Base Pairsfrom Magic Angle Spinning Liquid Crystal NMR and Nuclear Spin Relaxation J. AM. CHEM. SOC. 2009, 131, 9490–9491 

·         B. Chmura, Z. Lan, M. F. Rode and A. L. Sobolewski, Photochemistry of the water dimer: time-dependent quantum wave-packet description of the dynamics at the S1-S0 conical intersection. J . Chem. Phys. 131, 134307 (13 pages) (2009). [link]  

·         Z. Lan, E. Fabiano and W. Thiel, Photoinduced nonadiabatic dynamics of 9H-guanine. ChemPhysChem. 10, 1225-1229 (2009). [link]  

·         Z. Lan, E. Fabiano and W. Thiel, Photoinduced nonadiabatic dynamics of pyrimidine nucleobases: on-the-y surface-hopping study with semiempirical methods. J. Phys. Chem. B 113, 3548-3555 (2009). [link] 

·         Xu, L.; Yan, S. H.; Choi, E.-Y.; Lee, J. Y.; Kwon, Y.-U.  Product Control by Halide Ions of Ionic Liquids in the Ionothermal Syntheses of Ni-based Metal-Organic Frameworks  Chem. Comm. 2009, 3431-3433.  

·         Jung, H. S.; Kwon, P. S.; Lee, J. W.; Kim, J. I.; Hong, C. S.; Kim, J.; Yan, S. H.; Lee, J. Y.; Lee, J. H.; Joo, T.; Kim, S.;  Coumarin-Derived Cu2+ Selective Fluorescence Sensor: Synthesis, Mechanisms, and Applications in Living Cells  J. Am. Chem. Soc. 2009, 131, 2008-2012.  

·         Yan, S. H.; Lee, J. Y.  Solvated Excess Electron in LiAlH4 Clusters: Implication for Hydrogen Storage  J. Phys. Chem. C 2009, 113, 1104-1108.  

·         Wang, Y. F., Yang, G. and Liu, C. B. Electron transfers in proteins: Investigations with a modified through-bond coupling model. Phys. Rev. E 80, 021927 (1-8) (2009). 

·          Wang, Y. F., Yu, Z. Y., Wu, J. and Liu, C. B. Electron Delocalization and Charge Transfer in Polypeptide Chains. J. Phys. Chem. A 113, 10521-10526 (2009). 

·         Xue, Y. M., Yu, J. J. And Song, X. F. Hydrolysis of soy isoflavone glycosides by recombinant β-glucosidase from hyperthermophile Thermotoga maritima. J. Ind. Microbiol. Biot. 36, 1401-1408 (2009). 

·         Xue, Y. M., Peng, J. J., Wang, R. L. and Song, X. F. Construction of the trifunctional enzyme associating the Thermoanaerobacter ethanolicus xylosidase-arabinosidase with the Thermomyces lanuginosus xylanase for degradation of arabinoxylan. Enzyme Microb.Tech. 45, 22-27 (2009). 

·         Xue, Y. M., Song, X. F. and Yu, J. J. Overexpression of β-glucosidase from Thermotoga maritima for the production of highly purified aglycone isoflavones from soy flour. World J.Microb. Biot. 25, 2165-2172 (2009). 

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