NEW BOOK

Title:      Molecular Dynamics and Optimization Studies of alpha-synuclein Protein Structures

Subtitle: Mechanism Underlying the Parkinson's Disease and Movement Disorders

RECENT BOOK: https://youtu.be/Bzb9VzR2JPw

Teaching experiences

1. Theory of Computation

2. Advanced Algebra

3. Mathematics Modeling

4. Model Building and Solving and Software

5. Programming Languages, and Data Structures

6.  Computing Chemistry and Advanced Organic Chemistry

7. Tutoring experiences in many courses of Mathematics, Statistics, and Computer Computing.  

Publications

PhD thesis

• Zhang JP, Derivative-Free Hybrid Methods in Global Optimization and Their Applications, PhD thesis, The University of Ballarat (Australia), February 2005,  http://researchonline.federation.edu.au/vital/access/HandleResolver/1959.17/137122

MSc thesis

• Zhang JP, A global and superlinearly convergent algorithm for nonlinear nondifferential convex programming problems with a generalized Armijo line-search, Masters (rsearch) degree thesis, Institute of Operations Research (at Qufu Normal University China), 1996, arXiv1309.0931

Springer Monographs

•  Zhang JP (2023) Optimization-based Molecular Dynamics Studies of SARS-CoV-2 Molecular Structures - Research on COVID-19, Springer Cham, ISBN 978-3-031-36772-4, xx+953 pages. (Hardcover ISBN 978-3-031-36772-4, Softcover ISBN 978-3-031-36775-5, eBook ISBN 978-3-031-36773-1, DOI: 10.1007/978-3-031-36773-1)

• Zhang JP (2018) Molecular Dynamics Analyses of Prion Protein Structures - The Resistance to Prion Diseases Down Under, Springer Singapore, ISBN 978-981-10-8814-8, xxix+375 pages, NLM ID 101746134.   (Hardcover ISBN 978-981-10-8814-8 published on 07/08/2018, Softcover ISBN 978-981-13-4247-9 published on 23/12/2018, eBook ISBN 978-981-10-8815-5 published on 20/07/2018, MyCopy softcover ISBN 978-981-10-8816-2, DOI: 10.1007/978-981-10-8815-5)

• Zhang JP (2015) Molecular Structures and Structural Dynamics of Prion Proteins and Prions - Mechanism Underlying the Resistance to Prion Diseases, Springer Dordrecht, ISBN 978-94-017-7317-1, xix+355 pages (Association for Computing Machinery wrote 2 pages' Book Review), NLM ID 101676710.  (Hardcover ISBN 978-94-017-7317-1 published on 25/09/2015, Softcover ISBN 978-94-024-0445-6 published on 29/10/2016, eBook ISBN 978-94-017-7318-8 published on 14/09/2015, MyCopy softcover ISBN 978-94-017-7319-5, DOI: 10.1007/978-94-017-7318-8)

Journal Papers (selected)

• Zhang JP (2024) Molecular dynamics studies of frog prion protein wild types,

• Zhang JP (2024) Molecular dynamics studies of horse prion protein wild type and its S167D mutant, arXiv:2110.00365,

• Zhang JP (2023) Two polar contacts between GLU290 and ARG4 linking the two monomers of SARS-CoV-2 3CLpro, arXiv: 5182254. Current Topics in Biotechnology 14: 19-33. RT/BT/151, http://www.researchtrends.net/tia/abstract.asp?in=0&vn=14&tid=48&aid=7232&pub=2023&type=3 

• Zhang JP (2021) Molecular dynamics studies of dog prion protein wild-type and its D159N mutant, Journal of Biomolecular Structure and Dynamics 39 (12): 4234-4242, PMID 32496928, DOI: 10.1080/07391102.2020.1776155. https://www.tandfonline.com/eprint/XEJ6FRKGEUFFY8IM6R7A/full?target=10.1080/07391102.2020.1776155

• Zhang JP (2020) Molecular dynamics studies of the bufallo prion protein structured region at higher temperatures, The Open Bioinformatics Journal 13: 129-136. DOI: 10.2174/1875036202013010129 (Associate Editorial Board Membership annual paper) https://benthamopen.com/contents/pdf/TOBIOIJ/TOBIOIJ-13-129.pdf, https://youtu.be/5PrSq-xBr5Y

• Zhang JP (2020) The classical Minkowski problem: an optimization description, Asia-Pacific Journal of Mathematics and Statistics 2(1):1-4, DOI: 10.11648/10045508 (Editorial Board Membership paper)

• Zhang JP (2019) The polar clasps of a bank vole PrP(168–176) prion protofibril revisiting, Journal of Molecular Modeling 25 (5) 108, PMID 30937536, DOI: 10.1007/s00894-019-3981-z https://rdcu.be/buml4

• Zhang JP (2018) Molecular Dynamics Analyses of Prion Protein Structures (1st ed. 2018 Edition) Springer, ISBN 978-981-10-8814-8, 2018, DOI: 10.1007/978-981-10-8815-5, NLM ID 101746134.

• Zhang JP, Chatterjee S, Wang F (2017) Using graph theory and optimization theory to do data mining the large-scale buffalo prion protein structure database, Operations Research Transactions 21 (2) 73-83, DOI: 10.15960/j.cnki.issn.1007-6093.2017.02.009

• Zhang JP, Wang F (2016) A review on the salt bridge ASP177-ARG163 (O-N) of wild-type rabbit prion protein, Journal of Biomolecular Structure and Dynamics 34 (5) 1020-1028, PMID 26103085, DOI: 10.1080/07391102.2015.1064832. arXiv1408.5269

• Zhang JP, Chatterjee S, Wang F (2016) Molecular dynamics studies on the buffalo prion protein, Journal of Biomolecular Structure and Dynamics 34 (4) 762-777, PMID 26043781, DOI: 10.1080/07391102.2015.1052849. arXiv1503.00051

• Zhang JP, Wang F, Zhang YL (2015) Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions, Journal of Biomolecular Structure and Dynamics 33 (6) 1326-1335, PMID 25105226, DOI: 10.1080/07391102.2014.947325. arXiv1407.6221

• Zhang JP (2015) Molecular Structures and Structural Dynamics of Prion Proteins and Prions, Springer, ISBN 978-94-017-7317-1, 2015, DOI: 10.1007/978-94-017-7318-8, NLM ID 101676710.

• Zhang JP, Zhang YL (2014) Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins, Journal of Theoretical Biology 343 (1) 70-82, PMID 24184221, DOI: 10.1016/j.jtbi.2013.10.005. arXiv1304.7633

• Zhang JP, Wang F (2014) A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins, Current Pharmaceutical Biotechnology 15 (11) 1026-1048, PMID 25373387, DOI: 10.2174/1389201015666141103020004 https://youtu.be/ikL0gh7jYJM. arXiv1409.6104

• Zhang JP, Zhang YL (2013) Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136), Acta Biochimica et Biophysica Sinica 45(6) 509-519, PMID 23563221, DOI: 10.1093/abbs/gmt031 Free. arXiv1301.0117

• Zhang JP, Hou YT, Wang YJ, Wang CY, Zhang XS (2012) The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils, Natural Science 4(12A) 1097-1108, DOI: 10.4236/ns.2012.412A138. arXiv1206.1755

• Zhang JP (2011) The structural stability of wild-type horse prion protein, Journal of Biomolecular Structure and Dynamics 29 (2) 369-377, PMID 21875155, DOI: 10.1080/07391102.2011.10507391. arXiv1104.4616

• Zhang JP, Gao DY, Yearwood J (2011) A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling, Journal of Theoretical Biology 284 (1) 149-157, PMID 21723301, DOI: 10.1016/j.jtbi.2011.06.024. arXiv1107.4104

• Zhang JP, Sun J, Wu CZ (2011) Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils, Journal of Theoretical Biology 279 (1) 17-28, PMID 21420420, DOI: 10.1016/j.jtbi.2011.02.012. arXiv1012.2504

• Zhang JP, Liu DDW (2011) Molecular dynamics studies on the structural stability of wild-type dog prion protein, Journal of Biomolecular Structure and Dynamics 28 (6) 861-869, PMID 21469747, DOI: 10.1080/07391102.2011.10508613

• Zhang JP (2011) An effective simulated annealing refined replica exchange Markov chain Monte Carlo Algorithm for the infectious disease model of H1N1 influenza pandemic, World Journal of Modelling and Simulation 7(1) 29-39.

• Zhang JP (2011) Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins, Journal of Theoretical Biology 269(1) 88-95‏, PMID 20970434, DOI: 10.1016/j.jtbi.2010.10.020

• Zhang JP (2011) Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing, Journal Molecular Modelling 17 (1) 173-179, PMID 20411399, DOI: 10.1007/s00894-010-0691-y

• Zhang JP (2010) Studies on the structural stability of rabbit prion protein probed by molecular dynamics simulations of its wild-type and mutants, Journal of Theoretical Biology 264 (1) 119-122, PMID 20109469, DOI: 10.1016/j.jtbi.2010.01.024

• Bagirov AM, Rubinov AM, Zhang JP (2009) A multidimensional descent method for global optimization, Optimization 58 (5) 611-625, DOI: 10.1080/02331930902943483

• Zhang JP (2009) Studies on the structural stability of rabbit prion protein probed by molecular dynamics simulations, Journal of Biomolecular Structure and Dynamics 27 (2) 159-162, PMID 19583441, DOI: 10.1080/07391102.2009.10507305. with corrections

• Bagirov AM, Rubinov AM, Zhang JP (2005) Local optimization method with global multidimensional search, Journal of Global Optimization 32 (2) 161-179, DOI: 10.1007/s10898-004-2700-0. 

• Ghosh R, Rubinov AM, Zhang JP (2005) Optimization approach for clustering datasets with weights, Optimization Methods and Software 20 335-351, DOI: 10.1080/10556780512331318191

• Bagirov AM, Rubinov AM, Zhang JP (2004) Local Optimization Method with Global Multidimensional Search for Descent, Optimization Online 2004. http://www.optimization-online.org/DB_FILE/2004/01/808.pdf

• Abbass HA, Bagirov AM, Zhang JP (2003) The discrete gradient evolutionary strategy method for global optimization, IEEE The 2003 Congress on Evolutionary Computation, 2003 (CEC '03) Vol 1, pp. 435-442, DOI: 10.1109/CEC.2003.1299608 

• Bagirov AM, Zhang JP (2003) Comparative analyses of the cutting angle and simulated annealing methods in global optimization, Optimization 52 (4-5) 363-378, DOI: 10.1080/02331930310001611565

• Sun J, Zhang JP (2001) Global convergence of conjugate gradient methods without line search, Annals of Operations Research 103 161-173 DOI: 10.1023/A:1012903105391

Some Papers Linking PubMed:

Molecular dynamics studies of dog prion protein wild-type and its D159N mutant.

Zhang J. J Biomol Struct Dyn. 2021 Aug;39(12):4234-4242. doi: 10.1080/07391102.2020.1776155. Epub 2020 Jun 16.

PMID: 32496928    https://www.tandfonline.com/eprint/XEJ6FRKGEUFFY8IM6R7A/full?target=10.1080/07391102.2020.1776155

The polar clasps of a bank vole PrP(168-176) prion protofibril revisiting.

Zhang J. J Mol Model. 2019 Apr 2;25(5):108. doi: 10.1007/s00894-019-3981-z.

PMID: 30937536 https://rdcu.be/buml4

A review on the salt bridge ASP177-ARG163 (O-N) of wild-type rabbit prion protein.

Zhang J, Wang F. J Biomol Struct Dyn. 2016 May;34(5):1020-8. doi: 10.1080/07391102.2015.1064832. Epub 2016 Jan 26.

PMID: 26103085

Molecular dynamics studies on the buffalo prion protein.

Zhang J, Wang F, Chatterjee S. J Biomol Struct Dyn. 2016;34(4):762-77. doi: 10.1080/07391102.2015.1052849. Epub 2015 Jul 10.

PMID: 26043781

A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins.

Zhang J, Wang F. Curr Pharm Biotechnol. 2014;15(11):1026-48. doi: 10.2174/1389201015666141103020004.

PMID: 25373387  https://youtu.be/ikL0gh7jYJM

Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions.

Zhang J, Wang F, Zhang Y. J Biomol Struct Dyn. 2015;33(6):1326-35. doi: 10.1080/07391102.2014.947325. Epub 2014 Aug 8.

PMID: 25105226

Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins.

Zhang J, Zhang Y. J Theor Biol. 2014 Feb 7;342:70-82. doi: 10.1016/j.jtbi.2013.10.005. Epub 2013 Oct 31.

PMID: 24184221

Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136).

Zhang J, Zhang Y. Acta Biochim Biophys Sin (Shanghai). 2013 Jun;45(6):509-19. doi: 10.1093/abbs/gmt031. Epub 2013 Apr 5.

PMID: 23563221 Free

The structural stability of wild-type horse prion protein.

Zhang J. J Biomol Struct Dyn. 2011 Oct;29(2):369-77. doi: 10.1080/07391102.2011.10507391.

PMID: 21875155

A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling.

Zhang J, Gao DY, Yearwood J. J Theor Biol. 2011 Sep 7;284(1):149-57. doi: 10.1016/j.jtbi.2011.06.024. Epub 2011 Jun 28.

PMID: 21723301

Molecular dynamics studies on the structural stability of wild-type dog prion protein.

Zhang J, Liu DD. J Biomol Struct Dyn. 2011 Jun;28(6):861-9. doi: 10.1080/07391102.2011.10508613.

PMID: 21469747

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils.

Zhang J, Sun J, Wu C. J Theor Biol. 2011 Jun 21;279(1):17-28. doi: 10.1016/j.jtbi.2011.02.012. Epub 2011 Mar 21.

PMID: 21420420

Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins.

Zhang J. J Theor Biol. 2011 Jan 21;269(1):88-95. doi: 10.1016/j.jtbi.2010.10.020. Epub 2010 Oct 21.

PMID: 20970434

Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing.

Zhang J. J Mol Model. 2011 Jan;17(1):173-9. doi: 10.1007/s00894-010-0691-y. Epub 2010 Apr 22.

PMID: 20411399

Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants.

Zhang J. J Theor Biol. 2010 May 7;264(1):119-22. doi: 10.1016/j.jtbi.2010.01.024. Epub 2010 Jan 28.

PMID: 20109469

Studies on the structural stability of rabbit prion probed by molecular dynamics simulations.

Zhang J. J Biomol Struct Dyn. 2009 Oct;27(2):159-62. doi: 10.1080/07391102.2009.10507305.

PMID: 19583441

In Japanese

イヌプリオンタンパク質野生型とそのD159N変異体の分子動力学研究

Molecular Dynamics Studies of Dog Prion Protein Wild-type and Its D159N Mutant. Zhang Jiapu. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2020Jun04

銀行のボールPRP（168-176）プリオンプロトフィブリルの再訪の極地留め金

The polar clasps of a bank vole PrP(168-176) prion protofibril revisiting. Zhang Jiapu. Journal of molecular modeling(J Mol Model)2019Apr02

野生型ウサギプリオンタンパク質の塩橋Asp177-Arg163（O - N）のレビュー

A review on the salt bridge ASP177-ARG163 (O-N) of wild-type rabbit prion protein. Zhang Jiapu, Wang Feng. Journal of biomolecular structure & dynamics(J Biomol Struct Dyn)2016May01

バッファロープリオンタンパク質の分子動力学研究

Molecular dynamics studies on the buffalo prion protein. Zhang Jiapu, Wang Feng, Chatterjee Subhojyoti. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2016

プリオンタンパク質の（中央）疎水性領域に関する調査と分子動力学研究

A survey and a molecular dynamics study on the (central) hydrophobic region of prion proteins. Zhang Jiapu, Wang Feng. Current pharmaceutical biotechnology(Curr Pharm Biotechnol)2014

ウサギプリオンタンパク質野生型および変異体のNMR構造に関する分子動力学研究：表面静電荷分布。

Molecular dynamics studies on the NMR structures of rabbit prion protein wild type and mutants: surface electrostatic charge distributions. Zhang Jiapu, Wang Feng, Zhang Yuanli. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2015

ウサギプリオンタンパク質のNMRおよびX線構造に関する分子動力学研究

Molecular dynamics studies on the NMR and X-ray structures of rabbit prion proteins. Zhang Jiapu, Zhang Yuanli. Journal of theoretical biology(J. Theor. Biol.)2014Feb07

疎水性領域PRP（109~136）の3D構造に関する分子動力学研究

Molecular dynamics studies on 3D structures of the hydrophobic region PrP(109-136). Zhang Jiapu, Zhang Yuanli. Acta biochimica et biophysica Sinica(Acta Biochim. Biophys. Sin. (Shanghai))2013Jun01

野生型馬プリオンタンパク質の構造安定性

The structural stability of wild-type horse prion protein. Zhang Jiapu. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2011Oct01

プリオンAGAAAAGAアミロイドフィブリル分子モデリングのための新しい標準的な二重計算アプローチ。

A novel canonical dual computational approach for prion AGAAAAGA amyloid fibril molecular modeling. Zhang Jiapu, Gao David Y, Yearwood John. Journal of theoretical biology(J. Theor. Biol.)2011Sep07

野生型イヌプリオンタンパク質の構造安定性に関する分子動力学研究

Molecular dynamics studies on the structural stability of wild-type dog prion protein. Zhang Jiapu, Liu David D W. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2011Jun01

プリオンAGAAAAGAアミロイドフィブリルの最適な原子分解能構造。

Optimal atomic-resolution structures of prion AGAAAAGA amyloid fibrils. Zhang Jiapu, Sun Jie, Wu Changzhi. Journal of theoretical biology(J. Theor. Biol.)2011Jun21

ウサギプリオンタンパク質とヒトおよびマウスプリオンタンパク質の構造安定性の比較研究。

Comparison studies of the structural stability of rabbit prion protein with human and mouse prion proteins. Zhang Jiapu. Journal of theoretical biology(J. Theor. Biol.)2011Jan21

シミュレーテッドアニーリングによってフォーマットされたプリオンAGAAAAGAアミロイドフィブリルの最適な分子構造。

Optimal molecular structures of prion AGAAAAGA amyloid fibrils formatted by simulated annealing. Zhang Jiapu. Journal of molecular modeling(J Mol Model)2011Jan01

野生型および変異体の分子動力学シミュレーションによって調査されたウサギプリオンの構造安定性に関する研究。

Studies on the structural stability of rabbit prion probed by molecular dynamics simulations of its wild-type and mutants. Zhang Jiapu. Journal of theoretical biology(J. Theor. Biol.)2010May07

分子動力学シミュレーションによって調べられたウサギプリオンの構造安定性に関する研究。

Studies on the structural stability of rabbit prion probed by molecular dynamics simulations. Zhang Jiapu. Journal of biomolecular structure & dynamics(J. Biomol. Struct. Dyn.)2009Oct01

Zhang JP (2023) My Father's Diaries 1966-1971: A Cherish Literature and History Material - now published (ISBN 978-620-2-41346-6, ISBN-10 6202413468) by the Golden iris, Golden Light Academic Publishing, on 2023-02-08, ii+82 pages. It's English version's ISBN number is 978-620-0-64379-7 by the Globe EDIT Publishing on 2023-03-17, ii+112 pages. 

https://my.goldenlight-publishing.com/catalog/details//store/gb/book/978-620-2-41346-6/%E5%AE%B6%E7%88%B6%E6%97%A5%E8%AE%B01966-1971 

https://my.globeedit.com/catalog/details//store/gb/book/978-620-0-64379-7/my-father-s-diaries-1966-1971