Dr Jiapu Zhang

Transmissible spongiform encephalopathies (TSEs) - wikipedia.org Reference [36]: Zhang, Jiapu (25 April 2012), The nature of the infectious agents: PrP models of resistant species to prion diseases (dog, rabbit and horses), arXiv:1106.4628

https://www.technologyreview.com/2011/06/27/193403/prion-disease-secret-of-immunity-revealed/

New Books: [1] Computational Studies of Amyloid-β and τ Proteins: Mechanism underlying Alzheimer's Disease (chapter example); [2] Stochastic Programming: with Recourse(s), Local Search and Global Search; [3] Molecular Dynamics Studies of Prion resistant Proteins: Longer Simulations;

https://link.springer.com/book/10.1007/978-981-10-8815-5

https://link.springer.com/book/10.1007/978-94-017-7318-8

https://link.springer.com/book/9783031367724

https://link.springer.com/book/9783032212801

https://youtu.be/ikL0gh7jYJM, https://youtu.be/5PrSq-xBr

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

8. ..

Publications

PhD thesis

Zhang JP, Derivative-Free Hybrid Methods in Global Optimization and Their Applications, PhD thesis, The University of Ballarat (Australia), February 2005. (Identifier http://researchonline.federation.edu.au/vital/access/HandleResolver/1959.17/34054

Identifier vital:3522 Identifier https://library.federation.edu.au/search/a?searchtype=t&searcharg=Derivative-free+hybrid+methods+in+global+optimization+and+their+&searchscope=4&SORT=D) "Revolutionary optimization methods that pushed the boundaries of global optimization, forever changing the game." - a review from KW.

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 (2026) Molecular Dynamics and Optimization Studies of α-Synuclein Protein Structures - Mechanism Underlying the Parkinson's Disease and Movement Disorders, Springer Cham, ISBN 978-3-032-21280-1, xx+1861 pages, Hardcover ISBN 978-3-032-21280-1, softcover ISBN 978-3-032-21283-2, eBook ISBN 978-3-032-21281-8, DOI: 10.1007/978-3-032-21281-8), https://link.springer.com/book/9783032212801

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, NLM Unique ID 9918863688806676. (Hardcover ISBN 978-3-031-36772-4 published on 17/10/2023, Softcover ISBN 978-3-031-36775-5 published on 30/10/2024, eBook ISBN 978-3-031-36773-1 published on 16/10/2023, DOI: 10.1007/978-3-031-36773-1). A book review from ACM Computing Reviews

https://www.computingreviews.com/review/review_review.cfm?review_id=147951; Support Material 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 Unique 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) "Unlocking the secrets of prion proteins, revealing insights into the resistance against prion disesese." - a review from KW

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 Unique 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). A book review from ACM Computing Reviews

https://www.computingreviews.com/review/review_review.cfm?review_id=144750

Journal Papers (selected)

Zhang JP (2026) Cubic-spline-function based minimisation of the Lennard-Jones potential (arXiv version 1 of 31-Jul-2026).

A cubic spline is a piecewise cubic polynomial function that is smoothly joined at specified grid points; it provides a highly accurate and stable approximation of a smooth function. The function of Lennard-Jones potential is just a smooth function. In this article we will optimise the Lennard-Jones potential in the use of cubic spline function approximations.

Zhang JP (2026) Molecular dynamics and optimization studies of bat prion protein (bat-PrPC) (manuscript of 31-Jan-2026).

In the article [Tran et al. (2026) First report of novel single-nucleotide polymorphisms and genetic characteristics of the prion protein gene (PENP) in bats, to appear in journal Frontiers in Veterinary Science], the authors reported that "the bat PrP protein (comprising 248 amino acids, with a few specific amino acid residues uniquely presented in bats, including Q27, R36, S79, M132, K159, E162, H219, and R222) in the structured region contains three α-helical regions (residues 139-147, 167-189, and 195-228) and two β-sheet regions (residues 124-126 and 156-158), and in the unstructured region the K29R substitution is likely to be functionally neutral, without notable alterations in protein solubility or secondary structure. " For bat prion protein, as the authors reported in their article, there are highlights (i)-(iii): (i) bats are evolutionarily unique as the only mammals able to perform sustained flight, distinguishing them from avian species; (ii) they are also recognised as natural reservoirs for a large range of zoonotic viruses, including coronaviruses, filoviruses, and lyssaviruses, many of which can induce severe diseases in humans; and (iii) bats, a taxonomically and ecologically diverse mammalian group, do not naturally occurring prion disease - investigating prion-related genetic variation in bats may provide new insights into interspecies barriers and molecular mechanisms of resistance to prion diseases. In our article of MD (molecular dynamics) and Opt (optimization) studies of bat prion protein, we will report some detailed and interesting MD and Opt research results.

Zhang JP (2024) Classifications of Mathematical Studies of Prion(s).

This article is to do research on the classifications of prions in the MathSciNet database. Observations from the discussion of this article allow us to obtain at least six classes of MathSciNet study for prion(s). These classes are at different levels of study: (i) at disease population level, (ii) at brain or neurons-nerves-or-spine level, (iii) at cell level, (iv) at molecule level, (v) at polymer level, and (vi) with presence of others. These classifications may be helpful to us for the prion disease treatments.

(i) At disease population level [1, 13, 19, 31, 33, 47, 49], the populations of Sup35 prion yeast [1], with Parkinson’s disease (PD) [13], prion Creutzfeldt-Jacob Disease (CJD) [19], Chronic wasting disease (CWD) [33], etc. are studied. (ii) The studies at at brain or neurons-nerves-or-spine level can be seen from [3, 5, 2, 42-43, 59]. (iii) The studies at cell level are mainly considering yeast prion cells [20, 34, 36, 38, 48, 60]. Most of the models are in the class that is at molecule level [2, 14, 15, 16, 21, 23, 25, 27-29, 37,40-41, 44, 46, 50-57, 61]; some models are prions in the presence of chaperone [4, 6, 8, 11, 24, 51], interferons [10], suPrP [12], strains/variants [17, 22, 35, 40, 45, 46], interacting with Aβ [7, 13, 18, 30], and evolution with impulse effects [32]; prions are also used as a test/detecting/diagnosis to MD, optimization, PMCA technologies [9, 26, 35, 39].

Zhang JP (2024) Molecular dynamics, optimisation, and AlphaFold studies of wild-type frog prion proteins (frog-PrPCs), (invited paper).

In Section 5.3 of Springer eBook ISBN 978-981-10-8815-5 entitled "Molecular Dynamics Analyses of Prion Protein Structures", the molecular dynamics (MD) studies on the NMR structure of African clawed frog (Xenopus laevis) prion protein (frog-PrPC, with PDB entry 1XU0) are presented; where the author found that for frog-PrPC its α-helix 1 is not stable and the two β-strands are longer than usual. This research article is to present furthermore MD, optimisation, and AlphaFold results of frog-PrPCs.

Zhang JP (2024) Molecular dynamics and optimization studies of horse prion protein wild type and its S167D mutant (invited paper), arXiv:2110.00365, MDPI journal Zoonotic Diseases 4(3): 187-200, DOI:10.3390/zoonoticdis4030017. https://www.mdpi.com/2813-0227/4/3/17 Études de dynamique moléculaire de la protéine prion de cheval de type sauvage et de son mutant S167D By Jiapu Zhang Les maladies à prions, ou encéphalopathies spongiformes transmissibles (EST), sont des maladies neurodégénératives mortelles. Cependant, la maladie à prions n'a pas été signalée chez les chevaux jusqu'à présent; par conséquent, les chevaux sont connus pour être une espèce résistante aux maladies à prions. Le résidu S167 dans la protéine prion du cheval a été cité comme résidu protecteur essentiel pour les chevaux contre les maladies à prions. Comprendre la dynamique conformationnelle des protéines prions est essentiel pour développer des thérapies efficaces. Cet article vise à faire des études de dynamique moléculaire sur la protéine prion de cheval de type sauvage (WT) et son mutant S167D (Mutant) pour comprendre leur dynamique conformationnelle; des résultats intéressants seront discutés. Молекулярно-динамические исследования прионного белка лошади дикого типа и его мутанта S167D By Jiapu Zhang Прионные заболевания, или так называемые трансмиссивные губчатые энцефалопатии (ТГЭ), являются смертельными нейродегенеративными заболеваниями. Однако до настоящего времени о прионных заболеваниях у лошадей не сообщалось, поэтому известно, что лошади являются видом, устойчивым к прионным заболеваниям. Остаток S167 в прионном белке лошади считается важнейшим защитным элементом для лошадей от прионных заболеваний. Понимание конформационной динамики прионных белков является ключом к разработке эффективных методов лечения. Цель этой статьи - провести молекулярно-динамические исследования лошадиного прионного белка дикого типа (WT) и его мутанта S167D (Mutant), чтобы понять их конформационную динамику; будут обсуждаться интересные результаты. Prion diseases or called transmissible spongiform encephalopathies are fatal neurodegenerative diseases characterised by the accumulation of an abnormal prion protein isoform (rich in beta-sheets - about 30% alpha-helix and 43% beta-sheet), which is converted from the normal prion protein (predominant in alpha-helix - about 42% alpha-helix and 3% beta-sheet). However, prion disease has not been reported in horses up to now; therefore, horses are known to be a species resistant to prion diseases. Residue S167 in horse has been cited as critical protective residue for encoding prion protein conformational stability in prion-resistance. According to the protein-only hypothesis, abnormal prion protein is responsible for both spongiform degeneration of the brain and disease transmissibility. Thus, understanding the conformational dynamics of abnormal prion protein from normal prion protein is a key to developing effective therapies. This article is to do molecular dynamics and optimization studies on the horse normal prion protein wild-type and its S167D mutant respectively to understand their conformational dynamics and optimized confirmation; interesting results will be discussed. 野生型马朊病毒蛋白及其突变体S167D的分子动力学研究 by Jiapu Zhang 朊病毒病或传染性海绵状脑病 (TSE) 是致命的神经退行性疾病。然而，迄今为止，还没有关于马感染朊病毒病的报道。因此，马被认为是对朊病毒疾病有抵抗力的物种。马朊病毒蛋白中的残基S167被认为是马对抗朊病毒疾病的重要保护残基。了解朊病毒蛋白的构象动力学对于开发有效的疗法至关重要。本文旨在对野生型（WT）马朊病毒蛋白及其突变体S167D（Mutant）进行分子动力学研究，了解其构象动力学；将讨论有趣的结果。Molekulardynamische Untersuchungen des Pferde-Prionenproteins Wildtyp und seiner S167D-Mutante by Jiapu Zhang Prionenkrankheiten oder transmissible spongiforme Enzephalopathien (TSE) genannt, sind tödliche neurodegenerative Erkrankungen. Eine Prionenkrankheit wurde jedoch bisher bei Pferden nicht gemeldet; Daher ist bekannt, dass Pferde eine Spezies sind, die gegen Prionenkrankheiten resistent ist. Der Rückstand S167 im Prionenprotein von Pferden wurde als kritischer Schutzrückstand für Pferde gegen Prionenkrankheiten angeführt. Das Verständnis der Konformationsdynamik von Prionproteinen ist der Schlüssel zur Entwicklung wirksamer Therapien. Dieser Artikel soll molekulardynamische Studien am Pferde-Prionenprotein-Wildtyp (WT) und seiner S167D-Mutante (Mutante) durchführen, um ihre Konformationsdynamik zu verstehen; Interessante Ergebnisse werden diskutiert. Estudios de dinámica molecular de la proteína priónica de caballo de tipo salvaje y su mutante S167D by Jiapu Zhang. Las enfermedades priónicas, o llamadas encefalopatías espongiformes transmisibles (EET), son enfermedades neurodegenerativas fatales. Sin embargo, hasta ahora no se ha informado de enfermedades priónicas en caballos; por lo tanto, se sabe que los caballos son una especie resistente a las enfermedades priónicas. El residuo S167 en la proteína priónica de caballo se ha citado como residuo protector crítico para caballos contra enfermedades priónicas. Comprender la dinámica conformacional de las proteínas priónicas es clave para desarrollar terapias efectivas. El objetivo de este artículo es realizar estudios de dinámica molecular en la proteína priónica de caballo de tipo silvestre (WT) y su mutante S167D (Mutante) para comprender su dinámica conformacional; se discutirán resultados interesantes./ウマプリオン蛋白質野生型とそのS167D変異体の分子動力学と最適化研究 by Jiapu Zhang 感染性海綿状脳症と呼ばれるプリオン病は,正常なプリオン蛋白質(主にαヘリックス~約42%のαヘリックスと3%のβシート)から変換される異常なプリオン蛋白質アイソフォーム(βシート~約30%のαヘリックスと43%のβシートに富む)の蓄積により特徴付けられる致死的神経変性疾患である。しかし,プリオン病は現在までウマで報告されていない;したがって,ウマはプリオン病に抵抗性の種であることが知られている。ウマの残基S167はプリオン耐性におけるプリオン蛋白質立体配座安定性をコードする重要な保護残基として挙げられている。蛋白質のみの仮説によると,異常なプリオン蛋白質は脳の海綿状変性と疾患伝達性の両方に関与する。したがって,正常プリオン蛋白質由来の異常プリオン蛋白質の立体配座動力学の理解は効果的な治療法開発の鍵である。本論文は,ウマ正常プリオン蛋白質野生型とそのS167D突然変異体に関する分子動力学と最適化研究を,それぞれ,それらの立体配座動力学を理解し,確認を最適化することである。興味深い結果を論じた。

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

Ten short articles invited and published by some open access journals:

1. Zhang J (2015) A Complete List of Kernels Used in Support Vector Machines. Biochem Pharmacol (Los Angel) 4(5):195. doi:10.4172/2167-0501.1000195.

2. Zhang J (2015) A Survey on π-π Stackings and π-Cations in Prion Protein Structures. Biochem Pharmacol (Los Angel) 4: e175. doi:10.4172/2167-0501.1000e175.

3. Zhang J (2015) An Optimization Model of Molecular Voronoi Cells in Computational Chemistry. Research and Reviews: Journal of Pharmacy and Pharmaceutical Sciences. RRJPPS | Volume 4 | Issue 2 | April - June, 2015. e-ISSN: 2320-1215, p-ISSN: 2322-0112. 97-100.

4. Zhang J (2016) Mathematical Formulas for Prion All Cross-Structures Listed in the Protein Data Bank. Med chem (Los Angeles) 6: 179-188. doi:10.4172/2161-0444.1000343.

5. Zhang J (2016) Mathematical Formulas for Some Cross-Β Structures of Human Aβ Protein. Med chem (Los Angeles) 6: 349-355. doi:10.4172/2161-0444.1000369.

6. Zhang J (2014) Molecular dynamics studies of rabbit, dog, horse, human, mouse and elk prion proteins. Nat Prod Chem Res 2014, 2:5. doi: 10.4172/2329-6836.S1.005.

7. Zhang J (2016) Packing Rectangular-Box Cells Optimally for the Crystal Structure. Med chem 6: 039. doi:10.4172/2161-0444.1000320.

8. Zhang J (2013) Recent Advances in the Immunity Research of Rabbits to Prion Diseases. Biochem & Pharmacol 2:e143. doi:10.4172/2167-0501.1000e143.

9. Zhang J (2015) The Hybrid Idea of (Energy Minimization) Optimization Methods Applied to Study Prion Protein Structures Focusing on the beta2-alpha2 Loop. Biochem Pharmacol (Los Angel) 4: 175. doi:10.4172/2167-0501.1000175.

10. Zhang J (2014) Recent Research Advances in the Glycine xxx-Glycine Motif of Mammalian Prion Proteins. Biochem Pharmacol 3: e151. doi:10.4172/2167-0501.1000e151.

Five invited book-chapters by the NOVA Science Publishers:

1. Zhang JP (2014) Simulated annealing: in mathematical global optimization computations, hybrid with local or global search and practical applications in crystallography & molecular modelling of prion amyloid fibrils, in [Simulated Annealing: Strategies, Potential Uses and Advantages, Editors Prof. Dr. Marcos Tsuzuki & Prof. Dr. Thiago de Castro Martins, NOVA Science Publishers, ISBN 978-1-63117-268-7], Chapter 1, pp. 1-34.

2. Zhang JP (2013) A survey on the studies of rabbit prion proteins, in [Rabbits: Biology, Diet and Eating Habits and Disorders, Gianni Adamo & Albert Costanza (editors), NOVA Science Publishers, ISBN 978-1-62948-268-2 (eBook), ISBN 978-1-62948-267-5 (paper Book)], Chapter II, pp. 29-44.

3. Zhang JP (2012) Molecular dynamics studies on the structural stability of wild-type rabbit prion protein: Surface Electrostatic Charge Distributions, in [Bioinformatics Research: New Developments, Editors Chiheb Battik and Khalil Belhassine, NOVA Science Publishers, Feb 15th 2012, ISBN 978-1-61942-363-3, Hardcover], Chapter 7, pp. 131-138.

4. Zhang JP (2012) Atomic-resolution structures of prion AGAAAAGA amyloid fibrils, in [Amyloids: Composition, Functions and Pathology, Editors Irene P. Halcheck and Nancy R. Vernon, NOVA Science Publishers, Hauppauge, N.Y., March 1st 2012, ISBN 978-1-62100-538-4, hardcover,], Chapter 10, pp.177-186.

5. Zhang JP (2012) The nature of the infectious agents: PrP models of resistant species to prion diseases (dog, rabbit and horses), in [Prions and Prion Diseases: New Developments, Editor Jean-Michel Verdier, NOVA Publishers, 2012 2nd Quarter, ISBN 978-1-62100-027-3, Hard cover, June 15th 2012], arXiv1106.4628v2, Chapter 2, pp. 41-48.

Two invited book-chapters by the InTech Open Publisher (http://www.intechopen.com/):

1. Computational Studies of the Structural Stability of Rabbit Prion Protein Compared to Human and Mouse Prion Proteins, DOI: 10.5772/28858, Chapter 14 pages 301-310 of Book " 'Advanced Understanding of Neurodegenerative Diseases', book edited by Raymond Chuen-Chung Chang, ISBN 978-953-307-529-7, Published: December 16, 2011 under CC BY 3.0 license." download at website http://cdn.intechopen.com/pdfs-wm/25213.pdf

2. Computational Potential Energy Minimization Studies on the Prion AGAAAAGA Amyloid Fibril Molecular Structures, DOI: 10.5772/47733, Chapter 12 pages 297-312 of Book " 'Recent Advances in Crystallography', book edited by Jason B. Benedict, ISBN 978-953-51-0754-5, Published: September 19, 2012 under CC BY 3.0 license.", download at website http://cdn.intechopen.com/pdfs-wm/39124.pdf

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

-----------------Literatures: ------------------

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.

Zhang JP (2025) 张家普博士百篇科普论文集(卷一),II+xx+565页, https://youtu.be/qVJv2h8m4f4, ⓒsciencenet . - A recent youtube 关于Hopfield神经网络的一个小注解(张家普)

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