Publications

Peer-reviewed original articles:

1. Shengjie Huang, Sijie Yang, Jianqiao Yi, Honghan Chen, Haoyang Guan, Rui Zheng, Haocong Liao, Muzammal Hussain,Yaoquan Tu, Xiaoyun Lu, Yang Zhou, "Generative Replica Exchange: A flow-based framework for accelerating replica-exchange simulations", Journal of Chemical Theory and Computation 22, 6387(2026).
2. Yaoquan Tuand Aatto Laaksonen, "RADE: A reduced approach to density-functional expansion",The Journal of Chemical Physics 162, 054101 (2025).
3. Yiling Liu, Jundong Tan, Shiliang Hu, Muzammal Hussain, Chang Qiao, Yaoquan Tu, Xiaoyun Lu, and Yang Zhou, "Dynamics playing a key role in the covalent binding of inhibitors to focal adhesion kinase",  Journal of Chemical Information and Modeling 64, 6053(2024).
4. Yihao Zhao, Jintu Zhang, Haotian Zhang, Shukai Gu, Yafeng Deng,Yaoquan Tu, Tingjun Hou, and Yu Kang, "Sigmoid Accelerated Molecular Dynamics: An efficient enhanced sampling method for biosystems",The Journal of Physical Chemistry Letters14, 1103(2023).
5. Jiachen Li, Hao Chen, Zhengzhong Kang, Yingchun Liu, Yaoquan Tu, Qi Wang, and Jie Fan, "A combined computational and experimental approach predicts thrombin adsorption to zeolites",Colloids and Surfaces B: Biointerfaces221, 11307(2023).
6. Yang Zhou, Junhao Li, Glib Baryshnikov, and Yaoquan Tu, "Unravelling the abnormal molecular mechanism of suicide inhibition of cytochrome P450 3A4", Journal of Chemical Information and Modeling 62, 6172(2022)
7. Jiachen Li, Qi Wang, andYaoquan Tu, "Binding modes of prothrombin cleavage site sequences to the factor Xa catalytic triad: insights from atomistic simulations", Computational and Structural Biotechnology Journal 20, 5401(2022).
8. Dan Teng, Yang Zhou, Yun Tang, Guixia Liu, and Yaoquan Tu, "Mechanistic studies on the stereoselectivity of FFAR1 modulators", Journal of Chemical Information and Modeling 62, 3664(2022).
9. Sangram Nag, Patricia Miranda-Azpiazu, Zhisheng Jia, Prodip Datta, Ryosuke Arakawa, Mohammad Mahdi Moein, Zhou Yang, Yaoquan Tu, Laetitia Lemoine, Hans Ågren, Agneta Nordberg, Bengt Långström, and Christer Halldin, "Development of 11C-labeled ASEM analogues for the detection of neuronal nicotinic acetylcholine receptors (α7-nAChR)", ACS Chemical Neuroscience13, 352(2022).
10. Junhao Li, Yue Chen, Yun Tang, Weihua Li, andYaoquan Tu, "Homotropic cooperativity of midazolam metabolism by cytochrome P450 3A4: insight from computational studies", Journal of Chemical Information and Modeling 61, 2481(2021).
11. Yao Fu, Zhengzhong Kang, Weicheng Cao, Jinglin Yin,Yaoquan Tu, Jianhua Li, Hanxi Guan, Yiran Wang, Qi Wang, and Xueqian Kong, "Defect‐assisted loading and docking conformations of pharmaceuticals in metal‐organic frameworks",Angewandte Chemie International Edition 60, 7719(2021).
12. Yang Zhou,  Guanglin Kuang,  Junhao Li, Christer Halldin, Agneta Nordberg, Bengt Långström, Yaoquan Tu, and Hans Ågren, "In silico studies of ASEM analogues targeting α7-nAChR and experimental verification",RSC Advances 11, 3942(2021). 
13. Junhao Li, Yang Zhou, Yun Tang, Weihua Li, andYaoquan Tu,"Dissecting the structural plasticity and dynamics of cytochrome P450 2B4 by molecular dynamics simulations", Journal of Chemical Information and Modeling60, 5026(2020).
14. Rongfeng Zou, Yang Zhou, Yong Wang, Guanglin Kuang, Hans Ågren, Junchen Wu, andYaoquan Tu, "Free energy profile and kinetics for coupled folding and binding of the intrinsically disordered protein p53 with MDM2",Journal of Chemical Information and Modeling 60, 1551(2020).
15. Yamin Wang, Yingchun Liu,Yaoquan Tu, and Qi Wang, "Reductive decomposition of solvents and additives toward solid-electrolyte interphase formation in lithium-ion battery",Journal of Physical Chemistry C124, 9099(2020).
16. Junhao Li, Yun Tang, Weihua Li, andYaoquan Tu, "Mechanistic insights into the regio- and stereoselectivities of testosterone and dihydrotestosterone hydroxylation catalyzed by CYP3A4 and CYP19A1", Chemistry - A European Journal26, 6214(2020).
17. Yang Zhou, Rongfeng Zou, Guanglin Kuang, Bent Långström, Christer Halldin, Hans Ågren, andYaoquan Tu, "Enhanced sampling simulations of ligand unbinding kinetics controlled by protein conformational changes", Journal of Chemical Information and Modeling59, 3910(2019).
18. Yao Fu, Zhengzhong Kang, Jinglin Yin, Weicheng Cao,Yaoquan Tu, Qi Wang and Xueqian Kong,"Duet of acetate and water at the defects of metal-organic frameworks",Nano Letters19, 1618(2019).
19. Rongfeng Zou, Guanglin Kuang, Hans Ågren, Agneta Nordberg, Bengt Långström, andYaoquan Tu, "Free energy profile for penetration of Pittsburgh Compound-B into the amyloid β fibril", ACS Chemical Neuroscience10, 1783(2019).
20. Junhao Li, Hongxiao Zhang, Guixia Liu, Yun Tang,Yaoquan Tu, and Weihua Li, "Computational insight into vitamin K1 ω-hydroxylation by cytochrome P450 4F2", Frontiers in Pharmacology-Experimental Pharmacology and Drug Discovery9, 1065(2018).
21. Yang Zhou, Muzammal Hussain, Guanglin Kuang, Jiancun Zhang, andYaoquan Tu, "Mechanistic insights into peptide and ligand binding of ATAD2-bromodomain via atomistic simulations disclose a role of induced fit and conformational selection",Physical Chemistry Chemical Physics20, 23222 (2018).
22. Xin Zhao, Runfeng Li, Yang Zhou, Mengjie Xiao, Chunlong Ma, Zhongjin Yang, Shaogao Zeng, Qiuling Du, Chunguang Yang, Haiming Jiang, Yanmei Hu, Kefeng Wang, Chris Ka Pun Mok, Ping Sun, Jianghong Dong, Wei Cui, Jun Wang,Yaoquan Tu, Zifeng Yang, and Wenhui Hu, "Discovery of highly potent pinanamine-based inhibitors against amantadine- and oseltamivir-resistant influenza A viruses",Journal of Medicinal Chemistry61, 5187(2018).
23. Rongfeng Zou,Xiaomin Zhu,Yaoquan Tu, Junchen Wu, and Markita P. Landry,“Activity of antimicrobial peptide aggregates decreases with increased cell membrane embedding free energy cost”,Biochemistry57, 2606(2018).
24. Zejun Wang, Yao Fu, Zhengzhong Kang, Xiaoguo Liu, Nan Chen, Qi Wang,Yaoquan Tu, Lihua Wang, Shiping Song, Daishun Ling, Haiyun Song, Xueqian Kong, and Chunhai Fan, "Organelle-specific triggered release of immunostimulatory oligonucleotides from intrinsically coordinated DNA-metal-organic frameworks with soluble exoskeleton",Journal of the American Chemical Society139, 15784(2017).
25. Shang Li, Rongfeng Zou,Yaoquan Tu, Junchen Wu, Markita P. Landry, “Cholesterol-directed nanoparticle assemblies based on single amino acid peptide mutations activate cellular uptake and decrease tumor volume”,Chemical Science8, 7552(2017).
26. Xianqiang Sun, Genevieve Laroche, Xu Wang, Hans Ågren, Gregory R. Bowman, Patrick M. Giguère, andYaoquan Tu, “Propagation of the allosteric modulation induced by sodium in the δ opioid receptor”,Chemistry - A European Journal 23, 4615(2017).
27. Guanglin Kuang, Yang Zhou, Rongfeng Zou, Christer Halldin, Agneta Nordberg, Bent Långström, Hans Ågren, andYaoquan Tu, “Characterization of the binding mode of the PET tracer [18F]ASEM to a chimera structure of the α7 nicotinic acetylcholine receptor”,RSC Advances 7, 19787(2017).
28. Yan Wang, Malin Bergenstråhle-Wohlert,Yaoquan Tu, Hans Ågren, Lar A. Berglund, and Jakob Wohlert, “Swelling and dimensional stability of xyloglucan/montmorillonite nanocomposites in moist conditions from molecular dynamics simulations”,Computational Material Science128, 191(2017).
29. Guanglin Kuang, Xu Wang, Christer Halldin, Agneta Nordberg, Bent Långström, Hans Ågren, andYaoquan Tu, “Theoretical study of the binding profile of the allosteric modulator NS-1738 with a chimera structure of the α7 nicotinic acetylcholine receptor”,Physical Chemistry Chemical Physics18, 28003(2016).
30. Guanglin Kuang, Lijun Liang, Christian Brown, Qi Wang, Vincent Bulone, andYaoquan Tu, “Insight into the adsorption profiles of thesaprolegnia monoicachitin synthase MIT domain on POPA and POPC membranes by molecular dynamics simulation studies”,Physical Chemistry Chemical Physics18, 5281(2016).
31. Christian Brown, Scarlett Szpryngiel, Guanglin Kuang, Vaibhav Srivastava, Weihua Ye, Lauren S. McKee,Yaoquan Tu, Lena Mäler, and Vincent Bulone, “Structural and functional characterization of the microtubule interacting and trafficking domains of two oomycete chitin synthases”,The FEBS Journal283, 3072(2016).
32. Guanglin Kuang, Vincent Bulone, andYaoquan Tu, “Computational studies of the binding profile of phosphoinositide PtdIns(3,4,5)P3 with the pleckstrin homology domain of an oomycete cellulose synthase”,Scientific Reports6, 20555(2016).
33. Jianxin Cheng, Xianqiang Sun, Weihua Li, Guixia Liu,Yaoquan Tu, and Yun Tang, “Molecular switches of the κ opioid receptor triggered by 6'-GNTI and 5'-GNTI”,Scientific Reports6, 18913(2016).
34. Guanglin Kuang, N. Arul Murugan,Yaoquan Tu, Agneta Nordberg, and Hans Ågren, “Investigation of the binding profiles of AZD2184 and Thioflavin T with amyloid-β(1-42) fibril by molecular docking and molecular dynamics methods”,Journal of Physical ChemistryB119, 11560(2015).
35. Yan Wang, Jakob Wohlert, Malin Bergenstråhle-Wohlert,Yaoquan Tu, and Hans Ågren, “Molecular mechanisms for the adhesion of chitin and chitosan to montmorillonite clay”,RSC Advances5, 54580(2015).
36. Xu Wang, Xianqiang Sun, Guanglin Kuang, Hans Ågren, andYaoquan Tu, “A theoretical study on the molecular determinants of the affibody protein ZAβ3 bound to an amyloid β peptide”,Physical Chemistry Chemical Physics17, 16886(2015).
37. Xianqiang Sun, Jianxin Cheng, Xu Wang, Yun Tang, Hans Ågren, andYaoquan Tu, “Residues remote from the binding pocket control the antagonist selectivity towards the corticotropin-releasing factor receptor-1”,Scientific Reports5, 8066(2015).
38. Lu Sun, Xin Li,Yaoquan Tu, and Hans Ågren, “Origin of ion selectivity at the air/water interface”,Physical Chemistry Chemical Physics17, 4311(2015).
39. Changchun Shi, Zhe Kong, Tianyang Sun, Lijun Liang, Jiawei Shen, Zhengyan Zhao, Qi Wang, Zhengzhong Kang, Hans Ågren, andYaoquan Tu, “Molecular dynamics simulations of DNA sequencing with graphene nanopores indicate that DNA bases can be identified by their translocation times”,RSC Advances5, 9389(2015).
40. Yan Wang, Jakob Wohlert, Malin Bergenstråhle-Wohlert, Joby Jose Kochumalayil, Lars A. Berglund,Yaoquan Tu, and Hans Ågren, “Molecular adhesion at clay nanocomposite interfaces depends on counterion hydration — molecular dynamics simulations of montmorillonite/xyloglucan”,Biomacromolecules16, 257(2015).
41. Xianqiang Sun, Hans Ågren, andYaoquan Tu, “Microsecond molecular dynamics simulations provide insight into the allosteric mechanism of the Gs protein uncoupling from the β2 adrenergic receptor”,Journal of Physical ChemistryB118, 14737(2014).
42. Lu Sun, Xin Li, Thomas Hede,Yaoquan Tu, Caroline Leck, and Hans Ågren, “Molecular dynamics simulations reveal the assembly mechanism of polysaccharides in marine aerosols”,Physical Chemistry Chemical Physics16, 25935(2014).
43. Lijun Liang, Zhisen Zhang, Jiawei Shen, Zhe Kong, Qi Wang, Tao Wu, Hans Ågren, andYaoquan Tu, “Theoretical studies on the dynamics of DNA fragment translocation through multilayer graphene nanopores”,RSC Advances4, 50494(2014).
44. Xianqiang Sun, Hans Ågren, andYaoquan Tu, “Functional water molecules in rhodopsin activation”,Journal of Physical ChemistryB118, 10863(2014).
45. Yu Kang, Zhisen Zhang, Hui Shi, Junqiao Zhang, Lijun Liang, Qi Wang, Hans Ågren, andYaoquan Tu, “Na+ and K+ ion selectivity by size-controlled biomimetic graphene nanopores”,Nanoscale6, 10666(2014).
46. Yan Wang, Jakob Wohlert, Lars A. Berglund,Yaoquan Tu, and Hans Ågren, “Molecular dynamics simulations of strong interaction mechanisms at wet interfaces in clay-polysaccharide nanocomposites”,Journal of Materials ChemistryA2, 9541(2014).
47. Zhisen Zhang, Jiawei Shen, Hongbo Wang, Qi Wang, Junqiao Zhang, Lijun Liang, Hans Ågren, andYaoquan Tu, “Effect of graphene nanopore geometry on DNA sequencing”,Journal of Physical Chemistry Letters5, 1602(2014).
48. Xianqiang Sun, Lei Cheng, Yaozong Li, Weihua Li, Guixia Liu,Yaoquan Tu, and Yun Tang, “Structure-based ensemble QSAR building: A new approach to the study of the EGFR tyrosine kinase and its inhibitors”,Acta Pharmacologica Sinica35, 301(2014).
49. Lu Sun, Thomas Hede,Yaoquan Tu, Caroline Leck, and Hans Ågren, “Combined effect of glycine and sea salt on aerosol cloud droplet activation predicted by molecular dynamics simulations”,Journal of Physical ChemistryA117, 10746(2013).
50. Xin Li, Caroline Leck, Lu Sun, Thomas Hede,Yaoquan Tu, and Hans Ågren, “Cross-linked polysaccharide assemblies in marine gels − an atomistic simulation”,Journal of Physical Chemistry Letters4, 2637(2013).
51. Li Gao, Xianqiang Sun,Yaoquan Tu, Hans Ågren, and Leif A. Eriksson, “Modification of the anti-cancer drug tamoxifen to avoid CYP2D6 polymorphism”,CanadianJournal of Chemistry91, 916(2013).
52. Xin Li, Thomas Hede, Caroline Leck,Yaoquan Tu, and Hans Ågren, “Cloud droplet activation mechanisms of amino acid aerosol particles: insight from molecular dynamics simulations”,TELLUSB65, 20476(2013).
53. Thomas Hede, Caroline Leck, Lu Sun,Yaoquan Tu, and Hans Ågren, “A theoretical study revealing the promotion of light-absorbing carbon particles solubilization by natural surfactants in nanosized water droplets”,Atmospheric Science Letters14, 86(2013).
54.  Lijun Liang, Peng Cui, Qi Wang, Tao Wu, Hans Ågren, andYaoquan Tu, “Theoretical study on key factors in DNA sequencing with graphene nanopores”,RSC Advances3, 2445(2013).
55. Li Gao,Yaoquan Tu, Hans Ågren, and Leif A. Eriksson, “Characterization of agonist binding to His524 in the estrogen receptor α ligand binding domain”,Journal of Physical ChemistryB116, 4823(2012).
56.  Lu Sun, Xin Li, Thomas Hede,Yaoquan Tu, Caroline Leck, and Hans Ågren, “Molecular dynamics simulations of the surface tension and structure of salt solutions and clusters”,Journal of Physical ChemistryB116, 3198(2012).
57. Li Gao,Yaoquan Tu, and Leif A. Eriksson, “More stable, more estrogenic: the SERM-ERα LBD complex”,Journal of Biophysical Chemistry2, 233(2011).
58. Li Gao,Yaoquan Tu, Pia Wegman, Sten Wingren, and Leif A. Eriksson, “A mechanistic hypothesis for the cytochrome P450-catalyzed cis-trans isomerization of 4-hydroxytamoxifen – an unusual redox reaction”,Journal of Chemical Information and Modeling51, 2293 (2011).
59. Liming He, Yunxia Zhu, Meng Zhang, andYaoquan Tu, “A new relativistic Hartree-Fock calculation scheme and its application to the evaluation of fine-structure intervals for nd (n=3~40) series of sodium”,Journal of PhysicsB44, 225007(2011).
60. Qiong Zhang, Harry Brumer, Hans Ågren, andYaoquan Tu, “The adsorption of xyloglucan on cellulose: Effects of explicit water and side chain variation”,Carbohydrate Research346, 2595(2011).
61. Thomas Hede, Xin Li, Caroline Leck,Yaoquan Tu, and Hans Ågren, “Model HULIS compounds in nanoaerosol clusters — investigations of surface tension and aggregate formation using molecular dynamics simulations”,Atmospheric Chemistry and Physics11, 6549(2011).
62. Xin Li, Thomas Hede,Yaoquan Tu, Caroline Leck, and Hans Ågren, “Glycine in aerosol water droplets: A critical assessment of Köhler theory by predicting surface tension from molecular dynamics simulations”,Atmospheric Chemistry and Physics11, 519(2011).
63. Qiong Zhang, Vincent Bulone, Hans Ågren, andYaoquan Tu, “A molecular dynamics study of the thermal response of crystalline cellulose Iβ”,Cellulose18, 207(2011).
64. Li Gao,Yaoquan Tu, Pia Wegman, Sten Wingren, and Leif A. Eriksson, “Conformational enantiomerization and estrogen receptor α binding of anti-cancer drug tamoxifen and its derivatives”,Journal of Chemical Information and Modeling51, 306(2011).
65. Xin Li, Qiong Zhang,Yaoquan Tu, Hans Ågren, and He Tian, "Modulation of Iridium(III) phosphorescence via photochromic ligands: A density functional theory study”,Physical Chemistry Chemical Physics12, 13730(2010).
66. Yu Kang, Xin Li,Yaoquan Tu, Qi Wang, and Hans Ågren, "On the mechanism of protein adsorption onto hydroxylated and nonhydroxylated TiO2 surfaces",Journal of Physical ChemistryC114, 14496(2010).
67. Hui Lu,Yaoquan Tu, Xian Lin, Bin Fang, Duanbin Luo, and Aatto Laaksonen, “Effects of laser irradiation on the structure and optical properties of ZnO thin films”,Materials Letters64, 2072(2010).
68. Qiong Zhang,Yaoquan Tu, He Tian, Yanli Zhao, Fraser Stoddart, and Hans Ågren, “Working mechanism for a redox switchable molecular machine based on cyclodextrin: A free energy profiles approach”,Journal of Physical ChemistryB114, 6561(2010).
69. Xin Li,Yaoquan Tu, He Tian, and Hans Ågren, “Computer simulations of aqua metal ions for accurate reproduction of hydration free energies and structures”,Journal of Chemical Physics132, 104505(2010).
70. Xin Li, Thomas Hede,Yaoquan Tu, Caroline Leck, and Hans Ågren, “Surface-activecis-pinonic acid in atmospheric droplets: A molecular dynamics study”,The Journal of Physical Chemistry Letters1, 769(2010).
71. Boxue Tian,Yaoquan Tu, Åke Strid, and Leif A. Eriksson, “Hydroxylation and ring-opening mechanism of an unusual flavoprotein monooxygenase, 2-methyl-3-hydroxypyridine-5-carboxylic acid oxygenase: A theoretical study”,Chemistry – A European Journal16, 2557(2010).
72. Yaoquan Tu, Viviane Costa Felicíssimo, Freddy Fernandes Guimarães, Hans Ågren, and Faris Gel’mukhanov, “Mechanical action of infrared light on atoms and molecules through a rectification of the electric force”,Physica Scripta80, 055801(2009).
73. Xin Li, Zilvinas Rinkevicius,Yaoquan Tu, He Tian, and Hans Ågren, “Paramagnetic enhancement of 19F NMR chemical shifts in fluorinated cysteine by O2: A theoretical study”,Journal of Physical ChemistryB113, 10916(2009).
74. Ke Zhao,Yaoquan Tu, and Yi Luo, “Molecular dynamics and quantum chemistry study on conformations and optical properties of hydrogen bonded dipolar merocyanine dyes”,Journal of Physical ChemistryB113, 10271(2009).
75. Guangde Tu,Yaoquan Tu, Olav Vahtras, and Hans Ågren, “Core electron chemical shifts of hydrogen-bonded structures”,Chemical Physics Letters468, 294(2009).
76. Xin Li, Zilvinas Rinkevicius,Yaoquan Tu, He Tian, and Hans Ågren, “Nuclear magnetic shielding of 113Cd(II) ion in aqua solution: A combined molecular dynamics/density functional theory study”,Journal of Physical ChemistryB112, 11347(2008).
77. Yanli Feng, Qiong Zhang, Wenjuan Tan, Deqing Zhang,Yaoquan Tu, Hans Ågren, and He Tian, “A supramolecular photoswitch constructed by intermolecular hydrogen bond between BTEPy and TTF-COOH”,Chemical Physics Letters455, 256(2008).
78. Kai Liu, Yanhua Wang,Yaoquan Tu, Hans Ågren, and Yi Luo, “Two-photon absorption of hydrogen-bonded octupolar molecular clusters”,Journal of Physical ChemistryB112, 4387(2008).
79. Qiong Zhang,Yaoquan Tu, He Tian, and Hans Ågren, “Molecular dynamics simulations of polycarbonate doped with Lemke chromophores”,Journal of Physical ChemistryB111, 10645(2007).
80. Qiong Zhang,Yaoquan Tu, He Tian, and Hans Ågren, “Molecular dynamics simulations of local field factors”,Journal of Chemical Physics127, 014501(2007).
81. Kai Liu, Yanhua Wang,Yaoquan Tu, Hans Ågren, and Yi Luo, “Aggregation effects on two-photon absorption spectra of octupolar molecules”,Journal of Chemical Physics127, 026101(2007).
82. Yaoquan Tu,Qiong Zhang, and Hans Ågren, “Electric field poled polymeric nonlinear optical systems: Molecular dynamics simulations of poly(methyl methacrylate) doped with disperse red chromophores”,Journal of Physical ChemistryB111, 3591(2007).
83. Yaoquan Tu,Sven P. Jacobsson, and Aatto Laaksonen, “Efficientab initiotight-binding-like electronic structure calculation method”,Physical ReviewB74, 205104(2006).
84. Yaoquan Tu, Yi Luo, and Hans Ågren, “Molecular dynamics simulations applied to electric field induced second harmonic generation in dipolar chromophore solutions”,Journal of Physical ChemistryB110, 8971(2006).
85. Yaoquan Tu, Yi Luo, and Hans Ågren, “Can octupolar molecules be poled by an external electric field?”,Journal of Physical ChemistryB109, 16730(2005).
86. Yaoquan Tuand Aatto Laaksonen, “Quantum chemistry study of monomer electronic properties in water clusters and liquid water and methanol”,International Journal of Quantum Chemistry102, 888(2005).
87. Yaoquan Tu, Sven P Jacobsson, and Aatto Laaksonen, “Re-examination of the NDDO approximation and introduction of a new model beyond it”,Molecular Physics101, 3009(2003).
88. Yaoquan Tuand Aatto Laaksonen, “Atomic charges in molecular mechanical force field: A theoretical insight”,Physical ReviewE64, 026703-1(2001).
89. Yaoquan Tuand Aatto Laaksonen, “The electronic properties of water molecules in water clusters and liquid water”,Chemical Physics Letters329, 283(2000).
90. Yaoquan Tuand Aatto Laaksonen, “Combined Hartree-Fock quantum mechanical and molecular mechanical molecular dynamics simulations of water at ambient and supercritical conditions”,Journal of Chemical Physics113, 11264(2000).
91. Yaoquan Tuand Aatto Laaksonen, “On the effect of Lennard-Jones parameters on the quantum mechanical and molecular mechanical coupling in a hybrid molecular dynamics simulation of liquid water”,Journal of Chemical Physics111, 7519(1999).

Peer-reviewed conference contributions:

1. Yaoquan Tu, Lennart Nilsson, and Aatto Laaksonen, “A highly efficientab initiotight-binding-like approximate density-functional quantum mechanical method”,Lecture Notes in Computer Science4699, 100(2007).
2. Hans Ågren,Yaoquan Tu, and Yi Luo, “Modeling non-linear optical effects in guest-host systems”,Chinese Optical Letters3, S17(2005).

Review articles, book chapters:

1. Muzammal Hussain, Yang Zhou, Yu Song, H.M. Adnan Hameed, Hao Jiang,Yaoquan Tu, and Jiancun Zhang, "ATAD2 in cancer: A pharmacologically challenging but tractable target",Expert Opinion on Therapeutical Targets22, 85(2017).
2. Lijun Liang, Qi Wang, Hans Ågren, andYaoquan Tu, “Computational studies of DNA sequencing with solid-state nanopores: key issues and future prospects”,Frontiers in Chemistry2, 5(2014).
3. Yaoquan Tuand Aatto Laaksonen, “Implementing quantum mechanics into molecular mechanics: combined QM/MM calculation methods”, inAdvances in Quantum Chemistry59(Elsevier Academic Press Inc., San Diego, 2010), pp. 1-15.  
4. Alexander Lyubartsev,Yaoquan Tu, and Aatto Laaksonen, “Hierarchical multiscale modelling scheme from first principles to mesoscale”,Journal of Computational and Theoretical Nanoscience6, 951(2009).
5. Hans Ågren andYaoquan Tu, “Modeling of non-linear optical properties of guest-host systems”,Nonlinear Optics, Quantum Optics35, 39(2006).
6. Yaoquan Tuand Aatto Laaksonen, “Towards fast and reliable quantum chemical modelling of macromolecules”, in “New Algorithms of Macromolecular Simulations”, Lecture Notes in Computational Science and Engineering49(Springer Press 2005), pp. 315-341.
7. Aatto Laaksonen andYaoquan Tu, “Methods of incorporating quantum mechanical calculations into molecular dynamics simulations”, in“Molecular Dynamics: From Classical to Quantum Methods”(Elsevier Science, Amsterdam, 1999), pp. 1-29.