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Publications with KeyLAB affiliation

  1. Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, Toan T. Nguyen*, and Mai Suan Li*, 2024, Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2, Journal of Chemical Physics, 160(5), 055101, DOI: 10.1063/5.0188053. Highlighted in Scilight 2024, 051107 (2024), DOI: 10.1063/10.0024758
  2. Simone Albani, Elisa Costanzi, Gia Linh Hoang, Maria Kuzikov, Marcus Frings, Narjes Ansari, Nicola Demitri, The Toan Nguyen, Valerio Rizzi, Jörg Bernhard Schulz, Carsten Bolm, Andrea Zaliani, Paolo Carloni, Paola Storici, Giulia Rossett, 2023, Unexpected single ligand occupancy and negative cooperativity in the SARS-CoV-2 Main protease, Journal of Chemical Information and Modeling, 64(3), 892–904, selected for Front Cover. DOI: 10.1021/acs.jcim.3c01497.
  3. Thuy-Trang Nguyen*, Cao Cong-Phuong, Phong Le-Hoang, Linh Nguyen-Hoang, Nam Vu-Hoang, Toan Nguyen The, and Thang Phan Bach, 2023, H2 adsorption isotherms of Mg-MOF-74 isoreticulars: An integrated approach utilizing a thermochemical model and density functional theory, Communication in Physics, 33(4), 421-443, 10.15625/0868-3166/18859.
  4. Thong Nguyen-Minh Le*, Thu Nguyen-Bao Le, Phat Nguyen Tan, Trang Nguyen Thuy, Quang Ngoc Tran, Toan Nguyen The, Yoshiyuki Kawazoe, Thang Phan Bach, Duc Nguyen Manh, 2023, Insight into the direct conversion of methane to methanol on modified ZIF-204 from the perspective of DFT-based calculations, RSC Advances, 13, 15926-15933, DOI: 10.1039/d3ra02650g.
  5. Hien T. T. Lai, and Toan T. Nguyen*, 2023, Investigating structural features of dimeric SARS-CoV-2 Mpro catalytic site with bound covalent ligands at physiological temperature, J. Phys. Conf. Series, 2485(1), 012006, DOI: 10.1088/1742-6596/2485/1/012006.
  6. Trang Nguyen-Thuy*, Thong Le Nguyen Minh, Toan The Nguyen, Thang Bach Phan and Duc Nguyen-Manh, 2023, H2 physisorption in fluorinated MOF-74: Mutual influences between fluorine center and framework from the perspective of electronic structure calculations, Journal of Hydrogen Energy, 48(24), 8997-9007; DOI: 10.1016/j.ijhydene.2022.11.222
  7. Nam Hoang Vu*, Hieu Van Le, Thang Bach Phan, Nam Thoai, Toan The Nguyen, Hung Minh Le, Yoshiyuki Kawazoe, and Thi Minh Cao*, 2022, Emergence of Different Replica Dirac Cones and Intra- and Intervalley Scatterings in Short-Wavelength Graphene Superlattices Modulated by an Atomic-Scale Sharp Potential, J. Phys. Chem. C, 126(36), 15415-15423, DOI: 1021/acs.jpcc.2c03176
  8. Hien T. T. Lai, Ly H. Nguyen, Anh D. Phan, Agata Kranjc*, Toan T. Nguyen*, and Duc Nguyen-Manh, 2022, A comparative study of receptor interactions between SARS-CoV and SARS-CoV-2 from molecular modelling, Journal of Molecular Modelling, 28, 305, DOI: 1007/s00894-022-05231-7
  9. Hanh Hong Mai*, Van Huy Hoang, Manh Quynh Luu, Trong Tam Nguyen, Hoang Nam Nguyen, Do Xuan Tien, Giang Manh Khoi, Toan T. Nguyen, Youngwoon Choi, Wonshik Choi, Van Duong Ta, 2022, Magnetic nanoparticles embedded in microlasers for controlled transport in different sensing media, Journal of Physics D: Applied Physics, 55, 405106, DOI: 10.1088/1361-6463/ac835f
  10. Toan T. Nguyen*, Tran Huu Phat, 2022, Asymptotic critical behavior of holographic superconductor phase transition – the spectrum of excited states becomes continuous at T=0, Journal of High Energy Physics, 2022(6), 04, DOI: 10.1007/JHEP06(2022)004.
  11. Hien T. T. Lai, Ha M. Do∗, and Toan T. Nguyen*, 2022, Evaluation of Colchicine’s interaction with the ATP-binding region of mice NLRP3-NACHT domain using molecular docking and dynamics simulation, J. Phys. Conf. Series, 2269, 012012, DOI: 10.1088/1742-6596/2269/1/012012.
  12. Oanh P. Pham, Hien T. T. Lai, Duong B. Tran, Linh T. P. Le, Anh Thi Van Nguyen*, Hang Thi Thu Nguyen, Toan T. Nguyen*, 2022, Investigation of Allopurinol binding mechanism to allele HLA-A*33:03 by using Molecular Dynamics simulation, J. Phys. Conf. Series, 2269, 012011, DOI:10.1088/1742-6596/2269/1/012011.
  13. Linh Hoang, Jonas Goßen, Riccardo Capelli*, Toan T. Nguyen, Zhaoxi Sun, Ke Zuo, Jörg B. Schulz, Giulia Rossetti*, Paolo Carloni, 2022, Multiple poses and thermodynamics of ligands targeting protein surfaces: the case of furosemide binding to mitoNEET in aqueous solution, Frontiers in Cell and Developmental Biology, 10, 886568, DOI:10.3389/fcell.2022.886568.
  14. Hanh Hong Mai, Trong Tam Nguyen, Tien Thinh Nguyen, Thanh Thuy To, Toan T. Nguyen, Youngwoon Choi, Wonshik Choi, Van Duong Ta, 2022, Random lasers from the natural inverse photonic glass structure of Artemia eggshells, Journal of Physics D: Applied Physics, 55(29), 295104, DOI: 10.1088/1361-6463/ac6a25.
  15. Viet-Anh Tran, Phuong-Anh Tran, Hung Q. Nguyen, Giang H. Bach*, Toan T. Nguyen, 2022, Boundary-scattering induced Seebeck coefficient enhancement in thin films within relaxation time approximation, Physica B, 635, 413800, DOI: 10.1016/j.physb.2022.413800
  16. Thanh Tung Bui*, Bao Kim Nguyen, Minh Ngoc Le, The Toan Nguyen, The Hai Pham, 2021, In silico screening of drug inhibitors of SARS-CoV-2 RNA-dependent RNA polymerase target, Vietnam Journal of Science, Technology, and Engineering, 63(4), 47, DOI: 10.31276/VJSTE.63(4).47-54
  17. Vu Dang Hoang*, Cao Phuong Cong, Hung Huu Tran, Hue Minh Thi Nguyen, Toan T. Nguyen*, 2021, Influence of fatty alcohol mixing ratios on physicochemical properties of stearyl–cetyl–polysorbate 60–water ternary system: Insights from experiments and computer simulations, Colloid and Polymer Science, 299(5), 1885–1900, DOI:10.1007/s00396-021-04874-x
  18. D. N. Dung, Anh D. Phan*, Toan T. Nguyen, and Vu D. Lam, 2021, Effects of surface charge and environmental factors on the electrostatic interaction of fiber with virus-like particle: A case of coronavirus, AIP Advances, 11, 105008, DOI:10.1063/5.0065147
  19. Tran Huu Phat*, Toan T. Nguyen, 2021, On the holographic phase transitions at finite topological charge, European Physical Journal C, 81(5), 428, DOI: 10.1140/epjc/s10052-021-09141-5
  20. Hien T. T. Lai, Toan T. Nguyen*, 2021, Construction of dimeric hTSPO protein model using homology modelling and molecular dynamics, J. Phys. Conf. Ser., 1932, 012016, DOI: 10.1088/1742-6596/1932/1/012016
  21. Hien T. T. Lai, Alejandro Giorgetti, Giulia Rossetti, Toan T. Nguyen*, Paolo Carloni, Agata Kranjc*, 2021, The Interplay of Cholesterol and Ligand Binding in hTSPO from Classical Molecular Dynamics Simulations, Molecules, 26 (5), 1250, DOI: 10.3390/molecules26051250
  22. Trang Thuy Nguyen*, Phong Hoang Le, Nam Hoang Vu, Thong Nguyen-Minh Le, Tan Le Hoang Doan, Jer-Lai Kuo, Toan The Nguyen*, Thang Bach Phan and Duc Nguyen-Manh, 2020, Hydrogen adsorption mechanism of MOF-74 metal organic frameworks: An insight from first principles calculations, RCS Advances; 10(72), 43940-43949, DOI:10.1039/d0ra08864a
  23. Kim My Tran, Dinh Phuc Do, Hoang Nam Vu, Toan T Nguyen, Bach Thang Phan, Kieu Hanh Ta Thia*, Kim Ngoc Pham*, (2020), Experimental Combined Theoretical Study On Chemical Interactions Of Graphene Oxide with Chitosan and its Resistive-switching Effect, Materials Science & Engineering B, 262, 114788; DOI: 10.1016/j.mseb.2020.114788
  24. Hanh Hong Mai*, Tam Trong Nguyen, Khoi Manh Giang, Xuan Tien Do, Toan Nguyen, Hieu Chi Hoang, Duong Ta*, (2020), Chicken albumen based whispering gallery mode microlasers, Soft Matter, 16(39), 9069-9073; DOI: 10.1039/D0SM01091J
  25. Thao TT Nguyen, Linh T Dang, Giang H Bach, Tung H Dang, Kien T Nguyen, Hong T Pham, Thuat T Nguyen, Tuyen V Nguyen, Toan T Nguyen, Hung Q Nguyen*, (2020), Enhanced thermoelectricity at the ultra-thin film limit, Appl. Phys. Lett., 117(8), 083104; DOI: 10.1063/5.0010274
  26. Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, Toan T. Nguyen, Shikha Nangia, Phuong Nguyen*, Molecular mechanism of ultrasound interaction with a blood brain barrier mode, (2020), J. Chem. Phys., 153(4), 045104; DOI:10.1063/5.0010667
  27. Tran Ky Thanh, Toan T. Nguyen*, (2020), Computational study of μ-opioid receptor embedded in a realistic membrane, J. Phys. Conf. Series, 1506, 012023; DOI: 10.1088/1742-6596/1506/1/012023
  28. Le Thi Hai Yen, Tran Thanh Tuyen, Nguyen Viet Duc, Nguyen Quang Bau, Toan T. Nguyen* (2020), Numerical solution for the counterions distribution in a hexagonal DNA lattice within mean field theory using finite element method, Materials Transactions, 61(8), 1455-1461; DOI: 10.2320/matertrans.MT-MN2019020
  29. Vu H. Nam*, Le V. Hieu, Phan B. Thang, Nguyen T. Toan, Thoai, Nam, Cao, Thi Minh (2020), Effect of Surface States and Breakdown of the Schottky-Mott Limit of Graphene/Silicon van der Waals Heterostructure, Journal of Physical Chemistry C, 124 (16) 8958-8970; DOI: 10.1021/acs.jpcc.0c01257
  30. Ly H. Nguyen, Tuyen T. Tran, Lien Thi Ngoc Truong, Hanh Hong Mai, and Toan T. Nguyen*, (2020), Overcharging of zinc ion in the structure of zinc−finger protein is needed for DNA binding stability, Biochemistry, 59(13), 1378-1390; DOI: 10.1021/acs.biochem.9b01055, selected as cover story for April 2020 issues of Biochemistry.
  31. Hien T. T. Lai, Ha M Do*, Duc Manh Nguyen, and Toan T. Nguyen*, (2020), Homology modeling of mouse NLRP3 NACHT protein domain and molecular dynamics simulation of its ATP binding properties, International Journal of Modern Physics C, 31(3), 2050036; DOI: 10.1142/S0129183120500369.
  32. Vu Dang Hoang, Tran Huu Hung, Cao Phuong Cong, Hue Minh Thi Nguyen, and Toan T. Nguyen*, (2020), Investigating molecular mechanism for the stability of ternary systems containing cetrimide, fatty alcohol and water by using computer simulation, Journal of Molecular Graphics and Modeling, 95, 107500; DOI: 10.1016/j.jmgm.2019.107500, Jeffry D. Madura Memorial Graphics Prize 2021.
  33. Hien T. T. Lai, L. H. Nguyen, A. Kranjc, Toan T. Nguyen, D. Nguyen-Manh (2020), Elucidating the differences in the molecular mechanism of receptor binding between 2019-nCoV and the SARS-CoV viruses using computational tools, bioRxiv preprint, DOI: 10.1101/2020.04.21.053009
  34. Nguyen Viet Duc, Ly Hai Nguyen, Hien T. T. Lai, Toan T. Nguyen* (2019), Computational study of the effect of protonation states of PSA protein zinc fingers on its DNA binding, J. Phys. Conf. Series, 1274, 012002; DOI: 10.1088/1742-6596/1274/1/012002
  35. Nguyen Viet Duc, Toan T. Nguyen* (2019), Size Effect in Grand-canonical Monte-Carlo Simulation of Solutions of Electrolyte, VNU Journal of Science, Math.-Phys. 35, 13-21; DOI: 10.25073/2588-1124/vnumap.4296
  36. Nguyen Vu Nhan*, Nguyen Viet Duc, Toan T. Nguyen, (2019), The phenomena of charge inversion and effective attraction between the spherical macromolecules in electrolyte solvent, Scientific journal of Hanoi Metropolitan University, 35, 42-53.
  37. Fabrizio Fierro, Alejandro Giorgetti, Paolo Carloni, Wolfgang Meyerhof & Mercedes Alfonso-Prieto, Dual binding mode of “bitter sugars” to their human bitter taste receptor target, Scientific Report, 9, 8437.
  38. Mercedes Alfonso-Prieto, Luciano Navarini, Paolo Carloni, 2019, Understanding Ligand Binding to G-Protein Coupled Receptors Using Multiscale Simulations, Frontiers in Molecular Bioscience, 6, 29.
  39. Mercedes Alfonso-Prieto, Alejandro Giorgetti, Paolo Carloni, 2019, Multiscale simulations of human Frizzled and Taste2 GPCRs, Current Opinion in Structural Biology, 55, 8-16.
  40. Hoang Gia Linh*, Nguyen Thuy Trang, Nguyen The Toan, Doan Le Hoang Tan, and Nguyen Manh Duc (2018), A systematic study of electronic structure for anti-cancer drug molecule 5-Fluorouracil within various solvents from first-principles calculations” V. Van Toi et al. (eds.), 7th International Conference on the Development of Biomedical Engineering in Vietnam (BME7), IFMBE Proceedings 69, 721-726.
  41. Dung Nguyen Trong*, Cuong Nguyen Chinh, Toan Nguyen The, Hung Pham Khac, (2018), Factors on the Magnetic Properties of the Iron Nanoparticles by Classical Heisenberg Model, Physica B, 532, 144.
  42. Jakob Schneider, Ksenia Korshunova, Francesco Musiani, Mercedes Alfonso-Prieto, Alejandro Giorgettia, Paolo Carloni, 2018, Predicting ligand binding poses for low-resolution membrane protein models: prespectives frommultiscale simulations, Biochemical and Biophysical Research Communications, 498(2), 366-374.
  43. Viet Duc Nguyen, Toan T. Nguyen*, Paolo Carloni, (2017), DNA like-charge attraction and overcharging by divalent counterions in the presence of divalent co-ions, J. Biol. Phys., 43, 185–195.
  44. Nguyen V Duc, Toan T Nguyen* (2017), Grand−canonical Monte−Carlo simulation of DNA condensation in equilibrium with a salt mixture containing 2:2 salt, J. Phys. Conf. Ser., 865, 012010.
  45. Eda Suku, Fabrizio Fierro, Alejandro Giorgetti, Mercedes Alfonso-Prieto, Paolo Carloni, 2017, Multi-scale simulations of membrane proteins: The case of bitter taste receptors, Journal of Science: Advanced Materials and Devices, 2, 15-21.
  46. Vu Van Quyen, Vu Thi Hai Yen, Toan T. Nguyen* (2016), Screening of a small spherical macroion by oppositely charged flexible polyelectrolyte, Comm. Phys. 26, 287.
  47. Nguyen, T. T., (2016), Grand-canonical simulation of DNA condensation with two salts, effect of divalent counterion size, Journal of Chemical Physics 144(6), 065102, DOI:10.1063/1.4940312.

Preprints

  1. Hien T. T. Lai, L. H. Nguyen, A. Kranjc, Toan T. Nguyen, D. Nguyen-Manh, 2020, Elucidating the differences in the molecular mechanism of receptor binding between 2019-nCoV and the SARS-CoV viruses using computational tools,bioRxiv preprint, DOI: 10.1101/2020.04.21.053009.
  2. Toan T. Nguyen, 2017, Grand-canonical Monte-Carlo simulation of solutions of salt mixtures: theory and implementation, arxiv:1705.08840 [cond-mat.soft].

Publications related to the KeyLAB

  1. Duc Minh Tran, Van-Duy Nguyen, Le Bin Ho, Hung Q. Nguyen, 2023, Increased success probability in Hardy’s nonlocality: Theory and demonstration (Editors’ Suggestion), Physical Review A 107, 042210.
  2. Phuong Thuy Bui, and Trinh Xuan Hoang, 2020, Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape, J. Chem. Phys. 153, 045105, DOI: 10.1063/5.0008292.
  3. Le Sy Vinh, Nguyen Duc Canh, Bui Ngoc Thang, Duong Quoc Chinh, Tran Cong Hoang, Do Thi Thu Hang, Le Ba Hong Minh, Pham Thi Dieu Linh, 2018, Genomedics: Whole exome analysis system for clinical studies, The 9th International Conference on Knowledge and Systems Engineering, IEEE CPS, 142.
  4. Sy Vinh Le, Phan Hoang Truc Le, Thi Khanh Van Le, Thi Thuy Kieu Huynh, Thi Thu Hang Do, 2017, A mutation in GABRB3 associated with Dravet syndrome, Am J Med Genet Part A., 9999:1–6, DOI: 10.1002/ajmg.a.38282