2024

  1. Thu, T. T. M.; Phung, H. N. T.; Co, N. T.; Kloczkowski, A.; Li, M. S. Key factors controlling fibril formation of proteins. Acta Physica Polonica A, 2024, 145(3). DOI: 10.12693/APhysPolA.145.S21.
  2. Nguyen, H. L.; Nguyen, T. Q.; Li, M. S. SARS-CoV-2 Omicron subvariants do not differ much in binding affinity to human ACE2: A molecular dynamics study. J. Phys. Chem. B, 2024, 128, 14, 3340–3349. DOI: 10.1021/acs.jpcb.3c06270.
  3. Lan, P. D.; Nissley, D. A.; Sitarik, I.; Vu, Q. V.; Jiang, Y.; To, P.; Xia, Y.; Fried, S. D.; Li, M. S.; O'Brien, E. P. Synonymous mutations can alter protein dimerization through localized interface misfolding involving self-entanglements. J. Mol. Biol., 168487 (2024). DOI: 10.1016/j.jmb.2024.168487.
  4. Lan, P. D.; Nissley, D. A.; O'Brien, E. P.; Nguyen, T. T.; Li, M. S. Deciphering the free energy landscapes of SARS-CoV-2 wild type and Omicron variant interacting with human ACE2. J. Chem. Phys. 160, 055101 (2024). DOI: 10.1063/5.0188053. This work is highlighted in Scilight. DOI: 10.1063/10.0024758.

    5. 2023

  5. Nguyen, H.; Nguyen, H. L.; Lan, P. D.; Thai, N. Q.; Sikora, M.; Li, M. S. Interaction of SARS-CoV-2 with Host Cells and Antibodies: Experiment and Simulation. Chem. Soc. Rev. 2023, 52 (18), 6497–6553. DOI: 10.1039/D1CS01170G
  6. Pawel Krupa, Giovanni La Penna, and Mai Suan Li. Amyloid-β Tetramers and Divalent Cations at the Membrane/Water Interface: Simple Models Support a Functional Role. Int. J. Mol. Sci. 2023, 24(16), 12698. DOI: 10.3390/ijms241612698
  7. Ritaban Halder, Daniel A. Nissley, Ian Sitarik, Yang Jiang, Yiyun Rao, Quyen V. Vu, Mai Suan Li, Justin Pritchard, and Edward P. O’Brien. How soluble misfolded proteins bypass chaperones at the molecular level. Nat. Commun. 14, 3689 (2023). DOI: 10.1038/s41467-023-38962-z
  8. Alexander M Gabovich, Alexander I Voitenko, Toshikazu Ekino, Akira Sugimoto, Daiki Yoshida, Takeshi Saito, Mai Suan Li, Henryk Szymczak. Coexistence of superconductivity and charge-density waves: evidence from tunneling studies. Low Temperature Physics/Fizyka Nyzkykh Temperatur, 2023, Vol. 49, No. 7, pp. 881–898. Read more
  9. Quyen V. Vu, Daniel A. Nissley, Yang Jiang, Edward P. O’Brien, and Mai Suan Li. Is Posttranslational Folding More Efficient Than Refolding from a Denatured State: A Computational Study. J. Phys. Chem. B 2023, 127, 21, 4761–4774. DOI: 10.1021/acs.jpcb.3c01694
  10. Ankur Gupta, Pawel Krupa, Oskar Engberg, Magdalena Krupa, Ankur Chaudhary, Mai Suan Li, Daniel Huster, and Sudipta Maiti. Unusual Robustness of Neurotransmitter Vesicle Membranes against Serotonin-Induced Perturbations. J. Phys. Chem. B 2023, 127, 9, 1947–1955. DOI: 10.1021/acs.jpcb.2c07464

    11. 2022

  11. Nguyen Hoang Linh, Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux, Thi Ly Mai, and Phuong H. Nguyen. Molecular dynamics simulation of cancer cell membrane perforated by shockwave induced bubble collapse , J. Chem. Phys. 157, 225102 (2022). DOI: 10.1063/5.0105675
  12. Hoang Linh Nguyen, Nguyen Quoc Thai and Mai Suan Li. Identifying inhibitors of NSP16-NSP10 of SARS-CoV-2 from large databases , Journal of Biomolecular Structure and Dynamics. DOI: 10.1080/07391102.2022.2114941
  13. Pamela Smardz, Adam K. Sieradzan, and Paweł Krupa. Mechanical Stability of Ribonuclease A Heavily Depends on the Redox Environment. J. Phys. Chem. B 2022, 126, 33, 6240–6249. DOI: 10.1021/acs.jpcb.2c04718
  14. Tran Thi Minh Thu and Mai Suan Li. Protein aggregation rate depends on mechanical stability of fibrillar structure , J. Chem. Phys. 157, 055101 (2022). DOI: 10.1063/5.0088689
  15. A. M. Gabovich , M. S. Li, H. Szymczak , A. I. Voitenko. Charge-charge interaction in three-layer systems: Classical approach , Phys.Rev. B 105, 115415 (2022). DOI: 10.1103/PhysRevB.105.115415
  16. Hoang Linh Nguyen, Nguyen Quoc Thai, Phuong H. Nguyen, and Mai Suan Li. SARS-CoV-2 Omicron Variant Binds to Human Cells More Strongly than the Wild Type: Evidence from Molecular Dynamics Simulation , J. Phys. Chem. B 2022, 126, 25, 4669–4678. DOI: https://doi.org/10.1021/acs.jpcb.2c01048
  17. Hung Nguyen & Mai Suan Li. Antibody–nanobody combination increases their neutralizing activity against SARS-CoV-2 and nanobody H11-H4 is effective against Alpha, Kappa and Delta variants , Scientific Reports volume 12, Article number: 9701 (2022). DOI: https://doi.org/10.1038/s41598-022-14263-1
  18. Hoang Linh Nguyen, Huynh Quang Linh, Pawel Krupa, Giovanni La Penna, and Mai Suan Li Amyloid β Dodecamer Disrupts the Neuronal Membrane More Strongly than the Mature Fibril: Understanding the Role of Oligomers in Neurotoxicity , J. Phys. Chem. B 2022, 126, 20, 3659–3672. DOI: https://doi.org/10.1021/acs.jpcb.2c01769
  19. Hoang Linh Nguyen, Nguyen Quoc Thai, Mai Suan Li. Determination of Multidirectional Pathways for Ligand Release from the Receptor: A New Approach Based on Differential Evolution , J. Chem. Theory Comput. 2022. DOI: https://doi.org/10.1021/acs.jctc.1c01158
  20. Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, and Mai Suan Li. Cocktail of REGN Antibodies Binds More Strongly to SARS-CoV-2 Than Its Components, but the Omicron Variant Reduces Its Neutralizing Ability , J. Phys. Chem. B 2022, 126, 15, 2812–2823. DOI: https://doi.org/10.1021/acs.jpcb.2c00708
  21. Hoang Linh Nguyen, Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, Phuong H Nguyen. Elastic moduli of normal and cancer cell membranes revealed by molecular dynamics simulations , Phys. Chem. Chem. Phys., 2022, 24, 6225-6237. DOI: https://doi.org/10.1039/D1CP04836H
  22. Nguyen Truong Co, Mai Suan Li, Pawel Krupa. Computational Models for the Study of Protein Aggregation , Computer Simulations of Aggregation of Proteins and Peptides, Methods in Molecular Biology 2340, 51 (2022) DOI: 10.1007/978-1-0716-1546-1_4
  23. Lan Pham Dang, Daniel Allen Nissley, Ian Sitarik, Quyen Vu Van, Yang Jiang, Mai Suan Li, Edward P. O’Brien. Synonymous mutations can alter protein dimerization through localized interface misfolding involving self-entanglements , biorxiv., 2021. Preprint Available.

    24. 2021

  24. Adam Liwo, Adam K. Sieradzan, Agnieszka S. Karczyńska, Emilia A. Lubecka, Sergey A. Samsonov, Cezary Czaplewski, Paweł Krupa & Magdalena Mozolewska. Physics-Based Coarse-Grained Modeling in Bio- and Nanochemistry , Practical Aspects of Computational Chemistry V pp 31–69. DOI: https://doi.org/10.1007/978-3-030-83244-5_2
  25. Sarah E. Leininger, Judith Rodriguez, Quyen V. Vu, Yang Jiang, Mai Suan Li, Carol Deutsch, and Edward P. O’Brien. Ribosome Elongation Kinetics of Consecutively Charged Residues Are Coupled to Electrostatic Force , Biochemistry 2021, 60, 43, 3223–3235. DOI: https://doi.org/10.1021/acs.biochem.1c00507
  26. P. Krupa (co-author). Modeling the Structure, Dynamics, and Transformations of Proteins with the UNRES Force Field , Protein Folding, Methods in Molecular Biology 2376, 399 (2021), DOI: https://doi.org/10.1007/978-1-0716-1716-8_23
  27. P. Krupa (co-author). Modeling protein structures with the coarse-grained UNRES force field in the CASP14 experiment , Journal of Molecular Graphics and Modelling 108, 108008 (2021), DOI: https://doi.org/10.1016/j.jmgm.2021.108008
  28. Hong An Pham, Duc Toan Truong, and Mai Suan Li. Dependence of Work on the Pulling Speed in Mechanical Ligand Unbinding , Phys Chem B 125, 30, 8325–8330 (2021), DOI: https://doi.org/10.1021/acs.jpcb.1c01818
  29. Quyen V. Vu, Yang Jiang, Mai Suan Li, Edward O'Brien. The Driving Force for Co-translational Protein Folding is Weaker In the Ribosome Vestibule due to Greater Water Ordering , Chemical Science 2021. 12, 11851-11857. DOI: https://doi.org/10.1039/D1SC01008E
  30. Adolfo B. Poma*, Tran Thi Minh Thu, Lam Tang Minh Tri, Hoang Linh Nguyen, and Mai Suan Li*. Nanomechanical Stability of Aβ Tetramers and Fibril-like Structures: Molecular Dynamics Simulations , J. Phys. Chem. B 2021. DOI: https://doi.org/10.1021/acs.jpcb.1c02322
  31. Hung Nguyen, Pham Dang Lan, Daniel A. Nissley, Edward P. O’Brien, and Mai Suan Li*. Electrostatic Interactions Explain the Higher Binding Affinity of the CR3022 Antibody for SARS-CoV-2 than the 4A8 Antibody , J. Phys. Chem. B 2021. DOI: https://doi.org/10.1021/acs.jpcb.1c03639
  32. Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, Junmei Wang, and Phuong H. Nguyen*. Molecular Mechanism of Ultrasound-Induced Structural Defects in Liposomes: A Nonequilibrium Molecular Dynamics Simulation Study , Langmuir 2021, 37, 26, 7945–7954. DOI: https://doi.org/10.1021/acs.langmuir.1c00555. PDF
  33. N.T. Co and M. S. Li. Effect of Surface Roughness on Aggregation of Polypeptide Chains: A Monte Carlo Study , Biomolecules 11(4), 596 (2021). DOI: https://doi.org/10.3390/biom11040596
  34. Martina Banchelli, Roberta Cascella, Cristiano D’Andrea, Giovanni La Penna*, Mai Suan Li, Fabrizio Machetti, Paolo Matteini, and Silvia Pizzanelli. Probing the Structure of Toxic Amyloid-β Oligomers with Electron Spin Resonance and Molecular Modeling , ACS Chem. Neurosci. 2021, 12, 7, 1150–1161. DOI: https://doi.org/10.1021/acschemneuro.0c00714
  35. Mai Suan Li (co-author). Amyloid Oligomers: A Joint Experimental/Computational Perspective on Alzheimer’s Disease, Parkinson’s Disease, Type II Diabetes, and Amyotrophic Lateral Sclerosis , Chem. Rev. 2021. DOI: https://doi.org/10.1021/acs.chemrev.0c01122
  36. Daniela Marasco, Caterina Vicidomini, Pawel Krupa, Federica Cioffi, Pham Dinh Quoc Huy, Mai Suan Li, Daniele Florio, Kerensa Broersen, Maria Francesca De Pandis, and Giovanni N.Roviello. Plant isoquinoline alkaloids as potential neurodrugs: A comparative study of the effects of benzo[c]phenanthridine and berberine based compounds on β-amyloid aggregation, Chemico-Biological Interactions, 334, (2021). LINK
  37. P. Krupa, M. Spodzieja, A.K. Sieradzan. Prediction of CD28-CD86 protein complex structure using different level of resolution approach , Journal of Molecular Graphics and Modelling 103, 107802 (2021), doi: 10.1016/j.jmgm.2020.107802 https://doi.org/10.1016/j.jmgm.2020.107802
  38. P. Krupa, A.G. Karczyńska, M.A. Mozolewska, A. Liwo, C. Czaplewski. UNRES-Dock - protein-protein and peptide-protein docking by coarse-grained replica-exchange MD simulations , Bioinformatics 37, 1613 (2021), DOI: 10.1093/bioinformatics/btaa897 https://doi.org/10.1093/bioinformatics/btaa897

    39. 2020

  39. P. Krupa (co-author). Improved consensus-fragment selection in template-assisted prediction of protein structures with the UNRES force field in CASP13 , Journal of Chemical Information and Modeling 2020, 60, 3, 1844-1864 https://doi.org/10.1021/acs.jcim.9b00864
  40. Hoang Linh Nguyen, Thai Nguyen, Duc Toan Truong, and Mai Suan Li. Remdesivir Strongly Binds to both RNA-dependent RNA Polymerase and Main Protease of SARS-CoV-2: Evidence from Molecular Simulations, J. Phys. Chem. B 2020, 124, 50, 11337–11348. LINK
  41. Hoang Linh Nguyen, Pham Dang Lan, Nguyen Quoc Thai, Daniel A. Nissley, Edward P. O’Brien, and Mai Suan Li. Does SARS-CoV-2 Bind to Human ACE2 More Strongly Than Does SARS-CoV? J. Phys. Chem. B 2020, 124, 34, 7336–7347. LINK
  42. Hoang Linh Nguyen, Huynh Quang Linh, Paolo Matteini, Giovanni La Penna, and Mai Suan Li. Emergence of Barrel Motif in Amyloid-β Trimer: A Computational Study,J. Phys. Chem. B 2020, 124, 47, 10617–10631. LINK
  43. Man Viet Hoang, Mai Suan Li, Philippe Derreumaux, Junmei Wang, Toan T. Nguyen, S. Nangia, and Phuong H. Nguyen. Molecular mechanism of ultrasound interaction with a blood brain barrier model, J. Chem. Phys. 153, 045104 (2020). LINK
  44. Subramanian Boopathi, Pham Dinh Quoc Huy, Wendy Gonzalez, Panagiotis E. Theodorakis, Mai Suan Li. Zinc binding promotes greater hydrophobicity in Alzheimer's Aβ42 peptide than copper binding: Molecular dynamics and solvation thermodynamics studies, Proteins: Structure, Function, and Bioinformatics (2020). PDF
  45. Mai Suan Li (co-author). Nanoscopic insights into the surface conformation of neurotoxic amyloid β oligomers,RSC Advances, 10(37), pp.21907-21913. PDF
  46. Nguyen Quoc Thai, Panagiotis E. Theodorakis, and Mai Suan Li. Fast Estimation of the Blood–Brain Barrier Permeability by Pulling a Ligand through a Lipid Membrane,Journal of Chemical Information and Modeling (2020). PDF
  47. Kiet Ho, Duc Toan Truong, and Mai Suan Li. How Good is Jarzynski’s Equality for Computer-Aided Drug Design? ,The Journal of Physical Chemistry B (2020). PDF
  48. Dinh Quoc Huy Pham, Pawel Krupa, Hoang Linh Nguyen, Giovanni La Penna, and Mai Suan Li. Computational Model to Unravel the Function of Amyloid‐β Peptides in Contact with a Phospholipid Membrane, J. Phys. Chem. B. PDF
  49. Daniel A. Nissley, Quyen V. Vu, Fabio Trovato, Nabeel Ahmed, Yang Jiang, Mai Suan Li, and Edward P. O’Brien. Electrostatic Interactions Govern Extreme Nascent Protein Ejection Times from Ribosomes and Can Delay Ribosome Recycling, J. Am. Chem. Soc. 142, 13, 6103-6110 (2020).PDF
  50. Nguyen Truong Co, Pham Dang Lan, Pham Dinh Quoc Huy, and Mai Suan Li. Heat-induced degradation of fibrils: Exponential vs logistic kinetics, J. Chem. Phys. 152, 115101 (2020).PDF
  51. Miroslav Gancar, Kiet Ho, Sk. Abdul Mohid, Nguyen Quoc Thai, Zuzana Bednarikova, H. Linh Nguyen, Anirban Bhunia, Eugenie Nepovimova, Mai Suan Li, and Zuzana Gazova. 7-Methoxytacrine and 2-Aminobenzothiazole Heterodimers: Structure–Mechanism Relationship of Amyloid Inhibitors Based on Rational Design, ACS Chem. Neurosci 11, 5, 715-729 (2020). PDF

    52. 2019

  52. J. Liwo, A. Sieradzan, A. Karczyńska, A. Lipska, A. Giełdoń, C. Sikorska, C. Czaplewski, E. Lubecka, K. Zięba, M. Mozolewska, M. Ślusarz, P. Krupa, R. Slusarz, S. Samsonov, S. N. Crivelli, U. Uciechowska, Ł. Golon. Evaluation of the scale-consistent UNRES force field in template-free prediction of protein structures in the CASP13 experiment , Journal of Molecular Graphics and Modelling 2019, 92, 154-166 https://doi.org/10.1016/j.jmgm.2019.07.013
  53. Pawel Krupa (co-author). Blind prediction of homo- and hetero-protein complexes: The CASP13-CAPRI experiment , Proteins: Structure, Function, and Bioinformatics 2019, 87, 1200-1221 https://doi.org/10.1002/prot.25838
  54. Adam Liwo, Cezary Czaplewski, Adam K Sieradzan, Emilia A Lubecka, Agnieszka G Lipska, Łukasz Golon, Agnieszka Karczyńska, Paweł Krupa, Magdalena A Mozolewska, Mariusz Makowski, Robert Ganzynkowicz, Artur Giełdoń, Maciej Maciejczyk. Scale-consistent approach to the derivation of coarse-grained force fields for simulating structure, dynamics, and thermodynamics of biopolymers , Progress in molecular biology and translational science, 170, 73-122. https://doi.org/10.1016/bs.pmbts.2019.12.004
  55. Tran Thi Minh Thu, Shu-Hsiang Huang, Ly Anh Tu, Shang-Ting Fang, Mai Suan Li, Yi-Cheng Chen. G37V mutation of Aβ42 induces a nontoxic ellipse-like aggregate: An in vitro and in silico study, Neurochemistry International 129, 104512 (2019).PDF
  56. Hoang Linh Nguyen, Pawel Krupa, Nguyen Minh Hai, Huynh Quang Linh, Mai Suan Li. Structure and Physicochemical Properties of the Aβ42 Tetramer: Multiscale Molecular Dynamics Simulations, J. Phys. Chem. B 123, 34, 7253-7269 (2019).PDF
  57. Pawel Krupa , Pham Dinh Quoc Huy, and Mai Suan Li. Properties of monomeric Aβ42 probed by different sampling methods and force fields: Role of energy components ,J. Chem. Phys. 151, 055101 (2019). PDF
  58. Tran Thi Minh Thu, Nguyen Truong Co, Ly Anh Tu and Mai Suan Li. Aggregation rate of amyloid beta peptide is controlled by beta-content in monomeric state , J. Chem. Phys. 150, 225101 (2019). PDF
  59. Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux and Phuong H. Nguyen. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level , J. Chem. Phys. 150, 215101 (2019). PDF
  60. Hoang Linh Nguyen, Pham Hong An, Nguyen Quoc Thai, Huynh Quang Linh and Mai Suan Li. Erythromycin, Cethromycin and Solithromycin display similar binding affinities to the E. coli's ribosome: A molecular simulation study, Journal of Molecular Graphics and Modelling 91 (2019) 80-90. PDF
  61. Viet Hoang Man, Mai Suan Li, Junmei Wang, Philippe Derreumaux and Phuong H. Nguyen. Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion, J. Chem. Phys. 151, 024103 (2019). PDF
  62. Giovanni La Penna and Mai Suan Li. Computational models explain how copper binding to amyloid-β peptide oligomers enhances oxidative pathways, Phys Chem Chem Phys 21, 8774-8784 (2019). PDF
  63. Viet Hoang Man, Phan Minh Truong, Mai Suan Li, Junmei Wang, Nguyen-Thi Van-Oanh, Philippe Derreumaux , and Phuong H. Nguyen. Molecular Mechanism of the Cell Membrane Pore Formation Induced by Bubble Stable Cavitation, J Phys Chem B 123, 71−78 (2019). PDF
  64. Adolfo B. Poma, Horacio V. Guzman, Mai Suan Li and Panagiotis E. Theodorakis. Mechanical and thermodynamic properties of Aβ42, Aβ40, and α-synuclein fibrils: a coarse-grained method to complement experimental studies , Beilstein Journal of Nanotechnology 10, 500–513 (2019). PDF

    65. 2018

  65. E Gołaś, M Mozolewska, P Krupa, C Czaplewski, HA Scheraga, JA Liwo. Use of coarse-grained and all-atom molecular dynamics to study Hsp70 and Hsp40 chaperone action Frontiers in Structural Biology, Role of Molecular Chaperones in Structural Folding , Biological Functions, and Drug Interactions of Client Proteins http://dx.doi.org/10.2174/97816810861561180101
  66. EA Lubecka, AK Sieradzan, C Czaplewski, P Krupa, A Liwo. High performance computing with coarse grained model of biological macromolecules Supercomputing , Frontiers and Innovations 5 (2), 63-75 http://dx.doi.org/10.14529/jsfi180206
  67. A. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, K.K. Bojarski, B. Zaborowski, A. Liwo, R. Ślusarz, M. Ślusarz, J. Lee, K. Joo, and C. Czaplewski. of the UNRES force field in template-assisted prediction of proteins structures and the refinement of server models: test with CASP12 targets , Journal of Molecular Graphics and Modelling 2018, 83, 92-99 https://doi.org/10.1016/j.jmgm.2018.05.008
  68. Pawel Krupa (co-author). Formative assessment of WeFold: a framework of international collaborative pipelines for protein structure prediction , Scientific Reports 2018, 8, Article number: 9939 https://doi.org/10.1038/s41598-018-26812-8
  69. P. Krupa, D. Wales, A.K. Sieradzan. Computational Studies of the Mechanical Stability for Single-Strand Break DNA , Journal of Physical Chemistry B 2018, 122, 8166-8173 https://doi.org/10.1021/acs.jpcb.8b05417
  70. E. Faraggi, P. Krupa, M.A. Mozolewska, A. Liwo, A. Kloczkowski. Re-optimized UNRES Potential for Protein Model Quality Assessment , Genes 2018, 9, 601 https://doi.org/10.3390/genes9120601
  71. A.S. Karczyńska, M.A. Mozolewska, P. Krupa, A. Giełdoń, A. Liwo, C. Czaplewski. of protein structure with the coarse-grained UNRES force field assisted by small X-ray scattering data and knowledge-based information , Proteins: Structure, Function, and Bioinformatics 2018, 86 (S1), 228–239 https://doi.org/10.1002/prot.25421
  72. A. B.Poma, Mai Suan Li, and P. E. Theodorakis. Generalization of the elastic network model for the study of large conformational changes in biomolecules , Phys Chem Chem Phys 20, 17020-17028 (2018). PDF
  73. Pham Dang Lan, Maksim Kouza, Andrzej Kloczkowski, and Mai Suan Li. A topological order parameter for describing folding free energy landscapes of proteins , The Journal of Chemical Physics 149, 175101 (2018). PDF
  74. Huy Dinh Quoc Pham, Nguyen Quoc Thai, Zuzana Bednarikova, Huynh Quang Linh, Zuzana Gazova and Mai Suan Li. Bexarotene cannot reduce amyloid beta plaques through inhibition of production of amyloid beta peptides: in silico and in vitro study , Physical Chemistry Chemical Physics, 2018, 20, 24329. PDF
  75. Dinh Quoc Huy Pham, Mai Suan Li, and Giovanni La Penna . Copper Binding Induces Polymorphism in Amyloid-β Peptide: Results of Computational Models , Journal of Physical Chemistry B, 122 (29), 7243–7252 (2018). PDF
  76. Nguyen Quoc Thai, Zuzana Bednarikova, Miroslav Gancar, Huynh Quang Linh, Chin-Kun Hu, Mai Suan Li, and Zuzana Gazova. Compound CID 9998128 Is a Potential Multitarget Drug for Alzheimer’s Disease , ACS Chemical Neuroscience. PDF
  77. Maksim Kouza, Nguyen Truong Co, Mai Suan Li, Sebastian Kmiecik, Andrzej Kolinski, Andrzej Kloczkowski, and Irina Alexandra Buhimschi. Kinetics and mechanical stability of the fibril state control fibril formation time of polypeptide chains: A computational study , The Journal of Chemical Physics 148, 215106 (2018). PDF
  78. Hoang Linh Nguyen, Dang Lan Pham, Edward P. O’Brien & Mai Suan Li. Erythromycin leads to differential protein expression through differences in electrostatic and dispersion interactions with nascent proteins , Scientific Reports, volume 8, Article number: 6460. PDF
  79. Truong Duc Toan and Mai Suan Li. Probing the binding affinity by Jarzynski’s non-equilibrium free energy and unbinding times , J. Phys. Chem. B, appeared online, DOI 10.1021/acs.jpcb.8b02137 (2018). PDF
  80. G. La Penna and Mai Suan Li. Towards High‐Throughput Modelling of Copper Reactivity Induced by Structural Disorder in Amyloid Peptides , Chemistry: A European Journal; 24, 1-13 (2018). PDF
  81. Michał Wojciechowski, Bartosz Różycki, Pham Dinh Quoc Huy, Mai Suan Li, Edward A. Bayer & Marek Cieplak. Dual binding in cohesin-dockerin complexes: the energy landscape and the role of short, terminal segments of the dockerin module , Scientific Reports 8:5051 (2018), PDF
  82. Viet Hoang Man, Mai Suan Li, Philippe Derreumaux, and Phuong H. Nguyen. Rayleigh-Plesset equation of the bubble stable cavitation in water: A nonequilibrium all-atom molecular dynamics simulation study , J. Chem. Phys. 148(9), 09450 (2018), PDF
  83. Nguyen Quoc Thai, Ngan Quy Nguyen, Chuong Nguyen, Truong Quy Nguyen, Kiet Ho, Trung Tin Nguyen, and Mai Suan Li. Screening potential inhibitors for cancer target LSD1 from natural products by steered molecular dynamics , Molecular Simulation 44, 335-342 (2018),
    DOI: 10.1080/08927022.2017.1380802 PDF

    84. 2017

  84. P. Krupa, A.K. Sieradzan, M.A. Mozolewska, H. Li, A. Liwo, and H.A. Scheraga. Dynamics of Disulfide-Bond Disruption and Formation in the Thermal Unfolding of Ribonuclease A , Journal of Chemical Theory and Computation 2017, 13 (11), 5721–5730 https://doi.org/10.1021/acs.jctc.7b00724
  85. P. Krupa, A. Hałabis, W. Żmudzińska, S. Ołdziej, H.A. Scheraga, A. Liwo. Maximum Likelihood Calibration of the UNRES Force Field for Simulation of Protein Structure and Dynamics, Journal of Chemical Information and Modeling 2017, 57 (9), 2364-2377 https://doi.org/10.1021/acs.jcim.7b00254
  86. A.S. Karczyńska, C. Czaplewski, P. Krupa, M.A. Mozolewska, K. Joo, J. Lee, A. Liwo. Ergodicity and model quality in template-restrained canonical and temperature/Hamiltonian replica exchange coarse-grained molecular dynamics simulations of proteins , Journal of Computational Chemistry 2017, 38 (31), 2730-2746 https://doi.org/10.1002/jcc.25070
  87. M. Baranowski, C. Czaplewski, E.I. Gołas, Y. He, D. Jagieła, P. Krupa, A. Liwo, G.G. Maisuradze, M. Makowski, M.A Mozolewska, A. Niadzvedtski, A.J. Niemi, S. Rackovsky, R. Slusarz, A.K Sieradzan, S. Ołdziej, T. Wirecki, Y. Yin, B. Zaborowski, H.A. Scheraga. Microscopic Physics-Based Models of Proteins and Nucleic Acids, UNRES and NARES Coarse-Grained Modeling of Biomolecules https://doi.org/10.1201/9781315374284
  88. L. Ahmed, B. Rasulev, S. Kar, P. Krupa, M.A. Mozolewska, J. Leszczynski. Inhibitors or Toxins? Large Library Target-Specific Screening of Fullerene-based Nanoparticles for Drug Design Purpose Nanoscale 2017, 9 (29), 10263-10276. https://doi.org/10.1021/acs.jpcb.6b08780
  89. M.A. Mozolewska, A.K. Sieradzan*, A. Niadzvedstki, C. Czaplewski, A. Liwo, P. Krupa. Role of the sulfur to α-carbon thioether bridges in thurincin H Journal of Biomolecular Structure & Dynamics 2017, 35 (13), 2868-2879 https://doi.org/10.1080/07391102.2016.1234414
  90. A.K. Sieradzan, P. Krupa, D. Wales. What Makes Telomeres Unique? The Journal of Physical Chemistry B 2017, 121(10), 2207-2219 https://doi.org/10.1021/acs.jpcb.6b08780
  91. Mai Suan Li. Ligand migration and steered molecular dynamics in drug discovery: Comment on Ligand diffusion in proteins via enhanced sampling in molecular dynamics by Jakub Rydzewski and Wieslaw Nowak , Physics of Life Reviews 22-23, 79-81 (2017),
    DOI: http://dx.doi.org/10.1016/j.plrev.2017.08.006, PDF
  92. Thai Nguyen QuocNguyen Hoang Linh Huynh Quang Linh, and Mai Suan Li. Protocol for fast screening of multi-target drug candidates: Application to Alzheimer's disease , Journal of Molecular Graphics and Modelling 77, 121-129 (2017),
    DOI: 10.1016/j.jmgm.2017.08.002, PDF
  93. Pham Dinh Quoc Huy, Nguyen Quoc Thai, Zuzana Bednarikova, Le Huu Phuc, Huynh Quang Linh, Zuzana Gazova, and Mai Suan Li. Bexarotene does not clear amyloid beta plaques but delays fibril growth: Molecular mechanisms , ACS Chem Neuroscience 8 (9) 1960-1969 (2017).
    DOI: 10.1021/acschemneuro.7b00107 PDF
  94. Nguyen Hoang Linh, Tran Thi Minh Thu, Ly Anh Tu, Chin-Kun Hu, and Mai Suan Li. Impact of Mutations at C-Terminus on Structures and Dynamics of Ab40 and Ab42: A Molecular Simulation Study , J. Phys. Chem B 121, 4341-4354 (2017). PDF
  95. Maksim Kouza, Pham Dang Lan, A. M. Gabovich, A. Kolinski, and Mai Suan Li. Switch from thermal to force-driven pathways of protein refolding , J. Chem. Phys. 146, 135101 (2017). PDF

    96. 2016

  96. Quan Van Vuong, Pham Dinh Quoc Huy, Giovanni La Penna, Peter Faller, and Mai Suan Li. Impact of Cu(II) binding on Structures and Dynamics of Ab42 Monomer and Dimer: Molecular Dynamics Study , ACS Chem. Neurosci., 2016, 7 (10), pp 1348–1363. PDF
  97. Nguyen Quoc Thai, Ning-Hsuan Tseng, Mui Thi Vu, Tin Trung Nguyen, Huynh Quang Linh, Chin-Kun Hu, Yun-Ru Chen, and Mai Suan Li. Discovery of DNA dyes Hoechst 34580 and 33342 as Good Candidates for Inhibiting Amyloid Beta Formation: In silico and in vitro Study , J. Computer-Aided Mol Design (2016)
    DOI:10.1007/s10822-016-9932-1. PDF
  98. Nguyen Hoang Linh, Tran Thi Minh Thu, Phan Minh Truong, Pham Dang Lan, Man Hoang Viet, Phuong H. Nguyen, T. Ly Anh, Y-C. Chen, and Mai Suan Li. Ab41 Aggregates More Like Ab40 Than Like Ab42: In silico and in vitro Study , J. Phys. Chem B 120 (30), 7371-7379 (2016). PDF
  99. Yu-Jen Chang, Nguyen Hoang Linh, Hui-Ming Yu, Mai Suan Li, and Yun-Ru Chen. Alzheimer's Amyloid-beta Sequesters Caspase-3 via its C-terminal Tail , ACS Chemical Neuroscience 7 (8), 1097-1106 (2016). PDF
  100. Tin Trung Nguyen, Duy Phuoc Tran, Huy Dinh Quoc Pham, Zung Hoang, Paolo Carloni, Phuc Van Pham, Chuong Nguyen, and Mai Suan Li. Ligand binding to anti-cancer target CD44 investigated by molecular simulations , Journal of Molecular Modeling 22 (7), Article Number: 165 (2016). PDF
  101. Z. Bednarikova, PDQ Huy, M.M. Mocanu, D. Fedunova, M.S. Li, and Z. Gazova. Fullerenol C-60(OH)(16) prevents amyloid fibrillization of A beta(40) - in vitro and in silico approach , Phys Chem Chem Phys 18 (28), 18855-18867 (2016). PDF
  102. Son Tung Ngo, Shang-Ting Fang, Shu-Hsiang Huang, Chao-Liang Chou, Pham Dinh Quoc Huy, Mai Suan Li, and Yi-Cheng Chen. Anti-arrhythmic medication Propafenone is potential drug for Alzheimer's disease by inhibiting aggregation of Abeta: in silico and in vitro studies , Journal of Chem Inf Model. 56 (7), 1344-1356 (2016)
    DOI: 10.1021/acs.jcim.6b00029 . PDF
  103. M.H. Viet, N.T.V. Oanh, Philippe Derreumaux, Mai Suan Li, Christopher Roland,Celeste Sagui and Phuong H. Nguyen. Picosecond infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of virus , Phys. Chem. Chem. Phys. 18, 11951-11958 (2016). PDF

    104. 2015

  104. Quan Van Vuong, Tin Trung Nguyen, and Mai Suan Li. A New Method for Navigating Optimal Direction for Pulling Ligand from Binding Pocket: Application to Ranking Binding Affinity by Steered Molecular Dynamics , J. Chem. Info. Model. 55, 2731-2738 (2015). PDF
  105. Man Hoang Viet, Philippe Derreumaux, Mai Suan Li, Christopher Roland,Celeste Sagui and Phuong H. Nguyen. Picosecond dissociation of amyloid fibrils with infrared laser: a nonequilibrium simulation study , J. Chem. Phys. 143, 155101 (2015). PDF
  106. Man Hoang Viet, Phan Minh Truong, Philippe Derreumaux, Mai Suan Li, Christopher Roland,Celeste Sagui and Phuong H. Nguyen. Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study , Phys. Chem. Chem. Phys. 17, 27275 (2015). PDF
  107. Minh D. Pham, Ya-Ping Lin, Quan Van Vuong, Penumaka Nagababu, Brian T.-A. Chang, Kok Yaoh Ng, Chein-Hung Chen, Chau-Chung Han, Chung-Hsuan Chen, Mai Suan Li, Steve S.-F. Yu, Sunney I. Chan . Inactivation of the particulate methane monooxygenase (pMMO) in Methylo- coccus capsulatus (Bath) by acetylene , BBA - Proteins and Proteomics 1854, 1842-1852 (2015). PDF
  108. J. Nasica-Labouze , O. Berthoumieu, P. Nguyen, F. Sterpone, N-V. Buchete, S. Cote, A. De Simone, A. Doig, P. Faller, A. Garcia, A. Laio, Mai Suan Li, S. Melchionna, N. Mousseau, Y. Mu, A. Paravastu, S. Pasquali, D. Rosenman, B. Strodel, B. Tarus, J. Viles, T. Zhang, C. Wang, and P. Derreumaux. Amyloid beta-protein and Alzheimer's disease: when computer simulations complement experimental studies , Chemical Reviews 115, 3518-3563 (2015),
    DOI: 10.1021/cr500638n. PDF
  109. M. Kouza, N.T. Co, P.H. Nguyen, A. Kolinski, and Mai Suan Li. Preformed template fluctuations promote fibril formation: Insights from lattice and all-atom models , J. Chem. Phys. 142, 145104, 2015 (
    DOI:10.1063/1.4917073). PDF
  110. M.H. Viet, K. Siposova, Z. Bednarikova, A. Antosova, T.T. Nguyen, Z. Gazova, and Mai Suan Li. In silico and in vitro study of binding affinity of tripeptides to amyloid beta fibrils: Implications for Alzheimer's disease , J. Phys. Chem. B 119, 5145 (2015). PDF
  111. Quan Van Vuong, Zuzana Bednarikova, Andrea Antosova, Pham Dinh Quoc Huy, Katarina Siposova, Mai Suan Li, and Zuzana Gazova. Inhibition of Insulin Amyloid Fibrillization by Glyco-Acridines: In vitro and in silico Study , MedChemComm 6, 810 (2015),
    DOI:10.1039/C5MD00004A. PDF
  112. Son Tung Ngo, Binh Khanh Mai, Dinh Minh Hiep, and Mai Suan Li. Estimation of the binding free energy of AC1NX476 to HIV-1 protease wild-type and mutations using free energy perturbation method , Chem. Biol. Drug Design 86, 546-558 (2015). PDF

    113. 2014

  113. Pham Dinh Quoc Huy, and Mai Suan Li. Binding of fullerenes to amyloid beta fibrils: Size matters , Phys. Chem. Chem. Phys 16, 20030-20040 (2014). PDF
  114. Phan Minh Truong, Man Hoang Viet, Phuong H. Nguyen, C. K. Hu, and Mai Suan Li. Effect of Taiwan Mutation (D7H) on Structures of Amyloid Beta Peptides: Replica Exchange Molecular Dynamics Study , J. Phys. Chem. B 118, 8972-8981 (2014). PDF
  115. Man Hoang Viet, Phuong H. Nguyen, P. Derreumaux, and Mai Suan Li. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Abeta and Abeta42 , ACS Chem Neurosci. 5, 646-657 (2014). PDF
  116. Arthitaya Meeprasert, Thanyada Rungrotmongkol, Mai Suan Li, Supot Hannongbua. Exploring the potent inhibitors against NS3/4A protease of hepatitis C virus using steered molecular dynamics technique , Current Pharmaceutical Design 20 (Nr 21), 3465 (2014). PDF
  117. P.h. Nguyen, Mai Suan Li, and P. Derreumaux. Amyloid oligomer structure characterization from simulations: A general method , J. Chem. Phys. 140, 094105 (2014). PDF
  118. Truc Trang Nguyen, M.H. Viet,and Mai Suan Li. Effects of water models on binding affinity: Evidences from all-atom simulation of binding of Tamiflu to A/H5N1 neuraminidase , The Scientific World Journal 2014, paper A536084 (2014). PDF

    119. 2013

  119. M.H. Viet, P.H. Nguyen, S.T. Ngo, Mai Suan Li, and P. Derreumaux, Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers of Ab40 and Ab42 , ACS Neuroscience 4, 1446-1457 (2013). PDF
  120. M. H. Viet, C-Y. Chen, C-K. Hu, Y-R. Chen, and Mai Suan Li, Discovery of Dihydrochalcone as potential lead for Alzheimer's disease: in silico and in vitro study , Plos One 8(11), e79151 (2013). PDF
  121. M. Kouza, C-K. Hu, Mai Suan Li, and A. Kolinski, A structure-based model fails to probe the mechanical unfolding pathways of the titin I27 domain , J. Chem. Phys. 139, 065103 (2013). PDF
  122. H. -L. Chiang, S. T. Ngo, C. -J. Chen, C.-K. Hu, M. S. Li, Oligomerization of peptides LVEALYL and RGFFYT and their binding affinity to insulin , Plos One, 8, 65358 (2013). PDF
  123. Nguyen Truong Co, Chin-Kun Hu, and Mai Suan Li, Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models, J. Chem. Phys. 138, 185101 (2013). PDF
  124. V.Q. Vuong, K. Siposova,T.T. Nguyen, A. Antosova, L. Balogova, L. Drajna,J. Imrich, M. S. Li, and Z. Gazova, Binding of glyco-acridine derivatives to lysozyme leads to inhibition of amyloid fibrillization, Biomacromolecules 14 (4), 1035-1043 (2013). PDF
  125. Son Tung Ngo and M. S. Li, Top-Leads from natural products for treatment of Alzheimer's disease: Docking and molecular dynamics study, Molecular Simulation 39, 279-291 (2013) . PDF
  126. P.D.Q. Huy, Y-C. Yu, Son Tung Ngo, Tran Van Thao, C-P Chen, M. S. Li, and Y-C Chen, In silico and in vitro characterization of anti-amyloidogenic activity of vitamin K3 analogues for Alzheimer's disease, BBA-General Subjects 1380, 2960 (2013). PDF

    127. 2012

  127. Nguyen Truong Co and M. S. Li, New method for determining size of critical nucleus of fibril formation of polypeptide chains, J. Chem. Phys. 137, 095101 (2012) . PDF
  128. Son Tung Ngo and M. S. Li, Curcumin binds to Ab40 peptides and fibrils stronger than ibuprofen and naproxen, J.Phys. Chem. B 116, 10165 (2012) . PDF
  129. M. H. Viet and M. S. Li, Amyloid peptide Ab40 inhibits aggregation of Ab42: evidence from molecular dynamics simulations, J. Chem. Phys. 136, 245105 (2012) . PDF
  130. M. S. Li and B. K. Mai, Steered molecular dynamics - a promising tool for drug design, Current Bioinformatics 7, 342 (2012) . PDF

    131. 2011

  131. M. C. Wu, M. S. Li, W. J. Ma, M. Kouza, and C. K. Hu, Universal geometrical factor of protein conformations as a consequence of energy minimization, Europhys. Lett. 96, 68005 (2011) . PDF
  132. R. K. Mishra, G. Mishra, M. S. Li and S. Kumar, Effect of shear force on the separation of double stranded DNA, Phys. Rev. E 84, 032903 (2011) . PDF
  133. P. K. Ghosh, M. S. Li, and B. C. Bag, Periodic force induced stabilization or destabilization of the denaturated state of a protein , J. Chem. Phys. 135, 114101 (2011) . PDF
  134. Truc Trang Nguyen, Binh Khanh Mai, and M. S. Li, Study of Tamiflu sensitivity to variants of A/H5N1 virus using different force fields, J. Chem. Info. Model. 51, 2266 (2011) . PDF
  135. G. Mishra, D. Giri, M. S. Li and S. Kumar, Role of loop entropy in the force induced melting of DNA hairpin, J. Chem. Phys. 135, 035102 (2011) . PDF
  136. Binh Khanh Mai and Mai Suan Li, Neuraminidase inhibitor R-125489 -- a promising drug for treating influenza virus: Steered molecular dynamics approach, Biochemical and Biophysical Research Communications 410, 688 (2011) . PDF
  137. Man Hoang Viet, Son Tung Ngo, Nguyen Sy Lam , and Mai Suan Li, Inhibition of aggregation of amyloid peptides by beta-sheet breaker peptides and their binding affinity, J. Phys. Chem. B 115, 7433 (2011) . PDF
  138. Phuong Hoang Nguyen, Philippe Derreumaux, and Mai Suan Li, Effects of all-atom force fields on amyloid oligomerization: Replica exchange molecular dynamics simulations of the Ab16-22 dimer and trimer, Phys. Chem. Chem. Phys. 13, 9778 (2011). PDF

    139. 2010

  139. Binh Khanh Mai, Man Hoang Viet, and Mai Suan Li, Top-leads for swine influenza A/H1N1 virus revealed by steered molecular dynamics approach, J. Chem. Inf. Model. 50,2236 (2010). PDF
  140. Mai Suan Li, N.T. Co, G. Reddy, C-K Hu and D. Thirumalai, Factors governing fibrillogenesis of polypeptide chains revealed by lattice models, Phys. Rev. Lett. 105, 218101 (2010). PDF
  141. Zh. S. Gevorkian, Mai Suan Li, and C-K Hu, Sample to sample fluctuations in heterogeneous DNA, Journal of Polymer Science Part B 48, 2432 (2010). PDF
  142. H.-L. Chen, Jack C.-C. Hsu, Man Hoang Viet, Mai Suan Li, Chin-Kun Hu, Chia-Hsun Liu, Frederick Y. Luh, Silvia Si-Wei Chen, Evan S.-H. Chang, Andrew H.-J. Wang, Min-Feng Hsu, Wunshain Fann, Rita P.-Y. Chen, Studying the fast folding kinetics of an antifreeze protein RD1 using a photolabile caging strategy and time-resolved photoacoustic calorimetry on a nanosecond time scale, Proteins: Structures, Functions, and Bioinformatics 78, 2973 (2010). PDF
  143. Bidhan Chandra Bag, Chin-Kun Hu, and Mai Suan Li, Colored noise, folding rates and departure from Kramers' behavior, Phys. Chem. Chem. Phys. 12, 11753 (2010). PDF
  144. G. Arad-Haase, S.G. Chuartzman, S. Dagan, R. Nevo, M. Kouza, B.K. Mai, H.T. Nguyen, Mai Suan Li, and Z. Reich, Mechanical unfolding of acylphosphatase studied by single-molecule force spectroscopy and MD simulations, Biophys. J 99, 238 (2010). PDF
  145. H.B. Nam, M. Kouza, H. Zung, and Mai Suan Li, Relationship between population of the fibril-prone conformation in the monomeric state and oligomer formation times of peptides: Insights from all-atom simulations, J. Chem. Phys. 132, 165104 (2010). PDF
  146. S. Kumar, and Mai Suan Li, Biomolecules under mechanical force, Physics Reports 486, 1 (2010)(This review is among top 10 most downloaded). PDF

    147. Before 2010

  147. M. Kouza, C.K. Hu, H. Zung and Mai Suan Li, Protein mechanical unfolding: importance of non-native interactions, J. Chem. Phys. 131, 215103 (2009). PDF
  148. A.M. Gabovich, and Mai Suan Li, Mechanical stability of proteins, J. Chem Phys. 131, 024121 (2009). PDF
  149. Mai Suan Li, and M. Kouza, Dependence of protein mechanical unfolding pathways on pulling speeds, J. Chem Phys. 130, 145102 (2009). PDF
  150. Huey-Jen Fang, Yong-Zhong Chen, Mai Suan Li, Ming-Chya Wu, Chun-Ling Chang, Chung-ke Chang, Yen-lan Hsu, Tai-huang Huang, Hueih-Min Chen, Tian-Yow Tsong, and Chin-Kun Hu, Thermostability of the N-terminal RNA-binding domain of the SARS-CoV nucleocapsid protein: Experimental study and numerical simulations, Biophys. J. 96, 1892 (2009). PDF
  151. Mai Suan Li, D. K. Klimov, J.E. Straub, and D. Thirumalai, Probing the mechanisms of fibril formation using lattice models, J. Chem. Phys. 129, 175101 (2008). PDF
  152. Mai Suan Li, A.M. Gabovich, and A.I. Voitenko, New method for deciphering free energy landscape of three-state proteins, J. Chem. Phys. 129, 105102 (2008). PDF
  153. Maksim Kouza, Chin-Kun Hu, and Mai Suan Li, New force replica exchange method and protein folding pathways probed by force-clamp technique, J. Chem. Phys 128, 045103 (2008). PDF
  154. Mai Suan Li, Secondary structure, mechanical stability and location of transition state of proteins, Biophys J. 93, 2644 (2007). ps
  155. P. H. Nguyen, Mai Suan Li, G. Stock, J.E. Straub, and D. Thirumalai, Monomer adds to preformed structured oligomers of Abeta-peptides by a two-stage dock-lock mechanism, Proc Natl Acad Sci USA 104, 111 (2007). PDF
  156. Mai Suan Li, Maksim Kouza, Chin-Kun Hu, Refolding upon force quench and pathways of mechanical and thermal unfolding of ubiquitin, Biophysical J. 92, 547 (2007). PDF
  157. M. S. Li, C.-K. Hu, D. K. Klimov, and D. Thirumalai, Multiple step wise refolding of immunoglobulin domain I27 upon force quench depends on initial conditions, Proc Natl Acad Sci USA 103, 93 (2006). PDF
  158. M. Kouza, M. S. Li, E. P. O'Brien Jr., C.-K. Hu and D. Thirumalai. Effect of finite size on cooperativity and rates of protein folding, J. Phys. Chem. A 110, 671 (2006). PDF
  159. M. Kouza, C.-F. Chang, S. Hayryan, T.-H. Yu, M. S. Li, T.-H. Huang, and C.-K. Hu. Folding of the protein domain hbSBD, Biophysical J. 89, 3353 (2005). PDF
  160. P. H. Nguyen, G. Stock, E. Mittag, C.K. Hu, and M. S. Li, Free energy landscape and folding mechanism of beta-hairpin in explicit water: a replica exchange molecular dynamics study, Proteins: Structures, Functions, and Bioinformatics 61, 795 (2005). PDF
  161. M. S. Li, D. K. Klimov, and D. Thirumalai, Finite size effects on calorimetric cooperativity of two-state proteins, Physica A 350, 38 (2005). PDF
  162. M. S. Li, D. K. Klimov, and D. Thirumalai, Finite size effects on thermal denaturation of globular proteins, Phys. Rev. Lett. 93, 268107 (2004). PDF
  163. M. S. Li, D. K. Klimov, and D. Thirumalai, Thermal denaturation and folding rates of single domain proteins: size matters, Polymer 45, 573 (2004). PDF
  164. M. S. Li, D. K. Klimov, and D. Thirumalai, Dependence of folding rates on protein length, J. Phys. Chem. B 106, 8302 (2002). PDF
  165. M. S. Li and M. Cieplak, Simple models of proteins with repulsive non-native contacts, Eur. Phys. J. B 14, 787 (2000). PDF
  166. M. Cieplak, T. X. Hoang, and M. S. Li, Scaling of folding properties in simple models of proteins, Phys. Rev. Lett. 83, 1684 (1999). PDF
  167. M. S. Li and M. Cieplak, Folding in two-dimensional off-lattice models of proteins, Phys. Rev. E 59, 970 (1999). PDF
  168. M. S. Li and M. Cieplak, De1ineation of the native basin in continuum models of proteins, J. Phys. A 32, 5577 (1999). PDF

    169. Statistical and Condensed Matter Physics

  169. Ekino, T., Gabovich, A.M., Li, M.S., Szymczak, H. and Voitenko, A.I., Break-junction tunneling spectra of Bi2212 superconducting ceramics: Influence of inhomogeneous d-wave-Cooper-pairing and charge-density-wave order parameters , Low Temperature Physics, 46(4), pp.400-413, 2020. PDF
  170. Gabovich, A.M., Li, M.S., Szymczak, H. and Voitenko, A.I., Electric dipole image forces in three-layer systems: The classical electrostatic model , The Journal of Chemical Physics, 152(9), p.094705,2020. PDF
  171. Gabovich, A.M., Li, M.S., Szymczak, H. and Voitenko, A.I., Non-Coulombic behavior of electrostatic charge-charge interaction in three-layer heterostructures , Journal of Electrostatics, 102, p.103377, (2019). PDF
  172. T. Ekino, A.M. Gabovich, Mai Suan Li, H. Szymczak and A. I. Voitenko, Quasiparticle conductance-voltage characteristics for break junctions involving d-wave superconductors: charge-density-wave effects , J. Phys. Cond. Matter 29 (50), Article Number: 505602 (2017). PDF
  173. T. Ekino, A.M. Gabovich, Mai Suan Li, H. Szymczak and A. I. Voitenko, Influence of the spatially inhomogeneous gap distribution on the quasiparticle current in c-axis junctions involving d-wave superconductors with charge density waves , J. Phys. Cond. Matter 28 (44), Article Number: 445701 (2016). PDF
  174. A.M. Gabovich, A.I. Voitenko, Mai Suan Li, and H. Szymczak, Quasiparticle current along the c axis in junctions involving d-wave superconductors partially gapped by charge density waves , Phys. Rev. B 92, 054512 (2015). PDF
  175. A.M. Gabovich, A.I. Voitenko, Mai Suan Li, and H. Szymczak, Stationary Josephson current as a tool to detect charge density waves in high-Tc oxides , Physica C 516, 62-73 (2015). PDF
  176. A.M. Gabovich, Mai Suan Li, H. Szymczak, and A.I. Voitenko, Stationary Josephson current in junctions involving d-wave superconductors with charge density waves: the temperature dependence and deviations from the law of corresponding states , European Phys J B 87, 115 (2014). PDF
  177. A.M. Gabovich, Mai Suan Li, H. Szymczak, and A.I. Voitenko, Orientation percularities of dc Josephson tunneling between d-wave superconductors with charge density wave , Phys. Rev. B 87, 104503 (2013). PDF
  178. A.M. Gabovich, Mai Suan Li, H. Szymczak, and A.I. Voitenko, Image forces for a point-like dipole near a plane metal surface: An account of the spatial dispersion of dielectric permittivity , Surface Science 606, 510 (2012). PDF
  179. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, d-Wave superconductivity and s-wave charge density waves: coexistence between order parameters of different origin and symmetry , Symmetry 3, 699 (2011). PDF
  180. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, The phase diagram for coexisting d-wave superconductivity and charge-density waves: cuprates and beyond, J. Phys. Condens. Matter 23, 385701 (2011). PDF
  181. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, Competition of superconductivity and charge density waves in cuprates: Recent evidence and interpretation, Advances in Condensed Matter Physics, Vol. 2010 (2010), Article ID 681070. ps
  182. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, Temperature-dependent pseudogap-like features in tunnel spectra of high_Tc cuprates as a manifestation of charge-density waves, J. Phys.: Cond. Matter 20, 425218 (2008). ps
  183. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, Tunnel spectra of junctions involving BSCCO and other cuprates: Superconducting and charge-density-wave gapping, Physica C 468, 1145 (2008). ps
  184. T. Ekino, A.M. Gabovich, Mai Suan Li, M. Pekala, H. Szymczak, and A.I. Voitenko, Analysis of the pseudogap-related structure in tunneling spectra of superconducting Bi2Sr2CaCu2O, Phys. Rev. B 76, 180503R (2007). ps
  185. Z. R. Struzik, A. Glatz, and Mai Suan Li, 1/f Noise in one-dimensional charge density wave system, Europhys. Lett. 66, 385 (2004). PDF
  186. A. M. Gabovich, Mai Suan Li and A. I. Voitenko, New method of the spin-polarization detection in tunnel junctions ferromagnet/insulator/charge-density-wave metal, Pis'ma v ZhETP 80, 55 (2004). PDF
  187. M. S. Li and T. Nattermann, Flux lattice melting in two-dimensional disordered superconductors, Phys. Rev. B 67, 184520 (2003). PDF
  188. M. S. Li, Paramagnetic Meissner effect and related dynamical phenomena, Physics Reports. 376, 133-223 (2003). PDF
  189. M. S. Li, H. Zung and D. Dominguez, Nonlinear AC resistivity in s-wave and d-wave disordered granular superconductors, Phys. Rev. Lett. 88, 257004 (2002). PDF
  190. M. S. Li, Microwave absorption in s- and d-wave disordered superconductors, Phys. Rev. B 64, 144501 (2001). PDF
  191. A. Glatz, S. Kumar and M. S. Li, Collective dynamics of one-dimensional charge density waves, Phys. Rev. B 64, 184301 (2001). PDF
  192. M. S. Li, P. Nordblad and H. Kawamura, Aging effect in ceramic superconductors, Phys. Rev. Lett. 86, 1339 (2001). PDF
  193. H. Kawamura and M. S. Li, Nature of the ordering of the three-dimensional XY spin glasses, Phys. Rev. Lett. 87, 187204 (2001). PDF
  194. M. S. Li and D. Dominguez, AC resistivity of d-wave ceramic superconductors, Phys. Rev. B 62, 14554 (2000). PDF
  195. M. S. Li, Second harmonics and compensation effect in high-Tc ceramic superconductors, Phys. Rev. B 60, 118 (1999). PDF
  196. M. S. Li, Surface growth with spatially correlated noise, Phys. Rev. E 55, 1178 (1997). PDF
  197. H. Kawamura and M. S. Li, An equilibrium phase with broken time-reversal symmetry in ceramic high-Tc superconductors, Phys. Rev. Lett. 78, 1556 (1997). PDF
  198. H. Kawamura and M. S. Li, Chiral glass: a new equilibrium phase of ceramic high-T_c superconductors, J. Phys. Soc. Jpn 66, 2110 (1997). PDF
  199. M. S. Li, T. Nattermann, H. Rieger and M. Schwartz, Vortex lines in three-dimensional XY model with positional disorder, Phys. Rev. B 54, 16024 (1996). PDF
  200. H. Kawamura and M. S. Li, Monte Carlo studies of the ordering of ceramic superconductors - chiral glass, orbital glass and nonlinear susceptibility, Phys. Rev. B 54, 619 (1996). PDF
  201. T. Nattermann, S. Scheidl, S. E. Korshunov and M. S. Li, Absence of reentrance in the two-dimensional XY-model with random phase shift , J. Physique I 5, 565 (1995). PDF
  202. M. S. Li, and M. Cieplak, Renormalization group study of the coupled XY-Ising models, Phys.Rev.B 50, 955 (1994). PDF
  203. M. Cieplak, M. S. Li, and J. R. Banavar, Universality and chaos in XY spin glasses, Phys.Rev.B 47, 5022 (1993). PDF
  204. M. Cieplak, J. R. Banavar, M. S. Li, and A. Khurana, Frustration, scaling and local gauge invariance, Phys.Rev.B 45, 786 (1992). PDF
  205. M. S. Li, Spin glass in two-sublattice model, Zh.Eksp.Teor.Fiz. 95,569 (1989) (Sov.Phys. JETF 68 (1989) 319). PDF
  206. M. S. Li, Critical dynamics in three dimensional space , Zh.Eksp.Teor.Fiz. 84 (1983) 985 ( Sov.Phys. JETF 57, 572 (1983)). PDF