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Publications of Trinh Xuan Hoang

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In journals

SCI journals

  1. Phuong Thuy Bui and Trinh Xuan Hoang, Hydrophobic and electrostatic interactions modulate protein escape at the ribosomal exit tunnel, Biophysical Journal 120 (21), 4798-4808 (2021); DOI: 10.1016/j.bpj.2021.09.027
  2. Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti, Amos Maritan, and Jayanth R. Banavar, Marginally compact phase and ordered ground states in a model polymer with side spheres, Physical Review E 104, L012501 (2021); DOI: 10.1103/PhysRevE.104.L012501
  3. Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti, Amos Maritan, and Jayanth R. Banavar, Spontaneous dimensional reduction and ground state degeneracy in a simple chain model, Physical Review E 104, L012101 (2021); DOI: 10.1103/PhysRevE.104.L012101
  4. Phuong Thuy Bui and Trinh Xuan Hoang, Protein escape at the ribosomal exit tunnel: Effect of the tunnel shape, Journal of Chemical Physics 153, 045105 (2020); DOI: 10.1063/5.0008292
  5. Tatjana Skrbic, Trinh Xuan Hoang, Amos Maritan, Jayanth R. Banavar and Achille Giacometti, Local symmetry determines the phases of linear chains: a simple model for the self-assembly of peptides, Soft Matter 15, 5596-5613 (2019); DOI: 10.1039/c9sm00851a
  6. Anh D. Phan, Trinh X. Hoang, The pH-dependent electrostatic interaction of a metal nanoparticle with the MS2 virus-like particles, Chemical Physics Letters 730, 84-88 (2019); DOI: 10.1016/j.cplett.2019.05.045
  7. Tatjana Škrbić, Trinh X. Hoang, Amos Maritan, Jayanth R. Banavar, Achille Giacometti, The elixir phase of chain molecules, Proteins: Structure, Function and Bioinformatics 87 (3), 176-184 (2019); DOI: 10.1002/prot.25619
  8. Phuong Thuy Bui, and Trinh Xuan Hoang, Protein escape at the ribosomal exit tunnel: Effects of native interactions, tunnel length, and macromolecular crowding, Journal of Chemical Physics 149, 045102 (2018); DOI: 10.1063/1.5033361
  9. Nguyen Ba Hung, Duy-Manh Le, and Trinh X. Hoang, Sequence dependent aggregation of peptides and fibril formation, Journal of Chemical Physics 147, 105102 (2017); DOI: 10.1063/1.5001517
  10. Tatjana Škrbić, Trinh X. Hoang, and Achille Giacometti, Effective stiffness and formation of secondary structures in a protein-like model, Journal of Chemical Physics 145, 084904 (2016); DOI: 10.1063/1.4961387
  11. V. Hung Nguyen, Trinh X. Hoang, P. Dollfus and J.-C. Charlier, Transport properties through graphene grain boundaries: strain effects versus lattice symmetry, Nanoscale 8, 11658 (2016); DOI: 10.1039/c6nr01359g
  12. Tatjana Skrbic, Artem Badasyan, Trinh Xuan Hoang, Rudolf Podgornik and Achille Giacometti, From polymers to proteins: the effect of side chains and broken symmetry on the formation of secondary structures within a Wang–Landau approach, Soft Matter 12, 4783 (2016); DOI: 10.1039/c6sm00542j
  13. Phuong Thuy Bui and Trinh Xuan Hoang, Folding and escape of nascent proteins at ribosomal exit tunnel, Journal of Chemical Physics 144, 095102 (2016); DOI: 10.1063/1.4943042
  14. Trinh X. Hoang, Hoa Lan Trinh, Achille Giacometti, Rudolf Podgornik, Jayanth R. Banavar, and Amos Maritan, Phase diagram of the ground states of DNA condensates, Physical Review E (Rapid Communications) 92, 060701(R) (2015); DOI: 10.1103/PhysRevE.92.060701
  15. Trinh Xuan Hoang, Achille Giacometti, Rudolf Podgornik, Nhung T. T. Nguyen, Jayanth R. Banavar, and Amos Maritan, From toroidal to rod-like condensates of semiflexible polymers, JOURNAL OF CHEMICAL PHYSICS 140, 064902 (2014); DOI: 10.1063/1.4863996
  16. Anh D. Phan, Trinh X. Hoang, The-Long Phan, and Lilia M. Woods, Repulsive interactions of a lipid membrane with graphene in composite materials, Journal of Chemical Physics 139, 184703 (2013); DOI: 10.1063/1.4828939
  17. Anh D. Phan, Trinh X. Hoang, Thi H. L. Nghiem, and Lilia M. Woods, Surface plasmon resonances of protein-conjugated gold nanoparticles on graphitic substrates, Applied Physics Letters 103, 163702 (2013); DOI: 10.1063/1.4826514
  18. Trinh X. Hoang, Antonio Trovato, Flavio Seno, Jayanth R. Banavar, and Amos Maritan, Sequence repeats and protein structure, Phys. Rev. E (Rapid Communications) 86, 050901(R) (2012)
  19. Trinh X. Hoang, Jayanth R. Banavar and Amos Maritan, Shapes of hydrophobic thick membranes, EPL 98 (5), 56006 (2012); DOI: 10.1209/0295-5075/98/56006
  20. Jayanth R. Banavar, T. X. Hoang, F. Seno, A. Trovato, A. Maritan, Protein Sequence and Structure: Is One More Fundamental than the Other?, Journal of Statistical Physics 148, 636 (2012)
  21. J. R. Banavar, M. Cieplak, T. X. Hoang, A. Maritan, First-principles design of nanomachines, Proc. Natl. Acad. Sci. USA 106, 6900-6903 (2009); DOI: 10.1073/pnas.0901429106
  22. T. X. Hoang, F. Seno, A. Trovato, J. R. Banavar, A. Maritan, Inference of the solvation energy parameters of amino acids using maximum entropy approach, Journal of Chemical Physics 129, 035102 (2008); DOI: 10.1063/1.2953691
  23. A.Trovato, T. X. Hoang, J. R. Banavar, and A. Maritan, Symmetry, shape and order, Proc. Natl. Acad. Sci. USA 104, 19187 (2007); DOI: 10.1073/pnas.0707523104
  24. J. R. Banavar, T. X. Hoang, J. H. Maddocks, A. Maritan, C. Poletto, A. Stasiak, and A. Trovato, Structural motifs of biomolecules, Proc. Natl. Acad. Sci. USA 104, 17283 (2007); DOI: 10.1073/pnas.0704594104
  25. T. X. Hoang, A. Trovato, F. Seno, J. R. Banavar and A. Maritan, Marginal compactness of protein native structures, J. Phys.: Condens. Matter 18, S297 - S306 (2006)
  26. T. X. Hoang, L. Marsella, A. Trovato, F. Seno, J. R. Banavar, A. Maritan, Common attributes of native-state structures of proteins, disordered proteins, and amyloid, Proc. Natl. Acad. Sci. USA 130, 6883-6888 (2006); DOI: 10.1073/pnas.0601824103
  27. J. R. Banavar, M. Cieplak, A. Flammini, T. X. Hoang, R. D. Kamien, T. Lezon, D. Marenduzzo, A. Maritan, F. Seno, Y. Snir and A. Trovato, Geometry of proteins: Hydrogen bonding, sterics, and marginally compact tubes, Phys. Rev. E 73, 031921 (2006); DOI: 10.1103/PhysRevE.73.03192
  28. D. Marenduzzo, T. X. Hoang, F. Seno, M. Vendruscolo and A. Maritan, Form of growing strings, Phys. Rev. Lett. 95, 098103 (2005); DOI: 10.1103/PhysRevLett.95.098103
  29. M. Cieplak, A. Pastore and T. X. Hoang, Mechanical properties of the domains of titin in a Go-like model, J. Chem. Phys. 112, 05906 (2005); DOI: 10.1063/1.1839572
  30. A. Rosa, T. X. Hoang, D. Marenduzzo and A. Maritan, A new interpolation formula for semiflexible polymers, Biophys. Chem. 115, 251-254 (2005); DOI: 10.1016/j.bpc.2004.12.030
  31. T. X. Hoang, A. Trovato, F. Seno, J. R. Banavar and A. Maritan, Geometrical model for the native-state folds of proteins, Biophys. Chem. 115, 289-294 (2005); DOI: 10.1016/j.bpc.2004.12.036
  32. A. Trovato, T. X. Hoang, J. R. Banavar, A. Maritan and F. Seno, What determines the structures of native folds of proteins?, J. Phys.: Cond. Matt. 17, S1515-S1522 (2005); DOI: 10.1088/0953-8984/17/18/009
  33. J. R. Banavar, T. X. Hoang and A. Maritan, Protein and polymers, J. Chem. Phys. 112, 234910 (2005); DOI: 10.1063/1.1940059
  34. M. Cieplak, T. X. Hoang, and M. O. Robbins, Stretching of proteins in the entropic limit, Phys. Rev. E 69, 011912 (2004); DOI: 10.1103/PhysRevE.69.011912
  35. M. Cieplak, T. X. Hoang, and M. O. Robbins, Thermal Effects in Stretching of Go-like Models of Titin and Secondary Structures, Proteins 56, 285-297 (2004); DOI: 10.1002/prot.20081
  36. M. Cieplak, T. X. Hoang, and M. O. Robbins, Stretching of homopolymers and contact order, Phys. Rev. E 70, 011917 (2004); DOI: 10.1103/PhysRevE.70.011917
  37. J.R. Banavar, T.X. Hoang, A. Maritan, F. Seno, and A. Trovato, Unified perspective on proteins: A physics approach, Phys. Rev. E 70, 041905 (2004); DOI: 10.1103/PhysRevE.70.041905
  38. T. X. Hoang, A. Trovato, F. Seno, J. R. Banavar, and A. Maritan, Geometry and symmetry pre-sculpt the free energy landscape of proteins, Proc. Natl. Acad. Sci. USA. 101, 7960 (2004); DOI: 10.1073/pnas.0402525101
  39. A. Rosa, T. X. Hoang, D. Marenduzzo and A. Maritan, Elasticity of semiflexible polymers with and without interactions, Macromolecules 36, 10095-10102 (2003); DOI: 10.1021/ma0348831
  40. M. Cieplak, T.X. Hoang, Folding of proteins in Go models with angular interactions, Physica A 330, 195 (2003)
  41. T. X. Hoang, F. Seno, J.R. Banavar, M. Cieplak, A. Maritan, Assembly of protein tertiary structures from secondary structures using optimized potentials, Proteins: Struct. Func. Gen. 52, 155 (2003)
  42. M. Cieplak and T. X. Hoang, Universality classes in protein folding times, Biophysical Journal 84, 475 (2003)
  43. M. Cieplak, T. X. Hoang, M. O. Robbins, Folding and stretching in a Go-like model of titin, Proteins: Struct. Func. Gen. 49, 114-124 (2002)
  44. M. Cieplak, T. X. Hoang, M. O. Robbins, Thermal folding and mechanical unfolding pathways of protein secondary structures, Proteins: Struct. Func. Gen. 49, 104-113 (2002)
  45. T. X. Hoang, M. Cieplak, J. R. Banavar, A. Maritan, Prediction of protein secondary structures from conformational biases, Proteins: Struct. Func. Gen. 48, 558-565 (2002)
  46. M. Cieplak and T. X. Hoang, The range of contact interactions and the kinetics of the Go models of proteins, International Journal of Modern Physics C 13, 1231-1242 (2002)
  47. G. Settanni, T. X. Hoang, C. Micheletti, A. Maritan, Folding pathways of prion and doppel, Biophysical Journal 83, 3533-3541 (2002)
  48. M. Cieplak, T. X. Hoang, Kinetic nonoptimality and vibrational stability of proteins, Proteins: Struct. Func. Gen. 44, 20-25 (2001)
  49. T. X. Hoang, N. Sushko, M. S. Li, M. Cieplak, Spin analogues of proteins: scaling of ‘folding’ properties, J. Phys. A: Math. Gen. 33, 3977-3987 (2000)
  50. T. X. Hoang, M. Cieplak, Sequencing of folding events in Go-type proteins, Journal of Chemical Physics 113, 8319-8328 (2000)
  51. T. X. Hoang, M. Cieplak, Molecular dynamics of folding of secondary structures in Go-type models of proteins, Journal of Chemical Physics 112, 6851-6862 (2000)
  52. P. Garstecki, T. X. Hoang, M. Cieplak, Energy landscapes, supergraphs, and ‘‘folding funnels’’ in spin systems, Physical Review E 60, 3219-3226 (1999)
  53. M. Cieplak, T. X. Hoang, M. S. Li, Scaling of folding properties in simple models of proteins, Physical Review Letters 83, 1684-1687 (1999)
  54. M. Cieplak, T. X. Hoang, Coarse grained description of protein folding, Phys. Rev. E 58, 3589-3596 (1998)
  55. T. X. Hoang, M. Cieplak, Protein folding and models of dynamics on the lattice, J. Chem. Phys. 109, 9192-9196 (1998)

SCIE journals

  1. V Hung Nguyen, Trinh X Hoang and J-C Charlier, Electronic properties of twisted multilayer graphene, Journal of Physics: Materials 5 (3), 034003 (2022); DOI: 10.1088/2515-7639/ac6c4a
  2. Tatjana Škrbić, Trinh Xuan Hoang, Achille Giacometti, Amos Maritan and Jayanth R. Banavar, Proteins — a celebration of consilience, International Journal of Modern Physics B 36, 2140051 (2022); DOI: 10.1142/S0217979221400518
  3. Trinh X. Hoang, Ha T. H. Mai, Anthony B. Brennan & Ly Le, Effects of inter-organism interactions in biofouling on microtopographic surfaces, Biofouling 35 (6), 684-695 (2019); DOI: 10.1080/08927014.2019.1650918
  4. Anh D. Phan, Justyna Knapik-Kowalczuk, Marian Paluch, Trinh X. Hoang, and Katsunori Wakabayashi, Theoretical Model for the Structural Relaxation Time in Coamorphous Drugs, Molecular Pharmaceutics 16, 2992−2998 (2019); DOI: 10.1021/acs.molpharmaceut.9b00230
  5. M. Cieplak, T. X. Hoang, Scaling of folding properties in Go models of proteins, Journal of Biological Physics 26, 273-294 (2000)

Non-SCI journals

  1. Nhung T. T. Nguyen, Phuong Thuy Bui, Trinh Xuan Hoang, Effects of macromolecular crowding on folding of small globular proteins, Communications in Physics 32, (2022); DOI: 10.15625/0868-3166/16830
  2. Nhung T. T. Nguyen and Trinh Xuan Hoang, Aggregation of zoospores on sharklet microtopographic surfaces, Communications in Physics 31 (3), 279-287 (2021); DOI: 10.15625/0868-3166/15668
  3. Phuong Thuy Bui and Trinh Xuan Hoang, Protein escape at an atomistic model of the ribosomal exit tunnel, Journal of Physics: Conference Series 1506, 012022 (2020); DOI: 10.1088/1742-6596/1506/1/012022
  4. Nguyen Ba Hung, Trinh Xuan Hoang, SAMPLING THE FOLDING TRANSITION STATE ENSEMBLE IN A TUBE-LIKE MODEL OF PROTEIN, Communications in Physics 29 (2), 129-139 (2019); DOI: 10.15625/0868-3166/29/2/13670
  5. Phuong Thuy Bui and Trinh Xuan Hoang, ADDITIVE EFFECTS OF MACROMOLECULAR CROWDING AND CONFINEMENT ON PROTEIN STABILITY, Communications in Physics 28 (4), 351-360 (2018); DOI: 10.15625/0868-3166/28/4/13194
  6. Oanh T. P. Kim, Manh D. Le, Hoang X. Trinh and Hai V. Nong, In silico studies for the interaction of tumor necrosis factor-alpha (TNF-α) with different saponins from Vietnamese ginseng (Panax vietnamesis), Biophysics and Physicobiology 13, 173-180 (2016); DOI: 10.2142/biophysico.13.0_173
  7. Anh D. Phan, Trinh X. Hoang, Cascaded plasmon resonant field enhancement in protein-conjugated gold nanoparticles: Role of protein shell, Journal of Science: Advanced Materials and Devices 1, 61-64 (2016); DOI: 10.1016/j.jsamd.2016.03.002
  8. Nguyen Ba Hung and Trinh Xuan Hoang, Aggregation of peptides in the tube model with correlated sidechain orientations, Journal of Physics: Conference Series 627, 012028 (2015); DOI: doi:10.1088/1742-6596/627/1/012028
  9. Bui Phuong Thuy, Hoang Thi Thu Huong and Trinh X Hoang, Effects of macromolecular crowding on protein folding, Journal of Physics: Conference Series 627, 012027 (2015); DOI: doi:10.1088/1742-6596/627/1/012027
  10. Nguyen Ba Hung, Trinh Xuan Hoang, Folding of proteins in presculpted free energy landscape, Communications in Physics 23 (4), 313-320 (2013)
  11. Bui Phuong Thuy and Trinh Xuan Hoang, Effects of ribosomal exit tunnel on protein, Communications in Physics 23 (3), 219-225 (2013)
  12. Bui Phuong Thuy and Trinh Xuan Hoang, Evolution of protein-protein interaction networks in duplication-divergence model, Communications in Physics 22, 7-14 (2012)

In conference proceedings

  1. T. X. Hoang, N. T. T. Nhung, J. R. Banavar, and A. Maritan, Symmetry and Folded Structures of Biomolecules, IFMBE Proceedings of 4th International Conference on Biomedical Engineering in Vietnam (Springer) 40, 372-375 (2013); DOI: 10.1007/978-3-642-32183-2_90
  2. J. R. Banavar, T. X. Hoang, A. Maritan, A. Trovato, Spin glasses, tubes and proteins, Proceedings of the International School of Physics "Enrico Fermi" Volume 165, 135-143 (2007); DOI: 10.3254/978-1-58603-792-5-135
  3. T. X. Hoang, Một số mô hình vật lý trong mô phỏng cuốn Protein, Tuyển tập các báo cáo hội nghị vật lý toàn quốc lần thứ 6, 20 - 23 (2006)

Book chapters

Books