Phuong Nguyen

Chargé de Recherche - CNRS

 

Education

Post-doc:  Theoretical Biochemistry-Biophysics, Institute of Physical and Theoretical Chemistry, Frankfurt University, Germany

PhD:        Condensed Matter Theory, Physics Department, Bielefeld University, Germany
                Condensed Matter Theory, Physics Department, Mainz University, Germany
                Condensed Matter Theory, Max-Planck Institute for Polymer Research, Germany    

Diploma:  Condensed Matter Theory, International Centre for Theoretical Physics (ICTP), Trieste, Italy

BSc:         Solid State Theory, Physics Department, Hue University, Vietnam

Contact

Laboratoire de Biochimie Theorique - UPR 9080, CNRS
Institute de Biologie Physico-Chimique

13 rue Pierre et Marie Currie, F-75005 Paris

Office:  +33 (0) 1 58 41 51 81
Mobile: +33 (0) 6 21 20 20 83
Email:phuong.nguyen@ibpc.fr

Research

Development and application of efficient and physically rigorous theoretical methods for studying equlibrium and nonequilibrium structure, dynamics and thermodynamics of protein and RNA at all-atom and coarse-grained levels.

Publications

Book chapters

1. Nonequilibrium molecular dynamics simulation of photoinduced energy flow in peptides: theory meets experiment
P.H. Nguyen and P. Hamm and  G. Stock
in: Proteins: Energy, Heat and Signal Flow, eds. D. Leitner and J. Straub, CRC Press, 151 (2009)

2. Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations
G. Stock and A. Jain and L. Riccardi and P.H. Nguyen
eds. R. Schweitzer-Stenner, Wiley (2011)

3. Energy transport in peptide helices around the glass transitionE. H. G. Backus and P. H. Nguyen and V. Botan and R. Pfister and A. Moretto and M. Crisma and C. Toniolo and G. Stock and P. Hammin: ULTRAFAST PHENOMENA XVI  Book Series: Springer Series in Chemical Physics   Volume: 92   Pages: 532-534 (2009)

Papers

65. Coarse-grained and All-atom Simulations towards the Early and Late Steps of Amyloid Fibril Formation

Chiricotto, M. and Tran, T. T. and Nguyen, Phuong H. and Melchionna, S. and Sterpone, F.  and Derreumaux, P.
ISRAEL JOURNAL OF CHEMISTRY (DOI: 10.1002/ijch.201600048, 2016)

64. Abeta41 aggregates more like Abeta40 than like Ab42: In silico and in vitro study

Nguyen, Hoang Linh. and Tran, Minh Thu and Phan, Minh Truong and Man, Viet and Nguyen, Phuong H. and Ly, Anh Tu and Chen, Yi-Cheng and Li, Mai Suan.
JOURNAL OF PHYSICAL CHEMISTRY B 120, 7371 (2016)

63. Impact of A2V mutation on the heterozygous and homozygous Abeta140 dimer structures from atomistic simulations

Nguyen, Phuong H. and Sterpone, Fabio and Campanera, Jose Maria and Nasica-Labouze, Jessica and  Derreumaux, Philippe.
ACE CHEMICAL NEUROSCIENCE (submitted 2016)

62. Lattice model for amyloid peptides: OPEP force field parametrization and applications to the nucleus size of Alzheimer's peptides

Thanh Thuy, Tran  and Nguyen, Phuong H. and Derreumaux, Philippe.
JOURNAL OF CHEMICAL PHYSICS 144, 205103 (2016)

61. Nonequilibrium all-atom molecular dynamics simulation of the ultrasound induced bubble vibration and application to dissociate amyloid fibrils

Viet, Man  and Derreumaux, Philippe and  Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS (accepted 2016)

60. Communication: Picosecond Infrared laser-induced all-atom nonequilibrium molecular dynamics simulation of dissociation of viruses

Viet, Man  and Nguyen-Thi, Van-Oanh and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and  Nguyen, Phuong H.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 18, 11951 (2016)

59. Communication: Picosecond melting of peptide nanotubes using an infrared laser: a nonequilibrium simulation study
Viet, Man  and Phan, Truong and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and  Nguyen, Phuong H.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 17, 27275 (2015)

58. Communication: Multiple atomistic force fields in a single enhanced sampling simulation
Viet, Man  and Derreumaux, Philippe and  Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 143, 021101 (2015)

57. Structures of the Alzheimer's wild-type Abeta1-40 dimer from atomistic simulations
Tarus, Bogdan and Tran, Thanh and Nassica-Labouze, Jessica and Sterpone, Fabio and Nguyen, Phuong H. and Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY 119, 10478 (2015)

56. Folding atomistic proteins in explicit solvent using simulated tempering
Zhang, Tong and Nguyen, Phuong H. and Nassica-Labouze, Jessica and Mu, Yuguang and Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY B 119, 6941 (2015)

55. Picosecond dissociation of amyloid fibrils with infrared laser: a nonequilibrium simulation study
Viet, Man  and Derreumaux, Philippe and Li, Mai Suan and Roland, Christopher and Sagui, Celeste and  Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 143, 155101 (2015)

54. Combined experimental and simulation study suggests a revised mode of action of the anti-Alzheimer disease drug NQ-Trp
Berthoumieu, Olivia and  Nguyen, Phuong H. and  del Castillo-Frias  Maria and Ferre, Sabrina and Tarus, Bogdan and Nasica-Labouze , Jessica and Noel, Sabrina and  Saurel, Olivier and Rampon, Claire and  Doig, Andrew and Derreumaux, Philippe and Faller, Peter.
CHEMISTRY 21, 12657 (2015)

53. Amyloid beta-protein and Alzheimer's disease: when computer simulations complement experimental studies
J. Nasica-Labouze , Nguyen, Phuong H., O. Berthoumieu, 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.
CHEMICAL REVIEWS 115, 3518 (2015)

52. Preformed template fluctuations promote fibril formation: insights from lattice and all-atom models
Kouza, Masksim and Truong, Co and Nguyen, Phuong H. and Kolinski, Andrzej and Li, Mai Suan.
JOURNAL OF CHEMICAL PHYSICS 142, 145104 (2015)

51. Effect of the English familial disease mutation (H6R) on the monomers and dimers of Abeta40 and Abeta42.
Viet, Man and Nguyen, Phuong H. and Derreumaux, Philippe and Li, Mai Suan.
 ACS CHEMICAL NEUROSCIENCE 5, 646 (2014)

50. Molecular Structure of the NQTrp inhibitor with the Alzheimer Aβ1-28 monomer.
Tarus, Bogdan and Nguyen, Phuong H. Berthoumieu, Olivia and Faller, Peter and Doig, Andrew J. and Derreumaux, Philippe
Eur. J. MED. CHEM. 91, 43 (2015)

49. Replica Exchange Molecular Dynamics Simulation for Understanding the Initial Process of Amyloid Peptide Aggregation.
Nishikawa, Naohiro and Nguyen, Phuong H. and Derreumaux, Philippe and Okamoto, Yuko
MOLECULAR SIMULATION (DOI:10.1080/08927022.2014.938445, 2014)

48. Effect of Taiwan mutation (D7H) on Structures of Amyloid beta peptides: replica exchange molecular dynamics study.
Truong, Phan Minh and Viet, Man and Nguyen, Phuong H. and Hu, Chin-Kun  and Li, Mai Suan.
JOURNAL OF PHYSICAL CHEMISTRY B 118, 8972 (2014)

47. The OPEP coarse-grained Protein Model: From Single Molecules, Amyloid Formation, Role of Macromolecular Crowding and Hydrodynamics to RNA/DNA Complexs.

Sterpone, Fabio and Melchionna, Simone and Tuffery, Pierre and Pasquali, and Mousseau, Normand and Cragnolini, Tristan and Chebaro, Yassmine and Saint-Pierre, Jean-Francois, and Kalimeri Maria, and Barducci, Alessandro and Laurin, Yohan and Tek, Alex and Baaden, Marc and Nguyen, Phuong H. and Derreumaux, Philippe.
CHEMICAL SOCIETY REVIEWS (accepted 2014, DOI:10.1039/C4CS00048J)

45. Amyloid Oligomer Structure Characterization from Simulations: A General Method
Nguyen, Phuong H. and Li, Mai Suan and Derreumaux, Philippe
JOURNAL OF CHEMICAL PHYSICS 140, 094105 (2014)

44. The familial Alzheimer A2V mutation reduces the intrinsic disorder and completely changes the free energy landscape of the Aβ1-28 monomer
Nguyen, Phuong H. and Tarus, B. and Derreumaux, Philippe
JOURNAL OF PHYSICAL CHEMISTRY B 118, 501 (2014)

43. Understanding amyloid fibril nucleation and Abeta oligomer/drug interactions from computer simulations
Nguyen, Phuong H. and Derreumaux, Philippe
ACCOUNTS OF CHEMICAL RESEARCH 47(2):603-11 (2014)

42. Effect of the Tottori familial disease mutation (D7N) on the monomers and dimers Abeta40 and Abeta42
Viet, Man and Nguyen, Phuong H. and Ngo, Son and Li, Mai and Derreumaux, Philippe
ACS CHEMICAL NEUROSCIENCE 4, 1446 (2013)

41. Important of the ion-pair interactions in the OPEP coarse-grained force field: parametrization and validation
Sterpone, Fabio and Nguyen, Phuong H. and Kalimeri, Maria and Derreumaux, Philippe
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 9, 4574 (2013)

40. Conformational ensemble and polymorphism of the all-atom Alzheimer's Abeta(37-42) amyloid peptide oligomers
Nguyen, Phuong H, and Derreumaux, Philippe
JOURNAL OF PHYSICAL CHEMISTRY B 117, 5831 (2013)

39. Communication: Simulated tempering with fast on-the-fly weight determination
Nguyen, Phuong H, and Okamoto, Yuko, and Derreumaux, Philippe
JOURNAL OF CHEMICAL PHYSICS  138, 061102 (2013)

38. Construction of the Free Energy Landscape of Peptide Aggregation from Molecular Dynamics Simulations
Riccardi, Laura and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF CHEMICAL THEORY AND COMPUTATION  8, 1471 (2012)

37. Structures of Aβ17–42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure
Chebaro, Yassmine and Jiang, Ping and Zang, Tong and Mu, Yuguang and  Nguyen, Phuong H. and Mousseau, Normand and Derreumaux, Philippe
JOURNAL OF PHYSICAL CHEMISTRY B (2012)

36. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature
Nguyen, Phuong H. and Derreumaux, Philippe
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 14, 877 (2012)

35. Simulation of transient infrared spectra of a photoswitchable peptide
Kobus, Maja and Lieder, Martin and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS, 135, 225102 (2011)

34. Real Time Observation of Ultrafast Peptide Conformational Dynamics: Molecular Dynamics Simulation vs Infrared Experiment
Nguyen, Phuong H. and Staudt, Heike and Wachtveitl, Josef and Stock, Gerhard
JOURNAL OF PHYSICAL CHEMISTRY B 115, 13084 (2011)

33. Coherent vibrational energy transfer along a peptide helix
Kobus, Maja and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 134, 124518 (2011)

32. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer
Nguyen, Phuong H. and Li, Mai Suan and Derreumaux, Philippe
PHYSICAL CHEMISTRY CHEMICAL PHYSICS 13, 9778 (2011)

31. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study
Kobus, Maja and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 133, 034512 (2010)

30. Replica exchange simulation method using temperature and solvent viscosity
Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 132, 144109 (2010)

29. Nonequilibrium molecular dynamics simulation of the energy transport  through a peptide helix
Nguyen, Phuong H. and Park, Sang-Min and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 132, 025102 (2010)

28. Free-Energy Landscape of RNA Hairpins Constructed via Dihedral Angle Principal Component Analysis
Riccardi, Laura and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF PHYSICAL CHEMISTRY B 113, 16660 (2010)

27. Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent
Park, Sang-Min and Nguyen, Phuong H. and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 131, 184503 (2009)

26. Energy Flow and Long-Range Correlations in Guanine-Binding Riboswitch: A Nonequilibrium Molecular Dynamics Study
Nguyen, Phuong H. and Derreumaux, Philippe and Stock, Gerhard
JOURNAL OF PHYSICAL CHEMISTRY B 113, 9340 (2009)

25. Estimating configurational entropy of complex molecules: A novel variable transformation approach
Nguyen, Phuong H.
CHEMICAL PHYSICS LETTERS 468, 90 (2009)

24. Structural Flexibility of a Helical Peptide Regulates Vibrational Energy Transport Properties
Backus, Ellen H. G. and Nguyen, Phuong H. and Botan, Virgiliu and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Zerbe, Oliver and Stock, Gerhard and Hamm, Peter
JOURNAL OF PHYSICAL CHEMISTRY B 112, 15487 (2009)

23. Energy transport in peptide helices: A comparison between high- and low-energy excitations
Backus, Ellen H. G. and Nguyen, Phuong H. and Botan, Virgiliu and Pfister, Rolf and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Stock, Gerhard and Hamm, Peter
JOURNAL OF PHYSICAL CHEMISTRY B 112, 9091 (2008)

22. Construction of the free energy landscape of biomolecules via dihedral angle principal component analysis
Altis, Alexandros and Otten, Moritz and Nguyen, Phuong H. and Hegger, Rainer and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 128, 245102 (2008)

21. Nonadiabatic vibrational dynamics and spectroscopy of peptides: A quantum-classical description
Kobus, Maja and Gorbunov, Roman D. and Nguyen, Phuong H. and Stock
CHEMICAL PHYSICS 347, 208, 2008

20. Energy transport in peptide helices
Botan, Virgiliu and Backus, Ellen H. G. and Pfister, Rolf and Moretto, Alessandro and Crisma, Marco and Toniolo, Claudio and Nguyen, Phuong H. and Stock, Gerhard and Hamm, Peter
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104, 12749 (2007)

19. Dihedral angle principal component analysis of molecular dynamics simulations
Altis, Alexandros and Nguyen, Phuong H. and Hegger, Rainer and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 126, 244111 (2007)

18. Conformational states and folding pathways of peptides revealed by principal-independent component analyses
Nguyen, Phuong H.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 67,579 (2007)

17. Structure and dynamics of the homologous series of alanine peptides: A joint molecular dynamics/NMR study
Graf, Juergen and Nguyen, Phuong H. and Stock, Gerhard and Schwalbe,  Harald
JOURNAL OF THE AMERICAN CHEMICAL SOCIETY 129, 1179 (2007)

16. Quantum-classical description of the amide I vibrational spectrum of  trialanine
Gorbunov, Roman D. and Nguyen, Phuong H. and Kobus, Maja and Stock, Gerhard
JOURNAL OF CHEMICAL PHYSICS 126, 054509 (2007)

15. How complex is the dynamics of peptide folding?
Hegger, Rainer and Altis, Alexandros and Nguyen, Phuong H. and Stock, Gerhard
PHYSICAL REVIEW LETTERS 98, 028102 (2007)

14. Monomer adds to preformed structured oligomers of A beta-peptides by a two-stage dock-lock mechanism
Nguyen, Phuong H. and Li, Mai Suan and Stock, Gerhard and Straub, John E. and Thirumalai, D.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 104, 111 (2007)

13. Complexity of free energy landscapes of peptides revealed by nonlinear principal component analysis
Nguyen, Phuong H.
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 65, 898 (2006)

12. Photoinduced conformational dynamics of a photoswitchable peptide: A nonequilibrium molecular dynamics simulation study
Nguyen, Phuong H. and Gorbunov, Roman D. and Stock, Gerhard
BIOPHYSICAL JOURNAL 91, 1224 (2006)

11. Improved Wang-Landau sampling through the use of smoothed potential-energy surfaces
Nguyen, PH and Mittag, E and Torda, AE and Stock, G
JOURNAL OF CHEMICAL PHYSICS 124, 154107 (2006)

10. Nonequilibrium molecular dynamics simulation of a photoswitchable peptide
Nguyen, PH and Stock, G
CHEMICAL PHYSICS 323, 36 (2006)

9. Free energy landscape and folding mechanism of a beta-hairpin in explicit water: A replica exchange molecular dynamics study
Nguyen, PH and Stock, G and Mittag, E and Hu, CK and Li, MS
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 61, 795 (2005)

8. Structure and energy landscape of a photoswitchable peptide: A replica exchange molecular dynamics study
Nguyen, PH and Mu, YG and Stock, G
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 60, 485 (2005)

7. Reply to the Comment on "Energy Landscape of a Small Peptide Revealed by Dihedral Angle Principal Component Analysis
Mu, YG and Nguyen, PH and Stock, G
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 64, 798 (2006) 7

6. Energy landscape of a small peptide revealed by dihedral angle principal component analysis
Mu, YG and Nguyen, PH and Stock, G
PROTEINS-STRUCTURE FUNCTION AND BIOINFORMATICS 58, 45 (2005)

5. Nonequilibrium molecular-dynamics study of the vibrational energy relaxation of peptides in water
Nguyen, PH and Stock, G
JOURNAL OF CHEMICAL PHYSICS 119, 11350 (2003)

4. Local structure in nematic and isotropic liquid crystals
Phuong, NH and Schmid, F
JOURNAL OF CHEMICAL PHYSICS 119, 1214 (2003)

3. The direct correlation function in nematic liquid crystals from computer simulation
Phuong, NH and Germano, G and Schmid, F
COMPUTER PHYSICS COMMUNICATIONS 147, 350 (2002)

2. Spatial order in liquid crystals: Computer simulations of systems of ellipsoids
Schmid, F and Phuong, NH
MORPHOLOGY OF CONDENSED MATTER: PHYSICS AND GEOMETRY OF SPATIALLY COMPLEX SYSTEMS, Lecture Notes in Physics 600, 172 (2002)

1. Elastic constants from direct correlation functions in nematic liquid crystals: A computer simulation study
Phuong, NH and Germano, G and Schmid, F
JOURNAL OF CHEMICAL PHYSICS 115, 7227 (2001)