Phuong Nguyen

Chargé de Recherche - CNRS

Education
 

Habilitation a Diriger des Recherches,   Laboratoire de Chimie Physique,  Universite Paris Sud, France

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: nguyen@ibpc.fr

Research

Phuong H. Nguyen is a permanent CNRS researcher at the Laboratory of Theoretical Biochemistry (LBT) in France. His research primarily revolves around employing standard or advanced molecular dynamics methods to gain a deeper understanding of the early and late stages of aggregation in the mechanism of amyloid-β and tau proteins within various environments at the atomistic level. Recently, Phuong H. Nguyen has shifted his focus towards addressing the challenges associated with ultrasound-induced bubble cavitation to enhance drug delivery and regulate mitochondrial function. This line of inquiry involves the development of simulation approaches to model the bubble stable cavitation, and cell response over large and long time scales that bridge the current gap between all-atom MD simulations and experiments. Furthermore, he works on constructing multi-scale models of plasma cell membranes composed of lipid bilayers and cytoskeletons. 

Conference organization

Multiscale Investigation of Bubble-Cell Interaction Mechanisms for Enhanced Drug Delivery

• Dates

 ​28 Oct - 31 Oct 2024

• Location

Paris

• Organisers

Michaela Cooley: Case Western Reserve University, USA

Claude Inserra: Laboratory of Therapeutic Applications of Ultrasound, LabTAU, Inserm U1032, Lyon , France

Phuong Nguyen: Laboratoire de Biochimie Théorique, LBT, CNRS UPR9080, Paris , France

• Description 

Ultrasound (US)  in combination with nano/microbubbles  is a promising method to improve the delivery of drugs and genes into living cells. The basic idea is that under US exposure, bubbles may stably compress and expand, a regime called stable cavitation, which generates liquid flows around the bubbles. Bubbles may also oscillate non-linearly and expand until collapse, called the inertial cavitation regime, generating jetting and shock waves. These hydrodynamic effects cause different biophysical and biochemical cell responses, which could facilitate the delivery of drugs and genes into cells.

The noninvasive nature, low toxicity, local application, cost effectiveness and potential to achieve imaging-guided therapy are significant advantages of the US mediated drug delivery method. Therefore, in the last two decades, both experimental and theoretical studies have been intensively performed to get in-depth understanding on how the ultrasound-induced drug uptake is influenced by the properties of bubbles and cells, by acoustical driving parameters and bubble/cell micro-environment. Despite advances in the field, there are still large discrepancies among in-vitro, in-vivo and modelling studies. Moreover, there are variations in drug delivery outcomes, and the delivery efficiency is still rather low. However, the method has been tried in a brute manner to treat various diseases such as Alzheimer’s disease, cardiovascular disease, infections and cancer. However, why this emerging drug delivery paradigm has not yet reached widespread clinical use? The entire process from bubble cavitation up to animal and human clinical therapeutic effects spans over very large spatiotemporal scales, from picoseconds to days, thus a deep understanding of the bubble-cell interaction mechanism is challenge.

Currently, microscopy-based techniques are ideal for capturing the spatiotemporal dynamics of bubble dynamics and cell response in the microsecond and micrometer scales. However, experimental approaches are difficult to access simultaneously to the bubble dynamics and cell response in the earlier stages, which especially happen in the picosecond-microsecond range, and nanometer length scale. In principle, MD simulation has the potential to reveal the mechanisms of bubble cavitation and cell response at the atomistic/molecular levels and short timescales. However, there is a scarcity of MD simulation studies specifically focused on bubble cavitation and cell response. This could be attributed to the limitations of MD simulation when it comes to large spatiotemporal scales. The particle based simulation and mathematical modelling can address intriguing problems of bubble behaviour and cell response across both short and large spatiotemporal scales. However, these approaches often lack molecular-level details in their analyses. As a result, there is a gap between MD simulation and experimental observations. One of our objectives through this workshop is to explore how MD simulation can complement theoretical modelling and experiment, thereby enhancing its role in the field of bubble cavitation for improved drug delivery. Additionally, we will explore topics such as nanobubble cavitation-controlled regimes for effective molecular internalization, optimization of ultrasound and bubble parameters, and the molecular mechanisms underlying drug uptake.

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 transition.

E. 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. Hamm

in: ULTRAFAST PHENOMENA XVI  Book Series: Springer Series in Chemical Physics   Volume: 92   Pages: 532-534 (2009)

4. Aggregation of short disease-related peptides. 

P. H. Nguyen and F. Sterpone and P. Derreumaux.

in Computational approaches for understanding dynamical systems: Protein folding and assembly. Prog. Mol. Biol Transl. Sci. 170, 435 (2020)

5. Computer Simulations Aimed at Exploring Protein Aggregation and Dissociation.

P. H. Nguyen and P. Derreumaux.

in: Li, M. S, Kloczkowski, A, Cieplak, A. Kouza, M. (eds) Computer Simulations of Aggregation of Proteins and Peptides.  Methods in Molecular Biology, vol. 2340. Humana, New York, NY (2022)

6. Dynamics of Amyloid Formation from Simplified Representation to Atomistic Simulations. 

P. H. Nguyen and Tufféry and P. Derreumaux.

in: Simonson, T. (eds) Computational Peptide Science. Methods in Molecular Biology, vo.l 2405. Humana, New York, N.Y (2022) 

Paper

112. Double mutation K16F/E22F promotes the oligomerization but not beta-sheet formation of Abeta peptides: a molecular dynamics simulation study

Viet, Man and He, Xibing  and Nguyen, Phuong H. and Wang, Junmei.   (2024)

111.Stability and Cavitation of Nanobubble: Insights from Large-Scale Atomistic Molecular Dynamics Simulations

Viet, Man and Li, Mai Suan and Derreumaux, Philippe and Nguyen, Phuong H. 

JOURNAL OF CHEMICAL PHYSICS  (accepted 2024)

110. Modeling stable cavitation of coated microbubbles: A framework integrating smoothed dissipative particle dynamics and the Rayleigh-Plesset equation.

Nguyen, Phuong H.

JOURNAL OF CHEMICAL PHYSICS 161, 064110 (2024)

109. Molecular Docking, Drug-Likeness, ADMET, Molecular dynamic simulation studies of GHSR inhibitors: Promising Anti-childhood obesity agents.

80. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.
Nguyen, Phuong H. and Campanera, Josep M. and Ngo, Son T. and Loquet, Antoine and  Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY B 123, 6750 (2019)

79. Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.
Nguyen, Phuong H. and Campanera, Josep M. and Ngo, Son T. and Loquet, Antoine and  Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY B 123, 3643 (2019)

78. Nonequilibrium atomistic molecular dynamics simulation of tubular nano-motor propelled by bubble propulsion.
Viet, Man and Li, Mai Suan and Junmei, Wang and Derreumaux, Philippe  and Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 151, 024103 (2019)

77. Interaction mechanism between the focused ultrasound and lipid membrane at the molecular level.
Viet, Man and Li, Mai Suan and Junmei, Wang and Derreumaux, Philippe and Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 150, 215101 (2019)

76. Amyloid-β(29-42) Dimeric Conformations in Membranes Rich in Omega-3 and Omega-6 Polyunsaturated Fatty Acids.

Lu, Yan and Shi  Xiaofeng and Nguyen, Phuong H. and Sterpone, Fabio and Salsbury Jr., Freddie and Derreumaux, Philippe.

JOURNAL OF PHYSICAL CHEMISTRY B 123, 2687 (2019)

75. Effects of All-Atom Molecular Mechanics Force Fields on Amyloid Peptide Assembly: The Case of Aβ16-22 Dimer
Viet, Man and He Xibing and Derreumaux, Philippe and Ji, Beihong and  Xie, Xiang-Qun and Nguyen, Phuong H. and Junmei, Wang
JOURNAL OF CHEMICAL THEORY AND COMPUTATION 15, 1440 (2019)

74. Molecular mechanism of the cell membrane pore formation induced by bubble stable cavitation
Viet, Man  and Phan, Minh Truong and Li, Mai Suan and Junmei, Wang and Van-Oanh, Nguyen-Thi and Derreumaux, Philippe and  Nguyen, Phuong H.
JOURNAL OF PHYSICAL CHEMISTRY B 123, 71 (2019)

73. Breaking down cellulose fibrils with a mid-infrared laser
Domin, Dominik and Viet, Man  and Van-Oanh, Nguyen-Thi and Junmei, Wang and Kawasaki, Takayasu and Derreumaux, Philippe and  Nguyen, Phuong H.
CELLULOSE, DOI:10.1007/s10570-018-1973-2 (2018)

72. Amyloid-β/Drug Interactions from Computer Simulations and Cell-Based Assays.
Nguyen, Phuong H. and del Castillo-Frias, Maria P. and Berthoumieux, Olivia and Faller, Peter and Doig, Andrew J. and  Derreumaux, Philippe

JOURNAL OF ALZHEIMER'S DISEASE (2018)

71. Rayleigh-Plesset equation of the bubble stable cavitation in water: a nonequilibrium all-atom molecular dynamics simulation study.
Viet, Man and Li, M. Suan and Derreumaux, Philippe and Nguyen, Phuong H.
JOURNAL OF CHEMICAL PHYSICS 148, 094505 (2018)

70. Multi-scale simulations of biological systems using the OPEP coarse-grained model.
F. Sterpone and S. Doutreligne and T. T. Tran and S. Melchionna and M. Baaden and Nguyen, Phuong H. and P. Derreumaux.
BIOCHEM BIOPHYS RES. COMMUN. 17, 31739 (2017)

69. Why Is Research on Amyloid-beta Failing to Give New Drugs for Alzheimer's Disease?
Doig, A. J. Doig and del Castillo-Frias, M. P and Berthoumieu, O. and Tarus, B. and Nasica-Labouze, J. and Sterpone, F. and Nguyen, Phuong H. and Hooper, N. M. and Faller, P. and Derreumaux, P.
ACS CHEMICAL NEUROSCIENCE 8, 1435 (2017) .

68. High-resolution structures of the amyloid-beta1-42 dimers from the comparison of four atmistic force fields.
Viet, Man  and Nguyen, Phuong H. and Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY B 121, 2434 (2017).

67. Conformational Ensembles of the Wild-Type and S8C Abeta1-42 Dimers.
Viet, Man  and Nguyen, Phuong H. and Derreumaux, Philippe.
JOURNAL OF PHYSICAL CHEMISTRY B 121, 2434 (2017).

66. Dimerization mechanism of Alzheimer Abeta40 peptides: the high content of intrapeptide-stabilized conformations in A2V and A2T heterozygous dimers retards amyloid fibril formation

Nguyen, Phuong H. and Sterpone, Fabio and Pouplana, Ram and Derreumaux, Philippe and Campanera, Jose Maria.
JOURNAL OF PHYSICAL CHEMISTRY B 120, 12111 (2016)

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 56, 1 (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.
ACS CHEMICAL NEUROSCIENCE 7, 823 (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 145, 174113 (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)