Publications

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Park S-M, Nguyen PHoang, Stock G.  2009.  Molecular dynamics simulation of cooling: Heat transfer from a photoexcited peptide to the solvent. J. Chem. Phys.. 131
Parody-Morreale A, Robert CH, Bishop GA, Gill SJ.  1987.  Calorimetric studies of oxygen and carbon monoxide binding to human hemoglobin. Sequential binding heats for oxygen. J. Biol. Chem.. 262:10994–10999.
Parody-Morreale A., Robert C.H, Gill S.J.  1987.  Calorimetric analysis of oxygen binding to lobster hemocyanin. Invertebrate Oxygen Carriers.
Parton D.L, Tek A., Baaden M, Sansom M.S.  2013.  Formation of raft-like assemblies within clusters of influenza hemagglutinin observed by MD simulations. Plos Comput. Biol.. 9:e1003034.
Pasquali S., Maggs A.C..  2008.  Fluctuation-induced interactions between dielectrics. J. Chem. Phys.. 129:014703.
Pasquali S., Percus J.K.  2009.  Mean field and the confined single homopolymer. Mol. Phys.. 107:1303–1312.
Pasquali S., Percus J.K..  2006.  Mapping a Homopolymer onto a Model Fluid. J. Chem. Phys.. 125:064906.
Pasquali S., Maggs A.C..  2009.  Numerical studies of Lifshitz interactions between dielectrics. Phys. Rev. A. 79:020102(R).
Pasquali S, Derreumaux P.  2010.  HiRE-RNA: A High Resolution Coarse-Grained Energy Model for RNA. J. Phys. Chem. B. 114:11957–11966.
Pasquali S., Nitti F., Maggs A.C..  2008.  Numerical methods for fluctuation driven interactions between dielectrics. Phys. Rev. E. 77:016705.
Pasquali S., Gan H.H., Schlick T..  2005.  Modular RNA architecture revealed by computational analysis of existing pseudoknots and ribosomal RNAs. Nuc. Acids Res.. 33:1384–1398.
Peoc'h K, Levavasseur E, Delmont E, Laffont-Proust ADe Simone, Privat N, Chebaro Y, Bedoucha CChapuis Pi, Brandel J-P, Laquerriere A, Hauw J-LKemeny Jea et al..  2012.  Substitutions at residue 211 in the prion protein drive a switch between CJD and GSS syndrome, a new mechanism governing inherited neurodegenerative disorders. Hum. Mol. Genet.. 21:5417–5428.
Perales-Calvo J, Giganti D, Stirnemann G, Garcia-Manyes S.  2018.  The force-dependent mechanism of DnaK-mediated mechanical folding. Sci Adv. 4:eaaq0243.
Perez S., Tubiana T., Imberty A., Baaden M.  2015.  Three-dimensional representations of complex carbohydrates and polysaccharides–SweetUnityMol: a video game-based computer graphic software. Glycobiology. 25:483–491.
PETICOLAS WL, WILSON KJ, Derreumaux P, VERGOTEN G.  1989.  RAMAN-SPECTROSCOPY, MOLECULAR-FORCE FIELDS, AND THE DYNAMICS OF BIOLOGICAL MOLECULES. Chemica Scripta. 29A:113–122.
Petroff JT, Dietzen NM, Santiago-McRae E, Deng B, Washington MS, Chen LJ, K. Moreland T, Deng Z, Rau M, Fitzpatrick JAJ et al..  2022.  Open-channel structure of a pentameric ligand-gated ion channel reveals a mechanism of leaflet-specific phospholipid modulation. Nature Communications. 13
Petuhov M.G, Dorofeyev V.E, Abagyan R.A, Mazur AK.  1992.  Global optimization of conformation energy of polypeptides by tunnel algorithm. Biophysics. 37:226–230.
Petuhov M.G, Mazur AK.  1992.  Modeling of the possible binding modes of substrates in the active site of Taka-Amylase A. Mol. Biol.. 26:292–299.
Petukhov MG, Mazur AK, Elyakova LA.  1995.  Investigation of the conformational properties of a {$\beta$}-(1-3) branched {$\beta$}-(1-6) heptasacchardie elicitor and its analogues by internal coordinate stochastic dynamics. Carbohydr. Res.. 279:41–57.
Phillips J, Hardy D, Maia J, Stone J, Ribeiro J, Bernardi R, Buch R, Fiorin G, Hénin J, Jiang W et al..  2020.  Scalable molecular dynamics on CPU and GPU architectures with NAMD. The Journal of Chemical Physics. 153
Phuong NH, Schmid F.  2003.  Local structure in nematic and isotropic liquid crystals. J. Chem. Phys.. 119:1214–1222.
Phuong NH, Germano G, Schmid F.  2001.  Elastic constants from direct correlation functions in nematic liquid crystals: A computer simulation study. J. Chem. Phys.. 115:7227–7234.
Phuong NH, Germano G, Schmid F.  2002.  The direct correlation function in nematic liquid crystals from computer simulation. Comput. Phys. Commun.. 147:350–353.
Pizzitutti F, Marchi M, Sterpone F, Rossky PJ.  2007.  How protein surfaces induce anomalous dynamics of hydration water. J. Phys. Chem. B. 111:7584–90.
Pons S, Sallette J, Bourgeois JP, Taly A, Changeux J-P, Devillers-Thiéry A.  2004.  Critical role of the C-terminal segment in the maturation and export to the cell surface of the homopentameric $\alpha$7–5HT3A receptor. Eur. J. Neurosci.. 20:2022–2030.

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