Publications

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2019
Chiricotto M, Melchionna S, Derreumaux P, Sterpone F.  2019.  Multiscale Aggregation of the Amyloid Aβ16–22 Peptide: From Disordered Coagulation and Lateral Branching to Amorphous Prefibrils. The Journal of Physical Chemistry Letters. 10:1594-1599.
Man VHoang, Li MSuan, Wang J, Derreumaux P, Nguyen PH.  2019.  Nonequilibrium atomistic molecular dynamics simulation of tubular nanomotor propelled by bubble propulsion. The Journal of chemical physics. 151:024103.
da Silva FLuis Barro, Sterpone F, Derreumaux P.  2019.  OPEP6: A New Constant-pH Molecular Dynamics Simulation Scheme with OPEP Coarse-Grained Force Field. Journal of Chemical Theory and Computation. 15:3875-3888.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Physics-based oligomeric models of the yeast mitofusin Fzo1 at the molecular scale in the context of membrane docking. Mitochondrion. 49:234–244.
Li C, Danilowicz C, Tashjian TF, Godoy VG, Prévost C, Prentiss M.  2019.  The positioning of Chi sites allows the RecBCD pathway to suppress some genomic rearrangements. Nucleic Acids Res. 47:1836-1846.
Ngo STung, Derreumaux P, Vu VV.  2019.  Probable Transmembrane Amyloid α-Helix Bundles Capable of Conducting Ca Ions.. J Phys Chem B. 123(12):2645-2653.
Mason P.E., Jungwirth P., Duboué-Dijon E.  2019.  Quantifying the Strength of a Salt Bridge by Neutron Scattering and Molecular Dynamics. J. Phys. Chem. Lett.. 10
Martinez X, Krone M, Baaden M.  2019.  QuickSES: A Library for Fast Computation of Solvent Excluded Surfaces. Workshop on Molecular Graphics and Visual Analysis of Molecular Data.
Tashjian TF, Danilowicz C, Molza A-E, Nguyen BH, Prévost C, Prentiss M, Godoy VG.  2019.  Residues in the fingers domain of the translesion DNA polymerase DinB enable its unique participation in error-prone double-strand break repair. J Biol Chem. 294:7588-7600.
Lu D, Danilowicz C, Tashjian TF, Prévost C, Godoy VG, Prentiss M.  2019.  Slow extension of the invading DNA strand in a D-loop formed by RecA-mediated homologous recombination may enhance recognition of DNA homology. J Biol Chem. 294:8606-8616.
Gnutt D, Timr S, Ahlers J, König B, Manderfeld E, Heyden M, Sterpone F, Ebbinghaus S.  2019.  Stability Effect of Quinary Interactions Reversed by Single Point Mutations. Journal of the American Chemical Society. 141:4660-4669.
Brandner A, De Vecchis D, Baaden M, Cohen MM, Taly A.  2019.  Structural dataset from microsecond-long simulations of yeast mitofusin Fzo1 in the context of membrane docking.. Data Brief. 26:104460.
Nguyen PH, Campanera JM, Ngo STung, Loquet A, Derreumaux P.  2019.  Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. II. In Aqueous Solution.. J Phys Chem B. 123(31):6750-6756.
Nguyen PH, Campanera JM, Ngo STung, Loquet A, Derreumaux P.  2019.  Tetrameric Aβ40 and Aβ42 β-Barrel Structures by Extensive Atomistic Simulations. I. In a Bilayer Mimicking a Neuronal Membrane.. J Phys Chem B. 123(17):3643-3648.
Baaden M.  2019.  Visualizing Biological Membrane Organization and Dynamics.. J Mol Biol. 431(10):1889-1919.
Boyer B, Danilowicz C, Prentiss M, Prévost C.  2019.  Weaving DNA strands: structural insight on ATP hydrolysis in RecA-induced homologous recombination. Nucleic Acids Res. 47:7798-7808.
2018
Nguyen PH, Del Castillo-Frias MP, Berthoumieux O, Faller P, Doig AJ, Derreumaux P.  2018.  Amyloid-β/drug interactions from computer simulations and cell-based assays. Journal of Alzheimer's Disease. 64:S659–S672.
Esque J, Sansom MSP, Baaden M, Oguey C.  2018.  Analyzing protein topology based on Laguerre tessellation of a pore-traversing water network.. Sci Rep. 8(1):13540.
Baaden M, Barboiu M, Borthakur MPratim, Chen C-L, Coalson R, Davis J, Freger V, Gong B, Hélix-Nielsen C, Hickey R et al..  2018.  Applications to water transport systems: general discussion.. Faraday Discuss. 209:389-414.
Baaden M, Barboiu M, Bill RM, Chen C-L, Davis J, Di Vincenzo M, Freger V, Fröba M, Gale PA, Gong B et al..  2018.  Biomimetic water channels: general discussion.. Faraday Discuss. 209:205-229.
Taly A.  2018.  Is the boundary of fun redefined in a mixed-reality serious game?
Domin D, Man VHoang, Van-Oanh N-T, Wang J, Kawasaki T, Derreumaux P, Nguyen PH.  2018.  Breaking down cellulose fibrils with a mid-infrared laser. Cellulose. 25:5553–5568.
Guerin ME, Stirnemann G, Giganti D.  2018.  Conformational entropy of a single peptide controlled under force governs protease recognition and catalysis. Proc Natl Acad Sci U S A. 115:11525-11530.
Hitaishi VPratap, Clement R, Bourassin N, Baaden M, de Poulpiquet A, Sacquin-Mora S, Ciaccafava A, Lojou E.  2018.  Controlling Redox Enzyme Orientation at Planar Electrodes. Catalysts. 8
Wang YJian, Rico-Lastres P, Lezamiz A, Mora M, Solsona C, Stirnemann G, Garcia-Manyes S.  2018.  DNA Binding Induces a Nanomechanical Switch in the RRM1 Domain of TDP-43. J Phys Chem Lett. 9:3800-3807.

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