Publications
] .
2010. Infrared signatures of the peptide dynamical transition: A molecular dynamics simulation study. J. Chem. Phys.. 133
.
2010. Nonequilibrium molecular dynamics simulation of the energy transport through a peptide helix. J. Chem. Phys.. 132
.
2010. Replica exchange simulation method using temperature and solvent viscosity. J. Chem. Phys.. 132
.
2011. Coherent vibrational energy transfer along a peptide helix. J. Chem. Phys.. 134
.
2011. Effects of all-atom force fields on amyloid oligomerization: replica exchange molecular dynamics simulations of the A beta(16-22) dimer and trimer. Phys. Chem. Chem. Phys.. 13:9778–9788.
.
2011. Exploring the energy landscape of small peptides and proteins by molecular dynamics simulations.
.
2011. Simulation of transient infrared spectra of a photoswitchable peptide. J. Chem. Phys.. 135
.
2012. Configurational entropy: an improvement of the quasiharmonic approximation using configurational temperature. Phys. Chem. Chem. Phys.. 14:877–886.
.
2012. Structures of A beta 17-42 Trimers in Isolation and with Five Small-Molecule Drugs Using a Hierarchical Computational Procedure. J. Phys. Chem. B. 116:8412–8422.
.
2013. Communication: Simulated tempering with fast on-the-fly weight determination. J. Chem. Phys.. 138:061102.
.
2013. Conformational Ensemble and Polymorphism of the All-Atom Alzheimer's A beta(37-42) Amyloid Peptide Oligomers. J. Phys. Chem. B. 117:5831–5840.
.
2013. Effect of the Tottori Familial Disease Mutation (D7N) on the Monomers and Dimers of A beta(40) and A beta(42). Acs Chem. Neurosci.. 4:1446–1457.
.
2013. Importance of the Ion-Pair Interactions in the OPEP Coarse-Grained Force Field: Parametrization and Validation. J. Chem. Theory Comput.. 9:4574–4584.
.
2013. Replica-exchange molecular dynamics simulations of the amyloid-beta(16-22) fragments. European Biophysics Journal with Biophysics Letters. 42:S68.
.
2014. Amyloid oligomer structure characterization from simulations: A general method. J. Chem. Phys.. 140:094105.
.
2014. Effect of the English Familial Disease Mutation (H6R) on the Monomers and Dimers of A beta 40 and A beta 42. Acs Chem. Neurosci.. 5:646–657.
.
2014. Familial Alzheimer A2 V Mutation Reduces the Intrinsic Disorder and Completely Changes the Free Energy Landscape of the A beta 1-28 Monomer. J. Phys. Chem. B. 118:501–510.
.
2014. The OPEP protein model: from single molecules, amyloid formation, crowding and hydrodynamics to DNA/RNA systems. Chem. Soc. Rev.. 43:4871–4893.
.
2015. Amyloid beta Protein and Alzheimer’s Disease: When Computer Simulations Complement Experimental Studies. Chem. Rev.. 115:3518–3563.
.
2015. Combined Experimental and Simulation Studies Suggest a Revised Mode of Action of the Anti-Alzheimer Disease Drug NQ-Trp. Chemistry-a European Journal. 21:12657–12666.
.
2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation.. The Journal of Chemical Physics. 143:021101–021101.
.
2015. Communication: Multiple atomistic force fields in a single enhanced sampling simulation. J. Chem. Phys.. 143:021101.
.
2015. Folding Atomistic Proteins in Explicit Solvent Using Simulated Tempering. J. Phys. Chem. B. 119:6941–6951.
.
2015. Molecular structure of the NQTrp inhibitor with the Alzheimer A beta 1-28 monomer. Eur. J. Med. Chem.. 91:43–50.
.
2015. Picosecond dissociation of amyloid fibrils with infrared laser: A nonequilibrium simulation study. J. Chem. Phys.. 143:155101.