Torras, Juan; Seabra, Gustavo; Deumens, Erik; Trickey, S. B.; Roitberg, Adrian E.. A versatile AMBER-Gaussian QM/MM interface through PUPIL Journal of Computational Chemistry, 2008-02-12 Abstract: The PUPIL package (Program for User Package Interfacing and Linking) originally was developed to interface… Read More
Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy, and electrochemistry.
Castro, Maria Ana; Roitberg, Adrian E.; Cukiernik, Fabio D.. Theoretical and experimental studies of diruthenium tetracarboxylates structure, spectroscopy, and electrochemistry. Inorganic Chemistry., 2008-05-06 Abstract: Quantum mechanical calculations at the density functional theory (DFT) level have been performed on diruthenium tetracarboxylates… Read More
Exchange frequency in replica exchange molecular dynamics.
Sindhikara, Daniel; Meng, Yilin; Roitberg, Adrian E.. Exchange frequency in replica exchange molecular dynamics. Journal of Chemical Physics, 2008-01-10 Abstract: The effect of the exchange-attempt frequency on sampling efficiency is studied in replica exchange molecular dynamics (REMD). We show that… Read More
Simulating Temperature Jumps for Protein Folding
Kim, Seonah; Roitberg, Adrian E.. Simulating Temperature Jumps for Protein Folding Journal of Physical Chemistry B, 2008-01-15 Abstract: We present a new computational methodology aimed to calculate the thermodynamics and kinetics of peptide folding. We focus in particular on temperature… Read More
Hydrologic modeling, uncertainty, and sensitivity in the Okavango Basin: Insights for scenario assessment
Linhoss, A.C., R. Muñoz-Carpena, G. Kiker, D. Hughes. Hydrologic modeling, uncertainty, and sensitivity in the Okavango Basin: Insights for scenario assessment Journal of Hydrologic Engineering., 2012-12-12 Abstract: The development of watershed models with minimal quantified uncertainty under non-stationary conditions is… Read More
Shorebird patches as fingerprints of fractal coastline fluctuations due to climate change
Convertino, M., A. Bockelie, G.A Kiker, R. Muñoz-Carpena and I. Linkov. Shorebird patches as fingerprints of fractal coastline fluctuations due to climate change 2012. Ecological Processes 1:9, 2012-10-30 Abstract: The Florida coast is one of the most species-rich ecosystems in… Read More
Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra
Corey N. Stedwell, Johan F. Galindo, Kerim Gulyuz, Adrian E. Roitberg and Nicolas C. Polfer . Crown Complexation of Protonated Amino Acids: Influence on IRMPD Spectra J. Phys. Chem. A, Article ASAP, 2012-08-14 Abstract: We report infrared multiple photon dissociation… Read More
Adenine Formation without HCN
Kenneth M. Merz Jr., Eduardo C. Aguiar and Joao Bosco P. da Silva. Adenine Formation without HCN J. Phys. Chem. A 2014, 118, 3637-3644., 2014-05-05 Abstract: From a historic point of view adenine was always presumed to be the product… Read More
Discovery of the {beta}-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs
Satoshi Kimura; Kenjyo Miyauchi; Yoshiho Ikeuchi; Patrick C. Thiaville; Valerie de Crecy-Lagard; Tsutomu Suzuki. Discovery of the {beta}-barrel-type RNA methyltransferase responsible for N6-methylation of N6-threonylcarbamoyladenosine in tRNAs Nucleic Acids Research, 2014-07-24 Abstract: Methylation is a versatile reaction involved in the… Read More
Validation and Time Step Determination of Discrete Element Modeling of Flexible Fibers
Y. Guo, C. Wassgren, B. Hancock, W. Ketterhagen, J. Curtis. Validation and Time Step Determination of Discrete Element Modeling of Flexible Fibers Powder Technology, 2013-11-01 Abstract: In this paper, a flexible fiber model, based on the Discrete Element Method (DEM)… Read More