Molecular simulations, insight from

Paulsson M, Frederiksen T, Brandbyge M (2010) Molecular electronics insight from first-principles transport simulations. Chimia 64 350-355... 

Mechanochemical Coupling in Molecular Motors Insights from Molecular Simulations of the Myosin Motor Domain... 

It should not be forgotten that quantum-chemical calculations can provide physical and chemical understanding in addition to hard numbers. Often, such an insight obtained from an electronic structure calculation leads to a useful concept or approximation in subsequent molecular simulation or analytical model building. 

Colombo, G., Roccatano, D., and Mark, A. E. (2002). Folding and stability of the three-stranded beta-sheet peptide betanova Insights from molecular dynamics simulations. Proteins Strud. Fund. Genet. 46, 380—392. 

CT, 1999, pp. 441—451. The Dynamics of Non-Crystalline Silica Insight from Molecular Dynamics Computer Simulations. 

Meli, M., Morra, G., Colombo, G. Investigating the mechanism of peptide aggregation insights from mixed Monte Carlo-molecular dynamics simulations. Biophys. J. 2008, 94, 4414-26. 

John Prausnitz I d like to make one quick addendum. I want to defend the use of molecular simulations because we have gained insight from them as well. Let me mention one outstanding example. Until about 20 years ago, we believed that you could only condense a phase with attractive forces, and no one ever questioned that myth. Then computer simulations were done in the 1960s by Bemi Alder and his associates. The results showed that even for hard spheres, without any attractive forces, you can get a phase transition. This was never present in the van der Waals theory. I want to emphasize that simulations also add to our conceptual knowledge. 

Insights into the Role of Conformational Transitions and Metal Ion Binding in RNA Catalysis from Molecular Simulations... 

X. Biarmes, J. Nieto, A. Planas, and C. Rovira, Substrate distortion in the Michaelis complex of Bacillus 1,3-1,4-/i-glucanase. Insight from first principles molecular dynamics simulations, J. Biol. Chem., 281 (2006) 1432-1441. 

DeMarco ML, Daggett V (2009) Characterization of cell-surface prion protein relative to its recombinant analogue insights from molecular dynamics simulations of diglycosylated, membrane-bound human prion protein. J Neurochem 109 60... 

Homak V, Ahuja S, Eilers M et al (2010) Light activation of rhodopsin insights from molecular dynamics simulations guided by solid-state NMR distance restraints. J Mol Biol 396 510-527... 

Thomas, A. et al. Pressure-driven Water Flow through Carbon Nanotubes Insights from Molecular Dynamics Simulation, Carnegie Mellon University, USA, Department of Mechanical Engineering 2009. 

H. N. Chen, Y. J. Wu, and G. A. Voth. Proton transport behavior through the influenza A M2 channel Insights from molecular simulation. Biophys. 1, 93 3470-3479, 2007. 

Utmmala, N.R., Risko, C., Bruner, C., Dauskardt, R.H., Br Das, J.L., 2015. Entanglements in P3HT and their influence on thin-film mechanical properties insights from molecular dynamics simulations. 

Fig. 2. The 2.0-A resolution crystal structure of the 6Fe-containing form of zinc-containing ferre-doxin from Sulfolobus sp. strain (PDB entry, IXER [T. Fujii, Y. Hata, T. Wakagi, N. Tanaka, and T. Oshima, Nat. Struct. Biol. 3, 834 (1996) T. Fujii, Y. Hata, M. Oozeki, H. Moriyama, T. Wakagi, N. Tanaka, and T. Oshima, Biochemistry 36, 1505 (1997)]). Important residues are labeled. The model was drawn using the Insight II software (Molecular Simulations Inc.).

Bedrov, D., J. Vatamanu, and Z. Z. Hu. 2015. Ionic liquids at charged surfaces Insight from molecular simulations. Journal of Non-Crystalline Solids 407 339-348. 

The initial DNA structures were built in the standard B-DNA conformation within QUANTA (Molecular Simulations, Inc 1992). The sodium ions were placed along the O-P-0 bisector, SA away from the P atom. The systems thus assembled were solvated with the overlay procedure within Insight II (Biosym Technologies 1993), and the final simulation cells were trimmed to hexagonal prisms of 24A side and Ilk length with Simulaid 26). 

Rotenberg, B., J.-P. Morel, V. Marry, P. Turq, and N. Morel-Desrosiers. 2009. On the driving force of cation exchange in clays Insights from combined microcalorimetry experiments and molecular simulation. Geochimica et Cosmochimica Acta Ti, no. 14 4034-4044. doi 10.1016/j.gca.2009.04.012. 

---