Insights from Simulations

In addition to the above examples, modeling of translocation with computer simulations has become an important tool, particularly because the experimental data are only the cumulative results from many contributing factors. On the other hand, effects from selected factors can be individually monitored in computer simulations. A full review of these new developments is beyond the scope of the present discussion. Nevertheless, we briefly mention a few key points below. 

Most of the simulations on polymer translocation involve uncharged flexible chains, focusing on the dependence of the average translocation time on the chain length. The exponent a in the relation. 

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We expect more insight from simulations in the future, particularly in situations where these multicomponent systems show effects of coupling between the different degrees of freedom, surface tensions depending on temperature and concentration, hydrodynamic flow induced by concentration gradients in addition to thermal buoyancy. 

Wade RC, Gabdoulline RR, Ludemann SK, et al. Electrostatic steering and ionic tethering in enzyme-hgand binding insights from simulations. Proc Natl Acad Sci USA 1998 95 5942-5949. 

Berkowitz ML, Bostick DL, Pandit S. Aqueous solutions next to phospholipid membrane surfaces insights from simulations. Chem. Rev. 2006 106 1527-1539. 

USA), 95, 5942 (1998). Electrostatic Steering and Ionic Tethering in Enzyme-ligand Binding Insights from Simulations. 

C. Moon, R. E. Hawtin, and P. M. Rodger, Faraday Discussion, 136,367 (2007). Nucleation and Control of Clathrate Hydrates Insights from Simulation. 

Akdim, B., Pachter, R., Kim, S.S., et al. Electronic properties of a graphene device with peptide adsorption insight from simulation. ACS Appl. Mater. Interfaces 5, 7470-7477 (2013). doi 10.1021/am401731c... 

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. 

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

A STRUCTURAL CONTEXT FOR THE ACTIVATION MECHANISM OF GPCRS INSIGHTS FROM MODELING AND COMPUTATIONAL SIMULATIONS... 

Pohorille, A., New, M. H., Schweighofer, K. and Wilson, M. A. (1999). Insights from computer simulations into the interactions of small molecules with lipid bilayers. In Membrane Permeability, Vol. 48 100 Years Since Ernest Overton, eds. Deamer, D. W., Kleinzeller, A. and Fambrough, D. M., Academic Press, San Diego pp. 50-76. 

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

Gale JD, Rohl. AL (2003) The General Utility Lattice Program (GULP). Mol Simul 29 291-341 Galy A, Bar-Matthews M, Halicz L, O Nions RK (2002) Mg isotopic composition of carbonate insight from speleothem formation. Earth and Planet Sci Lett 201 1-11 Gao YQ, Marcus RA (2002) On the theory of the strange and unconventional isotopic effects in ozone formation. J Chem Phys 116 137-154... 

Zott, C. 2003. Dynamic capabilities and the emergence of intraindustry differential firm performance insights from a simulation study. Strategic Management Journal, 24 97-125. 

Information gained from simulations can reveal key insights that explain gaps or contradictions in information. The time line is a useful tool in this development. For incidents of unexpected chemical reactions, it is common to attempt a lab scale simulation of the conditions involved in the exotherm or explosion. Many chemical processes can be modeled and duplicated dynamically by computer algorithms. Accelerated rate calorimeters (ARC) have proven to he highly useful tools for studying exothermic or overpressure runaway reactions. 

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. 

Ballauff M, Likos CN. Dendrimers in solution insight from theory and simulation. Angew Chem Int Ed 2004 43 2998-3020. 

Boresch, S. 2002. The Role of Bonded Energy Terms in Free Energy Simulations - Insights from Analytical Results , Mol. Sim., 28, 13. 

Ambrose, P. G. Monte Carlo simulation in the evaluation of susceptibility breakpoints predicting the future insights from the society of infectious diseases pharmacists. Pharmacotherapy 2006, 26 129-134. 

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. 

Gao, J., Energy components of aqueous solution Insight from hybrid QM/MM simulations using a polarizable solvent model. J. Comput. Chem. (1997) 18 1061—1071. 

Fawcett P. J., Agustdottir A. M., Alley R. B., and Shuman C. A. (1997) The Younger Dryas termination and north Atlantic deepwater formation insight from climate model simulations and Greenland ice core data. Paleocanography 12, 23-38. 

Computer modeling techniques are a substantial aid in zeolite structure solutions or refinements, and a means of extracting structural insight from difiraction or other anal ftical experiments. Sorption results, particle shapes in some cases, diffraction or scattering data, as well as optical, NMB and EXAFS spectra can all be simulated based on an atomic structure and, conversely, analytical data of these various types can be used to guide the development or detailing of an appropriate structural model. 

Gould C, Wong CF. 2002. Designing specific protein kinase inhibitors insights from computer simulations and comparative sequence/structure analysis. Pharmacol. Ther. In press... 

M. Sulpizi, A. Laio, J. VandeVondele, U. Rothlisberger, A. Cattaneo, and P. Carloni (2003) Reaction Mechanism of Caspases Insights from Mixed QM/MM Car-Parrinello Simulations. Proteins-Structure, Function and Genetics 52, p. 212... 

A. Kolinski, B. Ilkowski, J. Skolnick (1999) Dynamics and thermodynamics of beta-hairpin assembly Insights from various simulation techniques. Biophys. J. 77, pp. 2942-2952... 

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