Activity coefficients for liquid organic reactions : towards a better understanding of true kinetics with the synthesis of jasmin aldehyde as showcase

The aldol condensation of benzaldehyde and heptanal is taken as an example of reversible liquid phase organic reactions to show that inclusion of activity coefficients reveal distinct differences in conversion and product distribution when different solvents methanol, ethanol, n-propanol, or n-butanol are used. The purpose of this work is to show a pronounced solvent effect for a given set of identical kinetic parameters, i.e., the same liquid phase kinetics can result in different conversion and yield values, depending on the choice of solvent. It was shown that subsequent parameter estimation without inclusion of the activity coefficients resulted in a pronounced deviation from the true' kinetics, up to a factor of 30. It is proposed that the usage of average activity coefficients gives already a significant improvement, resulting in acceptable parameter estimates

Native geometry and the dynamics of protein folding

In this paper we investigate the role of native geometry on the kinetics of protein folding based on simple lattice models and Monte Carlo simulations. Results obtained within the scope of the Miyazawa-Jernigan indicate the existence of two dynamical folding regimes depending on the protein chain length. For chains larger than 80 amino acids the folding performance is sensitive to the native state's conformation. Smaller chains, with less than 80 amino acids, fold via two-state kinetics and exhibit a significant correlation between the contact order parameter and the logarithmic folding times. In particular, chains with N=48 amino acids were found to belong to two broad classes of folding, characterized by different cooperativity, depending on the contact order parameter. Preliminary results based on the G\={o} model show that the effect of long range contact interaction strength in the folding kinetics is largely dependent on the native state's geometry.Comment: Proceedings of the BIFI 2004 - I International Conference, Zaragoza (Spain) Biology after the genome: a physical view. To appear in Biophysical Chemistr

Correlations in nano-scale step fluctuations: comparison of simulation and experiments

We analyze correlations in step-edge fluctuations using the Bortz-Kalos-Lebowitz kinetic Monte Carlo algorithm, with a 2-parameter expression for energy barriers, and compare with our VT-STM line-scan experiments on spiral steps on Pb(111). The scaling of the correlation times gives a dynamic exponent confirming the expected step-edge-diffusion rate-limiting kinetics both in the MC and in the experiments. We both calculate and measure the temperature dependence of (mass) transport properties via the characteristic hopping times and deduce therefrom the notoriously-elusive effective energy barrier for the edge fluctuations. With a careful analysis we point out the necessity of a more complex model to mimic the kinetics of a Pb(111) surface for certain parameter ranges.Comment: 10 pages, 9 figures, submitted to Physical Review

Effects of Surfactant Solubility on the Hydrodynamics of a Viscous Drop in a DC Electric Field

The physico-chemistry of surfactants (amphiphilic surface active agents) is often used to control the dynamics of viscous drops and bubbles. Surfactant sorption kinetics has been shown to play a critical role in the deformation of drops in extensional and shear flows, yet to the best of our knowledge these kinetics effects on a viscous drop in an electric fieldhave not been accounted for. In this paper we numerically investigate the effects of sorption kinetics on a surfactant-covered viscous drop in an electric field. Over a range of electric conductivity and permittivity ratios between the interior and exterior fluids, we focus on the dependence of deformation and flow on the transfer parameter $J$, and Biot number $\text{Bi}$ that characterize the extent of surfactant exchange between the drop surface and the bulk. Our findings suggest solubility affects the electrohydrodynamics of a viscous drop in distinct ways as we identify parameter regions where (1) surfactant solubility may alter both the drop deformation and circulation of fluid around a drop, and (2) surfactant solubility affects mainly the flow and not the deformation

Kinetics of bond formation in crosslinked gelatin gels

In chemical crosslinking of gelatin solutions, two different time scales affect the kinetics of the gel formation in the experiments. We complement the experimental study with Monte Carlo numerical simulations of a lattice model. This approach shows that the two characteristic time scales are related to the formation of single bonds crosslinker-chain and of bridges between chains. In particular their ratio turns out to control the kinetics of the gel formation. We discuss the effect of the concentration of chains. Finally our results suggest that, by varying the probability of forming bridges as an independent parameter, one can finely tune the kinetics of the gelation via the ratio of the two characteristic times.Comment: 8 pages, 9 figures, revised versio