A bibliometric analysis of the Journal of Molecular Graphics and Modelling

This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported

Modeling the vapor-liquid equilibrium and association of nitrogen dioxide/dinitrogen tetroxide and its mixtures with carbon dioxide

We have used in this work the crossover soft-SAFT equation of state to model nitrogen dioxide/dinitrogen tetraoxide (NO2/N2O4), carbon dioxide (CO2) and their mixtures. The prediction of the vapor – liquid equilibrium of this mixture is of utmost importance to correctly assess the NO2 monomer amount that is the oxidizing agent of vegetal macromolecules in the CO2 + NO2 / N2O4 reacting medium under supercritical conditions. The quadrupolar effect was explicitly considered when modeling carbon dioxide, enabling to obtain an excellent description of the vapor-liquid equilibria diagrams. NO2 was modeled as a self associating molecule with a single association site to account for the strong associating character of the NO2 molecule. Again, the vapor-liquid equilibrium of NO2 was correctly modeled. The molecular parameters were tested by accurately predicting the very few available experimental data outside the phase equilibrium. Soft-SAFT was also able to predict the degree of dimerization of NO2 (mimicking the real NO2/N2O4 situation), in good agreement with experimental data. Finally, CO2 and NO2 pure compound parameters were used to predict the vapor – liquid coexistence of the CO2 + NO2 / N2O4 mixture at different temperatures. Experimental pressure – CO2 mass fraction isotherms recently measured were well described using a unique binary parameter, independent of the temperature, proving that the soft-SAFT model is able to capture the non-ideal behavior of the mixture

Modeling, Simulating, and Parameter Fitting of Biochemical Kinetic Experiments

In many chemical and biological applications, systems of differential equations containing unknown parameters are used to explain empirical observations and experimental data. The DEs are typically nonlinear and difficult to analyze, requiring numerical methods to approximate the solutions. Compounding this difficulty are the unknown parameters in the DE system, which must be given specific numerical values in order for simulations to be run. Estrogen receptor protein dimerization is used as an example to demonstrate model construction, reduction, simulation, and parameter estimation. Mathematical, computational, and statistical methods are applied to empirical data to deduce kinetic parameter estimates and guide decisions regarding future experiments and modeling. The process demonstrated serves as a pedagogical example of quantitative methods being used to extract parameter values from biochemical data models.Comment: 23 pages, 9 figures, to be published in SIAM Revie