Kinetic Modeling and Parameter Estimation of a Prebiotic Peptide Reaction Network.

Although our understanding of how life emerged on Earth from simple organic precursors is speculative, early precursors likely included amino acids. The polymerization of amino acids into peptides and interactions between peptides are of interest because peptides and proteins participate in complex interaction networks in extant biology. However, peptide reaction networks can be challenging to study because of the potential for multiple species and systems-level interactions between species. We developed and employed a computational network model to describe reactions between amino acids to form di-, tri-, and tetra-peptides. Our experiments were initiated with two of the simplest amino acids, glycine and alanine, mediated by trimetaphosphate-activation and drying to promote peptide bond formation. The parameter estimates for bond formation and hydrolysis reactions in the system were found to be poorly constrained due to a network property known as sloppiness. In a sloppy model, the behavior mostly depends on only a subset of parameter combinations, but there is no straightforward way to determine which parameters should be included or excluded. Despite our inability to determine the exact values of specific kinetic parameters, we could make reasonably accurate predictions of model behavior. In short, our modeling has highlighted challenges and opportunities toward understanding the behaviors of complex prebiotic chemical experiments.

Natural Rubber Blend Optimization via Data-Driven Modeling: The Implementation for Reverse Engineering.

Natural rubber formulation methodologies implemented within industry primarily implicate a high dependence on the formulator's experience as it involves an educated guess-and-check process. The formulator must leverage their experience to ensure that the number of iterations to the final blend composition is minimized. The study presented in this paper includes the implementation of blend formulation methodology that targets material properties relevant to the application in which the product will be used by incorporating predictive models, including linear regression, response surface method (RSM), artificial neural networks (ANNs), and Gaussian process regression (GPR). Training of such models requires data, which is equal to financial resources in industry. To ensure minimum experimental effort, the dataset is kept small, and the model complexity is kept simple, and as a proof of concept, the predictive models are used to reverse engineer a current material used in the footwear industry based on target viscoelastic properties (relaxation behavior, tanδ, and hardness), which all depend on the amount of crosslinker, plasticizer, and the quantity of voids used to create the lightweight high-performance material. RSM, ANN, and GPR result in prediction accuracy of 90%, 97%, and 100%, respectively. It is evident that the testing accuracy increases with algorithm complexity; therefore, these methodologies provide a wide range of tools capable of predicting compound formulation based on specified target properties, and with a wide range of complexity.