One of the challenges in understanding polymer flammability is the lack of information about microscopic events that lead to macroscopically observed species, and Reactive Molecular Dynamics is a promising approach to obtain this crucially needed information. The development of a predictive method for condensed-phase reaction kinetics can provide significant insight into polymer ammability, thus helping guide future synthesis of fire-resistant polymers. Through this dissertation, a new reactive forcefield, RMDff, and Reactive Molecular Dynamics program, RxnMD, have been developed and used to simulate such material chemistry. It is necessary to have accurate description of chemical kinetics to describe quantitative chemical kinetics. Typical equilibrium forcefields are inadequate for describing chemical reactions due to the inability to represent bonding transformations. This issue was resolved by developing a new method, RMDff, that allows standard equilibrium forcfields to describe reactive transitions. The chemical reactions are described by employing switching functions that permit smooth transitions between the reactant and product descriptions available from traditional forcefields. Because all of the chemical motions are described, a complete potential energy surface is obtained for the course of the reaction. Descriptions of scission, addition/beta-scission, and abstraction reactions were developed for hydrocarbon species. Reactive potentials were developed using a representative reaction involving small molecules. It is shown that the overall geometric and energetic changes are transferable to larger and substituted molecules. The main source of error found in RMDff resulted from errors within the equilibrium forcefield descriptions. In order to simulate the chemical kinetics, it was necessary to create a molecular dynamics program that could implement the reactions from RMDff. RxnMD was developed as a new C++-based Reactive Molecular Dynamics code to simulate the dynamics using RMDff. Polymer kinetics were predicted for high-density polyethylene and used to test the method and code. Conformational changes and polymer length in the initial polyethylene molecules did not significantly alter the backbone decomposition kinetics. The results also revealed that the backbone carbon-carbon bonds could break with an activation energy approximately 100 kJ/mol below the carbon-carbon bond dissociation energy. This decrease was believed to occur from intramolecular polymer stress, which is relieved via backbone scission. Such stress was also observed to increase the beta-scission reaction rate at high temperatures, apparently because the scission reaction alone is not always sufficient to remove the energy associated with the polymer stress concentrated near the scission location. Finally, the RMD method was also shown to be transferable and applicable in describing the decomposition of novel fire-resistant polymers.

Οι ζεόλιθοι ανήκουν στα νανοπορώδη υλικά ή αλλιώς και μοριακά κόσκινα. Βρίσκουν δε εφαρμογή σε πληθώρα εφαρμογών, καλύπτοντας ένα μεγάλο θερμοκρασιακό φάσμα. Η γνώση της απόκρισής τους κατά τις μεταβολές της θερμοκρασίας είναι καθοριστικής σημασίας για την αποδοτικότητά τους, ακόμα περισσότερο όταν εμφανίζονται ανώμαλα φαινόμενα, όπως αρνητικός συντελεστής θερμικής διαστολής. Η παρούσα εργασία επικεντρώνεται στην ερμηνεία αυτού του φαινομένου με την χρήση προσομοιώσεων και πειραμάτων σκέδασης ακτίνων Χ. Ένα νέο πεδίο δυνάμεων αναπτύχθηκε και χρησιμοποιήθηκε σε προσομοιώσεις δυναμικής πλέγματος, όπου για πρώτη φορά προβλέπεται η συστολή της μοναδιαίας κυψελίδας του σιλικαλίτη, όπως και η διαστολή της μοναδιαίας κυψελίδας του αργιλοπυριτικού φωγιασίτη (NaX) πάνω από την θερμοκρασία δωματίου. Περαιτέρω ανάλυση των αποτελεσμάτων δείχνει πως υπεύθυνες για την συστολή κατά την θέρμανση είναι οι περιστροφές των τετραέδρων SiO4 και AlO4 από τα οποία απαρτίζεται η δομή. Αυτό το αποτέλεσμα είναι σύμφωνο με τον μηχανισμό των περιστροφών άκαμπτων μονάδων που προτείνεται στην βιβλιογραφία (R.U.M.). Στη συνέχεια υπολογίζονται μηχανικές ιδιότητες του υλικού, όπως το μέτρο Young και το μέτρο ελαστικότητας όγκου. Τέλος μελετήθηκε η απόκριση της δομής των ζεολίθων σε ερεθίσματα πέραν της θερμοκρασίας, όπως μεταβολή πίεσης και ρόφηση μορίων. Χαρακτηριστικά καταλήγουμε πως η δομή αποκρίνεται στην άσκηση της πίεσης μέσω του ίδιου μηχανισμού που καθορίζει της θερμοκρασιακή της απόκριση, δηλαδή τις περιστροφές των άκαμπτων ή σχεδόν άκαμπτων τετραέδρων. Επίσης, σε ό, τι αφορά την επίδραση της ρόφησης, η παρουσία των μορίων εξανίου, παρόλο επιφέρει δομικές αλλαγές που βελτιώνουν την αποδοτικότητα των ζεολιθικών μεμβρανών, αυτές οι αλλαγές δεν επηρεάζουν τις ροφητικές ιδιότητες στο εσωτερικό του κρυστάλλου. / Zeolites are nanoporous materials, otherwise called molecular sieves. The knowledge of the response of a zeolite structure to temperature changes or to the presence of host molecules in the pore system is of critical significance for the performance of zeolites as molecular sieves, especially if they are prepared in the form of membranes. Crack formation or grain boundary openings may appear between the substrate and the membrane due to a mismatch between the thermal expansion coefficient of the two materials, affecting the sorption and selectivity properties of the membrane. The problem is enhanced when the zeolite shows negative thermal expansion coefficient. The present work focuses in the mechanism that lies behind contraction upon heating, with the use of simulations and powder XRD experiments. A new force field was developed and was implemented in lattice dynamics simulations. It’s the first time that simulations predict the contraction of silicalite unit cell as well as the expansion of aluminosilicate faujasite (NaX) unit cell above room temperature. Further analysis of the simulation data shows that the Rigid Unit Mode (R.U.M.) mechanism that is proposed in the literature is the dominant mechanism of thermal contraction of the zeolite. Furthermore, mechanical properties such as Young modulus and bulk modulus were computed with the use of the newly derived force field. Finally, the response of framework upon pressure change and sorption of molecules was investigated. The zeolite structure response upon pressure change is similar to this of the temperature response, meaning that the volume and atomic positions change with the help of the rotations of the rigid AlO2/SiO2 tetrahedra. Concerning the response upon sorption, is was found with the help of theoretical calculations that although unit cell size variations that are induced by temperature changes and/or sorption may affect the efficiency of silicalite-1 membrane performance through alteration of the size of the non-zeolitic pores, such changes appear to affect negligibly the bulk sorption capacity of the silicalite-1 crystals.

The selection of the forcefield is a crucial issue in any MD related work and there is no clear indication as to which of the many available forcefields is the best for protein analysis. Many recent literature surveys indicate that MD work may be hindered by two limitations, namely conformational sampling and forcefields used (inaccuracies in the potential energy function may bias the simulation toward incorrect conformations). However, the advances in computing infrastructures, theoretical and computing aspects of MD have paved the way to carry out a sampling on a sufficiently longtime scale, putting a need for the accuracies in the forcefield. Because there are established differences in MD results when using forcefields, we have sought to ask how we could assess common mobility segments from a protein by analysis of trajectories using three forcefields in a similar environment. This is important because, disparate fluctuations appear to be more at flexible regions compared to stiff regions; in particular, flexible regions are more relevant to functional activities of the protein molecule. Therefore, we have tried to assess the similarity in the dynamics using three well-known forcefields ENCAD, CHARMM27 and AMBERFF99SB for 61 monomeric proteins and identify the properties of dynamic residues, which may be important for function. The comparison of popular forcefields with different parameterization philosophy may give hints to improve some of the currently existing agnostics in forcefields and characterization of mobile regions based on dynamics of proteins with diverse folds. These may also give some signature on the proteins at the level of dynamics in relation to function, which can be used in protein engineering studies. Nanosecond level MD simulation(30ns) on 61 monomeric proteins were carried out using CHARMM and AMBER forcefields and the trajectories with ENCAD forcefield obtained from Dynameomics database. The trajectories were first analyzed to check whether structural and dynamic properties from the three forcefields similar choosing few parameters in each case. The gross dynamic properties calculated (root mean square deviation (RMSD), TM-score derived RMSD, radius of gyration and accessible surface area) indicated similarity in many proteins. Flexibility index analysis on 17 proteins, which showed a notable difference in the flexibility, indicated that tertiary interactions (fraction of nonnative stable hydrogen bonds and salt bridges) might be responsible for the difference in the flexibility index. The normalized subspace overlap and shape overlap score taken based on the covariance matrices derived from trajectories indicated that majority of the proteins show a range between 0.3-0.5 indicating that the first principal components from these proteins in different combinations may not match well. These results indicate that although dynamic properties in general are similar in many proteins. However, flexibility index and normalized subspace overlap score indicate that subspaces on the first principal component in many proteins may not match completely. The number of proteins showing a better correlation is higher in CHARMM-AMBER combinations than the other two. The structural features from trajectories have been computed in terms of fraction of secondary structure, hydrogen bonds, salt bridges and native contacts. Although secondary structures and native contacts are well preserved during the simulations, the tertiary interactions (hydrogen bonds) are lost in many proteins and may be responsible for the difference in the some of properties among forcefields. Comparison of simulation results to experimental structures in terms of Root mean square fluctuations, Accessible surface area and radius of gyration indicates that the simulations results are on par with the ones derived from experimental structures. We have tried to assess the flexibility in the proteins using normalized Root mean square fluctuations (nRMSF), which for a residue is the ratio of RMSF from simulation to that of crystal structure. We have selected a threshold for this nRMSF to indicate the mobile regions in a protein based on secondary structure analysis. Based on the threshold of nRMSF and conformational properties (deviation in the dihedral angles), we have classified the residue and evaluated the properties of rigid hinge residues and corresponding mobile residues in terms of residue propensity, secondary structure preference and accessible surface area ranges. Since the rigid dynamic residues represent the inherent mobility, they might be important for function. Therefore, we have tried to assess the functional relevance considering the dynamic mobile residues from each protein from each forcefield simulation with the residues important for the function (taken from literature and databases). It is observed that some residues found to be mobile from the simulation are found to match with the experimental ones, although in many cases the number of these mobile residues is higher compared to the experimental ones. In summary, an analysis of protein simulation trajectories using three forcefields on a set of monomeric protein has shown that the gross structural properties and secondary structures from many proteins remain similar, but there are differences as may be seen from flexibility index. However correlation in parameters from CHARMM and AMBER force field is better compared to other two combinations. The differences seen in some of structural properties may arise mainly due to the loss of few tertiary interactions as indicated by the fraction of native hydrogen bonds and salt bridges. Based on the nRMSF, mobile segments obtained from the simulations were identified, and some of the mobile segments are found to match the functionally important residues from the experimental ones. Our work indicates that there are still some differences in the properties from the simulations, which indicates that care must be exercised when choosing a forcefield, especially assessing the functionally relevant residues from the simulations.