Molecular Dynamics Simulation of Surface Nucleation during Growth of an Alkane Crystal

Crystal growth from the melt of n-pentacontane (C50) was studied by molecular dynamics simulation. Quenching below the melting temperature gives rise to propagation of the crystal growth front into the C50 melt from a crystalline polyethylene surface. By tracking the location of the crystal–melt interface, crystal growth rates between 0.02 and 0.05 m/s were observed, for quench depths of 10–70 K below the melting point. These growth rates compare favorably with those from a previous study by Waheed et al. [ Polymer 2005, 46, 8689−8702]. Next, surface nucleation was identified with the formation of two-dimensional clusters of crystalline sites within layers parallel to the propagating growth front. Critical nucleus sizes, waiting times, and rates for surface nucleation were estimated by a mean first passage time analysis. A surface nucleation rate of ∼0.05 nm⁻² ns⁻¹ was observed, and it was nearly temperature-independent. Postcritical “spreading” of the surface nuclei to form a completely crystallized layer slowed with deeper supercooling.National Science Foundation (U.S.) Division of Civil, Mechanical and Manufacturing Innovation (CMMI-1235109

Molecular modeling of polymer crystallization and the effect of nucleating agents

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2017.Cataloged from PDF version of thesis.Includes bibliographical references (pages 145-156).The microstructure in a semicrystalline polymer material ultimately determines its material properties. Despite the abundance of research into the semicrystalline microstructure and its evolution during crystallization, a clear description of its development remains elusive. The advent of advanced computing and algorithms, however, have promoted molecular modeling of polymer crystallization, providing a new perspective on the development of the microstructure. This thesis revisits and challenges many aspects of microstructural development in macromolecular materials by applying new modeling techniques and recent technologies. Through atomistic simulations of n-alkane crystallization, this thesis presents new molecular evidence of surface nucleation processes that contribute to the propagation of the crystal growth front in a macromolecular system. Crystallization in polymeric systems has long been theorized to proceed by "secondary nucleation." In this work, molecular dynamics (MD) simulations were engineered to probe this surface nucleation process by systematically inducing crystal growth for a system of macromolecules. In a novel application of mean first passage time analysis, the critical surface nucleus sizes, waiting times, and surface nucleation rates were extracted from atomically-detailed molecular trajectories using a layer-by-layer approach. Insight from MD simulations was used to build a new kinetic model to describe the structure and rate of advancement of the growth front during crystallization. In the model, solidification occurs through the mechanisms of surface nucleation and lateral spreading of the solid phase within layers in the vicinity of the growth front. Transformation within each layer is described by an equation similar to the two-dimensional variant of the Johnson-Mehl-Avrami equation. The kinetic model is computationally efficient and predictive of important macroscopic observables. Finally, this thesis presents the first computational screening of nucleating agents for macromolecular crystallization. Screens were conducted for two families of crystal materials: tetrahedrally coordinated materials isomorphic to diamond and silicon, and 2D, hexagonally coordinated materials isomorphic to graphene. The induction time for heterogeneous nucleation was shown to depend strongly on crystallographic registry between the nucleating agent and the critical nucleus, but the severity of this registry requirement weakened with increasing strength of attraction to the surface of the nucleating agent. In an unprecedented find, the substrate rigidity significantly influenced heterogeneous nucleation. The molecular organization of nalkane chains at the nucleating surface was also investigated to build a fundamental understanding of the mechanisms for heterogeneous nucleation and spreading.by Alexander Jules Bourque.Ph. D

Heterogeneous nucleation of an n-alkane on graphene-like materials

Nucleating agents are materials that enhance crystallization through their role in heterogeneous nucleation. They are frequently used to control kinetics and morphology in polymer crystallization. However, selection and design of nucleating agents is hindered by a lack of detailed, atomistic level information about the relationship between physicochemical properties and heterogeneous nucleation activity. We examined heterogeneous nucleation of n-pentacontane – a model surrogate for polyethylene – induced by graphene, and the family of 2D hexagonally coordinated nanoplatelet materials to which it belongs, using molecular dynamics simulation. High throughput computational screening was performed by systematic variation of the parameters that define the 2D nanoplatelet. Nucleation activity is characterized by induction time. These computations confirm the utility of graphene as a nucleating agent for n-pentacontane and, by extension, polyethylene. We identify a set of heuristics for the design of efficient nucleating agents. These include: epitaxial matching, material compatibility as measured by adhesive interactions, and optimal rigidity. We also observed a three-fold degeneracy in the orientation of epitaxial matches between the nucleating agent and the crystallizing organic, which increased the induction time. This study advances the prospect of high-throughput computation to build a “materials genome” of nucleating agents for polymers

Heterogeneous Nucleation of an n-Alkane on Tetrahedrally Coordinated Crystals

Heterogeneous nucleation refers to the propensity for phase transformations to initiate preferentially on foreign surfaces, such as vessel walls, dust particles, or formulation additives. In crystallization, the form of the initial nucleus has ramifications for the crystallographic form, morphology, and properties of the resulting solid. Nevertheless, the discovery and design of nucleating agents remains a matter of trial and error because of the very small spatiotemporal scales over which the critical nucleus is formed and the extreme difficulty of examining such events empirically. Using molecular dynamics simulations, we demonstrate a method for the rapid screening of entire families of materials for activity as nucleating agents and for characterizing their mechanism of action. The method is applied to the crystallization of n-pentacontane, a model surrogate for polyethylene, on the family of tetrahedrally coordinated crystals, including diamond and silicon. A systematic variation of parameters in the interaction potential permits a comprehensive, physically based screening of nucleating agents in this class of materials, including both real and hypothetical candidates. The induction time for heterogeneous nucleation is shown to depend strongly on crystallographic registry between the nucleating agent and the critical nucleus, indicative of an epitaxial mechanism in this class of materials. Importantly, the severity of this registry requirement weakens with decreasing rigidity of the substrate and increasing strength of attraction to the surface of the nucleating agent. Employing this method, a high-throughput computational screening of nucleating agents becomes possible, facilitating the discovery of novel nucleating agents within a broad “materials genome” of possible additives.National Science Foundation (U.S.) (Award CMMI-1235109

Sex differences in oncogenic mutational processes

Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research.Peer reviewe

Sex differences in oncogenic mutational processes

Funder: Canadian Network for Research and Innovation in Machining Technology, Natural Sciences and Engineering Research Council of Canada (NSERC Canadian Network for Research and Innovation in Machining Technology); doi: https://doi.org/10.13039/501100002790Funder: Genome Canada (Génome Canada); doi: https://doi.org/10.13039/100008762Funder: Canada Foundation for Innovation (Fondation canadienne pour l'innovation); doi: https://doi.org/10.13039/501100000196Funder: Terry Fox Research Institute (Institut de Recherche Terry Fox); doi: https://doi.org/10.13039/501100004376Abstract: Sex differences have been observed in multiple facets of cancer epidemiology, treatment and biology, and in most cancers outside the sex organs. Efforts to link these clinical differences to specific molecular features have focused on somatic mutations within the coding regions of the genome. Here we report a pan-cancer analysis of sex differences in whole genomes of 1983 tumours of 28 subtypes as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium. We both confirm the results of exome studies, and also uncover previously undescribed sex differences. These include sex-biases in coding and non-coding cancer drivers, mutation prevalence and strikingly, in mutational signatures related to underlying mutational processes. These results underline the pervasiveness of molecular sex differences and strengthen the call for increased consideration of sex in molecular cancer research

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

Funder: NCI U24CA211006Abstract: The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts

Retrospective evaluation of whole exome and genome mutation calls in 746 cancer samples

The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that ~80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAF < 15%) and clonal heterogeneity contribute up to 68% of private WGS mutations and 71% of private WES mutations. We observe that ~30% of private WGS mutations trace to mutations identified by a single variant caller in WES consensus efforts. WGS captures both ~50% more variation in exonic regions and un-observed mutations in loci with variable GC-content. Together, our analysis highlights technological divergences between two reproducible somatic variant detection efforts.The Cancer Genome Atlas (TCGA) and International Cancer Genome Consortium (ICGC) curated consensus somatic mutation calls using whole exome sequencing (WES) and whole genome sequencing (WGS), respectively. Here, as part of the ICGC/TCGA Pan-Cancer Analysis of Whole Genomes (PCAWG) Consortium, which aggregated whole genome sequencing data from 2,658 cancers across 38 tumour types, we compare WES and WGS side-by-side from 746 TCGA samples, finding that -80% of mutations overlap in covered exonic regions. We estimate that low variant allele fraction (VAFPeer reviewe