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Abstract The formation of biomolecular materials via dynamical interfacial processes, such as self-assembly and fusion, for diverse compositions and external conditions can be efficiently probed using ensemble Molecular Dynamics (MD). However, this approach requires many simulations when investigating a large composition phase space. In addition, there is difficulty in predicting whether each simulation will yield biomolecular materials with the desired properties or outcomes and how long each simulation will run. These difficulties can be overcome by rules-based management systems, including intermittent inspection, variable sampling, and premature termination or extension of the individual MD simulations. Automating such a management system can significantly improve runtime efficiency and reduce the burden of organizing large ensembles of MD simulations. To this end, a computational framework, the Pipelines for Automating Compliance-based Elimination and Extension (PACE²), is proposed for high-throughput ensemble biomolecular materials simulations. The PACE²framework encompasses Candidate pipelines, where each pipeline includes temporally separated simulation and analysis tasks. When a MD simulation is completed, an analysis task is triggered, which evaluates the MD trajectory for compliance. Compliant simulations are extended to the next MD phase with a suitable sample rate to allow additional, detailed analysis. Non-compliant simulations are eliminated, and their computational resources are reallocated or released. The framework is designed to run on local desktop computers and high-performance computing resources. Preliminary scientific results enabled by the use of PACE²framework are presented, which demonstrate its potential and validates its function. In the future, the framework will be extended to address generalized workflows and investigate composition-structure-property relations for other classes of materials. 

The formation of biomolecular materials via dynamical interfacial processes such as self-assembly and fusion, for diverse compositions and external conditions, can be efficiently probed using ensemble Molecular Dynamics. However, this approach requires a large number of simulations when investigating a large composition phase space. In addition, there is difficulty in predicting whether each simulation is yielding biomolecular materials with the desired properties or outcomes and how long each simulation will run for. These difficulties can be overcome by rules-based management systems which include intermittent inspection, variable sampling, premature termination and extension of the individual Molecular Dynamics simulations. The automation of such a management system can significantly reduce the overhead of managing large ensembles of Molecular Dynamics simulations. To this end, a high-throughput workflows-based computational framework, Pipeline for Automating Compliance-based Elimination and Extension (PACE2), for biomolecular materials simulations is proposed. The PACE2 framework encompasses Simulation-Analysis Pipelines. Each Pipeline includes temporally separated simulation and analysis tasks. When a Molecular Dynamics simulation completes, an analysis task is triggered which evaluates the Molecular Dynamics trajectory for compliance. Compliant Molecular Dynamics simulations are extended to the next Molecular Dynamics phase with a suitable sample rate to allow additional, detailed analysis. Non-compliant Molecular Dynamics simulations are eliminated, and their computational resources are either reallocated or released. The framework is designed to run on local desktop computers and high performance computing resources. In the future, the framework will be extended to address generalized workflows and investigate other classes of materials. 

Harnessing the self-assembly of peptide sequences has demonstrated great promise in the domain of creating high precision shape-tunable biomaterials. The unique properties of peptides allow for a building block approach to material design. In this study, self-assembly of mixed systems encompassing two peptide sequences with identical hydrophobic regions and distinct polar segments is investigated. The two peptide sequences are diphenylalanine and phenylalanine-asparagine-phenylalanine. The study examines the impact of molecular composition (namely, the total peptide concentration and the relative tripeptide concentration) on the morphology of the self-assembled hybrid biological material. We report a rich polymorphism in the assemblies of these peptides and explain the relationship between the peptide sequence, concentration and the morphology of the supramolecular assembly. 

The interactions between a DPPC lipid membrane and a PAMAM dendron-grafted surface.