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Full-Text Articles in Engineering
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Molecular Dynamic Studies Of Dye–Dye And Dye–Dna Interactions Governing Excitonic Coupling In Squaraine Aggregates Templated By Dna Holliday Junctions, German Barcenas, Austin Biaggne, Olga A. Mass, William B. Knowlton, Bernard Yurke, Lan Li
Materials Science and Engineering Faculty Publications and Presentations
Dye molecules, arranged in an aggregate, can display excitonic delocalization. The use of DNA scaffolding to control aggregate configurations and delocalization is of research interest. Here, we applied Molecular Dynamics (MD) to gain an insight on how dye–DNA interactions affect excitonic coupling between two squaraine (SQ) dyes covalently attached to a DNA Holliday junction (HJ). We studied two types of dimer configurations, i.e., adjacent and transverse, which differed in points of dye covalent attachments to DNA. Three structurally different SQ dyes with similar hydrophobicity were chosen to investigate the sensitivity of excitonic coupling to dye placement. Each dimer configuration was …
Probing Dna Structural Heterogeneity By Identifying Conformational Subensembles Of A Bicovalently Bound Cyanine Dye, Matthew S. Barclay, Azhad U. Chowdhury, Austin Biaggne, Jonathan S. Huff, Nicholas D. Wright, Paul H. Davis, Lan Li, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Daniel B. Turner
Probing Dna Structural Heterogeneity By Identifying Conformational Subensembles Of A Bicovalently Bound Cyanine Dye, Matthew S. Barclay, Azhad U. Chowdhury, Austin Biaggne, Jonathan S. Huff, Nicholas D. Wright, Paul H. Davis, Lan Li, William B. Knowlton, Bernard Yurke, Ryan D. Pensack, Daniel B. Turner
Materials Science and Engineering Faculty Publications and Presentations
DNA is a re-configurable, biological information-storage unit, and much remains to be learned about its heterogeneous structural dynamics. For example, while it is known that molecular dyes templated onto DNA exhibit increased photostability, the mechanism by which the structural dynamics of DNA affect the dye photophysics remains unknown. Here, we use femtosecond, two-dimensional electronic spectroscopy measurements of a cyanine dye, Cy5, to probe local conformations in samples of single-stranded DNA (ssDNA–Cy5), double-stranded DNA (dsDNA–Cy5), and Holliday junction DNA (HJ–DNA–Cy5). A line shape analysis of the 2D spectra reveals a strong excitation–emission correlation present in only the dsDNA–Cy5 complex, which is …
General-Purpose Coarse-Grained Toughened Thermoset Model For 44dds/Dgeba/Pes, Michael M. Henry, Stephen Thomas, Mone’T Alberts, Carla E. Estridge, Brittan Farmer, Olivia Mcnair, Eric Jankowski
General-Purpose Coarse-Grained Toughened Thermoset Model For 44dds/Dgeba/Pes, Michael M. Henry, Stephen Thomas, Mone’T Alberts, Carla E. Estridge, Brittan Farmer, Olivia Mcnair, Eric Jankowski
Materials Science and Engineering Faculty Publications and Presentations
The objective of this work is to predict the morphology and material properties of crosslinking polymers used in aerospace applications. We extend the open-source dybond plugin for HOOMD-Blue to implement a new coarse-grained model of reacting epoxy thermosets and use the 44DDS/DGEBA/PES system as a case study for calibration and validation. We parameterize the coarse-grained model from atomistic solubility data, calibrate reaction dynamics against experiments, and check for size-dependent artifacts. We validate model predictions by comparing glass transition temperatures measurements at arbitrary degree of cure, gel-points, and morphology predictions against experiments. We demonstrate for the first time in molecular simulations …
Perspective On Coarse-Graining, Cognitive Load, And Materials Simulation, Eric Jankowski, Nealee Ellyson, Jenny W. Fothergill, Michael M. Henry, Mitchell H. Leibowitz, Evan D. Miller, Mone't Alberts, Jamie D. Guevara, Chris D. Jones, Mia Klopfenstein, Kendra K. Noneman, Rachel Singleton, Matthew L. Jones
Perspective On Coarse-Graining, Cognitive Load, And Materials Simulation, Eric Jankowski, Nealee Ellyson, Jenny W. Fothergill, Michael M. Henry, Mitchell H. Leibowitz, Evan D. Miller, Mone't Alberts, Jamie D. Guevara, Chris D. Jones, Mia Klopfenstein, Kendra K. Noneman, Rachel Singleton, Matthew L. Jones
Materials Science and Engineering Faculty Publications and Presentations
The predictive capabilities of computational materials science today derive from overlapping advances in simulation tools, modeling techniques, and best practices. We outline this ecosystem of molecular simulations by explaining how important contributions in each of these areas have fed into each other. The combined output of these tools, techniques, and practices is the ability for researchers to advance understanding by efficiently combining simple models with powerful software. As specific examples, we show how the prediction of organic photovoltaic morphologies have improved by orders of magnitude over the last decade, and how the processing of reacting epoxy thermosets can now be …
Optimization And Validation Of Efficient Models For Predicting Polythiophene Self-Assembly, Evan D. Miller, Matthew L. Jones, Michael M. Henry, Paul Chery, Kyle Miller, Eric Jankowski
Optimization And Validation Of Efficient Models For Predicting Polythiophene Self-Assembly, Evan D. Miller, Matthew L. Jones, Michael M. Henry, Paul Chery, Kyle Miller, Eric Jankowski
Materials Science and Engineering Faculty Publications and Presentations
We develop an optimized force-field for poly(3-hexylthiophene) (P3HT) and demonstrate its utility for predicting thermodynamic self-assembly. In particular, we consider short oligomer chains, model electrostatics and solvent implicitly, and coarsely model solvent evaporation. We quantify the performance of our model to determine what the optimal system sizes are for exploring self-assembly at combinations of state variables. We perform molecular dynamics simulations to predict the self-assembly of P3HT at ~350 combinations of temperature and solvent quality. Our structural calculations predict that the highest degrees of order are obtained with good solvents just below the melting temperature. We find our model produces …
Computationally Connecting Organic Photovoltaic Performance To Atomistic Arrangements And Bulk Morphology, Matthew L. Jones, Eric Jankowski
Computationally Connecting Organic Photovoltaic Performance To Atomistic Arrangements And Bulk Morphology, Matthew L. Jones, Eric Jankowski
Materials Science and Engineering Faculty Publications and Presentations
Rationally designing roll-to-roll printed organic photovoltaics requires a fundamental understanding of active layer morphologies optimized for charge separation and transport, and which ingredients can be used to self-assemble those morphologies. In this review article we discuss advances in three areas of computational modeling that provide insight into active layer morphology and the charge transport properties that result. We explain the computational bottlenecks prohibiting atomistically-detailed simulations of device-scale active layers and the coarse-graining and hardware acceleration strategies for overcoming them. We review coarse-grained simulations of organic photovoltaic active layers and show that high throughput simulations of experimentally-relevant length scales are now …
Simulation Of Plasticity In Nanocrystalline Silicon, M. J. Demkowicz, A. S. Argon, D. Farkas, Megan Frary
Simulation Of Plasticity In Nanocrystalline Silicon, M. J. Demkowicz, A. S. Argon, D. Farkas, Megan Frary
Materials Science and Engineering Faculty Publications and Presentations
Molecular dynamics investigation of plasticity in a model nanocrystalline silicon system demonstrates that inelastic deformation localizes in intergranular regions. The carriers of plasticity in these regions are atomic environments that can be described as high-density liquid-like amorphous silicon. During fully developed flow, plasticity is confined to system-spanning intergranular zones of easy flow. As an active flow zone rotates out of the plane of maximum resolved shear stress during deformation to large strain, new zones of easy flow are formed. Compatibility of the microstructure is accommodated by processes such as grain rotation and formation of new grains. Nano-scale voids or cracks …