XSEDE: Accelerating Scientific Discovery

Towns, John; Cockerill, T. M.; Dahan, Maytal; Foster, Ian; Gaither, Kelly; Grimshaw, Andrew S.; Hazlewood, Victor; Lathrop, Scott; Lifka, David; Peterson, Gregory D.; Roskies, Ralph; Scott, James R.; Wilkins‐Diehr, Nancy

doi:10.1109/mcse.2014.80

Cited by 3,193 publications

(2,069 citation statements)

References 16 publications

Supporting

Mentioning

2,033

Contrasting

Order By: Relevance

“…This work used the Extreme Science and Engineering Discovery Environment (XSEDE), which is supported by National Science Foundation grant number ACI-1053575 [155]. This material is based upon work supported by the National Science Foundation under Grant No.…”

Section: Acknowledgementsmentioning

confidence: 99%

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Jones

Jankowski

2017

Molecular Simulation

View full text Add to dashboard Cite

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 accessible. We describe a new Python package diffractometer that permits grazing-incidence X-ray scattering patterns of simulated active layers to be compared against experiments. We explain the accurate calculation of charge-carrier mobilities from coarse-grained active layer morphologies by using atomistic backmapping, quantum chemical calculations, and kinetic Monte Carlo simulations. We employ these simulations to show that ordering of poly(3-hexylthiophene-2,5-diyl) explains a factor of 1000 improvement in charge mobility. In concert, we present a suite of computational tools enabling large-scale electronic properties of organic photovoltaics to be studied and screened for by molecular simulations.

show abstract

Section: Acknowledgementsmentioning

confidence: 99%

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Jones

Jankowski

2017

Molecular Simulation

View full text Add to dashboard Cite

show abstract

“…Subsequent structure calculation and refinement steps were performed using single-and double-precision floatingpoint compilations of Relion-1.4. We used software and computational infrastructure maintained by SBgrid (19), as well as highperformance computing facilities available through the Stampede Supercomputer at Texas Advanced Computing Center (20).…”

Section: Significancementioning

confidence: 99%

Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis

Kulczyk

Moeller

Meyer

et al. 2017

Proc. Natl. Acad. Sci. U.S.A.

View full text Add to dashboard Cite

We present a structure of the ∼650-kDa functional replisome of bacteriophage T7 assembled on DNA resembling a replication fork. A structure of the complex consisting of six domains of DNA helicase, five domains of RNA primase, two DNA polymerases, and two thioredoxin (processivity factor) molecules was determined by single-particle cryo-electron microscopy. The two molecules of DNA polymerase adopt a different spatial arrangement at the replication fork, reflecting their roles in leading-and lagging-strand synthesis. The structure, in combination with biochemical data, reveals molecular mechanisms for coordination of leading-and laggingstrand synthesis. Because mechanisms of DNA replication are highly conserved, the observations are relevant to other replication systems.cryo-EM structure | replisome | coordination of leading-and lagging-strands synthesis | DNA replication | DNA polymerase T he reverse polarity and antiparallel nature of the two strands in duplex DNA pose a topological problem for their simultaneous synthesis. The "trombone" model of DNA replication postulates that the lagging strand forms a loop such that the leading-and lagging-strand replication proteins contact one another (1). This replication loop contains a nascent Okazaki fragment and allows for coordination of leading-and laggingstrand synthesis. The bacteriophage T7 replisome has been studied extensively (2). Thus, the macromolecular complex of T7 replication proteins provides an excellent model for structural analysis of a replisome. Notably, the human mitochondrial and the T7 replication systems are similar (3).The phage T7 replisome is relatively simple. Four proteins are sufficient for reconstitution of the functional replisome, yet the assembled replisome recapitulates all of the key features of more complex prokaryotic and eukaryotic systems (2, 4). These proteins are the following: DNA polymerase (gp5) and its processivity factor, Escherichia coli thioredoxin (trx), single-stranded DNA (ssDNA)-binding protein (gp2.5), and the bifunctional DNA primase-helicase (gp4).Gp4 forms multiple oligomeric forms (5). The negative stain EM revealed that hexamers and heptamers are the most abundant (∼22% and ∼78%, respectively). Upon addition of ssDNA, the equilibrium between the two oligomeric forms changes (∼77% protein rings are now hexameric, and ∼18% are heptameric), indicative of DNA binding (6). The hexamer is an enzymatically active form of gp4. It binds to ssDNA, hydrolyzes nucleotides, translocates on ssDNA, and unwinds dsDNA (7-9). In contrast, the heptamer does not bind to ssDNA (6).Crystal structures of all of the individual T7 replication proteins have been determined (10-15). However, to date there is no structural information on the T7 replisome or its subassemblies. Consequently, intermolecular interactions involved in coordination of DNA synthesis have not been identified. We have therefore used cryo-electron microscopy (cryo-EM) and single-particle reconstruction methods to determine a structure of the T7 replisome. ResultsR...

show abstract

“…106 The O t Bu groups were simplified to OMe groups and the methyl groups of LA were replaced by H atoms during the propagation steps. For the oxidized…”

mentioning

confidence: 99%

A Comparison of Gallium and Indium Alkoxide Complexes as Catalysts for Ring-Opening Polymerization of Lactide

et al. 2017

View full text Add to dashboard Cite

ABSTRACT:The synthesis, characterization, and reactivity of an aluminum alkoxide complex supported by a ferrocene-based ligand, (thiolfan*)Al(O t Bu) (1 red , thiolfan* = 1,1'-di(2,4-di-tert-butyl-6-thiophenoxy)ferrocene), are reported. The homopolymers of L-lactide (LA), ε-caprolactone (CL), δ-valerolactone (VL), cyclohexene oxide (CHO), trimethylene carbonate (TMC), and their copolymers were obtained in a controlled manner by using redox reagents. Detailed DFT calculations and experimental studies were performed to investigate the mechanism. Mechanistic studies show that after the insertion of the first monomer, the coordination effect of the carbonyl group, which has usually been ignored in previous reports, can significantly change the energy barrier of the propagation steps, thus playing an important role in polymerization and copolymerization processes.

show abstract

XSEDE: Accelerating Scientific Discovery

Cited by 3,193 publications

References 16 publications

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Computationally connecting organic photovoltaic performance to atomistic arrangements and bulk morphology

Cryo-EM structure of the replisome reveals multiple interactions coordinating DNA synthesis

A Comparison of Gallium and Indium Alkoxide Complexes as Catalysts for Ring-Opening Polymerization of Lactide

Contact Info

Product

Resources

About