64 research outputs found
Toward Fully Automated High Performance Computing Drug Discovery: A Massively Parallel Virtual Screening Pipeline for Docking and Molecular Mechanics/Generalized Born Surface Area Rescoring to Improve Enrichment
In this work we announce and evaluate
a high throughput virtual
screening pipeline for <i>in-silico</i> screening of virtual
compound databases using high performance computing (HPC). Notable
features of this pipeline are an automated receptor preparation scheme
with unsupervised binding site identification. The pipeline includes
receptor/target preparation, ligand preparation, VinaLC docking calculation,
and molecular mechanics/generalized Born surface area (MM/GBSA) rescoring
using the GB model by Onufriev and co-workers [<i>J. Chem. Theory
Comput.</i> <b>2007</b>, <i>3</i>, 156â169].
Furthermore, we leverage HPC resources to perform an unprecedented,
comprehensive evaluation of MM/GBSA rescoring when applied to the
DUD-E data set (Directory of Useful Decoys: Enhanced), in which we
selected 38 protein targets and a total of âź0.7 million actives
and decoys. The computer wall time for virtual screening has been
reduced drastically on HPC machines, which increases the feasibility
of extremely large ligand database screening with more accurate methods.
HPC resources allowed us to rescore 20 poses per compound and evaluate
the optimal number of poses to rescore. We find that keeping 5â10
poses is a good compromise between accuracy and computational expense.
Overall the results demonstrate that MM/GBSA rescoring has higher
average receiver operating characteristic (ROC) area under curve (AUC)
values and consistently better early recovery of actives than Vina
docking alone. Specifically, the enrichment performance is target-dependent.
MM/GBSA rescoring significantly out performs Vina docking for the
folate enzymes, kinases, and several other enzymes. The more accurate
energy function and solvation terms of the MM/GBSA method allow MM/GBSA
to achieve better enrichment, but the rescoring is still limited by
the docking method to generate the poses with the correct binding
modes
Crystallization Behavior of Poly(ethylene oxide) in Vertically Aligned Carbon Nanotube Array
We
investigate the effect of the presence of vertically aligned
multiwalled carbon nanotubes (CNTs) on the orientation of polyÂ(ethylene
oxide) (PEO) lamellae and PEO crystallinity. The high alignment of
carbon nanotubes acting as templates probably governs the orientation
of PEO lamellae. This templating effect might result in the lamella
planes of PEO crystals oriented along a direction parallel to the
long axis of the nanotubes. The presence of aligned carbon nanotubes
also gives rise to the decreases in PEO crystallinity, crystallization
temperature, and melting temperature due to the perturbation of carbon
nanotubes to the crystallization of PEO. These effects have significant
implications for controlling the orientation of PEO lamellae and decreasing
the crystallinity of PEO and thickness of PEO lamellae, which have
significant impacts on ion transport in PEO/CNT composite and the
capacitive performance of PEO/CNT composite. Both the decreased PEO
crystallinity and the orientation of PEO lamellae along the long axes
of vertically aligned CNTs give rise to the decrease in the charge
transfer resistance, which is associated with the improvements in
the ion transport and capacitive performance of PEO/CNT composite
Additional file 2: Table S4a. of Different survival analysis methods for measuring long-term outcomes of Indigenous and non-Indigenous Australian cancer patients in the presence and absence of competing risks
Regression analysis of time trend after diagnosis using cause-specific mortality (Cox proportional hazard regression), relative survival (Poisson regression), and competing risk analysis (Fine-Gray regression), all cancers combined1, Australia NT, 1991âÂÂ2009 (full model). Description: Table S4a. including hazard ratios for specific cancer sites. (DOC 47Ă kb
Additional file 1: Table S3a. of Different survival analysis methods for measuring long-term outcomes of Indigenous and non-Indigenous Australian cancer patients in the presence and absence of competing risks
Regression analysis of cause-specific mortality (Cox proportional hazard regression), relative survival (Poisson regression), and competing risk (Fine-Gray regression), all cancers combined1, Australia NT, 1991âÂÂ2009 (full model). Description: Table S3a. including hazard ratios for specific cancer sites. (DOC 49Ă kb
Temporal Changes and Stereoisomeric Compositions of 1,2,5,6,9,10-Hexabromocyclododecane and 1,2-Dibromo-4-(1,2-dibromoethyl)cyclohexane in Marine Mammals from the South China Sea
Stereoisomeric compositions
of 1,2,5,6,9,10-hexabromocyclododecane
(HBCD) and 1,2-dibromo-4-(1,2-dibromoethyl)Âcyclohexane (TBECH) were
investigated in the blubber of two species of marine mammals, finless
porpoises (<i>Neophocaena phocaenoides</i>) and Indo-Pacific
humpback dolphins (<i>Sousa chinensis</i>), from the South
China Sea between 2005 and 2015. The concentrations of ÎŁHBCD
in samples of porpoise (<i>n</i> = 59) and dolphin (<i>n</i> = 32) ranged from 97.2 to 6,260 ng/g lipid weight (lw)
and from 447 to 45,800 ng/g lw, respectively, while those of ÎŁTBECH
were both roughly 2 orders of magnitude lower. A significant increasing
trend of ÎŁHBCD was found in dolphin blubber over the past decade.
The diastereomeric profiles exhibited an absolute predominance of
Îą-HBCD (mostly >90%), while the proportions of four TBECH
diastereomers
in the samples appeared similar. A preferential enrichment of the
(â)-enantiomers of Îą-, β-, and Îł-HBCD was
found in most blubber samples. Interestingly, the body lengths of
porpoises showed a significant negative correlation with the enantiomer
fractions of Îą-HBCD. Significant racemic deviations were also
observed for ι-, γ-, and δ-TBECH enantiomeric pairs.
This is the first report of the presence of TBECH enantiomers in the
environment. The estimated hazard quotient indicates that there is
a potential risk to dolphins due to HBCD exposure
Capillary Effect-Enabled Water Electrolysis for Enhanced Electrochemical Ozone Production by Using Bulk Porous Electrode
A significant overpotential necessary
for the electrochemical oxygen evolution reaction (OER) is one of
the most serious disadvantages in water electrolysis, which, on the
contrary, gives the probability to electrochemically produce ozone
alternative to the common corona discharge. To effectively suppress
the competitive OER and improve gaseous ozone escaping, here we present
a capillary effect-enabled electrolysis strategy by employing an unusual
partial-submersed mode of anode composed of a β-PbO<sub>2</sub> cuboids-loaded bulk porous Pb, and realize a much enhanced electrocatalytic
gaseous ozone production in comparison to the cases of solid Pb counterpart
and/or usual submersion operation. Detailed study reveals a capillary
pressure-induced âmolecular oxygen-locking effectâ in
the electrolyte fully filled in the porous structure of the electrode
area above the electrolyte pool level, which unexpectedly leads to
the production of unusual ¡O<sub>3</sub><sup>â</sup> intermediate.
Distinctive from the traditional electrochemical ozone production
(EOP) mechanism dependent on the essential reaction between the atomic
oxygen and molecular oxygen, the ¡O<sub>3</sub><sup>â</sup> intermediate generation favors the EOP process in the special case
where the capillary action is relevant for a porous bulk anode
Intrinsic Ferromagnetism in 2D Fe<sub>2</sub>H with a High Curie Temperature
The rational design of ferromagnetic materials is crucial
for the
development of spintronic devices. Using first-principles structural
search calculations, we have identified 73 two-dimensional transition
metal hydrides. Some of them show interesting magnetic properties,
even when combined with the characteristics of the electrides. In
particular, the P3Ě
m1 Fe2H monolayer is stabilized in a 1T-MoS2-type structure
with a local magnetic moment of 3 ÎźB per Fe atom,
whose robust ferromagnetism is attributed to the exchange interaction
between neighboring Fe atoms within and between sublayers, leading
to a remarkably high Curie temperature of 340 K. On the other hand,
it has a large magnetic anisotropic energy and spin-polarization ratio.
Interestingly, the above room-temperature ferromagnetism of the Fe2H monolayer is well preserved within a biaxial strain of 5%.
The structure and electron property of surface-functionalized Fe2H are also explored. All of these interesting properties make
the Fe2H monolayer an attractive candidate for spintronic
nanodevices
Low-Temperature Synthesis of Mesoporous Half-Metallic High-Entropy Spinel Oxide Nanofibers for Photocatalytic CO<sub>2</sub> Reduction
High-entropy oxides (HEOs) exhibit
great prospects owing to their
varied composition, chemical adaptability, adjustable light-absorption
ability, and strong stability. In this study, we report a strategy
to synthesize a series of porous high-entropy spinel oxide (HESO)
nanofibers (NFs) at a low temperature of 400 °C by a solâgel
electrospinning technique. The key lies in selecting six acetylacetonate
salt precursors with similar coordination abilities, maintaining a
high-entropy disordered state during the transformation from stable
sols to gel NFs. The as-synthesized HESO NFs of (NiCuMnCoZnFe)3O4 show a high specific surface area of 66.48 m2/g, a diverse elemental composition, a dual bandgap, half-metallicity
property, and abundant defects. The diverse elements provide various
synergistic catalytic sites, and oxygen vacancies act as active sites
for electronâhole separation, while the half-metallicity and
dual-bandgap structure offer excellent light absorption ability, thus
expanding its applicability to a wide range of photocatalytic processes.
As a result, the HESO NFs can efficiently convert CO2 into
CH4 and CO with high yields of 8.03 and 15.89 Îźmol
gâ1 hâ1, respectively, without
using photosensitizers or sacrificial agents
Low-Temperature Synthesis of Mesoporous Half-Metallic High-Entropy Spinel Oxide Nanofibers for Photocatalytic CO<sub>2</sub> Reduction
High-entropy oxides (HEOs) exhibit
great prospects owing to their
varied composition, chemical adaptability, adjustable light-absorption
ability, and strong stability. In this study, we report a strategy
to synthesize a series of porous high-entropy spinel oxide (HESO)
nanofibers (NFs) at a low temperature of 400 °C by a solâgel
electrospinning technique. The key lies in selecting six acetylacetonate
salt precursors with similar coordination abilities, maintaining a
high-entropy disordered state during the transformation from stable
sols to gel NFs. The as-synthesized HESO NFs of (NiCuMnCoZnFe)3O4 show a high specific surface area of 66.48 m2/g, a diverse elemental composition, a dual bandgap, half-metallicity
property, and abundant defects. The diverse elements provide various
synergistic catalytic sites, and oxygen vacancies act as active sites
for electronâhole separation, while the half-metallicity and
dual-bandgap structure offer excellent light absorption ability, thus
expanding its applicability to a wide range of photocatalytic processes.
As a result, the HESO NFs can efficiently convert CO2 into
CH4 and CO with high yields of 8.03 and 15.89 Îźmol
gâ1 hâ1, respectively, without
using photosensitizers or sacrificial agents
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