Now showing items 1-20 of 3970

• The Air–Water Interface of Condensed Water Microdroplets does not Produce H2O2

(arXiv, 2021-09-07) [Preprint]
Recent reports on the production of hydrogen peroxide (H2O2) on the surface of condensed water microdroplets without the addition of catalysts or additives have sparked significant interest. The underlying mechanism isspeculated to be ultrahigh electric fields at the air-water interface;smaller droplets present higher interfacial area and produce higher (detectable) H2O2 yields. Herein, we present an alternative explanation for these experimental observations. We compare H2O2 production in water microdroplets condensed from vapor produced via (i) heating water to 50–70℃ and (ii) ultrasonic humidification (as exploited in the original report). Water microdroplets condensed after heating do not show any enhancement in the H2O2 level in comparison to the bulk water, regardless of droplet size or the substrate wettability. In contrast, those condensed after ultrasonic humidification produce significantly higher H2O2 quantities. We conclude that the ultrasonication of water contributes to the H2O2 production, not droplet interfacial effects.
• A threefold approach including quantum chemical, molecular docking and molecular dynamic studies to explore the natural compounds from Centaurea jacea as the potential inhibitors for COVID-19

(Brazilian Journal of Biology, FapUNIFESP (SciELO), 2021-09-03) [Article]
Abstract In the current report, we studied the possible inhibitors of COVID-19 from bioactive constituents of Centaurea jacea using a threefold approach consisting of quantum chemical, molecular docking and molecular dynamic techniques. Centaurea jacea is a perennial herb often used in folk medicines of dermatological complaints and fever. Moreover, anticancer, antioxidant, antibacterial and antiviral properties of its bioactive compounds are also reported. The Mpro (Main proteases) was docked with different compounds of Centaurea jacea through molecular docking. All the studied compounds including apigenin, axillarin, Centaureidin, Cirsiliol, Eupatorin and Isokaempferide, show suitable binding affinities to the binding site of SARS-CoV-2 main protease with their binding energies -6.7 kcal/mol, -7.4 kcal/mol, -7.0 kcal/mol, -5.8 kcal/mol, -6.2 kcal/mol and -6.8 kcal/mol, respectively. Among all studied compounds, axillarin was found to have maximum inhibitor efficiency followed by Centaureidin, Isokaempferide, Apigenin, Eupatorin and Cirsiliol. Our results suggested that axillarin binds with the most crucial catalytic residues CYS145 and HIS41 of the Mpro, moreover axillarin shows 5 hydrogen bond interactions and 5 hydrophobic interactions with various residues of Mpro. Furthermore, the molecular dynamic calculations over 60 ns (6×106 femtosecond) time scale also shown significant insights into the binding effects of axillarin with Mpro of SARS-CoV-2 by imitating protein like aqueous environment. From molecular dynamic calculations, the RMSD and RMSF computations indicate the stability and dynamics of the best docked complex in aqueous environment. The ADME properties and toxicity prediction analysis of axillarin also recommended it as safe drug candidate. Further, in vivo and in vitro investigations are essential to ensure the anti SARS-CoV-2 activity of all bioactive compounds particularly axillarin to encourage preventive use of Centaurea jacea against COVID-19 infections.
• Mapping Drug-Induced Neuropathy through In-Situ Motor Protein Tracking and Machine Learning

(Journal of the American Chemical Society, American Chemical Society (ACS), 2021-09-01) [Article]
Chemotherapy can induce toxicity in the central and peripheral nervous systems and result in chronic adverse reactions that impede continuous treatment and reduce patient quality of life. There is a current lack of research to predict, identify, and offset drug-induced neurotoxicity. Rapid and accurate assessment of potential neuropathy is crucial for cost-effective diagnosis and treatment. Here we report dynamic near-infrared upconversion imaging that allows intraneuronal transport to be traced in real time with millisecond resolution, but without photobleaching or blinking. Drug-induced neurotoxicity can be screened prior to phenotyping, on the basis of subtle abnormalities of kinetic characteristics in intraneuronal transport. Moreover, we demonstrate that combining the upconverting nanoplatform with machine learning offers a powerful tool for mapping chemotherapy-induced peripheral neuropathy and assessing drug-induced neurotoxicity.
• Selective Hydrocracking Polyaromatics into Light Aromatics: the Separation of Hydrogenation Center and Cracking Center

(ACS Sustainable Chemistry & Engineering, American Chemical Society (ACS), 2021-09-01) [Article]
Serial combined catalysts with separated hydrogenation centers and cracking centers, which were composed of CoMo/Al2O3 and Ni/B, were synthesized and compared with the normal bifunctional catalysts of NiMo/Al2O3–Beta and CoMo/Al2O3–Beta. The properties of different catalysts were characterized by various methods. H2-TPR results demonstrated the existence of hydrogen spillover between a Co or Ni promoter, and Mo metals could facilitate the reducibility of oxide Mo species and hydrogenation of aromatics. The naphthalene hydrocracking performances were also evaluated and compared with different catalysts. The combined catalysts showed relatively high yields of light aromatics with high-octane values (<C10 aromatics) and low yields of cyclanes. The reason should be correlated to the synergistic effect of CoMo/Al2O3 (hydrogenation center) with a high selectivity of converting naphthalene into C10 aromatics and the Ni/B (cracking center) with high activity of cracking C10 aromatics into light aromatics. The kinetic and thermodynamic analyses confirmed that the naphthalene hydrocracking activity of the CoMo/Al2O3–Beta catalyst was the highest, and the combined catalysts showed higher selectivity of converting naphthalene into light aromatics than NiMo/Al2O3–Beta and CoMo/Al2O3–Beta catalysts.
• Specificity and Synergy at the Oil–Brine Interface: New Insights from Experiments and Molecular Dynamics Simulations

(Energy & Fuels, American Chemical Society (ACS), 2021-08-30) [Article]
The interfacial tension (IFT) between oil and brine is a key parameter affecting the enhanced oil recovery process. Despite the several theoretical and experimental investigations on the oil–brine system, the salinity effect on the IFT of oil–brine is still not fully understood. There is a contradiction in the literature rather than consistency. In the present study, we combine molecular dynamics (MD) simulations with the pendant drop method to investigate the molecular interactions at the oil–brine interface to better understand the salinity–IFT relationship. Herein, we are taking into account the complex composition of both crude oil and brine and the pH and total acid number. Different salinity conditions have been considered ranging from deionized water to connate (formation) water. We also consider the effects of individual brines of the main alkali salts (i.e., NaCl, MgCl2, and CaCl2) that are common in carbonate reservoirs. The specificity and synergy of the molecular interactions are observed via the confrontation of the results of the mixed brines (seawater and formation water) with those of the individual brines. We observed a significant impact of the divalent cations on the oil–brine interfacial tension. Due to the specificity of the organic acid–Ca2+ type of interaction and the synergy between the different ions, complete encapsulation of the Ca2+ ions has been observed within the formation water brine. This induces the depletion of the organic acids at the interface and thus increases the IFT. Such ionic encapsulation has not been observed in the individual brines because the cation–anion (Cl–) and the cation–water interactions are strong enough to prevent the cation–acid encapsulation. The interplay between the electrostatic interactions and the cations’ dehydration-free energies is the main parameter that controls their specificity and synergy, affecting the oil–brine interfacial properties. This work provides important details on the ionic interactions influencing the interfacial properties between crude hydrocarbons and brine.
• Environmental vulnerability of the global ocean epipelagic plankton community interactome.

(Science advances, American Association for the Advancement of Science (AAAS), 2021-08-28) [Article]
Marine plankton form complex communities of interacting organisms at the base of the food web, which sustain oceanic biogeochemical cycles and help regulate climate. Although global surveys are starting to reveal ecological drivers underlying planktonic community structure and predicted climate change responses, it is unclear how community-scale species interactions will be affected by climate change. Here, we leveraged $\textit{Tara}$ Oceans sampling to infer a global ocean cross-domain plankton co-occurrence network-the community interactome-and used niche modeling to assess its vulnerabilities to environmental change. Globally, this revealed a plankton interactome self-organized latitudinally into marine biomes (Trades, Westerlies, Polar) and more connected poleward. Integrated niche modeling revealed biome-specific community interactome responses to environmental change and forecasted the most affected lineages for each community. These results provide baseline approaches to assess community structure and organismal interactions under climate scenarios while identifying plausible plankton bioindicators for ocean monitoring of climate change.
• Diel pCO2 fluctuations alter the molecular response of coral reef fishes to ocean acidification conditions

(Molecular Ecology, Wiley, 2021-08-28) [Article]
Environmental partial pressure of CO2 (pCO2) variation can modify the responses of marine organisms to ocean acidification, yet the underlying mechanisms for this effect remain unclear. On coral reefs, environmental pCO2 fluctuates on a regular day–night cycle. Effects of future ocean acidification on coral reef fishes might therefore depend on their response to this diel cycle of pCO2. To evaluate the effects on the brain molecular response, we exposed two common reef fishes (Acanthochromis polyacanthus and Amphiprion percula) to two projected future pCO2 levels (750 and 1,000 µatm) under both stable and diel fluctuating conditions. We found a common signature to stable elevated pCO2 for both species, which included the downregulation of immediate early genes, indicating lower brain activity. The transcriptional programme was more strongly affected by higher average pCO2 in a stable treatment than for fluctuating treatments, but the largest difference in molecular response was between stable and fluctuating pCO2 treatments. This indicates that a response to a change in environmental pCO2 conditions is different for organisms living in a fluctuating than in stable environments. This differential regulation was related to steroid hormones and circadian rhythm (CR). Both species exhibited a marked difference in the expression of CR genes among pCO2 treatments, possibly accommodating a more flexible adaptive approach in the response to environmental changes. Our results suggest that environmental pCO2 fluctuations might enable reef fishes to phase-shift their clocks and anticipate pCO2 changes, thereby avoiding impairments and more successfully adjust to ocean acidification conditions.
• An Efficient ADER-DG Local Time Stepping Scheme for 3D HPC Simulation of Seismic Waves in Poroelastic Media

(arXiv, 2021-08-24) [Preprint]
Many applications from geosciences require simulations of seismic waves in porous media. Biot's theory of poroelasticity describes the coupling between solid and fluid phases and introduces a stiff source term, thereby increasing computational cost and motivating efficient methods utilising High-Performance Computing. We present a novel realisation of the discontinuous Galerkin scheme with Arbitrary DERivative time stepping (ADER-DG) that copes with stiff source terms. To integrate this source term with a reasonable time step size, we use an element-local space-time predictor, which needs to solve medium-sized linear systems - with 1000 to 10000 unknowns - in each element update (i.e., billions of times). We present a novel block-wise back-substitution algorithm for solving these systems efficiently. In comparison to LU decomposition, we reduce the number of floating-point operations by a factor of up to 25. The block-wise back-substitution is mapped to a sequence of small matrix-matrix multiplications, for which code generators are available to generate highly optimised code. We verify the new solver thoroughly in problems of increasing complexity. We demonstrate high-order convergence for 3D problems. We verify the correct treatment of point sources, material interfaces and traction-free boundary conditions. In addition, we compare against a finite difference code for a newly defined layer over half-space problem. We find that extremely high accuracy is required to resolve the slow P-wave at a free surface, while solid particle velocities are not affected by coarser resolutions. By using a clustered local time stepping scheme, we reduce time to solution by a factor of 6 to 10 compared to global time stepping. We conclude our study with a scaling and performance analysis, demonstrating our implementation's efficiency and its potential for extreme-scale simulations.
• Deep Context-Encoding Network For Retinal Image Captioning

(IEEE, 2021-08-23) [Conference Paper]
Automatically generating medical reports for retinal images is one of the promising ways to help ophthalmologists reduce their workload and improve work efficiency. In this work, we propose a new context-driven encoding network to automatically generate medical reports for retinal images. The proposed model is mainly composed of a multi-modal input encoder and a fused-feature decoder. Our experimental results show that our proposed method is capable of effectively leveraging the interactive information between the input image and context, i.e., keywords in our case. The proposed method creates more accurate and meaningful reports for retinal images than baseline models and achieves state-of-the-art performance. This performance is shown in several commonly used metrics for the medical report generation task: BLEUavg (+16%), CIDEr (+10.2%), and ROUGE (+8.6%).
• Multi-window SRS imaging using a rapid widely tunable fiber laser

(arXiv, 2021-08-19) [Preprint]
Spectroscopic stimulated Raman scattering (SRS) imaging has become a useful tool finding a broad range of applications. Yet, wider adoption is hindered by the bulky and environmentally-sensitive solid-state optical parametric oscillator (OPO) in current SRS microscope. Moreover, chemically-informative multi-window SRS imaging across C-H, C-D and fingerprint Raman regions is challenging due to the slow wavelength tuning speed of the solid-state OPO. In this work, we present a multi-window SRS imaging system based on a compact and robust fiber laser with rapid and widely tuning capability. To address the relative intensity noise intrinsic to fiber laser, we implemented auto-balanced detection which enhances the signal-to-noise ratio of stimulated Raman loss imaging by 23 times. We demonstrate high-quality SRS metabolic imaging of fungi, cancer cells, and Caenorhabditis elegans across the C-H, C-D and fingerprint Raman windows. Our re-sults showcase the potential of the compact multi-window SRS system for a broad range of applications.
• Antiscaling Evaluation and Quantum Chemical Studies of Nitrogen-Free Organophosphorus Compounds for Oilfield Scale Management

(Industrial & Engineering Chemistry Research, American Chemical Society (ACS), 2021-08-17) [Article]
• A New Stability Approach for Positivity-Preserving Patankar-type Schemes

(arXiv, 2021-08-16) [Preprint]
Patankar-type schemes are linearly implicit time integration methods designed to be unconditionally positivity-preserving by going outside of the class of general linear methods. Thus, classical stability concepts cannot be applied and there is no satisfying stability theory for these schemes. We develop a new approach to study stability properties of Patankar-type methods. In particular, we demonstrate problematic behavior of these methods that can lead to undesired oscillations or order reduction. Extreme cases of the latter manifest as spurious steady states. We investigate various classes of Patankar-type schemes based on classical Runge-Kutta methods, strong stability preserving Runge-Kutta methods, and deferred correction schemes using our approach. Finally, we strengthen our analysis with challenging applications including stiff nonlinear problems.
• Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

(Nature Communications, Springer Science and Business Media LLC, 2021-08-16) [Article]
AbstractIce nucleation on the surface plays a vital role in diverse areas, ranging from physics and cryobiology to atmospheric science. Compared to ice nucleation in the bulk, the water-surface interactions present in heterogeneous ice nucleation complicate the nucleation process, making heterogeneous ice nucleation less comprehended, especially the relationship between the kinetics and the structures of the critical ice nucleus. Here we combine Markov State Models and transition path theory to elucidate the ensemble pathways of heterogeneous ice nucleation. Our Markov State Models reveal that the classical one-step and non-classical two-step nucleation pathways can surprisingly co-exist with comparable fluxes at T = 230 K. Interestingly, we find that the disordered mixing of rhombic and hexagonal ice leads to a favorable configurational entropy that stabilizes the critical nucleus, facilitating the non-classical pathway. In contrast, the favorable energetics promotes the formation of hexagonal ice, resulting in the classical pathway. Furthermore, we discover that, at elevated temperatures, the nucleation process prefers to proceed via the classical pathway, as opposed to the non-classical pathway, since the potential energy contributions override the configurational entropy compensation. This study provides insights into the mechanisms of heterogeneous ice nucleation and sheds light on the rational designs to control crystallization processes.
• Temperature-dependent kinetic pathways of heterogeneous ice nucleation competing between classical and non-classical nucleation

(Nature Communications, Springer Science and Business Media LLC, 2021-08-16) [Article]
AbstractIce nucleation on the surface plays a vital role in diverse areas, ranging from physics and cryobiology to atmospheric science. Compared to ice nucleation in the bulk, the water-surface interactions present in heterogeneous ice nucleation complicate the nucleation process, making heterogeneous ice nucleation less comprehended, especially the relationship between the kinetics and the structures of the critical ice nucleus. Here we combine Markov State Models and transition path theory to elucidate the ensemble pathways of heterogeneous ice nucleation. Our Markov State Models reveal that the classical one-step and non-classical two-step nucleation pathways can surprisingly co-exist with comparable fluxes at T = 230 K. Interestingly, we find that the disordered mixing of rhombic and hexagonal ice leads to a favorable configurational entropy that stabilizes the critical nucleus, facilitating the non-classical pathway. In contrast, the favorable energetics promotes the formation of hexagonal ice, resulting in the classical pathway. Furthermore, we discover that, at elevated temperatures, the nucleation process prefers to proceed via the classical pathway, as opposed to the non-classical pathway, since the potential energy contributions override the configurational entropy compensation. This study provides insights into the mechanisms of heterogeneous ice nucleation and sheds light on the rational designs to control crystallization processes.
• Analysis of the development of the flame brush in turbulent premixed spherical flames

(Combustion and Flame, Elsevier BV, 2021-08-13) [Article]
The thickness of the turbulent flame brush is central to the modeling of premixed turbulent combustion and the theory of turbulent diffusion is often applied to explain the growth of the brush with varying success. However, numerous studies have shown that the brush evolves differently from the dispersion of material points on the account of flame propagation, density changes across the front, and hydrodynamic instabilities. Modifications to turbulent diffusion theory to incorporate these effects are challenging since the theory is Lagrangian. In this article, we present an alternate Eulerian framework based on the surface density formalism. We employ the proposed framework to analyze a database of direct numerical simulations of spherical turbulent premixed flames in decaying isotropic turbulence and recover mechanisms for which scaling laws are proposed and assessed against data. We characterize quantitatively two mechanisms: one related to the mean velocity gradient induced by thermal expansion and the other due to flame propagation in the presence of curvature. We demonstrate that the net effect of these two processes is to hinder the growth of the turbulent flame brush in the present configuration. Our analysis supports the notion that the turbulent flame brush does not grow indefinitely, rather it attains a maximum thickness.
• Rapid enzymatic hydrolysis of crambe oil catalyzed by castor seeds lipases

(Industrial Crops and Products, Elsevier BV, 2021-08-13) [Article]
Oil hydrolysis is an important industrial process that requires high temperatures and pressure, or expensive enzymatic catalysts; it is, therefore, necessary to seek the use of inexpensive raw materials and process enhancement. In this work, a rapid and eco-friendly method, using ultrasound power, was successfully employed to hydrolyze crambe (Crambe abyssinica Hochst.) oil using lipase enzymes directly from castor (Ricinus communis L.) seeds, in oil-free and fresh forms. A yield of 86 % conversion of triglycerides into free fatty acids (FFA) was achieved in 5 min using castor fresh seeds and 73 % of conversion when performing the reaction with oil-free seeds. The operational conditions of ultrasound power, mass ratio of buffer solution and oil, catalyst, and total substrate were evaluated using a central composite rotatable design (CCRD). The hydrolysis yield was optimized by response surface methodology (RSM). The optimum conditions were approximately 70 % of ultrasound power (350 W), 1.79 buffer solution/oil mass ratio, and 0.25 catalyst/substrate mass ratio for fresh seeds. For the oil-free seeds, the optimal conditions found were 68 % (340 W) of ultrasound power, 1.67 buffer solution/oil mass ratio, and 0.06 catalyst/substrate mass ratio. Mathematical modeling was applied to the experimental kinetic data, and it was possible to predict FFA concentration values from independent experiments.
• The plant microbiota: composition, functions, and engineering

(Current Opinion in Biotechnology, Elsevier BV, 2021-08-12) [Article]
• Diversification and distribution of gall crabs (Brachyura: Cryptochiridae: Opecarcinus) associated with Agariciidae corals

(Coral Reefs, Springer Science and Business Media LLC, 2021-08-12) [Article]
Coral reefs are home to the greatest diversity of marine life, and many species on reefs live in symbiotic associations. Studying the historical biogeography of symbiotic species is key to unravelling (potential) coevolutionary processes and explaining species richness patterns. Coral-dwelling gall crabs (Cryptochiridae) live in obligate symbiosis with a scleractinian host, and are ideally suited to study the evolutionary history between heterogeneous taxa involved in a symbiotic relationship. The genus Opecarcinus Kropp and Manning, 1987, like its host coral family Agariciidae, occurs in both Indo-Pacific and Caribbean seas, and is the only cryptochirid genus with a circumtropical distribution. Here, we use mitochondrial and nuclear DNA gene fragments of Opecarcinus specimens sampled from 21 Indo-Pacific localities and one Atlantic (Caribbean) locality. We applied several species delimitation tests to characterise species diversity, inferred a Bayesian molecular-clock time-calibrated phylogeny to estimate divergence times and performed an ancestral area reconstruction. Time to the most recent common ancestor (tMRCA) of Opecarcinus is estimated at 15−6 Mya (middle Miocene—late Miocene). The genus harbours ~ 15 undescribed species as well as several potential species complexes. There are indications of strict host-specificity patterns in certain Opecarcinus species in the Indo-Pacific and Atlantic, however, a robust phylogeny reconstruction of Agariciidae corals—needed to test this further—is currently lacking. The Indo-West Pacific was inferred to be the most probable ancestral area, from where the Opecarcinus lineage colonised the Western Atlantic and subsequently speciated into O. hypostegus. Opecarcinus likely invaded from the Indo-West Pacific across the East Pacific Barrier to the Atlantic, before the full closure of the Isthmus of Panama. The subsequent speciation of O. hypostegus, is possibly associated with newly available niches in the Caribbean, in combination with genetic isolation following the closure of the Panama Isthmus.
• Penetration depth of Cooper pairs in the IrMn antiferromagnet

(Physical Review B, American Physical Society (APS), 2021-08-10) [Article]
• Balanced photodetector nonlinearity for the short-pulse regime

(Applied Optics, The Optical Society, 2021-08-06) [Article]
Short-pulse lasers are used to characterize the nonlinear response of amplified photodetectors. Two widely used balanced detectors are characterized in terms of amplitude, area, broadening, and balancing the mismatch of their impulse response. The dynamic impact of pulses on the detector is also discussed. It is demonstrated that using photodetectors with short pulses triggers nonlinearities even when the source average power is well below the detector's continuous power saturation threshold.