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At least 523 records · Page 29

Representability of algebraic topology for biomolecules in machine learning based scoring and virtual screening

This work introduces a number of algebraic topology approaches, including multi-component persistent homology, multi-level persistent homology, and electrostatic persistence for the representation, characterization, and description of small molecules and biomolecular complexes. In contrast to the conventional persistent homology, multi-component persistent homology retains critical chemical and biological information during the topological simplification of biomolecular geometric complexity. Multi-level persistent homology enables a tailored topological description of inter- and/or intra-molecular interactions of interest. Electrostatic persistence incorporates partial charge information into topological invariants. These topological methods are paired with Wasserstein distance to characterize similarities between molecules and are further integrated with a variety of machine learning algorithms, including k-nearest neighbors, ensemble of trees, and deep convolutional neural networks, to manifest their descriptive and predictive powers for protein-ligand binding analysis and virtual screening of small molecules. Extensive numerical experiments involving 4,414 protein-ligand complexes from the PDBBind database and 128,374 ligand-target and decoy-target pairs in the DUD database are performed to test respectively the scoring power and the discriminatory power of the proposed topological learning strategies. It is demonstrated that the present topological learning outperforms other existing methods in protein-ligand binding affinity prediction and ligand-decoy discrimination.

Biochemistry & Molecular Biology↗

Turbulence of electrostatic electron cyclotron harmonic waves observed by Ogo 5.

Analysis of VLF emissions that have been observed near 3/2, 5/2, and 7/2 f sub H by Ogo 5 in the magnetosphere (f sub H is the electron cyclotron frequency) in the light of the mechanism used for the diffuse plasma resonance f sub Dn observed by Alouette 2 and Isis 1. The VLF emission is considered to be generated by nonlinear coupling mechanisms in certain portions of the observation as the f sub Dn is enhanced by its association with nonlinear wave-particle interaction of the electrostatic electron cyclotron harmonic wave, including the instability due to the nonlinear inverse Landau damping mechanism in the turbulence. The difference between the two observations is in the excitation mechanism of the turbulence; the turbulence in the plasma trough detected by Ogo 5 is due to natural origins, whereas the ionospheric topside sounder makes the plasma wave turbulence artificially by submitting strong stimulation pulses. Electron density values in the plasma trough are deduced by applying the f sub Dn-f sub N/f sub H relationship obtained from the Alouette 2 experiment as well as by applying the condition for the wave-particle nonlinear interactions. The electron density values reveal good agreement with the ion density values observed simultaneously by the highly sensitive ion mass spectrometer.

Oya, H.↗

Assessment of environmental effects on Space Station Freedom Electrical Power System

Analyses of EPS (electrical power system) interactions with the LEO (low earth orbit) environment are described. The results of these analyses will support EPS design so as to be compatible with the natural and induced environments and to meet power, lifetime, and performance requirements. The environmental impacts to the Space Station Freedom EPS include aerodynamic drag, atomic oxygen erosion, ultraviolet degradation, VXB effect, ionizing radiation dose and single event effects, electromagnetic interference, electrostatic discharge, plasma interactions (ion sputtering, arcing, and leakage current), meteoroid and orbital debris threats, thermal cycling effects, induced current and voltage potential differences in the SSF due to induced electric field, and contamination degradation.

Lu, Cheng-Yi↗

"Coulombic Viscosity" In Granular Materials: Planetary and Astrophysical Implications

The term "Coulombic viscosity" is introduced here to define an empirically observed phenomenon from experiments conducted in both microgravity, and in ground-based 1-g conditions. In the latter case, a sand attrition device was employed to test the longevity of aeolian materials by creating two intersecting grain-circulation paths or cells that would lead to most of the grain energy being expended on grain-to-grain collisions (simulating dune systems). In the areas in the device where gravitationally-driven grain-slurries recycled the sand, the slurries moved with a boundary-layer impeded motion down the chamber walls. Excessive electrostatic charging of the grains during these experiments was prevented by the use of an a.c. corona (created by a Tesla coil) through which the grains passed on every cycle. This created both positive and negative ions which neutralized the triboelectrically-generated grain charges. When the corona was switched on, the velocity of the wall-attached slurries increased by a factor of two as approximately determined by direct observation. What appeared to be a freely-flowing slurry of grains impeded only by intergranular mechanical friction, had obviously been significantly retarded in its motion by electrostatic forces between the grains; with the charging reduced, the grains were able to move past one another without a flow "viscosity" imposed by the Coulombic intergranular forces. A similar phenomenon was observed during microgravity experiments aboard Space Shuttle in USML-1 & USML-2 spacelabs where freely-suspended clouds of sand were being investigated for their potential to for-m aggregates. In this environment, the grains were also charged electrostatically (by natural processes prior to flight), but were free from the intervention of gravity in their interactions. The grains were dispersed into dense clouds by bursts of air turbulence and allowed to form aggregates as the ballistic and turbulent motions damped out. During this very brief (30-60 sec) damping period, motion of the grains was observed to be retarded by the electrostatic interactions. The fact that the grains almost instantly formed aggregates was evidence that their ballistic motions had been constrained and redirected by the dipole-dipole interactions that led to filamentary aggregate development. Undoubtedly, the "Coulombic viscosity" of the cloud assisted in damping grain motion so rapidly. The electrostatically-induced grain-cloud viscosity or drag exerted on grain motion, is a complex function of three major parameters: charge magnitude, charge sign, and mean intergranular distance. The above experiments illustrate one particular type of granular behavior. The discussion here will therefore be restricted to drag relationships: (a) between grains that are naturally charged triboelectrically and thus exhibit dipole-dipole attractions between one another even if there are slight net charges present (which can be overwhelmed by dipole coupling at short distances), and (b) between grains that are densely spaced where the intergranular distance varies between zero and some value (usually tens or hundreds of grain diameters) that permits each grain to detect the dipole moment of another grain -- the distance is not so great that other grains appears as neutral electrical "singularities. I. Aeolian transport: During motion of grains in a saltation cloud (on Earth, Mars, or Venus), triboelectric charging must occur as a result of multiple grain contacts, and by friction with the entraining air. A situation might develop that is similar to the one described above in the attrition device: grain motion becoming significantly retarded (reduced flux) as grains find it increasingly difficult to either separate from the surface, or to pass one another without Coulombic retarding forces. A "Coulombic drag" will exist at flux initiation and increase with time to work in direct opposition to the aerodynamic drag that drives the grain motion. It is predicted that this will lead to an increase with time of both the aerodynamic and bed-dilatancy thresholds (3). Because of Paschen discharge effects in the martian atmosphere, the electrostatic charging in a saltation cloud may be partially abated, but this will lead to greater grain mobility, more charging, and thus to a charge-discharge steady state mediated by mechanical interactions. II. Dry colluvial systems: Sand avalanches on dunes, dry debris flows, talus flows, avalanches, and pyroclastic surges are examples of gravity-driven, dense granular flows where rock/grain fragmentation and grain-to-grain interactions cause triboelectrification (sometimes augmented by other electrical charging processes), and where the grain densities of the systems are such that strong dipole-dipole interactions between grains might be expected to be present. Because it is expected that the Coulombic forces between grains will cause a sluggishness or enhanced granular-flow viscosity, the motion of a grain mass will be retarded or damped so that this will assist, ultimately, in terminating the flow. The greatest Coulombic viscosity will be created in the most highly charged systems, which will also be the most energetic. Thus, grain flows have some tendency to be self-limiting by internal energy partitioning; gravitational potential is converted to Coulombic potential, which manifests itself as a drag force between the grains. III. Volcanic eruption plumes and impact ejecta curtains: The violence of these systems leads to powerful electrical charging of particulates. Lightning storms emanating from volcanic plumes are a testimony to the levels of charging. As pyroclastic grains interact forcefully and frequently within eruption plumes, it is reasonable to predict that the internal turbulent motions of the plume will be significantly damped by the Coulombic viscosity exerted by grain charges. Additional information is contained in the original.

Marshall, J. R.↗

ISEE 1 observations of electrostatic ion cyclotron waves in association with ion beams on auroral field lines from about 2.5 to 4.5 R(E)

Quasi-monochromatic waves at about the hydrogen cyclotron frequency were observed as the ISEE 1 satellite traversed auroral field lines at radial distances of about 2.5-4.5 R(E) near midnight on June 19, 1981. Waves and both lower and higher frequencies were observed at higher altitudes, and possible electrostatic helium cyclotron and oxygen cyclotron waves occurred at lower altitudes. Upflowing hydrogen and oxygen beams and field-aligned currents occurred simultaneously. The features of the waves are most consistent with the current-driven mode. In addition, numerical studies of the linear dispersion relation, using parameters based on the observations, show that both the parallel and oblique two-stream modes and the ion-beam-driven modes were stable while oblique current-driven modes were unstable. The O(+) and H(+) distributions provide evidence for interactions with local electrostatic ion cyclotron waves and for the H(+)-O(+) two-stream instability at altitudes below the satellite.

Catell, C. A.↗

Superhydrophobic Phosphonium Modified Robust 3D Covalent Organic Framework for Preferential Trapping of Charge Dispersed Oxoanionic Pollutants

Abstract Charge dispersed and less hydrophilic anionic pollutants are often difficult to be preferentially captured by common cationic framework materials. A gamma radiation modification approach is employed to anchor a superhydrophobic phosphonium‐containing coating on a robust crystalline 3D covalent organic framework (COF). By regulating the surface hydrophobicity, the prepared 3DCOF‐ g ‐VBPPh 3 Cl is endowed with a strong affinity for charge dispersed and less hydrophilic oxoanions, such as MnO 4 − , TcO 4 − and ReO 4 − , to surmount the Hofmeister bias, which much favors remediation of oxoanionic pollutants in complex aqueous systems. Batch and column experiments with 3DCOF‐g‐VBPPh 3 Cl in both tap water and simulated groundwater are performed, and rapid sequestration is achieved with removal efficacy up to 99.995%, record‐high distribution coefficient of 1.0 × 10 8 mL g −1 , and desirable priority over competing anions such as Cl − , SO 4 2− , HCO 3 − , and NO 3 − , confirming promise for remediation of charge dispersed anionic pollutants. Theoretical calculations reveal a mechanism of preferential capture based on electrostatic and dispersion interaction between charge dispersed anions and 3DCOF‐g‐VBPPh 3 Cl that effectively competes with solvation of the aqueous anions.

Wang, Yue↗

2D Ionic Liquid-Like State of Charged Rare-Earth Clusters on a Metal Surface

Rare-earth complexes are vital for separation chemistry and useful in many advanced applications including emission and energy upconversion. Here, 2D rare-earth clusters having net charges are formed on a metal surface, enabling investigations of their structural and electronic properties on a one-cluster-at-a-time basis using scanning tunneling microscopy. While these ionic complexes are highly mobile on the surface at ≈100 K, their mobility is greatly reduced at 5 K and reveals stable and self-limiting clusters. In each cluster, a pair of charged rare-earth complexes formed by electrostatic and dispersive interactions act as a basic unit, and the clusters are chiral. Unlike other non-ionic molecular clusters formed on the surfaces, these rare-earth clusters show mechanical stability. Moreover, their high mobility on the surface suggests that they are in a 2D liquid-like state.

36 MATERIALS SCIENCE↗

Quantitative Protein Corona Composition and Dynamics on Carbon Nanotubes in Biological Environments

When nanoparticles enter biological environments, proteins adsorb to form the "protein corona" which alters nanoparticle biodistribution and toxicity. Herein, we measure protein corona formation on DNA-functionalized single-walled carbon nanotubes (ssDNA-SWCNTs), a nanoparticle used widely for sensing and delivery, in blood plasma and cerebrospinal fluid. We characterize corona composition by mass spectrometry, revealing high-abundance corona proteins involved in lipid binding, complement activation, and coagulation. We investigate roles of electrostatic and entropic interactions driving selective corona formation. Lastly, we study real-time protein binding on ssDNA-SWCNTs, obtaining agreement between enriched proteins binding strongly and depleted proteins binding marginally, while highlighting cooperative adsorption mechanisms. Knowledge of protein corona composition, formation mechanisms, and dynamics informs nanoparticle translation from in vitro design to in vivo application.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

From classical thermodynamics to phase-field method

Phase-field method is a density-based computational method at the mesoscale for modeling and predicting the temporal microstructure and property evolution during materials processes. The focus of this article is on connecting the most common phase-field equations to the very basic first and second laws of classical thermodynamics through rudimentary irreversible thermodynamics. It briefly discusses the relations of the continuum phase-field equations to their counter parts at the microscopic and atomic levels. It attempts to clarify the contributions of long-range elastic, electrostatic, and magnetic interactions to domain structure evolution during structural, ferroelectric, and ferromagnetic phase transformations by separating order parameter changes due to the presence of quasi-static fields and those arising from phase transformations. A few examples are presented to demonstrate the possibility of employing the phase-field method to provide guidance to designing materials for optimum properties or discovering novel mesoscale phenomena or new materials functionalities. Here, the article ends with a brief perspective on a number of potential future directions on the development and applications of phase-field method beyond its traditional applications to structural alloys.

36 MATERIALS SCIENCE↗

Lignin-enzyme interaction: A roadblock for efficient enzymatic hydrolysis of lignocellulosics

Efficiently producing second-generation biofuels from biomass is of strategic significance and meets sustainability targets, but it remains a long-term challenge due to the existence of biomass recalcitrance. Lignin contributes significantly to biomass recalcitrance by physically limiting the access of enzymes to carbohydrates, and this could be partially overcome by applying a pretreatment step to directly target lignin. However, lignin typically cannot be completely removed, and its structure is also significantly altered during the pretreatment. As a result, lignin residue in the pretreated materials still significantly hindered a complete conversion of carbohydrate to its monosugars by interacting with cellulase enzymes. The non-productive adsorption driven by hydrophobic, electrostatic, and/or hydrogen bonding interactions is widely considered as the major mechanism of action governing the unfavored lignin-enzyme interaction. One could argue this type of interaction between lignin residue and the activated enzymes is the major roadblock for efficient enzymatic hydrolysis of pretreated lignocellulosics. To alleviate the negative effects of lignin on enzyme performance, a deep understanding of lignin structural transformation upon different types of pretreatments as well as how and where does lignin bind to enzymes are prerequisites. In the last decade, the progress toward a fundamental understanding of lignin-enzyme interaction, structural characterization of lignin during pretreatment and/or conformation change of enzyme during hydrolysis is resulting in advances in the development of methodologies to mitigate the negative effect of lignin. Here in this review, the lignin structural transformation upon different types of pretreatments and the inhibition mechanism of lignin in the bioconversion of lignocellulose to bioethanol are summarized. Some technologies to minimize the adverse impact of lignin on the enzymatic hydrolysis, including chemical modification of lignin, adding blocking additives, and post-treatment to remove lignin were also introduced. The production of liquid biofuels from lignocellulosic biomass has shown great environmental benefits such as reducing greenhouse gas emissions and mitigate climate change. By addressing the root causes of lignin-enzyme interaction and how to retard this interaction, it is our hope that this comprehensive review will pave the way for significantly reducing the high cost associated with the enzymatic hydrolysis process, and ultimately achieving a cost-effective and sustainable biorefinery system.

09 BIOMASS FUELS↗

Surface modification induced cuprous oxide nanoparticle toxicity to duckweed at sub-toxic metal concentrations

Nanoparticle capping agents are critical for controlling the growth, oxidation state, and final particle size during aqueous synthesis. However, despite the known phytotoxicity of cetyltrimethylammonium bromide (CTAB) to plants, it is used to synthesize metal oxide nanoparticles of uniform size and with mesoporous structure. Among the few studies that have investigated how CTAB influences nanoparticle toxicity, CTAB has never been identified as the primary cause of nanoparticle toxicity in environmental systems; rather nanoparticle surface charge or morphology was identified as the driver of toxicity in environmentally relevant systems. In the current study, CTAB release from CTAB surface modified Cu 2 O nanoparticles (SM-Cu 2 O NPs) inhibited duckweed (Landoltia punctata) growth, even when administered at subtoxic Cu concentrations. Organic ligands, such as humic acid (HA) and ethylenediaminetetraacetic acid (EDTA), lessened growth inhibition associated with exposure to SM-Cu 2 O NPs, likely through electrostatic and hydrophobic interactions with CTAB. Finally, such results highlight the need for a more holistic approach to nanoparticle surface modification and improved communication between toxicologists and synthetic chemists to develop green alternatives for nanoparticle synthesis.

54 ENVIRONMENTAL SCIENCES↗

Depth-Dependent Emission from Silver Dopants in Single CdSe Nanoplatelets

Dopants in semiconductor nanostructures offer tremendous control over electronic, optical, and magnetic properties beyond what is achievable in bulk materials. We demonstrate that the broad dopant emission in semiconductor nanoplatelets effectively maps the electron wave function across the nanoplatelet thickness. Both the emission energy and lifetime of the dopant transition depend strongly on the depth of the dopant within the nanoplatelet. This dependence arises from the electrostatic self-interaction of the charged dopant, which varies with proximity to the dielectric discontinuity at the nanoplatelet surface. Through comprehensive single-particle spectroscopy of silver-doped CdSe nanoplatelets, we verify that acceptors near the center emit at higher energies with shorter lifetimes, while those near the surface emit at lower energies with longer lifetimes. This spatial mapping also reveals unusual two-color emission from individual nanoplatelets, with enhanced Auger recombination yielding exceptional photon antibunching (>90% purity) at room temperature, suggesting potential applications in quantum information technologies.

cadmium selenide↗

The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation

Yeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically-disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4 Å and 4.0 Å resolution in inward-facing open conformations that capture previously unobserved ordered states of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the Lasso motif. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide insights into how R-domains control ABCC transporter activity.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Thiocyanate complexes of the lanthanides, Am and Cm

In this work, the synthesis and single crystal structures of Am( III ) and Cm( III ) thiocyanate complexes are reported along with an isostructural series of lanthanide thiocyanate complexes. Because the complexes are isostructural, a comparative study of the metal–thiocyanate bonds was conducted using Raman spectroscopy indicating very similar and electrostatic metal–ligand interactions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

K–Co–Mo–S x chalcogel: high-capacity removal of Pb 2+ and Ag + and the underlying mechanisms

Chalcogenide-based aerogels, known as chalcogels, represent a novel class of nanoparticle-based porous amorphous materials characterized by high surface polarizability and Lewis base properties, exhibiting promising applications in clean energy and separation science. This work presents a K–Co–Mo–S x (KCMS) chalcogel as a highly efficient sorbent for heavy metal ions and details its sorption mechanisms. Its incoherent structure comprises Mo 2 V (S 2 ) 6 and Mo 3 IV S(S 6 ) 2 anion-like clusters with four- and six-coordinated Co–S polyhedra, forming a Co–Mo–S covalent network that hosts K + ions through electrostatic attraction. The interactions of KCMS with heavy metal ions, particularly Pb 2+ and Ag + , reveal that KCMS is exceptionally effective in removing these ions from ppm concentrations down to trace levels (≤5 ppb). KCMS rapidly removes Ag + (≈81.7%) and Pb 2+ (≈99.5%) within five minutes, achieving >99.9% removal within an hour, with a distribution constant K d ≥10 8 mL g -1 . KCMS exhibits an impressive removal capacity of 1378 mg g -1 for Ag + and 1146 mg g -1 for Pb 2+ , establishing it as one of the most effective materials known to date for heavy metal removal. This material is also effective for the removal of Ag + and Pb 2+ along with Hg 2+ , Ni 2+ , Cu 2+ , and Cd 2+ from various water sources even in the presence of highly concentrated and chemically diverse cations, anions, and organic species. Analysis of the post-interacted KCMS by synchrotron X-ray pair distribution function (PDF), X-ray photoelectron spectroscopy (XPS) and energy dispersive X-ray spectroscopy (EDS) revealed that the sorption of Pb 2+ , Ag + , and Hg 2+ mainly occurs by the exchange of K + and Co 2+ . Despite being amorphous, this material exhibits unprecedented ion-exchange mechanisms both for the ionically and covalently bound K + and Co 2+ , respectively. In conclusion, this discovery advances our knowledge of amorphous gels and guides material synthesis principles for the highly selective and efficient removal of heavy metal ions from water.

54 ENVIRONMENTAL SCIENCES↗