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At least 199 records · Page 11

Assembly of Building Blocks by Double-End-Anchored Polymers in the Dilute Regime Mediated by Hydrophobic Interactions at Controlled Distances

Hierarchical assembly of building blocks via competing, orthogonal interactions is a hallmark of many of nature’s composite materials that do not require highly specific ligand-receptor interactions. To mimic this assembly mechanism requires the development of building blocks capable of tunable interactions. In the present work, we explored the interplay between repulsive (steric and electrostatic) and attractive hydrophobic forces. The designed building blocks allow hydrophobic forces to effectively act at controlled, large distances, to create and tune the assembly of membrane-based building blocks under dilute conditions and affect their interactions with cellular membranes via physical cross-bridges. Specifically, we employed double-end-anchored poly(ethylene glycol)s (DEA-PEGs)—hydrophilic PEG tethers with hydrophobic tails on both ends. Using differential-interference-contrast optical microscopy, synchrotron small angle X-ray scattering (SAXS), and cryogenic electron microscopy, we investigated the ability of DEA-PEGs to mediate assembly in the dilute regime on multiple length scales and on practical time scales. The PEG length, anchor hydrophobicity, and molar fraction of DEA-PEG molecules within a membrane strongly affect the assembly properties. Additional tuning of the intermembrane interactions can be achieved by adding repulsive interactions via PEG-lipids (steric) or cationic lipids to the DEA-PEG-mediated attractions. Further, while the optical and electron microscope imaging methods provided qualitative evidence of the ability of DEA-PEGs to assemble liposomes, the SAXS measurements and quantitative line-shape analysis in dilute preparations demonstrated that the ensemble average of loosely organized liposomal assemblies maintains DEA-PEG concentration-dependent tethering on defined nanometer length scales. For cationic liposome–DNA nanoparticles (CL–DNA NPs), aggregation induced by DEA-PEGs decreased internalization of NPs by cells, but tuning the DEA-PEG-induced attractions by adding repulsive steric interactions via PEG-lipids limited aggregation and increased NP uptake. However, confocal microscopy imaging together with colocalization studies with Rab11 and LysoTracker as markers of intracellular pathways showed that modifying CL–DNA NPs with DEA-PEGs alters their interactions with the plasma and endosomal membranes.

- x-ray scattering↗

Self-interaction error overbinds water clusters but cancels in structural energy differences

Here, we gauge the importance of self-interaction errors in density functional approximations (DFAs) for the case of water clusters. To this end, we used the Fermi–Löwdin orbital self-interaction correction method (FLOSIC) to calculate the binding energy of clusters of up to eight water molecules. Three representative DFAs of the local, generalized gradient, and metageneralized gradient families [i.e., local density approximation (LDA), Perdew–Burke–Ernzerhof (PBE), and strongly constrained and appropriately normed (SCAN)] were used. We find that the overbinding of the water clusters in these approximations is not a density-driven error. We show that, while removing self-interaction error does not alter the energetic ordering of the different water isomers with respect to the uncorrected DFAs, the resulting binding energies are corrected toward accurate reference values from higher-level calculations. In particular, self-interaction–corrected SCAN not only retains the correct energetic ordering for water hexamers but also reduces the mean error in the hexamer binding energies to less than 14 meV/ H 2 O from about 42 meV/ H 2 O for SCAN. By decomposing the total binding energy into many-body components, we find that large errors in the two-body interaction in SCAN are significantly reduced by self-interaction corrections. Higher-order many-body errors are small in both SCAN and self-interaction–corrected SCAN. These findings suggest that orbital-by-orbital removal of self-interaction combined with a proper DFA can lead to improved descriptions of water complexes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Understanding the dynamic interactions of root-knot nematodes and their host: role of plant growth promoting bacteria and abiotic factors

Root-knot nematodes (Meloidogyne spp., RKN) are among the most destructive endoparasitic nematodes worldwide, often leading to a reduction of crop growth and yield. Insights into the dynamics of host-RKN interactions, especially in varied biotic and abiotic environments, could be pivotal in devising novel RKN mitigation measures. Plant growth-promoting bacteria (PGPB) involves different plant growth-enhancing activities such as biofertilization, pathogen suppression, and induction of systemic resistance. We summarized the up-to-date knowledge on the role of PGPB and abiotic factors such as soil pH, texture, structure, moisture, etc. in modulating RKN-host interactions. RKN are directly or indirectly affected by different PGPB, abiotic factors interplay in the interactions, and host responses to RKN infection. We highlighted the tripartite (host-RKN-PGPB) phenomenon with respect to (i) PGPB direct and indirect effect on RKN-host interactions; (ii) host influence in the selection and enrichment of PGPB in the rhizosphere; (iii) how soil microbes enhance RKN parasitism; (iv) influence of host in RKN-PGPB interactions, and (v) the role of abiotic factors in modulating the tripartite interactions. Furthermore, we discussed how different agricultural practices alter the interactions. Finally, we emphasized the importance of incorporating the knowledge of tripartite interactions in the integrated RKN management strategies.

59 BASIC BIOLOGICAL SCIENCES↗

Mass Spectral Imaging to Map Plant–Microbe Interactions

Plant–microbe interactions are of rising interest in plant sustainability, biomass production, plant biology, and systems biology. These interactions have been a challenge to detect until recent advancements in mass spectrometry imaging. Plants and microbes interact in four main regions within the plant, the rhizosphere, endosphere, phyllosphere, and spermosphere. This mini review covers the challenges within investigations of plant and microbe interactions. We highlight the importance of sample preparation and comparisons among time-of-flight secondary ion mass spectroscopy (ToF-SIMS), matrix-assisted laser desorption/ionization (MALDI), laser desorption ionization (LDI/LDPI), and desorption electrospray ionization (DESI) techniques used for the analysis of these interactions. Using mass spectral imaging (MSI) to study plants and microbes offers advantages in understanding microbe and host interactions at the molecular level with single-cell and community communication information. More research utilizing MSI has emerged in the past several years. We first introduce the principles of major MSI techniques that have been employed in the research of microorganisms. An overview of proper sample preparation methods is offered as a prerequisite for successful MSI analysis. Traditionally, dried or cryogenically prepared, frozen samples have been used; however, they do not provide a true representation of the bacterial biofilms compared to living cell analysis and chemical imaging. New developments such as microfluidic devices that can be used under a vacuum are highly desirable for the application of MSI techniques, such as ToF-SIMS, because they have a subcellular spatial resolution to map and image plant and microbe interactions, including the potential to elucidate metabolic pathways and cell-to-cell interactions. Promising results due to recent MSI advancements in the past five years are selected and highlighted. The latest developments utilizing machine learning are captured as an important outlook for maximal output using MSI to study microorganisms.

59 BASIC BIOLOGICAL SCIENCES↗

Emulating the impact of additional proton-proton interactions in the ATLAS simulation by pre-sampling sets of inelastic Monte Carlo events

The accurate simulation of additional interactions at the ATLAS experiment for the analysis of proton-proton collisions delivered by the Large Hadron Collider presents a significant challenge to the computing resources. During the LHC Run (2015-2018) there were up to 70 inelastic interactions per bunch crossing, which need to be accounted for in Monte Carlo (MC) production. In this document, a new method to account for these additional interactions in the simulation chain is described. Instead of sampling the inelastic interactions and adding their energy deposits to a hard-scatter interaction one-by-one, the inelastic interactions are presampled, independent of the hard scatter, and stored as combined events. Consequently, for each hard-scatter interaction only one such presampled event needs to be added as part of the simulation chain. For the Run 2 simulation chain, with an average of 35 interactions per bunch crossing, this new method provides a substantial reduction in MC production CPU needs of around 20%, while reproducing the properties of the reconstructed quantities relevant for physics analyses with good accuracy.

97 MATHEMATICS AND COMPUTING↗

Vortical interactions in turbulent thermoacoustic systems

This study examines the dynamics of vortical interactions and their implications for mitigating thermoacoustic instability in a turbulent combustor. The regions of intense vortical interactions are identified as vortical communities in the network space of weighted directed vortical networks constructed from two-dimensional experimental velocity data. One can expect vortical interactions in the combustor to be strongest near the moment of vortex shedding, as the shed vortices gradually weaken due to dissipation while convecting downstream. However, we show that, during the state of thermoacoustic instability, there is a non-trivial consistent phase lag of approximately 52° between the shedding of the coherent structures from the backward-facing step and the time instant when the vortical interactions attain their local maximum value. We explain this phase lag by investigating the correlation between acoustic pressure fluctuations, spatio-temporal dynamics of coherent structures and vortical interactions in the reaction field of the combustor. We also show the aperiodic variation of vortical interactions during the states of combustion noise and aperiodic epochs of intermittency. Furthermore, the spatio-temporal evolution of pairs of vortical communities with the maximum inter-community interactions provides insight into explaining the critical regions detected in the reaction field during the states of intermittency and thermoacoustic instability, also identified in previous studies. As a result, we further show that the most efficient suppression of thermoacoustic instability via air microjet injection is achieved when steady air jets are introduced to disrupt the maximum inter-community interactions present during the state of thermoacoustic instability.

Sahay, Ankit [Indian Institute of Technology Madra↗

Atomic-Scale Imaging Reveals Polar-π Interactions in Two-Dimensional Molecular Superlattices

Controlling coassembly of synthetic oligomers into binary superlattices at the atomic level is challenging. Here, we report a strategy for programming polar-π interactions in oligomeric peptoids, a class of sequence-defined peptidomimetics, facilitating the formation of homogeneous two-dimensional (2D) superlattices. N-2-phenylethyl and N-(2-perfluorophenyl)ethyl side chains, similar in size, but with contrasting electrostatic characteristics, were introduced at defined sequence positions to generate favorable dipolar aromatic interactions. The resulting nanosheets exhibit different crystal motifs depending on the side chain interactions: systems containing only one type of aromatic side chain form a parallel V-shaped motif driven by π-π interactions, whereas a combination of both types of aromatic side chains, either within one backbone or through the coassembly of two distinct peptoids, adopt an antiparallel V-shaped superlattice with higher thermal stability, driven by polar-π interactions. Cryogenic transmission electron microscopy directly resolved the packing arrangement of perfluorophenyl and phenyl rings in individual nanosheet superlattices, confirming that intermolecular polar-π interaction dominates the superlattice motifs and increases lattice stability. Molecular dynamics simulations and density functional theory calculations further substantiate the energetic favorability of polar-π interactions over π-π interactions, rationalizing the formation of homogeneous superlattices with enhanced thermal stability. Our discoveries establish a design principle for binary coassembly using sequence-defined oligomers, which enables control over unit cell geometry, lattice stability, and molecular registration through aromatic side chain polarization and sequence control. This ability to program atomic-scale binary superlattices opens new avenues for designing functional 2D soft materials.

Lee, Yen Jea [Lawrence Berkeley National Laborator↗

Genome-scale analysis of interactions between genetic perturbations and natural variation

Interactions between genetic perturbations and segregating loci can cause perturbations to show different phenotypic effects across genetically distinct individuals. To study these interactions on a genome scale in many individuals, we used combinatorial DNA barcode sequencing to measure the fitness effects of 8046 CRISPRi perturbations targeting 1721 distinct genes in 169 yeast cross progeny (or segregants). We identified 460 genes whose perturbation has different effects across segregants. Several factors caused perturbations to show variable effects, including baseline segregant fitness, the mean effect of a perturbation across segregants, and interacting loci. We mapped 234 interacting loci and found four hub loci that interact with many different perturbations. Perturbations that interact with a given hub exhibit similar epistatic relationships with the hub and show enrichment for cellular processes that may mediate these interactions. These results suggest that an individual’s response to perturbations is shaped by a network of perturbation-locus interactions that cannot be measured by approaches that examine perturbations or natural variation alone.

59 BASIC BIOLOGICAL SCIENCES↗

Structural insights into isoform-specific RAS-PI3Kα interactions and the role of RAS in PI3Kα activation

Abstract Mutations in RAS and PI3Kα are major drivers of human cancer. Their interaction plays a crucial role in activating PI3Kα and amplifying the PI3K-AKT-mTOR pathway. Disrupting RAS-PI3Kα interaction enhances survival in lung and skin cancer models and reduces tumor growth and angiogenesis, although the structural details of this interaction remain unclear. Here, we present structures of KRAS, RRAS2, and MRAS bound to the catalytic subunit (p110α) of PI3Kα, elucidating the interaction interfaces and local conformational changes upon complex formation. Structural and mutational analyses highlighted key residues in RAS and PI3Kα impacting binding affinity and revealed isoform-specific differences at the interaction interface in RAS and PI3K isoforms, providing a rationale for their differential affinities. Notably, in the RAS-p110α complex structures, RAS interaction with p110α is limited to the RAS-binding domain and does not involve the kinase domain. This study underscores the pivotal role of the RAS-PI3Kα interaction in PI3Kα activation and provides a blueprint for designing PI3Kα isoform-specific inhibitors to disrupt this interaction.

Science & Technology - Other Topics↗

A spectroscopic, structural, and computational study of Ag–oxo interactions in Ag + /UO 2 2+ complexes

For this work, twelve novel Ag + /UO 2 2+ heterometallic complexes have been prepared and characterized via structural, spectroscopic, and computational methods to probe the effects of Ag–oxo interactions on bonding and photophysical properties of the uranyl cation. Structural characterization reveals Ag–oxo interaction distances ranging from 2.475(3) Å to 4.287(4) Å. These interactions were probed using luminescence and Raman spectroscopy which displayed little effect on the luminescence intensity and the energy of the Raman active U═O symmetric stretch peak as compared to previously reported Pb–oxo interactions. Computational efforts via density functional theory-based natural bond orbital analysis revealed that the highest stabilization energy associated with the Ag–oxo interaction had a value of only 11.03 kcal mol –1 and that all other energy values fell at 7.05 kcal mol –1 or below indicating weaker interactions relative to those previously reported for Pb 2+ /UO 2 2+ heterometallic compounds. In contrast, quantum theory of atoms in molecules analysis of bond critical point electron density values indicated higher electron density in Ag–oxo interactions as compared to Pb–oxo interactions which suggests more covalent character with the Ag + . Overall, this data indicates that Ag + has a less significant effect on UO 2 2+ bonding and photophysical properties as compared to other Pb 2+ , likely due to the high polarizability of the cation.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Interactions of laser-driven tin ejecta microjets over phase transition boundaries

Ejecta microjets offer an experimental methodology to study high-speed particle laden-flow interactions, as microjets consist of millions of particulates traveling at velocities of several kilometers per second and are easily generated by most common shock drives. Previous experiments on the OMEGA Extended Performance laser found that collisions between two counter-propagating laser-driven tin ejecta microjets varied as a function of drive pressure; jets generated near shock pressures of 10 GPa passed through each other without interacting, whereas jets generated at shock pressures of over 100 GPa interacted strongly, forming a cloud around the center interaction point. In this paper, we present a more systematic scan of tin ejecta microjet collisions over intermediate pressure regimes to identify how and at what shock pressure interaction behavior onsets. Radiographs of interacting microjets at five different laser drive energies qualitatively demonstrate that interaction behavior onsets slowly as a function of laser drive energy. Quantitative mass and density metrics from each radiograph provide trends on jet characteristics and collisional mass dispersion. It is observed that jetting mass, jet densities, and mass dispersion increase with increasing drive pressures and that the increased jet density at the higher drive energies may account for the increased mass dispersion. This work provides an important step in the understanding of tin ejecta microjet collisions and paves the way for future studies on the physics dominating high-speed particle-laden flow interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Flavor-specific interaction favors strong neutrino self-coupling in the early universe

Flavor-universal neutrino self-interaction has been shown to ease the tension between the values of the Hubble constant measured from early and late Universe data. Here, we introduce a self-interaction structure that is flavor-specific in the three active neutrino framework. This is motivated by the stringent constraints on new secret interactions among electron and muon neutrinos from several laboratory experiments. Our study indicates the presence of a strongly interaction mode which implies a late-decoupling of the neutrinos just prior to matter radiation equality. Using the degeneracy of the coupling strength with other cosmological parameters, we explain the origin of this new mode as a result of better fit to certain features in the CMB data. We find that if only one or two of the three active neutrino flavors are interacting, then the statistical significance of the strongly-interacting neutrino mode increases substantially relative to the flavor-universal scenario. However, the central value of the coupling strength for this interaction mode does not change by any appreciable amount in the flavor-specific cases. We also briefly analyze a scenario with more than three neutrino species of which only one is self-interacting. In none of the cases, we find a large enough Hubble constant that could resolve the so-called Hubble tension.

79 ASTRONOMY AND ASTROPHYSICS↗

Constraints on long-ranged interactions between dark matter and the Standard Model

Dark matter's existence is known thanks to its gravitational interaction with Standard Model particles, but it remains unknown whether this is the only force present between them. While many searches for such new interactions with dark matter focus on short-range, contact-like interactions, it is also possible that there exist weak, long-ranged forces between dark matter and the Standard Model. In this work, we present two types of constraints on such new interactions. First, we consider constraints arising from the fact that such a force would also induce long range interactions between Standard Model particles themselves, as well as between dark matter particles themselves. Combining the constraints on these individual forces generally sets the strongest constraints available on new Standard Model-dark matter interactions. Second, we consider the possibility of constraining new long-ranged interactions between dark matter and the Standard Model using the effects of dynamical friction in ultrafaint dwarf galaxies, especially Segue I. Such new interactions would accelerate the transfer of kinetic energy from stars to their surrounding dark matter, slowly reducing their orbits; the present-day stellar half-light radius of Segue I therefore allows us to exclude new forces which would have reduced stars' orbital radii below this scale by now.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Dynamical friction in self-interacting ultralight dark matter

Here, we explore how dynamical friction in an ultralight dark matter (ULDM) background is affected by dark matter self-interactions. We calculate the force of dynamical friction on a point mass moving through a uniform ULDM background with self-interactions, finding that the force of dynamical friction vanishes for sufficiently strong repulsive self-interactions. Using the pseudospectral solver ultraDark.jl, we show with simulations that reasonable values of the ULDM self-interaction strength and particle mass cause $\mathcal{O}$(1) differences in the acceleration of an object like a supermassive black hole (SMBH) traveling near the center of a soliton, relative to the case with no self-interactions. For example, repulsive self-interactions with λ=10 -90 yield a deceleration due to dynamical friction ≈ 70% smaller than a model with no self-interactions. We discuss the observational implications of our results for SMBHs near soliton centers and for massive satellite galaxies falling into ultralight axion halos and show that outcomes are dependent on whether a self-interaction is present or not.

79 ASTRONOMY AND ASTROPHYSICS↗

Experimental Observations of Laser-Driven Tin Ejecta Microjet Interactions

The study of high-velocity particle-laden flow interactions is of importance for the understanding of a wide range of natural phenomena, ranging from planetary formation to cloud interactions. Experimental observations of particle dynamics are sparse given the difficulty of generating high-velocity flows of many particles. Ejecta microjets are micron-scale jets formed by strong shocks interacting with imprinted surfaces to generate particle plumes traveling at several kilometers per second. As such, the interaction of two ejecta microjets provides a novel experimental methodology to study interacting particle streams. In this Letter, we report the first time sequences of x-ray radiography images of two interacting tin ejecta microjets taken on a platform designed for the OMEGA Extended Performance (OMEGA EP) laser. We observe that the microjets pass through each other unattenuated for the case of 11.7±3.2 GPa shock pressures and jet velocities of 2.2±0.5 km/s but show strong interaction dynamics for 116.0±6.1 GPa shock pressures and jet velocities of 6.5±0.5 km/s. Furthermore, we find that radiation-hydrodynamic simulations of the experiments are able to capture many aspects of the collisional behavior, such as the attenuation of jet velocity in the direction of propagation, but are unable to match the full spread of the strongly interacting cloud.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Enhancing Thermal Transport in Polymeric Composites Via Engineered Noncovalent Filler–Polymer Interactions

Understanding thermal transport mechanisms in polymeric composites allows us to expand the boundaries of thermal conductivity in them, either increasing it for more efficient heat dissipation or decreasing it for better thermal insulation. But, these mechanisms are not fully understood. Systematic experimental investigations remain limited. Practical strategies to tune the interfacial thermal resistance (ITR) between fillers and polymers and the thermal conductivity of composites remain elusive. Here, we studied the thermal transport in representative polymer composites, using polyethylene (PE) or polyaniline (PANI) as matrices and graphite as fillers. PANI, with aromatic rings in its backbone, interacts with graphite through strong noncovalent π–π stacking interactions, whereas PE lacks such interactions. We can then quantify how π–π stacking interactions between graphite and polymers enhance thermal transport in composites. PE/graphite and PANI/graphite composites with the same 1.5% filler volume fractions show a ∼22.82% and ∼34.85% enhancement in thermal conductivity compared to pure polymers, respectively. Calculated ITRs in PE/graphite and PANI/graphite are ~6 x 10 -8 m 2 KW -1 and ~1 x 10 -8 m 2 KW -1 , respectively, highlighting how π–π stacking interactions reduce ITR. Molecular dynamics (MD) simulations suggest that π–π stacking interactions between PANI chains and graphite surfaces enhance alignment of PANI's aromatic rings with graphite surfaces. This allows more carbon atoms from PANI chains to interact with graphite surfaces at a shorter distance compared to PE chains. Finally, our work indicates that tuning the π–π stacking interactions between polymers and fillers is an effective approach to reduce the ITR and enhance the thermal conductivity of composites.

atoms↗

Momentum-exchange interactions in a Bragg atom interferometer suppress Doppler dephasing

Large ensembles of laser-cooled atoms interacting through infinite-range photon-mediated interactions are powerful platforms for quantum simulation and sensing. Here we realize momentum-exchange interactions in which pairs of atoms exchange their momentum states by collective emission and absorption of photons from a common cavity mode, a process equivalent to a spin-exchange or XX collective Heisenberg interaction. The momentum-exchange interaction leads to an observed all-to-all Ising-like interaction in a matter-wave interferometer. A many-body energy gap also emerges, effectively binding interferometer matter-wave packets together to suppress Doppler dephasing in analogy to Mössbauer spectroscopy. The tunable momentum-exchange interaction expands the capabilities of quantum interaction–enhanced matter-wave interferometry and may enable the realization of exotic behaviors, including simulations of superconductors and dynamical gauge fields.

Science & Technology - Other Topics↗

Improved recovery of cell-cycle gene expression in Saccharomyces cerevisiae from regulatory interactions in multiple omics data

Gene expression is regulated by DNA-binding transcription factors (TFs). Together with their target genes, these factors and their interactions collectively form a gene regulatory network (GRN), which is responsible for producing patterns of transcription, including cyclical processes such as genome replication and cell division. However, identifying how this network regulates the timing of these patterns, including important interactions and regulatory motifs, remains a challenging task. Results We employed four in vivo and in vitro regulatory data sets to investigate the regulatory basis of expression timing and phase-specific patterns cell-cycle expression in Saccharomyces cerevisiae . Specifically, we considered interactions based on direct binding between TF and target gene, indirect effects of TF deletion on gene expression, and computational inference. We found that the source of regulatory information significantly impacts the accuracy and completeness of recovering known cell-cycle expressed genes. The best approach involved combining TF-target and TF-TF interactions features from multiple datasets in a single model. In addition, TFs important to multiple phases of cell-cycle expression also have the greatest impact on individual phases. Important TFs regulating a cell-cycle phase also tend to form modules in the GRN, including two sub-modules composed entirely of unannotated cell-cycle regulators ( STE12-TEC1 and RAP1-HAP1-MSN4 ). Conclusion Our findings illustrate the importance of integrating both multiple omics data and regulatory motifs in order to understand the significance regulatory interactions involved in timing gene expression. This integrated approached allowed us to recover both known cell-cycles interactions and the overall pattern of phase-specific expression across the cell-cycle better than any single data set. Likewise, by looking at regulatory motifs in the form of TF-TF interactions, we identified sets of TFs whose co-regulation of target genes was important for cell-cycle expression, even when regulation by individual TFs was not. Overall, this demonstrates the power of integrating multiple data sets and models of interaction in order to understand the regulatory basis of established biological processes and their associated gene regulatory networks.

59 BASIC BIOLOGICAL SCIENCES↗