Nanoscale Interactions Research Articles

Investigating Nanoscale Interactions of Host–Guest Complexes Formed Between CB[7] and Atenolol by Quantum Chemistry and Ultrasensitive Vibrational Spectroscopy

Investigating Nanoscale Interactions of Host–Guest Complexes Formed Between CB[7] and Atenolol by Quantum Chemistry and Ultrasensitive Vibrational Spectroscopy

Illuminating cellular architecture and dynamics with fluorescence polarization microscopy.

Ever since Robert Hooke's 17th century discovery of the cell using a humble compound microscope, light-matter interactions have continuously redefined our understanding of cell biology. Fluorescence microscopy has been particularly transformative and remains an indispensable tool for many cell biologists. The subcellular localization of biomolecules is now routinely visualized simply by manipulating the wavelength of light. Fluorescence polarization microscopy (FPM) extends these capabilities by exploiting another optical property - polarization - allowing researchers to measure not only the location of molecules, but also their organization or alignment within larger cellular structures. With only minor modifications to an existing fluorescence microscope, FPM can reveal the nanoscale architecture, orientational dynamics, conformational changes and interactions of fluorescently labeled molecules in their native cellular environments. Importantly, FPM excels at imaging systems that are challenging to study through traditional structural approaches, such as membranes, membrane proteins, cytoskeletal networks and large macromolecular complexes. In this Review, we discuss key discoveries enabled by FPM, compare and contrast the most common optical setups for FPM, and provide a theoretical and practical framework for researchers to apply this technique to their own research questions.

Potential of plasmonics and nanoscale light-matter interactions for the next generation of optical neural interfaces.

Within the realm of optical neural interfaces, the exploration of plasmonic resonances to interact with neural cells has captured increasing attention among the neuroscience community. The interplay of light with conduction electrons in nanometer-sized metallic nanostructures can induce plasmonic resonances, showcasing a versatile capability to both sense and trigger cellular events. We describe the perspective of generating propagating or localized surface plasmon polaritons on the tip of an optical neural implant, widening the possibility for neuroscience labs to explore the potential of plasmonic neural interfaces.

Nanoscale interactions of arginine-containing dipeptide repeats with nuclear pore complexes as measured by transient scanning electrochemical microscopy.

The nuclear pore complex (NPC) plays imperative biological and biomedical roles as the sole gateway for molecular transport between the cytoplasm and nucleus of eukaryotic cells. The proteinous nanopore, however, can be blocked by arginine-containing polydipeptide repeats (DPRs) of proteins resulting from the disordered C9orf72 gene as a potential cause of serious neurological diseases. Herein, we report the new application of transient scanning electrochemical microscopy (SECM) to quantitatively characterize DPR-NPC interactions for the first time. Twenty repeats of neurotoxic glycine-arginine and proline-arginine in the NPC are quantified to match the number of phenylalanine-glycine (FG) units in hydrophobic transport barriers of the nanopore. The 1 : 1 stoichiometry supports the hypothesis that the guanidinium residue of a DPR molecule engages in cation-π interactions with the aromatic residue of an FG unit. Cation-π interactions, however, are too weak to account for the measured free energy of DPR transfer from water into the NPC. The DPR transfer is thermodynamically as favorable as the transfer of nuclear transport receptors, which is attributed to hydrophobic interactions as hypothesized generally for NPC-mediated macromolecular transport. Kinetically, the DPRs are trapped by FG units for much longer than the physiological receptors, thereby blocking the nanopore. Significantly, the novel mechanism of toxicity implies that the efficient and safe nuclear import of genetic therapeutics requires strong association with and fast dissociation from the NPC. Moreover, this work demonstrates the unexplored power of transient SECM to determine the thermodynamics and kinetics of biological membrane-molecule interactions.

Molecular Interactions in Atomically Precise Metal Nanoclusters.

For nanochemistry, precise manipulation of nanoscale structures and the accompanying chemical properties at atomic precision is one of the greatest challenges today. The scientific community strives to develop and design customized nanomaterials, while molecular interactions often serve as key tools or probes for this atomically precise undertaking. In this Perspective, metal nanoclusters, especially gold nanoclusters, serve as a good platform for understanding such nanoscale interactions. These nanoclusters often have a core size of about 2 nm, a defined number of core metal atoms, and protecting ligands with known crystal structure. The atomically precise structure of metal nanoclusters allows us to discuss how the molecular interactions facilitate the systematic modification and functionalization of nanoclusters from their inner core, through the ligand shell, to the external assembly. Interestingly, the atomic packing structure of the nanocluster core can be affected by forces on the surface. After discussing the core structure, we examine various atomic-level strategies to enhance their photoluminescent quantum yield and improve nanoclusters' catalytic performance. Beyond the single cluster level, various attractive or repulsive molecular interactions have been employed to engineer the self-assembly behavior and thus packing morphology of metal nanoclusters. The methodological and fundamental insights systemized in this review should be useful for customizing the cluster structure and assembly patterns at the atomic level.

The conformation of tetraspanins CD53 and CD81 differentially affects their nanoscale organization and interaction with their partners

Tetraspanins, including CD53 and CD81, are four-transmembrane proteins that affect the membrane organization to regulate cellular processes including migration, proliferation and signaling. However, it is unclear how the organizing function of tetraspanins is regulated at the molecular level. Here we investigated whether recently proposed ‘open’ and ‘closed’ conformations of tetraspanins regulate the nanoscale organization of the plasma membrane of B cells. We generated conformational mutants of CD53 (F44E) and CD81 (4A, E219Q) that represent the ‘closed’ and ‘open’ conformation, respectively. Surface expression of these CD53 and CD81 mutants was comparable to that of wildtype (WT) protein. Localization of mutant tetraspanins into nanodomains was visualized by super-resolution dSTORM microscopy. Whereas the size of these nanodomains was unaffected by conformation, the clustered fraction of ‘closed’ CD53 was higher and of ‘open’ CD81 lower than respective WT protein. In addition, knock-out cells lacking CD53 showed an increased likelihood of clustering of its partner CD45. Interestingly, ‘closed’ CD53 interacted more with CD45 than WT CD53. Absence of CD81 lowered the cluster size of its partner CD19, and ‘closed’ CD81 interacted less with CD19 than WT CD81, but ’open’ CD81 did not affect CD19 interaction. However, none of the tetraspanin conformations made significant impact on the nanoscale organization of their partners CD19 or CD45. Taken together, conformational mutations of CD53 and CD81 differentially affect their nanoscale organization, but not the organization of their partner proteins. This study improves the molecular insight into cell surface nanoscale organization by tetraspanins.

Bioarchitectonic Nanophotonics by Replication and Systolic Miniaturization of Natural Forms.

The mimesis of biological mechanisms by artificial devices constitutes the modern, rapidly expanding, multidisciplinary biomimetics sector. In the broader bioinspiration perspective, however, bioarchitectures may perform independent functions without necessarily mimicking their biological generators. In this paper, we explore such Bioarchitectonic notions and demonstrate three-dimensional photonics by the exact replication of insect organs using ultra-porous silica aerogels. The subsequent conformal systolic transformation yields their miniaturized affine 'clones' having higher mass density and refractive index. Focusing on the paradigms of ommatidia, the compound eye of the hornet Vespa crabro flavofasciata and the microtrichia of the scarab Protaetia cuprea phoebe, we fabricate their aerogel replicas and derivative clones and investigate their photonic functionalities. Ultralight aerogel microlens arrays are proven to be functional photonic devices having a focal length f ~ 1000 μm and f-number f/30 in the visible spectrum. Stepwise systolic transformation yields denser and affine functional elements, ultimately fused silica clones, exhibiting strong focusing properties due to their very short focal length of f ~ 35 μm and f/3.5. The fabricated transparent aerogel and xerogel replicas of microtrichia demonstrate a remarkable optical waveguiding performance, delivering light to their sub-100 nm nanotips. Dense fused silica conical clones deliver light through sub-50 nm nanotips, enabling nanoscale light-matter interactions. Super-resolution bioarchitectonics offers new and alternative tools and promises novel developments and applications in nanophotonics and other nanotechnology sectors.

Understanding Nanoscale Interactions between Minerals and Microbes: Opportunities for Green Remediation of Contaminated Sites.

In situ contaminant degradation and detoxification mediated by microbes and minerals is an important element of green remediation. Improved understanding of microbe-mineral interactions on the nanoscale offers promising opportunities to further minimize the environmental and energy footprints of site remediation. In this Perspective, we describe new methodologies that take advantage of an array of multidisciplinary tools─including multiomics-based analysis, bioinformatics, machine learning, gene editing, real-time spectroscopic and microscopic analysis, and computational simulations─to identify the key microbial drivers in the real environments, and to characterize in situ the dynamic interplay between minerals and microbes with high spatiotemporal resolutions. We then reflect on how the knowledge gained can be exploited to modulate the binding, electron transfer, and metabolic activities at the microbe-mineral interfaces, to develop new in situ contaminant degradation and detoxication technologies with combined merits of high efficacy, material longevity, and low environmental impacts. Two main strategies are proposed to maximize the synergy between minerals and microbes, including using mineral nanoparticles to enhance the versatility of microorganisms (e.g., tolerance to environmental stresses, growth and metabolism, directed migration, selectivity, and electron transfer), and using microbes to synthesize and regenerate highly dispersed nanostructures with desired structural/surface properties and reactivity.

Using Nanoscale Passports To Understand and Unlock Ion Channels as Gatekeepers of the Cell.

Natural ion channels are proteins embedded in the cell membrane that control many aspects of cell and human physiology by acting as gatekeepers, regulating the flow of ions in and out of cells. Advances in nanotechnology have influenced the methods for studying ion channels in vitro, as well as ways to unlock the delivery of therapeutics by modulating them in vivo. This review provides an overview of nanotechnology-enabled approaches for ion channel research with a focus on the synthesis and applications of synthetic ion channels. Further, the uses of nanotechnology for therapeutic applications are critically analyzed. Finally, we provide an outlook on the opportunities and challenges at the intersection of nanotechnology and ion channels. This work highlights the key role of nanoscale interactions in the operation and modulation of ion channels, which may prompt insights into nanotechnology-enabled mechanisms to study and exploit these systems in the near future.

Non-Fourier computations of heat and mass transport in nanoscale solid-fluid interactions using the Galerkin finite element method

PurposeTo improve the thermal performance of base fluid, nanoparticles of three types are dispersed in the base fluid. A novel theory of non-Fourier heat transfer is used for design and development of models. The thermal performance of sample fluids is compared to determine which types of combination of nanoparticles are the best for an optimized enhancement in thermal performance of fluids. This article aims to: (i) investigate the impact of nanoparticles on thermal performance; and (ii) implement the Galerkin finite element method (GFEM) to thermal problems.Design/methodology/approachThe mathematical models are developed using novel non-Fourier heat flux theory, conservation laws of computational fluid dynamics (CFD) and no-slip thermal boundary conditions. The models are approximated using thermal boundary layer approximations, and transformed models are solved numerically using GFEM. A grid-sensitivity test is performed. The accuracy, correction and stability of solutions is ensured. The numerical method adopted for the calculations is validated with published data. Quantities of engineering interest, i.e. wall shear stress, wall mass flow rate and wall heat flux, are calculated and examined versus emerging rheological parameters and thermal relaxation time.FindingsThe thermal relaxation time measures the ability of a fluid to restore its original thermal state, called thermal equilibrium and therefore, simulations have shown that the thermal relaxation time associated with a mono nanofluid has the most substantial effect on the temperature of fluid, whereas a ternary nanofluid has the smallest thermal relaxation time. A ternary nanofluid has a wider thermal boundary thickness in comparison with base and di- and mono nanofluids. The wall heat flux (in the case of the ternary nanofluids) has the most significant value compared with the wall shear stresses for the mono and hybrid nanofluids. The wall heat and mass fluxes have the highest values for the case of non-Fourier heat and mass diffusion compared to the case of Fourier heat and mass transfer.Originality/valueAn extensive literature review reveals that no study has considered thermal and concentration memory effects on transport mechanisms in fluids of cross-rheological liquid using novel theory of heat and mass [presented by Cattaneo (Cattaneo, 1958) and Christov (Christov, 2009)] so far. Moreover, the finite element method for coupled and nonlinear CFD problems has not been implemented so far. To the best of the authors’ knowledge for the first time, the dynamics of wall heat flow rate and mass flow rate under simultaneous effects of thermal and solute relaxation times, Ohmic dissipation and first-order chemical reactions are studied.

Nanoscale Structure, Interactions, and Dynamics of Centromere Nucleosomes.

Centromeres are specific segments of chromosomes comprising two types of nucleosomes: canonical nucleosomes containing an octamer of H2A, H2B, H3, and H4 histones and CENP-A nucleosomes in which H3 is replaced with its analogue CENP-A. This modification leads to a difference in DNA wrapping (∼121 bp), considerably less than 147 bp in canonical nucleosomes. We used atomic force microscopy (AFM) and high-speed AFM (HS-AFM) to characterize nanoscale features and dynamics for both types of nucleosomes. For both nucleosomes, spontaneous asymmetric unwrapping of DNA was observed, and this process occurs via a transient state with ∼100 bp DNA wrapped around the core, followed by a rapid dissociation of DNA. Additionally, HS-AFM revealed higher stability of CENP-A nucleosomes compared with H3 nucleosomes in which dissociation of the histone core occurs prior to the nucleosome dissociation. These results help elucidate the differences between these nucleosomes and the potential biological necessity for CENP-A nucleosomes.

Nanoscale Interaction of Endonuclease APE1 with DNA.

Apurinic/apyrimidinic endonuclease 1 (APE1) is involved in DNA repair and transcriptional regulation mechanisms. This multifunctional activity of APE1 should be supported by specific structural properties of APE1 that have not yet been elucidated. Herein, we applied atomic force microscopy (AFM) to characterize the interactions of APE1 with DNA containing two well-separated G-rich segments. Complexes of APE1 with DNA containing G-rich segments were visualized, and analysis of the complexes revealed the affinity of APE1 to G-rich DNA sequences, and their yield was as high as 53%. Furthermore, APE1 is capable of binding two DNA segments leading to the formation of loops in the DNA-APE1 complexes. The analysis of looped APE1-DNA complexes revealed that APE1 can bridge G-rich segments of DNA. The yield of loops bridging two G-rich DNA segments was 41%. Analysis of protein size in various complexes was performed, and these data showed that loops are formed by APE1 monomer, suggesting that APE1 has two DNA binding sites. The data led us to a model for the interaction of APE1 with DNA and the search for the specific sites. The implication of these new APE1 properties in organizing DNA, by bringing two distant sites together, for facilitating the scanning for damage and coordinating repair and transcription is discussed.

Thermally Stable 3D‐Metamaterial Designs with Advanced Hyperbolic Dispersion Manipulation and Magnetic Anisotropy

AbstractHybrid metamaterials (HMs) have attracted significant research interests owing to their unique optical properties and their ability to manipulate light‐matter interaction in a novel and controlled fashion beyond what any single material offers. Especially 3D HMs are of great interest due to their potential to provide advanced and precise control of such light‐matter interaction in nanoscale. In this study, a set of 3D HM nanocomposite films are designed by integrating three phases, i.e., vertically aligned CoFe2 nanosheets within the matrix of TiN/TaN multilayers. By increasing the number of TiN/TaN multilayers from 2 to 19, a high degree of tunability in optical property has been demonstrated, including well‐tailored optical permittivity, and tunable hyperbolic dispersion from Type‐II to Type‐I. Ferromagnetic CoFe2 nanosheets introduces novel magnetic responses, such as magnetic anisotropy and enhanced coercivity. Furthermore, in situ heating X‐ray diffraction (XRD) suggests good thermal stability of the 3D nanocomposite films up to the measured temperature of 600 °C. This three‐phase 3D nanocomposite design offers more flexibility in HM designs, multifunctionalities, and phase stability, compared with the typical two‐phase HMs toward future metamaterials by design.

Morphostructural studies of pure and mixed metal oxide nanoparticles of Cu with Ni and Zn

Nano-scale interactions between pure metal or metal-oxide components within an oxide matrix can improve functional performance over basic metal oxides. This study reports on the synthesis of monometallic (CuO), bimetallic (CuO–NiO) and trimetallic (CuO–NiO–ZnO) oxide nanoparticles (NPs) via the co-precipitation method and investigation of morphostructural properties. All of the synthesized metal oxide NPs were calcined at 550 °C temperature and annealed under vacuum. In this work, we applied Scherrer formula, modified Scherrer equation, Williamson-Hall plots, and Halder-Wagner plots to calculate the average crystallite size. The XRD data analysis showed that average crystallite sizes of the as-synthesized metal oxide phases were between 4 nm and 76 nm and average diameters calculated from SEM image were between 15 nm and 83 nm. The XRD studies also disclosed that average crystallite size and lattice microstrain of the CuO phases remain almost same (43 nm–46 nm and 2.074×10−3 to 2.665×10−3) for pure CuO and mixed CuO–NiO; but in case of mixed CuO–NiO–ZnO it is found to decrease in size to 11 nm where lattice microstrain increases to 9.653×10−3. Line broadening of diffraction peaks from microstrain contribution was between 0.02 and 0.01. Degree of crystallinity (%) of CuO phases found to decrease from 81 to 71. Dislocation density of CuO phases found to increase from 6.63×10−4nm−2 to 12.68×10−3nm−2. X-ray density of CuO phases increased from 6.48 to 6.53 g/cm3. Where this calculated small dislocation density well agreed with the high crystallinity. Crystal structure and specific surface area were determined from lattice constants and X-ray density. These synthesized nanopowders showed the existence of monoclinic, cubic, and hexagonal phases. The obtained NPs of multi-metal oxide explained more than one phases with different size, shape, and morphology at nano scale.

Probing Inherent Optical Anisotropy in Substrates via Direct Nanoimaging of Mie Scattering.

In this study, we investigated the optical properties of a transition metal dichalcogenide (TMD) substrate via Mie-scattering-induced surface analysis (MISA). Employing near-field optical microscopy and finite-difference time-domain (FDTD) simulations, we systemically prove and directly visualize the Mie scattering of superspherical gold nanoparticles (s-AuNPs) at the nanoscale. Molybdenum disulfide substrates exhibited optical isotropy, while rhenium disulfide (ReS2) substrates showed anisotropic behavior attributed to the interaction with incident light's electric field. Our study revealed substantial anisotropic trends in Mie scattering, particularly in the near-infrared energy range, with ReS2 exhibiting more pronounced spectral and angular responses in satellite peaks. Our results emphasize the application of Mie scattering, exploring the optical properties of substrates and contributing to a deeper understanding of nanoscale light-matter interactions.

Electron videography of a lipid-protein tango.

Biological phenomena, from enzymatic catalysis to synaptic transmission, originate in the structural transformations of biomolecules and biomolecular assemblies in liquid water. However, directly imaging these nanoscopic dynamics without probes or labels has been a fundamental methodological challenge. Here, we developed an approach for "electron videography"-combining liquid phase electron microscopy with molecular modeling-with which we filmed the nanoscale structural fluctuations of individual, suspended, and unlabeled membrane protein nanodiscs in liquid. Systematic comparisons with biochemical data and simulation indicate the graphene encapsulation involved can afford sufficiently reduced effects of the illuminating electron beam for these observations to yield quantitative fingerprints of nanoscale lipid-protein interactions. Our results suggest that lipid-protein interactions delineate dynamically modified membrane domains across unexpectedly long ranges. Moreover, they contribute to the molecular mechanics of the nanodisc as a whole in a manner specific to the protein within. Overall, this work illustrates an experimental approach to film, quantify, and understand biomolecular dynamics at the nanometer scale.

Emergent Properties from Three-Dimensional Assemblies of (Nano)particles in Confined Spaces.

The assembly of (nano)particles into compact hierarchical structures yields emergent properties not found in the individual constituents. The formation of these structures relies on a profound knowledge of the nanoscale interactions between (nano)particles, which are often designed by researchers aided by computational studies. These interactions have an effect when the (nano)particles are brought into close proximity, yet relying only on diffusion to reach these closer distances may be inefficient. Recently, physical confinement has emerged as an efficient methodology to increase the volume fraction of (nano)particles, rapidly accelerating the time scale of assembly. Specifically, the high surface area of droplets of one immiscible fluid into another facilitates the controlled removal of the dispersed phase, resulting in spherical, often ordered, (nano)particle assemblies. In this review, we discuss the design strategies, computational approaches, and assembly methods for (nano)particles in confined spaces and the emergent properties therein, such as trigger-directed assembly, lasing behavior, and structural photonic color. Finally, we provide a brief outlook on the current challenges, both experimental and computational, and farther afield application possibilities.

Cadmium pollution exacerbated by drought: Insights from the nanoscale interaction at the clay mineral surface

Drought is a global environmental problem, while the effect of drought-induced unsaturation on the fate of heavy metal ions is still poorly understood, particularly the lack of mechanistic information at the molecular level. This study used molecular dynamics simulations to investigate nanoscale interactions at the montmorillonite surface under different moisture conditions. Compared to the saturated condition, drought increased the amounts and strength of Cd2+ ions adsorbed on the montmorillonite (MMT) surface while decreased the diffusivity, which was especially obvious in extreme drought conditions (θv=21%−7%). This is closely related to the compressed electric double layer, overcompensation of surface charge, and increased ion pair interactions, resulting from the confinement of water films under drought stress. Further analysis showed that the decrease of hydration effect was responsible for the exacerbated cadmium pollution. Therefore, this study may break the stereotypes about the interactions between heavy metal ions and soil minerals. The results suggest that water management (e.g., irrigation) may be prioritized before beginning heavy metal remediation.

Hydrogen enhanced localised plasticity of single grain α titanium verified by in-situ hydrogen microcantilever bending

The effect of hydrogen on the micromechanical characteristics of pure grade 2 titanium was investigated by comparing prenotched microcantilever bending in air versus in-situ electrochemical hydrogen charging. The nanoscale interaction between hydrogen and the metal's defects was analysed in three different grain orientations, i.e. the top surface parallel to {101‾2}, {0001}, and {202‾1}. The subsequent high resolution post-mortem characterisation enabled to characterise the interplay between hydrogen in solid solution and the dislocations in the local deformation process. The results showed that hydrogen facilitated a localised plasticity mechanism, causing hydrogen assisted degradation at the applied low hydrogen concentration below the hydride formation threshold. Meanwhile, hydrogen provoked a reduction in defect formation energy, following the defactant concept, which was responsible for a softening effect on the yield stress and flow stress. Furthermore, due to the anisotropic characteristics of the α titanium hexagonal close packed crystal lattice, the susceptibility to hydrogen effects also depended on the grain orientation. This single grain in-situ micromechanical testing is complementing the existing macroscaled identification of hydrogen effects in α titanium.

Deep learning-enabled probing of irradiation-induced defects in time-series micrographs

Modeling time-series data with convolutional neural networks (CNNs) requires building a model to learn in batches as opposed to training sequentially. Coupling CNNs with in situ or operando techniques opens the possibility of accurately segmenting dynamic reactions and mass transport phenomena to understand how materials behave under the conditions in which they are used. In this article, in situ ion irradiation transmission electron microscopy (TEM) images are used as inputs into the CNN to assess the defect generation rate, defect cluster density, and saturation of defects. We then use the output segmentation maps to correlate with conventional TEM micrographs to assess the model’s ability to detail nanoscale interactions. Next, we discuss the implications of preprocessing and hyperparameters on model variability, accuracy when expanded to other datasets, and the role of regularization when controlling model variance. Ultimately, we eliminate human bias when extrapolating physical metrics, speed up analysis time, decouple reactions that happen at 100 ms intervals, and deploy models that are both accurate and transferable to similar experiments.