Formation Of Localized Structures Research Articles

Predicting the Sequence-Dependent Backbone Dynamics of Intrinsically Disordered Proteins.

How the sequences of intrinsically disordered proteins (IDPs) code for functions is still an enigma. Dynamics, in particular residue-specific dynamics, holds crucial clues. Enormous efforts have been spent to characterize residue-specific dynamics of IDPs, mainly through NMR spin relaxation experiments. Here we present a sequence-based method, SeqDYN, for predicting residue-specific backbone dynamics of IDPs. SeqDYN employs a mathematical model with 21 parameters: one is a correlation length and 20 are the contributions of the amino acids to slow dynamics. Training on a set of 45 IDPs reveals aromatic, Arg, and long-branched aliphatic amino acids as the most active in slow dynamics whereas Gly and short polar amino acids as the least active. SeqDYN predictions not only provide an accurate and insightful characterization of sequence-dependent IDP dynamics but may also serve as indicators in a host of biophysical processes, including the propensities of IDP sequences to undergo phase separation.

Hybrid Patterns and Solitonic Frequency Combs in Non-Hermitian Kerr Cavities.

We unveil a new scenario for the formation of dissipative localized structures in nonlinear systems. Commonly, the formation of such structures arises from the connection of a homogeneous steady state with either another homogeneous solution or a pattern. Both scenarios, typically found in cavities with normal and anomalous dispersion, respectively, exhibit unique fingerprints and particular features that characterize their behavior. However, we show that the introduction of a periodic non-Hermitian modulation in Kerr cavities hybridizes the two established soliton formation mechanisms, embodying the particular fingerprints of both. In the resulting novel scenario, the stationary states acquire a dual behavior, playing the role that was unambiguously attributed to either homogeneous states or patterns. These fundamental findings have profound practical implications for frequency comb generation, introducing unprecedented reversible mechanisms for real-time manipulation.

Surface-induced water crystallisation driven by precursors formed in negative pressure regions

Ice nucleation is a crucial process in nature and industries; however, the role of the free surface of water in this process remains unclear. To address this, we investigate the microscopic freezing process using brute-force molecular dynamics simulations. We discover that the free surface assists ice nucleation through an unexpected mechanism. The surface-induced negative pressure enhances the formation of local structures with a ring topology characteristic of Ice 0-like symmetry, promoting ice nucleation despite the symmetry differing from ordinary ice crystals. Unlike substrate-induced nucleation via water-solid interactions that occurs directly on the surface, this negative-pressure-induced mechanism promotes ice nucleation slightly inward the surface. Our findings provide a molecular-level understanding of the mechanism and pathway behind free-surface-induced ice formation, resolving the longstanding debate. The implications of our discoveries are of substantial importance in areas such as cloud formation, food technology, and other fields where ice nucleation plays a pivotal role.

Excellent piezoelectric response and low dielectric loss of PIN-PHT ceramics obtained through synergy of defect engineering and localized heterostructure

Pb-based piezoelectric ceramics with excellent piezoelectric response and low dielectric loss are crucial for advanced applications but still challenging to achieve. Herein, an approach based on synergistic effect of defect engineering and localized heterogeneous structures was developed to prepare 0.11 Pb(In0.5Nb0.5)O3-0.89 Pb(Hf0.47Ti0.53)O3+xmol%(Sb5++Nd3+) advanced piezoelectric ceramics by solid phase reaction method. Effects of ion co-doping on physical phase structures, defect concentrations, and electric domain morphologies of ceramics were all investigated. A mapping relationship between defect concentration, formation of localized heterogeneous structure, and modulation of piezoelectric and dielectric properties of ceramics was extracted. Values of d33, TC, εr, tanδ (%), and kp of ceramics obtained at x = 0.4 mol% were determined as respectively 607 pC/N, 313.1°C, 3407.81, 1.42, and 0.66, showing excellent overall performances. The doping of (Sb5++Nd3+) skillfully modulated the concentration of defects inside ceramics, resulting in excellent piezoelectric response and reduced dielectric loss. On the other hand, lattice distortion induced by doping generated nanodomains formed localized heterostructures and significantly reduced the Gibbs free-energy barrier, resulting in excellent piezoelectric response and dielectric properties. These effects can mainly be attributed to synergistic action of defect engineering and localized heterostructures. Overall, proposed ceramics and strategy look promising for preparing Pb-based piezoelectric ceramics with excellent comprehensive performance.

Inflection Point in Pressure Dependence of Ionic Conductivity as a Fingerprint of Local Structure Formation.

In this study, we employed dielectric spectroscopy to investigate the effect of temperature and pressure on the ion dynamics of phosphonium ionic liquids (ILs) differing by the length of an alkyl chain, [P666,n][TFSI] (n = 2, 6, 8, 12). We found that both temperature and pressure dependence of dc-conductivity (σdc) determined for all examined ILs herein exhibit unique characteristics, unusual for aprotic ILs. Two regions differing by ion self-organization have been identified from the derivative analysis of σdc(T-1) data. On the other hand, isothermal measurements performed at elevated pressure revealed a unique concave-convex character of σdc(P) dependences, resulting in a clear minimum in the pressure behavior of activation volume. Such an inflection point characterizing the pressure dependence of σdc in [P666,n][TFSI] ILs can be considered an inherent feature of ion dynamics governed by structural self-assembly. Our results offer a unique perspective to link the ion mobility at various T-P conditions to the nanostructural organization of ionic systems.

Dynamic responses of laminated and graded ZrC-Mo composites

It is of great significance to investigate the dynamic responses of functionally graded materials (FGMs). A series of experiments are conducted to evaluate the dynamic behaviors of the laminated and graded ZrC-Mo composites with three graded exponents (i.e., 0.69, 1.35, and 2.70) by the split Hopkinson pressure bar (SHPB) device. The graded composites with an exponent of 0.69 show the highest strength and best performances of the three. It results from the formation of local stress-transferring structures and the interaction of the ZrC component and Mo component. Based on the digital imaging correlation (DIC) method, different evolutions of local strains in the ZrC-rich and the Mo-rich regions are analyzed by changing the gradient directions of the composites. The transmission behaviors of stress waves in the laminated and graded composite with multi-interfaces are investigated theoretically. The finite element method (FEM) is used to evaluate influences of the plasticity of metal component, and the transmitted coefficient in theory is employed to optimize and evaluate the laminated and graded structures. It also indicates the special role of loading frequency. These results might be helpful for a profound understanding of the internal wave propagation and guide the structural designing optimization.

Mathematical modeling of rocks fracture within local structures

Soil massif fracturing has a significant impact on change in engineering and geological conditions and, as a result, on stability of structures. Development of tectonic fracturing of local structures, taking into account the history of the process, its mechanism, resulting stresses in the massif and subsequent deformations of the rocks, led to a change in their structure, composition and strength characteristics, activation of hypergenesis and exogenous processes. The above circumstances require careful attention to identification of areas of increased fracturing, as the most dangerous in terms of risks during the construction of engineering structures. Field methods for assessing the fracturing of rock masses are laborious. It is not always possible to conduct instrumental surveys that allow solving the final problem – establishing patterns and sizes of damaged areas within local structures. The existing mathematical models for assessing fracturing, as a rule, are used to solve local problems: assessing the stability of developed pits, water content of rock masses, degree of fragmentation of individual blocks, etc. This information is not sufficient when assessing the areal distribution of weakened zones and clarifying their boundaries, since it does not take into account the history of the development of the structure, its parameters (dimensions, amplitude of the foundation block uplift, deformation properties of rocks). Aim. To develop a mathematical model of formation of the red-colored strata tectonic fracturing zones based on deformation criterion of destruction and mechanism of development of local structures. Results. The authors have developed a new mathematical model for predicting damage (fracturing) of terrigenous rocks of the red-colored strata that make up local structures, based on the mechanism of formation of local tectonic structures of the 3rd order and the deformation criterion of destruction. The paper introduces the mathematical dependencies that make it possible to predict the size (area) of taxa based on the data on the uplift amplitude of local structures. The results of the research can be used in assessing the fracturing of massifs composed of terrigenous rocks, and make it possible to judge the regularities in distribution of weakened zones within the entire massif being assessed.

Influence of the discrete lattice spacing on the formation of intrinsic localized structures in the Salerno model

We report in this paper the influence of the discrete lattice spacing on the formation of intrinsic localized structures in the Salerno model. Through the linear stability analysis, appearance criterions of the modulation instability (MI) are derived. We show via the growth rate that, the discrete lattice spacing and the nonlinearity term can affect significantly the formation of instability zones. We find that for large values of the discrete lattice spacing, the MI is developed to increase the number instability zones whereas for very low values of this parameter, the MI growth rate is arisen up to enlarge the bandwidth. The theoretical findings have been numerically tested via the discrete spatial Fourier transform method and the direct simulations, and have been found to be in full agreement with the analytical prediction. Moreover, it has been revealed that a higher modulation index can dramatically modify the shape and the amplitude of the modulated waves.

INSTITUTIONAL ASPECT INNOVATIVE MODERNIZATION OF AGRICULTURAL PRODUCTION

The institutional determinants of innovative modernization of agricultural production are substantiated.
 It is established that the transformational features domestic agricultural production are monoculture agricultural production, its structural deformation, increased degradation of land and water resources, growing dependence of agricultural producers on imported inputs for the production process, and a reduction in the number of rural workers and the population of rural communities.
 It is argued that transformational changes in agro-industrial production should be focused on large-scale modernization changes in the production process in terms of restoring land fertility, improving the quality characteristics of food products, expanding the existing export potential of agricultural products and the share competitive products. 
 It is established that the threats to the recovery of agricultural production are the narrowing of the domestic consumer market; reduction of the purchasing power of the population with a decrease in its number; reduction and blocking of exports of agricultural products; rising costs of material resources and rising costs of agricultural products and food prices.
 It is substantiated that institutional support for the innovative modernization of agro-industrial production should be accompanied by the formation of effective basic and special institutions and institutions that meet the criteria of systematicity when they are included in the hierarchical structure of norms and institutions of innovation.
 It is emphasized that the institutional support for innovative modernization should implement the following key tasks: ensuring a favorable investment climate for attracting financial resources to processing enterprises and the formation of local regional structures with low capacity for processing agricultural raw materials; creating conditions for the inclusion of agricultural producers in global value chains.
 Institutional interventions should be aimed at stimulating the diffusion and development of product innovations; supporting and shaping organizational structures for vertical and horizontal integration; supporting and shaping organizational frameworks for vertical and horizontal integration; and restructuring forms of state support for agricultural production.
 The strategic guidelines for the innovative modernization of agro-industrial production are defined: introduction of motives and incentives for structural changes in agricultural production, intensification of the development of small forms of management, integration of production processes, and use of competitive advantages.

Solution-Processed Non-Crystalline Solid Electrolytes for Advanced Energy Storage

Advanced batteries containing a Li metal anode (LMA) are needed to enable the clean economy and meet ambitious climate targets. Currently, LMA batteries are limited by dendrite propagation due to the non-uniform plating and stripping of Li, which is detrimental to cell performance. The non-crystalline solid electrolyte (SE), lithium phosphorus oxynitride (LiPON) is unique in demonstrating stable Li plating/stripping at appreciable rates, but its synthesis requires costly and slow vacuum deposition methods. We use aqueous precursor solutions which are rapidly condensed during spin coating and gently annealed to produce dense, flat, Li metal oxide films without long-range order. However, such solution-processed SEs typically exhibit ionic conductivities (σ ion ) too low for energy storage applications (~10-8 S cm-1) and far lower than vacuum-deposited LiPON (~10-6 S cm-1).We will discuss various approaches to increase the σion of these materials, including compositional engineering and controlled processing conditions. Structure-property relationships have been elucidated using modelling of the local structure and interphase formation against Li evaluated by time-dependent electrochemical impedance spectroscopy and in situ X-ray photoelectron spectroscopy. Electrochemical testing of these films deposited onto a current collector in an anode-free cell will be used to evaluate their ability to facilitate stable deposition and stripping of Li.Initial exploration of processing parameters have yielded σion values > 10-7 S cm-1 [1] and the presence of medium-range order (nanocrystalline domains) in some cases. Beyond Li, new non-crystalline SEs for other ions will be discussed. As only limited chemical compositions and processing conditions of these materials have been reported, with no corresponding structural studies, our work provides insight to enable the optimisation and discovery of scalable non-crystalline SEs for advanced batteries.1. P. Vadhva, T. Gill, J. H. Cruddos, S. Said, M. Siniscalchi, S. Narayanan, M. Pasta, T.S. Miller, A.J.E. Rettie. Engineering solution-processed non-crystalline solid electrolytes for Li metal batteries. Chemistry of Materials, 2022, 35, 3, 1168–1176.

Dispersion engineering in a Brillouin fiber laser cavity for Kerr frequency comb formation

We conduct numerical and experimental investigations on Kerr comb generation in a nonlinear and non-reciprocal fiber cavity by leveraging both stimulated Brillouin backscattering and cascaded four-wave mixing. By engineering the net cavity dispersion to be either normal or anomalous, we enable the formation of diverse patterns and localized structures in the cavity field. The comb’s properties depend crucially on the mismatch between the frequency spacing of the bichromatic pump and the free spectral range of the Brillouin laser cavity in both cases. Particularly, in the anomalous regime, adjusting this parameter yields coherent, stable frequency combs in the modulation instability regime. This allows control and expansion of the spectral bandwidth up to 2 THz in normal dispersion and to 6 THz under anomalous net dispersion. This versatile and easily reconfigurable method holds potential for applications in high-speed communications and microwave synthesis.

Microstructural characterization and mechanical behavior of Aba Panu meteorite by correlative microscopy and nanoindentation

Meteorite samples that land on earth can provide important information about asteroid and meteors found in space. Thorough, multimodal, and multiscale microstructural analysis is necessary to provide clues about the formation history of these materials. Both 3D x-ray tomography and scanning electron microscopy, along with energy dispersive spectroscopy, were used to obtain detailed structural information from the Aba Panu meteorite. EDS was utilized to obtain elemental composition and identify existing minerals in the meteorite. The microstructural analysis enabled a proposed hypothesis of potential local structure formation processes supported by phase diagrams of the existing minerals. Mechanical properties of identified phases were measured using nanoindentation and Vickers hardness testing. By combining structural, compositional, and mechanical results, a comprehensive characterization and discussion of meteorite Aba Panu was obtained.

Isolas of localized structures and Raman–Kerr frequency combs in micro-structured resonators

We theoretically investigate the combined impact of the Kerr and stimulated Raman scattering effect on the formation of localized structures and frequency comb generation. We focus on the regime of traveling wave instability. We first perform a real-order parameter description by deriving a Swift–Hohenberg equation with nonlocal delayed feedback. Second, we characterize the motion of traveling wave periodic solutions by estimating their thresholds as well their speed. By using a numerical continuation method, we construct a bifurcation diagram showing the emergence of traveling wave periodic solutions, as well as bright and dark moving localized structures. Numerical simulations of the generalized Lugiato–Lefever equation confirm evidence of isolas of localized structures. More importantly, we show that the stimulated Raman scattering strongly impacts the dynamics of localized structures by creating isolas consisting of bright and dark localized structures, and by inducing a motion of these structures. Finally, we provide a geometrical interpretation of the formation of isola stacks based on dynamical systems theory.

Electrostatic lower hybrid turbulence due to magnetic islands and particle heating in magnetopause reconnection regions

This investigation presents a model to understand the magnetopause turbulence in the lower hybrid frequency range at reconnection regions as observed by the magnetospheric multiscale mission. We have modeled 3D electrostatic lower hybrid wave (LHW) in cold magnetized plasma in the presence of magnetic islands. In this model, we have developed the modified nonlinear Schrödinger equation, contemplating that nonlinear effects are due to ponderomotive force. The dynamical equation of the system thus obtained is solved using numerical simulation techniques. The simulation results illustrate the formation and evolution of localized structures and the current sheets. Due to the nonlinear effects and magnetic reconnection, the current sheets become turbulent with time. A semi-analytical model is also given to illustrate the scale size of current sheets. The turbulent power spectra have also been studied. The spectral index of the power spectrum is found to be −2.7 (approximately) in the perpendicular direction and −2.2 (approximately) in the parallel direction, indicating anisotropy. Using the Folker–Plank diffusion equation with the new velocity space diffusion coefficient, we find the distribution function of energetic electrons due to these turbulent structures. We propose that LHW may be responsible for plasma heating in magnetopause.

Spectroscopic behavior differences between lumazine and alloxazine in the DMSO-water mixture

The absorption and emission spectra were investigated for lumazine, alloxazine and their cyanated or fluorinated derivatives, respectively. The spectroscopic properties were modulated by varying water concentration in dimethyl sulfoxide (DMSO). Some intriguing experimental results were found for the samples containing 65 % of water and 35% of DMSO. This finding is consistent with previously published molecular dynamics (MD) simulations confirming the concept of the ‘local bulk’ model. In this case, a notable decrease in absorption and emission intensities was registered, even larger than the water quenching observed in other cases. The changes in midrange DMSO concentrations could be explained by the formation of local solvents structures as predicted by MD, specifically the formation of DMSO·2H2O dimers. Experimentally, the cyano-substituted lumazine has shown a remarkable sensitivity to DMSO concentration. The spectroscopic measurements were interpreted using the density functional theory where the implicit DMSO solvent model was combined with explicit water molecules. Together with its enhanced water solubility, the cyanated lumazine derivate could be used for non-destructive DMSO detection in vitro for applications such as drug uptake monitoring, since DMSO is often used in pharmaceutical practice.

Liquid Structures and Diffusion Dynamics of Alkyl-Pyrene Liquids Studied by Molecular Dynamics Simulations.

Functional molecular liquids (FMLs) based on alkylated π-conjugated molecules have attracted attention as solvent-free and nonvolatile liquid materials with prominent optoelectronic features. Recently, novel FML compounds containing pyrene as the functional core were synthesized, and their rheological and photochemical properties were investigated. Although the molecules differ only in the number of alkyl chain substituents and their substitution positions, their viscosity coefficients are largely different beyond the Stokes-Einstein relation on the assumption of identical microscopic friction, indicating that local microscopic molecular interactions are crucial for the macroscopic rheological properties. Here, we report a theoretical study on the rheological properties of the alkyl-pyrene liquids by means of atomistic molecular dynamics (MD) simulations. We performed long-time MD simulations for tens of microseconds to obtain ample statistical samples of the alkyl-pyrene liquids and analyzed their liquid structures and diffusion dynamics based on spatiotemporal correlation functions. We found the formation of characteristic local liquid structures of π-π stacking of the pyrene moieties and locally anisotropic and anomalous diffusion dynamics, which remarkably vary depending on the alkyl substituent patterns. The present results provide an atomistic insight into the macroscopic rheological properties of alkyl-π FMLs and molecular design strategy for them.

The Formation of β-Strand Nine (β9) in the Folding and Insertion of BamA from an Unfolded Form into Lipid Bilayers.

Transmembrane proteins span lipid bilayer membranes and serve essential functions in all living cells. Membrane-inserted domains are of either α-helical or β-barrel structure. Despite their biological importance, the biophysical mechanisms of the folding and insertion of proteins into membranes are not well understood. While the relative composition of the secondary structure has been examined by circular dichroism spectroscopy in folding studies for several outer membrane proteins, it is currently not known how individual β-strands fold. Here, the folding and insertion of the β-barrel assembly machinery protein A (BamA) from the outer membrane of Escherichia coli into lipid bilayers were investigated, and the formation of strand nine (β9) of BamA was examined. Eight single-cysteine mutants of BamA were overexpressed and isolated in unfolded form in 8 M urea. In each of these mutants, one of the residues of strand β9, from R572 to V579, was replaced by a cysteine and labeled with the fluorophore IAEDANS for site-directed fluorescence spectroscopy. Upon urea-dilution, the mutants folded into the native structure and were inserted into lipid bilayers of dilauroylphosphatidylcholine, similar to wild-type BamA. An aqueous and a membrane-adsorbed folding intermediate of BamA could be identified by strong shifts in the intensity maxima of the IAEDANS fluorescence of the labeled mutants of BamA towards shorter wavelengths, even in the absence of lipid bilayers. The shifts were greatest for membrane-adsorbed mutants and smaller for the inserted, folded mutants or the aqueous intermediates. The spectra of the mutants V573C-, L575C-, G577C-, and V579C-BamA, facing the lipid bilayer, displayed stronger shifts than the spectra recorded for the mutants R572C-, N574C-, T576C-, and K578C-BamA, facing the β-barrel lumen, in both the membrane-adsorbed form and the folded, inserted form. This alternating pattern was neither observed for the IAEDANS spectra of the unfolded forms nor for the water-collapsed forms, indicating that strand β9 forms in a membrane-adsorbed folding intermediate of BamA. The combination of cysteine scanning mutagenesis and site-directed fluorescence labeling is shown to be a valuable tool in examining the local secondary structure formation of transmembrane proteins.

A fermi acceleration model to study the electron acceleration in laser-produced plasma with localized structures formation and turbulence generation

This investigation presents a model based on the nonlinear coupling of waves for studying electron acceleration in laser-produced plasma. The impact of the localized structures formation and turbulence generation on electron acceleration is investigated via a second-order Fermi acceleration mechanism. For this purpose, the dynamical coupled equations of the extraordinary mode laser and the upper hybrid wave are formulated by taking into account relativistic and ponderomotive nonlinearity. These coupled equations are solved by laboratory simulations using pseudo-spectral and finite difference methods. The simulation results show the turbulent wavenumber spectrum associated with the localization of the laser beam. The power-law scaling of turbulence generation has been utilized to study the formation of the thermal tail of energetic electrons, which may be responsible for the acceleration of the electrons. A fractional diffusion method has been exploited to determine electron acceleration. This study also provides a simplified model for a better understanding of the nonlinear progression of the laser beam during propagation inside the magnetized plasma.

New measurement system based on small-angle neutron scattering for structural analysis of light-responsive materials

With the increasing importance of light-responsive materials, it is vital to analyze the relationship between function and structural changes induced by light irradiation. Small-angle scattering (SAS) is effective for such structural analysis. However, quantitatively capturing local molecular structure formation and molecular reactions at a scale of less than 1 nm via SAS is difficult. In this study, to analyze the structure of non-equilibrium phenomena in light-responsive materials, a new sample environment has been developed for a time-of-flight small- and wide-angle neutron scattering instrument (TAIKAN), comprising a UV–Vis irradiation system, UV–Vis absorption measurement equipment and photodetector. Simultaneous measurement of small-angle neutron scattering and UV–Vis absorption was achieved. This system was used to demonstrate the in situ observation of UV–Vis irradiation-induced structural change of micelles formed by 4-butylazobenzene-4′-(oxyethyl)trimethylammonium bromide, which is a light-responsive surfactant, in an aqueous solution. The results showed that the present measuring system provides direct information on the interplay between changes in micelle structure and changes in molecular configuration.

Synthesis of yttrium titanate stannate (Y2Ti2−xSnxO7, x = 0–2) pyrochlore glass–ceramics as potential nuclear waste form

AbstractY2Ti2−xSnxO7 (x = 0–2) pyrochlore sodium aluminoborosilicate glass–ceramics (GCs) are produced by calcining the pelletized Y–Ti–Sn oxide mixture and glass precursor at 1200 or 1300°C for 4 h. The metal oxide mixture is prepared by a soft chemistry route. X‐ray diffraction, Raman spectroscopy, and electron microscopy are employed to investigate the formation of pyrochlore GCs and local crystal structures. Near phase pure Ti‐rich pyrochlores are produced with minor phase SnO2 observed for Sn‐rich materials. The cell parameters of the pyrochlore structures refined by Le Bail fitting are in good agreement with the published data and increase linearly with the gradual increment of Sn substitution. With progressively increasing Sn proportion on pyrochlore B‐site, Raman characteristic bands of the pyrochlore structure become sharper and well defined. The Raman A1g peak position and its full width at half‐maximum are linearly progressed with increasing x (Sn). The presence of the melting glass facilitates the pyrochlore formation, with ceramic grain sizes ranging from submicron to microns. Transmission electron microscopy and selected area electron diffraction observations indicate the sample possesses a relatively high crystallographic perfection at the atomic level. This new series of pyrochlore GCs and the method disclosed herein may pave the way for further materials development as potential nuclear waste forms.