Interdomain Boundaries Research Articles

Interfacial Segregation, Structure, and Diffusion ofn-Alkane Mixture Films Adsorbed on Smooth and Rough Gold Surfaces

The compositional, structural, and diffusional properties of equal-weight mixtures of liquid n-hexane and n-hexadecane films supported on atomically smooth and rough gold surfaces are explored with the use of temperature-controlled, canonical, molecular dynamics simulations at 315 K. Preferential adsorption of n-hexadecane molecules is found in the region next to the solid surface. The selective molecular segregation effect is much stronger at the smooth Au(111) surface, where it is accompanied by pronounced layering exhibited in the density profile of the adsorbed film normal to the surface, which shows the formation of two well-defined interfacial liquid layers. For both the smooth and rough solid surfaces, in the region of the first layer located about 5 Å from the solid surface, the alkane molecules order with their axis oriented parallel to the adsorbing surface, thus maximizing the attractive physisorption energy. The orientational ordering is accompanied by the formation of ordered domains in the first liquid-film layer, with the molecules in each domain lying parallel to each other. The interfacial domain ordering is frustrated in the alkane mixture film adsorbed on the rough surface. Reduced diffusive motion is found for molecules located near the solid surfaces. However, in the region of the first adsorbed layer of the liquid film adsorbed on the smooth surface, the rate of diffusion, particularly of the hexane molecules, is larger than at the rough surface. It is found that the smaller, hexane, molecules diffuse through channels at the boundaries between the ordered domains formed by the hexadecane molecules. For the rough surface case, where the domain ordering is frustrated, such interdomain boundary channels do not form and consequently the domain boundary-assisted diffusion of the smaller molecules is not operative there, resulting in a smaller diffusion rate.

Modeling and Simulation of Unsteady Flow in Multistage Compressors Using Interdomain Boundaries

In this paper, a model for simulating the intrinsic fast dynamics of flow in a multistage, axi-centrifugal compressor is presented. The model treats the flow through the stage elements, i.e., rotors and stators, as curved stream-tube elements along the mean line. The model captures unsteady flow dynamics in respective frames for stators and rotors of individual stages, alternating between stationary and rotating frames as needed. Accelerations associated with the rotating frames are represented as body forces. Unique characteristics-based compact interfaces that account for the transformations between the frames (and also serve as compact loss zones) are used. Simulation results for an industrial four-stage axial compressor are presented that illustrate the propagation of waves through the compressor segments as the throttle is moved. In particular, the dynamic processes that can lead a compressor to either of the opposite ends of its operation, i.e., loss of stability or choked flow, are investigated. Simulation results demonstrate that the model accounts for the acoustic impedance that is responsible for choked flow. In throttling toward stall, the simulation results show, as expected, that with large plenum the compressor loses stability when it is driven beyond the peak of its characteristics. Further, the capabilities of the developed model as a diagnostic tool are demonstrated by analyzing “pseudomeasured” pressure signals in two possible scenarios of stability loss.

Features of magnetostriction in carbon steels

Magnetostriction of the tempered 60G steel in the magnetic field of a solenoid is studied. A technique is proposed for dividing magnetostriction into components, namely those induced by the displacement of interdomain boundaries and those caused by the mechanism of rotation of spin magnetic moments. The dependences of the magnetostriction components on the tempering temperature of the hardened steel are constructed. This contributes to an increase in the effectiveness (accuracy) of evaluating elastic stresses in a steel structure by magnetoelastic methods. The essence of the technique lies in the application of the Langevin function to describing the experimental magnetostriction curves of the tempered 60G steel.

Transformations of Thermosensitive Hyperbranched Poly(ionic liquid)s Monolayers.

We synthesized amphiphilic hyperbranched poly(ionic liquid)s (HBPILs) with asymmetrical peripheral composition consisting of hydrophobic n-octadecylurethane arms and hydrophilic, ionically linked poly(N-isopropylacrylamide) (PNIPAM) macrocations and studied low critical solution temperature (LCST)-induced reorganizations at the air-water interface. We observed that the morphology of HBPIL Langmuir monolayers is controlled by the surface pressure with uniform well-defined disk-like domains formed in a liquid phase. These domains are merged and transformed to uniform monolayers with elevated ridge-like network structures representing coalesced interdomain boundaries in a solid phase because the branched architecture and asymmetrical chemical composition stabilize the disk-like morphology under high compression. Above LCST, elevated individual islands are formed because of the aggregation of the collapsed hydrophobized PNIPAM terminal macrocations in a solid phase. The presence of thermoresponsive PNIPAM macrocations initiates monolayer reorganization at LCST with transformation of surface mechanical contrast distribution. The heterogeneity of elastic response and adhesion distributions for HBPIL monolayers in the wet state changed from highly contrasted two-phase distribution below LCST to near-uniform mechanical response above LCST because of the hydrophilic to hydrophobic transformation of the PNIPAM phase.

A non-overlapping DDM combined with the characteristic method for optimal control problems governed by convection–diffusion equations

In this paper, we consider a non-overlapping domain decomposition method combined with the characteristic method for solving optimal control problems governed by linear convection–diffusion equations. The whole domain is divided into non-overlapping subdomains, and the global optimal control problem is decomposed into the local problems in these subdomains. The integral mean method is utilized for the diffusion term to present an explicit flux calculation on the inter-domain boundary in order to communicate the local problems on the interfaces between subdomains. The convection term is discretized along the characteristic direction. We establish the fully parallel and discrete schemes for solving these local problems. A priori error estimates in $$L^2$$ -norm are derived for the state, co-state and control variables. Finally, we present numerical experiments to show the validity of the schemes and verify the derived theoretical results.

Hsp90 shapes protein and RNA evolution to balance trade-offs between protein stability and aggregation

Acquisition of mutations is central to evolution; however, the detrimental effects of most mutations on protein folding and stability limit protein evolvability. Molecular chaperones, which suppress aggregation and facilitate polypeptide folding, may alleviate the effects of destabilizing mutations thus promoting sequence diversification. To illuminate how chaperones can influence protein evolution, we examined the effect of reduced activity of the chaperone Hsp90 on poliovirus evolution. We find that Hsp90 offsets evolutionary trade-offs between protein stability and aggregation. Lower chaperone levels favor variants of reduced hydrophobicity and protein aggregation propensity but at a cost to protein stability. Notably, reducing Hsp90 activity also promotes clusters of codon-deoptimized synonymous mutations at inter-domain boundaries, likely to facilitate cotranslational domain folding. Our results reveal how a chaperone can shape the sequence landscape at both the protein and RNA levels to harmonize competing constraints posed by protein stability, aggregation propensity, and translation rate on successful protein biogenesis.

Cellular Proliferative Domains: Barriers to Migration

An important aspect of the analysis of the proliferation of cell populations as composed of a set of intercommunicating logistic domains is the nature of the barriers between adjacent domains and the regulation of cellular migration between them. The nature of these inter-domain boundaries is discussed in relation to the central role of L-type calcium channels in the control of cell motility and it is proposed that domain boundaries are determined by proteoglycans which act as calcium chelators and hence regulate the local extracellular Ca⁺⁺ concentration. The selective migratory advantage gained by overexpression of calcium channels is briefly alluded to.

A Non-overlapping DDM for Optimal Boundary Control Problems Governed by Parabolic Equations

In this paper, we consider a non-overlapping domain decomposition method for solving optimal boundary control problems governed by parabolic equations. The whole domain is divided into non-overlapping subdomains, and the global optimal boundary control problem is decomposed into the local problems in these subdomains. The integral mean method is utilized to present an explicit flux calculation on the inter-domain boundary in order to communicate the local problems on the interface between subdomains. We establish the fully parallel and discrete schemes for solving these local problems. A priori error estimates in $$L^2$$ -norm are derived for the state, co-state and control variables. Finally, we present numerical experiments to show the validity of the schemes and verify the derived theoretical results.

Intra-domain periodic defects in monolayer MoS2

We present an ultra-high vacuum scanning tunneling microscopy study of structural defects in molybdenum disulfide thin films grown on silicon substrates by chemical vapor deposition. A distinctive type of grain boundary periodically arranged inside an isolated triangular domain, along with other inter-domain grain boundaries of various types, is observed. These periodic defects, about 50 nm apart and a few nanometers in width, remain hidden in optical or low-resolution microscopy studies. We report a complex growth mechanism that produces 2D nucleation and spiral growth features that can explain the topography in our films.

Domain decomposition approach for parallel improvement of tetrahedral meshes

Presently, a tetrahedral mesher based on the Delaunay triangulation approach may outperform a tetrahedral improver based on local smoothing and flip operations by nearly one order in terms of computing time. Parallelization is a feasible way to speed up the improver and enable it to handle large-scale meshes. In this study, a novel domain decomposition approach is proposed for parallel mesh improvement. It analyses the dual graph of the input mesh to build an inter-domain boundary that avoids small dihedral angles and poorly shaped faces. Consequently, the parallel improver can fit this boundary without compromising the mesh quality. Meanwhile, the new method does not involve any inter-processor communications and therefore runs very efficiently. A parallel pre-processing pipeline that combines the proposed improver and existing parallel surface and volume meshers can prepare a quality mesh containing hundreds of millions of elements in minutes. Experiments are presented to show that the developed system is robust and applicable to models of a complication level experienced in industry.

Formation of a bidomain structure in lithium niobate wafers for beta-voltaic alternators

The possibility of increasing the efficiency of a beta-voltaic generator due to using a single-crystal bimorph element made of lithium niobate as a piezoelectric converter. The known beta voltaic alternators consist of a piezoelectric cantilever and a source of β-electrons. The cantilever represents a resilient member made, for example, of silicon, on which a piezoelectric element made of PZT piezoceramics is mounted. It is proposed to replace the silicon cantilever structure with a piezoelectric element by a uniform cantilever that represents a thin wafer made of a bidomain single-crystal lithium niobate. Due to this, the efficiency of the mechanical oscillation conversion into electrical power, the system Q-factor, and the stability of the operating parameters simultaneously increase; and the operation temperature range also significantly increases (by several hundred degrees). The solution of the main problem—the formation of a bidomain structure in a thin wafer of lithium niobate—is considered in detail. A method for the high-temperature annealing of samples in a nonuniform electric field is proposed. It is demonstrated that one can predict the domain structure based on the developed model. Samples are obtained having the occurrence depth of the interdomain boundary ranging from 120 to 150 μm. At the same time, it is shown that the sharpness of the boundary depends on the potential difference between the striated electrodes of the technological cell and the external electrode. The method is efficient for manufacturing a bidomain structure in a wafer up to 300 μm thick.

Fine-grained parallel algorithm for unstructured surface mesh generation

A parallel surface meshing algorithm is proposed by exploiting the parallelism within the meshing process of a surface, which is more efficient than the conventional scheme that meshes surfaces individually. One integral part is the domain decomposition approach adopted, which ensures no small inter-domain angles; therefore, the parallel meshing procedure can fix the inter-domain boundary without compromising mesh quality. Combining the parallel surface mesher with the parallel tetrahedral mesher and improver developed previously, a parallel preprocessing pipeline for large-scale simulations is set up. It only consumes minutes to prepare a mesh containing hundreds of millions of elements.

An interdomain boundary in RAG1 facilitates cooperative binding to RAG2 in formation of the V(D)J recombinase complex.

V(D)J recombination assembles functional antigen receptor genes during lymphocyte development. Formation of the recombination complex containing the recombination activating proteins, RAG1 and RAG2, is essential for the site-specific DNA cleavage steps in V(D)J recombination. However, little is known concerning how complex formation leads to a catalytically-active complex. Here, we combined limited proteolysis and mass spectrometry methods to identify regions of RAG1 that are sequestered upon association with RAG2. These results show that RAG2 bridges an interdomain boundary in the catalytic region of RAG1. In a second approach, mutation of RAG1 residues within the interdomain boundary were tested for disruption of RAG1:RAG2 complex formation using fluorescence-based pull down assays. The core RAG1 mutants demonstrated varying effects on complex formation with RAG2. Interestingly, two mutants showed opposing results for the ability to interact with core versus full length RAG2, indicating that the non-core region of RAG2 participates in binding to core RAG1. Significantly, all of the RAG1 interdomain mutants demonstrated altered stoichiometries of the RAG complexes, with an increased number of RAG2 per RAG1 subunit compared to the wild type complex. Based on our results, we propose that interaction of RAG2 with RAG1 induces cooperative interactions of multiple binding sites, induced through conformational changes at the RAG1 interdomain boundary, and resulting in formation of the DNA cleavage active site.

Single site suppressors of a fission yeast temperature-sensitive mutant in cdc48 identified by whole genome sequencing.

The protein called p97 in mammals and Cdc48 in budding and fission yeast is a homo-hexameric, ring-shaped, ubiquitin-dependent ATPase complex involved in a range of cellular functions, including protein degradation, vesicle fusion, DNA repair, and cell division. The cdc48+ gene is essential for viability in fission yeast, and point mutations in the human orthologue have been linked to disease. To analyze the function of p97/Cdc48 further, we performed a screen for cold-sensitive suppressors of the temperature-sensitive cdc48-353 fission yeast strain. In total, 29 independent pseudo revertants that had lost the temperature-sensitive growth defect of the cdc48-353 strain were isolated. Of these, 28 had instead acquired a cold-sensitive phenotype. Since the suppressors were all spontaneous mutants, and not the result of mutagenesis induced by chemicals or UV irradiation, we reasoned that the genome sequences of the 29 independent cdc48-353 suppressors were most likely identical with the exception of the acquired suppressor mutations. This prompted us to test if a whole genome sequencing approach would allow us to map the mutations. Indeed genome sequencing unambiguously revealed that the cold-sensitive suppressors were all second site intragenic cdc48 mutants. Projecting these onto the Cdc48 structure revealed that while the original temperature-sensitive G338D mutation is positioned near the central pore in the hexameric ring, the suppressor mutations locate to subunit-subunit and inter-domain boundaries. This suggests that Cdc48-353 is structurally compromized at the restrictive temperature, but re-established in the suppressor mutants. The last suppressor was an extragenic frame shift mutation in the ufd1 gene, which encodes a known Cdc48 co-factor. In conclusion, we show, using a novel whole genome sequencing approach, that Cdc48-353 is structurally compromized at the restrictive temperature, but stabilized in the suppressors.

FORMATION OF BIDOMAIN STRUCTURE IN LITHIUM NIOBATE WAFERS FOR BETAVOLTAIC ALTERNATORS

The possibility of increasing the efficiency of a beta-voltaic generator due to using a single-crystal bimorph element made of lithium niobate as a piezoelectric converter. The known beta voltaic alternators consist of a piezoelectric cantilever and a source of β-electrons. The cantilever represents a resilient member made, for example, of silicon, on which a piezoelectric element made of PZT piezoceramics is mounted. It is proposed to replace the silicon cantilever structure with a piezoelectric element by a uniform cantilever that represents a thin wafer made of a bidomain single-crystal lithium niobate. Due to this, the efficiency of the mechanical oscillation conversion into electrical power, the system Q-factor, and the stability of the operating parameters simultaneously increase; and the operation temperature range also significantly increases (by several hundred degrees). The solution of the main problem—the formation of a bidomain structure in a thin wafer of lithium niobate—is considered in detail. A method for the high-temperature annealing of samples in a nonuniform electric field is proposed. It is demonstrated that one can predict the domain structure based on the developed model. Samples are obtained having the occurrence depth of the interdomain boundary ranging from 120 to 150 μm. At the same time, it is shown that the sharpness of the boundary depends on the potential difference between the striated electrodes of the technological cell and the external electrode. The method is efficient for manufacturing a bidomain structure in a wafer up to 300 μm thick.

Implementation of an interior point source in the ultra weak variational formulation through source extraction

The Ultra Weak Variational Formulation (UWVF) is a powerful numerical method for the approximation of acoustic, elastic and electromagnetic waves in the time-harmonic regime. The use of Trefftz-type basis functions incorporates the known wave-like behaviour of the solution in the discrete space, allowing large reductions in the required number of degrees of freedom for a given accuracy, when compared to standard finite element methods. However, the UWVF is not well disposed to the accurate approximation of singular sources in the interior of the computational domain. We propose an adjustment to the UWVF for seismic imaging applications, which we call the Source Extraction UWVF. Differing fields are solved for in subdomains around the source, and matched on the inter-domain boundaries. Numerical results are presented for a domain of constant wavenumber and for a domain of varying sound speed in a model used for seismic imaging.

Domain decomposition procedures combined with [formula omitted]-Galerkin mixed finite element method for parabolic equation

Non-overlapping domain decomposition procedures are considered for parabolic equation. These procedures are combined with using H1-Galerkin mixed finite element method in the sub-domains to approximate the primary variable u and its flux σ simultaneously. Explicit calculations are built by using integral mean methods to present the inter-domain boundary conditions for the flux. Thus, the parallelism can be achieved by these procedures. Two approximation schemes are established. Time step constraints are proved necessary to preserve stability, which are less severe than that of fully explicit Galerkin finite element method. The mixed finite element spaces are allowed to be of different polynomial degrees and not subject to the LBB-consistency condition. New nonstandard elliptic projections are defined and analyzed. Optimal error estimates for the variable u in H1-norm and its flux σ in L2-norm and are derived for these schemes. Numerical experiments are presented to confirm the theoretical results.

Probing structural inhomogeneity of graphene layers via nonlinear optical scattering

Incoherent optical second harmonic generation (SHG) is studied from series of multilayer graphene samples of various thickness manufactured by chemical vapor deposition technique and deposited over 150 μm thick glass slides. Two different values of the correlation lengths are obtained from the linear and SHG indicatrices and reveal the existence of two types of optical scatterers. The first one is associated with homogeneous graphene areas, while the second one originates from wrinkles at the interdomain boundaries. Second harmonic imaging microscopy used to map the distribution of the second-order polarization at the nanoscale confirms the results of the nonlinear scattering data.

Parallel Nonoverlapping DDM Combined with the Characteristic Method for Incompressible Miscible Displacements in Porous Media

Two types of approximation schemes are established for incompressible miscible displacements in porous media. First, standard mixed finite element method is used to approximate the velocity and pressure. And then parallel non-overlapping domain decomposition methods combined with the characteristics method are presented for the concentration. These methods use the characteristic method to handle the material derivative term of the concentration equation in the subdomains and explicit flux calculations on the interdomain boundaries by integral mean method or extrapolation method to predict the inner-boundary conditions. Thus, the velocity and pressure can be approximated simultaneously, and the parallelism can be achieved for the concentration equation. The explicit nature of the flux prediction induces a time step limitation that is necessary to preserve stability. These schemes hold the advantages of nonoverlapping domain decomposition methods and the characteristic method. Optimal error estimates in L2-norm are derived for these two schemes, respectively.

Seepage analysis in multi-domain general anisotropic media by three-dimensional boundary elements

Abstract A three-dimensional boundary element solution for the seepage analysis in multi-domain general anisotropic media has been developed based on the transformation approach. Using analytical eigenvalues and eigenvectors of the hydraulic conductivity tensor, a closed-form coordinate transformation matrix has been provided to transform the quadratic form of governing equation of seepage for the general anisotropic media to the Laplace equation. This transformation allows the analysis to be carried out using any standard BEM codes for the potential theory on the transformed space by adding small pre- and post-processing routines. With this transformation, any physical quantity like the total head remains unchanged at corresponding nodes on the physical and transformed space, and the normal gradient across the domain boundaries should also be transformed. In multi-domain problems, compatibility equations (equality of the potential on corresponding nodes on the interface) and equilibrium equations (conservation of the flux across the interface boundaries of adjacent domains) on the corresponding nodes of interface between two neighbor domains are needed for boundary element method. In the transformed space, the compatibility equation remains unchanged. However, due to the distortion of boundaries in the mapped space and therefore misalignment of the unit outward normal vectors along the inter-domain boundaries, the equilibrium of the normal fluxes have to be transformed accordingly. Based on the proposed transformation, the normal to boundary flux boundary conditions in the mapped space and the transformed equilibrium equation for interface of adjacent zones have been given in this paper. Examples have been solved with the proposed scheme and the results were verified with the finite element method. Excellent agreement of the results shows the veracity of the proposed transformation and the formulas given for transformation of equilibrium equation for multi-domain general anisotropic media.