Geometry Of Interaction Research Articles

Anisotropy of acousto-optic figure of merit for the case of a Bragg-diffracted wave propagating along an optic axis in optically biaxial crystals: Tl3AsS4 crystals.

In the present work, we analyze acousto-optic (AO) interactions under the condition when a diffracted optical wave propagates along one of the optic axes in optically biaxial crystals. We find that the number of AO interaction types is reduced from nine, which is typical for the most general case, to six, since some of the isotropic and anisotropic diffraction types manifest themselves simultaneously. We reveal that, in the case of the interactions of quasi-ordinary and quasi-extraordinary optical waves, the dependences of effective elasto-optic coefficients and AO figure of merit on the tracing angle of an incident optical beam around the optic axis are symmetric with respect to the plane that is perpendicular to the plane of optic axes and contains the principal axis Z. We determine the geometry of AO interactions at which the highest AO figure of merit can be expected. Finally, we show that, in the case of propagation of diffracted light along one of the optic axes in the biaxial Tl3AsS4 crystals, the highest AO figures of merit, M2=1290×10-15s3/kg and M2=1305×10-15s3/kg, can be reached when the quasi-longitudinal acoustic wave interacts with the quasi-ordinary or quasi-extraordinary optical waves in the plane of optic axes.

Balancing Density Functional Theory Interaction Energies in Charged Dimers Precursors to Organic Semiconductors.

The pursuit of an increasingly accurate description of intermolecular interactions within the framework of Kohn-Sham density functional theory (KS-DFT) has motivated the construction of numerous benchmark databases over the past two decades. By far, the largest efforts have been spent on closed-shell, neutral dimers for which today the interaction energies and geometries can be accurately reproduced by various combinations of dispersion-corrected density functional approximations (DFAs). In sharp contrast, charged, open-shell dimers remain a challenge as illustrated by the analysis of the OREL26rad benchmark set, composed of π-dimer radical cations. Aside from the methodological aspect, achieving a proper description of radical cationic complexes is appealing due to their role as models for charge carriers in organic semiconductors. In the interest of providing an assessment of more realistic dimer systems, we construct a data set of large radical cationic dimers (CryOrel9) and jointly train the 19 parameters of a dispersion corrected, range-separated hybrid density functional (ωB97X-dDsC). The main objective of ωB97X-dDsC is to provide the maximum balance between the treatment of long-range London dispersion and reduction of the delocalization error, which are essential conditions to obtain accurate energy profiles and binding energies of charged, open-shell dimers. The performance of ωB97X-dDsC, its parent ωB97X functional series, and a selection of wave function-based methods is reported for the CryOrel9 data set. The robustness of the reoptimized variant (ωB97X-dDsC) is also tested on other GMTKN30 data sets.

On positive geometries of quartic interactions: Stokes polytopes, lower forms on associahedra and world-sheet forms

In [1], two of the present authors along with P. Raman attempted to extend the Amplituhedron program for scalar field theories [2] to quartic scalar interactions. In this paper we develop various aspects of this proposal. Using recent seminal results in Representation theory [3, 4], we show that projectivity of scattering forms and existence of kinematic space associahedron completely capture planar amplitudes of quartic interaction. We generalise the results of [1] and show that for any n-particle amplitude, the positive geometry associated to the projective scattering form is a convex realisation of Stokes polytope which can be naturally embedded inside one of the ABHY associahedra defined in [2, 5]. For a special class of Stokes polytopes with hyper-cubic topology, we show that they have a canonical convex realisation in kinematic space as boundaries of kinematic space associahedra.We then use these kinematic space geometric constructions to write world-sheet forms for \U0001d7194 theory which are forms of lower rank on the CHY moduli space. We argue that just as in the case of bi-adjoint \U0001d7193 scalar amplitudes, scattering equations can be used as diffeomorphisms between certain frac{n-4}{2} forms on the world-sheet and frac{n-4}{2} forms on ABHY associahedron that generate quartic amplitudes.

Insight into 1:1 complexes of H2O with NF3 and CF2Cl2: a quantum chemical approach

The competition of hydrogen, halogen and pnicogen bonding to the stability of the atmospheric complexes is interesting, especially where the molecules by the most abundant greenhouse effect in the atmosphere are subject of interest. In the present work, we have computationally studied the addition of H2O to the NF3 and CF2Cl2 molecules to reveal the electronic and structural features of the NF3-H2O and CF2Cl2-H2O complexes through DFT, MP2 and CCSD (T) methods. The interaction energies, geometry and electronic properties including charge transfer, energy gap, NEDA and AIM analyses of all the complexes were calculated to discuss the nature and strength of intermolecular interactions. The results indicate that the role of halogen bonding is more obvious than that of hydrogen and pnicogen bonding, and compared with the NF3, CF2Cl2 is more effectively stabilized by the H2O molecules. In the present work, we have studied the addition of H2O molecule to the NF3 and CF2Cl2 molecules to reveal the electronic and structural features of the NF3-H2O and CF2Cl2-H2O complexes through DFT, MP2 and CCSD (T) methods.

Estimating the Parameters of Monocrystal-Based Acousto-Optic Devices for Terahertz Radiation Control

The acoustic and optical properties of a number of monocrystals transparent in the terahertz range are systematized. Acousto-optic (AO) figure of merit is calculated for the quasi-orthogonal and collinear geometries of AO interaction. The parameters of AO deflectors and filters of THz radiation are determined.

Model of Geometry Realistic Learning Development with Interactive Multimedia Assistance in Elementary School

Initial research results indicate there are problems in learning mathematics, especially in geometry material in elementary schools. Students still have not had the opportunity to build their own knowledge. The purpose of this study is to produce a realistic learning model of interactive multimedia-assisted geometry to improve the reasoning ability of fourth grade elementary school students who meet valid, practical and effective criteria. This research is a design research that combines the Plomp and Gravemeijer & Cobb development model which consists of three phases: preliminary research (experimental preparation), prototyping phase (conducting experiments, retrospective analysis) and assessment phase. The subjects of the study were students of grade four SD thirty seven Pekanbaru. The results of the study indicate that the learning design developed has fulfilled valid, practical and effective. Valid in terms of content and construction. Practical in terms of implementation, convenience and time required. Effective in terms of potential impact on reasoning ability.

Balancing DFT Interaction Energies in Charged Dimers Precursors to Organic Semiconductors

Accurately describing intermolecular interactions within the framework of Kohn-Sham density functional theory (KS-DFT) has resulted in numerous benchmark databases over the past two decades. By far, the largest efforts have been spent on closed-shell, neutral dimers for which today, the interaction energies and geometries can be accurately reproduced by various combinations of dispersion-corrected density functional approximations (DFAs). In sharp contrast, charged, open-shell dimers remain a challenge as illustrated by the analysis of the OREL26rad benchmark set consisting of pi-dimer radical cations. Aside from the methodological aspect, achieving a proper description of radical cationic complexes is appealing due to their role as models for charge carriers in organic semiconductors. In the interest of providing an assessment of more realistic dimer systems, we construct a dataset of large radical cationic dimers (CryOrel) and jointly train the 19 parameters of a dispersion corrected, range-separated hybrid density functional (wB97X-dDsC), with the objective of providing the maximum balance between the treatment of long-range London dispersion and reduction of the delocalization error. These conditions are essential to obtain accurate energy profiles and binding energies of charged, open-shell dimers. Comparisons with the performance of the parent wB97X functional series and state-of-the-art wavefunction based methods are provided.

Phase Separation in Atomistic Simulations of Model Membranes.

Understanding the lateral organization in plasma membranes remains an open problem despite a large body of research. Model membranes with coexisting micrometer-size domains are routinely employed as simplified models of plasma membranes. Many molecular dynamics simulations have investigated phase separation in model membranes at the coarse-grained level, but atomistic simulations remain computationally challenging. We simulate DPPC:DOPC and DPPC:DOPC:cholesterol lipid bilayers to investigate phase transitions at temperatures from 310 to 270 K. In this temperature range, the binary mixture forms a liquid phase (Lα) and a coexistence of Lα and either gel or ripple phases. The ternary mixture forms a liquid disordered (Ld) phase and a coexistence of liquid ordered (Lo) and either Ld or gel phases. We quantify the coexisting phases and discuss their properties against the background of experimental results. We observe partial registration of growing domains in both mixtures. We characterize specific cholesterol-cholesterol and cholesterol-phospholipid interaction geometries underlying its increased partitioning and the smoothed phase transition in the ternary mixture compared to the binary mixture. By comparing coexisting domains with homogeneous bilayers of the same composition, we demonstrate how domain coexistence affects their properties. Our simulations provide important insights into the lipid-lipid interactions in model lipid bilayers and improve our understanding of the lateral organization in plasma membranes with higher compositional complexity.

Enhancement of laser-driven ion acceleration in non-periodic nanostructured targets

Using particle-in-cell simulations, we demonstrate an improvement of the target-normal-sheath acceleration (TNSA) of protons in non-periodically nanostructured targets with micron-scale thickness. Compared to standard flat foils, an increase in the proton cutoff energy by up to a factor of two is observed in foils coated with nanocones or perforated with nanoholes. The latter nano-perforated foils yield the highest enhancement, which we show to be robust over a broad range of foil thicknesses and hole diameters. The improvement of TNSA performance results from more efficient hot-electron generation, caused by a more complex laser–electron interaction geometry and increased effective interaction area and duration. We show that TNSA is optimized for a nanohole distribution of relatively low areal density and that is not required to be periodic, thus relaxing the manufacturing constraints.

Influence of the position of the methyl substituent and N-oxide formation on the geometry and intermolecular interactions of 1-(phenoxyethyl)piperidin-4-ol derivatives.

Aminoalkanol derivatives have attracted much interest in the field of medicinal chemistry as part of the search for new anticonvulsant drugs. In order to study the influence of the methyl substituent and N-oxide formation on the geometry of molecules and intermolecular interactions in their crystals, three new examples have been prepared and their crystal structures determined by X-ray diffraction. 1-[(2,6-Dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 1, and 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol, C15H23NO2, 2, crystallize in the orthorhombic system (space groups P212121 and Pbca, respectively), with one molecule in the asymmetric unit, whereas the N-oxide 1-[(2,3-dimethylphenoxy)ethyl]piperidin-4-ol N-oxide monohydrate, C15H23NO3·H2O, 3, crystallizes in the monoclinic space group P21/c, with one N-oxide molecule and one water molecule in the asymmetric unit. The geometries of the investigated compounds differ significantly with respect to the conformation of the O-C-C linker, the location of the hydroxy group in the piperidine ring and the nature of the intermolecular interactions, which were investigated by Hirshfeld surface and corresponding fingerprint analyses. The crystal packing of 1 and 2 is dominated by a network of O-H...N hydrogen bonds, while in 3, it is dominated by O-H...O hydrogen bonds and results in the formation of chains.

Interactive E-Module Model Of Transformation Geometry Based On Case (Creative, Active, Systematic, Effective) As A Practical And Effective Media To Support Learning Autonomy And Competence.

This study aims to develop an interactive e-module of Transformation Geometry based on some principles, e.g. creative, active, systematic, and effective (CASE) as a teaching material to support learning autonomy and student’s competence. In this research and development study includes some steps, e.g. preliminary study, product design and development (model), and product testing and assessment. In the preliminary study, based on student’s needs analysis, it was shown that most students were more interested in Transformation Geometry session by using interactive emodule as the teaching materials as it may enable the students to learn independently and understand easily. Therefore, it is necessary to develop an interesting and easily-understood teaching material model in the form of an interactive e-module. In the designing step, the initial draft produced a model with a systematic: introduction (instructions for using e-modules, material descriptions, prerequisites, learning objectives), learning activities that include: a description of the material and examples of questions, problem training, summaries, competency tests, instructions for practice answers, feedback, and reference lists. In product development (model), CASE-based interactive e-module models covering Transformation Geometry topic was created. The results of the product review by experts indicate that the product (model) has fulfilled in terms of validity. The product testing results showed that the interactive e-module model Transformation Geometry developed in this study is as the teaching material model that supports learning independence and has met the criteria of a practical and effective model.

Coarse-grained and atomic resolution biomolecular docking with the ATTRACT approach.

The ATTRACT protein-protein docking program has been employed to predict protein-protein complex structures in CAPRI rounds 38-45. For 11 out of 16 targets acceptable or better quality solutions have been submitted (~70%). It includes also several cases of peptide-protein docking and the successful prediction of the geometry of carbohydrate-protein interactions. The option of combining rigid body minimization and simultaneous optimization in collective degrees of freedom based on elastic network modes was employed and systematically evaluated. Application to a large benchmark set indicates a modest improvement in docking performance compared to rigid docking. Possible further improvements of the docking approach in particular at the scoring and the flexible refinement steps are discussed.

A review of non-polar liquids as materials for bulk acousto-optic devices operating with terahertz radiation

In this paper, the acoustic and optical properties of a number of liquids transparent in the terahertz range are systematized. The acousto-optic quality is calculated for the quasi-orthogonal and collinear geometry of the acousto-optic interaction. The parameters of acousto-optic deflectors and filters of terahertz radiation are determined. The diagrams linking the resolution for the filter and the maximum number of resolvable elements for the deflector with the diffraction efficiency are given.

Interaction Geometry Causes Spectral Line-Shape Broadening at the Solid/Liquid Interface

Line-shape broadness in vibrational spectra is usually associated with structural heterogeneity of the surrounding environment. At the solid/liquid interface, surface-sensitive sum-frequency generation spectroscopy (SFG) has shown a variety of distributions of the vibrational frequency for sapphire surface hydroxyl groups in contact with several liquids. Even though the broadness in SFG spectra could be associated with the surface heterogeneity and diverse interfacial interactions, the origin remains elusive in experiments. To better understand the physical picture of interfacial interactions, and hence broadness, we perform SFG along with molecular dynamics (MD) simulations of liquid molecules in contact with sapphire. In the SFG spectra, line-shape broadness of the sapphire hydroxyl group vibrational frequency increases in the following order: chloroform, acetone and dimethyl sulfoxide. The broadness in the interaction energy distributions calculated from the MD simulations for the molecules interacting...

On the glass transition temperature Tg against molar volume Vm plotting in arsenoselenide glasses

Dependence of glass transition temperature Tg (K) on overall mean bonding energy E (kJ/mol) in arsenoselenide glass reexamined under per-atom calculations is shown to obey linearized master equation Tg ≅ 418⋅(E–1.13). Compositional variations in Tg against molar volume Vm are plotted for g-AsxSe100-x taken within (0 ≤ x ≤ 65) domain assuming preferential cohesive Van der Waals (VDW) bonding between network-constituting entities. The Tg values are found to vary as inverse-αth power of Vm, attaining distinct values for different networks, in part, 0D-molecular (α = =6/3 = 2), 1D-chained (α = =5/3), 2D-layered (α = =4/3), and 3D-spatial (α = =3/3 = 1). These variations originated from macroscopic geometry of VDW interaction are linearized in log-log presentation for networks dominated with chain-like 1D-entities (0 ≤ x<~8) and cross-linked 3D-entities (~8 < x< 30–33), while demonstrate non-linear behaviour for cross-linked 3D- and layered 2D-entities (30–33 < x < 40), and layered 2D- and molecular 0D-entities (40 < x < 65). Appearance of molecular entities in g-AsxSe100-x (40 < x < 65) results in self-terminated loop in log–log plotting of Tg(1/Vm) dependence.

Metal−π Interactions in Light of Geometry-Corrected Statistical Analysis

Statistical analysis on metal−π interactions has been performed, and a geometrical correction, named as offset correction, has been incorporated into the analysis to nullify the geometrical bias to understand the geometrical preference for this interaction. The population distributions of these interactions before and after offset correction with respect to the offset from the centroid of the benzenoid ring are completely different. In the cases of alkali metal−π interactions, the population is maximum at offset zero or near zero. However, in the case of transition metal−π interactions, the offset for the maximum population is found near the carbon atom of the benzenoid ring. Interestingly, alkaline earth metals, which lie in between the alkali and transition metals in the periodic table, behave in between these two metals when metal−π interaction geometry is concerned.

Improved Modeling of Cation-π and Anion-Ring Interactions Using the Drude Polarizable Empirical Force Field for Proteins.

Cation-π interactions are noncovalent interactions between a π-electron system and a positively charged ion that are regarded as a strong noncovalent interaction and are ubiquitous in biological systems. Similarly, though less studied, anion-ring interactions are present in proteins along with in-plane interactions of anions with aromatic rings. As these interactions are between a polarizing ion and a polarizable π system, the accuracy of the treatment of these interactions in molecular dynamics (MD) simulations using additive force fields (FFs) may be limited. In the present work, to allow for a better description of ion-π interactions in proteins in the Drude-2013 protein polarizable FF, we systematically optimized the parameters for these interactions targeting model compound quantum mechanical (QM) interaction energies with atom pair-specific Lennard-Jones parameters along with virtual particles as selected ring centroids introduced to target the QM interaction energies and geometries. Subsequently, MD simulations were performed on a series of protein structures where ion-π pairs occur to evaluate the optimized parameters in the context of the Drude-2013 FF. The resulting FF leads to a significant improvement in reproducing the ion-π pair distances observed in experimental protein structures, as well as a smaller root-mean-square differences and fluctuations of the overall protein structures from experimental structures. Accordingly, the optimized Drude-2013 protein polarizable FF is suggested for use in MD simulations of proteins where cation-π and anion-ring interactions are critical. © 2019 Wiley Periodicals, Inc.

Removal of Bacteria from Solids by Bubbles: Effect of Solid Wettability, Interaction Geometry, and Liquid-Vapor Interface Velocity.

Air bubbles are a promising means of controlling fouling for a range of applications, particularly delaying fouling in marine environments. This work investigates the mechanism by which the collision of an air bubble with a solid removes adsorbed bacteria. A key feature of the work is that the numbers of bacteria were monitored via video microscopy throughout the collision; so, we were able to explore the mechanism of bacteria removal. When a bubble collides with a solid, an air-liquid interface crosses the solid twice, and we were able to distinguish the effects of the first and second air-liquid interfaces. The bacterium Pseudomonas aeruginosa was allowed to adhere to smooth poly(dimethylsiloxane) and then a collision with a bubble was investigated for one of three different approach geometries: perpendicular, parallel, and oscillating parallel to the solid surface. Other factors examined were the speed of the bubble, the duration of bacterial adhesion on the solid surface, and the wettability of the solid. Surface wettability was identified as the most significant factor. When the solid dewet, almost all bacteria were removed from hydrophobic surfaces upon the passage of the first air-liquid interface. In contrast, when a thin liquid film remained between the solid and the bubble (a hydrophilic solid), variable amounts of bacteria remained. Although almost all bacteria were initially removed from hydrophobic solids, many bacteria were redeposited on hydrophobic surfaces upon the passage of the second air-liquid interface, especially when the first and second air-liquid interfaces moved in opposite directions. As described previously, a lower velocity of the bubble allows more time for the thin liquid film to drain and improved removal efficiency on hydrophilic solids. A rougher solid (8 μm diameter hemispherical protrusions) decreased the detachment efficiency because bacteria and liquid were able to shelter in concavities.

Molecular interaction of the triazole fungicide propiconazole with homology modelled superoxide dismutase and catalase

To understand the plasmid mediated biodegradation of propiconazole and enzymatic antioxidant activity, the plasmid cured PS-4C strain was utilized against the propiconazole for its dissolution in the liquid medium, further, the molecular docking studies against the Pseudomonas aeruginosa superoxide dismutase (SOD) as well as catalase (CAT) was undertaken. An acridine orange based LD50 concentration of the propiconazole was found at 50 µg ml−1 and hence the plasmid of PS-4C strain was cured at this dose. Homology modeling using Swiss modeler was applied to generate 3D structure of both SOD and CAT. Active sites were predicted using CastP server and molecular docking was performed by AutodockVina program and thereby calculated binding free energy. Ligand docked against the SOD and CAT enzymes was found to bind with strong hydrophobic interaction. Propiconazole showed strong binding affinity with CAT compared to SOD. Thus, propiconazole resistant plasmid degenerated bacterium PS-4C strain can be a potent candidate for the safer remediation of pollutants and the conformation of propiconazole exploits the interactive geometry along with the molecule size sufficient for spanning the two enzymes to which they will bind making it a good starting point for designing library of antioxidants.

Wave properties and band gap analysis of deploying pipes conveying fluid with periodic varying parameters

Wave propagation and band gap (BG) characteristics of deploying long pipes conveying fluid are investigated based on a phononic crystal (PC) pipe model. The dispersion relation of the corresponding time-variant uniform pipe system is first derived in terms of the traveling wave feature of axially moving structures. Basic wave properties, such as the propagating and evanescent waves and the phase velocity and group velocity of propagating waves, are discussed to demonstrate the great effects of the flow velocity and deploying speed. The band structures of deploying pipe conveying fluid with periodic varying parameters are then investigated based on the Bragg scattering mechanism and treated by the transfer matrix method. A complex propagation constant is used to measure the band distribution. The fluid–structure interaction, deploying motion and component geometry are all found to have significant effects on the location and width of the BGs of the pipe. The deploying speed and flow velocity mainly influence the lower BGs while the component geometry acts much on the higher ones.