Geometry Of Interaction Research Articles

Negative-pressure-induced helimagnetism in ferromagnetic cubic perovskites Sr1−xBaxCoO3

Helimagnetic materials are identified as promising for novel spintronic applications. Since helical spin order is manifested as a compromise of competing magnetic exchange interactions, its emergence is limited by unique constraints imposed by the crystalline lattice and the interaction geometries, as exemplified by the multiferroic perovskite manganites with large orthorhombic distortion. Here we show that a simple cubic perovskite SrCoO$_3$ with room-temperature ferromagnetism has the potential to host helimagnetic order upon isotropic lattice expansion. Increasing the Ba content $x$ in Sr$_{1-x}$Ba$_x$CoO$_3$ continuously expands the cubic lattice, eventually suppressing the ferromagnetic order near $x$=0.4, where helimagnetic correlations are observed as incommensurate diffuse magnetic scattering by neutron diffraction measurements. The emergence of helimagnetism is semi-quantitatively reproduced by first-principles calculations, leading to the conjecture that a simple cubic lattice with strong $d$-$p$ hybridisation can exhibit a variety of novel magnetic phases originating from competing exchange interactions.

Mechanically Responsive Crystalline Coordination Polymers with Controllable Elasticity.

Crystalline coordination polymers tend to be brittle and inelastic, however, we now describe a family of such compounds that are capable of displaying mechanical elasticity in response to external pressure. The design approach successfully targets structural features that are critical for producing the desired mechanical output. The elastic crystals all comprise 1D cadmium(II) halide polymeric chains with adjacent metal centres bridged by two halide ions resulting in the required stacking interactions and short "4 Å" crystallographic axes. These polymeric chains (structural "spines") are further organized via hydrogen bonds and halogen bonds perpendicular to the direction of the chains. By carefully altering the strength and the geometry of these non-covalent interactions, we have demonstrated that it is possible to control the extent of elastic bending in crystalline coordination compounds.

Anti-HLA antibodies with complementary and synergistic interaction geometries promote classical complement activation on platelets.

High titers of HLA antibodies are associated with platelet refractoriness, causing poor platelet increments after transfusions in a subset of patients with HLA antibodies. Currently, we do not know the biological mechanisms that explain the variability in clinical responses in HLA alloimmunized patients receiving platelet transfusions. Previously we showed that a subset of anti-HLA IgG-antibodies induces FcγRIIa-dependent platelet activation and enhanced phagocytosis. Here, we investigated whether anti-HLA IgG can induce complement activation on platelets. We found that a subset of anti-HLA IgG induced complement activation via the classical pathway, causing C4b and C3b deposition and formation of the membrane-attack complex. This resulted in permeabilization of platelet membranes and increased calcium influx. Complement activation also caused enhanced α-granule release, as measured by CD62P surface exposure. Blocking studies revealed that platelet activation was caused by FcγRIIa-dependent signaling as well as HLA antibody induced complement activation. Synergistic complement activation employing combinations of monoclonal IgGs suggested that assembly of oligomeric IgG complexes strongly promoted complement activation through binding of IgGs to different antigenic determinants on HLA. In agreement with this, we observed that preventing anti-HLA-IgG hexamer formation using an IgG-Fc:Fc blocking peptide, completely inhibited C3b and C4b deposition. Our results show that HLA antibodies can induce complement activation on platelets including membrane attack complex formation, pore formation and calcium influx. We propose that these events can contribute to fast platelet clearance in vivo in patients refractory to platelet transfusions with HLA alloantibodies, who may benefit from functional-platelet matching and treatment with complement inhibitors.

Effect of deviation from purely transverse and longitudinal polarization states of acoustic waves on the anisotropy of acousto-optic figure of merit: the case of Tl3AsS4 crystals.

We analyze the effect of acoustic wave (AW) polarization states deviation from purely longitudinal and transverse on the anisotropy of the acousto-optic (AO) figure of merit for the case of AO interactions occurring in the principal crystallographic planes. In particular, we obtain phenomenological relations that describe the effective elasto-optic coefficient for the six types of AO interactions, which exhaust all of the possible isotropic AO diffractions. These relations are compared for the alternative cases when the deviations of polarization of the AWs from purely longitudinal and transverse ones are either taken into consideration or completely neglected. Our analysis carried out on the example of Tl3AsS4 crystals reveals that the deviation of AW polarization from its pure states influences the anisotropy of the AO figure of merit only when the AO interactions with quasi-transverse AWs are dealt with. This fact is caused by the peculiar acoustic and elasto-optic properties of Tl3AsS4. On the other hand, the situation can become different for other crystalline materials, where the angular dependences of the AO figure of merit can differ significantly in cases in which the deviation angle increases. This holds true for the AO interactions with both quasi-transverse and quasi-longitudinal AWs. Under these conditions, non-orthogonality of the AWs (or deviation from their longitudinal polarization states) affects essentially the AO characteristics. Finally, we determine the geometries of AO interactions for which the highest AO figures of merit are reached for the Tl3AsS4 crystals.

Focal spot characteristics of Thomson scattering x-ray sources

With the recent rapid development of x-ray imaging using Thomson scattering x-ray sources, there is an increasing demand for knowledge of the focal spot characteristics of this type of light source. This is because imaging quality is closely related to focal spot characteristics. In this paper, an analytical expression of the focal spot size and beam parameters at arbitrary interaction angles is derived. Based on this, the focal spot can be optimized in a straightforward manner by adjusting the laser and electron focusing at a fixed interaction geometry. As the beam focusing increases, a smaller focal spot and a higher photon yield are obtained, while the bandwidth of scattered x rays deteriorates, leading to a compromise of the above three physical parameters. Considering the beam position and time fluctuations, the focal spot will be broadened and the photon yield will be reduced. Using typical beam parameters at the Tsinghua Thomson scattering x-ray source, it is shown that a micrometer-sized focal spot can be easily achieved. The results will help one to develop the x-ray imaging field, especially in micro-computed tomography applications based on Thomson light sources.

Neural networks to fit potential energy curves from asphaltene-asphaltene interaction data

Neural networks methodology is a tool that allows to get the potential energy curve in cases where the data dispersion does not fit a discrete distribution; hence, a binding energy fitting can be found with this methodology. A data distribution of the intermolecular pair interaction potential in vacuum has been previously accomplished between asphaltene-asphaltene (UAA) systems by using compass classical force field. In the latter, all possible interaction geometries are taken into account between the species: random, face-to-face, t-shape and edge to edge. In one of these cases, a potential energy curve is gotten when the geometry of interaction is face-to-face using a statistical fit. Focusing in these data distribution, neural networks have been applied on the following cases: i) face-to-face distribution of asphaltene-asphaltene interactions; ii) the complete asphaltene-asphaltene discrete distribution of energy vs contact distance (the minimum distance at which the interacting species is not equal to zero) where all-geometries were used, and iii) the random distribution of geometries of asphaltene-asphaltene interactions. In addition, using an asphaltene model molecule reported by Speight and taking into account two possible asphaltene interactions (face-to-face and random), firstly the data distribution of energy as a function of distance is obtained, and secondly neural networks are applied to fit the corresponding potential energy curve.

DFT study of arsine (AsH3) gas adsorption on pristine, Stone-Wales-defected, and Fe-doped single-walled carbon nanotubes

To find the possible way of adsorption and detecting the toxic gas of AsH3, we have studied the interactions between AsH3 molecule and modified (5,5) single-walled carbon nanotubes by using the method of density functional theory (DFT). The interaction distances, adsorption energies, and geometry and electronic changes of structures were investigated to explore the sensitivity of variety of models of single-walled carbon nanotubes (SWCNTs) with Fe doping, Stone-Wales defects, and a combination of them toward AsH3 molecule. From calculated results, it was found that AsH3 molecule was more likely to be absorbed on Fe-doped CNTs with relatively higher adsorption energy and higher charge transfer and shorter interaction distance compared with that on the pristine and defected SWCNTs.

Placement of Water Molecules in Protein Structures: From Large-Scale Evaluations to Single-Case Examples.

Water molecules are of great importance for the correct representation of ligand binding interactions. Throughout the last years, water molecules and their integration into drug design strategies have received increasing attention. Nowadays a variety of tools are available to place and score water molecules. However, the most frequently applied software solutions require substantial computational resources. In addition, none of the existing methods has been rigorously evaluated on the basis of a large number of diverse protein complexes. Therefore, we present a novel method for placing water molecules, called WarPP, based on interaction geometries previously derived from protein crystal structures. Using a large, previously compiled, high-quality validation set of almost 1500 protein-ligand complexes containing almost 20 000 crystallographically observed water molecules in their active sites, we validated our placement strategy. We correctly placed 80% of the water molecules within 1.0 Å of a crystallographically observed one.

Benchmarking of the R-7 Anisotropic Dispersion Energy Term on the S22 Dimer Test Set.

The effects of including the anisotropic E7 term to the dispersion energy in addition to the leading E6 term are examined by using the effective fragment potential (EFP) method on the S22 test set. In this study, the full anisotropic E7 term is computed whereas the isotropic and spherical approximations are used for the E6 term. It is found that the E7 term is positive for hydrogen-bonded complexes and has a magnitude that can be as large as 50% of E6, giving rise to larger intermolecular distances than those obtained with E6 alone. The large positive value of E7 is analyzed for the hydrogen-bonded uracil dimer; it is found to originate from the large magnitude of the dynamic polarizability tensors as well as the proximity of the LMOs involved in hydrogen bonding. Conversely, E7 tends to be negative for dispersion-dominant complexes, and it has a very small magnitude for such complexes. The optimized geometries for these systems are therefore not greatly affected by the presence of the E7 term. For the mixed systems in the S22 test set, an intermediate behavior is observed. Overall, the E7 term is most important for systems with hydrogen bonding interactions and mixed systems. A full anisotropic treatment of the E6 term and higher order terms may need to be included to obtain more accurate interaction energies and geometries.

2D finite-element elastic models of transtensional pull-apart basins

A set of two-dimensional finite-element elastic models are presented to provide insights on the evolution of transtensional pull-apart basins between two right-stepping, right-lateral fault segments. Three representative fault segment interaction geometries are modelled, showing underlapping, neutral and overlapping segments. Despite the simplifications of the 2D model, overall results are obtained that might help understanding the formation of pull-apart basins. Firstly, the orientations of the local σ1 and σ3 tensional stress directions markedly depend on the segment's position. Secondly, the mean normal stress is extensional in a transtensional basin between segments, while the region outside the step is characterized by more compressive mean normal stresses. Thirdly, the angle of offset between the fault segments is one of the most important parameters controlling the geometries of the transtensional pull-apart basins: connected depocenters with basin high and lozenge shape in the case of underlapping steps, spindle shape or lazy S or Z shape in the case of neutral steps, and broadly elongate rhomboidal to sigmoidal basins in the case of overlapping steps. Generally, en-échelon basin margin system, dual opposing asymmetric depocenter, intrabasin relative structural high, and wide basin width can be used as indicators that a pull-apart basin is developing in transtension zones.

Virtual human bone modelling by interactive sculpting, mesh morphing and force-feedback

The paper deals with an investigation on the role of interactive sculpting and radial basis function (RBF) mesh morphing in the field of biomechanical computer-aided simulations. In this context, mesh morphing can be effectively used in predictive medicine workflows where a patient-specific numerical model is taken as reference to understand the physics of interest by means of simulation-driven techniques. The proposed methodology is intended for addressing the interactive geometry modification in combination with a force-feedback device and it is applied to anatomical structures. The concept is demonstrated showing a fast remodelling workflow of the human femur. The interactive process allows to steer the morphing of a template FEA model onto the patient geometry by positioning a set of landmark points. A first morphing action allows to warp the solid model according to the RBF deformation field produced by landmarks, a final projection on the target surface is performed to complete the task. The approach proven to be quick, effective and ergonomic thanks to the haptic device and the high level of interactivity. New patient specific CAE models are generated in a very short time preserving the very good quality of the computational mesh.

A survey of methionine-aromatic interaction geometries in the oxidoreductase class of enzymes: What could Met-aromatic interactions be doing near metal sites?

Redox reactions of the aromatic amino acids tyrosine (Tyr) and tryptophan (Trp) are crucial for the biological functions of many metalloproteins. An important question is how biological systems can use the protein environment to move electrons through proteins in a controlled manner. Methionine (Met)-aromatic interactions are common in proteins, but little is known about redox reactions of such motifs. Here, we explore methionine sulfur-aromatic interactions in the oxidoreductase (EC 1) class of proteins and their proximity to metal sites. We also propose a new metric for classifying Met-aromatic interactions called “interaction order.” Over 12,000 protein structures from the Protein Data Bank were analyzed. A linear algebraic heuristic was used to classify the interaction of Met‑sulfur with tyrosine, tryptophan, and phenylalanine. We found that 83% of oxidoreductase proteins contained aromatic interactions meeting our criteria, with a preferential angle of about 60° between Met‑sulfur lone pairs and aromatic planes. A total of 41% of Met-aromatic interactions meeting our criteria were found to be within 20 Å of a metal site, and 6% were found within 10 Å. A surprising number of “bridging” interactions, involving two aromatic residues and one Met also were identified. Finally, selected examples of potentially important Met-aromatic redox motifs are outlined. On the basis of our results, we suggest that Met-aromatic interactions should be considered as mediators of electron transfer reactions, as well as their more widely recognized roles as structural motifs.

Book review: Exploring Classical Greek Construction Problems with Interactive Geometry Software

Book review: Exploring Classical Greek Construction Problems with Interactive Geometry Software

Investigation of the interactions between 1-butyl-3-methylimidazolium-based ionic liquids and isobutylene using density functional theory.

To identify ionic liquids (ILs) that could be used as solvents in isobutylene (IB) polymerization, the interactions between IB and eight different ILs based on the 1-butyl-3-methylimidazolium cation ([Bmim]+) were investigated using density functional theory (DFT). The anions in the ILs were chloride, hexafluorophosphate, tetrafluoroborate, bis[(trifluoromethyl)sulfonyl]imide, tetrachloroaluminate ([AlCl4]-), tetrachloroferrate, acetate, and trifluoroacetate. The interaction geometries were explained by changes in the total energy, intermolecular distances, Hirshfeld charges, and the electrostatic potential surface. The IL solvents were screened by comparing their interaction intensities with IB to the interaction intensities of reference ILs ([AlCl4]--based ILs) with IB. The microscopic mechanism for IB dissolution was rationalized by invoking a previously reported microscopic mechanism for the dissolution of gases in ILs. Computation results revealed that hydrogen (H) bonding between C2-H on the imidazolium ring and the anions plays a key role in ion pair (IP) formation. The addition of IB leads to slight changes in the dominant interactions of the IP. IB molecules occupied cavities created by small angular rearrangements of the anions, just as CO2 does when it is dissolved in an IL. The limited total free space in the ILs and the much larger size of IB than CO2 were found to be responsible for the poor solubility of IB compared with that of CO2 in the ILs.

Coupling Influences SMM Properties for Pure 4 f Systems.

Increasing both the energy barrier for magnetization reversal and the coercive field of the hysteresis loop are significant challenges in the field of single-molecule magnets (SMMs). Coordination geometries of lanthanide ions and magnetic interactions between lanthanide ions are both important for guiding the magnetic behavior of SMMs. We report a high energy barrier of 657 K (457 cm-1 ) in a diamagnetic-ion-diluted lanthanide chain compound with a constrained bisphenoid symmetry (D2d ); this energy barrier is substantially higher than the barrier of 567 K (394 cm-1 ) of the non-diluted chain compound with intrachain ferromagnetic interactions. Although intrachain magnetic interaction lowers the energy barrier for magnetization reversal, it can greatly enhance the coercive fields and zero-field remanence of the hysteresis loops, which is crucial for the rational design of high-performance SMMs. Factors related to the coordination sphere of the lanthanide center, which govern the high magnetic relaxation barriers through the second excited Kramer's doublets and the magnetic interactions that affect the hysteresis loops, were revealed through ab initio calculations.

A Comprehensive Analysis of Anion-Quadrupole Interactions in Protein Structures.

The edgewise interactions of anions with phenylalanine (Phe) aromatic rings in proteins, known as anion-quadrupole interactions, have been well studied. However, the anion-quadrupole interactions of the tyrosine (Tyr) and tryptophan (Trp) rings have been less well studied, probably because these have been considered weaker than interactions of anions hydrogen bonded to Trp/Tyr side chains. Distinguishing such hydrogen bonding interactions, we comprehensively surveyed the edgewise interactions of certain anions (aspartate, glutamate, and phosphate) with Trp, Tyr, and Phe rings in high-resolution, nonredundant protein single chains and interfaces (protein-protein, DNA/RNA-protein, and membrane-protein). Trp/Tyr anion-quadrupole interactions are common, with Trp showing the highest propensity and average interaction energy for this type of interaction. The energy of an anion-quadrupole interaction (-15.0 to 0.0 kcal/mol, based on quantum mechanical calculations) depends not only on the interaction geometry but also on the ring atom. The phosphate anions at DNA/RNA-protein interfaces interact with aromatic residues with energies comparable to that of aspartate/glutamate anion-quadrupole interactions. At DNA-protein interfaces, the frequency of aromatic ring participation in anion-quadrupole interactions is comparable to that of positive charge participation in salt bridges, suggesting an underappreciated role for anion-quadrupole interactions at DNA-protein (or membrane-protein) interfaces. Although less frequent than salt bridges in single-chain proteins, we observed highly conserved anion-quadrupole interactions in the structures of remote homologues, and evolutionary covariance-based residue contact score predictions suggest that conserved anion-quadrupole interacting pairs, like salt bridges, contribute to polypeptide folding, stability, and recognition.

Phenylboronic Acid Derivatives as Validated Leads Active in Clinical Strains Overexpressing KPC-2: A Step against Bacterial Resistance.

The emergence and dissemination of multidrug resistant (MDR) pathogens resistant to nearly all available antibiotics poses a significant threat in clinical therapy. Among them, Klebsiella pneumoniae clinical isolates overexpressing KPC-2 carbapenemase are the most worrisome, extending bacterial resistance to last-resort carbapenems. In this study, we investigate the molecular recognition requirements in the KPC-2 active site by small phenylboronic acid derivatives. Four new phenylboronic acid derivatives were designed and tested against KPC-2. For the most active, despite their simple chemical structures, nanomolar affinity was achieved. The new derivatives restored susceptibility to meropenem in clinical strains overexpressing KPC-2. Moreover, no cytotoxicity was detected in cell-viability assays, which further validated the designed leads. Two crystallographic binary complexes of the best inhibitors binding KPC-2 were obtained at high resolution. Kinetic descriptions of slow binding, time-dependent inhibition, and interaction geometries in KPC-2 were fully investigated. This study will ultimately lead toward the optimization and development of more-effective KPC-2 inhibitors.

Efficient Implementation of Evaluation Strategies via Token-Guided Graph Rewriting

In implementing evaluation strategies of the lambda-calculus, both correctness and efficiency of implementation are valid concerns. While the notion of correctness is determined by the evaluation strategy, regarding efficiency there is a larger design space that can be explored, in particular the trade-off between space versus time efficiency. We contributed to the study of this trade-off by the introduction of an abstract machine for call-by-need, inspired by Girard's Geometry of Interaction, a machine combining token passing and graph rewriting. This work presents an extension of the machine, to additionally accommodate left-to-right and right-to-left call-by-value strategies. We show soundness and completeness of the extended machine with respect to each of the call-by-need and two call-by-value strategies. Analysing time cost of its execution classifies the machine as "efficient" in Accattoli's taxonomy of abstract machines.

Exploring vacuum birefringence based on a 100 PW laser and an x-ray free electron laser beam

Exploring vacuum birefringence with the station of extreme light at Shanghai Coherent Light Facility is considered. Laser pulses of intensity beyond 1023 W cm−2 are capable of polarizing the vacuum due to the ultra-strong electro-magnetic fields. The subtle difference of the vacuum refractive indexes along electric and magnetic fields leads to a birefringence effect for lights propagating through. The vacuum birefringence effect can now be captured by colliding a hard x-ray free electron laser (XFEL) beam with a high-power laser. The initial XFEL beam of pure linear polarization is predicated to gain a very small ellipticity after passing through the laser stimulated vacuum. Various interaction geometries are considered, showing that the estimated ellipticity lies between 1.8 × 10−10 and 10−9 for a 100 PW laser interacting with a 12.9 keV XFEL beam, approaching the threshold for todays’ polarity detection technique. The detailed experimental set-up is designed, including the polarimeter, the focusing compound refractive lens and the optical path. When taking into account the efficiencies of the x-ray instruments, it is found that about 10 polarization-flipped x-ray photons can be detected for a single shot for our design. Considering the background noise level, accumulating runs are necessary to obtain high confident measurement.

Charting the Replica Symmetric Phase

Diluted mean-field models are spin systems whose geometry of interactions is induced by a sparse random graph or hypergraph. Such models play an eminent role in the statistical mechanics of disordered systems as well as in combinatorics and computer science. In a path-breaking paper based on the non-rigorous `cavity method', physicists predicted not only the existence of a replica symmetry breaking phase transition in such models but also sketched a detailed picture of the evolution of the Gibbs measure within the replica symmetric phase and its impact on important problems in combinatorics, computer science and physics [Krzakala et al.: PNAS 2007]. In this paper we rigorise this picture completely for a broad class of models, encompassing the Potts antiferromagnet on the random graph, the $k$-XORSAT model and the diluted $k$-spin model for even $k$. We also prove a conjecture about the detection problem in the stochastic block model that has received considerable attention [Decelle et al.: Phys. Rev. E 2011].