Geometry Of Interaction Research Articles

On geometry of interaction for polarized linear logic

We present Geometry of Interaction (GoI) models for Multiplicative Polarized Linear Logic, MLLP, which is the multiplicative fragment of Olivier Laurent's Polarized Linear Logic. This is done by uniformly adding multi-points to various categorical models of GoI. Multi-points are shown to play an essential role in semantically characterizing the dynamics of proof networks in polarized proof theory. For example, they permit us to characterize the key feature of polarization, focusing, as well as being fundamental to our construction of concrete polarized GoI models.Our approach to polarized GoI involves following two independent studies, based on different categorical perspectives of GoI: (i)Inspired by the work of Abramsky, Haghverdi and Scott, a polarized GoI situation is defined in which multi-points are added to a traced monoidal category equipped with a reflexive object U. Using this framework, categorical versions of Girard's execution formula are defined, as well as the GoI interpretation of MLLP proofs. Running the execution formula is shown to characterize the focusing property (and thus polarities) as well as the dynamics of cut elimination.(ii)The Int construction of Joyal–Street–Verity is another fundamental categorical structure for modelling GoI. Here, we investigate it in a multi-pointed setting. Our presentation yields a compact version of Hamano–Scott's polarized categories, and thus denotational models of MLLP. These arise from a contravariant duality between monoidal categories of positive and negative objects, along with an appropriate bimodule structure (representing ‘non-focused proofs’) between them.Finally, as a special case of (ii) above, a compact model of MLLP is also presented based on Rel (the category of sets and relations) equipped with multi-points.

Gluonic hot spots and spatial correlations inside the proton

In this work, largely based on [J. L. Albacete, A. Soto-Ontoso, Hot spots and the hollowness of proton-proton interactions at high energies, arXiv:1605.09176; J. L. Albacete, H. Petersen, A. Soto-Ontoso, Correlated wounded hot spots in proton-proton interactions, arXiv:1612.06274], we present a novel initial state geometry for proton-proton interactions. We rely on gluonic hot spots as effective degrees of freedom whose transverse positions inside the proton are correlated. We explore the impact of these non-trivial spatial correlations on the eccentricity and triangularity of the system following a Monte Carlo Glauber approach.

Revised CHARMM force field parameters for iron-containing cofactors of photosystem II.

Photosystem II is a complex protein-cofactor machinery that splits water molecules into molecular oxygen, protons, and electrons. All-atom molecular dynamics simulations have the potential to contribute to our general understanding of how photosystem II works. To perform reliable all-atom simulations, we need accurate force field parameters for the cofactor molecules. We present here CHARMM bonded and non-bonded parameters for the iron-containing cofactors of photosystem II that include a six-coordinated heme moiety coordinated by two histidine groups, and a non-heme iron complex coordinated by bicarbonate and four histidines. The force field parameters presented here give water interaction energies and geometries in good agreement with the quantum mechanical target data. © 2017 Wiley Periodicals, Inc.

Optimization of acousto-optic interaction geometry in KRS-5 crystal for far-infrared applications

Acousto-optic figures of merit of TlBr-TlI solid solution (KRS-5) crystals are calculated for different propagation directions and polarizations of interacting waves. The transverse, collinear, and semicollinear regimes of acousto-optic interaction are considered in this paper. Optimal diffraction configurations applicable in acousto-optic devices operating in the far-infrared region of spectrum are found in the cases of longitudinal and shear acoustic waves in the cubic crystalline material.

Amplification of coherent synchrotron high harmonic emission from ultra-thin foils in relativistic light fields

We report on a remarkable enhancement of high harmonic (HH) radiation emitted from the interaction of an ultra-intense laser pulse with ultra-thin foils by a manipulation of foil pre-plasma conditions. With a strong counter-propagating pre-pulse, we introduce a concerted expansion of the ultrathin foil target, and this significantly raises the efficiency of the HH generation process. Our experimental results show how the emission efficiency can be easily controlled by the intensity and delay time of the pre-pulse. The results give an important insight into the high harmonic generation process from solid dense plasmas when spatially limited. 1D particles in cell simulations confirm our experimental findings and show a significant dependency of the HH emission efficiency on the plasma density. The simplicity of the ultra-thin foil target and interaction geometry hold promise for specifically compact realization of imaging experiments with ultra-short and bright extreme ultra violet-pulses.

Accurate DFT-D3 Calculations in a Small Basis Set.

Calculations of interaction energies of noncovalent interactions in small basis sets are affected by the basis set superposition error and dispersion-corrected DFT-D methods and are thus usually parametrized only for triple-ζ and larger basis sets. Nevertheless, some smaller basis sets could also perform well. Among many combinations tested, we obtained excellent results with the DZVP-DFT basis and newly parametrized D3 dispersion correction. The accuracy of interaction energies and geometries is close to significantly more expensive calculations.

Anion Recognition Strategies Based on Combined Noncovalent Interactions.

This review highlights the most significant examples of an emerging field in the design of highly selective anion receptors. To date, there has been remarkable progress in the binding and sensing of anions. This has been driven in part by the discovery of ways to construct effective anion binding receptors using the dominant N-H functional groups and neutral and cationic C-H hydrogen bond donors, as well as underexplored strong directional noncovalent interactions such as halogen-bonding and anion-π interactions. In this review, we will describe a new and promising strategy for constructing anion binding receptors with distinct advantages arising from their elaborate design, incorporating multiple binding sites able to interact cooperatively with anions through these different kinds of noncovalent interactions. Comparisons with control species or solely hydrogen-bonding analogues reveal unique characteristics in terms of strength, selectivity, and interaction geometry, representing important advances in the rising field of supramolecular chemistry.

Halogen Bonding in Nucleic Acid Complexes.

Halogen bonding (X-bonding) has attracted notable attention among noncovalent interactions. This highly directional attraction between a halogen atom and an electron donor has been exploited in knowledge-based drug design. A great deal of information has been gathered about X-bonds in protein-ligand complexes, as opposed to nucleic acid complexes. Here we provide a thorough analysis of nucleic acid complexes containing either halogenated building blocks or halogenated ligands. We analyzed close contacts between halogens and electron-rich moieties. The phosphate backbone oxygen is clearly the most common halogen acceptor. We identified 21 X-bonds within known structures of nucleic acid complexes. A vast majority of the X-bonds is formed by halogenated nucleobases, such as bromouridine, and feature excellent geometries. Noncovalent ligands have been found to form only interactions with suboptimal interaction geometries. Hence, the first X-bonded nucleic acid binder remains to be discovered.

Syntheses and Photophysical Properties of Schiff Base Ni(II) Complexes: Application for Sustainable Antibacterial Activity and Cytotoxicity

Five new imine-linked ligands (H2L1, H4L2, and L3–L5) were synthesize in two step reactions and final products were fully characterized with spectroscopic techniques. The binding behavior of these ligands was evaluated with the library of metal ions. However, substantial photophysical modulations were observed with the coordination of [Ni2+] ion to the ligand pocket. The fact that Ni2+ induced remarkable modulation in photophysical studies encouraged us to prepare the nickel complexes of respective ligands. The resultant coordination complexes offered interesting properties like tunable coordination geometry, variable stereochemistry, and possibility of electrostatic interactions which are important for biomolecular recognition. These properties of coordination complexes encouraged us to evaluate the antimicrobial activity of nickel complexes. All nickel complexes have shown appreciable antibacterial activity against Staphylococcus aureus and methicillin-resistant S. aureus (MRSA). The SEM imaging studies...

Pseudo-invariants contributing to inverse energy cascades in three-dimensional turbulence

Three-dimensional (3D) turbulence is characterized by a dual forward cascade of both kinetic energy and helicity, a second inviscid flow invariant, from the integral scale of motion to the viscous dissipative scale. In helical flows, however, such as strongly rotating flows with broken mirror symmetry, an inverse energy cascade can be observed analogous to that of two-dimensional turbulence (2D) where a second positive-definite flow invariant, enstrophy, unlike helicity in 3D, effectively blocks the forward cascade of energy. In the spectral-helical decomposition of the Navier-Stokes equation it has previously been show that a subset of three-wave (triad) interactions conserve helicity in 3D in a fashion similar to enstrophy in 2D, thus leading to a 2D-like inverse energy cascade in 3D. In this work, we show both theoretically and numerically that an additional subset of interactions exist conserving a new pseudo-invariant in addition to energy and helicity, which contributes either to a forward or inverse energy cascade depending on the specific triad interaction geometry.

Bis-chlorinated aromatics adsorption in Faujasites investigated by molecular simulation-influence of Na+ cation

Molecular simulations have been employed in order to explore at the microscopic scale the adsorption of bis-chlorinated aromatics (1,2- and 1,3-dichlorobenzene) in Faujasite, a large pore openings zeolite. Both, the purely siliceous and the sodium cation exchanged forms of zeolite structures have been respectively considered, aiming to clearly determine the role of the charge compensating cation in the adsorption phenomenon of the investigated aromatics. A suited combination of classical and electronic structure simulation tools provided a clear overall picture of the adsorption process, from both local and global points of view, well matching with the accessible experimental data. The adsorbate preferential locations, adsorbate/zeolite interaction nature and geometry as well as the adsorption energy were extracted from Density Functional Theory calculations. Furthermore, on the basis of classical force fields, the Gibbs ensemble Monte Carlo simulations allowed predicting the room temperature (298 K) adsorption isotherms for the investigated molecules in Faujasite, within the purely siliceous and Na+ exchanged form, with mobile extra-framework cations upon the adsorption process. Finally, we accomplished a detailed analysis of the microscopic mechanism in play along the whole adsorption process, with a special highlight to the understanding of the interaction geometry of the molecule with the sodium cation, in function of its crystallographic site. Location of the charge compensating cation has been found to influence the nature of interaction with the adsorbate molecule.

Large-Scale Analysis of Hydrogen Bond Interaction Patterns in Protein-Ligand Interfaces.

Protein-ligand interactions are the fundamental basis for molecular design in pharmaceutical research, biocatalysis, and agrochemical development. Especially hydrogen bonds are known to have special geometric requirements and therefore deserve a detailed analysis. In modeling approaches a more general description of hydrogen bond geometries, using distance and directionality, is applied. A first study of their geometries was performed based on 15 protein structures in 1982. Currently there are about 95 000 protein-ligand structures available in the PDB, providing a solid foundation for a new large-scale statistical analysis. Here, we report a comprehensive investigation of geometric and functional properties of hydrogen bonds. Out of 22 defined functional groups, eight are fully in accordance with theoretical predictions while 14 show variations from expected values. On the basis of these results, we derived interaction geometries to improve current computational models. It is expected that these observations will be useful in designing new chemical structures for biological applications.

Scale transition using dislocation dynamics and the nudged elastic band method

Microstructural features such as precipitates or irradiation-induced defects impede dislocation motion and directly influence macroscopic mechanical properties such as yield point and ductility. Dislocation-defect interactions involve both atomic scale and long range elastic interactions. Thermally assisted dislocation bypass of obstacles occurs when thermal fluctuations and driving stresses contribute sufficient energy to overcome the energy barrier. The Nudged Elastic Band (NEB) method is typically used in the context of atomistic simulations to quantify the activation barriers for a given reaction. In this work, the NEB method is generalized to coarse-grain continuum representations of evolving microstructure states beyond the discrete particle descriptions of first principles and atomistics. This method enables the calculation of activation energies for a 1/2[111](11¯0) glide dislocation bypassing a [001] self-interstitial atom loop of size in the range of 4–10 nm with a spacing larger than 150 nm in α-iron for a range of applied stresses and interaction geometries. Further, the study is complemented by a comparison between atomistic and continuum based prediction of barriers.

Development of the concept of natural geometry for physical interactions

We analyze the development of the concept of natural geometry for the gravitational field in Logunov’s works. We discuss the application of this concept to vacuum nonlinear electrodynamics and show that defining the natural geometry for a nonlinear theory and finding its metric tensor permit obtaining sufficiently complete information about the propagation laws for electromagnetic field pulses in background electromagnetic fields.

Engineering Efficient p‐Type TMD/Metal Contacts Using Fluorographene as a Buffer Layer

P‐type transistors based on high work function transition metal dichalcogenide (TMD) monolayers such as MoS2 are to date difficult to produce, owing to the strong Fermi level pinning at the semiconductor/contact metal interfaces. In this work, the potential of halogenated graphenes is demonstrated as a new class of efficient hole injection layers to TMDs such as MoS2 and WSe2 by taking fluorographene (or GF) as a model buffer layer. Using first‐principles computations, two commonly obtained GF stoichiometries, C2F and CF, have been studied as buffer layers between MoS2 and Pt. In particular, for high work function TMDs such as MoS2, it has been shown that C2F forms an ohmic contact, while CF leads to a significant p‐SBH value. On the other hand, for low work function TMDs such as WSe2, both C2F and CF lead to p‐type ohmic contacts. This analysis shows that the ability of these buffer layers to form p‐type contacts depends crucially on the charge redistribution at the GF/metal interface, which is dictated by their chemical interaction and equilibrium geometry. The fundamental electronic structures between the different semiconductor/insulator/metal interfaces which are part of this study have also been investigated.

Assessing DFT-D3 Damping Functions Across Widely Used Density Functionals: Can We Do Better?

With the aim of improving the utility of the DFT-D3 empirical dispersion correction, we herein generalize the DFT-D3 damping function by optimizing an additional parameter, an exponent, which controls the rate at which the dispersion tail is activated. This method - DFT-D3(op), shorthand for "optimized power," where power refers to the newly introduced exponent - is then parametrized for use with ten popular density functional approximations across a small set of noncovalent interactions and isomerization energies; the resulting methods are then evaluated across a large independent test set of 2475 noncovalent binding energies and isomerization energies. We find that the DFT-D3(op) tail represents a substantial improvement over existing damping functions, as it affords significant reductions in errors associated with noncovalent interaction energies and geometries. The revPBE0-D3(op) and MS2-D3(op) methods in particular stand out, and our extensive testing indicates they are competitive with other modern density functionals.

High-average-power, 2-μm femtosecond optical parametric oscillator synchronously pumped by a thin-disk, mode-locked laser.

A high-energy, extended-cavity femtosecond BiBO optical parametric oscillator synchronously pumped by a 1.0-ps, 1030-nm Yb:YAG, thin-disk pump laser is presented. The oscillator operated near degeneracy in a noncollinear interaction geometry, producing signal wavelength tunability from 1.99 to 2.20 μm. The signal pulses have an average power exceeding 2 W, producing 455-fs pulses at 7.08 MHz with energies up to 350 nJ, showing increased potential for tunable sources of scalable ultrafast pulses in the infrared.

A grasp-based passivity signature for haptics-enabled human-robot interaction: Application to design of a new safety mechanism for robotic rehabilitation

In this paper, the biomechanical capability of the human upper limb in absorbing physical interaction energy during human-robot interaction is analyzed. The outcome is a graphical map that can quantitatively correlate the extent of the grasp pressure and the geometry of interaction to the extent of hand passivity. For this purpose, a user study has been conducted for 11 healthy human subjects to characterize the energy absorption capability in their arm and wrist. The above correlation is statistically validated. The identified user-specific grasp-based passivity signature map can be used as a graphical tool to assess the biomechanical capabilities of the upper limb in absorbing interaction energy. In this paper, the proposed grasp-based passivity signature map is utilized in the design of a new stabilizer for haptic systems, that takes into account the variation in energy absorption during haptic task execution. The goal is to optimize the haptic system fidelity while guaranteeing human-robot interaction stability despite the potential existence of delays and a non-passive environment. The controller is termed grasp-based passivity signature map stabilizer. If the user provides minimum to no energy absorption during the interaction, the controller makes the force reflection gate tight to guarantee stability. However, when the user demonstrates high capability in absorbing interaction energy, the controller allows the forces to be reflected. The grasp-based passivity signature map stabilizer is an alternative for both conventional stabilizers of haptic/telerobotic systems and fixed conservative force limits in rehabilitation systems where patient-robot interaction safety is a crucial requirement. This provides the practical motivation for this work. Experimental results are presented.

Acoustic field structure simulation in quasi-collinear acousto-optic cells with ultrasound beam reflection

Ultrasound wave reflection from one of the crystal faces is the convenient way to arouse the acoustic beam with a desired propagation direction in acousto-optic cells with collinear and quasi-collinear interaction geometries. The reflection process effects on the ultrasound field amplitude and phase structure. The method to simulate the reflected finite ultrasound beam structure in the case of acoustically anisotropic media is presented in this paper. The investigation is carried on the example of two quasi-collinear acousto-optic cells fabricated on the base of tellurium dioxide crystal. The cells have special geometry that allows to obtain extremely long acousto-optic interaction length and to achieve unprecedented spectral resolution. The influence of reflection process in the acousto-optic diffraction characteristics was also examined.

Application potential of paratellurite and iodic acid crystals for acousto-optics in the Terahertz range

The possibility of applying paratellurite, iodic acid, and lithium iodate crystals in acousto-optics in the THz range has been investigated. The transparency windows of these crystals and their refractive indices in the THz range have been determined. The acousto-optic figures of merit of these materials are calculated for different acousto-optic interaction geometries.