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At least 433 records · Page 24

Phosphorus recycling by mineral-catalyzed ribonucleotide cleavage on iron and manganese oxides

Abstract Phosphorus is an essential element influencing both food security via plant fertilization, and water pollution through excessive phosphorus use, yet the phosphorus cycle in ecosystems is poorly known. In particular, beyond adsorption, the role of iron and manganese oxides in catalyzing the abiotic dephosphorylation of biomolecules is debated. Here, we studied the reactions of ribonucleotides, containing different phosphate bonding, with goethite, hematite, and birnessite. We employed both high-resolution mass spectrometry of solution species and molecular modeling simulations of ribonucleotide-mineral complexes. Results disclose an up to fivefold preferential hydrolytic cleavage of a phosphoanhydride bond over a phosphoester bond, indicating that mineral-catalyzed reactions reflect the hierarchy reported for the activity of phosphatase enzymes. The fourfold higher catalytic reactivity of goethite and birnessite versus hematite is explained by mineral-specific binding rather than surface area differences. Corresponding simulated adsorbate conformations at the water–mineral interfaces are proposed. Overall, our findings provide new insights on the catalytic recycling of organic phosphorus species by mineral oxides.

58 GEOSCIENCES↗

Understanding geopolymer binder-aggregate interfacial characteristics at molecular level

The interfacial characteristics of geopolymer binder to aggregate composites are poorly understood, especially at molecular level. Herein, molecular models are developed to study, for the first time, the geopolymer-aggregate interface. Chemically, various forms of interfacial bonding are characterized, including Al-O-Si bonding through condensation reactions, NaO and H-bonding. An atomic-level interfacial transition zone (ITZ) is identified, attributed to the concentration of –OH groups. Increasing the Si/Al ratio of geopolymer is found to decrease the ITZ density, but have limited effect on the ITZ width. A heterogeneous diffusion characteristic occurs in geopolymer, due to the weak interfacial interaction. Mechanically, lowering the Si/Al ratio promotes the interfacial strength due to the stronger interfacial interaction and higher cross-linking degree in geopolymer. Under loading the interfacial fracture undergoes three stages: crack propagation, chain bridging (including aluminosilicate and ionic bridging) and breakage. The above atomic-level findings may facilitate a better design of geopolymer concrete in engineering.

36 MATERIALS SCIENCE↗

Solvation of furfural at metal–water interfaces: Implications for aqueous phase hydrogenation reactions

Metal–water interfaces are central to understanding aqueous-phase heterogeneous catalytic processes. However, the explicit modeling of the interface is still challenging as it necessitates extensive sampling of the interfaces’ degrees of freedom. Herein, we use ab initio molecular dynamics (AIMD) simulations to study the adsorption of furfural, a platform biomass chemical on several catalytically relevant metal–water interfaces (Pt, Rh, Pd, Cu, and Au) at low coverages. We find that furfural adsorption is destabilized on all the metal–water interfaces compared to the metal–gas interfaces considered in this work. This destabilization is a result of the energetic penalty associated with the displacement of water molecules near the surface upon adsorption of furfural, further evidenced by a linear correlation between solvation energy and the change in surface water coverage. To predict solvation energies without the need for computationally expensive AIMD simulations, we demonstrate OH binding energy as a good descriptor to estimate the solvation energies of furfural. Using microkinetic modeling, we further explain the origin of the activity for furfural hydrogenation on intrinsically strong-binding metals under aqueous conditions, i.e., the endothermic solvation energies for furfural adsorption prevent surface poisoning. In conclusion, our work sheds light on the development of active aqueous-phase catalytic systems via rationally tuning the solvation energies of reaction intermediates.

aqueous-phase hydrogenation↗

Deep potential molecular dynamics simulations of low-temperature plasma-surface interactions

Machine learning approaches to potential generation for molecular dynamics (MD) simulations of low-temperature plasma-surface interactions could greatly extend the range of chemical systems that can be modeled. Empirical potentials are difficult to generalize to complex combinations of multiple elements with interactions that might include covalent, ionic, and metallic bonds. This work demonstrates that a specific machine learning approach, Deep Potential Molecular Dynamics (DeepMD), can generate potentials that provide a good model of plasma etching in the Si-Cl-Ar system. Comparisons are made between MD results using DeepMD models and empirical potentials, as well as experimental measurements. Pure Si properties predicted by the DeepMD model are in reasonable agreement with experimental results. Simulations of Si bombardment by Ar + ions demonstrate the ability of the DeepMD method to predict sputtering yields as well as the depth of the amorphous-crystalline interface. Etch yields as a function of flux ratio and ion energy for simultaneous Cl 2 and Ar + impacts are in good agreement with previous simulation results and experiment. Predictions of etch yields and etch products during plasma-assisted atomic layer etching of Si-Cl 2 -Ar are shown to be in good agreement with MD predictions using empirical potentials and with experiment. Finally, good agreement was also seen with measurements for the spontaneous etching of Si by Cl atoms at 300 K. Further, the demonstration that DeepMD can reproduce results from MD simulations using empirical potentials is a necessary condition to future efforts to extend the method to a much wider range of systems for which empirical potentials may be difficult or impossible to obtain.

70 PLASMA PHYSICS AND FUSION TECHNOLOGY↗

Metastable Clusters and Competitive Solvation Tune Ion Pairing at Liquid Interfaces

The balance of hydrophobic and hydrophilic interactions underlies emergent phenomena in complex multicomponent chemical systems. Here, we show that a supposedly ‘non–interacting’ nonpolar phase can be used to competitively solvate amphiphilic molecules at an oil/aqueous interface. This solvation, as probed by surface specific nonlinear spectroscopy and simulations, results in a molecularly thin corrugated phase boundary featuring metastable assemblies that alter the hydrogen bonding networks of water and the apparent ‘hard/soft’ descriptors used to describe ionic interactions. We show that competitive solvation enhances amphiphile mobility, opening up otherwise energetically inaccessible complexes that transiently interact with aqueous phase ions. These transient species impact ensemble binding affinities and may represent the molecular agents responsible for aspects of ionic transport and function. In conclusion, the result of this work highlights how seemingly unrelated nonpolar interactions feedback onto aqueous phase chemical phenomena, providing a pathway to tune phase separation and self-assembly to access new reaction pathways using interfaces for a range of chemical and biological systems.

Anions↗

Direct Observation of Ultrafast Hydrogen Bond Strengthening in Liquid Water

Water is one of the most important, yet least understood, liquids in nature. Many anomalous properties of liquid water originate from its well-connected hydrogen bond network, including unusually efficient vibrational energy redistribution and relaxation. An accurate description of the ultrafast vibrational motion of water molecules is essential for understanding the nature of hydrogen bonds and many solution-phase chemical reactions. Most existing knowledge of vibrational relaxation in water is built upon ultrafast spectroscopy experiments. However, these experiments cannot directly resolve the motion of the atomic positions and require difficult translation of spectral dynamics into hydrogen bond dynamics. Here we measured the ultrafast structural response to the excitation of the OH stretching vibration in liquid water with femtosecond temporal and atomic spatial resolution using liquid ultrafast electron scattering. We observed a transient hydrogen bond contraction of roughly 0.04 Å on a timescale of 80 femtoseconds, followed by a thermalization on a timescale of ~1 picosecond. Molecular dynamics simulations reveal the need to treat the distribution of the shared proton in the hydrogen bond quantum mechanically to capture the structural dynamics on the femtosecond timescales. Our experiment and simulations unveiled the intermolecular character of the water vibration preceding the relaxation of the OH stretch.

36 MATERIALS SCIENCE↗

Epoxide Alcoholysis over M-BEA Zeolites: Effects of Alcohol Chain Length on Rates and Regioselectivities

The structures of nucleophilic reactants affect their coordination behavior among solvent molecules and kinetics of reactions with surface intermediates within the confines of fluidfilled pores of zeolites and other microporous materials. Consequently, rates and regioselectivities of diverse chemistries may depend sensitively on nucleophile identity in manners not observed for classic fluid phase reactions. Here, we examine the impact of varying the primary alcohol (ROH) chain length on the kinetics of 1,2-epoxybutane (C 4 H 8 O) ring-opening within Brønsted (Al-BEA) and Lewis acid (Zr-BEA) zeolites. Turnover rates increase by factors of ∼6 (Al-BEA) and 4-fold (Zr-BEA) between methanol and 1-hexanol, yet the reaction mechanisms remain comparable. Despite modest rate differences, apparent activation enthalpies calculated from rates and activities of solvated reactants decrease linearly by 12 (Al-BEA) to 33 kJ mol −1 (Zr- BEA) with increased proton affinity, which suggests bond formation energies for the nucleophile strongly influence rate increases. The molecular interpretation of these trends demonstrates, however, that the solvation of ring-opening transition states by zeolite pore structures and solvent molecules also governs rates. The impact of local solvating interactions appears most directly as changes in regioselectivities, which tend to enhance terminal alcohol formation with increasing ROH chain length. Regioselectivities largely do not vary with differences in fluid composition for a given ROH. The addition of H 2 O increases the number of hydrogen bonds among reactive species, and trends in regioselectivities imply that the decreased hydrogen bonding ability of longer chain ROH, and not the nucleophile strength or steric bulk, determines the regioselectivities of the resulting products. This work provides direct experimental evidence that nucleophilicity and hydrogen bonding influence reaction barriers and regioselectivities in zeolitecatalyzed epoxide ring-opening, offering pathways to better control reaction kinetics.

acidic zeolites↗

On the mechanism of intermolecular nitrogen-atom transfer from a lattice-isolated diruthenium nitride intermediate

Catalyst confinement within microporous media provides the opportunity to site isolate reactive intermediates, enforce intermolecular functionalization chemistry by co-localizing reactive intermediates and substrates in molecular-scale interstices, and harness non-covalent host–guest interactions to achieve selectivities that are complementary to those accessible in solution. As part of an ongoing program to develop synthetically useful nitrogen-atom transfer (NAT) catalysts, we have demonstrated intermolecular benzylic amination of toluene at a Ru 2 nitride intermediate confined within the interstices of a Ru2-based metal–organic framework (MOF), Ru 3 (btc) 2 X 3 (btc = 1,3,5-benzenetricarboxylate, i.e., Ru-HKUST-1 for X = Cl). Nitride confinement within the extended MOF lattice enabled intermolecular C–H functionalization of benzylic C–H bonds in preference to nitride dimerization, which was encountered with soluble molecular analogues. Detailed study of the kinetic isotope effects (KIEs, i.e., k H /k D ) of C–H amination, assayed both as intramolecular effects using partially labeled toluene and as intermolecular effects using a mixture of per-labeled and unlabeled toluene, provided evidence for restricted substrate mobility on the time scale of interstitial NAT. Analysis of these KIEs as a function of material mesoporosity provided approximate experimental values for functionalization in the absence of mass transport barriers. Here, we disclose a combined experimental and computational investigation of the mechanism of NAT from a Ru 2 nitride to the C–H bond of toluene. Computed kinetic isotope effects for a H-atom abstraction (HAA)/radical rebound (RR) mechanism are in good agreement with experimental data obtained for C–H amination at the rapid diffusion limit. These results provide the first detailed analysis of the mechanism of intermolecular NAT to a C–H bond, bolster the use of KIEs as a probe of confinement effects on NAT within MOF lattices, and provide mechanistic insights unavailable by experiment because rate-determining mass transport obscured the underlying chemical kinetics.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Hydrogen Bonding Inside Anionic Polymeric Brush Layer: Machine Learning-Driven Exploration of the Relative Roles of the Polymer Steric Effect, Charging, and Type of Screening Counterions

This paper employs a combination of all-atom molecular dynamics (MD) simulations and unsupervised machine learning (ML) for studying the water-water hydrogen bonds (HBs) inside the anionic poly-acrylic acid (PAA) brushes modeled using all-atom MD simulations. PAA brush layer with different charge fraction (f), namely f=0, f=0.25, and f=1, is considered. Water-water interactions, both inside and outside the brush layer, are represented through distinct clusters of tupules of variables representing distances associated with the interacting water molecules. While clusters representing the HBs are present for water inside and outside the brushes, several clusters representing the long-range water-water interactions are missing for the water molecules inside the highly charged (f=1) PAA brushes. More importantly, inside highly charged brushes, the edge of the clusters representing the water-water HBs is progressively shortened, as compared to that in the bulk. Both these results stem from the presence of the PAA brushes imparting the steric effect and the charge effect, or the effect associated with enhanced interactions of water molecules with PE charges and counterions, thereby disrupting the water connectivity. This water-charged-species interaction also increases the water-water HB angle, i.e., makes the water-water HBs less stable inside the highly charged PAA brush layer. The narrowing of the clusters representing the HBs and the alteration of the angle characterizing the HBs confirm that the conditions defining the water-water HBs change inside the PAA brush layer as a function of the charges on the PAA brush layer. Furthermore, we show that the use of the generic definition of HBs, as compared to using our simulation-motivated modified definition of water-water HBs, overpredict the number of water-water HBs inside the PAA brush layer. Finally, we employ this all-atom-MD-ML framework to quantify the effect of other types of screening counterions (Li + , Ca 2+ , and Y 3+ ions) in determining the water-water interactions and water-water HB properties inside the PAA brush layer. Furthermore, the findings of the present study, confirming the weakening of water-water HBs inside the PAA brush layer, points to the possibility that the water molecules will be more available for hydrating the brush layer and counterions, thereby leading to a more pronounced wetting of the PAA brush layer.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Low-Temperature Non-Oxidative Coupling of Methane on Atomically Dispersed Titanium–Aluminum–Boron Nanopowder

Nonoxidative coupling of methane represents a long-standing challenge in heterogeneous catalysis, as it requires activation of the carbon–hydrogen (C–H) bond, controlled carbon–carbon (C–C) bond formation, and effective hydrogen management without relying on oxidants. Here, we report a low-temperature C–H activation and nonoxidative C–C coupling of methane over atomically dispersed titanium–aluminum–boron nanopowder (Ti–Al–B NP) utilizing a catalytic microreactor coupled to synchrotron single-photon photoionization reflectron time-of-flight mass spectrometry. The soft-ionization, in situ probing method detects the nascent reaction products and radical intermediates under operando conditions, including methyl radical, C2 hydrocarbons, and molecular hydrogen. Methane activation is initiated at 800 K, approximately 700 K below the gas-phase decomposition threshold, leading predominantly to ethylene formation with selectivity reaching up to 78% among the C–C coupled products. Electronic structure calculations on model Ti–Al–B clusters elucidate a cooperative catalytic mechanism in which titanium enables methane adsorption and C–H activation, boron acts as a reversible hydrogen reservoir, and aluminum stabilizes methylene intermediates, thereby facilitating selective C–C coupling and dehydrogenation. These findings establish a distinct catalyst architecture for nonoxidative methane coupling based on earth abundant elements alternative to expensive platinum and other noble metal-containing conventional catalysts and provide molecular-level design principles for controlling dehydrogenation and subsequent C–C bond formation in challenging light alkane conversions.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Polyphenols Weaken Pea Protein Gel by Formation of Large Aggregates with Diminished Noncovalent Interactions

Polyphenols are well-known native cross-linkers and gel strengthening agents for many animal proteins. However, their role in modifying plant protein gels remains unclear. In this study, multiple techniques were applied to unravel the influence of green tea polyphenols (GTP) on pea protein gels and the underlying mechanisms. We found that the elasticity and viscosity of pea protein gels decreased with increased GTP. The protein backbone became less rigid when GTP was present based on shortened T 1ρ H in relaxation solid-state NMR measurements. Electron microscopy and small-angle X-ray scattering showed that gels weakened by GTP possessed disrupted networks with the presence of large protein aggregates. Solvent extraction and molecular dynamic simulation revealed a reduction in hydrophobic interactions and hydrogen bonds among proteins in gels containing GTP. The current findings may be applicable to other plant proteins for greater control of gel structures in the presence of polyphenols, expanding their utilization in food and biomedical applications.

59 BASIC BIOLOGICAL SCIENCES↗

Proton switching molecular magnetoelectricity

Abstract The convergence of proton conduction and multiferroics is generating a compelling opportunity to achieve strong magnetoelectric coupling and magneto-ionics, offering a versatile platform to realize molecular magnetoelectrics. Here we describe machine learning coupled with additive manufacturing to accelerate the design strategy for hydrogen-bonded multiferroic macromolecules accompanied by strong proton dependence of magnetic properties. The proton switching magnetoelectricity occurs in three-dimensional molecular heterogeneous solids. It consists of a molecular magnet network as proton reservoir to modulate ferroelectric polarization, while molecular ferroelectrics charging proton transfer to reversibly manipulate magnetism. The magnetoelectric coupling induces a reversible 29% magnetization control at ferroelectric phase transition with a broad thermal hysteresis width of 160 K (192 K to 352 K), while a room-temperature reversible magnetic modulation is realized at a low electric field stimulus of 1 kV cm −1 . The findings of electrostatic proton transfer provide a pathway of proton mediated magnetization control in hierarchical molecular multiferroics.

36 MATERIALS SCIENCE↗

Electrokinetic comparison of CaF 2 and AgCl from a MDS perspective

CaF 2 has limited electrokinetic sensitivity to fluoride ions in solution and the positive CaF 2 surface charge is not reversed at high fluoride ion concentration. Similar insensitivity of surface charge to high fluoride ion concentration has been observed for other alkali and alkaline earth fluoride salts. On the contrary, chloride ions act as potential determining ions for AgCl and reverse the surface charge, as expected. FTIR-IRS results indicate that the AgCl/water interface has a water structure-breaking tendency, whereas the CaF 2 /water interface has a structure-making tendency. Here, it is speculated that the strong hydrogen bonding between fluoride ions and water prevents the accommodation of excess fluoride ions at surface lattice sites of fluorite, and therefore explains the low sensitivity of the fluorite surface charge sign and magnitude to fluoride ion concentration. However, this speculation has not been examined at the molecular level and is evaluated by molecular dynamics simulations (MDS) in the research presented in this paper. Higher hydrogen bond density at the CaF 2 mineral/water interface confirms that the water structure has stronger hydrogen bonding at both the CaF 2 mineral surface and with the F - ion in solution. In this way, the interaction of the F - ion with the CaF 2 surface is inhibited.

36 MATERIALS SCIENCE↗

Effects of pore size on water dynamics in mesoporous silica

Water confined in mesoporous silica plays a central role in its many uses ranging from gas sorption to nanoconfined chemical reactions. Here in this paper, the influence of pore diameter (2.5–5.4 nm) on water hydrogen bond (H-bond) dynamics in MCM41 and SBA15 mesoporous silicas is investigated using femtosecond infrared vibrational spectroscopy and molecular dynamics simulations on selenocyanate (SeCN-) anions dissolved in the pores. As shown recently, SeCN- spectral diffusion is a reliable probe of surrounding water H-bond structural motions. Additionally, the long CN stretch vibrational lifetime facilitates measurement of the full range of confined dynamics, which are much slower than in bulk water. The simulations shed light on quantitative details that are inaccessible from the spatially averaged observables. The dependence of SeCN- orientational relaxation and that of spectral diffusion on the distance from the silica interface are quantitatively described with an exponential decay and a smoothed step-function, respectively. The distance-dependence of both quantities is found to be independent of the diameter of the pores, and the spatial distribution of SeCN- is markedly non-uniform, reaching a maximum between the interface and the pore center. The results indicate that the commonly invoked two-state, or core–shell, model is a more appropriate description of spectral diffusion. Using these insights, we model the full time-dependence of the measured dynamics for all pore sizes and extract the “core” and “shell” dynamical correlation functions and SeCN- spatial probability distributions. The results are critically compared to those for water confined in reverse micelles.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Breakthrough Conductivity Enhancement in Deep Eutectic Solvents via Grotthuss–Type Proton Transport

There is an increasing demand for the development of ion-conducting electrolytes for energy storage systems. Much attention is directed toward deep eutectic solvents as potential candidates. In the search for highly conductive systems, the possibility of designing deep eutectic solvents with Grotthuss-type proton transport is widely overlooked. Herein, ethaline, a mixture of choline chloride and ethylene glycol is used in a 1:2 molar ratio, to induce a significant conductivity increase with the addition of water and sulfuric acid (H 2 SO 4 ). The achieved breakthrough conductivity is analyzed experimentally and simulated with ab initio molecular dynamics (AIMD). At sufficient water content, an H-bonding network is formed that leads to a significant breakthrough conductivity based on H 2 SO 4 -derived proton transfer following the long-established Grotthuss proton transport mechanism. This result is substantiated by the positive deviation from the ideal KCl line in the Walden plot. Specifically, the data series positioned above the reference line indicates a Grotthuss mechanism in action. The AIMD simulations demonstrate proton transfer between water and ethylene glycol, supported by simulation frames captured at various times.

36 MATERIALS SCIENCE↗

Electricity-driven recycling of ester plastics using one-electron electro-organocatalysis

Here, we report the catalytic use of electrochemically generated one-electron reducing agents to produce ester anion radicals that can decompose to acids and alcohols in the presence of oxygen. Through this approach, we demonstrate that molecular analogs of polyethylene terephthalate (PET) can be deconstructed into their molecular components. We additionally show efficient reductive scission of ester bonds in PET plastic using catalytically regenerated reducing agents based on benzimidazolium cations.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Molecular packing modulation enabling optimized blend morphology and efficient all small molecule organic solar cells

The molecular planarity of a small molecule donor is one of the key factors affecting its molecular packing behavior, the morphology of the related active blend and thus the photovoltaic properties of all small molecule organic solar cells (ASM-OSCs). Here, a series of new benzodithiophene (BDT)-based A-π-D-π-A type small molecules were developed, namely SD1, SD2 and SD3, by combining the chemical modification of side chain (sulfuration), π-bridge (alkoxy groups introducing) and end group (different type or different alkyl chain). The sulfuration of the BDT side chains and introducing alkoxy group to the π-bridge could induce intermolecular S … S and intramolecular S … O non-covalent interactions for higher planarity of these small molecules. The rhodanine and cyanoacetate end groups showed less effect on the optical and electronic properties but significantly affected the molecular packing behavior and blend morphology. From SD1:Y6-T to SD2:Y6-T and SD3:Y6-T, the face-to-face packing was gradually reduced, while the face-to-edge packing was increased, which resulted in lowered exciton dissociation efficiency, further decreased the device performance. SD1:Y6-T blend exhibited more favorable face-to-face packing and ideal morphology for efficient charge dissociation and transport, contributing to a champion PCE of 10.12%. This work provided a deep insight of the donor and acceptor packing behavior effect on the photovoltaic property by molecular design.

36 MATERIALS SCIENCE↗

Explicitly antisymmetrized neural network layers for variational Monte Carlo simulation

The combination of neural networks and quantum Monte Carlo methods has arisen as a promising path forward for highly accurate electronic structure calculations. Previous proposals have combined equivariant neural network layers with a final antisymmetric layer in order to satisfy the antisymmetry requirements of the electronic wavefunction. However, to date it is unclear if one can represent antisymmetric functions of physical interest, and it is difficult to precisely measure the expressiveness of the antisymmetric layer. Here, this work attempts to address this problem by introducing explicitly antisymmetrized universal neural network layers. This approach has a computational cost which increases factorially with respect to the system size, but we are nonetheless able to apply it to small systems to better understand how the structure of the antisymmetric layer affects its performance. We first introduce a generic antisymmetric (GA) neural network layer, which we use to replace the entire antisymmetric layer of the highly accurate ansatz known as the FermiNet. We demonstrate that the resulting FermiNet-GA architecture can yield effectively the exact ground state energy for small atoms and molecules. We then consider a factorized antisymmetric (FA) layer which more directly generalizes the FermiNet by replacing the products of determinants with products of antisymmetrized neural networks. We find, interestingly, that the resulting FermiNet-FA architecture does not significantly outperform the FermiNet. This strongly suggests that the sum of products of antisymmetries is a key limiting aspect of the FermiNet architecture. To explore this further, we investigate a slight modification of the FermiNet, called the full determinant mode, which replaces each product of determinants with a single combined determinant. We find that the full single-determinant FermiNet closes a large part of the gap between the standard single-determinant FermiNet and FermiNet-GA on small atomic and molecular problems. Surprisingly, on the nitrogen molecule at a dissociating bond length of 4.0 Bohr, the full single-determinant FermiNet can outperform the largest standard FermiNet calculation with 64 determinants.

97 MATHEMATICS AND COMPUTING↗