Diffuse Functions Research Articles

The Effective Fragment Molecular Orbital Method: Achieving High Scalability and Accuracy for Large Systems.

The effective fragment molecular orbital (EFMO) method has been developed to predict the total energy of a very large molecular system accurately (with respect to the underlying quantum mechanical method) and efficiently by taking advantage of the locality of strong chemical interactions and employing a two-level hierarchical parallelism. The accuracy of the EFMO method is partly attributed to the accurate and robust intermolecular interaction prediction between distant fragments, in particular, the many-body polarization and dispersion effects, which require the generation of static and dynamic polarizability tensors by solving the coupled perturbed Hartree-Fock (CPHF) and time-dependent HF (TDHF) equations, respectively. Solving the CPHF and TDHF equations is the main EFMO computational bottleneck due to the inefficient (serial) and I/O-intensive implementation of the CPHF and TDHF solvers. In this work, the efficiency and scalability of the EFMO method are significantly improved with a new CPU memory-based implementation for solving the CPHF and TDHF equations that are parallelized by either message passing interface (MPI) or hybrid MPI/OpenMP. The accuracy of the EFMO method is demonstrated for both covalently bonded systems and noncovalently bound molecular clusters by systematically examining the effects of basis sets and a key distance-related cutoff parameter, Rcut. Rcut determines whether a fragment pair (dimer) is treated by the chosen ab initio method or calculated using the effective fragment potential (EFP) method (separated dimers). Decreasing the value of Rcut increases the number of separated (EFP) dimers, thereby decreasing the computational effort. It is demonstrated that excellent accuracy (<1 kcal/mol error per fragment) can be achieved when using a sufficiently large basis set with diffuse functions coupled with a small Rcut value. With the new parallel implementation, the total EFMO wall time is substantially reduced, especially with a high number of MPI ranks. Given a sufficient workload, nearly ideal strong scaling is achieved for the CPHF and TDHF parts of the calculation. For the first time, EFMO calculations with the inclusion of long-range polarization and dispersion interactions on a hydrated mesoporous silica nanoparticle with explicit water solvent molecules (more than 15k atoms) are achieved on a massively parallel supercomputer using nearly 1000 physical nodes. In addition, EFMO calculations on the carbinolamine formation step of an amine-catalyzed aldol reaction at the nanoscale with explicit solvent effects are presented.

Insights into pyrolysis of ginger via TG-FTIR and Py-GC/MS analyses: Thermochemical behaviors, kinetics, evolved gas, and products

One of the key leverages for lessening the heavy reliance on fossil fuels is the conversion of non-food biomass into bioenergy and high value-added products. This study aimed to quantify the bioenergetic, emission, and biochar performances of ginger (Zb) pyrolysis. The main pyrolysis stage of Zb occurred in the range of 127–540 °C, releasing gaseous products, primarily CO2, in significant quantities between 200–600 °C. The dominant pyrolysis products were CO functional groups, accounting for 52.18–62.68% of the total. As the temperature rose, the primary pyrolysis products transitioned from ketones to benzene and its derivatives. Through the application of three model-free and three model-fitting methods, the most suitable mechanism identified for the main pyrolysis stage (0.2 < conversion degree < 0.7) was the three-dimensional diffusion (spherically symmetric) function, serving as an internal diffusion mechanism. Results of this study provide impactful and actionable insights into control over the generation of bioenergy potential, gas emissions, and value-added products via the Zb pyrolysis.

BTS-ADCNN: brain tumor segmentation based on rapid anisotropic diffusion function combined with convolutional neural network using MR images

BTS-ADCNN: brain tumor segmentation based on rapid anisotropic diffusion function combined with convolutional neural network using MR images

Stochastic Generalized Porous Media Equations Over $$\sigma $$-finite Measure Spaces with Non-continuous Diffusivity Function

Stochastic Generalized Porous Media Equations Over $$\sigma $$-finite Measure Spaces with Non-continuous Diffusivity Function

Spectroscopic properties, crystal structure, Hirshfeld surface analysis and DFT study of a new Cu(II) complex based on quinazolinone O,N,O-donor ligand

A quinazolinone-based Schiff base ligand 3-[(2‑hydroxy-5-methoxybenzylidene)amino]-2-(2‑hydroxy-5-methoxyphenyl)-2,3-dihydroquinazolin-4-one (L1) and its new mononuclear copper(II) complex [Cu(L1)Cl(H2O)] (1) were synthesised and fully characterised by various spectroscopic techniques (NMR, FTIR, UV–Vis) and single-crystal X-ray diffraction study. The aspherical model of the crystal structure of the ligand L1 as well as of the copper(II) complex 1 was refined by the Hirshfeld Atom Refinement method. The crystal structure of the copper(II) complex shows the existence of a substitution disorder at the position of the water molecule, which represents two different complex molecules [Cu(L1)Cl(H2O)] (1a) and [Cu(L1)Cl] (1b) with different coordination polyhedra around the copper atom. The majority of the mononuclear complex [Cu(L1)Cl(H2O)] (1a) in the crystal structure contains a coordinated water molecule, but the minority in the crystal structure contains a mononuclear complex [Cu(L1)Cl] (1b) and a water molecule is outside the coordination sphere around the copper atom. The crystal structure of complex 1 showed a penta-coordinated (1a) or tetra-coordinated (1b) Cu atom in the shape of a tetragonal pyramid (1a) or square planar (1b) formed by a chloride atom in the equatorial plane, and a Schiff base bound as an O,N,O-tridentate ligand, and an additional water molecule in the axial position (only 1a). A detailed analysis of the intermolecular interactions was investigated using three-dimensional 3D Hirshfeld surfaces and their associated two-dimensional 2D fingerprint plots. Hirshfeld surface analysis was performed for both crystal structures. Furthermore, theoretical DFT analysis has been performed in order to interpret the experimental data. In order to obtain high quality DFT data, we present here a new basis set B1MH, which is an extension of the LanL2DZ basis with incorporated polarisation and diffusion functions for heavy atoms (C, N, O, Cl and Cu) and added ECPs for Cl and Cu atoms. The presented B1MH basis set allowed us to obtain better theoretical results than those previously published.

Development of a universal method for vibrational analysis of the terminal alkyne C≡C stretch.

The terminal alkyne C≡C stretch has a large Raman scattering cross section in the "silent" region for biomolecules. This has led to many Raman tag and probe studies using this moiety to study biomolecular systems. A computational investigation of these systems is vital to aid in the interpretation of these results. In this work, we develop a method for computing terminal alkyne vibrational frequencies and isotropic transition polarizabilities that can easily and accurately be applied to any terminal alkyne molecule. We apply the discrete variable representation method to a localized version of the C≡C stretch normal mode. The errors of (1) vibrational localization to the terminal alkyne moiety, (2) anharmonic normal mode isolation, and (3) discretization of the Born-Oppenheimer potential energy surface are quantified and found to be generally small and cancel each other. This results in a method with low error compared to other anharmonic vibrational methods like second-order vibrational perturbation theory and to experiments. Several density functionals are tested using the method, and TPSS-D3, an inexpensive nonempirical density functional with dispersion corrections, is found to perform surprisingly well. Diffuse basis functions are found to be important for the accuracy of computed frequencies. Finally, the computation of vibrational properties like isotropic transition polarizabilities and the universality of the localized normal mode for terminal alkynes are demonstrated.

A New Algorithm Framework for the Influence Maximization Problem Using Graph Clustering

Given a social network modelled by a graph, the goal of the influence maximization problem is to find k vertices that maximize the number of active vertices through a process of diffusion. For this diffusion, the linear threshold model is considered. A new algorithm, called ClusterGreedy, is proposed to solve the influence maximization problem. The ClusterGreedy algorithm creates a partition of the original set of nodes into small subsets (the clusters), applies the SimpleGreedy algorithm to the subgraphs induced by each subset of nodes, and obtains the seed set from a combination of the seed set of each cluster by solving an integer linear program. This algorithm is further improved by exploring the submodularity property of the diffusion function. Experimental results show that the ClusterGreedy algorithm provides, on average, higher influence spread and lower running times than the SimpleGreedy algorithm on Watts–Strogatz random graphs.

A fast computational technique based on a novel tangent sigmoid anisotropic diffusion function for image-denoising

A fast computational technique based on a novel tangent sigmoid anisotropic diffusion function for image-denoising

Diffusion Monte Carlo method for barrier heights of multiple proton exchanges and complexation energies in small water, ammonia, and hydrogen fluoride clusters.

Proton exchange reactions are of key importance in many processes in water. However, it is nontrivial to achieve reliable barrier heights for multiple proton exchanges and complexation energies in hydrogen-bonded systems theoretically. Performance of the fixed-node diffusion quantum Monte Carlo (FN-DMC) with the single-Slater-Jastrow trial wavefunction on total energies, barrier heights of multiple proton exchanges, and complexation energies of small water, ammonia, and hydrogen fluoride clusters is investigated in this study. Effects of basis sets and those of locality approximation (LA), T-move approximation (T-move), and determinant localization approximation (DLA) schemes in dealing with the nonlocal part of pseudopotentials on FN-DMC results are evaluated. According to our results, diffuse basis functions are important in achieving reliable barrier heights and complexation energies with FN-DMC, although the cardinal number of the basis set is more important than diffuse basis functions on total energies of these systems. Our results also show that the time step bias with DLA and LA is smaller than T-move; however, the time step bias of DMC energies with respect to time steps using the T-move is roughly linear up to 0.06a.u., while this is not the case with LA and DLA. Barrier heights and complexation energies with FN-DMC using these three schemes are always within chemical accuracy. Taking into account the fact that T-move and DLA are typically more stable than LA, FN-DMC calculations with the T-move or DLA scheme and basis sets containing diffuse basis functions are suggested for barrier heights of multiple proton exchanges and complexation energies of hydrogen-bonded clusters.

Conformational and Chiroptical Properties of Salicylamide-Based Peptidomimetics

Optical rotation (OR), the most frequently used chiroptical method, is used for the characterization of newly synthesized or isolated compounds. Computational predictions of OR are, however, mainly used for the determination of the absolute configurations of chiral compounds, but they may also be used for the verification of conformational analysis results if the experimental values are known. Our computational study deals with the conformational analysis of flexible salicylamide-based peptidomimetics, starting with a conformation search, then a low-level ab initio preoptimization of the hundreds of conformations found, and, finally, a higher-level DFT optimization. For the resulting minima structures, Boltzmann populations were calculated, followed by OR calculations for all the populated conformers using the DFT method with various basis sets with diffuse functions. Weighted averages of the ORs were compared with experimental values, and the agreement, which ranged from excellent to moderate for various compounds, served as a verification of the conformational analysis results.

Novel complex compounds of nickel with 3-(1-phenyl-2,3-dimethyl-pyrazolone-5)azopentadione-2,4: synthesis, NBO analysis, reactivity descriptors and in silico and in vitro anti-cancer and bioactivity studies

A synthesized azo compound based on 4-amino antipyrine and its complexes with Ni(II) in solution and solid phase is reported. The structures of these compounds have been testified by IR and NMR spectroscopy. The combined experimental and theoretical approach was used. To study the structure and properties of the synthesized compound, as well as its possible complex formation with the Ni(II), ab initio quantum-chemical calculations were carried out using the Hartree-Fock (HF) method with the 6-31 G basis set and the electron density functional theory (DFT) method with hybrid three-parameter potential B3LYP and extended basis set 6-311++G(d,p) taking into account polarization and diffuse functions for all atoms. The geometric, energy, and electronic parameters were calculated and analyzed. The HOMO-LUMO energy gap has been calculated to determine chemical activity. Both complexes had effective inhibition against butyrylcholinesterase and acetylcholinesterase. IC50 values were found as 19.43 and 27.08 µM for AChE, 2.37 and 7.40 µM for BChE, respectively. For the anticancer outcome, high doses of compound E1 inhibited viability by about 40–45%, while this rate was around 65–70% for compound E2 at the same doses. Anticholinesterase and anticancer potential of compounds E1 and E2 also evaluated by in silico techniques. Both compounds show strong binding to VEGFR1, with E2 exhibiting superior inhibitory activity in hAChE and hBChE through shorter and stronger interactions. MD simulations suggest that E2 forms more stable complexes with hAChE and hBChE compared to E1, making it a promising candidate for further exploration in anticancer and anticholinesterase therapies. Communicated by Ramaswamy H. Sarma

Theoretical Investigation on excited dipole bound states of alkali-containing diatomic anions

Abstract Information about electronic excited states of molecular anions plays an important role in investigating the electron attachment and detachment processes. Here we present a high-level theoretical study on the electronic structures of twelve alkali-metal-containing diatomic anions MX- (MX = LiH, LiF, LiCl, NaF, NaCl, NaBr, RbCl, KCl, KBr, RbI, KI, and CsI). The equation-of-motion electron-attachment coupled-cluster singles and doubles (EOM-EA-CCSD) method is carried out to calculate the electron binding energies (EBEs) of 10 electronic excited states of each of the twelve molecule anions. With addition of different s-/p-/d- diffusion functions in the basis set, we have identified possible excited dipole bound states (DBSs) of each anion. With the investigation of EBEs on the twelve MXs with dipole moment (DM) up to 12.1 D, we evaluate the dependence of the number of anionic excited DBSs on molecular DM. The results indicate that, there exists at least two or three DBSs of anions with the molecular DM larger than 7 D and a molecule with DM &gt; 10 D can sustain a π-DBS of the anion. Our study would shed some implications on the excited DBSs electronic states of alkali-metal-containing diatomic molecules.

Improved target detection method for space-based optoelectronic systems

The detection of faint and small targets by space-based surveillance systems is difficult owing to the long distances, low energies, high speeds, high false alarm rates, and low algorithmic efficiencies involved in the process. To improve space object detection and help prevent collisions with critical facilities such as satellites, this study proposes an improved method for the detection of faint and small space-based targets. The proposed method consists of two components: star atlas preprocessing and space-based target detection. The star atlas preprocessing step applies multi-exposure image pyramidal weighted fusion to the original image containing the faint and small space-based target. After obtaining the image pyramidal weighted fusion result atlas, the algorithm employs threshold segmentation to improve the overall image clarity, highlight image details, and provide additional information for target detection. The detection of targets partially relies on the local symmetry of the image. Accordingly, a diffusion function describing the local symmetry is established to precisely locate stars by measuring the symmetry factor in a small area surrounding each pixel in the star atlas. This effectively removes the background stars while retaining high-definition and high-contrast images. The efficacy of the algorithm is validated using simulated datasets consisting of space-based and real images. The results demonstrate that the proposed technique improves the applicability of the multistage hypothesis testing (MHT) method in the context of a complex space environment, thus improving the performance of the space-based electro-optical detection system to better catalogue, identify, and track space targets.

RAZOR A Lightweight Block Cipher for Security in IoT

Rapid technological developments prompted a need to do everything from anywhere and that is growing due to modern lifestyle. The Internet of Things (IoT) technology is helping to provide the solutions by inter-connecting the smart devices. Lightweight block ciphers are deployed to enable the security in such devices. In this paper, a new lightweight block cipher RAZOR is proposed that is based on a hybrid design technique. The round function of RAZOR is designed by mixing the Feistel and substitution permutation network techniques. The rotation and XOR based diffusion function is applied on 32-bit input with 8 branches and branch number 7 to optimize the security. The strength of RAZOR is proved against differential, linear, and impossible differential attacks. The number of active S-boxes in any 5-round differential characteristic of RAZOR is 21 in comparison to the 10, 6, 4, 7, and 6 for PRESENT, Rectangle, LBlock, GIFT, and SCENERY respectively. RAZOR provides better security than the existing lightweight designs. The average throughput of 1.47 mega bytes per second to encrypt the large files makes it a better choice for software oriented IoT applications.

A failure of double hybrid density functional method: Out‐of‐plane bending vibrations for the carbon‐carbon double‐bonded molecules

AbstractIn this work, we report anomalous descriptions of bending modes of the carbon–carbon double bonded molecules with double hybrid density functional theories. The harmonic frequencies of the out‐of‐plane modes are found to be extremely low, and the anharmonicities are found to be very large. The unphysical large anharmonities of these modes increase significantly with a basis set having diffuse function. Increasing basis set size does not necessarily reduce or eliminate the problem. We observe that the problem with the double hybrid functional is in‐built due to the presence of the part of the second‐order perturbation terms in the functional.

Utilizing a pseudo-random Linear Congruential Generator (LCG) S-Box for encoding color images through genetic crossover

This article introduces a novel algorithm crafted for encrypting color images. The algorithm leverages chaotic principles and harnesses fresh substitution tables derived from independent linear congruence generators. These generators are dynamically sized based on pseudo-random vectors used in this technology. The proposed method initiates with the original image, vectorization, employing selected chaotic maps. The primary goal revolves around implementing a genetic operator tailored for image encryption, who integrates an enhanced Vigenère technique, incorporating novel confusion and diffusion functions derived from the previously established substitution tables. To gauge the effectiveness of this approach, numerous color images of varying dimensions and formats underwent testing using our algorithm. The yielded outcomes are both promising and gratifying, furnishing heightened security against recognized attacks.

On the structure of weak solutions of the Riemann problem for a degenerate nonlinear diffusion equation

An explicit form of weak solutions to the Riemann problem for a degenerate nonlinear parabolic equation with a piecewise constant diffusion coe cient is found. It is shown that the lines of phase transitions (free boundaries) correspond to the minimum point of some strictly convex and coercive function of a nite number of variables. A similar result is true for Stefan’s problem. In the limit, when the number of phases tends to in nity, there arises a variational formulation of self-similar solutions to the equation with an arbitrary nonnegative diffusion function.

Insight into the Binding of Argon to Cyclic Water Clusters from Symmetry-Adapted Perturbation Theory.

This work systematically examines the interactions between a single argon atom and the edges and faces of cyclic H2O clusters containing three-five water molecules (Ar(H2O)n=3-5). Full geometry optimizations and subsequent harmonic vibrational frequency computations were performed using MP2 with a triple-ζ correlation consistent basis set augmented with diffuse functions on the heavy atoms (cc-pVTZ for H and aug-cc-pVTZ for O and Ar; denoted as haTZ). Optimized structures and harmonic vibrational frequencies were also obtained with the two-body-many-body (2b:Mb) and three-body-many-body (3b:Mb) techniques; here, high-level CCSD(T) computations capture up through the two-body or three-body contributions from the many-body expansion, respectively, while less demanding MP2 computations recover all higher-order contributions. Five unique stationary points have been identified in which Ar binds to the cyclic water trimer, along with four for (H2O)4 and three for (H2O)5. To the best of our knowledge, eleven of these twelve structures have been characterized here for the first time. Ar consistently binds more strongly to the faces than the edges of the cyclic (H2O)n clusters, by as much as a factor of two. The 3b:Mb electronic energies computed with the haTZ basis set indicate that Ar binds to the faces of the water clusters by at least 3 kJ mol-1 and by nearly 6 kJ mol-1 for one Ar(H2O)5 complex. An analysis of the interaction energies for the different binding motifs based on symmetry-adapted perturbation theory (SAPT) indicates that dispersion interactions are primarily responsible for the observed trends. The binding of a single Ar atom to a face of these cyclic water clusters can induce perturbations to the harmonic vibrational frequencies on the order of 5 cm-1 for some hydrogen-bonded OH stretching frequencies.

Fisher-Shannon Investigation of the Effect of Nonlinearity of Discrete Langevin Model on Behavior of Extremes in Generated Time Series.

Diverse forms of nonlinearity within stochastic equations give rise to varying dynamics in processes, which may influence the behavior of extreme values. This study focuses on two nonlinear models of the discrete Langevin equation: one with a fixed diffusion function (M1) and the other with a fixed marginal distribution (M2), both characterized by a nonlinearity parameter. Extremes are defined according to the run theory with thresholds based on percentiles. The behavior of inter-extreme times and run lengths is examined by employing Fisher's Information Measure and the Shannon Entropy. Our findings reveal a clear relationship between the entropic and informational measures and the nonlinearity of model M1-these measures decrease as the nonlinearity parameter increases. Similar relationships are evident for the M2 model, albeit to a lesser extent, even though the background data's marginal distribution remains unaffected by this parameter. As thresholds increase, both the values of Fisher's Information Measure and the Shannon Entropy also increase.

Improving the bioactive content in honeydew melon by impregnation with Hibiscus extract/sucrose solutions: A coupled mass transfer analysis

This study investigated the bioactive content enrichment of honeydew melon cuts (hemispheres) immersed into Hibiscus extract/sucrose solutions (HESS). A face-centered design (FCD) was initially conducted to explore the effect of time (30–210 min), solution concentration (20–60°Bx) and temperature (40–60 °C) on water loss (WL), solids gain (SG), as well as in the increase of anthocyanins (ANT), phenolics (PHE), and antioxidant capacity (AXC) of melon. WL and SG were also investigated with pure sucrose syrups (SS) for comparison purposes. Processing conditions were further optimized by a Pareto approach to maximize both WL and bioactive content enrichment with minimal SG. Then, impregnation kinetics, conducted around the optimal experimental conditions, were analyzed with a 2D diffusive model, considering the anisotropic shrinkage of melon and solved under four complexity levels to examine coupled mass transfer (including constant diffusivities, main plus cross diffusion terms or nonlinear diffusivity functions of local water content). HESS favored a higher WL and lower SG than SS during FCD. The optimal condition occurred at 30 min, 20°Bx and about 50 °C, where melon gained ANT not originally present in it, and PHE and AXC increased by factors of 4.5 and 6.1 in comparison with untreated fruit, respectively. No evidence of significant coupling among WL, SG and bioactive transfer was found (p>0.05), with diffusivities for ANT, PHE, AXC, water and solids ranging from 3.26 to 3.45, 12.8–14.4, 1.24–5.19, 0.82–1.36, and 1.19–4.26 (×10−10) m2/s, respectively.