Theoretical Computational Methods Research Articles

Enhancing risk and crisis communication with computational methods: A systematic literature review.

Recent developments in risk and crisis communication (RCC) research combine social science theory and data science tools to construct effective risk messages efficiently. However, current systematic literature reviews (SLRs) on RCC primarily focus on computationally assessing message efficacy as opposed to message efficiency. We conduct an SLR to highlight any current computational methods that improve message construction efficacy and efficiency. We found that most RCC research focuses on using theoretical frameworks and computational methods to analyze or classify message elements that improve efficacy. For improving message efficiency, computational and manual methods are only used in message classification. Specifying the computational methods used in message construction is sparse. We recommend that future RCC research apply computational methods toward improving efficacy and efficiency in message construction. By improving message construction efficacy and efficiency, RCC messaging would quickly warn and better inform affected communities impacted by current hazards. Such messaging has the potential to save as many lives as possible.

Optical materials enhancing the chemical reactivity characteristics of N-benzyloxycarbonyl-L-phenylalanine: Spectroscopic, electronic properties, natural bond orbital, stability, electron-hole, Topology and molecular docking analyses

In the field of organic chemistry, the exploration of heterocyclic compounds is considered as vital, with roots in medicinal chemistry and the synthesis of organic composites. The optimized structural configuration with the geometrical values was obtained and related to the experimental data. The theoretical computational methods were carried out using a versatile basis set, B3LYP/6–311++G(d,p). The spectroscopic insights of N-Benzyloxycarbonyl-l-Phenylalanine (NBCLP) were performed, and the simulated assigned vibrational wavenumbers (PED contributions) were compared with the experimental information. Further, employing the optimized structure of FMO's molecular orbitals, energy parameters were attained for the various solvents. The detailed theoretical interpretations were assessed on the UV–Vis absorption spectra (TD-DFT/M062X) for different solvents, and their respective values were related to the experimental value. The electronic properties of the FMO's orbitals match the experimental UV–Vis absorption energy value. The reactivity regions (nucleophilic and electrophilic) were obtained using the MEP map, and the corresponding lone pair/donor-acceptor transitions along with the higher stabilization energies were discussed using NBO analysis. Moreover, using the Multiwave function analyzer interface, electron-hole analysis for the excited states, along with parameters such as excitation energy, charge transfer length, H, t, and Δr indices for the above-mentioned solvents, and topological analysis, viz., ELF, LOL, and RDG, were discussed for the header composite. To enhance the biological behavior, molecular docking-in silico analysis was accomplished, suitable protein receptors were attained, and the results show the measure of binding energy in the ligand-protein interactions. Consequently, the present investigations imply that NBCLP may be designated as a potent and satisfying medication for the ailment of tuberculosis.

Computational analysis of the Covid-19 model using the continuous Galerkin–Petrov scheme

Abstract Epidemiological models feature reliable and valuable insights into the prevention and transmission of life-threatening illnesses. In this study, a novel SIR mathematical model for COVID-19 is formulated and examined. The newly developed model has been thoroughly explored through theoretical analysis and computational methods, specifically the continuous Galerkin–Petrov (cGP) scheme. The next-generation matrix approach was used to calculate the reproduction number ( R 0 ) ({R}_{0}) . Both disease-free equilibrium (DFE) ( E 0 ) ({E}^{0}) and the endemic equilibrium ( E ⁎ ) ({E}^{\ast }) points are derived for the proposed model. The stability analysis of the equilibrium points reveals that ( E 0 ) ({E}^{0}) is locally asymptotically stable when R 0 < 1 {R}_{0}\lt 1 , while E ⁎ {E}^{\ast } is globally asymptotically stable when R 0 > 1 {R}_{0}\gt 1 . We have examined the model’s local stability (LS) and global stability (GS) for endemic equilibrium \text{ } and DFE based on the number ( R 0 ) ({R}_{0}) . To ascertain the dominance of the parameters, we examined the sensitivity of the number ( R 0 ) ({R}_{0}) to parameters and computed sensitivity indices. Additionally, using the fourth-order Runge–Kutta (RK4) and Runge–Kutta–Fehlberg (RK45) techniques implemented in MATLAB, we determined the numerical solutions. Furthermore, the model was solved using the continuous cGP time discretization technique. We implemented a variety of schemes like cGP(2), RK4, and RK45 for the COVID-19 model and presented the numerical and graphical solutions of the model. Furthermore, we compared the results obtained using the above-mentioned schemes and observed that all results overlap with each other. The significant properties of several physical parameters under consideration were discussed. In the end, the computational analysis shows a clear image of the rise and fall in the spread of this disease over time in a specific location.

A spring-mass-damper model based on separated phase flow mode for pulsating heat pipe with adjustive-structured channels

Pulsating heat pipe (PHP) is a kind of efficient passive phase-change cooling device. The pulsating behaviors of the two-phase flow inside PHP significantly affect the heat transfer performance for PHP, the investigation of which will greatly contribute to the optimal design of PHP for electronic heat dissipation in small space. In the present work, the heat transfer performance of PHP is optimized via structure analysis and modeling calculation. A new “spring-mass-damper” model in terms of separated phase flow mode is established, where the frictional pressure loss of the real two-phase flow pattern − slug flow in PHP is considered. Besides, a prototype of PHP with adjustive-structured channel (ASCPHP) is proposed. The heat transfer performance of ASCPHP is evaluated with the newly established model. With theoretical computation method, the frequency of ASCPHP the superiority of ASPHP is also confirmed by comparison with other types of PHPs.

CO2 adsorption on a K-promoted MgO surface: A DFT theoretical study

The primary cause of global warming is the emission of greenhouse gases such as CO2. So reducing CO2 emissions is vital. This paper investigates the impact of the atom K as a promoter of MgO on the CO2 adsorption properties using the DFT theoretical computational method. By analyzing the adsorption energy, bader charge as well as the density of states and COHP, it was found that K-promoting the MgO (100) surface resulted in a redistribution of charge on the MgO surface and enhanced CO2 adsorption compared to the pure MgO surface. The presence of K atoms causes orbital hybridization among O (CO2) and Mg atoms, O (CO2) atoms and K atoms, and the surface O atoms and K atoms. These interactions lead to the formation of (MgO)Mg-O(CO2) and (CO2)O−K−O(MgO) chemical bonds. The adsorption energy of CO2 on the K-promoted MgO surface increased from -0.32 eV to -1.01 eV compared to the pure surface, enhancing the adsorption of CO2.

Grape seeds waste activated carbon as an adsorber of paracetamol drug residue: Experimental and theoretical approaches

Activated carbon (AC) derived from grape seeds wastes and chemically activated with phosphoric acid was employed to remove paracetamol (PCT); from an aqueous solution; as a pharmaceutical compound model. The AC was characterized using several techniques, and a series of batch adsorption experiments were conducted. Additionally, a theoretical study investigated the interactions of PCT with various functional groups present on the AC surface. The results demonstrated that the developed AC possessed a well-developed pore structure and a high specific surface area (SBET = 543 m2/g). The AC also exhibited an acidic surface and a low pHpzc (2.5). Adsorption experiments revealed that the pseudo-second-order (PSO) and Freundlich models provided the best fits for experimental kinetic and equilibrium data, respectively. The maximum adsorption capacity of AC for PCT was found to be 17.3 mg/g. Thermodynamic analysis suggested endothermic, favorable, and spontaneous adsorption; with low enthalpy values (ΔH° = 8.099 kJ/mol), supporting physisorption. The DLPNO-CCDT(T)/6-311G(d,p) calculation method yielded the most reliable adsorption energy (Eads) and Gibbs free energy (ΔGads) values between PCT and functional groups on the carbon surface, indicating strong interactions between the acid phosphate group of AC and the acetamide fragment of PCT (ΔGads = −7.60 kcal/mol), and strong interactions between the ketone groups and lactone cycles with the hydroxyl (ΔGads = −3.40 kcal/mol), and acetamide (ΔGads = −1.91 kcal/mol) groups of PCT, respectively. The obtained results indicated, first, that the use of activated carbon from waste is an effective alternative adsorbent for the treatment of wastewater containing pharmaceutical compounds. Second, the application of theoretical computational methods in quantum chemistry provides a thorough understanding of the mechanism of the absorption of PCT at the carbon surface.

A Theoretical-Computational Study of Phosphodiester Bond Cleavage Kinetics as a Function of the Temperature.

The hydrolysis of the phosphodiester bond is an important chemical reaction involved in several biological processes. Here, we study the cleavage of this bond by means of a theoretical-computational method in a model system, the dineopentyl phosphate. By such an approach, we reconstructed the kinetics and related thermodynamics of this chemical reaction along an isochore. In particular, we evaluated the kinetic constants of all the reaction steps within a wide range of temperatures, mostly corresponding to conditions where no experimental measures are available due to the extremely slow kinetics. Our results, in good agreement with the experimental data, show the robustness of our theoretical-computational methodology which can be easily extended to more complex systems.

Spatial Modelling of Urban Wind Characteristics: Review of Contributions to Sustainable Urban Development

Wind, a renewable resource with growing importance in the contemporary world, is considered a capable tool for addressing some of the problems linked with rapid urbanization, unsustainable development, and climate change. As such, understanding modelling approaches to wind characteristics in cities becomes crucial. While prior reviews delve into the advancements in reduced-scale models and computational fluid dynamics simulations, there is scant literature evaluating large-scale spatial modelling of urban wind environments. This paper aims to consolidate the understanding of spatial modelling approaches to wind characteristics in cities by conducting a systematic literature review with the PRISMA protocol to capture the contributions to sustainable urban development. The reviewed articles are categorized under two distinctive approaches: (a) studies adopting the wind morphometric approach, encompassing theoretical foundations, input factors, and computation methods and (b) studies adopting the urban climate mapping approach, centering on the amalgamation of wind with urban microclimate analysis. The findings suggest that wind morphometric methodologies hold considerable promise due to their straightforward calculations and interpretability. Nonetheless, issues related to data precision and accuracy challenge the validity of these models. This review also probes into the implications of these two distinctive approaches for urban planning and policymaking, advocating for more sustainable urban development.

The experimental and theoretical study on the spatial‐temporal distribution of electromagnetic radiation from JO‐8 explosions.

AbstractThe detonating fuse in the multistage warhead will be subjected to strong electromagnetic interference, derived from electromagnetic radiation generated by explosion of the shaped charge warhead, which may cause premature detonation or misfire. In order to explore the possible electromagnetic environment surrounded the detonating fuse, the spatial‐temporal distribution of electromagnetic radiation after the explosion of JO‐8 explosive was investigated in this paper. The electromagnetic radiation signal was collected and its frequency coverage was analyzed in the far‐field area by the field blast test. Moreover, based on electromagnetic theory, a theoretical model of electromagnetic radiation generated by the explosion of JO‐8 explosive was established, and the spatial‐temporal distribution of the electric field intensity was illustrated in detail for several typical positions after the explosion. The better agreement between experimental and theoretical results indicates that the proposed theoretical model and computational method are reasonable. On this basis, the distributions of electric field intensity for different positions and various explosive weights were predicted respectively by using distance and explosive weight as variables. This study is expected to provide a reference for the research on the electromagnetic radiation for explosive explosion and anti‐explosive electromagnetic interference.

Theoretical progress of MXenes as electrocatalysts for the hydrogen evolution reaction

We reviewed recent theoretical progress in MXenes as HER electrocatalysts, covering structural and electronic properties, terminal group tunability, heteroatom doping, crucial activity descriptors, and advances in theoretical computational methods.

Observation of Continuum State Dissociation Enables the Determination of N2 Bond Dissociation Energy to Spectroscopic Accuracy.

Nitrogen (N) is one of the most fundamental elements of life. Precise determination of the bond dissociation energy (BDE) of the corresponding homonuclear diatomic molecule N2 is not only important for calculating the enthalpies of formation for any N-containing molecules but also provides the best benchmark for evaluating theoretical computational methods. Thus, it has attracted many experimental and theoretical studies, while controversies still exist. Here, we report the observation of continuum state dissociation of N2 into the channel N(2D5/2,3/2)+N(2D5/2,3/2) for the first time by using the vacuum ultraviolet (VUV)-pump-VUV-probe time-sliced velocity-mapped imaging setup. The quantum-state-resolved images enable the direct visualization of the dissociation onsets corresponding to each of the correlated spin-orbit fine-structure channels within a few tenths of wavenumber. The BDEs of 14N2 and 15N2 are directly determined to be 78691.8 ± 0.3 cm-1 and 78731.5 ± 0.3 cm-1, respectively, which should represent the most accurate BDE of N2 thus far.

An accurate and universal protein-small molecule batch docking solution using Autodock Vina

As an important theoretical computation method in computer-aided drug design, molecular docking has significantly shifted the paradigm of drug discovery. As one of the open-source docking software, Autodock Vina (Vina) is widely popular, but the lack of relevant experience and inappropriate docking parameters make it unable to perform optimally in practical application scenarios, which leads to potential failure risks in the early stage of drug discovery. In order to simplify the docking steps and determine the most appropriate docking parameters, a universal solution for rigid receptor docking using Vina has been proposed in this paper, and a user-friendly software for the entire process of molecular docking using Vina is developed. The case studies show that our docking solution is able to be applied to different docking scenarios to facilitate a more accurate, faster, and more convenient new drug discovery process.

Coating of pseudo-plastic material in reverse roll-coating: Mathematical analysis

This paper describes a theoretical framework and computational methods of a thin layer coating of a non-Newtonian polymeric material while it moves through a tiny space among two inverted rollers. Order of magnitude is accustomed to clarify the nondimensional forms of the governing equations. Semi-analytical solutions of pressure gradient, velocity profile and rate of the flow are acquired via optimal homotopy asymptotic method (OHAM). The graphical representation depicts the physical quantities of the effects of velocity profile ratio k and Weissenberg number We. It is observed that by increasing the values of k and We, velocity profile decreases while pressure distribution increases.

Rational Design of Hydrogels for Cationic Antimicrobial Peptide Delivery: A Molecular Modeling Approach.

In light of the growing bacterial resistance to antibiotics and in the absence of the development of new antimicrobial agents, numerous antimicrobial delivery systems over the past decades have been developed with the aim to provide new alternatives to the antimicrobial treatment of infections. However, there are few studies that focus on the development of a rational design that is accurate based on a set of theoretical-computational methods that permit the prediction and the understanding of hydrogels regarding their interaction with cationic antimicrobial peptides (cAMPs) as potential sustained and localized delivery nanoplatforms of cAMP. To this aim, we employed docking and Molecular Dynamics simulations (MDs) that allowed us to propose a rational selection of hydrogel candidates based on the propensity to form intermolecular interactions with two types of cAMPs (MP-L and NCP-3a). For the design of the hydrogels, specific building blocks were considered, named monomers (MN), co-monomers (CM), and cross-linkers (CL). These building blocks were ranked by considering the interaction with two peptides (MP-L and NCP-3a) as receptors. The better proposed hydrogel candidates were composed of MN3-CM7-CL1 and MN4-CM5-CL1 termed HG1 and HG2, respectively. The results obtained by MDs show that the biggest differences between the hydrogels are in the CM, where HG2 has two carboxylic acids that allow the forming of greater amounts of hydrogen bonds (HBs) and salt bridges (SBs) with both cAMPs. Therefore, using theoretical-computational methods allowed for the obtaining of the best virtual hydrogel candidates according to affinity with the specific cAMP. In conclusion, this study showed that HG2 is the better candidate for future in vitro or in vivo experiments due to its possible capacity as a depot system and its potential sustained and localized delivery system of cAMP.

Stability analysis of soft–hard-interbedded anti-inclined rock slope

The instability of rock slope is still a very frequent geological disaster, which seriously affects people's life and production activities. Previous studies have mainly focused on deformation mechanism, prediction, and control of hard rock with single lithology, while there are limited studies on the theoretic computational method of the stability for soft–hard interbedded anti-inclined rock strata. In this study, a geomechanical model for the toppling failure of soft–hard-interbedded anti-inclined rock slope is established. The modes of failure for soft and hard rock strata are analyzed, the computational formula of the downward thrust for each anti-inclined rock stratum is derived, and the stability safety factor of each rock stratum is defined. A theoretical computational method for determining the potentially most dangerous failure surface of soft–hard-interbedded anti-inclined rock slope is proposed. By comparing with the existing research results, the theoretical solving method proposed in this study can well solve the location of the potentially most dangerous failure surface of soft–hard-interbedded anti-inclined rock slope. The potentially most dangerous failure surface of this kind of slope is approximately planar, and the angle between it and the normal plane of the rock strata is an acute angle within 30°. It provides theoretical support for the stability analysis of this kind of slope.

The Interplay Between Experimental Spectroscopy, Theoretical, and Computational Quantum Chemistry

Advances in technology led to development of sophisticated experimental techniques for studying new chemical systems and processes on the molecular levels. Such experimental observations required advanced computational and theorical studies to enable observations and analysis of the data. This led to evolution of new theoretical models and computational methods that have been proven valuable in aiding experimental detection and interpretation of results. Collaborative research between theorists and experimentalists became essential in the various areas chemistry, such as identification and determination of properties of new important hydrogen-bonded and chemically-bonded chemical species. These molecular systems are of importance in the atmospheric chemistry, development of new materials from large clusters, drug design, reactions and interactions in biological systems. This mini review provides examples of the author’s theoretical work for two different types of new chemical systems, in collaboration with experimental spectroscopists. These selected studies will be used to emphasis importance of the interplay between theory, computational chemistry, and high-resolution molecular spectroscopy in gas phase.

A co-word analysis of museum tourism experience via hierarchy of needs: Case study of the China Block Printing Museum at Yangzhou

Studies on tourism experience frequently emphasize antecedents, neglect consequences, and lack systematisation, which motivated us to explore an application of semantic co-word analysis based on the hierarchy of needs theory in the systematic research of tourism experience. We collected the texts of visitors’ online comments of the China Block Printing Museum at Yangzhou and conducted an empirical research, the results indicated that tourists’ activity-environment needs had three levels; experience of the tourism setting was positive overall; the experience of tourism activities required improvement; and the benefits of the tourism experience were unfavourable. The museum should enhance the ‘participation-dynamic setting’ to create an experience space for tourists, improve ungazed spaces to enhance leisure benefits, innovate the museum guide system to facilitate educational benefits, and develop an ‘exploring-expanding setting’ to create unique all-for-one tourism products. The innovation of the combination of theoretical tools and computational methods in this study is a necessary exploration to use qualitative materials to objectively reveal the operation mechanism of tourism experience.

Theoretical-Computational Modeling of Gas-State Thermodynamics in Flexible Molecular Systems: Ionic Liquids in the Gas Phase as a Case Study.

A theoretical-computational procedure based on the quasi-Gaussian entropy (QGE) theory and molecular dynamics (MD) simulations is proposed for the calculation of thermodynamic properties for molecular and supra-molecular species in the gas phase. The peculiarity of the methodology reported in this study is its ability to construct an analytical model of all the most relevant thermodynamic properties, even within a wide temperature range, based on a practically automatic sampling of the entire conformational repertoire of highly flexible systems, thereby bypassing the need for an explicit search for all possible conformers/rotamers deemed relevant. In this respect, the reliability of the presented method mainly depends on the quality of the force field used in the MD simulations and on the ability to discriminate in a physically coherent way between semi-classical and quantum degrees of freedom. The method was tested on six model systems (n-butane, n-butane, n-octanol, octadecane, 1-butyl-3-methylimidazolium hexafluorophosphate and 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide ionic pairs), which, being experimentally characterized and already addressed by other theoretical-computational methods, were considered as particularly suitable to allow us to evaluate the method's accuracy and efficiency, bringing out advantages and possible drawbacks. The results demonstrate that such a physically coherent yet relatively simple method can represent a further valid computational tool that is alternative and complementary to other extremely efficient computational methods, as it is particularly suited for addressing the thermodynamics of gaseous systems with a high conformational complexity over a large range of temperature.

Performance of a Novel Enhanced Sparrow Search Algorithm for Engineering Design Process: Coverage Optimization in Wireless Sensor Network

Burgeoning swarm intelligence techniques have been creating a feasible theoretical computational method for the modeling, simulation, and optimization of complex systems. This study aims to increase the coverage of a wireless sensor network (WSN) and puts forward an enhanced version of the sparrow search algorithm (SSA) as a processing tool to achieve this optimization. The enhancement of the algorithm covers three aspects. Firstly, the Latin hypercube sampling technique is utilized to generate the initial population to obtain a more uniform distribution in the search space. Secondly, a sine cosine algorithm with adaptive adjustment and the Lévy flight strategy are introduced as new optimization equations to enhance the convergence efficiency of the algorithm. Finally, to optimize the individuals with poor fitness in the population, a novel mutation disturbance mechanism is introduced at the end of each iteration. Through numerical tests of 13 benchmark functions, the experimental results show that the proposed enhanced algorithm can converge to the optimum faster and has a more stable average value, reflecting its advantages in convergence speed, robustness, and anti-local extremum ability. For the WSN coverage problem, this paper established a current optimization framework based on the swarm intelligence algorithms, and further investigated the performance of nine algorithms applied to the process. The simulation results indicate that the proposed method achieves the highest coverage rate of 97.66% (on average) among the nine algorithms in the calculation cases, which is increased by 13.00% compared with the original sparrow search algorithm and outperforms other methods by 1.47% to 15.34%.

DNA Interaction, DNA Photocleavage, Photocytotoxicity In Vitro, and Molecular Docking of Naphthyl-Appended Ruthenium Complexes.

With the development of metal-based drugs, Ru(II) compounds present potential applications of PDT (photodynamic therapy) and anticancer reagents. We herein synthesized two naphthyl-appended ruthenium complexes by the combination of the ligand with naphthyl and bipyridyl. The DNA affinities, photocleavage abilities, and photocytotoxicity were studied by various spectral methods, viscosity measurement, theoretical computation method, gel electrophoresis, and MTT method. Two complexes exhibited strong interaction with calf thymus DNA by intercalation. Production of singlet oxygen (1O2) led to obvious DNA photocleavage activities of two complexes under 365 nm light. Furthermore, two complexes displayed obvious photocytotoxicity and low dark cytotoxicity towards Hela, A549, and A375 cells.