Computation

22 pages, 4834 KiB

Open AccessArticle

Computer Aided Structure-Based Drug Design of Novel SARS-CoV-2 Main Protease Inhibitors: Molecular Docking and Molecular Dynamics Study

by Dmitry S. Kolybalov, Evgenii D. Kadtsyn and Sergey G. Arkhipov

Computation 2024, 12(1), 18; https://doi.org/10.3390/computation12010018 - 20 Jan 2024

Cited by 1 | Viewed by 2581

Abstract

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus syndrome caused the recent outbreak of COVID-19 disease, the most significant challenge to public health for decades. Despite the successful development of vaccines and promising therapies, the development of novel drugs is still in the [...] Read more.

Severe acute respiratory syndrome Coronavirus 2 (SARS-CoV-2) virus syndrome caused the recent outbreak of COVID-19 disease, the most significant challenge to public health for decades. Despite the successful development of vaccines and promising therapies, the development of novel drugs is still in the interests of scientific society. SARS-CoV-2 main protease M^pro is one of the key proteins for the lifecycle of the virus and is considered an intriguing target. We used a structure-based drug design approach as a part of the search of new inhibitors for SARS-CoV-2 M^pro and hence new potential drugs for treating COVID-19. Four structures of potential inhibitors of (4S)-2-(2-(1H-imidazol-5-yl)ethyl)-4-amino-2-(1,3-dihydroxypropyl)-3-hydroxy-5-(1H-imidazol-5-yl)pentanal (L¹), (2R,4S)-2-((1H-imidazol-4-yl)methyl)-4-chloro-8-hydroxy-7-(hydroxymethyl)octanoic acid (L²), 1,9-dihydroxy-6-(hydroxymethyl)-6-(((1S)-1,7,7-trimethylbicyclo [2.2.1]heptan-2-yl)amino)nonan-4-one (L³), and 2,4,6-tris((4H-1,2,4-triazol-3-yl)amino)benzonitrile (L⁴) were modeled. Three-dimensional structures of ligand–protein complexes were modeled and their potential binding efficiency proved. Docking and molecular dynamic simulations were performed for these compounds. Detailed trajectory analysis of the ligands’ binding conformation was carried out. Binding free energies were estimated by the MM/PBSA approach. Results suggest a high potential efficiency of the studied inhibitors. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Biology)

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43 pages, 19694 KiB

Open AccessArticle

Influence of Gyrotactic Microorganisms on Bioconvection in Electromagnetohydrodynamic Hybrid Nanofluid through a Permeable Sheet

by Ahmed S. Rashed, Ehsan H. Nasr and Samah M. Mabrouk

Computation 2024, 12(1), 17; https://doi.org/10.3390/computation12010017 - 20 Jan 2024

Cited by 2 | Viewed by 1885

Abstract

Many biotechnology sectors that depend on fluids and their physical characteristics, including the phenomenon of bioconvection, have generated a great deal of discussion. The term “bioconvection” describes the organized movement of microorganisms, such as bacteria or algae. Microorganisms that participate in bioconvection display [...] Read more.

Many biotechnology sectors that depend on fluids and their physical characteristics, including the phenomenon of bioconvection, have generated a great deal of discussion. The term “bioconvection” describes the organized movement of microorganisms, such as bacteria or algae. Microorganisms that participate in bioconvection display directed movement, frequently in the form of upward or downward streaming, which can lead to the production of distinctive patterns. The interaction between the microbes’ swimming behavior and the physical forces acting on them, such as buoyancy and fluid flow, is what drives these patterns. This work considers the laminar-mixed convection incompressible flow at the stagnation point with viscous and gyrotactic microorganisms in an unsteady electrically conducting hybrid nanofluid (Fe₃O₄-Cu/water). In addition, hybrid nanofluid flow over a horizontal porous stretched sheet, as well as external and induced magnetic field effects, can be used in biological domains, including drug delivery and microcirculatory system flow dynamics. The governing system has been reduced to a set of ordinary differential equations (ODEs) through the use of the group technique. The current research was inspired by an examination of the impacts of multiple parameters, including Prandtl number,

P r

, magnetic diffusivity,

η_{0}

, shape factor

, n

, microorganism diffusion coefficient,

D_{n}

, Brownian motion coefficient,

D_{B}

, thermophoresis diffusion coefficient,

D_{T}

, bioconvection Peclet number,

P e

, temperature difference,

δ t

, and concentration difference,

δ c

. The results show that as

P r

rises, temperature, heat flux, and nanoparticles all decrease. In contrast, when the

η_{0}

value increases, the magnetic field and velocity decrease. Heat flow, bacterial density, and temperature decrease as the

D_{B}

value rises, yet the number of nanoparticles increases. As the

D_{T}

value increases, the temperature, heat flow, and concentration of nanoparticles all rise while the density of bacteria decreases. Even though temperature, heat flux, nanoparticles, and bacterial density all decrease as

δ c

values climb, bacterial density rises as

D_{n}

values do although bacterial density falls with increasing,

δ t

and

P e

values; on the other hand, when n values increase, temperature and heat flow increase but the density of bacteria and nanoparticle decrease. The physical importance and behavior of the present parameters were illustrated graphically. Full article

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17 pages, 5592 KiB

Open AccessArticle

Computational Fluid Dynamics Analysis of Varied Cross-Sectional Areas in Sleep Apnea Individuals across Diverse Situations

by W. M. Faizal, C. Y. Khor, Suhaimi Shahrin, M. H. M. Hazwan, M. Ahmad, M. N. Misbah and A. H. M. Haidiezul

Computation 2024, 12(1), 16; https://doi.org/10.3390/computation12010016 - 17 Jan 2024

Viewed by 1957

Abstract

Obstructive sleep apnea (OSA) is a common medical condition that impacts a significant portion of the population. To better understand this condition, research has been conducted on inhaling and exhaling breathing airflow parameters in patients with obstructive sleep apnea. A steady-state Reynolds-averaged Navier–Stokes [...] Read more.

Obstructive sleep apnea (OSA) is a common medical condition that impacts a significant portion of the population. To better understand this condition, research has been conducted on inhaling and exhaling breathing airflow parameters in patients with obstructive sleep apnea. A steady-state Reynolds-averaged Navier–Stokes (RANS) approach and an SST turbulence model have been utilized to simulate the upper airway airflow. A 3D airway model has been created using advanced software such as the Materialize Interactive Medical Image Control System (MIMICS) and ANSYS. The aim of the research was to fill this gap by conducting a detailed computational fluid dynamics (CFD) analysis to investigate the influence of cross-sectional areas on airflow characteristics during inhale and exhale breathing in OSA patients. The lack of detailed understanding of how the cross-sectional area of the airways affects OSA patients and the airflow dynamics in the upper airway is the primary problem addressed by this research. The simulations revealed that the cross-sectional area of the airway has a notable impact on velocity, Reynolds number, and turbulent kinetic energy (TKE). TKE, which measures turbulence flow in different breathing scenarios among patients, could potentially be utilized to assess the severity of obstructive sleep apnea (OSA). This research found a vital correlation between maximum pharyngeal turbulent kinetic energy (TKE) and cross-sectional areas in OSA patients, with a variance of 29.47%. Reduced cross-sectional area may result in a significant TKE rise of roughly 10.28% during inspiration and 10.18% during expiration. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Heat and Mass Transfer (ICCHMT 2023))

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22 pages, 3189 KiB

Open AccessArticle

A Technical Comparative Heart Disease Prediction Framework Using Boosting Ensemble Techniques

by Najmu Nissa, Sanjay Jamwal and Mehdi Neshat

Computation 2024, 12(1), 15; https://doi.org/10.3390/computation12010015 - 16 Jan 2024

Cited by 2 | Viewed by 3253

Abstract

This paper addresses the global surge in heart disease prevalence and its impact on public health, stressing the need for accurate predictive models. The timely identification of individuals at risk of developing cardiovascular ailments is paramount for implementing preventive measures and timely interventions. [...] Read more.

This paper addresses the global surge in heart disease prevalence and its impact on public health, stressing the need for accurate predictive models. The timely identification of individuals at risk of developing cardiovascular ailments is paramount for implementing preventive measures and timely interventions. The World Health Organization (WHO) reports that cardiovascular diseases, responsible for an alarming 17.9 million annual fatalities, constitute a significant 31% of the global mortality rate. The intricate clinical landscape, characterized by inherent variability and a complex interplay of factors, poses challenges for accurately diagnosing the severity of cardiac conditions and predicting their progression. Consequently, early identification emerges as a pivotal factor in the successful treatment of heart-related ailments. This research presents a comprehensive framework for the prediction of cardiovascular diseases, leveraging advanced boosting techniques and machine learning methodologies, including Cat boost, Random Forest, Gradient boosting, Light GBM, and Ada boost. Focusing on “Early Heart Disease Prediction using Boosting Techniques”, this paper aims to contribute to the development of robust models capable of reliably forecasting cardiovascular health risks. Model performance is rigorously assessed using a substantial dataset on heart illnesses from the UCI machine learning library. With 26 feature-based numerical and categorical variables, this dataset encompasses 8763 samples collected globally. The empirical findings highlight AdaBoost as the preeminent performer, achieving a notable accuracy of 95% and excelling in metrics such as negative predicted value (0.83), false positive rate (0.04), false negative rate (0.04), and false development rate (0.01). These results underscore AdaBoost’s superiority in predictive accuracy and overall performance compared to alternative algorithms, contributing valuable insights to the field of cardiovascular health prediction. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Engineering)

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16 pages, 530 KiB

Open AccessArticle

Cutting-Edge Computational Approaches for Approximating Nonlocal Variable-Order Operators

by Nayereh Tanha, Behrouz Parsa Moghaddam and Mousa Ilie

Computation 2024, 12(1), 14; https://doi.org/10.3390/computation12010014 - 12 Jan 2024

Cited by 1 | Viewed by 1527

Abstract

This study presents an algorithmically efficient approach to address the complexities associated with nonlocal variable-order operators characterized by diverse definitions. The proposed method employs integro spline quasi interpolation to approximate these operators, aiming for enhanced accuracy and computational efficiency. We conduct a thorough [...] Read more.

This study presents an algorithmically efficient approach to address the complexities associated with nonlocal variable-order operators characterized by diverse definitions. The proposed method employs integro spline quasi interpolation to approximate these operators, aiming for enhanced accuracy and computational efficiency. We conduct a thorough comparison of the outcomes obtained through this approach with other established techniques, including finite difference, IQS, and B-spline methods, documented in the applied mathematics literature for handling nonlocal variable-order derivatives and integrals. The numerical results, showcased in this paper, serve as a compelling validation of the notable advantages offered by our innovative approach. Furthermore, this study delves into the impact of selecting different variable-order values, contributing to a deeper understanding of the algorithm’s behavior across a spectrum of scenarios. In summary, this research seeks to provide a practical and effective solution to the challenges associated with nonlocal variable-order operators, contributing to the applied mathematics literature. Full article

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21 pages, 3017 KiB

Open AccessArticle

A Novel Model for Economic Recycle Quantity with Two-Level Piecewise Constant Demand and Shortages

by El-Awady Attia, Md Maniruzzaman Miah, Abu Sayeed Arif, Ali AlArjani, Mahmud Hasan and Md Sharif Uddin

Computation 2024, 12(1), 13; https://doi.org/10.3390/computation12010013 - 11 Jan 2024

Viewed by 1704

Abstract

This paper focuses on the production systems that may produce a proportion of recyclable defective products. The developed model is called an Economic Recycle Quantity (ERQ) model with the assumption of a full recovery of defective items. The defective parts are collected during [...] Read more.

This paper focuses on the production systems that may produce a proportion of recyclable defective products. The developed model is called an Economic Recycle Quantity (ERQ) model with the assumption of a full recovery of defective items. The defective parts are collected during the production-off time and can be used during the next production cycle of the same category. The demand rate of the non-defective items is a two-level piecewise factor—one during the production-run time and another during the production-off time. The developed model aims to optimize the total inventory cost, the order quantity, and the amount of recyclable defective items that represent the ERQ. The mathematical formulations of the model are deduced theoretically. The model was solved analytically, and the optimal results are illustrated. Sensitivity analysis is carried out to investigate the effect of varying system parameters and validate the proposed model. Results of the sensitivity analysis show that the consideration of defective part recycling reduces the total inventory cost where the raw material is reduced. The cost reduction is about 1%; of course, the environmental impact is more appreciated. Furthermore, the managerial implications are described, and the future perspectives are discussed. Full article

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16 pages, 7982 KiB

Open AccessArticle

Hydraulic Performance Optimization of a Submersible Drainage Pump

by Md Rakibuzzaman, Sang-Ho Suh, Hyung-Woon Roh, Kyung Hee Song, Kwang Chul Song and Ling Zhou

Computation 2024, 12(1), 12; https://doi.org/10.3390/computation12010012 - 10 Jan 2024

Cited by 1 | Viewed by 2180

Abstract

Small submersible drainage pumps are used to discharge leaking water and rainwater in buildings. In an emergency (e.g., heavy rain or accident), advance monitoring of the flow rate is essential to enable optimal operation, considering the point where the pump operates abnormally when [...] Read more.

Small submersible drainage pumps are used to discharge leaking water and rainwater in buildings. In an emergency (e.g., heavy rain or accident), advance monitoring of the flow rate is essential to enable optimal operation, considering the point where the pump operates abnormally when the water level is increased rapidly. Moreover, pump performance optimization is crucial for energy-saving policy. Therefore, it is necessary to meet the challenges of submersible pump systems, including sustainability and pump efficiency. The final goal of this study was to develop an energy-saving and highly efficient submersible drainage pump capable of performing efficiently in emergencies. In particular, this paper targeted the hydraulic performance improvement of a submersible drainage pump model. Prior to the development of driving-mode-related technology capable of emergency response, a way to improve the performance characteristics of the existing submersible drainage pump was found. Disassembling of the current pump followed by reverse engineering was performed instead of designing a new pump. Numerical simulation was performed to analyze the flow characteristics and pump efficiency. An experiment was carried out to obtain the performance, and it was validated with numerical results. The results reveal that changing the cross-sectional shape of the impeller reduced the flow separation and enhanced velocity and pressure distributions. Also, it reduced the power and increased efficiency. The results also show that the pump’s efficiency was increased to 5.56% at a discharge rate of 0.17 m³/min, and overall average efficiency was increased to 6.53%. It was concluded that the submersible pump design method is suitable for the numerical designing of an optimized pump’s impeller and casing. This paper provides insight on the design optimization of pumps. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Heat and Mass Transfer (ICCHMT 2023))

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15 pages, 5308 KiB

Open AccessArticle

Analytical and Numerical Investigation of Two-Dimensional Heat Transfer with Periodic Boundary Conditions

by İrem Bağlan and Erman Aslan

Computation 2024, 12(1), 11; https://doi.org/10.3390/computation12010011 - 10 Jan 2024

Viewed by 2065

Abstract

A two-dimensional heat diffusion problem with a heat source that is a quasilinear parabolic problem is examined analytically and numerically. Periodic boundary conditions are employed. As the problem is nonlinear, Picard’s successive approximation theorem is utilized. We demonstrate the existence, uniqueness, and constant [...] Read more.

A two-dimensional heat diffusion problem with a heat source that is a quasilinear parabolic problem is examined analytically and numerically. Periodic boundary conditions are employed. As the problem is nonlinear, Picard’s successive approximation theorem is utilized. We demonstrate the existence, uniqueness, and constant dependence of the solution on the data using the generalized Fourier method under specific conditions of natural regularity and consistency imposed on the input data. For the numerical solution, an implicit finite difference scheme is used. The results obtained from the analytical and numerical solutions closely match each other. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Heat and Mass Transfer (ICCHMT 2023))

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20 pages, 357 KiB

Open AccessArticle

Corporate Bankruptcy Prediction Models: A Comparative Study for the Construction Sector in Greece

by Kanellos Toudas, Stefanos Archontakis and Paraskevi Boufounou

Computation 2024, 12(1), 9; https://doi.org/10.3390/computation12010009 - 9 Jan 2024

Cited by 1 | Viewed by 2985

Abstract

This study focuses on testing the efficiency of alternative bankruptcy prediction models (Altman, Ohlson, Zmijewski) and on assessing the possible reasons that led to the confirmation or not of the prevailing model. Data from financial statements of listed (Greek) construction companies before the [...] Read more.

This study focuses on testing the efficiency of alternative bankruptcy prediction models (Altman, Ohlson, Zmijewski) and on assessing the possible reasons that led to the confirmation or not of the prevailing model. Data from financial statements of listed (Greek) construction companies before the economic crisis were utilized. The results showed that Altman’s main predictive model as well as the revised models have low overall predictability for all three years before bankruptcy. Full article

(This article belongs to the Special Issue Quantitative Finance and Risk Management Research)

21 pages, 5167 KiB

Open AccessArticle

Enhancement of Machine-Learning-Based Flash Calculations near Criticality Using a Resampling Approach

by Eirini Maria Kanakaki, Anna Samnioti and Vassilis Gaganis

Computation 2024, 12(1), 10; https://doi.org/10.3390/computation12010010 - 9 Jan 2024

Cited by 4 | Viewed by 2114

Abstract

Flash calculations are essential in reservoir engineering applications, most notably in compositional flow simulation and separation processes, to provide phase distribution factors, known as k-values, at a given pressure and temperature. The calculation output is subsequently used to estimate composition-dependent properties of interest, [...] Read more.

Flash calculations are essential in reservoir engineering applications, most notably in compositional flow simulation and separation processes, to provide phase distribution factors, known as k-values, at a given pressure and temperature. The calculation output is subsequently used to estimate composition-dependent properties of interest, such as the equilibrium phases’ molar fraction, composition, density, and compressibility. However, when the flash conditions approach criticality, minor inaccuracies in the computed k-values may lead to significant deviation in the dependent properties, which is eventually inherited to the simulator, leading to large errors in the simulation. Although several machine-learning-based regression approaches have emerged to drastically accelerate flash calculations, the criticality issue persists. To address this problem, a novel resampling technique of the ML models’ training data population is proposed, which aims to fine-tune the training dataset distribution and optimally exploit the models’ learning capacity across various flash conditions. The results demonstrate significantly improved accuracy in predicting phase behavior results near criticality, offering valuable contributions not only to the subsurface reservoir engineering industry but also to the broader field of thermodynamics. By understanding and optimizing the model’s training, this research enables more precise predictions and better-informed decision-making processes in domains involving phase separation phenomena. The proposed technique is applicable to every ML-dominated regression problem, where properties dependent on the machine output are of interest rather than the model output itself. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Engineering)

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19 pages, 10224 KiB

Open AccessArticle

Analysis of Effectiveness of Combined Surface Treatment Methods for Structural Parts with Holes to Enhance Their Fatigue Life

by Olexander Grebenikov, Andrii Humennyi, Serhii Svitlychnyi, Vasyl Lohinov and Valerii Matviienko

Computation 2024, 12(1), 8; https://doi.org/10.3390/computation12010008 - 8 Jan 2024

Cited by 1 | Viewed by 1807

Abstract

The typical and most widespread stress concentrators in the lower wing panels of aircraft are the drain holes located on the stringer vertical ribs. These are prime sources for the initiation and development of fatigue cracks, which lead to early failure of the [...] Read more.

The typical and most widespread stress concentrators in the lower wing panels of aircraft are the drain holes located on the stringer vertical ribs. These are prime sources for the initiation and development of fatigue cracks, which lead to early failure of the wing structure. Therefore, improving fatigue life in these critical areas is one of the significant issues for research. Two combined methods of surface plastic treatment in the location around drain holes are discussed in this paper. Using the finite element method and ANSYS software, we created a finite element model and obtained nonlinear solution results in the case of tension in a plate with three holes. In addition, the development of residual stress due to the surface plastic treatment of the hole-adjacent areas was taken into account. In this paper, it is shown that after surface treatment of the corresponding areas of the holes, residual stress, which exceeds the yield stress for the plate material, is induced. When combined with alternative tensile stress, these reduce the amplitude of the local stresses, thus increasing the number of stress cycles before failure. The benefits of this technology were confirmed by fatigue test results, which include the fatigue failure types of the plates. Graphs showing the impact of applicable surface treatment combined methods on the number of cycles to failure were also plotted. Full article

(This article belongs to the Special Issue Integrated Computer Technologies in Mechanical Engineering – Synergetic Engineering Ⅱ)

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17 pages, 922 KiB

Open AccessArticle

A New Mixed Fractional Derivative with Applications in Computational Biology

by Khalid Hattaf

Computation 2024, 12(1), 7; https://doi.org/10.3390/computation12010007 - 4 Jan 2024

Cited by 24 | Viewed by 2454

Abstract

This study develops a new definition of a fractional derivative that mixes the definitions of fractional derivatives with singular and non-singular kernels. This developed definition encompasses many types of fractional derivatives, such as the Riemann–Liouville and Caputo fractional derivatives for singular kernel types, [...] Read more.

This study develops a new definition of a fractional derivative that mixes the definitions of fractional derivatives with singular and non-singular kernels. This developed definition encompasses many types of fractional derivatives, such as the Riemann–Liouville and Caputo fractional derivatives for singular kernel types, as well as the Caputo–Fabrizio, the Atangana–Baleanu, and the generalized Hattaf fractional derivatives for non-singular kernel types. The associate fractional integral of the new mixed fractional derivative is rigorously introduced. Furthermore, a novel numerical scheme is developed to approximate the solutions of a class of fractional differential equations (FDEs) involving the mixed fractional derivative. Finally, an application in computational biology is presented. Full article

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21 pages, 6692 KiB

Open AccessReview

Thermal Analysis and Cooling Strategies of High-Efficiency Three-Phase Squirrel-Cage Induction Motors—A Review

by Yashwanth Reddy Konda, Vamsi Krishna Ponnaganti, Peram Venkata Sivarami Reddy, R. Raja Singh, Paolo Mercorelli, Edison Gundabattini and Darius Gnanaraj Solomon

Computation 2024, 12(1), 6; https://doi.org/10.3390/computation12010006 - 4 Jan 2024

Cited by 3 | Viewed by 3791

Abstract

In recent times, there has been an increased demand for electric vehicles. In this context, the energy management of the electric motor, which are an important constituent of electric vehicles, plays a pivotal role. A lot of research has been conducted on the [...] Read more.

In recent times, there has been an increased demand for electric vehicles. In this context, the energy management of the electric motor, which are an important constituent of electric vehicles, plays a pivotal role. A lot of research has been conducted on the optimization of heat flow through electric motors, thus reducing the wastage of energy via heat. Futuristic power sources may increasingly rely on cutting-edge innovations like energy harvesting and self-powered induction motors. In this context, effective thermal management techniques are discussed in this paper. Importance was given to the potential energy losses, hotspots, the influence of overheating on the motor efficiency, different cooling strategies, certain experimental approaches, and power control techniques. Two types of thermal analysis computation methods, namely the lumped-parameter circuit method (LPCM) and the finite element method (FEM), are discussed. Also, this paper reviews different cooling strategies. The experimental research showed that the efficiency was greater by 11% with the copper rotor compared to the aluminum rotor. Each rotor type was reviewed based on the temperature rise and efficiency at higher temperatures. The water-cooling method reduced the working temperatures by 39.49% at the end windings, 41.67% at the side windings, and by a huge margin of 56.95% at the yoke of the induction motor compared to the air-cooling method; hence, the water-cooling method is better. Lastly, modern cooling strategies are proposed to provide an effective thermal management solution for squirrel-cage induction motors. Full article

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21 pages, 2656 KiB

Open AccessArticle

Implicit and Explicit Solvent Effects on the Global Reactivity and the Density Topological Parameters of the Preferred Conformers of Caespitate

by Andrea Moreno-Ceballos, María Eugenia Castro, Norma A. Caballero, Liliana Mammino and Francisco J. Melendez

Computation 2024, 12(1), 5; https://doi.org/10.3390/computation12010005 - 3 Jan 2024

Cited by 3 | Viewed by 2196

Abstract

In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol [...] Read more.

In the search to cover the urgent need to combat infectious diseases, natural products have gained attention in recent years. The caespitate molecule, isolated from the plant Helichrysum caespititium of the Asteraceae family, is used in traditional African medicine. Caespitate is an acylphloroglucinol with biological activity. Acylphloroglucinols have attracted attention for treating tuberculosis due to their structural characteristics, highlighting the stabilizing effect of their intramolecular hydrogen bonds (IHBs). In this work, a conformational search for the caespitate was performed using the MM method. Posteriorly, DFT calculations with the APFD functional were used for full optimization and vibrational frequencies, obtaining stable structures. A population analysis was performed to predict the distribution of the most probable conformers. The calculations were performed in the gas phase and solution using the implicit SMD model for water, chloroform, acetonitrile, and DMSO solvents. Additionally, the multiscale ONIOM QM1/QM2 model was used to simulate the explicit solvent. The implicit and explicit solvent effects were evaluated on the global reactivity indexes using the conceptual-DFT approach. In addition, the QTAIM approach was applied to analyze the properties of the IHBs of the most energetically and populated conformers. The obtained results indicated that the most stable and populated conformer is in the gas phase, and chloroform has an extended conformation. However, water, acetonitrile, and DMSO have a hairpin shape. The optimized structures are well preserved in explicit solvent and the interaction energies for the IHBs were lower in explicit than implicit solvents due to non-covalent interactions formed between the solvent molecules. Finally, both methodologies, with implicit and explicit solvents, were validated with ¹H and ¹³C NMR experimental data. In both cases, the results agreed with the experimental data reported in the CDCl₃ solvent. Full article

(This article belongs to the Special Issue Calculations in Solution)

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16 pages, 4913 KiB

Open AccessArticle

LSTM Reconstruction of Turbulent Pressure Fluctuation Signals

by Konstantinos Poulinakis, Dimitris Drikakis, Ioannis W. Kokkinakis, S. Michael Spottswood and Talib Dbouk

Computation 2024, 12(1), 4; https://doi.org/10.3390/computation12010004 - 1 Jan 2024

Viewed by 2261

Abstract

This paper concerns the application of a long short-term memory model (LSTM) for high-resolution reconstruction of turbulent pressure fluctuation signals from sparse (reduced) data. The model’s training was performed using data from high-resolution computational fluid dynamics (CFD) simulations of high-speed turbulent boundary layers [...] Read more.

This paper concerns the application of a long short-term memory model (LSTM) for high-resolution reconstruction of turbulent pressure fluctuation signals from sparse (reduced) data. The model’s training was performed using data from high-resolution computational fluid dynamics (CFD) simulations of high-speed turbulent boundary layers over a flat panel. During the preprocessing stage, we employed cubic spline functions to increase the fidelity of the sparse signals and subsequently fed them to the LSTM model for a precise reconstruction. We evaluated our reconstruction method with the root mean squared error (RMSE) metric and via inspection of power spectrum plots. Our study reveals that the model achieved a precise high-resolution reconstruction of the training signal and could be transferred to new unseen signals of a similar nature with extremely high success. The numerical simulations show promising results for complex turbulent signals, which may be experimentally or computationally produced. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Engineering)

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28 pages, 3679 KiB

Open AccessArticle

Design of Inhibitors That Target the Menin–Mixed-Lineage Leukemia Interaction

by Moses N. Arthur, Kristeen Bebla, Emmanuel Broni, Carolyn Ashley, Miriam Velazquez, Xianin Hua, Ravi Radhakrishnan, Samuel K. Kwofie and Whelton A. Miller III

Computation 2024, 12(1), 3; https://doi.org/10.3390/computation12010003 - 27 Dec 2023

Viewed by 2483

Abstract

The prognosis of mixed-lineage leukemia (MLL) has remained a significant health concern, especially for infants. The minimal treatments available for this aggressive type of leukemia has been an ongoing problem. Chromosomal translocations of the KMT2A gene are known as MLL, which expresses MLL [...] Read more.

The prognosis of mixed-lineage leukemia (MLL) has remained a significant health concern, especially for infants. The minimal treatments available for this aggressive type of leukemia has been an ongoing problem. Chromosomal translocations of the KMT2A gene are known as MLL, which expresses MLL fusion proteins. A protein called menin is an important oncogenic cofactor for these MLL fusion proteins, thus providing a new avenue for treatments against this subset of acute leukemias. In this study, we report results using the structure-based drug design (SBDD) approach to discover potential novel MLL-mediated leukemia inhibitors from natural products against menin. The three-dimensional (3D) protein model was derived from Protein Databank (Protein ID: 4GQ4), and EasyModeller 4.0 and I-TASSER were used to fix missing residues during rebuilding. Out of the ten protein models generated (five from EasyModeller and I-TASSER each), one model was selected. The selected model demonstrated the most reasonable quality and had 75.5% of residues in the most favored regions, 18.3% of residues in additionally allowed regions, 3.3% of residues in generously allowed regions, and 2.9% of residues in disallowed regions. A ligand library containing 25,131 ligands from a Chinese database was virtually screened using AutoDock Vina, in addition to three known menin inhibitors. The top 10 compounds including ZINC000103526876, ZINC000095913861, ZINC000095912705, ZINC000085530497, ZINC000095912718, ZINC000070451048, ZINC000085530488, ZINC000095912706, ZINC000103580868, and ZINC000103584057 had binding energies of −11.0, −10.7, −10.6, −10.2, −10.2, −9.9, −9.9, −9.9, −9.9, and −9.9 kcal/mol, respectively. To confirm the stability of the menin–ligand complexes and the binding mechanisms, molecular dynamics simulations including molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) computations were performed. The amino acid residues that were found to be potentially crucial in ligand binding included Phe243, Met283, Cys246, Tyr281, Ala247, Ser160, Asn287, Asp185, Ser183, Tyr328, Asn249, His186, Leu182, Ile248, and Pro250. MI-2-2 and PubChem CIDs 71777742 and 36294 were shown to possess anti-menin properties; thus, this justifies a need to experimentally determine the activity of the identified compounds. The compounds identified herein were found to have good pharmacological profiles and had negligible toxicity. Additionally, these compounds were predicted as antileukemic, antineoplastic, chemopreventive, and apoptotic agents. The 10 natural compounds can be further explored as potential novel agents for the effective treatment of MLL-mediated leukemia. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Biology)

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20 pages, 2411 KiB

Open AccessArticle

MSVR & Operator-Based System Design of Intelligent MIMO Sensorless Control for Microreactor Devices

by Tatsuma Kato, Kosuke Nishizawa and Mingcong Deng

Computation 2024, 12(1), 2; https://doi.org/10.3390/computation12010002 - 25 Dec 2023

Viewed by 1926

Abstract

Recently, microreactors, which are tubular reactors capable of fast and highly efficient chemical reactions, have attracted attention. However, precise temperature control is required because temperature changes due to reaction heat can cause reactions to proceed differently from those designed. In a previous study, [...] Read more.

Recently, microreactors, which are tubular reactors capable of fast and highly efficient chemical reactions, have attracted attention. However, precise temperature control is required because temperature changes due to reaction heat can cause reactions to proceed differently from those designed. In a previous study, a single-input/output nonlinear control system was proposed using a model in which the microreactor is divided into three regions and the thermal equation is formulated considering the temperature gradient, but it could not control two different temperatures. In this paper, a multi-input, multi-output nonlinear control system was designed using operator theory. On the other hand, when the number of parallel microreactors is increased, a sensorless control method using M–SVR with a generalized Gaussian kernel was incorporated into the MIMO nonlinear control system from the viewpoint of cost reduction, and the effectiveness of the proposed method was confirmed via experimental results. Full article

(This article belongs to the Special Issue 10th Anniversary of Computation—Computational Engineering)

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15 pages, 8246 KiB

Open AccessArticle

Performance and Application Analysis of a New Optimization Algorithm

by Junlong Zheng, Chaiyan Jettanasen and Pathomthat Chiradeja

Computation 2024, 12(1), 1; https://doi.org/10.3390/computation12010001 - 20 Dec 2023

Viewed by 1895

Abstract

Our research focused on an optimization algorithm. Our work makes three contributions. First, a new optimization algorithm, the Maritime Search and Rescue Algorithm (MSRA), is creatively proposed. The algorithm not only has better optimization performance, but also has the ability to plan the [...] Read more.

Our research focused on an optimization algorithm. Our work makes three contributions. First, a new optimization algorithm, the Maritime Search and Rescue Algorithm (MSRA), is creatively proposed. The algorithm not only has better optimization performance, but also has the ability to plan the path to the best site. For other existing intelligent optimization algorithms, it has never been found that they have both of these performances. Second, the mathematical model of the MSRA was established, and the computer program pseudo-code was created. Third, the MSRA was verified by experiments. Full article

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Computation, Volume 12, Issue 1 (January 2024) – 18 articles

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