Computer Simulation Model Research Articles

Impact of arterial system alterations due to amputation on arterial stiffness and hemodynamics: a numerical study

Subjects with amputation of the lower limbs are at increased risk of cardiovascular mortality and morbidity. We hypothesize that amputation-induced alterations in the arterial tree negatively impact arterial biomechanics, blood pressure and flow behavior. These changes may interact with other biological factors, potentially increasing cardiovascular risk. To evaluate this hypothesis regarding the purely mechanical impact of amputation on the arterial tree, we used a simulation computer model including a detailed one-dimensional (1D) arterial network model (143 arterial segments) coupled with a zero-dimensional (0D) model of the left ventricle. Our simulations included five settings of the arterial network: (1) 4-limbs control, (2) unilateral amputee (right lower limb), (3) bilateral amputee (both lower limbs), (4) trilateral amputee (lower-limbs and right upper-limb), and (5) quadrilateral amputee (lower and upper limbs). Analysis of regional stiffness, as calculated by pulse wave velocity (PWV) for large-, medium- and small-sized arteries, showed that, while aortic stiffness did not change with increasing degree of amputation, stiffness of medium and smaller-sized arteries increased with greater amputation severity. Despite a staged decrease in cardiac output, the systolic and diastolic blood pressure values increased, resulting in an increase in both central and peripheral pulse pressures but with an attenuation of pulse pressure amplification. The most significant increase in peak systolic pressure and decrease in peak systolic blood flow was observed at the site of the abdominal aorta. Wave separation analysis indicated no changes in the shape of the forward and backward wave components. However, the results from wave intensity analysis showed that with extended amputation, there was an increase in peak forward wave intensity and a rise in the inverse peak of the backward wave intensity, suggesting potential alterations in cardiac hemodynamic load. In conclusion, this simulation study showed that biomechanical and hemodynamic changes in the arterial network geometry could interact with additional risk factors to increase the cardiovascular risk in patients with amputations.

Computational model for policy simulation and prediction of the regulatory impact of front-of-package food labels

Non-communicable diseases (NCDs), a significant cause of global mortality, necessitate targeted policy measures to reduce exposure to risk factors, particularly nutrition-related ones. Front-of-pack food labeling aims to shape consumer behavior and decrease exposure to nutritional risk factors. There are various forms of this policy, including traffic light (TL), nutrient profile model (NPM), and reference value (RV) labels. Mathematical models incorporating experimental and dose–response data support determining the most effective form. When selecting a modeling method, it is essential to consider the uncertainty involved in estimating risk factors. This study aims to create a computational model to predict the health and economic impacts of different policy options using an improved version of the Scarborough algorithm, incorporating a validation process to address potential uncertainties. The model shows that NPM was the most effective, reducing the estimated annual mortality rate from 514,247 cases to 447,394 cases (13% reduction). The following labels were TL (11% reduction) and RV (6% reduction). Economically, the RV label affects consumer spending the least, predicting an 8% increase in monthly spending per individual from the baseline. When assessed from both health and economic perspectives, the RV label has emerged as the most advantageous front-of-pack food labeling policy. The proposed model can aid policymakers in evaluating policy alternatives and thus selecting the most advantageous policies based on health and economic outcomes while ensuring the model's accuracy and applicability for the community.

Experimental Design and Modeling for Forward-Inverse Maps

In customer-driven design of systems or products, one has performance targets in mind and would like to determine values for product or system parameters that meet such targets. Engineering computer simulation models predict performance given design parameter values; meeting a target is done iteratively through an optimization search procedure, typically by optimizing a regression, neural network or other type of approximation metamodel of the computer model. We pose the thesis that, since forward metamodel construction is a key part of this strategy, constructing an inverse metamodel directly is advantageous. The inverse metamodel obviates the need for optimization in many settings. One can design experiments that allow simultaneous fitting of forward and inverse metamodels. We discuss the potential for this strategy, the connection with the calibration problem, and some of the issues that must be resolved to make the approach practical.

Outer hair cells stir cochlear fluids.

We hypothesized that active outer hair cells drive cochlear fluid circulation. The hypothesis was tested by delivering the neurotoxin, kainic acid, to the intact round window of young gerbil cochleae while monitoring auditory responses in the cochlear nucleus. Sounds presented at a modest level significantly expedited kainic acid delivery. When outer-hair-cell motility was suppressed by salicylate, the facilitation effect was compromised. A low-frequency tone was more effective than broadband noise, especially for drug delivery to apical locations. Computational model simulations provided the physical basis for our observation, which incorporated solute diffusion, fluid advection, fluid-structure interaction, and outer-hair-cell motility. Active outer hair cells deformed the organ of Corti like a peristaltic tube to generate apically streaming flows along the tunnel of Corti and basally streaming flows along the scala tympani. Our measurements and simulations coherently indicate that the outer-hair-cell action in the tail region of cochlear traveling waves is for cochlear fluid circulation.

Intelligence analysis of membrane distillation via machine learning models for pharmaceutical separation

This study investigates simulation of pharmaceutical separation via membrane distillation process by computational simulation and machine learning modeling strategy. The efficacy of three regression models, i.e., Multi-layer Perceptron (MLP), Gamma Regression, and Support Vector Regression (SVR) in predicting the solute concentration, C(mol/m³), was evaluated. The hyper-parameters were optimized by fine-tuning the models using the Red Deer Algorithm (RDA). Computational analyses were carried out for removal of pharmaceuticals from solution by membrane distillation in continuous mode. Mass transfer and machine learning models were implemented focusing on concentration of solute in the feed section of membrane. Results indicate that the Multi-layer Perceptron model achieved great accuracy with an R2 of 0.9955, an MAE of 0.0084, and an RMSE of 0.0148, effectively capturing complex nonlinear relationships in the data. Gamma Regression also performed acceptably, with fitting R2 of 0.9214, showing its suitability for positively skewed data. The Support Vector Regression model, while capturing the general trend, showed the lowest performance with an R2 of 0.8710. These findings suggest that the Multi-layer Perceptron is the most accurate model for this dataset, followed by Gamma Regression and Support Vector Regression. This underscores the importance of careful model selection and optimization in regression analysis in combination with computational simulation of membrane processes.

Kinematics and hydrodynamic performance of zebrafish C-type maneuvers: A comparison of two- and three-dimensional simulations

Two-dimensional (2D) and three-dimensional (3D) numerical models are commonly employed to investigate the kinematic and hydrodynamic characteristics of fish maneuvers. In this study, we captured the posture characteristics of zebrafish during C-type maneuvers using high-speed photography and constructed a midline curvature model via the tandem principal characteristics method, which exhibited a “double peak and single valley” structure. Based on this curvature model, self-propelled simulations were conducted using the immersed boundary method with adaptive mesh refinement. The results showed that, under identical deformation conditions, the 2D simulation exhibited a 16.8% higher centroid velocity, 6.1% greater overall angular velocity, and an 11.9% larger turning angle compared to the 3D simulation. This discrepancy is primarily due to the 2D model’s inability to accurately represent the fish body’s mass distribution and force characteristics, resulting in artificially elevated performance. Nevertheless, 2D simulations remain applicable for studying the propulsion performance of fish with elongated cross-sections and large fin areas. Comparison between the simulated and real motion performance reveals that, under the self-propelled computational model, both 2D and 3D numerical simulations consistently capture the qualitative motion patterns. The quantitative results also reflect the actual swimming performance of the fish within an acceptable margin of error.

РАЗРАБОТКА ПРОГРАММЫ РАСЧЕТА ПАРАМЕТРОВ СХЕМЫ ЗАМЕЩЕНИЯ ТРЕХФАЗНОГО АСИНХРОННОГО ЭЛЕКТРОДВИГАТЕЛЯ

The article is devoted to developing a program for calculating the parameters of a T-shaped equivalent circuit of three-phase asynchronous electric motors. The relevance of this work is due to the need to obtain reliable results of computer simulation modelling of electric drive systems in software packages. The aim of the study is to implement in a convenient software interface an analytical technique for calculating the parameters of an asynchronous motor equivalent circuit with minimal deviations from the catalogue data. For the software calculation of the equivalent circuit parameters the paper considers analytical approximation and iterative counting techniques, since they do not require experiments on industrial electrical equipment. A comparative analysis of such techniques is performed using the example of a three-phase asynchronous motor brand BA280S4 with a power of 110 kW. The results of the compar-ative analysis show that the highest reliability of the mechanical and electromechanical characteristics is achieved in the case of using the iterative counting technique with minimizing the objective function of the sum of the weighted squares of the deviations of the control point values from the catalogue data. The authors implement the program for calculating the equivalent circuit parameters according to the selected calculation method in the Embarcadero Delphi environment. The reliable values of the electric motor parameters calculated by the program will allow for computer to model electric drive systems that best matches real objects.

Study on the 2D equivalent nonlinear dynamics simulation model related to high speed precision bearing and spindle

The stiffness and contact stress of the bearing spindle system are the key factors affecting its machining accuracy and service life under the condition of high-speed service, which will be affected by different structural parameters and service conditions. It is essential to establish an efficient and accurate computational simulation model to understand the influence of complex factors on the nonlinear dynamic characteristics of the bearing spindle system. Firstly, in the paper, a 2D axisymmetric finite element model of the bearing, aims at the relationship between stiffness and contact stress of the bearing under high-speed service, has been built based on a classical dynamic analysis model and the reversed method of material parameters of equivalent rolling balls. Additionally, for the BT30 spindle, the 2D axisymmetric finite element model of the bearing spindle system also has been built and applied in mechanical analysis of spindle under different conditions of assembly and service, based on the bearing model. The results show that the axial force of bearings decreases as the rotational speed increases, and an augmentation in speed will result in a reduction in the axial stiffness of the BT30 spindle. In addition, the maximum contact stress exhibits a slight decline as the rotational speed increases. Furthermore, with an escalating preload, the stiffness and contact stress of the spindle undergo substantial increments, however, these parameters will cease to alter once a certain threshold is reached.

Methodology for Improving the Educational Process Based on Computer Simulation Models in Secondary Schools (In the Example of 11th Class Computer Science and Information Technology Science)

This article presents the scientific research conducted on the use of computer simulation models in the effective organization of the educational process in general education schools. Also, the stages of creating computer simulation models, recommendations on their use in teaching activities are given. Scientific publications of foreign scientists and CIS countries were analyzed

Validation and Verification of Computational Model for the Numerical Simulation of the Operational Principle of a Submerged Horizontal Plate Device

This study describes the validation and verification of a two-dimensional numerical wave channel with a Submerged Horizontal Plate (SHP). The SHP is a fixed, submerged structure with a dual function: it acts as a breakwater and as a wave energy converter. To carry out the validation and verification procedures for the computational modeling, experimental and numerical results obtained from the literature were used. A relative error of 2.14% for the maximum axial velocity below the SHP was obtained in the validation, while an average absolute error of 0.0043 m/s for the axial velocity variation below the SHP was identified in the verification. Therefore, it can be inferred that the validation and verification stages were carried out successfully. So, the model is suitable for the numerical simulation of the operational principle of the SHP, both on a laboratory scale and on a real scale, allowing the investigation of its fluid dynamic behavior.

Numerical analysis and Schlieren visualization of gas flow dynamics inside the plasma arc cut kerf with curved cutting fronts

In plasma arc cutting (PAC), the characteristics of the gas flow exiting the nozzle significantly influence the cut quality. The high-pressure jet in PAC forms complex shockwave structures when it is incident on the metal to be cut. In this study, the flow behavior inside the kerfs of various geometries derived from an actual PAC workpiece is assessed. The shape of the cutting front in the kerf varies with the changing cutting speed. A high cutting speed yields a curved cutting front, resulting in unwanted gas flow behavior and adversely influencing the cutting performance. In this study, a computational fluid dynamics simulation model was used to analyze the effects of a curved cutting front on the gas flow behavior during the PAC process. The gas flow patterns obtained from the numerical simulations were qualitatively compared with the Schlieren experiment results. The analysis results indicated that the curvature of the cutting fronts generated oblique shockwave structures that significantly reduced the flow velocity. In particular, the weak shock structures throughout the curved cutting front gradually decreased the flow velocity. The critical flow velocity was realized in the kerf with a highly curved cutting front, beyond which the vertical penetration of the material was not possible. The shear stress lines concurred with the striation patterns on the kerf walls, thereby validating the numerical analysis results.

Filling Process Optimization of a Fully Flexible Machine through Computer Simulation and Advanced Mathematical Modeling

Filling Process Optimization of a Fully Flexible Machine through Computer Simulation and Advanced Mathematical Modeling

Building-block-flow computational model for large-eddy simulation of external aerodynamic applications

Computational fluid dynamics is an essential tool for accelerating the discovery and adoption of transformative designs across multiple engineering disciplines. Despite its many successes, no single approach consistently achieves high accuracy for all flow phenomena of interest, primarily due to limitations in the modeling assumptions. Here, we introduce a closure model for wall-modeled large-eddy simulation to address this challenge. The model, referred to as the Building-block Flow Model (BFM), rests on the premise that a finite collection of simple flows encapsulates the essential missing physics necessary to predict more complex scenarios. The BFM is designed to: (1) predict multiple flow regimes, (2) unify the closure model at solid boundaries and the rest of the flow, (3) ensure consistency with numerical schemes and gridding strategies by accounting for numerical errors, (4) be directly applicable to arbitrary complex geometries, and (5) be scalable to model additional flow physics in the future. The BFM is utilized to predict key quantities in five cases, including an aircraft in landing configuration, demonstrating similar or superior capabilities compared to previous state-of-the-art models. The design of BFM opens up new opportunities for developing closure models that can accurately represent various flow physics across different scenarios.

3D Variability Analysis Reveals a Hidden Conformational Change Controlling Ammonia Transport in Human Asparagine Synthetase.

How motions in enzymes might be linked to catalytic function is of considerable general interest. Advances in X-ray crystallography and cryogenic electron microscopy (cryo-EM) offer the promise of elucidating functionally relevant conformational changes that are not easily studied by other biophysical methods. Here we use 3D variability analysis (3DVA) of the cryo-EM map for wild-type (WT) human asparagine synthetase (ASNS) to identify a functional role for the Arg-142 side chain as a gate that mediates ammonia access to a catalytically relevant intramolecular tunnel. Our 3DVA-derived hypothesis is assessed experimentally, using the R142I variant in which Arg-142 is replaced by isoleucine, and by molecular dynamics (MD) simulations on independent, computational models of the WT human ASNS monomer and its catalytically relevant, ternary complex with β-aspartyl-AMP and MgPPi. Residue fluctuations in the MD trajectories for the human ASNS monomer are consistent with those determined for 3DVA-derived structures. These MD simulations also indicate that the gating function of Arg-142 is separate from the molecular events that form a continuous tunnel linking the two active sites. Experimental support for Arg-142 playing a role in intramolecular ammonia translocation is provided by the glutamine-dependent synthetase activity of the R142 variant relative to WT ASNS. MD simulations of computational models for the R142I variant and the R142I/β-aspartyl-AMP/MgPPi ternary complex provide a possible molecular basis for this observation. Overall, the combination of 3DVA with MD simulations is a generally applicable approach to generate testable hypotheses of how conformational changes in buried side chains might regulate function in enzymes.

Optimizing Medical Care during a Nerve Agent Mass Casualty Incident Using Computer Simulation

IntroductionChemical mass casualty incidents (MCIs) pose a substantial threat to public health and safety, with the capacity to overwhelm healthcare infrastructure and create societal disorder. Computer simulation systems are becoming an established mechanism to validate these plans due to their versatility, cost-effectiveness and lower susceptibility to ethical problems.MethodsWe created a computer simulation model of an urban subway sarin attack analogous to the 1995 Tokyo sarin incident. We created and combined evacuation, dispersion and victim models with the SIMEDIS computer simulator. We analyzed the effect of several possible approaches such as evacuation policy (‘Scoop and Run’ vs. ‘Stay and Play’), three strategies (on-site decontamination and stabilization, off-site decontamination and stabilization, and on-site stabilization with off-site decontamination), preliminary triage, victim distribution methods, transport supervision skill level, and the effect of search and rescue capacity.ResultsOnly evacuation policy, strategy and preliminary triage show significant effects on mortality. The total average mortality ranges from 14.7 deaths in the combination of off-site decontamination and Scoop and Run policy with pretriage, to 24 in the combination of onsite decontamination with the Stay and Play and no pretriage.ConclusionOur findings suggest that in a simulated urban chemical MCI, a Stay and Play approach with on-site decontamination will lead to worse outcomes than a Scoop and Run approach with hospital-based decontamination. Quick transport of victims in combination with on-site antidote administration has the potential to save the most lives, due to faster hospital arrival for definitive care.

Synthesis and Molecular Dynamic Simulation of Novel Cationic and Non-cationic Pyrimidine Derivatives as Potential G-quadruplex-ligands.

Drug resistance has been a problem in cancer chemotherapy, which often causes shortterm effectiveness. Further, the literature indicates that telomere G-quadruplex could be a promising anti-cancer target. We synthesized and characterized two new pyrimidine derivatives as ligands for G-quadruplex DNA. The interaction of novel non-cationic and cationic pyrimidine derivatives (3a, b) with G-quadruplex DNA (1k8p and 3qsc) was explored by circular dichroism (CD) and ultraviolet-visible spectroscopy and polyacrylamide gel electrophoresis (PAGE) methods. The antiproliferative activity of desired compounds was evaluated by the MTT assay. Apoptosis induction was assessed by Propidium iodide (P.I.) staining and flow cytometry. Computational molecular modeling (CMM) and molecular dynamics simulation (MD) were studied on the complexes of 1k8p and 3qsc with the compounds. The van der Waals, electrostatic, polar solvation, solventaccessible surface area (SASA), and binding energies were calculated and analyzed. The experimental results confirmed that both compounds 3a and 3b interacted with 1k8p and 3qsc and exerted cytotoxic and proapoptotic effects on cancer cells. The number of hydrogen bonds and the RMSD values increased in the presence of the ligands, indicating stronger binding and suggesting increased structural dynamics. The electrostatic contribution to binding energy was higher for the cationic pyrimidine 3b, indicating more negative binding energies. Both experimental and MD results confirmed that 3b was more prone to form a complex with DNA G-quadruplex (1k8p and 3qsc), inhibit cell growth, and induce apoptosis, compared to the non-cationic pyrimidine 3a.

The role of the thermal properties of electrons on the dispersion properties of Alfvén waves in space plasmas

Context. The transition from left-hand to right-hand polarised Alfvén waves depends on the wavenumber, the ratio of kinetic to magnetic pressure, β, the temperature anisotropy, and the ion composition of the plasma. Along with the temperature anisotropy, the electron-to-proton temperature ratio, Te/Tp, is of great relevance for the characterisation of the thermal properties of a plasma. This ratio varies significantly between different space plasma environments. Thus, studying how variations in this ratio affect the polarisation properties of electromagnetic waves becomes highly relevant for our understanding of the dynamics of space plasmas. Aims. We present an extensive study on the effect of the thermal properties of electrons on the behaviour and characteristics of Alfvénic waves in fully kinetic linear theory, as well as on the transition from the electromagnetic ion-cyclotron wave to the kinetic Alfvén wave. Methods. We solved the fully kinetic dispersion relation for oblique electromagnetic waves of the Alfvén branch in a homogenous Maxwellian electron-proton plasma. We quantified the effect of the thermal properties of electrons by varying the electron-to-proton temperature ratio for different configurations of the propagation angle, βp = 8πnkTp/B2, and wavenumber. Results. We show that the temperature ratio, Te/Tp, has strong and non-trivial effects on the polarisation of the Alfvénic modes, especially at kinetic scales (k⊥ρL > 1, where k⊥ = k sin θ, θ is the propagation angle, and ρL = cs/Ωp, with cs the plasma sound speed and Ωp the proton’s gyrofrequency) and βe + βp > 0.5. We conclude that electron inertia plays an important role in the kinetic scale physics of the kinetic Alfvén wave in the warm plasma regime, and thus cannot be excluded in hybrid models for computer simulations.

Intelligent generation method of infection risk map and management system in hospital waiting room for respiratory infectious diseases

Respiratory infectious diseases, such as seasonal influenza, pose significant risks to public health safety through airborne transmission. This study aims to explore methods for controlling airborne infection risk in waiting rooms, a hotspot for cross-infection. A database of 990 samples was established by integrating the results of computational fluid dynamics and social force model simulations into the Wells-Riley equation. We introduced two indicators, Pr (Particle Removal Efficiency) and Hr (High-risk Area Ratio), to evaluate the cleanliness performance of waiting room spaces. Additionally, the Sci (Space Cleanliness Index) was proposed as a criterion for evaluating architectural designs and fine-tuning fresh air system operational parameters. We also unveiled the mapping relationship between spatial morphology parameters and ventilation design parameters in relation to the cleanliness performance of waiting rooms. An infection-risk prediction proxy model was established based on machine learning methods, suitable for rapid prediction of spatial infection risks in waiting rooms and optimization of fresh air system operational parameters. The findings can be applied to the selection of hospital design schemes and the optimization of ventilation operational control strategies, aiding in strengthening infectious disease control and reducing the public health safety risks of cross-infection from respiratory infections during peak seasons in hospitals.

The dynamics of Staphylococcal infection and their treatment with antibiotics and bacteriophage in the Galleria mellonella model system.

Critical to our understanding of infections and their treatment is the role the innate immune system plays in controlling bacterial pathogens. Nevertheless, many in vivo systems are made or modified such that they do not have an innate immune response. Use of these systems denies the opportunity to examine the synergy between the immune system and antimicrobial agents. In this study we demonstrate that the larva of Galleria mellonella is an effective in vivo model for the study of the population and evolutionary biology of bacterial infections and their treatment. To do this we test three hypotheses concerning the role of the innate immune system during infection. We show: i) sufficiently high densities of bacteria are capable of saturating the innate immune system, ii) bacteriostatic drugs and bacteriophages are as effective as bactericidal antibiotics in preventing mortality and controlling bacterial densities, and iii) minority populations of bacteria resistant to a treating antibiotic will not ascend. Using a highly virulent strain of Staphylococcus aureus and a mathematical computer-simulation model, we further explore how the dynamics of the infection within the short term determine the ultimate infection outcome. We find that excess immune activation in response to high densities of bacteria leads to a strong but short-lived immune response which ultimately results in a high degree of mortality. Overall, our findings illustrate the utility of the G. mellonella model system in conjunction with established in vivo models in studying infectious disease progression and treatment.

Modeling of microwave thawing and reheating of multiphase foods: A case study for packed rice

Microwave (MW) thawing and reheating of porous foods such as rice is a common practice, but uniform heating can be difficult to achieve. Computer simulation models were developed using the finite-element method to study MW thawing and reheating of packed rice. A method to obtain an apparent thermal conductivity was proposed, which accounts for heat distribution by water evaporation and condensation through the air pores in the sample. Reheating experiments of mashed compact rice and regular porous rice were carried out on a flatbed MW oven for 90 s. Similarly, thawing experiments were conducted on porous rice for 180 s. Good agreement between simulated and experimental results was obtained when correcting for thermal conductivity of the pores and for the volumetric power absorption between the frozen and thawed fractions This can help in the design of specifically designed porous foods and containers that allow for fast and homogeneous reheating.