Computational Dynamic Analysis Research Articles

Computational analysis of affinity dynamics between the variants of SARS-CoV-2 spike protein (RBD) and human ACE-2 receptor

The novel coronavirus SARS-CoV-2 resulted in a significant worldwide health emergency known as the COVID-19 pandemic. This crisis has been marked by the widespread of various variants, with certain ones causing notable apprehension. In this study, we harnessed computational techniques to scrutinize these Variants of Concern (VOCs), including various Omicron subvariants. Our approach involved the use of protein structure prediction algorithms and molecular docking techniques, we have investigated the effects of mutations within the Receptor Binding Domain (RBD) of SARS-CoV-2 and how these mutations influence its interactions with the human angiotensin-converting enzyme 2 (hACE-2) receptor. Further we have predicted the structural alterations in the RBD of naturally occurring SARS-CoV-2 variants using the tr-Rosetta algorithm. Subsequent docking and binding analysis employing HADDOCK and PRODIGY illuminated crucial interactions occurring at the Receptor-Binding Motif (RBM). Our findings revealed a hierarchy of increased binding affinity between the human ACE2 receptor and the various RBDs, in the order of wild type (Wuhan-strain) < Beta < Alpha < Gamma < Omicron-B.1.1.529 < Delta < Omicron-BA.2.12.1 < Omicron-BA.5.2.1 < Omicron-BA.1.1. Notably, Omicron-BA.1.1 demonstrated the highest binding affinity of -17.4 kcal mol−1 to the hACE2 receptor when compared to all the mutant complexes. Additionally, our examination indicated that mutations occurring in active residues of the Receptor Binding Domain (RBD) consistently improved the binding affinity and intermolecular interactions in all mutant complexes. Analysis of the differences among variants has laid a foundation for the structure-based drug design targeting the RBD region of SARS-CoV-2.

Deep learning and big data mining for Metal–Organic frameworks with high performance for simultaneous desulfurization and carbon capture

Carbon capture and desulfurization of flue gases are crucial for the achievement of carbon neutrality and sustainable development. In this work, the “one-step” adsorption technology with high-performance metal–organic frameworks (MOFs) was proposed to simultaneously capture the SO2 and CO2. Four machine learning algorithms were used to predict the performance indicators (NCO2+SO2, SCO2+SO2/N2, and TSN) of MOFs, with Multi-Layer Perceptron Regression (MLPR) showing better performance (R2 = 0.93). To address sparse data of MOF chemical descriptors, we introduced the Deep Factorization Machines (DeepFM) model, outperforming MLPR with a higher R2 of 0.95. Then, sensitivity analysis was employed to find that the adsorption heat and porosity were the key factors for SO2 and CO2 capture performance of MOF, while the influence of open alkali metal sites also stood out. Furthermore, we established a kinetic model to batch simulate the breakthrough curves of TOP 1000 MOFs to investigate their dynamic adsorption separation performance for SO2/CO2/N2. The TOP 20 MOFs screened by the dynamic performance highly overlap with those screened by the static performance, with 76 % containing open alkali metal sites. This integrated approach of computational screening, machine learning, and dynamic analysis significantly advances the development of efficient MOF adsorbents for flue gas treatment.

Molecular Dynamics of Hydration Shells of Adsorbates in Entropy-Driven Adsorption (Hydrophobic Bonding) to Activated Carbon Surfaces

Hydrophobic bonding is a phenomenon wherein the adsorption of solutes from aqueous solutions is driven largely by the desire of solvent molecules to interact with each other, thus squeezing out solute molecules onto the adsorbent surface. A novel computational analysis of hydration shell water dynamics was used to study the driving force for the hydrophobic bonding of five small drug molecules to activated carbon. It was demonstrated that the solvation of these drug molecules produced hydration shells of lower density and molecular mobility than bulk water, up to 10.5–14 Å distance. Excellent correlations were found between the simulated water-water hydrogen bonding lifetimes in the hydration shell and the experimental capacity constants of hydrophobic bonding (KHB) obtained from the Two-Mechanism Langmuir-Like Equation. KHB also correlated well with the solute-solvent vdW interaction energies in a manner that could allow future predictions of KHB values from simple simulations. Such correlations were not found with the capacity constant of the well-known enthalpy-driven adsorption. The driving force for hydrophobic bonding has entropic origins due to the elimination of water structuring in the hydration shells. However, unlike a typical entropy-driven process, hydrophobic bonding to activated carbon was also associated with a large exothermic enthalpy change when studied with isoperibol calorimetry.

Animalista, Narco-Cultural, Conservacionista. Visions of Nature Around the Case of Hippos in Colombia

AbstractSince their introduction in Colombia in the '80s for Pablo Escobar’s extravagant zoo, hippos have become an ecological problem around the basin of the Magdalena River. This article proposes an ecosemiotic discourse analysis of different visions of nature enacted by stakeholders and public opinion around the management of hippos in Colombia. Concretely, we focus on three particular discourses and visions of nature: animalista, narco-cultural, and conservacionista. In this article, we present the relevant social and ecological context of Colombia, the visions of nature theory and the impact of such visions on conservation measures regarding so-called invasive species; we describe and analyze the three visions of nature we center on, and present a computational analysis of discourse dynamics and controversies in Twitter between of such visions of nature; and we reflect on possible courses of action and recommendations about addressing the close interrelation of public discourses and ecosystem conservation by proposing an alternative view, based on the biosemiotic framework of semiocide, to the concept of invasive species.

Computational analysis of cilia-mediated flow dynamics of Jeffrey nanofluid in physiologically realistic geometries

Cilia play important roles in fluid transport and development by propagating metachronal waves along cell surfaces. This study numerically investigates the biomechanics of cilia-driven flow of Jeffrey nanofluid in a wavy curved channel. The orthogonal curvilinear coordinates are used for the mathematical formulation of the problem in a set of partial differential equations. The governing equations are simplified using the dimensionless numbers and stream functions and then reduced using the long wavelength and low Reynolds number assumptions. Shooting method is applied to determine velocity, temperature, and nanoparticle concentration profiles. The resultant velocity, temperature profiles, nanoparticle concentration profiles, and streamlines are interpreted and elucidated graphically. The parametric analyses systematically examine the impacts of channel curvature, thermal buoyancy forces, nanoparticle concentrations, Jeffrey fluid rheology, and cilia motion kinematics on transport phenomena. Key findings show temperature and concentration gradients strongly influenced by cilia beating. The study provides deeper insight into the influence of these parameters on the cilia-driven flow in a complex wavy curved channel, bearing potential applications in heat transfer systems, nanotechnology, and biotechnology, among other fields.

Modification of Polyamide 66 for a Media-Tight Hybrid Composite with Aluminum

Metal-plastic composites are becoming increasingly important in lightweight construction. As a combination, e.g., for transmission housings in automobiles, composites made of die-cast aluminum housings and Polyamide 66 are a promising material. The interface between metal and plastic and the properties of the plastic component play an important role with regard to media tightness against transmission oil. The mechanical properties of the plastic can be matched to aluminum by glass fibers and additives. In the case of fiber-reinforced plastics, the mechanical properties depend on the fiber length and their orientation. These structural properties were investigated using computer tomography and dynamic image analysis. In addition to the mechanical properties, the thermal expansion coefficient was also investigated since a strongly different coefficient of the joining partners leads to stresses in the interface. Polyamide 66 was processed with 30 wt% glass fibers to align the mechanical and thermal expansion properties to those of aluminum. In contrast to the reinforcement additives, an impact modifier to improve the toughness of the composite, and/or a calcium stearate to exert influence on the rheological behavior of the composite, were used. The combination of the glass fibers with calcium stearate in Polyamide 66 led to high stiffnesses (11,500 MPa) and strengths (200 MPa), which were closest to those of aluminum. The coefficient of thermal expansion was found to be 6.6 × 10-6/K for the combination of Polyamide 66 with 30 wt% glass fiber and shows a low expansion exponent compared to neat Polamid 66. It was detected that the use of an impact modifier led to less orientated fibers along the injection direction, which resulted in lower modulus and strength in terms of mechanical properties.

Triclocarban-contaminated wastewater treatment by innovative hybrid moving entrapped bead activated sludge reactor (HyMER): Continuous performance and computational dynamic simulation analysis

Triclocarban (TCC) has been used in consumer products and is a widespread contaminant in municipal wastewater treatment systems that ultimately accumulates in natural receiving water and soil. This work aims to apply an innovative hybrid moving entrapped bead activated sludge reactor (named “HyMER”) that integrates entrapped TCC-degrading microbes and freely suspended activated sludge to treat TCC-contaminated wastewater. A previously isolated TCC-degrading bacterium (Pseudomonas fluorescens strain MC46, called MC46) and barium alginate entrapment were applied. The synthetic TCC-contaminated wastewater treatment (with TCC concentration of 10 mg/L) was performed using 20-cycle fed-batch reactor operation with feeding times of 12 and 24 h and cycle times of 13 and 25 h. The results indicated that the HyMER effectively reduced chemical oxygen demand by up to 80 and 95 % and TCC by up to 53 and 83 %, respectively, with feeding times of 12 and 24 h. Three TCC degradation intermediate products were found—3,4-dichloroaniline, 4-chloroaniline, and aniline. Scanning electron microscopic analysis revealed shorter cells and bacterial appendage development as cell adaptations against TCC and its intermediates. The live/dead assay indicated high survival of entrapped MC46 in toxic conditions, with up to 84 % viable cells. Based on computational fluid dynamic analysis, no entrapped cell agglomeration showed in the reactor, indicating the potential application of HyMER for real wastewater treatment. These results exhibit the feasibility of HyMER and its applicability for future toxic wastewater treatment.

Nonlinear finite element free and forced vibrations of cellular plates having lattice-type metamaterial cores: a strain gradient plate model approach

The main objective of this paper is to develop a theoretically and numerically reliable and efficient methodology based on combining a finite element method and a strain gradient shear deformation plate model accounting for the nonlinear free and forced vibrations of cellular plates having lattice-type metamaterial cores. The proposed model provides a modelling framework computationally more efficient than framework of the conventional three-dimensional elasticity for the simulation of the underlying nonlinear dynamics of cellular plates with microarchitectures. The corresponding governing equations follow Mindlin’s strain gradient elasticity theory including the micro-inertia effect applied to the first-order shear deformation plate theory along with the nonlinear von Kármán kinematics. Standard and higher-order computational homogenization methods determine the classical and strain gradient material constants, respectively. A higher-order C1-continuous 6-node finite element is adopted for the discretization in the spatial domain, and an arc-length continuation technique along with time-periodic discretization is implemented to solve the resulting nonlinear time-dependent problem. Through a set of comparative studies with 3D full-field models as reliable validation references for triangularly prismatic example cores, the accuracy and efficacy of the proposed dimension reduction methodology are demonstrated for a diverse range of problem parameters for analyzing the large-amplitude dynamic structural response. The results show that the proposed strain gradient plate model can accurately capture the microarchitecture effects of cellular plates with low computational costs, which signifies a relevant contribution particularly to the computational analysis of nonlinear dynamics.

Computational analysis of water dynamics in AOT reverse micelles

Aerosols can be modeled for detailed investigations using reverse micelles in the laboratory as well as in computational simulations. A long-standing question in the description of confined water under these conditions is that of a two-state model of core – interface or a three-state model of core – intermediate – interface. In this work, we present results of analysis of water dynamics inside reverse micelles from fully atomistic molecular dynamics simulations. The size and composition of reverse micelles is expressed through w0, the ratio of the number of water molecules to the number of surfactant molecules. Reverse micelles of diverse sizes, with w0 ranging from 5 to 20, were constructed with Sodium bis(2-ethylhexyl) sulfosuccinate (AOT) surfactant and simulated within isooctane solvent. Residence time and diffusion coefficients, in the simulations, both behaved increasingly like bulk water with the increase in size of reverse micelles. Rotational anisotropy autocorrelation was modeled using exponential functions in the short time range of 10–20 ps and longer time data were modeled as a power law fit. Similarly, the diffusion of water in the reverse micelles was also modeled on a power law fit. All these metrics demonstrate a clear progression towards bulk water behavior as the reverse micelle size increases. Additionally, our results also support a 3-layer model of water in a reverse micelle of core – intermediate – interface. These results extend the understanding of water dynamics in reverse micelles and provide further evidence for the 3-layer model.

Computational analysis of vortex dynamics and aerodynamic performance in flying-snake-like gliding flight with horizontal undulation

This paper numerically studies the flow dynamics of aerial undulation of a snake-like model, which is adapted from the kinematics of the flying snake (Chrysopelea) undergoing a gliding process. The model applies aerial undulation periodically in a horizontal plane where a range of angle of attack (AOA) is assigned to model the real gliding motion. The flow is simulated using an immersed-boundary-method-based incompressible flow solver. Local mesh refinement mesh blocks are implemented to ensure the grid resolutions around the moving body. Results show that the undulating body produces the maximum lift at 45° of AOA. Vortex dynamics analysis has revealed a series of vortex structures including leading-edge vortices (LEV), trailing-edge vortices, and tip vortices around the body. Changes in other key parameters including the undulation frequency and Reynolds number are also found to affect the aerodynamics of the studied snake-like model, where increasing of undulation frequency enhances vortex steadiness and increasing of Reynolds number enhances lift production due to the strengthened LEVs. This study represents the first study of both the aerodynamics of the whole body of the snake as well as its undulatory motion, providing a new basis for investigating the mechanics of elongated flexible flyers.

Computational analysis of metal transfer mode, dynamics, and heat transfer under different pulsating frequencies in pulsed wire-arc additive manufacturing

Abstract A numerical model of the metal transfer process was developed using the thermomagnetohydrodynamic equations and the phase-field method to investigate the influence of pulse frequency on the metal transfer mode, dynamics, and thermal behavior in the pulsed wire-arc additive manufacturing (WAAM) process. The control of droplet transfer mode, dynamics, and thermal behavior is essential in WAAM; otherwise, several potential defects such as high residual stresses and distortion, poor dimensional accuracy, and surface quality may occur due to uneven heat input condition and process instability. Therefore, in this study, eight sets of pulse frequencies ranging from 50 to 225 Hz, in steps of 25 Hz, using identical power source parameters, such as pulse duty cycle and average current of 25.4% and 152 A, respectively, were considered and compared for a nearly square current waveform. The results reveal that only the current pulses with a medium frequency regime (100–175 Hz) achieve the one-droplet-per-pulse mode of metal transfer. Moreover, an increase in pulse frequency leads to a shorter necking length of the pendent droplet and a significantly lower average speed and temperature of the detached droplet. The results for the heat flux analysis indicate that Joule heating and arc heating decrease due to the increase in pulse frequency, whereas the sheath heating remains almost constant using different pulse frequencies. The proposed numerical scheme provides a detailed understanding of controlling and tailoring the different metal transfer modes and their metal transfer stability during WAAM, which benefits further process optimization and control.

Clinical Impact of Computational Heart Valve Models.

This paper provides a review of engineering applications and computational methods used to analyze the dynamics of heart valve closures in healthy and diseased states. Computational methods are a cost-effective tool that can be used to evaluate the flow parameters of heart valves. Valve repair and replacement have long-term stability and biocompatibility issues, highlighting the need for a more robust method for resolving valvular disease. For example, while fluid–structure interaction analyses are still scarcely utilized to study aortic valves, computational fluid dynamics is used to assess the effect of different aortic valve morphologies on velocity profiles, flow patterns, helicity, wall shear stress, and oscillatory shear index in the thoracic aorta. It has been analyzed that computational flow dynamic analyses can be integrated with other methods to create a superior, more compatible method of understanding risk and compatibility.

Computational representation and analysis of emotion dynamics

Computational representation and analysis of emotion dynamics

Induction of inverted morphology in brain organoids by vertical-mixing bioreactors

Organoid technology provides an opportunity to generate brain-like structures by recapitulating developmental steps in the manner of self-organization. Here we examined the vertical-mixing effect on brain organoid structures using bioreactors and established inverted brain organoids. The organoids generated by vertical mixing showed neurons that migrated from the outer periphery to the inner core of organoids, in contrast to orbital mixing. Computational analysis of flow dynamics clarified that, by comparison with orbital mixing, vertical mixing maintained the high turbulent energy around organoids, and continuously kept inter-organoid distances by dispersing and adding uniform rheological force on organoids. To uncover the mechanisms of the inverted structure, we investigated the direction of primary cilia, a cellular mechanosensor. Primary cilia of neural progenitors by vertical mixing were aligned in a multidirectional manner, and those by orbital mixing in a bidirectional manner. Single-cell RNA sequencing revealed that neurons of inverted brain organoids presented a GABAergic character of the ventral forebrain. These results suggest that controlling fluid dynamics by biomechanical engineering can direct stem cell differentiation of brain organoids, and that inverted brain organoids will be applicable for studying human brain development and disorders in the future.

Automatic 3D cluster modelling of COVID-19 through voxel-based redistribution

Computational analysis of virus dynamics provides a non-contact environment for the study of the vital object. Cluster modelling is an essential step to investigate the properties of a group of viruses, and an automatic approach is required for massive 3D data processing. The morphological complexity of individual virus limits the application of smooth function algorithms with a regular-shaped assumption. This paper proposed a voxel-based redistribution approach to generate the virus cluster with COVID-19 input automatically. Representative elementary volume analysis was performed to address the statistical influence from the digital sample size. Coordination number analysis and surface density measurement were conducted with COVID-19 input and spherical input for comparison. The proposed approach is in natural compatibility with the lattice Boltzmann method for fluid dynamics analysis. A virtual permeation simulation was performed with the COVID-19 cluster and spherical cluster to demonstrate the necessity to include spike protein structure in the cluster modelling.

Design and analysis of a radial centrifugal pump for cryogenic helium based application

A centrifugal pump is a rotordynamic machine that has wide spread application in industry. After analytical design, it is important to check the machine performance by some numerical method to be assured of machine performance before manufacturing. In the present study, a centrifugal pump conforming to a specific process requirement for cryogenic helium fluid has been developed in detail. This involves analytical design derivation of the stator and rotor part, computer aided design (CAD) modelling, meshing and detailed computational dynamic analysis (CFD) analysis. In line with analytical prediction, it is seen from simulation results that the designed machine meets the given requirements with an achieved hydraulic efficiency of 88%.

Shunt Implants – Past, Present and Future

The treatment of hydrocephalus has evolved over centuries from being an enigma to the use of complex bioprosthetics. Major developments have taken place in the past few decades in shunt hardware and technology, with the use of complex flow regulating valves and biomaterials such as medical-grade silicone having revolutionized the management of hydrocephalus. To discuss the evolution of shunts over the decades and how they will evolve in the future. In this article, we mention an overview of the evolution of shunt technology and hardware from the prehistoric, pre-shunt era to the modern shunt and a brief insight into the future of hydrocephalus treatment. We review the history, development, and pioneers in shunt development and discuss the various types and parts of a shunt system. Shunts have been developed from the works of Galen and Hippocrates to the latest technologies using in vivo flow biosensors, computational analysis of flow dynamics, and use of artificial intelligence. This has led to an individualized and appropriate management that can be provided to even the most complex cases of hydrocephalus.

Experimental and computational dynamic structural analysis of free-flight rockets

Aerospace vehicles’ designers often strive to approach the lightweight structures in order to improve flight performance without compromising vehicles durability. However, this goal may be achieved on the expense of structural rigidity of the vehicle. A missile with high slenderness ratio is a typical vehicle that should be considered as flexible body if precise dynamic behaviour analysis is sought. This analysis is crucial to identify the flight performance of such missile with high accuracy. The present paper discusses the results of a side-by-side experimental and numerical analysis of the vibration characteristics of a full-scale free-flight missile having 70mm caliber. The experimental modal analysis is conducted on the missile with empty motor to represent its unpowered flight regime. Experimental modal analysis setup involved accelerometer sensors while vibration excitation is achieved using an impact hammer. Modal analysis is also conducted numerically using a well-used high-fidelity commercial tool. Results of experimental modal analysis have shown that the first four modes as bending modes with frequencies of 134.4, 400.6, 819.4 and 1173.6 Hz, respectively. The results also demonstrate the close agreement between numerical and experimental approaches.

The development of marine biomaterial derived from decellularized squid mantle for potential application as tissue engineered urinary conduit

Tissue engineering is focusing research effort on search for new biomaterials that might be applied to create artificial urinary conduit. Nevertheless, the demanding biomechanical characteristics necessary for proper conduit function is difficult to be replicated. In this study, we are introducing novel marine biomaterial obtained by decellularization of squid mantle derived from Loligo vulgaris. Squid mantles underwent decellularization according to developed dynamic flow two-staged procedure. Efficacy of the method was confirmed by computational dynamic flow analysis. Subsequently Decellularized Squid Mantle (DSM) underwent extensive histological analysis and mechanical evaluation. Based on gained biomechanical data the computational modelling using finite element method was utilized to simulate behavior of DSM used as a urinary conduit. Taking into account potential application in reconstructive urology, the DSM was then evaluated as a scaffold for urothelial and smooth muscle cells derived from porcine urinary bladder. Conducted analysis showed that DSM created favorable environment for cells growth. In addition, due to polarized structure and natural external polysaccharide layer, it protected seeded cells from urine.

Impaired Myocardial Energetics Causes Mechanical Dysfunction in Decompensated Failing Hearts.

Cardiac mechanical function is supported by ATP hydrolysis, which provides the chemical-free energy to drive the molecular processes underlying cardiac pumping. Physiological rates of myocardial ATP consumption require the heart to resynthesize its entire ATP pool several times per minute. In the failing heart, cardiomyocyte metabolic dysfunction leads to a reduction in the capacity for ATP synthesis and associated free energy to drive cellular processes. Yet it remains unclear if and how metabolic/energetic dysfunction that occurs during heart failure affects mechanical function of the heart. We hypothesize that changes in phosphate metabolite concentrations (ATP, ADP, inorganic phosphate) that are associated with decompensation and failure have direct roles in impeding contractile function of the myocardium in heart failure, contributing to the whole-body phenotype. To test this hypothesis, a transverse aortic constriction (TAC) rat model of pressure overload, hypertrophy, and decompensation was used to assess relationships between metrics of whole-organ pump function and myocardial energetic state. A multiscale computational model of cardiac mechanoenergetic coupling was used to identify and quantify the contribution of metabolic dysfunction to observed mechanical dysfunction. Results show an overall reduction in capacity for oxidative ATP synthesis fueled by either fatty acid or carbohydrate substrates as well as a reduction in total levels of adenine nucleotides and creatine in myocardium from TAC animals compared to sham-operated controls. Changes in phosphate metabolite levels in the TAC rats are correlated with impaired mechanical function, consistent with the overall hypothesis. Furthermore, computational analysis of myocardial metabolism and contractile dynamics predicts that increased levels of inorganic phosphate in TAC compared to control animals kinetically impair the myosin ATPase crossbridge cycle in decompensated hypertrophy/heart failure.