Explicit Simulations Research Articles

THR Using a 3D Printed Custom Made Acetabulum Component: A Case Report

Introduction: THR is one of the commonly performed adult arthroplasties in the world. Over the past 6 decades, Charnley low friction arthroplasty has evolved in design and concept. One among those recent advances is the use of 3D printing technology in arthroplasties. Purpose of this article is to discuss and share the details of a hip arthroplasty case where a customized 3D printed acetabulum component was used. Case: A 3 year postop case of acetabulum fracture fixation presented with arthritis of hip. CT revealed a periacetabular massive bone loss. After considering all options, decision was made to use a 3D printed acetabulum shell. Discussion: Complex THRs with special instrumentation and augmented implants are frequently seen in revision surgeries and post acetabulum fracture cases. Based on the size and pattern of the defect, IlioIschial cages, Triflange cups, Trabecular metal augments, CupCage constructs, Jumbo cups are some common options at a surgeons disposal while tackling an acetabulum bone loss challenge. A 3D manufactured component can be of aid when the defect is too large. It gives the advantage of being anatomically contoured. It also allows a porous structure for bone ingrowth. Conclusion: Life size models of the pelvis and the component gives an explicit simulation of the surgery, including the component placement and trajectory of the screws. This effective preoperative planning can improve the surgical precision and reduce the complications. Literature on the survival rates and long term complications of such 3d printed acetabulum shells is limited. Studies on the long term outcomes with usage of these implants would be insightful Keywords: 3D Printing, Complex THR, Customised acetabular shell

Applicability of Multivariate Linear Regression in Building Energy Demand Estimation

The vision of the research project is to find an energy optimal building configuration, suitable for specified requirements and restrictions. The first step on this way is to create a measure to compare building configurations, faster than explicit energetic simulations. The current study examines the applicability of multivariate linear regression to support the solution of building optimization problems. During the study, multivariate linear regression models were created to estimate the expected annual heating energy demand of building configurations and examined their accuracy Between examinations, the models were modified so that the complexity was increased only to such an extent that the approximation was still sufficiently accurate. The result was a multivariate linear model that estimated the expected output for unknown descriptive variables with a 0% relative error and a 1.6% standard deviation. The R2 point of the estimates was 0.9884. Based on these, the model was considered applicable in the search space defined by the training patterns.

Equivalent discontinuum analysis of stress and displacement in underground rock masses

The complexity and high frequency of fractures in rock masses make discrete fracture network (DFN) models suffer from burdensome computational consumption when every fracture is explicitly simulated. Meanwhile, the uncertainty in the spatial distribution of fractures also leads to the unnecessary explicit simulation of small fractures to achieve more accurate results. In this study, an equivalent discontinuum analysis (EDA) method is proposed to deal with complexly fractured rock masses in the deep underground. An equivalent discrete fracture network (E-DFN) with simple geometric configurations is extracted based on a defined significance index of fractures. The influence of fractures that are neglected in E-DFNs is superposed on the remaining fractures by reassigning their material properties. Using the proposed EDA method, the anisotropy of the deformation modulus of the original DFN model is well represented by the E-DFN models. Compared with the equivalent continuum and discontinuum models, the E-DFN models with reassigned fracture properties have a better potential for maintaining stress variability and displacement discontinuity in rock masses.

The implementation of habitat destruction methods that promote native survival under invasion

Controlling invasive alien species invasion and maintaining the survival of native species have attracted increasing attention, and habitat destruction can be used to achieve these aims. However, whether and how to promote the long-term survival of native species facing invaders through the use of habitat destruction remain unclear. In this study, we developed a spatially explicit simulation model in which invaders and natives were exposed to habitat destruction with different properties, including the spatial structure and the introduction time of habitat destruction, the interval between two destruction events, and the proportion of destroyed habitat. The results showed the following: (1) introducing habitat destruction could promote the long-term survival of native species, especially for a clustered initial spatial distribution of species or long-distance dispersal; (2) the positive effect of habitat destruction on the survival of native species occurred only for a period of time after introduction, such that the destroyed habitats gradually encompassed natives and separated them from invaders, prior to which habitat destruction substantially decreased the abundance of native species; (3) intermediate to high levels of habitat destruction were the most beneficial to the protection of native species for the clustered spatial distribution of species at the initial time or the short dispersal distance; (4) and even when ignoring the proportion of destroyed habitats, introducing spatially dispersed habitat destruction at an earlier time and shortening the interval between two habitat destruction events were very beneficial to the protection of natives. These insights can help facilitate the protection of natives under invasion by adjusting the implementation method of habitat destruction.

Axial Deformation of Shells at Higher Strain Rates using Buckling Initiators

Deformation mode of cylindrical shells and their peak load reduction is of prime importance in impact damage mechanics. In this study, numerical investigation is carried out for triggering mechanism induced in the thin-walled axially compressed short stubby shells, considering the damage occurred in vehicle crash or in any other protective equipment. The shells are studied for their initial buckling response under varying impact velocities for two different triggering configurations. Explicit simulation is carried out using ABAQUS/Explicit® to study the initial buckling of the shells by modelling Split Hopkinson Pressure Bar (SHPB) test setup. Initially, numerical scheme is validated using previously available study. Present analysis is carried out using diamond shaped triggering notches and these are configured in such a way that the shell will deform in particular buckling mode, under the impact of three different velocities i.e. 9 m/s, 20 m/s and 40 m/s. Effect of these notches and their pattern of arrangement on reduction in peak load and energy absorption characteristics are studied. Moreover, comparison is made between commonly used circular hole and diamond notch type cut-outs, in order to study the effect of above said parameters along with the energy absorbed, energy efficiency and specific energy absorption for the shells considered herein. By numerically impacting the shells in SHPB, it is observed that peak load reduction is higher in diamond notched shells as compared to circular hole shells. This was due to the geometry and size of the cut-outs considered in this study. Parameters like peak collapse load, energy absorbed, energy efficiency along with stress concentration around the notch are also observed and studied in this work in order to observe and compare the two shapes of cut-outs.

An Effective Field Theory for large oscillons

We consider oscillons — localized, quasiperiodic, and extremely long-living classical solutions in models with real scalar fields. We develop their effective description in the limit of large size at finite field strength. Namely, we note that nonlinear long-range field configurations can be described by an effective complex field ψ(t,x) which is related to the original fields by a canonical transformation. The action for ψ has the form of a systematic gradient expansion. At every order of the expansion, such an effective theory has a global U(1) symmetry and hence a family of stationary nontopological solitons — oscillons. The decay of the latter objects is a nonperturbative process from the viewpoint of the effective theory. Our approach gives an intuitive understanding of oscillons in full nonlinearity and explains their longevity. Importantly, it also provides reliable selection criteria for models with long-lived oscillons. This technique is more precise in the nonrelativistic limit, in the notable cases of nonlinear, extremely long-lived, and large objects, and also in lower spatial dimensions. We test the effective theory by performing explicit numerical simulations of a (d + 1)-dimensional scalar field with a plateau potential.

Economic benefits of conservation biocontrol: A spatially explicit bioeconomic model for insect pest management in agricultural landscapes

Spatially explicit population dynamic models have been successfully used to explore management scenarios in terms of pest suppression across a wide range of systems. However, the economic implications of pest management, particularly in the case of biological control and non-crop management strategies, have not been well considered. A bioeconomic spatially explicit simulation model was developed, that integrates models of pest population dynamics, pest movement and economics of management. The utility of the model is demonstrated here usingNysius vinitor, a pest of grain crops in Australia. The model estimates the short- and long-term economic benefits of three pest management strategies: (1) in-field pesticide spray; (2) pest suppression through weed management in non-crop habitat; and (3) bolstering biocontrol through revegetation with, or maintenance of, native vegetation. Across all management types, high yield and low relative management cost resulted in a greater chance of a gross profit. The impacts of the pests themselves were shown to be non-linear, with an intermediate level of pest pressure maximizing the economic gain from management. Pest dispersal capacity influenced the profitability of management of non-crop vegetation, with lower pest dispersal resulting in a greater likelihood of benefit, as benefits from non-crop management are localized (e.g., increased beneficial insect populations). In an intensively cropped landscape, pesticide management was most profitable over the short-term. Once a 10-year horizon was reached, then the profitability of revegetation was greater and continued to increase. While weeding requirements are low, it is likely to always be profitable in the long-term to maintain or restore native vegetation in good condition to control this pest in an intensively cropped landscape. Using pesticide alongside revegetation gave some short-term gain, but the negative impact of pesticide on beneficials outweighed the benefit and in the long-term it is less profitable. These results do not hold in a low production landscape, due to increased pest pressure and costs of managing non-crop habitat. In summary, when quantified over a 10–20 year time horizon, revegetation or conserving native remnants in good (i.e., non-weedy) condition could be economically more beneficial to control an insect pest than ongoing pesticide use, in intensively cropped landscapes.

Numerical investigation on structural stability and explicit performance of high-pressure hydrogen storage cylinders

Hydrogen, a clean and renewable energy fuel is termed the fuel of the future. Although the production of hydrogen is well-established, its storage is a major concern. The conventional metallic cylinders are bulky and cause difficulties in transportation and long-term sustenance, calling for the exploration of alternatives that are durable, lightweight and easy to fabricate. Composite high-pressure cylinders appear to be a promising solution for the storage of gaseous hydrogen. In this work, weight optimization of Type 1, Type 3 and Type 4 cylinders have been performed using lightweight materials such as Titanium, Acrylonitrile Butadiene Styrene (ABS) and Carbon fibre. The stability of these cylinders has been confirmed via structural analysis. In addition, explicit analyses such as drop and crash tests have also been carried out to evaluate the performance of the cylinder. Type 1 shows the least deformation, however, failed both the crash as well as drop tests. Whereas, the type 4 cylinder exhibits better performance in both structural and explicit simulations and is 39.2% lighter than the Type 1 cylinder. Such type 4 cylinders can revolutionize the energy storage sector and can advance mobility to a great extent in the near future.

An implicit FFT-based method for wave propagation in elastic heterogeneous media

An FFT-based algorithm is developed to simulate the propagation of elastic waves in heterogeneous d-dimensional rectangular shape domains. The method allows one to prescribe the displacement as a function of time in a subregion of the domain, emulating the application of Dirichlet boundary conditions on an outer face. Time discretization is performed using an unconditionally stable beta-Newmark approach. The implicit problem for obtaining the displacement at each time step is solved by transforming the equilibrium equations into Fourier space and solving the corresponding linear system with a preconditioned Krylov solver. The resulting method is validated against analytical solutions and compared with implicit and explicit finite element simulations and with an explicit FFT approach. The accuracy of the method is similar to or better than that of finite elements, and the numerical performance is clearly superior, allowing the use of much larger models. To illustrate the capabilities of the method, some numerical examples are presented, including the propagation of planar, circular, and spherical waves and the simulation of the propagation of a pulse in a polycrystalline medium.

Aggregation propensities of proteins with varying degrees of disorder.

The hydration thermodynamics of a globular protein (AcP), three intrinsically disordered protein regions (1CD3, 1MVF, 1F0R) and a fully disordered protein (α-synuclein) is studied by an approach that combines an all-atom explicit water molecular dynamics simulations and three-dimensional reference interaction site model (3D-RISM) theory. The variation in hydration free energy with percentage disorder of the selected proteins is investigated through its nonelectrostatic and electrostatic components. A decrease in hydration free energy is observed with an increase in percentage disorder, indicating favorable interactions of the disordered proteins with the solvent. This confirms the role of percentage disorder in determining the aggregation propensity of proteins which is measured in terms of the hydration free energy in addition to their respective mean net charge and mean hydrophobicity. The hydration free energy is decoupled into energetic and entropic terms. A residue-wise decomposition analysis of the hydration free energy for the selected proteins is evaluated. The decomposition shows that the disordered regions contribute more than the ordered ones for the intrinsically disordered protein regions. The dominant role of electrostatic interactions is confirmed from the residue-wise decomposition of the hydration free energy. The results depict that the negatively charged residues contribute more to the total hydration free energy for the proteins with negative mean net charge, while the positively charged residues contribute more for proteins with positive mean net charge.

Explicit finite difference simulations for accelerating cross diffusion flow over a perpendicular shield with parabolic motion

The heat transfer phenomenon subject to thermos-diffusion effects convey important applications in the heating processes, extrusion systems, chemical processes and various engineering systems. The objective of current work is to observe the contribution of Soret and Dufour effects in oscillating shield for cross diffusion flow. The perpendicular shield with oscillating motion induced the flow. The magnitude of oscillations is assumed to be small so that laminar flow due to oscillating shield has been resulted. The motivations for addressing the thermos-diffusion phenomenon due to oscillating of shield are due to applications in oscillatory pumps, moving surface, metal detectors, power systems etc. The dimensionless problem is obtained via introducing the appropriate set of variables. The numerical outcomes are suggested by using the most interesting explicit finite difference scheme. The physical illustration for flow parameters is presented. Moreover, the aspect of physical quantities involving the flow are graphically reported.

Analiza granične nosivosti zidanih svođenih mostova

To accurately evaluate the ultimate bearing capacity of masonry arch structures, considering the friction and bonding relationships between different components, a finite element model was established in this study with cohesive zero-thickness elements. The model was analysed using explicit dynamic simulations and verified through a case study. The results indicate that the thickness of the arch backfill and ring has a quadratic positive correlation with the ultimate bearing capacity of the structure, whereas the rise-span ratio has a cubic relationship. In particular, there is an optimal rise-span ratio (f/l = 1/3.909) to increase the bearing capacity of the structure under the same conditions.

Land-use strategies of household-based agroforestry in Pendua Village, North Lombok

Competing needs for land resources are increasing as the world’s population grows. Indonesia ranks as the fourth most populous country in the world. The population of Lombok Island has increased more than double in ten years, from around 1.5 million people in 2010 to 3.8 million people in 2020. Home garden improvement has been regarded as one of the important strategies to enhance household food security. Home gardens are also part of local food systems in Lombok. Local people of Pendua Village, North Lombok, are using their home garden for apiculture to meet their needs. This research aims to understand the horizontal land-use allocation of home gardens practicing apiculture in Pendua Village, North Lombok. The horizontal land-use allocation was analyzed using Spatially Explicit Individual-based Forest Simulator (SExI-FS) in 26 home gardens. The result shows that most home gardens allocate an average of 20% of their area for bee’s forage plants, 5% for bee hives, 30% for building, and 40% are the potential open area for plants and bee hives enrichment. The highest important value index (IVI) for the tree is Mangifera indica (163.08%), for pole is Theobroma cacao (62.54%), for sapling and seedling is Dimocarpus longan (27.66% and 37.92%, respectively), and Capsicum frutescens (36,44%) for understory.

Ensemble Cloud Model Application in Simulating the Catastrophic Heavy Rainfall Event

An attempt has been made in the present research to simulate a deadly flash-flood event over the City of Skopje, Macedonia on 6 August 2016. A cloud model ensemble forecast method is developed to simulate a super-cell storm's initiation and evolutionary features. Sounding data are generated using an ensemble approach, that utilizes a triple-nested WRF model. A three-dimensional (3-D) convective cloud model (CCM) with a very fine horizontal grid resolution of 250-m is initialized, using the initial representative sounding data, derived from the WRF 1-km forecast outputs. CCM is configured and run with an open lateral boundary conditions LBC, allowing explicit simulation of convective scale processes. This preliminary study showed that the ensemble approach has some advantages in the generation of the initial data and the model initialization. The applied method minimizes the uncertainties and provides a more qualitative-quantitative assessment of super-cell storm initiation, cell structure, evolutionary properties, and intensity. A high-resolution 3-D run is capable to resolve detailed aspects of convection, including high-intensity convective precipitation. The results are significant not only from the aspect of the cloud model's ability to provide a qualitative-quantitative assessment of intense precipitation but also for a deeper understanding of the essence of storm development, its vortex dynamics, and the meaning of micro-physical processes for the production and release of large amounts of precipitation that were the cause of the catastrophic flood in an urban area. After a series of experiments and verification, such a system could be a reliable tool in weather services for very short-range forecasting (nowcasting) and early warning of weather disasters.

Thermodynamics of trans/gauche conformational equilibria and vibrational spectra of 1,2-dihaloethanes in various media.

The recently developed efficient protocols to implicit [Grimme et al., J. Phys. Chem. A 125, 4039-4054 (2021)] and explicit quantum mechanical modeling of non-rigid molecules in solution [Katsyuba et al., J. Phys. Chem. B 124, 6664-6670 (2020)] are used to describe conformational equilibria of 1,2-dichloroethane and 1,2-dibromoethane in various media. Two approaches for evaluation of trans/gauche free energy differences, ΔGt-g, are compared: (a) direct ΔGt-g computation in implicit solution; (b) the use, together with experimental intensities, of infrared absorption coefficients and Raman scattering cross sections computed for each explicitly modeled solution. The same cluster model of a solute surrounded by the first solvation shell of solvent molecules was used to simulate both Raman and IR spectra. The good agreement between the two approaches indicates the reliability of both methods. The importance of using correct absorption coefficients and Raman scattering factors for each medium is discussed. The ΔGt-g estimates from both implicit and explicit solvation simulations were combined with experimentally measured enthalpy differences ΔHt-g available in the literature to obtain condensed-state ΔSt-g estimates.

A short note on a 3D spectral analysis for turbulent flows on unstructured meshes

We propose two techniques for computing the energy spectra for 3D unstructured meshes that are consistent across different element types. These techniques can be particularly useful when assessing the dissipation characteristics and the suitability of several popular non-linear high-order methods for implicit large-eddy simulations (iLES). Numerical experiments demonstrate the performance of several element types for iLES of the Taylor-Green vortex, where a significantly different dissipation and dispersion mechanism for each element type is revealed. The energy spectra results are dependent on the technique selected for obtaining them, therefore an additional established technique from the literature is also included for comparison to further analyse their similarities and their differences. These techniques can be an integral tool for the tuning and calibration of non-linear high-order methods that can benefit both explicit and implicit large-eddy simulations (LES).

Molecular dynamics simulations of binary sphere mixtures.

Explicit simulations of fluid mixtures of highly size-dispersed particles are constrained by numerical challenges associated with identifying pair-interaction neighbors. Recent algorithmic developments have ameliorated these difficulties to an extent, permitting more efficient simulations of systems with many large and small particles of disperse sizes. We leverage these capabilities to perform molecular dynamics simulations of binary sphere mixtures with elastically stiff particles approaching the hard sphere limit and particle size ratios of up to 50, approaching the colloidal limit. The systems considered consist of 500 large particles and up to nearly 3.6×10^{6} small particles with total particle volume fractions up to 0.51. Our simulations confirm qualitative predictions for correlations between large particles previously obtained analytically and for simulations employing effective depletion interactions, but also reveal additional insights into the near-contact structure that result from the explicit treatment of the small particle solvent. No spontaneous crystal nucleation was observed during the simulations, suggesting that nucleation rates in the fluid-solid coexistence region are too small to observe crystal nucleation for feasible simulation system sizes and timescales.

Molecular dynamics and free energy calculations of clozapine bound to D2 and H1 receptors reveal a cardiometabolic mitigated derivative

Most atypical antipsychotics derive from a high dropout of drug treatments due to adverse cardiometabolic side effects. These side effects are caused, in part, by the H1 receptor blockade. The current work sought a clozapine derivative with a reduced affinity for the H1 receptor while maintaining its therapeutic effect linked to D2 receptor binding. Explicit molecular dynamics simulations and end-point free energy calculations of clozapine in complex with the D2 and H1 receptors embedded in cholesterol-rich lipid bilayers were performed to analyze the intermolecular interactions and address the relevance of clozapine-functional groups. Based on that, free energy perturbation calculations were performed to measure the change in free energy of clozapine structural modifications. Our results indicate the best clozapine derivative is the iodine atom substitution for chlorine. The latter is mainly due to electrostatic interaction loss for the H1 receptor, while the halogen orientation out of the D2 active site reduces the impact on the affinity. Communicated by Ramaswamy H. Sarma

Interactive Flexible-Receptor Molecular Docking in Virtual Reality Using DockIT.

Interactive docking enables the user to guide and control the docking of two biomolecules into a binding pose. It is of particular use when the binding site is known and is thought to be applicable to structure-based drug design (SBDD) and educating students about biomolecular interactions. For SBDD, it enables expertise and intuition to be brought to bear in the drug design process. In education, it can teach students about the most basic level of biomolecular function. Here, we introduce DockIT for virtual reality (VR) that uses a VR headset and hand-held controllers. Using the method of linear response on explicit solvent molecular dynamics simulations, DockIT can model both global and local conformational changes within the receptor due to forces of interaction with the ligand. It has real-time flexible molecular surface rendering and can show the real-time formation and breaking of hydrogen bonds, both between the ligand and receptor and within the receptor itself as it smoothly changes conformation.

Extending and validating bubble nucleation rate predictions in a Lennard-Jones fluid with enhanced sampling methods and transition state theory.

We calculate bubble nucleation rates in a Lennard-Jones fluid through explicit molecular dynamics simulations. Our approach-based on a recent free energy method (dubbed reweighted Jarzynski sampling), transition state theory, and a simple recrossing correction-allows us to probe a fairly wide range of rates in several superheated and cavitation regimes in a consistent manner. Rate predictions from this approach bridge disparate independent literature studies on the same model system. As such, we find that rate predictions based on classical nucleation theory, direct brute force molecular dynamics simulations, and seeding are consistent with our approach and one another. Published rates derived from forward flux sampling simulations are, however, found to be outliers. This study serves two purposes: First, we validate the reliability of common modeling techniques and extrapolation approaches on a paradigmatic problem in materials science and chemical physics. Second, we further test our highly generic recipe for rate calculations, and establish its applicability to nucleation processes.