Simulation Of Evolution Research Articles

Asymptotic boundary condition for numerical modeling of wave packets in a supersonic boundary layer

Within the framework of linear stability theory, a simple non-stationary boundary condition is developed to simulate the far-field asymptotic behavior of linear wave packets propagating in a compressible boundary layer. This condition allows us to skip the linear stage of instability evolution in direct numerical simulations (DNS) of laminar-turbulent transition. It is also suggested to perform numerical simulations of the linear stage without recalculating the Jacobi matrix in the Newton iteration procedure. Robustness and efficiency of the both approaches are evaluated by computations of the first-mode wave packet propagating in the boundary layer on a flat plate at freestream Mach number 2. DNS of the nonlinear stage show that the wave packet quickly breaks down into a turbulent spot, if its hump amplitude is umax′≥0.1U∞. This confirms an amplitude nature of the transition onset criterion. The spectral analysis indicates that the breakdown mechanism differs from the oblique, fundamental or subharmonic resonance and requires additional studies.

Synchronization of non-smooth chaotic systems via an improved reservoir computing

The reservoir computing (RC) is increasingly used to learn the synchronization behavior of chaotic systems as well as the dynamical behavior of complex systems, but it is scarcely applied in studying synchronization of non-smooth chaotic systems likely due to its complexity leading to the unimpressive effect. Here proposes a simulated annealing-based differential evolution (SADE) algorithm for the optimal parameter selection in the reservoir, and constructs an improved RC model for synchronization, which can work well not only for non-smooth chaotic systems but for smooth ones. Extensive simulations show that the trained RC model with optimal parameters has far longer prediction time than those with empirical and random parameters. More importantly, the well-trained RC system can be well synchronized to its original chaotic system as well as its replicate RC system via one shared signal, whereas the traditional RC system with empirical or random parameters fails for some chaotic systems, particularly for some non-smooth chaotic systems.

Coupling Effect and Chain Evolution of Urban Rail Transit Emergencies

Emergency events such as fire, flood and COVID-19 occurred in urban rail transit (URT) usually triggered chain effect and evolved into huge disaster. This kind of chain with complexity and uncertainty evolution brought great challenges to the safety management of the system. Thus, the coupling effects of emergencies and then its relationship with the chain evolution is necessary to analyze emphatically. A Graph Evaluation and Review Technique Simulation (GERTS) evolution network is firstly constructed to describe the coupling effect and chain evolution of emergencies. Then, considering the internal and external influencing factors of the emergency chain, a dynamic evolution model of the emergency chain based on Coupled Map Lattice (CML) is proposed. This paper takes fire chain of URT as an example to simulate the evolution process of emergency chain, and analyze the impact of different coupling effects and various influencing factors on the evolution of emergency chain. The results of numerical simulation show that the AND-coupling can significantly inhibit the evolution of emergency events, while the OR-coupling and CO-coupling can expand the impact scope of emergency events. In addition, the evolution speed of emergency events can be controlled by increasing the coupling action time and improving the URT repair ability. When an emergency event occurs, the analysis of coupling effect and the accompanied chain evolution will help managers to make scientific judgment on the development trend of the emergency events and make targeted emergency defense measures.

Multi-scale in silico analysis of the phase separation behavior of FUS mutants.

Fused in sarcoma (FUS) is an intrinsically disordered RNA-binding protein that helps to regulate transcription and RNA transport while reversibly assembling into membraneless organelles (MLOs). Some mutations of FUS can promote irreversible aggregation, contributing to neurodegenerative diseases. We previously reported a multi-scale computational framework combining a series of molecular dynamics simulations (MD) followed by lattice Monte Carlo (MC) simulations to describe the tendency and dynamics of the assembly and disassembly of intrinsically disordered proteins (IDPs) using wild-type (WT)-FUS as an illustrative example. In this study, we utilized our computational model to simulate three FUS mutants widely experimented with glycine point mutation G156E, arginine point mutation R244C, and deletion of the C-terminal nuclear localization signal (ΔNLS). MD simulation results conveyed that G156E has improved sticker contact probability compared to WT-FUS, while R244C has slightly lower contact probability, which is also complemented by change of net interactions according to the molecular mechanics Poisson Boltzmann surface area (MMPBSA) method. The MC simulation results revealed that G156E has a higher aggregation propensity than the WT-FUS, while ΔNLS has more liquid-like assemblies. R244C demonstrated higher dynamics at the beginning, while over the evolution of MC simulations, it tends to aggregate compared to WT-FUS. In addition, the G156E mutant has more stable protein aggregates, lacking the rapid dynamics shown in all other scenarios. From the peak height of radial distribution functions (RDFs) of the assemblies, the phase separation propensity in ascending order is ΔNLS < FUS-WT < R244C < G156E. Moreover, interpreting the dynamic assembly propensity (DAP) parameter over time, the fluidity of the assemblies in ascending order is G156E < FUS-WT < R244C < ΔNLS. The results obtained from this study support that the computational model is able to predict the effect of mutation down to single amino acid substitution on the phase separation behavior of FUS. This efficient in silico method can be generalized to investigate the phase separation propensity of other IDPs and their mutants.

Mo-doping heterojunction: interfacial engineering in an efficient electrocatalyst for superior simulated seawater hydrogen evolution.

Exploring economical, efficient, and stable electrocatalysts for the seawater hydrogen evolution reaction (HER) is highly desirable but is challenging. In this study, a Mo cation doped Ni0.85Se/MoSe2 heterostructural electrocatalyst, Mox-Ni0.85Se/MoSe2, was successfully prepared by simultaneously doping Mo cations into the Ni0.85Se lattice (Mox-Ni0.85Se) and growing atomic MoSe2 nanosheets epitaxially at the edge of the Mox-Ni0.85Se. Such an Mox-Ni0.85Se/MoSe2 catalyst requires only 110 mV to drive current densities of 10 mA cm-2 in alkaline simulated seawater, and shows almost no obvious degradation after 80 h at 20 mA cm-2. The experimental results, combined with the density functional theory calculations, reveal that the Mox-Ni0.85Se/MoSe2 heterostructure will generate an interfacial electric field to facilitate the electron transfer, thus reducing the water dissociation barrier. Significantly, the heteroatomic Mo-doping in the Ni0.85Se can regulate the local electronic configuration of the Mox-Ni0.85Se/MoSe2 heterostructure catalyst by altering the coordination environment and orbital hybridization, thereby weakening the bonding interaction between the Cl and Se/Mo. This synergistic effect for the Mox-Ni0.85Se/MoSe2 heterostructure will simultaneously enhance the catalytic activity and durability, without poisoning or corrosion of the chloride ions.

Simulation of tumor density evolution upon chemotherapy alone or combined with a treatment to reduce lactate levels

&lt;abstract&gt;&lt;p&gt;In this study, we introduced a mathematical model mimicking as much as possible the evolutions and interactions between glioma and lactate in the brain, in order to test different therapies and administration protocols. We simulated both glioma cell density evolution and lactate concentration, and considered two therapies: chemotherapy and a treatment targeting lactate production. Three different protocols for administrating the therapies were tested. We compared the efficiency of the combined therapies, depending on the administration protocols and the dosage of the drugs, in order to evaluate the importance of controlling lactate production. Results show that the use of an agent to reduce lactate concentration permits one to significantly reduce the dose of the chemotherapeutic drug.&lt;/p&gt;&lt;/abstract&gt;

Evolution of the Magnetic Field in High- and Low-β Disks with Initially Toroidal Fields

Abstract We present the results from a pair of high-resolution, long-timescale (∼105 GM/c 3), global, three-dimensional magnetohydrodynamical accretion disk simulations with differing initial magnetic plasma β in order to study the effects of the initial toroidal field strength on the production of a large-scale poloidal field. We initialize our disks in approximate equilibrium with purely toroidal magnetic fields of strength β 0 = 5 and 200. We also perform a limited resolution study. We find that simulations of differing field strengths diverge early in their evolution and remain distinct over the time studied, indicating that the initial magnetic conditions leave a persistent imprint in our simulations. Neither simulation enters the magnetically arrested disk regime. Both simulations are able to produce poloidal fields from initially toroidal fields, with the β 0 = 5 simulation evolving clear signs of a large-scale poloidal field. We make a cautionary note that computational artifacts in the form of large-scale vortices may be introduced in the combination of initially weak field and disk-internal mesh refinement boundaries, as evidenced by the production of an m = 1 mode overdensity in the weak field simulation. Our results demonstrate that the initial toroidal field strength plays a vital role in the simulated disk evolution for the models studied.

An accelerated scheme for solving inhomogeneous elasticity in phase-field method and application to Ni-based multi-component alloys

On the way towards realistic predictions of various material properties for engineering structural materials, efficient computational simulations of microstructural evolution play an indispensable role. In the present work, an in-house phase-field code with inhomogeneous elasticity has been developed aiming to deal with precipitation processes for multi-component alloys with high efficiency. Two different numerical iterative algorithms, named as Model A and B, are implemented to solve inhomogeneous elastic equations. The resulting simulated morphology and energy evolutions under different conditions show consistency for these two algorithms. In order to perform simulation efficiently, a parallel technique based on CUDA (Computer Unified Device Architecture) architecture is used, which greatly improves the computational efficiency. After estimating the computational efficiency of different acceleration techniques for different grid sizes, Model A is extended to simulate concentration and morphology evolutions in the precipitation and rafting processes of γ′ phase in a Ni-based five-component alloy of Ni−Co−Al−Mo−W. Meanwhile, the CALPHAD method and related databases are linked to provide thermodynamic and diffusivity data. Finally, the computation costs of the parallel technique for different simulation scales are explored, testifying that this technique is capable of performing larger scale simulations for multi-component multi-phase structural materials.

Acceleration of Morphodynamic Simulations Based on Local Trends in the Bed Evolution

Due to the significant mismatch in timescales associated with morphological and hydrodynamic processes in coastal environments, modellers typically resort to various techniques for speeding up the bed evolution in morphodynamic simulations. In this paper, we propose a novel method that differs from existing ones in several aspects. For example, unlike previous approaches that apply a global measure (such as a constant acceleration factor that uniformly amplifies the bed evolution everywhere), we track and extrapolate local trends in morphological changes. The present algorithm requires the setting of four different parameters, values for which we set through an extensive calibration process. The proposed method is compared against the simple acceleration technique built into the popular software XBeach (wherein it is called morfac) for eight different beach profiles (including linear, Dean, and measured profiles). While the accuracy of both methods is generally similar, the proposed algorithm consistently shows a greater reduction in computational time relative to morfac, with our algorithm-accelerated simulations being on average 2.6 times faster than morfac. In light of these results, and considering the algorithm’s potential for easy generalisation to address arbitrary coastal morphodynamic problems, we believe that this method represents an important addition to the toolbox available to the community interested in coastal modelling.

Research on the Mechanism and Evolution Law of Delayed Water Inrush Caused by Fault Activation with Mining

Confined water inrush caused by fault activation is the main form of water disaster in deep mining. With theoretical analysis and similar simulation tests, the mechanism and evolution law of delayed water inrush caused by fault activation are revealed. At the theoretical level, the expansion and extension of the internal microstructure in the fault zone under the action of the mining stress field and seepage field are the essential causes of fault activation. Overlying strata movement and surrounding rock creep failure are the basic reasons for delayed water inrush caused by fault activation, and delayed time caused by surrounding rock creep failure is much longer than that of overlying strata movement. A similar simulation test was carried out with self-development solid–liquid coupling with similar simulation materials; the results show that delayed water inrush caused by fault activation with mining includes three stages. Micro-activation stage: Water inrush weakness point is formed because of the expansion and extension of the micro-fissure and structure at the bottom of the fault zone. Macro-activation stage: With the change in the stress of the waterproof coal pillar and surrounding rock, the micro-fissures and structures in the stress relief area and tension area of the fault zone expand and extend sharply; meanwhile, water intrudes into the interlayer stratification of the floor in the stress relief area, forming a strong laminar flow phenomenon, and cracks in the floor form and expand; finally, water-conducting channels in the fault zone and floor are formed. Water inrush stage: The waterproof coal pillar and water-resisting layer fail and are destroyed, and the first confined water inrush point is located at the junction of the waterproof coal pillar and gob floor.

Pre-supernova outbursts by core magnetic activity

ABSTRACT We conduct one-dimensional stellar evolutionary numerical simulations under the assumption that an efficient dynamo operates in the core of massive stars years to months before core collapse and find that the magnetic activity enhances mass-loss rate and might trigger binary interaction that leads to outbursts. We assume that the magnetic flux tubes that the dynamo forms in the inner core buoy out to the outer core where there is a steep entropy rise and a molecular weight drop. There the magnetic fields turn to thermal energy, i.e. by reconnection. We simulate this energy deposition where the entropy steeply rises and find that for our simulated cases the envelope radius increases by a factor of ≃1.2–2 and luminosity by about an order of magnitude. These changes enhance the mass-loss rate. The envelope expansion can trigger a binary interaction that powers an outburst. Because magnetic field amplification depends positively on the core rotation rate and operates in cycles, not in all cases the magnetic activity will be powerful enough to change envelope properties. Namely, only a fraction of core-collapse supernovae experiences pre-explosion outbursts.

Target-based sedimentary diagenesis simulation and three-dimensional diagenesis evolution modeling

Deposition and diagenesis are important factors affecting the quality of oil and gas reservoirs. Previously reported diagenesis studies mainly involve qualitative analysis, such as the determination of diagenetic events and diagenetic evolution sequences and modeling of two-dimensional diagenetic evolution, with less effort devoted to quantitative numerical simulation and three-dimensional diagenetic evolution models. This study proposes a new method for target-based diagenesis simulation by integrating the discrete element method, the quartet structure generation set method, and morphological algorithms. This new hybrid method can quantitatively simulate the effects of mineral grain deposition, compaction, cementation, dissolution, and replacement. Since specific minerals can undergo specific diagenetic alterations through mineral labeling, the sequence and path of diagenesis can be predefined in this method. Taking the sandstone reservoir of Lower Member 3 of the Shahejie Formation in Linnan Sag, Huimin Depression, Bohai Bay Basin, East China as an example, the new simulation method used the constructed diagenetic evolution sequence based on thin section identification and geochemical analysis to systematically simulate deposition and diagenesis in the study area and to construct a three-dimensional diagenetic evolution model. The predicted porosity, permeability, and pore size distribution of the simulated digital rocks are in good agreement with the experimental values, which validates the high accuracy of the simulation method. Based on these three-dimensional multi-mineral evolution models, the evolution trends of porosity and permeability during the sedimentation and diagenesis process were elucidated, revealing the variation in reservoir quality in the studied area and indicating reservoir sweet spots. The constructed 3D diagenesis evolution models are widely applicable and can be used not only for permeability simulation but also for the study of electrical, acoustic, and mechanical properties of reservoirs.

Numerical modelling of the evolution of a river reach with a complex morphology to help define future sustainable restoration decisions

Abstract. The prediction of river morphology evolution is very complicated, especially in the case of mountain and Piedmont rivers with complex morphologies, steep slopes, and heterogeneous grain sizes. The Lac des Gaves (LDG) reach, located within the Gave de Pau River in the Hautes-Pyrénées department, France, has precisely the complex morphological characteristics mentioned above. This reach has gone through severe sediment extractions for over 50 years, leading to the construction of two weirs for riverbed stabilisation. Two large floods resulted in changes in the LDG's hydromorphological characteristics as it went from a single channel river section to a braided river reach. In this study, a 2D hydromorphological model is developed with the TELEMAC-MASCARET system to reproduce the evolution of the channel following a flood that occurred in 2018. The model's validity is assessed by comparing the simulated topographic evolution to the observed one. The results reveal the challenge to choose well-fitted sediment transport equations and friction laws that would make it possible to reproduce such complex morphology. Although the exact localisation of the multiple channels forming the braided nature of the LDG was challenging to reproduce, our model was able to provide reliable volumetric predictions as it reproduces the filling of the LDG correctly. The influence of the two weirs on the river's current and future morphology is also studied. The aim is to provide decision-makers with more reliable predictions to design suitable restoration measures for the LDG reach.

Recent progress in the microstructurally based creep modelling of Ni-based alloy 617

ABSTRACT Solid solution strengthened (SSS) Ni-based superalloys, such as A617, show superior creep resistance at 700°C. Established for many years in land- and aero-based gas turbines, these materials are increasingly being considered for use in high-temperature thermal power plants. Apart from SSS, the creep strength in A617 stems from γ’ and carbide precipitates. In this work, a microstructurally based creep model for A617 is presented. Mobile dislocations in the model interact with fine grain-interior precipitates, and grain boundaries act as dislocation sources/sinks. The model is capable of simulating creep curves and time-to-rupture (TTR) diagrams based on the evolution of mobile dislocations. At lower stresses, the accuracy of modelled TTR can be improved by adding diffusion creep to dislocation creep. The simulated evolution of dislocation densities is realistic compared to the literature data. The reduction of area of ruptured samples was included in a damage factor, enabling the consideration of creep ductility.

The role of abiotic and biotic factors in the unequal body shape diversification of a Gondwanan fish radiation (Otophysi: Characiformes).

Understanding why some clades diversify greatly while others do not is a major goal of evolutionary biology. Both abiotic and biotic factors are important in driving unequal morphological diversity across the tree of life. However, few studies have quantified how abiotic habitat and community composition differences influence unequal morphological diversification in spatiotemporally diffuse radiations. We use geometric morphometrics, abiotic habitat data generated by Geographic Information Systems (GIS) analyses, evolutionary simulations, and phylogenetic comparative methods to determine whether random evolution, habitat variation, competition for niches, or a combination of factors influenced the unequal body shape diversity of a Gondwanan freshwater fish radiation. We find that Neotropical characiform lineages, which exhibit substantially more body shape diversity than their African counterparts, occupy significantly more slope and elevation habitats than African lineages. Differences in habitat occupation between the continental radiations occur through a combination of likely competition with cypriniform fishes in Africa restricting access to higher slope and elevation habitats and significantly more low-elevation and slope habitats available in the Neotropics. Our findings suggest that spatiotemporally widespread radiations, like Characiformes, do not diversify across homogenized habitats and biotic assemblages, with differences in community structure and physical habitat playing an important role in driving unequal morphological diversification.

Cellular automata simulation of interlayer microstructure for alumina ceramic sintering process formed by vat photopolymerization

The layered structure of the green parts formed by additive manufacturing considerably influences the densification and sintering process. This work focused on the interlayer microstructure evolution during the sintering of alumina ceramics formed by vat photopolymerization as well as its influencing factors and patterns. A cellular automata (CA) model combined with a back propagation neural network (BPNN) was developed to simulate the sintering process. The BPNN+CA model successfully predicted the porosity with an error of less than 12 % for specific particle size gradations (3 µm/0.5 µm and above) and sintering temperature. The simulated interlayer microstructure evolution was in agreement with the experimental results. The validated model showed that smaller particle size and higher sintering temperature induce stronger sensitivity to the interlayer gap. This simulated system is of great assistance in predicting interlayer microstructure evolution and change of porosity during sintering for ceramics manufactured by vat photopolymerization.

Multi-phase simulation for understanding morphodynamics of gravel beaches

This paper presents the use of an Eulerian–Eulerian multi-phase model to examine sediment transport over a gravel beach under regular waves. A previously published full-scale experiment is reproduced numerically; the simulated wave deformation, flow velocity, pore pressure, and morphological evolution are consistent with measurements. The multi-phase model can produce berm formation for smaller waves and beach erosion for larger waves as observation in previous field studies. The sensitivity analysis suggests that the nonlinear component of drag has significant effect on the berm formation through infiltration and exfiltration. The two simulated forces applied on the sediment (drag and buoyancy) are examined. The drag is the main force directly for sediment transport; therefore the sediment transport rate has high correlation with depth-averaged flow velocity. The buoyancy that is caused by plunging flow impacting beach face can push the sediment landward in the bore front, where the flow acceleration has its peak. The flow acceleration is considered in some previous sediment transport models empirically for simulating morphological evolution of gravel beach under waves. The buoyancy links the flow acceleration and sediment transport rate in the bore front.

Transient polymorphisms in parental care strategies drive divergence of sex roles

The parental roles of males and females differ considerably between and within species. By means of individual-based evolutionary simulations, we strive to explain this diversity. We show that the conflict between the sexes creates a sex bias (towards maternal or paternal care), even if the two sexes are initially identical. When including sexual selection, there are two outcomes: either female mate choice and maternal care or no mate choice and paternal care. Interestingly, the care pattern drives sexual selection and not vice versa. Longer-term simulations exhibit rapid switches between alternative parental care patterns, even in constant environments. Hence, the evolutionary lability of sex roles observed in phylogenetic studies is not necessarily caused by external changes. Overall, our findings are in striking contrast to the predictions of mathematical models. We show that the discrepancies are caused by transient within-sex polymorphisms in parental strategies, a factor largely neglected in current sex-role theory.

The Adaptation Front Equation Explains Innovation-Driven Taxonomic Turnovers and Living Fossilization.

AbstractEvolutionary taxonomic turnovers are often associated with innovations beneficial in various ecological niches. Such innovations can repeatedly occur in species occupying optimum niches for a focal species group, resulting in their repeated diversifications and species flows from optimum to suboptimum niches, at the expense of less innovated ones. By combining species packing theory and adaptive dynamics theory, we develop an equation that allows analytical prediction for such innovation-driven species flows over a niche space of arbitrary dimension under a unimodal carrying capacity distribution. The developed equation and simulated evolution show that central niches (with the highest carrying capacities) tend to attain the fastest innovation speeds to become biodiversity sources. Species that diverge from the central niches outcompete the indigenous species in peripheral niches. The outcompeted species become extinct or evolve directionally toward far more peripheral niches. Because of this globally acting process over niches, species occupying the most peripheral niches are the least innovated and have deep divergence times from their closest relatives, and thus they correspond to living fossils. The extension of this analysis for multiple geographic regions shows that living fossils are also expected in geographically peripheral regions for the focal species group.

Evolutionary game theory and simulations based on doctor and patient medical malpractice under government regulation

Physicians-patients are the two crucial participants in medical malpractice. The government, as the central authority responsible for addressing medical malpractices, plays a pivotal role in this matter. Guided by governmental agencies, its regulations, administrative orders, and policies serve as the primary governance mechanisms to address medical malpractice, providing an effective means to balance the doctor-patient relationship and foster social harmony and stable development. A doctor-patient evolutionary game model developed based on the principles of information asymmetry and finite rationality. The study explores the strategic decision-making process of these two players within the context of medical malpractice. Through the manipulation of various parameters, the model's evolutionary equilibrium strategy is demonstrated using Vensim PLE Version 6.4 simulation. The findings reveal that government regulation, patient cognition, and the benefits associated with standardized medical practices are the pivotal factors influencing the doctor-patient evolutionary game system under government regulation. It is possible to mitigate medical malpractice through adjusting relative weights of differing strategic options, adding penalties for unlawful conduct, and normalizing malpractice charges on the basis of physicians' income from standardized practice. To effectively address medical malpractice, proposed measures include adjusting the regulatory framework, reasonably determining the strength of regulations regarding medical practitioners' illegal practices and patient medical malpractice behavior, diversifying regulatory approaches, establishing comprehensive physician–patient management systems for information to resolve medical malpractices.