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With the aim of finding the plant-derived allosteric inhibitors of caspase-3/-7, we conducted computational investigations of bioactive compounds present in various berry fruits. In a molecular docking study, perulactone demonstrated excellent binding affinity scores of −12.1 kcal/mol and −9.1 kcal/mol for caspase 7 and 3, respectively, whereas FDA-approved allosteric inhibitors (DICA and FICA) were found to show lower docking scores (−5.6 and −6.1 kcal/mol) against caspase 7 while (−5.0 and −5.1 kcal/mol) for caspase 3, respectively. MD simulations were used to validate the binding stability of perulactone in the active sites of caspase-7/-3, and the results showed outstanding stability with lower ligand RMSDs of 1.270–3.088 Å and 2.426–9.850 Å against the targeted receptor. Furthermore, we performed MMGBSA free binding energy, where the perulactone values of ΔGBind were determined to be −63.98 kcal/mol and −66.32 kcal/mol for both receptors (3IBF and 1NME), which are significantly better than the −45.16 kcal/mol and −39.51 kcal/mol for DICA as well as −26.37 kcal/mol and −15.50 kcal/mol for FICA, respectively. The drug resemblance of perulactone was effectively evaluated by ADMET. Thus, our findings indicated that perulactone could be an orally administered therapeutic candidate for regulating apoptosis in a variety of disorders. However, there may be an urgent need to study using in vitro and in vivo experiments. [ABSTRACT FROM AUTHOR]

Recently, Egypt had seismic activity. These seismic events have affected the stability of minarets, especially historical ones. Weight is one of the minaret's main stability factors. The main objective of the current research is to perform a three-dimensional (3D) assessment of an existing minaret, determine its accurate spatial model, document its current condition, examine its stability in the event of earthquakes, and identify the requisite measures to safeguard the minaret from any potential damage. The masonry to construct the minaret was used by extracting and examining specimens of this substance to determine its physical characteristics. The current work created three-dimensional models of the Abou-Ghanam El-Bialy minaret using a terrestrial laser scanner (TLS) to document its current condition, as well as minaret was subjected to a free vibration analysis using 3D finite element modeling. Finally, the minaret's seismic behavior was assessed utilizing mode forms, base responses, and normal stresses. The surveying method effectively documented the Minarets' existing case. The 3D seismic analysis showed that the minaret responded dynamically to earthquake loading, with mode shapes, base reactions, and normal stresses being crucial characteristics. Based on these data, we may suggest procedures to protect the minaret during seismic events. [ABSTRACT FROM AUTHOR]

In view of the current problems of slow crystallization rate, varying grain sizes, complex process conditions, and low safety in the preparation of CL−20/TNT cocrystal explosives in the laboratory, an opposite spray crystallization method is provided to quickly prepare ultrafine explosive cocrystal particles. CL−20/TNT cocrystal explosive was prepared using this method, and the obtained cocrystal samples were characterized by electron microscopy morphology, differential thermal analysis, infrared spectroscopy, and X-ray diffraction analysis. The effects of spray temperature, feed ratio, and preparation method on the formation of explosive cocrystal were studied, and the process conditions of the pneumatic atomization spray crystallization method were optimized. The crystal plane binding energy and molecular interaction forces between CL−20 and TNT were obtained through molecular dynamic simulation, and the optimal binding crystal plane and cocrystal mechanism were analyzed. The theoretical calculation temperature of the binding energy was preliminarily explored in relation to the preparation process temperature of cocrystal explosives. The mechanical sensitivity of ultrafine CL−20/TNT cocrystal samples was tested. The results showed that choosing acetone as the cosolvent, a spraying temperature of 30 °C, and a feeding ratio of 1:1 was beneficial for the formation and growth of cocrystal. The prepared CL−20/TNT cocrystal has a particle size of approximately 10 μm. The grain size is small, and the crystallization rate is fast. The impact and friction sensitivity of ultrafine CL−20/TNT cocrystal samples were significantly reduced. The experimental process conditions are simple and easy to control, and the safety of the preparation process is high, providing certain technical support for the preparation of high-quality cocrystal explosives. [ABSTRACT FROM AUTHOR]

The steelmaking–continuous casting process (SCCP) is a complex manufacturing process which exhibits the distinct features of process manufacturing. The SCCP involves a variety of production elements, such as multiple process routes, a wide array of smelting and auxiliary devices, and a variety of raw and auxiliary materials. The production-simulation of SCCP holds a natural advantage in being able to accurately depict the intricate production behavior involved, and this serves as a crucial tool for optimizing the production operation of the SCCP. This paper thoroughly considers the various production elements involved in the SCCP, such as the fluctuation of the converter smelting cycle, fluctuation of heat weight, and ladle operation. Based on the Plant Simulation software platform, a dynamic simulation model of the SCCP is established and detailed descriptions are provided regarding the design of an SCCP using dynamic-operation rules. Additionally, a dynamic operational control program for the SCCP is developed using the SimTalk language, one which ensures the continuous operation of the caster in the SCCP, using the discrete simulation platform. The effectiveness of the proposed dynamic simulation model is verified by the total completion time of the production plan, the transfer time of the heat among the different processes, and the frequency of ladle turnover. The simulation's results indicate that the dynamic simulation model has a satisfactory effect in simulating the actual production process. On this basis, the application effects of different schedules are compared and analyzed. Compared with a heuristic schedule, the optimized schedule based on the "furnace–machine coordinating" mode reduces the weighted value of total completion time by 8.7 min, reduces the weighted value of transfer waiting time by 45.5 min, and the number of rescheduling times is also reduced, demonstrating a better application effect and verifying the optimizing effect of the "furnace–machine coordinating" mode on the schedule. [ABSTRACT FROM AUTHOR]

Ceramic slurry is the raw material used in stereolithography, and its performance determines the printing quality. Rheological behavior, one of the most important physical factors in stereolithography, is critical in ceramic printing, significantly affecting the flow, spreading, and printing processes. The rheological behavior of SiO2 slurry used in stereolithography technology is investigated in the current research using different powder diameters and temperatures. The results present the apparent non-Newtonian behavior. The yielding characteristics occur in all cases. For single-powder cases, the viscosity decreases when the powder diameter is increased. When the nano-sized and micro-sized powders are mixed in different proportions, a more significant proportion of micron-sized powders will decrease the viscosity. With an increase in the nano-sized powders, the slurry exhibits the shear thinning behavior; otherwise, the shear thickening behavior is observed. Thus, the prediction model is built based on the use of the pelican optimization algorithm-deep extreme learning machine (POA-DELM), and the model in then compared with the fitted and traditional models to validate the effectiveness of the method. A more accurate viscosity prediction model will contribute to better fluid dynamic simulation in future work. [ABSTRACT FROM AUTHOR]

Peridynamics describes the material in a non-local form and is very suited for the simulation of dynamic fracture. However, one significant effect regarding dynamic fracture is the correct handling of elastic deformation, like the pressure and tension waves inside a body, due to dynamic boundary conditions like an impact or impulse. Many peridynamic material formulations have been developed with differences in this regard. This study investigates the elastic wave propagation characteristics of bond-based, ordinary state-based, continuum kinematics-inspired peridynamics and a local continuum consistent correspondence formulation. Multiple parameters of a longitudinal pressure wave inside an elastic bar are studied. While all formulations demonstrate adequate wave propagation handling, all except the correspondence formulation are sensitive to incomplete horizons. The local continuum consistent formulation does not suffer from the surface effect and models the wave propagation with perfect accuracy. [ABSTRACT FROM AUTHOR]

Unveiling the dynamic active site of defective carbon-based electrocatalysts for hydrogen peroxide production. [Display omitted] Defective carbon materials have emerged as promising candidates for the electrocatalysis of oxygen reduction reaction (ORR) to selectively produce H 2 O 2. However, distinguishing the roles of oxygenates and carbon defects in carbon for 2e- ORR remains to be challenging. In a recent issue of Nature Communications, Yao and coworkers pinpointed the major active sites in oxygenated carbon materials and identified the key intermediate employing a series of dynamic and simulation techniques. In addition to highlight the proposed work, this comment article also discussed pioneering methodologies to characterize structure dynamics and probe the integral active center for rational design of carbon based catalysts with atomic precision. [ABSTRACT FROM AUTHOR]

Carbon nanotube (CNT) is a material with high modulus, high tensile strength, good flexibility and large specific surface area. This material has become very popular and has been also applied as an asphalt modifier. In the current research, multi-walled carbon nanotubes (MWCNTs) and styrene-butadiene-styrene (SBS) were employed as modifiers to fabricate MWCNTs/SBS composite-modified asphalt binder (hereinafter referred to as MCSA). The technical performance of MCSA was evaluated by performance tests and the optimal content of MWCNTs was determined. MCSA dispersion characteristics and interactions of components were investigated by microscopic test methods. Interactions of molecules and tensile behavior of MWCNTs in MCSA were explored by molecular dynamics (MD) simulation. The modification mechanism of MWCNTs was studied at the macro, micro and molecular levels. The following conclusions were drawn: According to macroscopic test results, the optimal content range of MWCNTs was 0.4% to 0.6%. MWCNTs modification process on asphalt binder was a physical modification. MWCNTs enhanced interactions among components and this effect was most obvious when MWCNTs content was 0.6%. The results of the macroscopic test were verified by the microscopic test. MWCNTs molecules could couple with SBS modifier as well as asphalt component molecules, thereby enhancing the interaction of each component in the system. MWCNTs mainly enhanced molecular interactions by increasing van der Waals energy in MCSA system, to make it more stable. MWCNTs do not break during the pull-out process. The molecules of asphalt component, SBS modifier and MWCNTs penetrated each other, which enhanced system stability to resist external loads and improved the mechanical properties of MCSA. [ABSTRACT FROM AUTHOR]

The building industry requires the development of a ductile lateral force resisting system made of mass timber to help mass timber to continue to grow in popularity as the primary structural building material. The OpenSees framework was used to develop a numerical model of a single-story timber frame with a timber buckling-restrained brace, which was validated by the results of a previously completed series of quasistatic cyclic timber buckling-restrained brace (TBRB) component and subassembly tests. The experimental validation included a model developed for the hysteretic behavior of the TBRB and the rotational capacity of beam–column joints made with mass ply lam (MPL) panels, two slotted-in steel plates, and a number of steel dowels. The single-story model TBRB braced frame was then expanded to a numerical model of an eight-story mass timber buckling-restrained braced frame. The TBRB frame was analyzed with static pushover, quasistatic cyclic loads, and earthquake simulations. During the simulation of eleven design-level earthquake ground motions, the building experienced a peak interstory drift at of 2.54% at the first-floor level and a peak floor acceleration of 1.7g at the roof. The numerical model developed in this research of a timber buckling-restrained braced frame with TBRBs is novel and could be used to design timber buckling-restrained braced frames as a ductile lateral force resisting solution for mass timber buildings in seismic regions. [ABSTRACT FROM AUTHOR]

[Display omitted] Hypothesis : Understanding the rules that control the assembly of nanostructured soft materials at interfaces is central to many applications. We hypothesize that electrolytes can be used to alter the hydration shell of amphiphilic oligomers at the air-aqueous interface of Langmuir films, thereby providing a means to control the formation of emergent nanostructures. Experiments : Three representative salts – (NaF, NaCl, NaSCN) were studied for mediating the self-assembly of oligodimethylsiloxane methylimidazolium (ODMS-MIM+) amphiphiles in Langmuir films. The effects of the different salts on the nanostructure assembly of these films were probed using vibrational sum frequency generation (SFG) spectroscopy and Langmuir trough techniques. Experimental data were supported by atomistic molecular dynamic simulations. Findings : Langmuir trough surface pressure – area isotherms suggested a surprising effect on oligomer assembly, whereby the presence of anions affects the stability of the interfacial layer irrespective of their surface propensities. In contrast, SFG results implied a strong anion effect that parallels the surface activity of anions. These seemingly contradictory trends are explained by anion driven tail dehydration resulting in increasingly heterogeneous systems with entangled ODMS tails and appreciable anion penetration into the complex interfacial layer comprised of headgroups, tails, and interfacial water molecules. These findings provide physical and chemical insight for tuning a wide range of interfacial assemblies. [ABSTRACT FROM AUTHOR]

Seismological studies have exposed numerous ultralow velocity zones (ULVZs) exhibiting extraordinary physical attributes at Earth's core-mantle boundary, yet their compositions and origins remain controversial. Water-iron reaction can generate unique phases under lowermost-mantle conditions and likely plays a crucial role in forming ULVZs. Through first-principles molecular dynamic simulations with machine learning techniques, we determine that iron hydride, the product of water-iron reaction, is stable as a superionic phase at the core-mantle boundary. This superionic iron hydride has much slower velocities and a higher density than the ambient mantle under lowermost-mantle conditions. Accumulation of iron hydride, created through either a chemical reaction between subducted water and iron or solidification of core material entrained in the lower mantle by convection, can explain the seismic observations of ULVZs particularly those associated with subduction. This work suggests that water may have a substantial role in creating seismic heterogeneities at the core-mantle boundary. [ABSTRACT FROM AUTHOR]

By addressing the phenomenon of carbody abnormal vibrations in the field, the acceleration of the carbody and bogie was measured using accelerometers, and the diamond mode of the carbody was identified. The equivalent conicity of the wheelset and the acceleration at the frame end indicated that the shaking of the carbody was caused by bogie hunting. In the SIMPACK simulation, the acceleration frequency and amplitude at the frame end and midsection of the side beam were calculated. The lateral deformation amplitude of the side beam in the finite element model was extracted, and a modal shape function for the diamond-shaped mode was established. By utilizing the modal vibration equation, the modal generalized forces of the carbody were computed, revealing that, during carbody shaking, the yaw damper force contributed significantly among the forces of the secondary suspension, with the phase difference between the front and rear bogies approaching 180°. This insight offers a novel perspective for subsequent active control strategies. Subsequently, these modal generalized forces were applied as external excitation to a coupled vibration model encompassing both the carbody and transformer. Aiming to reduce the acceleration amplitude at the side beam, the transformer was treated as a dynamic vibration absorber, allowing for the optimization of its lateral suspension parameters. As a result, the lateral and vertical acceleration amplitudes at the side beam were concurrently reduced, with the maximum decrease reaching 58.5%, significantly enhancing the ride comfort. [ABSTRACT FROM AUTHOR]

Introduction: Muscles play a critical role in supporting joints during activities of daily living, owing, in part, to the phenomenon of short-range stiffness. Briefly, when an active muscle is lengthened, bound cross-bridges are stretched, yielding forces greater than what is predicted from the force length relationship. For this reason, short-range stiffness has been proposed as an attractive mechanism for providing joint stability. However, there has yet to be a forward dynamic simulation employing a cross-bridge model, that demonstrates this stabilizing role. Therefore, the purpose of this investigation was to test whether Huxley-type muscle elements, which exhibit short-range stiffness, can stabilize a joint while at constant activation. Methods: We analyzed the stability of an inverted pendulum (moment of inertia: 2.7 kg m2) supported by Huxley-type muscle models that reproduce the short-range stiffness phenomenon. We calculated the muscle forces that would provide sufficient short-range stiffness to stabilize the system based in minimizing the potential energy. Simulations consisted of a 50 ms long, 5 Nm square-wave perturbation, with numerical simulations carried out in ArtiSynth. Results: Despite the initial analysis predicting shared activity of antagonist and agonist muscles to maintain stable equilibrium, the inverted pendulum model was not stable, and did not maintain an upright posture even with fully activated muscles. Discussion & conclusion: Our simulations suggested that short-range stiffness cannot be solely responsible for joint stability, even for modest perturbations. We argue that short-range stiffness cannot achieve stability because its dynamics do not behave like a typical spring. Instead, an alternative conceptual model for short-range stiffness is that of a Maxwell element (spring and damper in series), which can be obtained as a first-order approximation to the Huxley model. We postulate that the damping that results from short-range stiffness slows down the mechanical response and allows the central nervous system time to react and stabilize the joint. We speculate that other mechanisms, like reflexes or residual force enhancement/depression, may also play a role in joint stability. Joint stability is due to a combination of factors, and further research is needed to fully understand this complex system. [ABSTRACT FROM AUTHOR]

3,4-bis(3-nitrofurazan-4-yl) furoxan (DNTF) is an explosive with excellent performance, and the use of DNTF as a high-energy component is of great significance for improving the comprehensive performance of weapons. To explore the effect of DNTF on low-melting-point molten carrier explosives, the compatibility between DNTF and other low-melting-point explosives was analyzed by differential scanning calorimetry, and mechanical sensitivity was tested. The compatibility and cohesive energy density between DNTF and other low-melting-point explosives were calculated by Materials Studio. The results showed that DNTF has good compatibility with most low-melting-point explosives, and the peak temperature change of the mixed system formed by melt-casting is not obvious. Among them, DNTF has the best compatibility with MTNP, TNT, and DNAN; moderate compatibility with DFTNAN and DNP; and the worst compatibility with DNMT. The sensitivity test results indicate that the combination of DNTF and TNT has the most significant reduction in mechanical sensitivity. DFTNAN and MTNP have better stability than DNTF and can generate strong interaction forces with DNTF. Other low-melting-point explosives mixed with DNTF have lower intermolecular forces than DNTF. The DNTF/MTNP system requires the most energy to phase change when heated compared to other mixed systems and is the least sensitive to heat. The DNTF/DNMT system has the lowest cohesive energy density and is the most sensitive to heat. [ABSTRACT FROM AUTHOR]

This work focuses on the well-known issue of mass conservation in the context of the finite element technique for computational fluid dynamic simulations. Specifically, non-conventional finite element families for solving Navier–Stokes equations are investigated to address the mathematical constraint of incompressible flows. Raviart–Thomas finite elements are employed for the achievement of a discrete free-divergence velocity. In particular, the proposed algorithm projects the velocity field into the discrete free-divergence space by using the lowest-order Raviart–Thomas element. This decomposition is applied in the context of the projection method, a numerical algorithm employed for solving Navier–Stokes equations. Numerical examples validate the approach's effectiveness, considering different types of computational grids. Additionally, the presented paper considers an interface advection problem using marker approximation in the context of multiphase flow simulations. Numerical tests, equipped with an analytical velocity field for the surface advection, are presented to compare exact and non-exact divergence-free velocity interpolation. [ABSTRACT FROM AUTHOR]

Cells store triacylglycerol (TAG) within lipid droplets (LDs). A dynamic model describing complete LD formation at the endoplasmic reticulum (ER) membrane does not yet exist. A biochemical‐biophysical model of LD synthesis is proposed. It describes the time‐dependent accumulation of TAG in the ER membrane as the formation of a potential LD (pLD) bounded by spherical caps of the inner and outer monolayers of the membrane. The expansion rate of the pLD depends on the TAG supply, the elastic properties of the ER membrane, and the recruitment of phospholipids (PLs) to the cap‐covering monolayers. Model simulations provided the following insights: (a) Marginal differences in the surface tension of the cap monolayers are sufficient to fully drive the expansion of the pLD towards the cytosol or lumen. (b) Selective reduction of PL supply to the luminal monolayer ensures stable formation of cytosolic LDs, irrespective of variations in the elasto‐mechanical properties of the ER membrane. (c) The rate of TAG supply to the cytosolic monolayer has a major effect on the size and maturation time of LDs but has no significant effect on the TAG export per individual LD. The recruitment of additional PLs to the cap monolayers of pLDs critically controls the budding direction, size, and maturation time of LDs. The ability of cells to acquire additional LD initiation sites appears to be key to coping with acutely high levels of potentially toxic free fatty acids. [ABSTRACT FROM AUTHOR]

This paper presents a novel adaptation of the conventional approximate Bayesian computation sequential Monte Carlo (ABC-SMC) sampling algorithm for parameter estimation in the presence of uncertainties, coined combinatorial ABC-SMC. Inference of this type is used in situations where there does not exist a closed form of the associated likelihood function, which is replaced by a simulating model capable of producing artificial data. In the literature, conventional ABC-SMC is utilised to perform inference on continuous parameters. The novel scheme presented here has been developed to perform inference on parameters that are high-dimensional binary, rather than continuous. By altering the form of the proposal distribution from which to sample candidates in subsequent iterations (referred to as waves), high-dimensional binary variables may be targeted and inferred by the scheme. The efficacy of the proposed scheme is demonstrated through application to vibration data obtained in a structural dynamics experiment on a fibre-optic sensor simulated as a finite plate with uncertain boundary conditions at its edges. Results indicate that the method provides sound inference on the plate boundary conditions, which is validated through subsequent application of the method to multiple vibration datasets. Comparisons between appropriate forms of the metric function used in the scheme are also developed to highlight the effect of this element in the schemes convergence. [ABSTRACT FROM AUTHOR]

Living organisms are constructed from proteins that assemble into biomolecular complexes, each with a unique shape and function. Our knowledge about the structure–activity relationship of these complexes is still limited, mainly because of their small size, complex structure, fast processes, and changing environment. Furthermore, the constraints of current microscopic tools and the difficulty in applying molecular dynamic simulations to capture the dynamic response of biomolecular complexes and long-term phenomena call for new supplementary tools and approaches that can help bridge this gap. In this paper, we present an approach to comparing biomolecular and origami hierarchical structures and apply it to comparing bacterial microcompartments (BMCs) with spiral-based origami models. Our first analysis compares proteins that assemble the BMC with an origami model called "flasher", which is the unit cell of an assembled origami model. Then, the BMC structure is compared with the assembled origami model and based on the similarity, a physical scaled-up origami model, which is analogous to the BMC, is constructed. The origami model is translated into a computer-aided design model and manufactured via 3D-printing technology. Finite element analysis and physical experiments of the origami model and 3D-printed parts reveal trends in the mechanical response of the icosahedron, which is constructed from tiled-chiral elements. The chiral elements rotate as the icosahedron expands and we deduce that it allows the BMC to open gates for transmembrane passage of materials. [ABSTRACT FROM AUTHOR]

Several computational methods have been developed to identify neutralizing antibodies (NAbs) covering four dengue virus serotypes (DENV-1 to DENV-4); however, limitations of the dataset and the resulting performance remain. Here, we developed a new computational framework to predict potent and stable NAbs against DENV-1 to DENV-4 using only antibody (CDR-H3) and epitope sequences as input. Specifically, our proposed computational framework employed sequence-based ML and molecular dynamic simulation (MD) methods to achieve more accurate identification. First, we built a novel dataset (n = 1108) by compiling the interactions of CDR-H3 and epitope sequences with the half maximum inhibitory concentration (IC50) values, which represent neutralizing activities. Second, we achieved an accurately predictive ML model that showed high AUC values of 0.879 and 0.885 by tenfold cross-validation and independent tests, respectively. Finally, our computational framework could be applied to filter approximately 2.5 million unseen antibodies into two final candidates that showed strong and stable binding to all four serotypes. In addition, the most potent and stable candidate (1B3B9_V21) was evaluated for its development potential as a therapeutic agent by molecular docking and MD simulations. This study provides an antibody computational approach to facilitate the high-throughput identification of NAbs and accelerate the development of therapeutic antibodies. [ABSTRACT FROM AUTHOR]

The dynamic control of an active magnetic bearing (AMB) rotor after the rotor falls to its touch-down bearings has always been a difficult problem for applications such as flywheel energy storage. The rotor drop process has obvious nonlinear dynamic characteristics. This paper first discusses the structure of AMBs and the basic principles of their control. Starting from the electromagnetic forces that electromagnets can provide, the problem is simplified to the influence of an electromagnetic force with constant damping characteristics on the dynamic characteristics of a dropped rotor. A dynamic model of an AMB rotor with touch-down bearings was built and the contact force model between the rotor and the touch-down bearings was determined. A constant damping electromagnetic force was applied in two ways to verify the dynamic control feasibility of a dropped rotor through magnetic bearings. The simulation results show that the dropped rotor recovery control is feasible by applying a reasonable electromagnetic force. [ABSTRACT FROM AUTHOR]

Crushing is a critical operation in mineral processing, and its efficient performance is vital for minimizing energy consumption, maximizing productivity, and maintaining product quality. However, due to variations in feed material characteristics and safety constraints, achieving the intended circuit performance can be challenging. In this study, a centralized control strategy based on a finite state machine (FSM) is developed to improve the operations of an iron ore crushing circuit. The aim is to increase productivity by manipulating the closed-side-setting (CSS) of cone crushers and the speed of an apron feeder while considering intermediate storage silo levels and cone crusher power limits, as well as product quality. A dynamic simulation was conducted to compare the proposed control strategy with the usual practice of setting CSS to a constant value. Four scenarios were analyzed based on variations in bond work index (BWI) and particle size distribution. The simulation results demonstrate that the proposed control strategy increased average productivity by 6.88% and 48.77% when compared to the operation with a constant CSS of 38 mm and 41 mm, respectively. The proposed strategy resulted in smoother oscillation without interlocking, and it maintained constant flow rates. This ultimately improved circuit reliability and predictability, leading to reduced maintenance costs. [ABSTRACT FROM AUTHOR]

One of the most challenging issues scientists face is finding a suitable non-invasive treatment for cancer, as it is widespread around the world. The efficacy of phytochemicals that target oncogenic pathways appears to be quite promising and has gained attention over the past few years. We investigated the effect of docking phytochemicals isolated from the rhizomes of the Cimicifuga foetida plant on different domains of the IκB kinase alpha (IKK1/alpha) protein. The Cimicifugoside H-2 phytochemical registered a high docking score on the activation loop of IKK1/alpha amongst the other phytochemicals compared to the positive control. The interaction of the protein with Cimicifugoside H-2 was mostly stabilized by hydrogen bonds and hydrophobic interactions. A dynamic simulation was then performed with the Cimicifugoside H-2 phytochemical on the activation loop of IKK1/alpha, revealing that Cimicifugoside H-2 is a possible inhibitor of this protein. The pharmacokinetic properties of the drug were also examined to assess the safety of administering the drug. Therefore, in this in silico study, we discovered that the Cimicifugoside H-2 phytochemical inhibits the actively mutated conformation of IKK1/alpha, potentially suppressing the nuclear factor kappa light chain enhancer of activated B cells (NF-κB) pathway. [ABSTRACT FROM AUTHOR]

Flemingia macrophylla has traditionally been applied to relieve inflammation, diabetes, and circulatory complications. The leaf extract of F. macrophylla and its fractions were investigated for their in-vitro antioxidant and anti-diabetic properties. The phytochemical screening showed valuable phytochemicals, including glycosides, flavonoids, saponins, etc. GC-MS analysis of the phytochemicals in the methanol extract detected 19 bioactive compounds. Among the diverse fractions, the ethyl acetate fraction (EFM) exhibited the highest phenol and flavonoid contents of 557 mg GAE/g and 326 mg QCE/g, respectively. The total antioxidant content of EFM was found to be 292.41±19.16 mg AAE/g, while its antidiabetic study showed the greatest level of α -glucosidase (IC50: 11.27±1.25 µg/mL) and α -amylase (IC50: 10.04±0.63 µg/mL) inhibitory effects. The docking results showed that C6 had the highest binding scores of -9.0, -7.4, and -7.6 kcal/mol against antioxidant (6NGJ), α-glucosidase (5NN5), and α-amylase (4GQR) proteins, respectively. The dynamics simulation disclosed that C6-receptor protein complexes remained stable at the binding pocket under human body conditions and retained their stiff morphology for 100 nanoseconds (ns). ADMET results demonstrated their noncarcinogenic and well-absorbed properties, where PASS prediction data confirmed their efficacy as an antioxidant, antiulcerative, thrombolytic, and antidiabetic. Therefore, F. macrophylla has potential health benefits. [ABSTRACT FROM AUTHOR]

This research introduces the NeuRaiSya (Neural Railway System Application), an innovative railway signaling system integrating deep learning for passenger analysis. The objectives of this research are to simulate the NeuRaiSya and evaluate its effectiveness using the GreatSPN tool (graphical editor for Petri nets). GreatSPN facilitates evaluations of system behavior, ensuring safety and efficiency. Five models were designed and simulated using the Petri nets model, including the Dynamics of Train Departure model, Train Operations with Passenger Counting model, Timestamp Data Collection model, Train Speed and Location model, and Train Related-Issues model. Through simulations and modeling using Petri nets, the study demonstrates the feasibility of the proposed NeuRaiSya system. The results highlight its potential in enhancing railway operations, ensuring passenger safety, and maintaining service quality amidst the evolving railway landscape in the Philippines. [ABSTRACT FROM AUTHOR]

High-frequency non-physical oscillations may occur due to shock waves in seismic wavefield and dynamic rupture simulation. In this study, we introduced the alternative flux finite-difference weighted essentially non-oscillatory scheme to address potential shock wave issues in computational seismology effectively. The wavefield of the body-fitted curvilinear domain was accurately computed through conservative grid mapping, ensuring accurate implementation of free surface boundary conditions on irregular surfaces using characteristic boundary conditions and minimizing artificial boundary reflections with exponential decay absorbing layers. Finally, we compared our scheme with the GRTM for flat surfaces and the CGFDM3D-EQR for irregular surfaces to demonstrate its correctness and accuracy, and validated its non-oscillatory characteristics. The aforementioned scheme is anticipated to assume a significant function in simulating more intricate seismic wavefields or dynamic ruptures. [ABSTRACT FROM AUTHOR]

The dynamics of milling circuits, particularly those involving Semi-Autogenous Grinding (SAG) mills, are not adequately studied, despite their critical importance in mineral processing. This paper aims to investigate the dynamic behavior of an SAG mill pebble recycling circuit under varying feed ore conditions, focusing on both uncontrollable parameters (such as ore hardness) and controllable parameters (including circuit layout and pebble crusher configurations). The study is carried out with Simulink dynamic simulations. Our findings reveal several key insights. Firstly, plant designs based solely on static simulations may not be adequate for large or complex circuits, as they fail to account for the dynamic nature of milling processes. Second, incorporating stockpiles after pebble crushing can effectively mitigate the impact of dynamic fluctuations, leading to more stable circuit performance. Third, different circuit layouts can facilitate easier maintenance and operational flexibility. Notably, finer pebble crushing can enhance circuit throughput by 5% to 10%. [ABSTRACT FROM AUTHOR]

The research explores transition strategies of a coaxial compound helicopter transitioning to pure coaxial-rotor mode following a complete aft propeller failure. For that, a flight dynamics model is developed to predict the transition path, which is formulated as a multiphase trajectory optimization problem. Additionally, a revised aggressiveness indicator is proposed to quantify the transition difficulty. Next, the flight dynamics with and without the propeller and the accelerations at the propeller loss instant are discussed from a trim perspective. Finally, dynamic transitions are meticulously analyzed and compared using a multidimensional radar map to identify an effective strategy. Contrary to the static trim analysis, dynamic simulation results highlight the critical importance of pitch attitude control, longitudinal speed stability, and incidence instability. The potential threats include blade tip collision, significant height increase up to 300 m, and reverse longitudinal stick control regarding pitch attitude. To mitigate these risks and reduce pilot workload, we recommend gradually pitching up to enter the quasi-autorotation state. Additionally, slightly lowering the position of the propeller and maintaining a positive pitch attitude during normal flight can help improve aircraft transition stability. [ABSTRACT FROM AUTHOR]

Quercetin is a flavonoid with notable pharmacological effects and promising therapeutic potential. Quercetin plays a significant role in neuroinflammation, which helps reduce Alzheimer's disease (AD) severity. Quercetin (Q) and quercetin 3-O-glucuronide (Q3OG) are some of the most potent antioxidants available from natural sources. However, the natural form of quercetin converted into Q3OG when reacted with intestinal microbes. The study aims to ensure the therapeutic potential of Q and Q3OG. In this study, potential molecular targets of Q and Q3OG were first identified using the Swiss Target Prediction platform and pathogenic targets of AD were identified using the DisGeNET database. Followed by compound and disease target overlapping, 77 targets were placed in that AKT1, EGFR, MMP9, TNF, PTGS2, MMP2, IGF1R, MCL1, MET and PARP1 was the top-ranked target, which was estimated by CytoHubba plug-in. The Molecular docking was performed for Q and Q3OG towards the PDB:1UNQ target. The binding score of Q and Q3OG was − 6.2 kcal/mol and − 6.58 kcal/mol respectively. Molecular dynamics simulation was conducted for Q and Q3OG towards the PDB:1UNQ target at 200 ns. This study's results help identify the multiple target sites for the bioactive compounds. Thus, synthesizing new chemical entity-based quercetin on structural modification may aid in eradicating AD complications. [ABSTRACT FROM AUTHOR]

3-nitro-1,2,4-triazol-5-one (NTO) has been widely used as a kind of insensitive single-compound explosive owing to its excellent balance between safety and explosive energy. To reduce its possible acid corrosion and extend its application to insensitive ammunition, acid protection research on NTO-based explosives is significant. Traditionally, the acid protection effect was evaluated by metal corrosion, which is time-consuming and qualitative. An efficient and quantitative method is desirable for evaluating the acid protection effect and exploring novel protection materials. Herein, a polyimide of 4,4'-(hexafluoroisopropene)diphthalic anhydride (6FDA)/2,2-bis(trifluoromethyl)-4,4-diaminobiphenyl (TFMB) was synthesized by replacing the 4,4'-diaminodiphenyl ether (ODA) monomer with a TFMB monomer to act as an acid-protective coating material for NTO-based explosives. Compared with three other coating materials, polyvinylidene fluoride (PVDF), polyetherimide (PEI), and copolyimide (P84), the fluorinated polyimide exhibits the best acid protection effect. Moreover, a new method was constructed to obtain the pH time-dependent curve in order to evaluate efficiently the acid protection effect of the polymer materials. By the virtue of molecular dynamic simulation (Materials Studio 2023), the interfacial effects of the coating materials with NTO-based explosives were obtained. The study provides an interpretation of the acid protection effect on the molecular level, suggesting that the higher content of fluorine atoms is beneficial for stabilizing the active hydrogen atom of the NTO by forming intermolecular hydrogen bonds. [ABSTRACT FROM AUTHOR]

The Drosophila downstream receptor kinase (Drk), a homologue of human GRB2, participates in the signal transduction from the extracellular to the intracellular environment. Drk receives signals through the interaction of its Src homology 2 (SH2) domain with the phosphorylated tyrosine residue in the receptor tyrosine kinases (RTKs). Here, we present the solution NMR structure of the SH2 domain of Drk (Drk-SH2), which was determined in the presence of a phosphotyrosine (pY)-containing peptide derived from a receptor tyrosine kinase, Sevenless (Sev). The solution structure of Drk-SH2 possess a common SH2 domain architecture, consisting of three β strands imposed between two α helices. Additionally, we interpret the site-specific interactions of the Drk-SH2 domain with the pY-containing peptide through NMR titration experiments. The dynamics of Drk-SH2 were also analysed through NMR-relaxation experiments as well as the molecular dynamic simulation. The docking simulations of the pY-containing peptide onto the protein surface of Drk-SH2 provided the orientation of the peptide, which showed a good agreement with the analysis of the SH2 domain of GRB2. [ABSTRACT FROM AUTHOR]

Multiple drug-resistant fungal species are associated with the development of diseases. Thus, more efficient drugs for the treatment of these aetiological agents are needed. Rondonin is a peptide isolated from the haemolymph of the spider Acanthoscurria rondoniae. Previous studies have shown that this peptide has antifungal activity against Candida sp. and Trichosporon sp. strains, acting on their genetic material. However, the molecular targets involved in its biological activity have not yet been described. Bioinformatics tools were used to determine the possible targets involved in the biological activity of Rondonin. The PharmMapper server was used to search for microorganismal targets of Rondonin. The PatchDock server was used to perform the molecular docking. UCSF Chimera software was used to evaluate these intermolecular interactions. In addition, the I-TASSER server was used to predict the target ligand sites. Then, these predictions were contrasted with the sites previously described in the literature. Molecular dynamics simulations were conducted for two promising complexes identified from the docking analysis. Rondonin demonstrated consistency with the ligand sites of the following targets: outer membrane proteins F (id: 1MPF) and A (id: 1QJP), which are responsible for facilitating the passage of small molecules through the plasma membrane; the subunit of the flavoprotein fumarate reductase (id: 1D4E), which is involved in the metabolism of nitrogenous bases; and the ATP-dependent Holliday DNA helicase junction (id: 1IN4), which is associated with histone proteins that package genetic material. Additionally, the molecular dynamics results indicated the stability of the interaction of Rondonin with 1MPF and 1IN4 during a 10 ns simulation. These interactions corroborate with previous in vitro studies on Rondonin, which acts on fungal genetic material without causing plasma membrane rupture. Therefore, the bioprospecting methods used in this research were considered satisfactory since they were consistent with previous results obtained via in vitro experimentation. [ABSTRACT FROM AUTHOR]

Highlights: This review delves into the recent progress in high-performance and multifunctional neuromorphic devices for artificial intelligence applications from a novel perspective of plasticity modulation. It provides an in-depth discussion on the plasticity modulation strategies by chemical techniques, device structure design and physical signal modulation for advanced neuromorphic applications. It offers the prospects of exploring novel plasticity modulation mechanisms and techniques for scaled neural networks and examining their potentials in multimodal collaborative neuromorphic systems. Manipulating the expression of synaptic plasticity of neuromorphic devices provides fascinating opportunities to develop hardware platforms for artificial intelligence. However, great efforts have been devoted to exploring biomimetic mechanisms of plasticity simulation in the last few years. Recent progress in various plasticity modulation techniques has pushed the research of synaptic electronics from static plasticity simulation to dynamic plasticity modulation, improving the accuracy of neuromorphic computing and providing strategies for implementing neuromorphic sensing functions. Herein, several fascinating strategies for synaptic plasticity modulation through chemical techniques, device structure design, and physical signal sensing are reviewed. For chemical techniques, the underlying mechanisms for the modification of functional materials were clarified and its effect on the expression of synaptic plasticity was also highlighted. Based on device structure design, the reconfigurable operation of neuromorphic devices was well demonstrated to achieve programmable neuromorphic functions. Besides, integrating the sensory units with neuromorphic processing circuits paved a new way to achieve human-like intelligent perception under the modulation of physical signals such as light, strain, and temperature. Finally, considering that the relevant technology is still in the basic exploration stage, some prospects or development suggestions are put forward to promote the development of neuromorphic devices. [ABSTRACT FROM AUTHOR]

The primary aim of the current investigation is to contribute to SARS-CoV-2 research by identifying potential lead compounds for clinical applications, with a specific focus on inhibitors targeting the main protease (Mpro). In this research, molecular docking analysis was conducted using the software molecular operating environmental (MOE) to evaluate the potency of bioactive compounds sourced from medicinal plants as inhibitors of SARS--CoV-2 Mpro. Among 118 natural compounds with anti-HIV characteristics, the top seven candidates (h3, h84, h85, h87, h90, h108 and h110), were identified based on their superior binding energies with comparison to the reference ligand N3. These selected compounds exhibited binding affinities of -33.996, -35.336, -32.615, -32.154, -33.452, -31.903 and -40.360 kJ mol-1, respectively. To further refine our shortlist of potential candidates for human application, we examined the drug-likeness, and the pharmaceutical attributes of these compounds using the SwissADME web server. Among them, only two compounds, namely h85 and h87, demonstrated favorable pharmacological properties suitable for human administration. These two compounds were subsequently shortlisted for further investigation. To explore the conformational stability of ligands within the Mpro active site, we performed molecular dynamics (MD) simulations. These simulations showed reliable and steady trajectories, supported by analyses of root-mean-square-fluctuation (RMSF) and root--mean-square deviation (RMSD). These findings and favorable molecular properties as well as interaction profiles suggest that these two lead compounds may be promising SARS-CoV-2 therapeutic candidates. They present exciting starting points for further drug design. [ABSTRACT FROM AUTHOR]

As one of the core transmission components, axle-box bearings have been widely applied in urban rail vehicles and played a crucial role in their safe and stable operation. No matter in the starting and stopping stage or stable operation stage of the vehicle, the skidding phenomenon in axle-box bearings exists and impacts their own dynamic characteristics. Furthermore, as one of the main shape errors of the bearing surface, waviness may cause fluctuations for skidding characteristics of axle-box bearings. This study investigates the skidding dynamic analysis of axle-box bearings, taking into account race surface waviness. Firstly, a dynamics model for double-row cylindrical roller bearings is established, considering the cage flexibility and friction forces between different components. Then, this model is coupled with a three-dimension vehicle–track model, allowing for more precise dynamic simulation of axle-box bearings under actual running conditions. Furthermore, an excitation related to race surface waviness is added to the coupling model through time-varying displacement and contact stiffness. At last, the influence of race surface waviness on skidding characteristics of axle-box bearings is analyzed. The effectiveness of the proposed model is validated through theoretical analysis and field tests. Simulation results demonstrate that race surface waviness can impact the cage and roller slip ratio of axle-box bearings. Overall, this study provides valuable insights into the skidding dynamic analysis of axle-box bearings, highlighting the importance of considering race surface waviness in designing and maintaining axle-box bearings. [ABSTRACT FROM AUTHOR]

Ever since Varela and Maturana proposed the concept of autopoiesis as the minimal requirement for life, there has been a focus on cellular systems that erect topological boundaries to separate themselves from their surrounding environment. Here, we reconsider whether the existence of such a spatial boundary is strictly necessary for self-producing entities. This work presents a novel computational model of a minimal autopoietic system inspired by dendrites and molecular dynamic simulations in three-dimensional space. A series of simulation experiments where the metabolic pathways of a particular autocatalytic set are successively inhibited until autocatalytic entities that could be considered autopoietic are produced. These entities maintain their distinctness in an environment containing multiple identical instances of the entities without the existence of a topological boundary. This gives rise to the concept of a metabolic boundary which manifests as emergent self-selection criteria for the processes of self-production without any need for unique identifiers. However, the adoption of such a boundary comes at a cost, as these autopoietic entities are less suited to their simulated environment than their autocatalytic counterparts. Finally, this work showcases a generalized metabolism-centered approach to the study of autopoiesis that can be applied to both physical and abstract systems alike. [ABSTRACT FROM AUTHOR]

This study investigated the locomotion mechanism of foxtail robots, focusing on the frictional anisotropy of tilted bristles under the same friction coefficient and propulsion strategy using bristle diversity. Through dynamic analysis and simulations, we confirmed the frictional anisotropy of tilted bristles and elucidated the role of bristle diversity in generating propulsive force. The interaction between contact nonuniformity and frictional anisotropy was identified as the core principle enabling foxtail locomotion. Simulations of foxtail robots with multiple bristles demonstrated that variations in bristle length, angle, and deformation contribute to propulsive force generation and environmental adaptability. In addition, this study analyzed the influence of major design parameters on frictional anisotropy, highlighting the critical roles of body height, bristle length, stiffness, reference angle, and friction coefficient. The proposed guidelines for designing foxtail robots emphasize securing bristle nonuniformity and inducing contact nonuniformity. The simulation framework presented enables the quantitative prediction and optimization of foxtail robot performance. This research provides valuable insights into foxtail robot locomotion and lays a foundation for the development of efficient and adaptive next-generation robots for diverse environments. [ABSTRACT FROM AUTHOR]

The Cucumber Productivity Simulation Model (CPSM) was developed to precisely predict the dynamic process of cucumber productivity in a solar greenhouse. This research conducted a variety of sowing experiments and collected data on cucumber productivity and meteorological conditions from 2013 to 2015 and 2018 to 2020. Employing the principles of least squares, the relationship between cucumber productivity indicators and effective accumulated temperature (EAT) was fitted, determining key crop parameters and constructing the CPSM. Validation of the model was conducted using independent experimental data, evaluating its simulation accuracy. The results indicate that (1) CPSM can dynamically and meticulously simulate the formation process of different productivity indicators in cucumber. Normalized root mean square errors (NRMSE) ranged from 0.44% to 19.64%, and mean relative errors (MRE) ranged from 0.31% to 17.23% across different productivity indicator models. The models for organ water content, maximum root length, specific leaf area, and organ fresh weight distribution index demonstrated high simulation accuracy, while others showed relatively high accuracy. (2) Simulation accuracy varied with indicators and varieties. 19 indicators (34.55%) exhibited high simulation accuracy and 30 indicators (54.55%) showed relatively high accuracy. The JY35 variety (10.44 ± 8.49%) outperformed the JS206 variety (13.44 ± 8.50%) in terms of simulation accuracy. The JY35 variety had 39 superior productivity indicators (70.91%) while the JS206 variety had sixteen (29.09%). CPSM utilizes easily accessible temperature data as its input, allowing for precise and detailed simulation of productivity indicators for cucumber production in solar greenhouses. This research lays a theoretical foundation and provides technical support for guiding intelligent production management, efficient utilization of agricultural resources, and climate change productivity assessment in solar greenhouse cucumber production. [ABSTRACT FROM AUTHOR]

Nowadays, the dynamic behavior of rolling stocks is an essential problem. In dynamic simulation, the correct wheel-rail contact modeling is an important task. In this paper, the stiffness of the wheel-rail contact zone is found by a new, direct, and simplified formulation. This subject is developed by applying more details, such as surface roughness based on the surface topography and hardening effects of a real contact problem. These characteristics have not been considered altogether in other similar works. In this work, the contact stiffness and frequency results are obtained for different material properties and verified with analytical and experimental research. It is shown that the presented new direct method with an acceptable accuracy is easier to use than the complicated existing methods. This paper discusses the effects of contact parameter variations on contact stiffness and frequency. For example, it is shown that the contact stiffness decreases by increasing the surface roughness and increases by increasing the strain-hardening factor. [ABSTRACT FROM AUTHOR]

In aqueous and solid media, 2-HP-β/γ-CD inclusion complexes with poly aromatic hydrocarbon (PAH) Phenanthrene (PHN), Anthracene (ANT), Benz(a)pyrene (BaP), and Fluoranthene (FLT) were investigated for the first time. The inclusion complexes were characterized and investigated using fluorescence and 1HNMR spectroscopy. The most prevalent complexes consisting of both guests and hosts were those with a 1:1 guest-to-host ratio. The stability constants for the complexes of PHN with 2-HP-β-CD and 2-HP-γ-CD were 85 ± 12 M−1 and 49 ± 29 M−1, respectively. Moreover, the stability constants were found to be 502 ± 46 M−1 and 289 ± 44 M−1 for the complexes of ANT with both hosts. The stability constants for the complexes of BaP with 2-HP-β-CD and 2-HP-γ-CD were (1.5 ± 0.02) × 103 M−1 and (9.41 ± 0.03) × 103 M−1, respectively. The stability constant for the complexes of FLT with 2-HP-β-CD was (1.06 ± 0.06) × 103 M−1. However, FLT was observed to form a weak complex with 2-HP-γ-CD. Molecular dynamic (MD) simulations were used to investigate the mechanism and mode of inclusion processes, and to monitor the atomic-level stability of these complexes. The analysis of MD trajectories demonstrated that all guests formed stable inclusion complexes with both hosts throughout the duration of the simulation time, confirming the experimental findings. However, the flexible Hydroxypropyl arms prevented the PAHs from being encapsulated within the cavity; however, a stable exclusion complex was observed. The main forces that influenced the complexation included van der Waals interactions, hydrophobic forces, and C–H⋯π interaction, which contribute to the stability of these complexes. [ABSTRACT FROM AUTHOR]

Based on nanoarchitectonics and molecular dynamics simulations, we investigate the structural properties and diffusion pathway of Na atoms in sodium trisilicate over a wide temperature range. The structural and dynamics properties are analyzed through the radial distribution function (RDF), the Voronoi Si- and O-polyhedrons, the cluster function fCL(r), and the sets of fastest (SFA) and slowest atoms (SSA). The results indicate that Na atoms are not placed in Si-polyhedrons and bridging oxygen (BO) polyhedrons; instead, Na atoms are mainly placed in non-bridging oxygen (NBO) polyhedrons and free oxygen (FO) polyhedrons. Here BO, NBO, and FO represent O bonded with two, one, and no Si atoms, respectively. The simulation shows that O atoms in sodium trisilicate undergo numerous transformations: NBF0 ↔ NBF1, NBF1 ↔ NBF2, and BO0 ↔ BO1, where NBF is NBO or FO. The dynamics in sodium trisilicate are mainly distributed by the hopping and cooperative motion of Na atoms. We suppose that the diffusion pathway of Na atoms is realized via hopping Na atoms alone in BO-polyhedrons and the cooperative motion of a group of Na atoms in NBO- and FO-polyhedrons. [ABSTRACT FROM AUTHOR]

Context: A computational representation was used to model the doping and nanomodification of ZnO nanoparticles incorporated in Au/Fe nanocomposite. Au/Fe nanostructure was geometrically and discussed to investigate its electronic properties such electronic band structure and PDOS spectra. Moreover, the ZnO interacted with Au/Fe system was illustrated concerning the modified properties present on the surface of the nanocomposite as it may behave different attribution of band gap evaluated after ZnO modification included. Molecular dynamic simulation of the whole nano system was studied to predict the system stability concerning temperature and energy parameters during 100 ps simulation time. The most effective models under investigation were evaluated using adsorption annealing computations associated with the adsorption energy surface. A highly stable energetic adsorption system was anticipated by the periodic adsorption-annealing calculation. Methods: Au and Fe pure metals nanostructures were studied as a separate molecule with (0 0 1) plane surface for optimum energy minimization. Dmol3 module in/materials studio software was utilized for this protocol. The designed Au/Fe layers for nanostructure building material was computationally optimized, where DFT level was considered involving generalized gradient approximation (GGA) with Perdew–Burke–Ernzerh (PBE) exchange functional. In the computations of the structure matrix simulation, the global orbital cutoff was selected. To address the weak quantification of the standard DFT functionals, Tkatchenko-Schefer (TS) (DFT + D) was utilized to precisely correct the pairwise dispersion of the functionals. The electrical parameters were interpreted using the reciprocal space of the ultrasoft pseudopotential representation. To overcome the issues of self-electron interaction, the nonlocal hybrid functional with PBE0 method was utilized to calculate the electronic properties of the studied systems. The computations generated are predicated on a particular trajectory of the gamma k-point band energy interpolations proposed in this examination. An investigation into the position of adsorption came after geometric optimization. Adsorbed on an optimized Au/Fe surface, ZnO nanostructure was computationally explored using the Dmol3 simulation software. [ABSTRACT FROM AUTHOR]

Power system simulation is vital for designing and evaluating the performance of electrical system protection and control devices. Although several commercial simulators exist, most are expensive and not open-source code. It is essential to develop educational and research simulators that can prepare students, allow researchers to develop new methodologies, and assist system operators in making decisions. This paper aims to present a computer simulation platform called AnaDyn (dynamic analysis), a non-commercial and open-source platform. AnaDyn is an educational/research platform that allows dynamic (transient stability), quasi-steady-state simulation, modal, and power flow analysis. Short- and long-term studies of voltage, frequency, and rotor angle instability problems can be performed. The main characteristics of AnaDyn are quasi-steady-state simulation, in which the equations are not simplified; easy integration with other tools and toolboxes, since AnaDyn is developing in MATLAB; flexible modeling that allows the inclusion of new devices and controller tests. The detailed modeling of various power system devices, the description of the numerical solution method, and the interface are also presented in this work. The platform is validated by comparing a test system's results with those obtained with Brazil's most popular commercial software. The main potentials of quasi-steady-state simulation are also presented. The results indicate that AnaDyn is efficient for educational and research studies on the stability of short- and long-term electrical systems. [ABSTRACT FROM AUTHOR]

Rieske non-heme dioxygenase family enzymes play an important role in the aerobic biodegradation of nitroaromatic pollutants, but no active dioxygenases are available in nature for initial reactions in the degradation of many refractory pollutants like 2,4-dichloronitrobenzene (24DCNB). Here, we report the engineering of hotspots in 2,3-dichloronitrobenzene dioxygenase from Diaphorobacter sp. strain JS3051, achieved through molecular dynamic simulation analysis and site-directed mutagenesis, with the aim of enhancing its catalytic activity toward 24DCNB. The computationally predicted activity scores were largely consistent with the detected activities in wet experiments. Among them, the two most beneficial mutations (E204M and M248I) were obtained, and the combined mutant reached up to a 62-fold increase in activity toward 24DCNB, generating a single product, 3,5-dichlorocatechol, which is a naturally occurring compound. In silico analysis confirmed that residue 204 affected the substrate preference for meta-substituted nitroarenes, while residue 248 may influence substrate preference by interaction with residue 295. Overall, this study provides a framework for manipulating nitroarene dioxygenases using computational methods to address various nitroarene contamination problems. [ABSTRACT FROM AUTHOR]

Abnormal wear of stitch wires due to interference poses a serious threat to railway safety. To avoid this scenario, the concept of the dynamic envelope of the stitch wire was proposed, accompanied by an interference check method. A multi-node beam model of the stitch wire was established using the finite element method, employed to simulate the pantograph and catenary system, and validated by field test. The dynamic behaviour of the stitch wire was studied, and the concept of dynamic envelope was introduced. Moreover, factors affecting this envelope were analysed, and an interference check method was proposed. Results demonstrate that, the vibration of the stitch wire mainly occurs in the vertical direction and intensifies with increasing speed. Its vertical vibration increases from 70 mm to 137 mm as the train speed goes from 300 km/h to 400 km/h. Cantilever assembly errors and dropper installation issues are the main causes for the abnormal wear of stitch wires. A 100 mm assembly error reduces the clearance from 67 mm to 14 mm, while a 2 m dropper installation error eliminates the clearance entirely. This study provides valuable insights for enhancing the safety of catenary system. [ABSTRACT FROM AUTHOR]

The presented article deals with the issue of inventory management optimization through modelling and simulation in the software Tecnomatix Plant Simulation. Based on an in-depth analysis of the supply chain with an emphasis on inventory management, a simulation model was developed. It was optimized using the inventory theory methodology in combination with a discrete-event simulation approach. Dynamic simulation made it possible to perform experiments and optimize the existing state. The solution to the problem is elaborated on a case study to achieve the efficiency of the supply process of a specific operation of a clothing retail chain, which is struggling with the problems of excessive and inaccurate supply. [ABSTRACT FROM AUTHOR]

In this paper, we introduce a new method for exact decomposition of propagating, nonlinear magnetohydrodynamic (MHD) disturbances into their component eigenenergies associated with the familiar slow, Alfvén, and fast wave eigenmodes, and the entropy and field-divergence pseudoeigenmodes. First, the mathematical formalism is introduced, where it is illustrated how the ideal-MHD eigensystem can be used to construct a decomposition of the time variation of the total energy density into contributions from the eigenmodes. The decomposition method is then demonstrated by applying it to the output of three separate nonlinear MHD simulations. The analysis of the simulations confirms that the component wave modes of a composite wavefield are uniquely identified by the method. The slow, Alfvén, and fast energy densities are shown to evolve in exactly the way expected from comparison with known linear solutions and nonlinear properties, including processes such as mode conversion. Along the way, some potential pitfalls for the numerical implementation of the decomposition method are identified and discussed. We conclude that the exact, nonlinear decomposition method introduced is a powerful and promising tool for understanding the nature of the decomposition of MHD waves as well as analyzing and interpreting the output of dynamic MHD simulations. [ABSTRACT FROM AUTHOR]

Coal-resource-based cities, as one of the important types of typical resource-based cities in China, have strong characteristics of instability, sensitivity, and fragility, exhibiting a series of vulnerability features of the human-land system. Previous studies have lacked a deeper investigation into the vulnerability of such cities from the perspective of coupling feedback mechanisms among various elements or subsystems. This paper adopts Bohle et al.'s "Dual Structure Model" of vulnerability to establish an indicator system for vulnerability warning in coal-resource-based cities. Using Fushun City as a sample, a dynamic simulation model of vulnerability in coal-resource-based cities is constructed based on system dynamics for warning simulation calculations, analyzing the evolution trend of vulnerability in Fushun City from 2010 to 2022. The results show the following: (1) from 2010 to 2022, the urban vulnerability of Fushun City transitioned from a medium warning level to a relatively safe level, showing a trend of annual reduction and improvement, undergoing three development stages of significant reduction, fluctuation stabilization, and slight rebound. (2) Due to the causal relationships among various elements within the vulnerability subsystems of Fushun City, differences exist in the contribution levels of vulnerability subsystems during the period 2010–2022, under the combined effects of sensitivity and adaptability factors. The contribution rate of the natural subsystem was the highest from 2010 to 2014, while, from 2016 to 2019, urban vulnerability began to shift towards an economically and socially dominant type. Influenced by the pandemic, Fushun City's overall vulnerability has shown an upward trend since 2020 compared to the previous stage. Finally, specific policy suggestions are proposed for Fushun City to cope with vulnerability changes based on the analysis results, providing a theoretical basis for achieving sustainable development in such coal-resource-based cities. [ABSTRACT FROM AUTHOR]

Globally, rail transit is developing toward higher speeds, larger axle weights, and greater environmental friendliness. The more and more complex wheel–rail interaction will result in the dynamic responses of vehicles, tracks and other structures needing more in-depth theoretical research. However, most existing models for dynamic simulations of the vehicle–track coupling system need to extend the model on both sides of the concerned region to eliminate the boundary effect. To a certain extent, this kind of process method increases the computational effort. To overcome this disadvantage, a hybrid model combined with the analytical method and finite element method was proposed. The moving support system (including transition nodes) was specially established referring to the analytical solution of rail deflection based on the Winkler elastic foundation beam theory to realize the combination of the two methods. Two examples were presented to verify the stability and accuracy of the proposed model. The comparison results show that simulation results of vertical wheel–rail forces and track vibrations are almost consistent with the existing model. Furthermore, the calculation efficiency was discussed and certificated under different long-marshalling trains, with an obvious speedup factor that could be more than 2.5 for 16-marshalling train. The proposed model has a wide application prospect in the vehicle–track coupling analysis of long-marshalling trains, especially for heavy haul railways with hundreds of vehicles. [ABSTRACT FROM AUTHOR]

Phytophthora infestans (Mont.) de Bary, the oomycotic pathogen responsible for potato late blight, is the most devastating disease of potato production. The primary pesticides used to control oomycosis are phenyl amide fungicides, which cause environmental pollution and toxic residues harmful to both human and animal health. To address this, an antimicrobial peptide, NoPv1, has been screened to target Plasmopara viticola cellulose synthase 2 (PvCesA2) to inhibit the growth of Phytophthora infestans (P. infestans). In this study, we employed AlphaFold2 to predict the three-dimensional structure of PvCesA2 along with NoPv peptides. Subsequently, utilizing computational methods, we dissected the interaction mechanism between PvCesA2 and these peptides. Based on this analysis, we performed a saturation mutation of NoPv1 and successfully obtained the double mutants DP1 and DP2 with a higher affinity for PvCesA2. Meanwhile, dynamics simulations revealed that both DP1 and DP2 utilize a mechanism akin to the barrel-stave model for penetrating the cell membrane. Furthermore, the predicted results showed that the antimicrobial activity of DP1 was superior to that of NoPv1 without being toxic to human cells. These findings may offer insights for advancing the development of eco-friendly pesticides targeting various oomycete diseases, including late blight. [ABSTRACT FROM AUTHOR]

Motivation Simulating gut microbial dynamics is extremely challenging. Several computational tools, notably the widely used BacArena, enable modeling of dynamic changes in the microbial environment. These methods, however, do not comprehensively account for microbe–microbe stimulant or inhibitory effects or for nutrient–microbe inhibitory effects, typically observed in different compounds present in the daily diet. Results Here, we present BN-BacArena, an extension of BacArena consisting on the incorporation within the native computational framework of a Bayesian network model that accounts for microbe–microbe and nutrient–microbe interactions. Using in vitro experiments, 16S rRNA gene sequencing data and nutritional composition of 55 foods, the output Bayesian network showed 23 significant nutrient–bacteria interactions, suggesting the importance of compounds such as polyols, ascorbic acid, polyphenols and other phytochemicals, and 40 bacteria–bacteria significant relationships. With test data, BN-BacArena demonstrates a statistically significant improvement over BacArena to predict the time-dependent relative abundance of bacterial species involved in the gut microbiota upon different nutritional interventions. As a result, BN-BacArena opens new avenues for the dynamic modeling and simulation of the human gut microbiota metabolism. Availability and implementation MATLAB and R code are available in https://github.com/PlanesLab/BN-BacArena [ABSTRACT FROM AUTHOR]