Abstract: Development of the fast neutron radiography with higher penetration capability in Non-Destructive Testing (NDT) techniques is rapidly. The detection efficiency and the imaging spatial resolution are the main problem of the radiography detector for many fast neutron imaging systems. In this paper, a detector composed of pixelated EJ200 scintillator array，an 16 × 16 silicon-photomultipliers (SiPM) array, and a capacitive multiplexing network readout electronics is designed. Using Monte-Carlo simulations，the main parameters of the detector was optimization. Then the detector prototype was fabricated and tested at a 14 MeV D-T neutron source. The preliminary test results showed that the prototype has spatial resolution of 1.26 mm. Using pixelated scintillator structure，the conflict between spatial resolution and detect efficiency could improved. Moreover, SiPMs offer a flexibility for the expansion of application field of the imaging system due to their excellent photon detection performance, relatively low price and joint possibility for large area.

As a widely used plastic, the aging and degradation of polyethylene (PE) are inevitable problems, whether the goal is to prolong the life of PE products or address the issue of white pollution. Molecular simulation is a vital scientific tool in elucidating the mechanisms and processes of chemical reactions. To obtain the distribution and evolution process of PE's thermal oxidation products, this work employs the self-consistent charge density functional tight binding (SCC-DFTB) method to perform molecular simulations of the thermal oxidation of PE with different crystallinity and branched structures. We discovered that crystallinity does not affect the thermal oxidation mechanism of PE, but higher crystallinity makes PE more susceptible to cross-linking and carbon chain growth, reducing the degree of PE carbon chain breakage. The branched structure of PE results in differences in pore size between the carbon chains, with larger pores leading to a concentrated distribution of O2 and free radicals subsequently formed. The breakdown of PE is slowed down when free radicals are localized in low-density regions of the carbon chain. The specifics and mechanism of PE's thermal oxidation are clearly revealed in this paper, which is essential for understanding the process in-depth and for the development of anti-aging PE products.

Soccer is the leading cause of all sports-related ocular injuries in Europe and Israel and leads to blindness at a disproportionately high rate, especially among children (Thompson et al., 2019). With soccer being the most popular sport in the world, it is surprising the only solution to ocular injuries are sports glasses which can cause direct damage to the eye and impair peripheral vision by 15%, calling for an alternative (Smith & Jones, 2020). This work, based on an imported facial model, focuses on both the qualitative and quantitative aspects of building a personalized, low-cost (through optimizing material needed), superior apparatus to conventional sports glasses. The quantitative side examines a modified and model-validated (through a SRS of thirty unique extrapolated points) multivariate linear regression equation, based on horizontal and vertical rotation angles (n=60) trained with residual and computer simulation data, that can accurately extrapolate and quantify ocular impact from all horizontal and vertical rotation angles and a modified Hertzian Contact Stress Equation to determine the thickness of the apparatus using the elasticity modulus, impact force, and geometrical facial and soccer-ball features. The qualitative side examines where firstly, ocular impact is most prevalent, and secondly, where most impact is seen from rotating the ball horizontally and vertically through analysis of Pearson’s Correlation Coefficient at the supraorbital, medial canthus, infraorbital, and lateral canthus regions from both regression equations as well as a cost-benefit analysis for comparison with conventional sports glasses. The findings discovered in this work lay the groundwork for future research to build a customized low-cost ocular injury prevention device which can simultaneously ensure complete ocular safety while enhancing athletic performance for over 250,000,000 players (Johnson & Garcia, 2022).

The Active Distribution Networks (ADNs) are Multi-Input Multi-Output (MIMO) systems with coupled dynamics which cause interactions among the control loops of the Distributed Energy Resources (DERs). This undesired effect lead to performance degradation in the voltage control. To mitigate the effects of these unavoidable coupling, the present paper proposes a systematic design procedure based on the analysis of the interaction's sources. In details, each DER is equipped with a double loop PI to control the active and reactive powers output by the Voltage Source Converter (VSC) which connects the DER to the network's node. Furthermore, to guarantee Ancillary Services (ASs), the two loops are coupled by a simple mechanism of cooperation of the active power to voltage regulation realized by a filtered droop law. To achieve voltage regulation with reduced loop interactions, the PI parameters and the filter's pulse are designed according to a two sequential steps procedure based on the (Internal Model Control) IMC technique. Simulation studies are finally presented to demonstrate that the proposed design method achieves both reduction of the loop interaction and robust voltage control in presence of model parameter uncertainty in the MIMO model.

The “circular bioeconomy” offers numerous opportunities for the health, cosmetic, and nutrition sectors through the potential reuse of Castanea sativa by-products. This abundant and sustainable resource provides valuable bioactive secondary metabolites with antioxidants and anti-inflammatory properties. The transformation of these by-products into high-value products for human health can contribute to sustainable economic growth and reduce the environmental impact of traditional waste disposal practices, thus creating added value from previously underutilized resources. In the present study, we investigated the antioxidant capacity, phytochemical composition and in vitro antioxidant and anti-inflammatory activity of C. sativa burrs (CSB) aqueous extract. The spectrophotometric study yielded optimal total phenolic content (TPC) values, along with significant antioxidant and anti-radical properties. The utilization of UPLC-MS-MS techniques for phytochemical investigation resulted in the identification of a total of 56 metabolites, providing confirmation of the presence of phenolic compounds in CSB. In addition, CSB significantly downregulated pro-inflammatory mediators in LPS-stimulated RAW 264.7 macrophage cells without significant cell toxicity.

During the thinning process, in the semiconductor industry, residual stress from thin films can cause severe warpage in wafers, which can compromise their processability and packaging. This warpage can lead to bifurcation or buckling, making it important to understand this phenomenon for the manufacturing of large semiconductor wafers. We conducted a finite element analysis of the thinning process using ANSYS mechanical enterprise 2023/R2 to investigate the asymmetric curvatures resulting from bifurcation in a standard 300 mm Si (001) wafer. We induced an asymmetry in the system by applying a slight force on a point of the circumferential region perpendicularly to the substrate. We also simulated the compressive stress from the damaged layer formed during the thinning process and considered its influence on warpage and bifurcation in both linear and non-linear cases. We also included the influence of Earth's gravity induced deflection (GID) and investigated the influence of the compressive stress damaged layer on the grinding process of the whole wafer by adding a metal front layer to the ground back damaged wafer.

Here we propose a simple way in which one can considerably improve performance of the gas stripper setup at the GSI UNILAC. To do so, it will be enough to replace inside the main GSI stripper chamber the present nozzle and the short windowless storage gas cell (for pulsed gas-jet operation mode) by a simple conical diverging nozzle combined with a gas catcher tube placed on the axis of gas-jet at some distance downstream the nozzle exit. As a result, the background pressure in the main and differentially pumped adjacent vacuum chambers of the gas stripper at the GSI UNILAC will dramatically reduce, and it will make possible to achieve the required optimal thickness of gas targets. The pulsed gas stripper operation is simply realized by implementing a commercially available fast gas valve connected to the nozzle entrance. Moreover, the ion beam pulses repetition rate can be increased and it will allow for the considerably higher average intensity of the ion beams extracted from the GSI UNILAC. Performance of the proposed GSI UNILAC gas stripper modification we explored by means of detailed computer experiments, which give a realistic description of supersonic gas jets flowing out the nozzle into vacuum. Results of these computer experiments have presented and discussed.

The target area of the present study is the entrance to the Sulina channel in the Black Sea, the zero-kilometer of the Danube River. This represents the southern gate of the seventh Pan-European transport corridor and is subjected to high navigation traffic. The coastal environment at the Danube’s mouth is very often subjected to strong environmental conditions inducing high risks for navigation hazards. From this perspective, the objective of the present work is to provide a more comprehensive picture concerning the past and future expected dynamics of the environmental matrix in this area, including especially wind and wave conditions. An analysis of some in situ measurements performed at the zero kilometer of the Danube is first carried out for the 15 years 2009-2023. A second analysis is based on data provided by regional climate wind models. Two 30-year periods are considered, the recent past (1976-2005), when also comparisons with ERA5 reanalysis data were performed, and the near future (2041-2070), when two different models and three climate scenarios were considered. Finally, using as a forcing factor each of the wind fields before analyzed, simulations with a spectral wave model were carried out and the nearshore wave conditions were evaluated. The results show that both extreme wind and wave conditions are expected to be slightly enhanced in the future. Strong wind fields are characteristic in this area, with wind gusts exceeding on average with more than 70% the maximum hourly averaged wind speed. As regards the waves, due to the complex nearshore phenomena, considerable enhancements in terms of significant wave heights are induced. Furthermore, there is also a high risk of rogue wave’s occurrence.

Computational modeling (CM) is a versatile scientific methodology used to examine the properties and behavior of complex systems, such as polymeric materials for biomedical bioengineering. CM has emerged as a primary tool for predicting, setting up, and interpreting experimental results. Integrating in silico and in vitro experiments accelerates scientific advancements, yielding quicker results at a reduced cost. While CM is a mature discipline, its recent prominence in Bio-medical Engineering for biopolymer materials has recently gained prominence. In biopolymer biomedical engineering, CM focuses on three key research areas: A) Computer-aided design (CAD/CAM), B) Finite Element Analysis, and C) Molecular Dynamic Simulations. This review centers on Molecular Dynamics (MD) simulations in biopolymers, analyzing structural, functional, and evolutionary aspects of biomolecular systems over time. MD simulations solve Newton's equations of motion for all-atom systems, generating spatial trajectories for each atom, providing insights into properties like water absorption on biopolymer surfaces and interactions with solid surfaces, crucial for biomaterial assessment. This review offers readers a comprehensive overview of the diverse applications of Molecular Dynamics (MD) simulations on biopolymers. Furthermore, it emphasizes the flexibility, robustness, and synergistic relationship between in silico and experimental techniques.

EV transmissions operate at high speeds, upto 30,000 rpm. High speed operation puts higher demands on bearings, seals, and gears. Bearings in EV transmissions are prone to electrically induced bearing damage and may exhibit signs of pitting and fluting. Surface-initiated rolling contact fatigue is another common problem gaining increased attention lately. Most EV transmissions require a coupling between an oil-lubricated gearbox to an electrical motor that runs with minimal lubrication at very high rpm. High mechanical and thermal stresses the seals are exposed to under starved lubrication conditions have a detrimental impact on their service life. Hence, proper lubrication is critical. In general, EV transmission fluids call for a somewhat different spectrum of properties compared to conventional ATF. Gear tribology simulations open new ways to the design and optimization of lubrication for EV transmissions. Additionally, such simulations can also provide valuable insights into the effects of different oil properties on cooling and lubrication efficiencies, thereby helping in matching the lubricant and hardware characteristics for optimal performance. In the present communication, we demonstrate the effects of different lubricants and surface finishing technologies on the tribology of high-speed gears using tribological tests and advanced thermal elastohydrodynamic (TEHD) simulations. Important roles of lubricity additives and surface finish optimization are highlighted in conjunction with a move towards ultralow viscosity EV transmission fluids.

Scaling up the production of power devices involves, in the semiconductor industry, the use of large semiconductor 8” and 12” wafers of Si or SiC. Their use implicates a successful an effective monitoring and control of wafer warpage, as the geometrical size of the substrate increases, as well as a command control on the degeneration of non-linear warpage into critical phenomena known as bifurcation or buckling.To mitigate the warpage, the use of taiko wafers, which consists of wafers having a thicker region on the rim region of the wafer, has been generally adopted in the production lines. In a previous work [1] we investigated the warpage of taiko wafers by introducing the concept of equivalent thickness, in the linear approximation, for the case of a front side metalized taiko wafer. However, as the thickness of the central semiconductor substrate region decreases the possibility that also the taiko wafer bifurcates emerges. For this reason, in this work we have investigated the occurrence of bifurcation or buckling in a taiko wafer. In particular, we implemented a finite element analysis method by using ANSYS Mechanical Enterprise 2023/R2 to investigate the phenomenon of bifurcation in a taiko wafer. The investigated system consisted of a 200 mm Si (001) front side metalized (FSM) taiko wafer, having a substrate thickness ranging from 100 µm to 400 µm, with a step height fixed to 450 µm. The FSM layer consisted of an Al layer of 4.5 µm thin. The system was subjected to a thermal load such that, getting cooled from a nominal temperature T to 25°C, the metal layer can develop a residual stress. To investigate the bifurcation, an asymmetry was induced in the system by applying a slight force on a point of the circumferential region perpendicularly to the substrate. The temperature investigated ranged from 30 °C to 170 °C. From this investigation, it results that also the bifurcation is mitigated by the taiko structure. Indeed, the bifurcation emerges at higher values of the stresses with respect to the case of flat wafers having the same size and thickness of the substrate. Moreover, the concept of equivalent thickness needs to be reformulated by taking into account of the bifurcation phenomenon. Indeed, from the warpage at the bifurcation point of the taiko wafer, we can determine an overall equivalent thickness of the taiko wafer.

Sustainable development of our society demands recycling of metallic wastes which may contain a variety of metallic impurities. Thus, it is desirable to develop a ‘universal’ structure, such as an amorphous alloy tolerating high concentrations of metallic pollutants. We performed ab initio molecular dynamics simulations to manufacture a novel multicomponent amorphous alloy of twenty elements (20e-HEAA). Analysis reveals both topological and chemical compositional short-range ordering in the obtained 20e-HEAA and formation of B-B clusters. Electronic structure calculations reveal the metallic nature of the amorphous alloy with its Fermi level falling in a valley in the density of states. Moreover, the Zn 3d and Cd 4d electrons exhibit a localized nature and thus, should be excluded from the valence electron concentration (VEC) analysis in the study of high-entropy alloys. The information obtained here is helpful to get insight into multicomponent high entropy materials, especially multicomponent high-entropy amorphous alloys as potential circular metals.

A new approach was presented in this study to simulate a stable atom along with subatomic particles in it. Subatomic particles in an atom are treated as conventional particles, exhibiting attraction and repulsion between them, giving a stable atom simulation. This new approach leads to developing new potentials for subatomic particles to simulate a stable atom. Subatomic particle dynamics (SPD) simulations were developed for within-atom simulations that give a stable atom structure for infinite time and provide many insights into electron trajectories and atom properties like energies and radius of the atom. The effect of protons and neutrons movement in the nucleus on electron trajectories was captured in SPD. Hydrogen and Carbon atom SPD were reported in this study. The Pilot-wave theory was implemented in this study to simulate the wave nature of subatomic particles in an atom. Electrons motion was guided by the interference pattern produced by the electron’s aether medium waves in SPD. SPD was implemented on molecules, resulting in a stable molecular structure giving insights into electron trajectories shared by multiple atoms.

Cholinesterase (ChE) and secretase (BACE) inhibitors, and fibril- and β-amyloid-suppressing medicines are used to treat Alzheimer's disease (AD) symptomatically. The prevalence and complex nature of AD have increased the urgent need for multi-targeted directed ligands (MTDLs). This is because MTDLs can prevent potential drug-drug interactions during poly-therapy and have a better therapeutic profile than single targeted agents. Using piperazine linker or spacer and two primary scaffolds, benzofuran and 8-hydroxyquinoline, a unique class of multi-targeted medicines was recently reported by our group. These compounds showed re-markable effectiveness in inhibiting Aβ1-42 aggregation and acting as iron chelators.The results prompted us to synthesize an additional series of compounds as multimodal anti-AD agents and investigate its inhibitor activities to ChE (AChE/BChE) and BACE1 enzymes. The resulting in-hibitory effects suggested that the compounds under study might be used to improve cognitive function. The docking analysis' findings revealed that the compounds bind to AChE and BChE by forming H-bond interactions with amino acid residues at binding sites and µ-stacking inter-actions with aromatic residues, whereas the binding to BACE1 only revealed H-bond interac-tions with amino acid residues at binding sites.

This study delves into the realm of potential therapeutics for breast cancer by conducting a comprehensive docking simulation and virtual screening analysis using Autodock Vina Algorithm. The focus based on the human epidermal growth factor receptor 2 (HER2), a key protein associated with various cancers, particularly in the context of breast cancer.The results reveal compelling insights into the binding interactions of several natural compounds and drugs with HER2. Notably, Acebilustat, Bemcentinib, and Amentoflavone exhibit outstanding binding energies, averaging around -10 kcal/mol, suggesting strong and favorable interactions with the HER2 target.These encouraging findings not only emphasize the potential biological significance of these compounds but also hint at their potential usefulness in fighting breast cancer.Their promising binding affinities with HER2 position them as potential candidates for further investigation and development as therapeutic agents against breast cancer.

The WORLD3 world model, which served as the basis for The Club of Rome report The Limits to Growth (1972), was criticized, among other things, for not being able to simulate social interactions. In order to remedy this shortcoming, a research group led by Karl Deutsch at the Berlin Science Center developed a far more comprehensive model between 1979 and 1988 entitled GLOBUS, which was supposed to be able to include political developments in the calculation. This article aims to explain the hopes that were attached to the creation of a further world model and the means by which attempts were made to assert its results. To this end, three genealogical lines of the model -I. as part of the world modeling community, II. as part of quantitative international relations research, III. as part of Karl Deutsch's cybernetic-political science research- will be presented. The data basis and the functioning of GLOBUS are then described. Finally, section VI is devoted to the research group's efforts to make the model "effective".

Explosive boiling is a fast phase transition from an ultra-thin liquid film to vapor under an extremely high heat flux, which typically has been studied using molecular dynamics simulation (MDS) method. The present MDS study investigated the explosive boiling of a liquid argon nanofilm over different solid copper surfaces with different nanowall patterns including parallel and cross nanowalls. For each surface, atomic motion trajectories, number of liquid and vapor argon atoms, heat flux, and, mainly, onset time of explosive boiling were investigated. The simulation results indicated that explosive boiling occurs earlier on parallel and cross nanowall surfaces than on an ideally smooth surface, regardless of the topology and configuration of nanowalls. Moreover, the results revealed that by using the cross nanowall surfaces, the onset time of explosive boiling decreased by 0.7–4% compared to the parallel nanowall surfaces. In addition, it was found that the onset time of explosive boiling strongly depends on the potential energy barrier and the movement space between nanowalls for both parallel and cross nanowall surfaces. Furthermore, simulation findings showed that even though increasing the height of cross nanowalls increases heat flux and temperature of the fluid argon domain, it does not necessarily result in a shorter onset time of explosive boiling. These findings demonstrate the capability of cross nanowall surfaces for explosive boiling, thereby could be utilized in future surface design for thermal management applications.

Despite being small and simple structured in comparison to their victims, virus particles have the potential to harm severly and even kill highly developed species such as humans. To face upcoming virus pandemics, detailed quantitative biophysical understanding of intracellular virus replication mechanisms is inevitable. Unveiling the relationship of form and function might allow to determine putative attack points relevant for the systematic development of direct antiviral agents (DAA) and potent vaccines. Biophysical investigations of spatio-temporal dynamics of intracellular virus replication so far are rare. We are developing a framework to allow for fully spatio-temporal resolved virus replication dynamics simulations based on partial differential equations models (PDE) and evaluated with advanced numerical mathematical methods on leading supercomputers. This study presents an advanced highly nonlinear model of the genome replication cycle of a specific RNA virus, the Hepatitis C virus (HCV). The diffusion-reaction model mimics the interplay of the major components of the viral RNA (vRNA) cycle, namely non structural viral proteins (NSP), vRNA and a generic host factor. Technically, we couple surface PDEs (sufPDEs) on the 3D embedded 2D Endoplasmatic Reticulum (ER) manifold with PDEs in the 3D membranous web (MW) and cytosol volume. (The MWs are the replication factories growing on the ER induced by NSPs.) The sufPDE/PDE model is evaluated at realistic reconstructed cell geometries which are based on experimental data. The simulations couple the effects of NSPs which are restricted to the ER surface with effects appearing in the volume. The volume effects include the host factor supply from the cytosol and the MW dynamics. Special emphasis is put to the exchange of components between ER surface, MWs and cytosol volume. As the vRNA spatial properties are not fully understood so far in experiment, the model allows for vRNA both restricted to the ER and moving in the cytosol. The visualization of the simulation resembles a look into some sort of fully 3D resolved “in silico microscopes” to mirror and complement in vitro / in vivo experiments for the intracellular vRNA cycle dynamics. The output data are quantitatively consistent with experimental data and provoke advanced experimental studies to validate the model.

Integrating photovoltaic (PV) systems plays a pivotal role in the global shift toward renewable energy, offering significant environmental benefits. In many instances, utility companies pay for both energy and peak demand. PV systems can effectively reduce energy consumption during their operational periods, while, their contribution during peak hours, particularly in the early morning and late evening, is often limited. To address this issue, battery storage systems are utilized for storing energy during off-peak hours and releasing it during peak times. However, finding the optimal size of PV-battery systems remains a challenge. This study proposes a novel statistical model to optimize PV-battery system sizing for enhanced peak demand reduction. The model aims to flatten 95% of peak demand days up to a certain demand threshold, ensuring consistent energy supply and financial benefit for utility companies. A straightforward and effective search methodology is employed to determine the optimal system sizes. Additionally, the model effectiveness is rigorously tested through a modified Monte Carlo simulation coupled with time series clustering to generate various scenarios to assess performance under different conditions. The results indicate that the optimal PV-battery system successfully flattens 95% of daily peak demand up to 2000 kW, yielding a financial benefit of $812,648 over 20 years.

This is the second paper in a cycle investigating the exact solution of loop equations in decaying turbulence. We perform numerical simulations of the Euler ensemble, suggested in the previous work, as a solution to the loop equations. We designed novel algorithms for simulation, which take a small amount of computer RAM so that only the CPU time grows linearly with the size of the system and its statistics. This algorithm allows us to simulate systems with billions of discontinuity points on our fractal curve, dual to the decaying turbulence. For the vorticity correlation function, we obtain \textbf{quantum fractal laws} with regime changes between universal discrete values of indexes. The traditional description of turbulence with fractal or multifractal scaling laws does not apply here. The measured conditional probabilities of fluctuating variables are smooth functions of the logarithm of scale, with statistical errors being negligible at our large number of random samples $T = 167,772,160$ with $N = 200,000,000$ points on a fractal curve. The quantum jumps arise from the analytical distribution of scaling variable $X = \frac{\cot^2(\pi p/q)}{q^2}$ where $\frac{p}{q}$ is a random fraction. This distribution is related to the totient summatory function and is a discontinuous function of $X$. In particular, the energy spectrum is a devil's staircase with tilted uneven steps with slopes between $-1$ and $-2.03$. The logarithmic derivative of energy decay $n(t)$ as a function of time is jumping down the stairs of universal levels between $1.50$ and $1.53$. The quantitative verification of this quantization would require more precise experimental data.

This study explores how the properties of heater materials impact nucleate pool boiling using a comprehensive simulation model. The model integrates well-known heat transfer mechanisms, allowing us to assess the effects of two distinct heater materials. Findings indicate that materials with higher thermal conductivity, such as copper, notably improve refrigeration efficiency in nucle- ate boiling. The study provides insights into the relationship between bubble growth, microlayer recovery beneath a bubble, temperature fluctuations, and heater properties. Comparisons between copper and silicon oxide underscore variations in bubble frequency, attributed to differences in bubble growth time, microlayer recovery time, and material-dependent behavior. The influence of neighboring bubbling sites, especially pronounced in silicon oxide due to its low thermal conductivity and diffusivity, was observed. Temperature variations in such materials became highly visible due to their significant inertia in recovery. Simulation results align well with empirical correlations, confirming the model’s versatility in capturing the intricate phenomena of nucleate pool boiling.

NiO-based nanomaterials have attracted a great deal of interest in view of various applications, that have stimulated the implementation of various synthetic approaches to control their chemico-physical properties as a function of the desired end-use. In this regard, their bottom-up preparation starting from suitable precursors plays an important role, but a molecular level in-sight into their reactivity remains an open challenge. In this study, we focus on the fragmentation of Ni(II) diketonate-diamine adducts, of interest as precursors for Ni(II) oxide systems, by com-bined electrospray ionization mass spectrometry (ESI-MS) with multiple collisional experiments (ESI-MSn) and theoretical calculations. The joint analyses revealed common features in the frag-mentation pattern of the target compounds: i) in the first-fragmentation, all three complexes form analogous base-peak cations by losing a negatively charged diketonate; in these cations, Ni-O and Ni-N interactions are stronger and the Ni positive charge is lower than in the neutral complexes; ii) the tendency of ligand electronic charge to migrate towards Ni further increases in the subsequent fragmentation processes, leading to the formation – in all three cases – of a tetracoordinated Ni environment involving an interesting cation-π intramolecular interaction.

The ability to simulate realistically the electronic structure of superconducting materials is important to understand and predict various properties emerging in both the superconducting topological and spintronics realms. We introduce a tight-binding implementation of the Bogoliubov-de Gennes method, parameterized from density functional theory, which we utilize to explore the bulk and thin films of Nb, known to host a significant superconducting gap. The latter is useful for various applications such as the exploration of trivial and topological in-gap states. Here, we focus on the simulations aspects of superconductivity and study the impact of temperature, Cooper-pair coupling and dimensionality on the size of the superconducting order parameter.

This study addresses the central question that how can a precise measurement of the gluon Parton Distribution Function (PDF) be attained, thereby enhancing our understanding of the intricate quark-gluon composition within nucleons? Through a dual approach involving Quantum Chromodynamics (QCD) and high-energy particle collisions, the research combines computational tools and experimental techniques, focusing on protons and neutrons. Scattering experiments and advanced detectors are utilized to probe nucleon structure. Theoretical frameworks like QCD equations and the Momentum Sum Rule investigate Parton Distribution Functions at specific momentum fractions and energy scales. The primary goal is to achieve an accurate measurement of the gluon PDF, crucial for unraveling strong force complexities and internal nucleon dynamics. The study's theoretical plots and equations illustrate hypothetical behaviors of gluon distribution, quark distribution, and splitting functions, contributing to a deeper understanding of fundamental particles.

The paper deals with an electrothermal model of a thermoelectric converter dedicated to performing simulations of coupled thermal and electrical phenomena taking place in harvesting processes. The proposed model is used to estimate the electrical energy gain from waste heat that would be sufficient to supply electronic circuits, in particular autonomous battery-less nodes of wireless sensor networks (WSN) and Internet of Things (IoT) devices. The developed model is not limited to low power electronic solutions such as WSN or IoT; it can also be scaled up and applied to simulations of considerably higher thermal power conversion. In the paper, a few practical case studies are presented that show the feasibility and suitability of the proposed model for complex simultaneous simulation processes, in both electrical and thermal domains. The first example deals with a combined simulation of the electrothermal model of a thermoelectric generator (TEG) and an electronic harvester circuit based on Analog Devices’ power management integrated circuit LTC3108. The second example relates to the thermalization effect in heat sink-less harvesting applications that could be mitigated by a pulse mode operation.

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as Euler arches and Duffing oscillators. Collective synchrony in bistable dynamics of molecular-sized systems has attracted immense attention as a potential pathway to amplify the output signals of molecular nanodevices. Recently, pyridin-furan oligomers of helical shape that are a few nanometers in size and exhibit bistable dynamics similar to a Duffing oscillator have been identified through molecular dynamics simulations. In this article, we present the case of dynamical synchronization of these bistable systems. We show that two pyridine-furan springs connected by a rigid oligomeric bridge spontaneously synchronize vibrations and stochastic resonance enhances the synchronization effect.

Australia is a unique continent surrounded by the ocean and the majority of catchments flow to the coast. Some of these catchments are gauged and others are ungauged. There are 405 gauged catchments covering 2,549,000 km2 across the coastal regions of 12 drainage divisions in Australia. Whereas there are 771 catchments conceptualised as ungauged covering additional 835,000 km2. The mean annual rainfall and PET and its spatial and temporal distribution vary significantly from one drainage division to another. We developed a continuous daily streamflow time series of all gauged and ungauged catchments from 1993 onwards. We applied the GR4J lumped conceptual model to these catchments. The performance of gauged catchments was analysed through (i) visual inspection of daily hydrographs, flow duration curves and daily scatter plots, and (ii) performance metrics including NSE and PBias. Based on the NSE and PBias, performance ratings of 80% and 96% of the models respectively were found 'good'. There was no relationship found between the catchment area and model performance. The ungauged catchments were divided into four categories based on distance from potential donor catchments where observed data are available for GR4J model calibration, and Köppen climate zone. The total ungauged catchments represent 24.7% of the total drainage division areas. The streamflow from ungauged catchments was estimated using GR4J model based on the parameters of their donor catchments. Overall, runoff ratios from ungauged catchments were found to be higher compared to their donor gauged catchments, likely driven by their higher rainfall and less PET. This tendency was particularly evident in two drainage divisions – the Carpentaria Coast (CC) and Tanami-Timor Sea Coast (TTS) where ungauged areas comprised 51% and 43% respectively. The mean gauged annual streamflow varied significantly across drainage divisions – 230 GL from South Australian Gulf (SAG) to 146,150 GL in TTS. The streamflow from all ungauged catchments was estimated at 232,200 GL per year. Overall, the average streamflow from all drainage divisions, including gauged and ungauged areas, across the coastal regions of Australia was estimated at 419,950 GL per year. This nationwide estimate of streamflow dataset could potentially enhance our understanding of coastal processes and improvements of marine modelling systems and tools.

Redox-flow batteries are rechargeable batteries that store energy in two liquid electrolytes, separated by a membrane. During charging and discharging, the electrolytes flow through the membrane and undergo chemical reactions that generate or consume electrical energy. These batteries are known for their scalability and long cycle life and are versatile energy storage technologies developed to enhance efficiency and lower costs. Deep Eutectic Solvents (DES) are eco-friendly alternatives to traditional electrolytes, and their properties have been studied to improve the performance of redox-flow batteries. We investigated choline chloride/ethylene glycol (ChlCl/Eg) mixtures with LiPF6 salt at four concentrations through experimental and MD simulations. The thermophysical and transport properties of the mixture, including density, diffusion coefficient, viscosity, and ionic conductivity, were calculated across a temperature range of 298.15–398.5 K. Our findings indicate that an increase in salt concentration leads to a decrease in diffusion coefficients and ionic conductivity, while increasing the viscosity of the deep eutectic solvent. This research provides valuable insights into the behavior of DES mixtures and can aid in the design and optimization of DES-based processes for use in redox-flow batteries.

Chest X-ray (CXR) is the first tool globally employed to detect cardiopulmonary pathologies. These acquisitions are highly affected by scattered photons due to the large field-of-view required. Scatter in CXRs introduces background in the images, which reduces their contrast. We developed three deep learning-based models to estimate and correct the scatter contribution to CXRs. We used a Monte Carlo (MC) ray-tracing model to simulate CXRs from human models obtained from CT scans using different configurations (depending on the availability of dual-energy acquisitions). The simulated CXRs contained the separated contribution of direct and scattered X-rays in the detector. These simulated datasets were then used as the reference for the supervised training of several NN. Three NN models (single and dual energy) were trained with the MultiResUNet architecture. The performance of the NN models was evaluated on CXRs obtained with the MC code from chest CTs of patients affected by COVID-19. The results showed that the NN models were able to estimate and correct the scatter contribution to CXRs with an error <5%, being robust to variations in the simulation setup and improving the contrast in soft tissue. The single-energy model was tested with real CXRs, providing robust estimations of the scatter-corrected CXRs.

This paper presents the results of laboratory tests of CFRP (carbon fibre-reinforced polymer) laminates, which allowed the development of numerical material models. The obtained data were used in a further stage to perform numerical simulations of four variants of medical tabletops differing, among other features, in the shape of the cross-section. Maximum deflections and effort in the composite material were analyzed. The final step was to perform a laboratory test for one of the tabletop versions, the results of which confirmed the correctness of the numerical calculations. This work is aimed at both researchers and designers involved in the practical application of fibre-reinforced polymer matrix composites.

The new coronavirus SARS-CoV-2 is the cause of the COVID-19 pandemic, which has created an incomparable global health problem. PLpro is a key protein involved in viral polyprotein processing and immune system evasion, making it a prime target for the development of antiviral drugs to combat COVID-19. The review begins by elucidating the functional and structural properties of SARS-CoV-2 PLpro, underscoring its significance in viral pathogenicity and replication. Employing homology modeling, a tertiary structure model of PLpro is constructed, laying the groundwork for subsequent investigations. To expedite the search for potential therapeutic candidates, the study harnesses computational methodologies. Molecular docking techniques are employed to explore binding sites for antiviral drugs within the catalytic region of PLpro. This computational approach not only aids in drug development but also provides crucial preliminary data before experimental research commences. The stability of drug-PLpro complexes is assessed through comprehensive all-atom molecular dynamics (MD) simulations, affording dynamic insights into drug-PLpro interactions. By evaluating binding energy estimates from MD simulations, stable drug-PLpro complexes with potential antiviral properties are identified. However, it is emphasized that experimental validation is imperative to confirm these computational findings, necessitating in vitro and in vivo tests to assess safety and efficacy. This pivotal stage bridges the computational realm with real-world clinical applications. The review emphasizes the imperative need for enhancements in the existing PLpro-targeting drugs currently on the market. Their actions are insufficient for clinical use and necessitate thorough characterization and improvement. The Supervised Molecular Dynamics (SuMD) simulation technique reveals critical information about drug unbinding pathways, shedding light on opportunities for refinement. In addition to optimizing existing drugs, the investigation of sub-structurally similar molecules emerges as a promising avenue for drug development. In conclusion, the review underscores the pivotal role of targeting SARS-CoV-2 PLpro in the ongoing battle against COVID-19. By integrating molecular dynamics simulations, structural modeling, and computational insights, a robust foundation is established for identifying promising antiviral drug candidates. The continual need for improvement in existing drugs and the exploration of novel compounds remain paramount in the global effort to combat COVID-19. The evolution and management of COVID-19 hinge on the symbiotic relationship between computational insights and experimental validation, illustrating the interdisciplinary synergy crucial to this endeavor.

Numerical simulations of standard situations in the transition region from gas kinetics to fluid dynamics at small Mach numbers indicate a clear dependence of the simulation results on the underlying kinetic model (here: nonlinear and linearized Boltzmann collision operator vs. BGK relaxation model). We develop an improved mathematical framework (trace theory) to explain these differences. In particular we reveal certain deficiencies for the classical BKG system as well as for the standard Navier Stokes approach.

In its prefusion state, the SARS-CoV-2 Spike protein (similarly to other class I viral fusion proteins) is metastable, which is considered to be an important feature for optimizing or regulating their functions. After the binding process of its S1 subunit (S1) with the ACE2, the Spike protein (S) suffers a dramatic conformational change where S1 splits from the S2 subunit, which then penetrates the membrane of the host cell, promoting the fusion of the viral and cell membranes. This results in the infection of the host cell. In a previous work, we showed -using large scale molecular dynamics simulations- that the application of external electric fields (EF) induces drastic changes and damage in the receptor-binding domain (RBD) of the wild type Spike protein, as well of the Alpha, Beta and Gamma variants, leaving a structure which cannot be recognized any more by ACE2. In this work, we first extend the study to the Delta and Omicron variants and confirm the high sensitivity and extreme vulnerability of S to moderate EF (as weak as 104 V m-1), but, more importantly, we also show that, in contrast, the postfusion state of the spike protein does not suffer structural damage even if electric field intensities four orders of magnitude higher are applied. These results provide a solid scientific basis to confirm the prefusion state metastability roots of the SARS-CoV-2 Spike protein susceptibility to be damaged by EF. After the virus docks to the ACE2 receptor, the stable and robust postfusion conformation develops, which exhibits a similar resistance to EF (damage threshold higher than 108 V m-1) like most globular proteins.

Road-embedded inductive power transfer (IPT) systems have the potential to accelerate the electrification of the transportation sector. For these systems to be economically viable however, they need to have a similar durability and lifespan compared to that of asphalt roads. One area that has lacked investigation is thermally induced stresses in a primary IPT pad, which is caused by the increase in temperature of the pad when it is energized and the differing thermal expansion of the materials within. This paper presents an experimental and a finite-element based methodology for investigating the thermal-mechanical behaviour of a ¼-scale double-D pad, which was energized while suspended in air, as well as energized when embedded in pavement. A focus was placed on the measurement and prediction of strains in the magnetic ferrite cores because of their brittleness. Ferrite strains were measured using a combination of resistive strain gauges and non-metallic Fibre Bragg Grating (FBG) sensors. Coupled electromagnetic-thermal-structural simulations were conducted to predict temperature and strains in the system, with temperature-dependent properties obtained through physical testing. At an ambient temperature of 50°C, the temperature in the middle of the copper litz wire coil was predicted to be 100°C in both the suspended and embedded case. There was excellent correlation to experimental results, with a difference of less than 10% for most temperature measurements. When energized, the pad was predicted to experience an upward bow due to its temperature rise, resulting bending strains in the ferrite cores. At an ambient temperature of 50°C, maximum tensile strain in the ferrites of the embedded pad was measured to be 62 microstrain (με), with a root-mean square error that was 18 με across three sensors. The experimental and validated numerical methodology can be applied to full-scale operational IPT pads to analyse and improve their thermal-mechanical performance.

It’s been reported that Mori Folium (MF) and Eucommiae Cortex (EC) exhibit pharmacological effects on the treatment of immunosuppression. However, the mechanism of MF and EC against immunosuppression remains unclear. This study aims to explore the mechanism of action of MF and EC for the treatment of immunosuppression through network pharmacology, molecular docking, molecular dynamics simulations and animal experiments. As a result, 11 critical components, 9 hub targets, and related-signaling pathways of treatment of immunosuppression were obtained based on network pharmacology. The molecular docking suggested that 11 critical components exhibited great binding affinity to 9 hub targets of immunosuppression. The molecular dynamics simulations results showed that (-)-Tabernemontanine-AR, beta-sitosterol-AR and Dehydrodieugenol-HSP90AA1 complexes are stably bound. Additionally, in the animal experiments, the treated group results compared to the control group suggest that MF and EC have a significant effect on the treatment of immunosuppression. Therefore, the MF and EC treatment for immunosuppression may take effects in a multi-component, multi-target, and multi-pathway manner. The results would provide novel insights into the treatment of immunosuppression in humans.

RANS simulations have been broadly used to investigate turbulence in the oceans and atmosphere. Within these environments there are a multitude of tracers undergoing reactions (eg. phytoplankton growth, chemical reactions). The distribution of these reactive tracers is strongly influenced by turbulent mixing. With a 50 member ensemble of two dimensional Rayleigh-Taylor induced turbulent mixing, we show that the dynamics of a reactive tracer growing according to Fisher’s equation are poorly captured by the mean. A fluctuation-dependent sink introduced by Reynolds averaging Fisher’s equation transfers concentration from the mean to the fluctuations. We compare the dynamics of the reactive tracer with those of a passive tracer. The reaction causes the concentration of reactive tracer to increase thereby increasing Fickian diffusion and allowing the reactive tracer to diffuse into turbulent structures that the passive tracer cannot reach. A positive feedback between turbulent mixing and fluctuation growth is identified. We show that eddy viscosity and diffusivity parameterizations fail to capture the bulk trends of the system and identify a need for negative eddy diffusivities. One must therefore be cautious when interpreting RANS results for reactive tracers.

With more and more transportation tunnels have been and will be constructed in loess areas in Northwest China with high earthquake potential, the overall stability of portal section under earthquakes actions and the related aseismic countermeasures attracted the attentions from both the scholars and engineers, especially the tunnels in the upper slope connecting the high bridges crossing rivers or valleys. In order to study the dynamic response characteristics and damage evolution of steep loess slope with a tunnel under the earthquake actions, a large-scale shaking table tests were performed on steep loess slope with a tunnel. Wenchuan-tangyu (WT) wave and El Centro (El) wave records were applied on the model to investigate the displacement response and acceleration response of loess slope with a tunnel under the horizontal (X) and the combined action of horizontal and vertical (X-Z) seismic loads, respectively. In particular, three-dimensional non-contact optical measurement techniques were used to obtain the slope surface displacements. The results showed that the main deformation pattern of the slope was horizontal movement and settlement when the seismic wave input was in the X and X-Z directions, respectively. However, the X direction seismic wave had a greater impact on the deformation of the slope, and the tunnel portal slope was destroyed under the action of a large horizontal seismic acceleration finally. Slope failure ahead of a tunnel could be divided into four stages, i.e. elastic deformation stage, plastic deformation accumulation stage, local failure stage, and overall failure stage. The peak ground displacement of X direction (PGDX) and peak ground displacement of Z direction (PGDZ) of the slope surface increased with the increasing of the input peak ground acceleration (PGA) when the input wave was same waveform and same direction. The existence of the tunnel had a great influence on the PGA and the PGA amplification factor (PGAAF) of the soil mass surrounding it. This was because the seismic waves encounter a tunnel surface with clear differences in the physical properties of the medium during their propagation in the slope, thereby forming a strong reflection and refraction effect, and the amplitude changed significantly. Numerical simulation results were basically consistent with the experimental results.

In the development of a digital twin (DT) for hydropower turbines, dynamic modeling of the system (e.g., penstock, turbine, speed control) is crucial, along with all the necessary data interface, virtualization, and dashboard designs. Since the DT must mimic the actual dynamics of the hydropower turbine accurately, adaptive learning is required to train these dynamic models online so that the models in the DT can effectively follow the representation of the actual hydropower turbine dynamics accurately and reliably. This study presents an adaptive learning method for obtaining the hydropower turbine models for DT development of hydropower systems using recursive least squares algorithm. To simplify the formulation, the hydropower turbine under consideration was assumed to operate near a fixed operating point, where the system dynamics can be well represented by a set of linear differential equations with constant parameters. In this context, the well-known six-coefficient model for the Francis turbine was formulated as the starting point to obtain input and output models for the turbine. Then, an adaptive learning mechanism was developed to learn model parameters using the real-time data from a hydropower turbine testing system. This led to a semi-physical modeling in which the first principles and data-driven modeling are integrated to produce dynamic models for the DT development. Applications to a pilot system at the Norwegian University of Science and Technology (NTNU) were made, and the models learned adaptively using the data collected from the university’s pilot system. Desired modeling and validation results were obtained.

Oleanolic acid (OA) being the ubiquitous compound in the plant kingdom is studied for both the neuroprotective and neurotoxic properties. The mechanism of acetylcholinesterase (AChE) inhibitory potential of OA is investigated using the molecular dynamic simulations (MD) and docking as well as membrane-like and in vitro tests. There are also applied SH-SY5Y human neuroblastoma cells as well as in vivo on the zebrafish tests. The inhibitory potential towards the AChE enzyme is examined using the TLC-bioautography assay (the IC50 value is 9.22 μM). The CH- interactions between the central fragment of the ligand molecule and the aromatic cluster created by the His440, Phe288, Phe290, Phe330, Phe331, Tyr121, Tyr334, Trp84 and Trp279 side chains are observed. The in vitro tests carried out on the SH-SY5Y cells indicates that the viability rate is reduced to 71.5%, 61%, and 43% at the concentrations of 100 µg/mL, 300 µg/mL, and 1000 µg/mL, respectively after 48 hours of incubation whereas cytotoxicity against the tested cell line with the IC50 value is 714.32 ± 32.40 µg/mL. The in vivo tests on the zebrafish prove that there is no difference between the control and experimental groups as regards the mortality rate and morphology (P>0.05).

A major public health emergency has been created by the COVID-19 pandemic, which is brought on by the SARS-CoV-2 virus. Due to its crucial function in viral replication, the primary protease (Mpro) of the virus is a prime target for therapeutic research. In this study, we used molecular modeling and molecular dynamics simulations to examine the potential therapeutic uses of Mpro inhibitors for the treatment of COVID-19. Using induced fit docking and molecular dynamics simulations, we confirmed the top compounds after screening a library of compounds for their ability to bind to Mpro. Simulation interaction diagrams were used to investigate protein-ligand interactions, and MM-GBSA was used to determine binding energies. The Swiss ADME server was used to predict ADME properties. According to our findings, numerous substances are strong COVID-19 medication candidates since they have excellent ADME features and high binding affinities. This work serves as a foundation for additional experimental research and drug development initiatives aimed at Mpro.

Macromolecular assemblies, such as protein complexes, undergo continuous structural dynamics, including global reconfigurations critical for their function. Two fast analytical methods are widely used to study these global dynamics, namely elastic network model normal mode analysis and principal component analysis of ensembles of structures. These approaches have found wide use in various computational studies, driving the development of complex pipelines in several software packages. One common one has been conformational sampling through hybrid simulations incorporating all-atom molecular dynamics and global modes of motion. However, wide functionality is only available for experienced programmers with limited capabilities for other users. We have, therefore, integrated one popular and extensively developed software for such analyses, the ProDy Python application programming interface, into the Scipion workflow engine. This enables a wider range of users to access a complete range of macromolecular dynamics pipelines beyond the core functionalities available in its command-line applications and the normal mode wizard in VMD. The new protocols and pipelines can be further expanded and integrated into larger workflows together with other software packages for cryo-electron microscopy image analysis and molecular simulations. We present the resulting plugin, Scipion-EM-ProDy, in detail, highlighting the rich functionality made available by its development.

COVID-19 pandemic has spurred intense research efforts to identify effective treatments for SARS-CoV-2. In silico studies have emerged as a powerful tool in the drug discovery process, particularly in the search for drug candidates that interact with various SARS-CoV-2 receptors. These studies involve the use of computer simulations and computational algorithms to predict the potential interaction of drug candidates with target receptors. The primary receptors targeted by drug candidates include the RNA polymerase, main protease, spike protein, ACE2 receptor, TMPRSS2, and AP2-associated protein kinase 1. In silico studies have identified several promising drug candidates, including Remdesivir, Favipiravir, Ribavirin, Ivermectin, Lopinavir/Ritonavir, and Camostat mesylate, among others. The use of in silico studies offers several advantages, including the ability to screen a large number of drug candidates in a relatively short amount of time, thereby reducing the time and cost involved in traditional drug discovery methods. Additionally, in silico studies allow for the prediction of the binding affinity of drug candidates to target receptors, providing insight into their potential efficacy. However, it is crucial to consider both the advantages and limitations of these studies and to complement them with experimental validation to ensure the efficacy and safety of identified drug candidates.

This paper is a further development of our “Proposal of a new double-nozzle technique for in-gas-jet laser resonance ionization spectroscopy” published in journal Atoms earlier in this year. Here, we propose to equip the proposed double-nozzle technique with the RF-only funnel and RF-buncher placed in the gas-jet chamber at 70 mm distance downstream the double-nozzle exit. It allows for highly effective extraction into vacuum heavy ion beams, produced in two-steps laser resonance ionization in the argon supersonic jet. We explored the operation of this new full version of the double-nozzle technique through detailed gas dynamic and then Monte Carlo trajectory simulations, which results are presented and discussed. In particularly, we have shown by calculations that more than 80% of all nobelium-254 neutral atoms, extracted by argon flow from the gas stopping cell through the double-nozzle into the supersonic jet can be extracted into vacuum in a form of pulsed ion beam having low transverse and longitudinal emittance.s dynamic and Monte Carlo simulations

The goal of this paper is the performance evaluation of a deep learning approach when deployed in fifth-generation (5G) millimeter wave (mmWave) multicellular networks. To this end, the optimum beamforming configuration is defined by two neural networks (NNs) that are properly trained, according to mean square error (MSE) minimization. The first network has as input the requested spectral efficiency (SE) per active sector, while the second network the corresponding energy efficiency (EE). Hence, channel and power variations can now be taken into consideration during adaptive beamforming. The performance of the proposed approach is evaluated with the help of a developed system level simulator via extensive Monte Carlo simulations. According to the presented results, machine learning (ML)-adaptive beamforming can significantly improve EE compared to the standard non-ML framework. Although this improvement comes at the cost of increased blocking probability (BP) and radiating elements (REs) for high data rate services, the corresponding increase ratios are significantly reduced compared to the EE improvement ratio. In particular, considering 21.6 Mbps per active user and ML adaptive beamforming, then EE can reach up to 5.3 Mbps/W, which is significantly improved compared to the non-ML case (0.9 Mbps/W). In this context, BP does not exceed 2.6%, which is slightly worse compared to 1.7% in the standard non-ML case. Moreover, approximately 20% additional REs are required, with respect to the non-ML framework.

In recent years, Machine Learning (ML) has become a buzzword in the petroleum industry with numerous applications which guide engineers in better decision-making. The most powerful tool that most production development decisions rely on is reservoir simulation with applications in numerous modeling procedures, such as individual simulation runs, history matching and production forecast and optimization. However, all these applications lead to considerable computational time and computer resources associated costs, rendering reservoir simulators as not fast and robust enough, thus introducing the need for more time-efficient and smart tools, like ML models which are able to adapt and provide fast and competent results that mimic the simulator’s performance within an acceptable error margin. The first part of the present study (Part I) offers a detailed review of ML techniques in the petroleum industry, specifically in subsurface reservoir simulation, for the cases of individual simulation runs and history matching, whereas the ML-based Production Forecast Optimization applications will be presented in Part II. This review can assist engineers as a complete source for applied ML techniques since, with the generation of large-scale data in everyday activities, ML is becoming a necessity for future and more efficient applications.

The microstructure of oil pipeline steels is polycrystalline due to the presence of a complex grain boundary (GB) network in them. The performance of them when exposed to stresses in corrosive environments is largely dictated by the interplay between the hydrogen (H) diffusion, the dislocation slip, and their interactions with the GBs. However, the slip-GB interaction in the presence of H and the subsequent cracking along the GBs remains not fully understood up to date. It is challenging to simultaneously resolve the collective dislocation motions away from the GBs together with the H diffusion near the atomically structured GBs using single-scale techniques. To address this challenge, taking bcc iron as a model material, here we present a a concurrent atomistic-continuum (CAC) computational analysis of the interaction between dislocation slip and a H-charged GB. With the large number of dislocations-mediated plastic flow away from the GB together with the atomistic structure evolution at the GB being simultaneously retained, several main findings from our simulations are: (i) the large number of dislocation-mediated pileup-induced internal stress nearby the H-charged GB can be as high as 3GPa; (ii) the more dislocations accumulated nearby the GB, the slower H diffusion ahead of the slip-GB intersection; (iii) H atoms diffuse fast behind the pileup tip, get trapped within the GB, and diffuse slow ahead of the pileup tip; (iv) the local stresses nearby the pileup tip exhibits a strong heterogeneity along the dislocation line direction. This differs from the common wisdom in many existing 2D theories/models. The buildup of such a high local stress heterogeneity leads to inhomogeneous H diffusion within the GB plane. The CAC simulation-predicted local H diffusivity, Dpileup−tip, and local stresses, σ, nearby the GB are then correlated with each other and consolidated into a mechanics model by considering the dislocation pileup as an Eshelby inclusion. These findings will provide researchers with opportunities to: (a) characterize the coupled dynamics between plasticity, H diffusion, and crack initiation underlying the hydrogen-induced cracking (HIC); (b) develop mechanism-based constitutive rules to be used in diffusion-plasticity coupling models for understanding the interplay between mechanical and mass transport in materials at the continuum level; and (c) connect the atomistic deformation physics of polycrystalline materials with their overall performance in aqueous environments, which is currently difficult to achieve in laboratory experiments.

Hoechst 33342 (H33342) is a fluorescent probe that is commonly used to stain DNA of living cells. To do so, it needs to interact with and permeate through cell membranes. The pH of biological media may vary quite significantly and this influences H33342 ionization state, and may change its rate of permeation through biomembranes. In this work, we address the effect of pH in the association of H33342 with lipid bilayers using a combined experimental and computational approach. The partition of H33342 to 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) lipid membranes was experimentally quantified using fluorescence spectroscopy and isothermal titration calorimetry (ITC) measurements. Quantum chemical calculations were performed to select the most stable isomer of H33342 for the overall charges 0, +1, and +2, expected to predominate across the 5 < pH < 10 range. The interaction of these isomers with POPC bilayers was then studied by both unrestrained and umbrella sampling molecular dynamics simulations. While probe insertion occurs for all ionization states, with similar overall equilibrium location, orientation was found to depend on the probe charge, with the neutral form lying mostly parallel and the doubly charged displaying a significant tilt relative to the membrane plane. Both experimental results and computational free energy profiles indicate that the partition coefficient of H33342 displays a small variation over a wide pH range, not exceeding one order of magnitude. The enthalpy of interaction is negative and is larger at lower pH values. This suggests efficient hydrogen bonding between the probe and the lipid, namely for the protonated +2 form. The relatively high lipophilicity obtained for the charged species contrasts with the decrease in their general hydrophobicity as estimated from water and octanol partition. This highlights the distinction between lipophilicity and hydrophobicity, and the importance of considering association with lipid bilayers when predicting the affinity for biomembranes.

The hot rolling in the process chain of the aluminium rolled products present the critical element of material quality and influence on productivity. The desire to increase the letter demand modifications of hot rolling, consequential changes of microstructure, crystallographic texture, mechanical and formability properties must be knowledge and consistently considered in planning the rolling process and rolled product. Achieving lower thicknesses of the hot-rolled band would enable fewer passes with cold rolling; consequently, hot rolling with the same number of passes will complete with lower temperatures. Microstructural and texture characterization with the optical microscope and scanning electron microscope for the hot-rolled band 3.25 mm the smaller grains appeared in the center of the cross-section, unlike for the hot-rolled band 6 mm, the smaller grains were detected on the upper and bottom position of the cross-section. Furthermore, the comparison shows also that the hot-rolled band 6 mm has 64 % of random texture components and 83 % of recrystallized grains, and the proportional adjustment for the hot-rolled band 3.25 mm has the 42 % of random texture components and 55 % of recrystallized grains. For the mechanical testing results, the elongation values in rolling and transverse directions significantly differ just in the case of a hot rolled band of 3.25 mm. Consequently, the earing results are more than 1.5 % higher for the hot-rolled band, 3.25 mm, than the hot-rolled band, 6 mm.

Pentagalloyl glucose (PGG) is currently being investigated as a non-surgical treatment for abdominal aortic aneurysms (AAA); however molecular mechanisms of action of PGG on the AAA matrix components and the intra-luminal thrombus (ILT) still need to be better understood. To assess these interactions, we utilized peptide fingerprinting and molecular docking simulations to predict the binding of PGG to vascular proteins in normal and aneurysmal aorta, including matrix metalloproteinases (MMPs), cytokines and fibrin. We performed PGG diffusion studies in pure fibrin gels and human ILT samples. PGG was predicted to bind with high affinity to most vascular proteins, the active sites of MMPs, and several cytokines known to be present in AAA. Finally, despite potential binding to fibrin, PGG was shown to diffuse readily through thrombus at physiologic pressures. In conclusion, PGG can bind to all the normal and aneurysmal aorta protein components with high affinity, potentially protecting the tissue from degradation and exerting anti-inflammatory activities. Diffusion studies showed that thrombus presence in AAA is not a barrier to endovascular treatment. Together, these results provide a deeper understanding of the clinical potential of PGG as a non-surgical treatment of AAA.

ORF6 is responsible for suppressing the immune response of cells infected by the SARS-CoV-2 virus. It is also the most toxic protein of SARS-CoV-2, and its actions are associated with the viral pathogenicity. Here we study in silico and in vitro the structure of the protein, its interaction with RAE1, and the mechanism of action behind its high toxicity. We show both computationally and experimentally that SARS-CoV-2 ORF6, embedded in the membranes of the endoplasmic reticulum, binds to RAE1 and sequesters it in the cytoplasm, thus depleting its availability in the nucleus and impairing nucleocytoplasmic mRNA transport. This negatively affects the cellular genome stability by compromising the cell cycle progression into the S-phase and by promoting the accumulation of RNA-DNA hybrids. Understanding the multiple ways in which ORF6 affects DNA replication may also have important implications for elucidating the pathogenesis of SARS-CoV-2 and developing therapeutic strategies to mitigate its deleterious effects on host cells.

Vernacular architecture constitutes a rich source of information and ancestral knowledge that can become a key resource for sustainable development through its passive design strategies, which effectively respond to local climatic and weather conditions using locally sourced materials for the construction of its supporting structure and enveloping elements, as well as spatial organization and the incorporation of a buffer area (patio) that optimize the use of renewable resources. This qualitative study analyzes a traditional housing typology with a central patio located in the Historic Center of Azogues city, Ecuador, to evaluate its interior thermal comfort through in-situ monitoring in the different building spaces. Using the open-source software Open Studio and EnergyPlus, a simulation model was built to assess the annual thermal performance of the house. Field records were used to verify the effectiveness of the strategies that respond to the climatic conditions of the area. The analysis carried out on the passive strategies used in the selected house with regard to natural ventilation, solar protection, and thermal insulation, which depend on various aspects of the building, such as its location, internal space arrangement, design of openings (doors and windows), among others. The thermal simulations reveal that the traditional house located in the Historic Center of Azogues city is well adapted to the local climate, although interior thermal comfort is not entirely satisfactory.

The β-amyloid cleaving enzyme 1 (BACE1) is regarded as an important target of drug design toward treatment of Alzheimer's disease (AD). In this study, three separate molecular dynamics (MD) simulations and calculations of binding free energies were carried out to comparatively probe identification mechanism of BACE1 on three inhibitors 60W, 954 and 60X. The analyses on MD trajectories indicate that the presence of three inhibitors influences structural stability, flexibility and internal dynamics of BACE1. Binding free energies calculated by using solvated interaction energy (SIE) and molecular mechanics generalized Born surface area (MM-GBSA) methods reveal that the hydrophobic interactions provide decisive forces for inhibitor-BACE1 binding. The calculations of residue-based free energy decomposition suggest that the sidechains of residues L91, D93, S96, V130, Q134, W137, F169 and I179 play key roles in inhibitor-BACE1 binding, which provides a direction for future drug design toward treatment of AD.

The main objective of this study is to find out the influence of cooperation and intra-specific competition in escaping predation through refuge of the prey population and the effect of the two intra-specific interactions on the dynamics of prey-predator systems. For this purposes, two mathematical models with Holling type-II functional response function have been proposed and analyzed. The first model includes cooperation among prey populations whereas the second one incorporates intra-specific competition. Existence conditions and stability of different equilibrium points of both models have been carried out for the qualitative behaviour of the systems. Refuge through intra-specific competition has a stabilizing role, whereas cooperation has a destabilizing role on the system dynamics. Periodic oscillations are observed in both the systems through Hopf bifurcation. From the analytical and numerical findings, we conclude that intra-specific competition affects the prey population and continuously checks the refuge class under a critical value, and thus it never becomes too large to cause predator extinction due to food scarcity. Conversely, cooperation leads maximum individuals to escape predation through the refuge so that predators will suffer from low predation success.

This research paper explores the transformative potential of immersive media, specifically virtual reality (VR), in enhancing empathy among users. Empathy is vital in fostering understanding, compassion, and social cohesion. Immersive media, with its ability to transport individuals into simulated environments and perspectives, offers unique opportunities to bridge the empathy gap. This paper examines how VR can boost empathy, including perspective-taking, emotional connection, experiential learning, breaking down barriers, and empathy-building simulations. It discusses existing studies and empirical evidence supporting the effectiveness of VR in promoting empathy. The paper acknowledges the ethical considerations and challenges associated with using VR for empathy enhancement, such as avoiding stereotype reinforcement and ensuring inclusive design. By highlighting the potential of immersive media in cultivating empathy, this research paper contributes to the growing field of empathy research and provides insights for the development and application of VR experiences aimed at fostering empathy and understanding in diverse contexts.

Infectious diseases continue to be a significant threat to human health and civilization, and finding effective methods to combat them is crucial. In this research, we investigate the impact of awareness campaigns and optimal control techniques on infectious diseases without proper vaccines. Specifically, we develop an SIRS type mathematical model that incorporates awareness campaigns through media and treatment for disease transmission dynamics and control. The model displays two equilibria, a disease-free equilibrium and an endemic equilibrium, and exhibits Hopf bifurcation when the bifurcation parameter exceeds its critical value, causing a switch in the stability of the system. We also propose an optimal control problem that minimizes the cost of control measures while achieving a desired level of disease control. By applying the minimum principle to the optimal control problem, we obtain analytical and numerical results that show how the infection rate of the disease affects the stability of the system and how awareness campaigns and treatment can maintain system stability. This study highlights the importance of awareness campaigns in controlling infectious diseases and demonstrates the effectiveness of optimal control theory in achieving disease control with minimal cost.

The successful handling of large semiconductor wafers is crucial for scaling up their production. Early-stage warpage control allows to prevent undesirable asymmetric warpage, known as wafer bifurcation or buckling. Indeed, even in a gravity-free environment, thinning an 8" or 12" semiconductor wafer can result in warpage and bifurcation. To mitigate this issue, the taiko method, which involves creating a thicker ring region around the rim of the wafer, has been widely used. Previous research has focused on the theoretical factors affecting the warpage of a backside metalized taiko wafer. This work extends the case to a front-side metalized taiko wafer and introduces the concept of the equivalent thickness of a taiko wafer. The equivalent thickness of a taiko wafer, influenced by the ring region, lies in between the thickness of the central region and that of the annular region. Because of the limited number of taiko wafers that can be produced on a production line, modelling can be beneficial. In this work we compared the results of a developed analytical model with those obtained from a finite element analysis (FEA) approach with ANSYSY® software to model the equivalent thickness of a taiko wafer. We investigated the curvature as a function of the stress of the metal layer, considering key design factors such as the substrate region thickness, the thickness of the thin metal film, the step height, and the width of the ring region. By systematically varying the thickness of the central region of the taiko wafer, we explored the curvature as a function of stress induced by thermal load in the linear regime and determined the slopes in the linear region of the curvature vs. stress curves. The aim of this study is to identify regularities and similarities with the Stoney equation and investigate the validity of the analytical approach for the case of a taiko substrate. It results that there is a good agreement between the analytical model of a taiko wafer and the numerical analysis gained by the FEA methods.

An extensive review of literature simulations of polymer melts is given, considering results that test aspects of the Rouse model in the melt. We focus on the mean-square amplitudes < (X_p(0))^{2} > and time correlation functions < X_p(0) X_p(t) > of the Rouse modes $X_p(t)$. Contrary to the Rouse model: (i) Mean-square Rouse mode amplitudes < (X_p(0))^2> do not scale as sin^{-2}(p \pi/2N), N being the number of beads in the polymer. For small p (say, p <= 3) < (X_p(0))^2> scales with p as p^{-2}$; for larger p it scales as p^{-3}. (ii) Rouse mode time correlation functions < X_p(t) X_p(0) > do not decay with time as exponentials; they instead decay as stretched exponentials exp(-a t^b)$. b depends on p, typically with a minimum near N/2 or N/4. (iii) Polymer bead displacements are not described by independent Gaussian random processes. (iv) For p not equal to q, < X_p(t) X_{q}(0) > is sometimes non-zero. (v) The response of a polymer coil to a shear flow is a rotation, not the affine deformation predicted by Rouse. Simulations thus conclusively demonstrate that the Rouse model is invalid in polymer melts. We also briefly consider the Kirkwood-Riseman polymer model.

This paper attempts to develop a Dynamic Mode Decomposition (DMD) based Reduced Order Model (ROMs) which can quickly but accurately predict the forces and moments experienced by a road vehicle such that they be used by an on-board controller to determine the vehicle's trajectory. DMD can linearize a large dataset of high-dimensional measurements by decomposing them into low-dimensional coherent structures and associated time-dynamics. This ROM then also can be applied to predict the future state of the fluid flow. Existing literature on DMD is limited to low Reynolds number applications. This paper presents DMD analyses of the flow around an idealized road vehicle, called the Ahmed body, at a Reynolds number of 2.7E6. The high dimensional dataset used in this paper was collected from a computational fluid dynamics (CFD) simulation performed using Menter's shear stress transport (SST) turbulence model within the context of Improved Delayed Detached Eddy Simulations (IDDES). The DMD algorithm, as available in literature, was found to suffer nonphysical dampening of the medium-to-high frequency modes. Enhancements to the existing algorithm were explored, and a modified DMD approach is presented in this paper which includes: (a) a requirement of higher sampling rate to obtain higher resolution of data, and (b) a custom filtration process to remove spurious modes. The modified DMD algorithm thus developed was applied to the high Reynolds number, separation dominated flow past the idealized ground vehicle. The effectiveness of the modified algorithm was tested by comparing future predictions of force and moment coefficients as predicted by the DMD-based ROM to the reference CFD simulation data, and found to offer significant improvement.

This work exclusively focuses on the assessment of the thermal performance of a multifunctional facade panel incorporating PCM in foam layers, recurring to a hot box heat flux meter method to determine the thermal transmittance (U-value). The experimental setup is based on the steady-state approach using climatic chambers, assuring a stable thermal environment. Even small fractions of PCM achieved a small reduction in thermal amplitude. Numerical simulations using Ansys Fluent were developed to evaluate the performance of PCM use over a wide range of temperature boundary conditions and operating modes. These numerical models were calibrated and validated using the results of experimental tests, achieving a correlation factor of 0.9674, thus accurately representing a real-world scenario. The decrement factor (f) was used to analyse the data. It was identified that the efficiency of the panel and size of the optimum region increased with the PCM fraction growth. The simulated behaviour was optimum when the input mean temperature is of 20 °C for a room temperature of between 18-20 °C. The results show the significant potential of the multi-layered panel and the thermal regulator effect of the PCM incorporated on indoor space temperature to reach good thermal comfort levels.

Multisource meteorological re-analyses are the most reliable forcing data for driving hydrological models to simulate streamflow. We aimed to assess the different hydrological responses through hydrological modeling in the upper Lancang-Mekong River Basin (LMRB) using the two gridded meteorological datasets, climate forecast system reanalysis (CFSR) and the China Meteorological Assimilation Driving Datasets for the SWAT model (CMADS). We selected the Pearson’s correlation coefficient (R), percent bias (PBIAS), and root mean square error (RMSE) indices to compare the six meteorological variables of the two datasets. The spatial distributions of the statistical indicators in the CFSR and CMADS, namely, the R, PBIAS, and RMSE values, were different. Furthermore, the soil and water assessment tool plus (SWAT+) model was used to do hydrological modeling based on CFSR and CMADS meteorological re-analyses in the upper LMRB. Different meteorological datasets resulted in significant differences of hydrological responses, which reflected by different sensitive parameters and their optimal value. These different calibrated optimal values of sensitive parameters further lead to the different simulated water balance components between CFSR- and CMADS-based SWAT+ model. These findings can help in a better understanding of the strengths and weaknesses of different meteorological re-analysis datasets and the roles on the hydrological modeling.

This study proposes a machine-learning-based framework for detecting mechanical damage in pipelines, utilizing physics-informed datasets collected from simulations for mechanical damage. The framework provides an effective workflow from dataset generation to damage detection and identification for three types of pipeline events: welds, clamps, and corrosion defects. While the study initially focused on optimizing the CNN structure using various advanced optimizers, it also investigated the impact of sensing systems on data classification and the effect of noise on classification performance. The study's analysis highlights the importance of selecting the appropriate sensing system for the specific application. The authors also found that the proposed framework is robust to experimentally relevant levels of noise, suggesting its applicability in real-world scenarios where noise is present. Overall, this study contributes to the development of a more reliable and effective method for detecting mechanical damage in pipelines. The proposed framework provides an effective workflow for damage detection and identification, and the findings on the impact of sensing systems and noise on classification performance add to its robustness and reliability.

1D spin crossover (SCO) solids which convert between the low-spin (LS) and the high-spin (HS) states are widely studied in the literature due to their diverse thermal and optical characters which allows obtaining many original behaviors, such as large thermal hysteresis, incomplete spin tran-sitions, as multi-step spin transitions with self-organized states. In the present work, we investigate the thermal behaviors of a system of two-elastically coupled 1D mononuclear chains, using the electro-elastic model, by including an elastic frustration in the nearest neighbors (nn) bond length distances of each chain. The chains are made of SCO sites that are coupled elastically through springs with their nn and next-nearest neighbors. The elastic inter-chain coupling includes diagonal springs, while the nn inter-chains distance is fixed to that of the high-spin state. The model is solved using MC simulations, performed on the spin states and the lattice distortions. When we only frustrate the first chain, we found a strong effect on the thermal-dependence of the HS fraction of the second chain, whose, by lowering its transition temperature which is also accompanied with the appearance of a significant residual HS fraction at low temperature. In the second step, we frustrate both chains by imposing different frustration rates and found that, for high frustration values, the thermal dependence of the total HS fraction exhibits three step and even four step spin transitions. The careful examination of the spin state structures in the plateau regions revealed the existence of special antiferro-elastic structure of type LSLS-HSHS-LSLS-HSHS along the first chain, and HSHS-LSLS-HSHS-LSLS along the second, also showing that the two chains seem to be antifer-ro-elastically coupled. This type of organization is interesting, because it anticipates the possible existence of periodic structures made of alternate 1D antiferro-like HS-LS strings coupled in the ferro-like fashion along the interchain direction in the 2D case.

In this paper a new double-nozzle technique for in-gas-jet laser resonance ionization spectroscopy is proposed. The functionality of this new technique we explored by detailed gas dynamic and Monte Carlo atom-trajectory simulations, which results are presented and discussed. The results of similar computer simulations for JetRIS setup (as a typical representative of the conventional nowadays in-gas-jet technique) are presented and discussed as well. The direct comparison of calculation results for proposed new technique with the conventional one shows that the double-nozzle technique has many advantages compared with that one used in the JetRIS setup at GSI for future high-resolution laser spectroscopic study of heaviest elements. To fully implement the proposed new technique to all existing (or under construction) setups for in-gas-jet laser resonance ionization spectroscopy, it will be enough just replace the used their supersonic nozzle by the miniature double-nozzle device described in the paper.

The dynamic and surface manipulation of the M13 bacteriophage meeting application demands enable a pathway to design efficient applications with high selectivity and responsivity rate. Herein, we report the role of the M13 bacteriophage thin film layer deposited on an optical nanostructure involving gold nanoparticles/SiO2/Si and its influence on optical and geometrical properties. The thickness of the M13 phage layer was either controlled by varying the concentration or humidity exposure levels, and optical studies were conducted. We designed a standard and dynamic model based upon three-dimensional finite-difference time-domain (3D FDTD) simulations distinguishing the necessity of each model under variable conditions. As seen from the experiments, the origin of respective peak wavelength positions is addressed in detail with the help of simulations. The importance of the dynamic model was noted when humidity-based experiments were conducted. Inexpensive, multi-wavelength optical characteristics from a single structure, reproducibility, and reversible properties are significant advantages of involving M13 bacteriophage. We believe this work will provide fundamental insight into understanding and interpreting the geometrical and optical properties of the nanostructures involving M13 bacteriophage.

This study investigates the possible mechanisms related to the wide range of relative humidity in cirrus clouds (RHi). Under the closed adiabatic assumption, the impacts of vertical motion and ice crystal deposition/sublimation on RHi are investigated through in situ observations and parcel model simulations. Vertical motion is an active external force that changes the RHi, and ice crystal deposition/sublimation plays a role in mitigating the change in RHi. They are the two most important mechanisms involved in controlling the RHi fluctuation during cirrus evolution and could well explain the wide range of RHi in wave-related cirrus clouds. Furthermore, a comparison of cloud statistical characteristics from both observations and simulations shows that a very low value (e.g., 0.001) for the water vapor ice deposition coefficient is highly unlikely.

This paper shows that by applying the Nyquist-Shannon sampling theorem, the spatial and temporal resolution of a simulation can be no more than half the resolution of the simulating reality. This has significant implications for not only the values of the observables in the simulation but also its physical laws. This progressive halving of nested simulations coupled with the minimum resolution compatible with the production of a simulation also sets a limit to the nestedness of a lineage of simulations (it is by no means infinite). The limit of nestedness is then used to calculate the probability that we are living in a simulation assuming a single base reality. This will be shown to be significantly lower than popular expectation. A Kardashev-like scale, with three variants, is also developed to gauge the technological advancement of a civilization in relation to the extent to which it can extract information from space and time.

Human behaviour was tipped as the mainstay in the control of further SARS-CoV-2 (COVID-19) spread especially after the lifting of restrictions by many countries. Countries in which restrictions were lifted soon after the first wave, had subsequent waves of the COVID-19 infections and it remains to be seen whether there will be more waves. In this paper, we formulate a deterministic model for COVID-19 incorporating dynamic non-pharmaceutical interventions, dubbed social dynamics. The model steady states are determined and their stability analysed. Numerical simulations are carried out to determine the pack of various parameters that influence the social dynamics. In South Africa, the first wave was the only wave in which the only interventions rested solely on human behavior. The model is thus fitted to COVID-19 data on the first wave in South Africa. The results presented in this paper have implications on the trajectory of the pandemic in the presence of changing social processes.

The natural product Salvinorin A (SalA) was the first nitrogen-lacking agonist discovered for the opioid receptors and exhibits high selectivity for the kappa opioid receptor (KOR) turning SalA into a promising analgesic to overcome the current opioid crisis. Since SalA’s suffers from poor pharmacokinetic properties, particularly the absence of gastrointestinal bioavailability, fast metabolic inactivation and subsequent short duration of action, the rational design of new tailored analogs with improved clinical usability is highly desired. Despite being known for decades, the binding mode of SalA within the KOR remains elusive as several conflicting binding modes of SalA were proposed hindering the rational design of new analgesics. In this study, we rationally determined the binding mode of SalA to the active state KOR by in silico experiments (docking, molecular dynamics simulations, dynophores) in the context of all available mutagenesis studies and structure-activity relationship (SAR) data. To the best of our knowledge this is the first comprehensive evaluation of SalA’s binding mode since the determination of the active state KOR crystal structure. SalA binds above the morphinan binding site with its furan pointing towards the intracellular core while the C2-acetoxy group is oriented towards the extracellular loop 2 (ECL2). SalA is solely stabilized within the binding pocket by hydrogen bonds (C210ECL2, Y3127.35, Y3137.36) and hydrophobic contacts (V1182.63, I1393.33, I2946.55, I3167.39). With the disruption of this interaction pattern or the establishment of additional interactions within the binding site we were able to rationalize the experimental data for selected analogs. We surmise the C2-substituent interactions as important for SalA and its analogs to be experimentally active, albeit moderate frequency within MD simulations of SalA. We further identified the non-conserved residues 2.63, 7.35, and 7.36 responsible for the KOR subtype selectivity of SalA. We are confident that the elucidation of the SalA binding mode will promote the understanding of KOR activation and the facilitate the development of novel analgesics that are urgently needed.

A series of cysteine-based perfluoroaromatic (hexafluorobenzene (I) and decafluorobiphenyl (II) were synthesized and established as a chemoselective and available core to simple or more complex systems since small molecules to biomolecules with interesting properties. As proof of concept of the potential application of perfluorinated derivatives as non-cleavable linkers, some antibody-perfluorinated conjugates were prepared via thiol, demonstrating that the bioconjugation process doesn’t affect to the macromolecular entity. Besides, some molecular properties of synthesized compounds are evaluated using a combination of spectroscopic characterization (FT-IR and 19F-NMR chemical shifts) and theoretical calculations. Moreover, molecular Docking was also developed to predict cysteine-based hexafluorobenzene and decafluorobiphenyl derivatives’ affinity against topoisomerase Il and cyclooxygenase 2 (COX-2). The results suggested that mainly cysteine-based decafluorobiphenyl derivatives could be potential topoisomerase II α and COX-2 inhibitors, becoming potential anticancer agents and candidates for anti-inflammatory treatment.

Since its introduction, back in the late 1970s, the non-affine or slip parameter, ξ, has been routinely employed by numerous constitutive models as a constant parameter. However, the evidence seems to imply that it should be a function of polymer deformation. In the present work, we phenomenologically modify a constitutive model for the rheology of unentangled polymer melts [P. S. Stephanou et al. J. Rheol. 53, 309 (2009)] to account for a non-constant slip parameter. The revised model predictions are compared against newly accumulated rheological data for a C48 polyethylene melt obtained via direct non-equilibrium molecular dynamics simulations in shear. We find that the conformation tensor data are very well predicted; however, the predictions of the material functions are noted to deviate from the NEMD data, especially at large shear rates.

Mesoscale imperfections, such as pores and voids, can strongly modify the properties and the mechanical response of materials under extreme conditions. Tracking the material response and microstructure evolution during void collapse is crucial for understanding its performance. In particular, imperfections in ablator materials, such as voids, can limit the efficiency of the fusion reaction and ultimately hinder ignition. To characterize how voids influence the response of materials during dynamic loading and seed hydrodynamic instabilities, we have developed a tailored fabrication procedure for designer targets with voids at specific locations. Our procedure uses SU-8 as a proxy for ablators materials and hollow silica microspheres as proxy for voids and pores. By using photolithography to design the targets’ geometry, we demonstrate precise and highly reproducible placement of a single void within the sample, which is key for a detailed understanding of its behavior under shock compression. This fabrication technique will benefit high-repetition rate experiments at x-ray and laser facilities. Insight from shock compression experiments will provide benchmarks for the next generation of microphysics modelling.

Eukaryotic cells contain membranes with various curvatures, from the near-plane plasma membrane to the highly curved membranes of organelles, vesicles, and membrane protrusions. These curvatures are generated and sustained by curvature-inducing proteins, peptides, and lipids, and describing these mechanisms is an important scientific challenge. In addition to that, some molecules can sense membrane curvature and a thereby be trafficked to specific locations. The description of curvature-sensing is another fundamental challenge. Curved lipid membranes and their interplay with membrane-associated proteins can be investigated with molecular dynamics (MD) simulations, given the right tools. Various methods for simulating curved membranes with MD are discussed here, including tools for setting up simulation of vesicles, and methods for sustaining membrane curvature. The latter are divided into methods that exploit scaffolding virtual beads, methods that use curvature-inducing molecules, and methods applying virtual forces. The variety of simulation tools allow the researcher to closely match the conditions of experimental studies of membrane curvatures.

The extremely controversial conclusions about the function of human interferon-gamma (hIFNγ) C-terminus as well as the lack of a consistent model explaining its role in the receptor binding prompted us to scrutinize the interaction of hIFNγ with its extracellular receptor hIFNGR1 in different scenarios by means of molecular dynamics simulations. We find that the two molecules alone fail to form a stable complex but the presence of heparan-sulfate-like oligosaccharides largely facilitates the process by both demobilizing the highly flexible C-termini of the cytokine and assisting in the proper positioning of its globule between the receptor subunits. An antiproliferative-activity essay on cells depleted from surface sulfation confirms qualitatively the simulation-based multistage complex-formation model. Our results reveal the key role of HS and its proteoglycans in all processes involving hIFNγ signalling.

This paper describes a novel concept of producing energy efficient ”Maroon enriched natural gas “ and then Pink hydrogen” from any hydrocarbon base. The key idea is the extraction of hydrogen from water in addition to that from the hydrocarbon in an optimal fashion. This has the benefit of higher water vapor to CO2 exhaust ratio than conventional carbonaceous fuels when generating energy via combustion, a prudent step in achieving Netzero goals in a shorter time, and creating energy independence in most places.. The process of production makes concentrated CO₂ available for use and or sequestration. The process also maximizes use of renewable electricity in hydrogen generation, and maximizes use of existing infrastructure, with a minimum capital cost by energy recycle in the process. The process design applies sound thermodynamic principles which evolved during the nineteenth century, and mimics the geochemical processes going on in some of the natural 'colorless hydrogen'.

Naltrexone (NTX) is a potent opioid antagonist with good blood-brain barrier permeability, targeting different endogenous opioid receptors, particularly the mu-opioid receptor (MOR). Therefore, it represents a promising candidate for drug development against drug addiction. However, the details of the molecular interactions of NTX and its derivatives with MOR are not fully understood, hindering ligand-based drug discovery. In the present study, taking advantage of the high-resolution X-ray crystal structure of the murine MOR (mMOR), we constructed a homology model of the human MOR (hMOR). A solvated phospholipid bilayer was built around the hMOR and submitted to microsecond (µs) molecular dynamics (MD) simulations to obtain an optimized hMOR model. NTX and its derivatives were docked into the optimized hMOR model and submitted to µs MD simulations in an aqueous membrane system. The MD simulation results were submitted to Molecular Mechanics Generalized-Born surface area (MMGBSA) binding free energy calculations and principal component analysis. Our results revealed that NTX and its derivatives showed differences in protein-ligand interactions; however, they shared contact with residues at TM2, TM3, H6, and TM7. The binding free energy and principal component analysis revealed the structural and energetic effects responsible for the higher potency of NTX compared to its derivatives.

The rational fabrication of low-dimensional materials with a well-defined topology and functions is an incredibly important aspect of nanotechnology. In particular, the on-surface synthesis (OSS) methods based on the bottom-up approach enable facile construction of sophisticated molecular architectures unattainable by traditional methods of wet chemistry. Among such supramolecular constructs especially interesting are surface-supported metal-organic networks (SMONs), composed of low-coordinated metal atoms and π-aromatic bridging linkers differing in size, shape and functionalization scheme. In this work, the lattice Monte Carlo (MC) simulation technique was used to extract the chemical information encoded in a family of Y-shaped positional isomers coadsorbed with trivalent metal atoms on a flat metallic surface with (111) geometry. For this purpose the investigated tritopic molecules/metal atoms were carefully mapped on a triangular lattice as interconnected/isolated segments with appropriatelly embedded anisotropic interactions. Depending on the intramolecular distribution of active centers (functional groups) within the simulated molecular bricks, we observed the metal-directed self-assembly of two-dimensional (2D) openwork patterns, aperiodic mosaics and metal-organic ladders. The obtained theoretical findings could be especially relevant for the scanning tunneling microscopy (STM) experimentalists interested in a surface-assisted construction of complex nanomaterials stabilized by directional coordination bonds.

The combination of interstitial hyperthermia treatment (IHT) with high dose rate brachytherapy (HDR-BT) for prostate cancer treatment and has the potential to improve clinical outcome, since it highly enhances the efficiency of cell kill, especially when applied simultaneously. Therefore, we have developed the ThermoBrachy applicators. To effectively apply optimal targeted IHT, treatment planning is considered essential. However, treatment planning in IHT is rarely applied since it is regarded difficult to accurately calculate the deposited energy in the tissue in a short enough time for clinical practice. In this study, we investigated various time-efficient methods for fast computation of the electromagnetic (EM) energy deposition resulting from the ThermoBrachy applicators. Initially, we investigated the use of an electro-quasistatic solver. Next, we extended our investigation to the application of geometric simplifications. Furthermore, we investigated the validity of the superpositioning principle, which can enable adaptive treatment plan optimization without the need for continuous recomputation of the EM field. Finally, we evaluated the accuracy of the methods by comparing them to the golden standard Finite-Difference Time-Domain calculation method using gamma-index analysis. The simplifications considerably reduced the computation time needed, improving from &gt;12 h to a few seconds. All investigated methods showed excellent agreement with the golden standard by showing a &gt;99% passing rate with 1%/0.5 mm Dose Difference and Distance-to-Agreement criteria. These results allow the proposed electromagnetic simulation method to be used for fast and accurate adaptive treatment planning.

A connection between the phenomenon of wafer bifurcation and that of spontaneous symmetry breaking (SSB) has been established. Indeed, by developing an analytical approximation of the elastic energy of a wafer coated with a thin layer (e.g. a metal), it is shown as the elastic potential energy, interpreted as a quantity contributing to the thermodynamic free energy, can be investigated within the framework of the Landau theory of the second order phase transitions. The elastic energy of a bifurcated wafer is a complex function of the stress and the curvatures in the two perpendicular directions. In this work, it is shown as a translation of the coordinate system of the curvatures allows to gain a potential which has a “Mexican hat” shape. This is a distinctive trait of the phenomenon of spontaneous symmetry breaking (SSB). Moreover, it is shown as the values of the coordinates at the minimum of the SSB potential agrees with those provided by the theory. Bifurcation is hence a phenomenon that can also be interpreted as a spontaneous symmetry breaking where the rotational symmetry of a disc shaped wafer is broken. It occurs because of a lowering of the wafer energy in the SSB broken symmetry configuration.

3D facial surface imaging is a useful tool in dentistry and in terms of diagnostics and treatment planning. Between-groups PCA (bgPCA) is a method that has been used to analyse shapes in biological morphometrics, although various “pathologies” of bgPCA have recently been proposed. Monte Carlo (MC) simulated datasets were created here in order to explore “pathologies” of multilevel PCA (mPCA), where mPCA with two levels is equivalent to bgPCA. The first set of MC experiments involved 300 uncorrelated normally distributed variables, whereas the second set of MC experiments used correlated multivariate MC data describing 3D facial shape. We confirmed previous results of other researchers that indicated that bgPCA (and so also mPCA) can give a false impression of strong differences in component scores between groups when there is none in reality. These spurious differences in component scores via mPCA reduced strongly as the sample sizes per group were increased. Eigenvalues via mPCA were also found to be strongly effected by imbalances in sample sizes per group, although this problem was removed by using weighted forms of covariance matrices suggested by the maximum likelihood solution of the two-level model. However, this did not solve problems of spurious differences between groups in these simulations, which was driven by very small sample sizes in one group here. As a “rule of thumb” only, all of our experiments indicate that reasonable results are obtained when sample sizes per group in all groups are at least equal to the number of variables. Interestingly, the sum of all eigenvalues over both levels via mPCA scaled approximately linearly with the inverse of the sample size per group in all experiments. Finally, between-group variation was added explicitly to the MC data generation model in two experiments considered here. Results for the sum of all eigenvalues via mPCA predicted the asymptotic amount for the total amount of variance correctly in this case, whereas standard “single-level” PCA underestimated this quantity.

Thermal simulations are an important part in the design of electronic systems, especially as systems with high power density become common. In simulation-based design approaches, a considerable amount of time is spent by repeated simulations. In this work, we present a proof-of-concept study of the application of convolutional neural networks to accelerate those thermal simulations. The goal is not to replace standard simulation tools but to provide a method to quickly select promising samples for more detailed investigations. Based on a training set of randomly generated circuits with corresponding Finite Element solutions, the full 3D steady-state temperature field is estimated using a fully convolutional neural network. A custom network architecture is proposed which captures the long-range correlations present in heat conduction problems. We test the network on a separate dataset and find that the mean relative error is around 2 % and the typical evaluation time is 35 ms per sample ( 2 ms for evaluation, 33 ms for data transfer). The benefit of this neural-network-based approach is that, once training is completed, the network can be applied to any system within the design space spanned by the randomised training dataset (which includes different components, material properties, different positioning of components on a PCB, etc.).

Cardiac myosin-binding protein C (MyBPC) is a thick-filament associated regulatory protein in the sarcomere. It regulates the sensitive contractile system of the myocardium by acting as a mechanical tether, sensitizing the thin filament or modulating myosin motor activity. Mutations in the MYBPC3 gene are a frequent cause for the development of hypertrophic cardiomyopathy, the most frequent cardiac disorder. Recently, the monoallelic double mutation MYBPC3Δ25bp/D389V has been discovered as a subset of the common MYBPC3Δ25bp variant in South Asia. MYBPC3Δ25bp/D389V carriers exhibit hyperdynamic features, which are considered an early finding for the development of hypertrophic cardiomyopathy. Using correlation-guided molecular dynamics simulations sampling, we show that the D389V mutation shifts the conformational distribution of the C2 domain of MyBPC. We further applied biochemical approaches to probe the effects of the D389V mutation on structure, thermostability and protein-protein interactions of MyBPC C2. The melting temperature (Tm) of MyBPC C2 D389V is decreased by 4 to 7 °C compared to wild type while the interaction of the C0-C2 domains with myosin and actin remains unchanged. Additionally, we utilized steered molecular dynamics (SMD) simulations to investigate the altered unfolding pathway of MyBPC C2 D389V. Based on our data, we propose a pathomechanism for the development of HCM in MYBPC3Δ25bp and MYBPC3Δ25bp/D389V carriers.

A quantitative analysis of X-ray emission from an electron cyclotron resonance (ECR) plasma was performed to probe the spatial properties of electrons having energy for effective ionisation. A series of measurements were taken by INFN-LNS and ATOMKI, capturing spatially and spectrally resolved X-ray maps as well as volumetric emissions from argon plasma. Comparing the former with model generated maps (involving space-resolved phenomenological electron energy distribution function and geometrical efficiency calculated using ray-tracing MC routine) furnished information on structural aspects of the plasma. Similarly, fitting a model composed of bremsstrahlung and fluorescence to the volumetric X-ray spectrum provided valuable insight into the density and temperature of confined and lost electrons. The latter can be fed back to existing electron kinetics models for simulating more relevant energies, consequently improving theoretical X-ray maps and establishing the method as an excellent indirect diagnostic tool for warm electrons, required for both fundamental and applied research in ECR plasmas.

Polyphenol ellagic acid (EA) possesses anti-oxidant, anti-inflammatory, anti-carcinogenic, anti-diabetic and cardio protection activities, remarking it an interesting multi-targeting profile. EA also controls the central nervous system (CNS) since it was proven to reduce the immobility time of mice in both the forced swimming and the tail-suspension tests, with an efficiency comparable to that of classic antidepressants. Interestingly, the anti-depressant-like effect was almost nulled by the concomitant administration of selective antagonists of the noradrenergic receptors, suggesting the involvement of these cellular targets in the central effects elicited by EA and its derivatives. By in silico and in vitro studies, we discuss how EA engages with human α2A-ARs and α2C-AR catalytic pockets, comparing EA behaviour with those ones of known agonist and antagonist. Structurally, the hydrophobic residues surrounding α2A-AR pocket confer specificity on the intermolecular interactions and hence lead to favourable binding of EA in the α2A-AR, with respect to α2C-AR. Moreover, EA seems to better accommodate within α2A-ARs into TM5 area, closely to S200 and S204 which play a crucial role for activation of aminergic GPCRs such as the α2-AR, highlighting its promising role as a partial agonist. Consistently, EA mimics clonidine in inhibiting noradrenaline exocytosis from hippocampal nerve endings in an yohimbine-sensitive fashion that confirms the engagement of naïve α2-ARs in the EA-mediated effect.

Heavy metal contamination of drinking water is a public health concern that requires the development of more efficient bioremediation techniques. Absorption technologies, including biosorption, provide opportunities for improvements to increase the diversity of metal ions removed and overall binding capacity. Microorganisms are a key component in wastewater treatment plants and they naturally bind metal ions through surface macromolecules but with limited capacity. The long-term goal of this work is to engineer capsule polymerases to synthesize molecules with novel functionalities. In previously published work, we showed that the Neisseria meningitidis serogroup W (NmW) galactose-sialic acid (Gal—NeuNAc) heteropolysaccharide binds lead effectively, thereby demonstrating the potential for using this capsular polysaccharide in environmental decontamination applications. In this study, computational analysis of the NmW capsule polymerase galactosyltransferase (GT) domain was used to gain insight into how the enzyme could be modified to enable the synthesis N-acetylgalactosamine-sialic acid (GalNAc—NeuNAc) heteropolysaccharide. Various computational approaches, including molecular modeling with I-TASSER and molecular dynamics simulations (MD) with NAMD, were utilized to identify key amino acid residues in the substrate binding pocket of the GT domain that may be key to conferring UDP-GalNAc specificity. Through these combined strategies and using BshA, a UDP-GlcNAc transferase, as a structural template, several NmW active site residues were identified as mutational targets to accommodate the proposed N-acetyl group in UDP-GalNAc. Thus, a rational approach for potentially conferring new properties to bacterial capsular polysaccharides is demonstrated.

Under the oxidative stress condition, the small RNA (sRNA) Oxys that acts as essential post-transcriptional regulators of gene expression is produced and plays a regulatory function with the assistance of the RNA chaperone Hfq protein. Interestingly, experimental studies found that the N48A mutation of Hfq protein could enhance the binding affinity with OxyS while resulting in defection of gene regulation. But, how the Hfq protein interacts with sRNA Oxys and the origin of the stronger affinity of N48A mutation are both unclear. In this paper, molecular dynamics (MD) simulations were performed on the complex structure of Hfq and OxyS to explore their binding mechanism. The molecular mechanics generalized Born surface area (MM/GBSA) and interaction entropy (IE) method were combined to calculate the binding free energy between Hfq and OxyS sRNA, and the computational result is in excellent correlation with the experimental result. Per-residue decomposition of the binding free energy revealed that the enhanced binding ability of the N48A mutation mainly comes from the increased van der Waals interactions (vdW). This research explores the binding mechanism between Oxys and chaperone protein Hfq, and revealed the origin of the strong binding affinity of N48A mutation. The results provided important insights on the mechanism of gene expression regulation affected by protein mutations.

Molecular Dynamics (MD) simulations model motion of molecules in atomistic detail and aid in drug design. While simulations on large systems may require several days to complete, analysis of terabytes of data generated in the process could also be time consuming. Recent studies captured exciting and dramatic drug-receptor interactions under cell-like complex conditions. Such advances make simulations of biomolecular interactions more realistic, insightful, and informative and have potential to make drug design more realistic. However, currently available resources and techniques do not provide, in reasonable time, a comprehensive understanding of events seen in simulations. We demonstrate that big data approach results in significant speedups, and provides rapid insights into simulations performed. Advancing this improvement, we propose a scalable, self-tuning, and responsive framework based on Cloud-infrastructure to accomplish the best possible MD studies with given priorities and within available resources.

We reveal the significance of plasmonic nanoparticle’s (NP) shape and its surface morphology en route to an efficient self-assembled plasmonic nanoparticle cluster. A simplified model is simulated in the form of free-space dimer and trimer nanostructures (NPs in shape of sphere, cube, and disk). A ~ 200 % to ~ 125% raise in near field strength (gap mode enhancement) is observed for spherical NPs in comparison with cubical NPs (from 2 nm to 8 nm gap sizes). Full-width three-quarter maximum reveals better broad-spectral optical performance in a range of ~ 100 nm (dimer) and ~ 170 nm (trimer) from spherical NPs as compared to a cube (~ 60 nm for dimer and trimer). These excellent properties for sphere-based nanostructures are merited from its dipole mode characteristics.

The analytical method for the calculation of the properties of a bolted connection established by the structural Eurocodes proposes the T-stub as a component for the characterization of the tension and compression zones in moment joints. In this article, a review of the state of the art on the T-stub component is developed, where the works developed since it was initially defined, and from the perspectives of formulation, experimentation and numerical simulation are summarized and discussed. Additionally, possible future lines of work are proposed.

Discrete, logic-based models are increasingly used to describe biological mechanisms. Initially introduced to study gene regulation, these models evolved to cover various molecular mechanisms, such as signalling, transcription factor cooperativity, and even metabolic processes. The abstract nature and amenability of discrete models to robust mathematical analyses make them appropriate for addressing a wide range of complex biological problems. Recent technological breakthroughs have generated a wealth of high throughput data. Novel, literature-based representations of biological processes and emerging algorithms offer new opportunities for model construction. Here, we review up-to-date efforts to address challenging biological questions by incorporating omic data into logic-based models, and discuss critical difficulties in constructing and analysing integrative, large-scale, logic-based models of biological mechanisms.

The sensitivity of macroscopic mechanical and thermal properties of grey cast iron is computationally investigated for a variety of graphite microstructures over a wide temperature range. In order to represent common graphite microstructures according to DIN EN ISO 945-1, a synthetic approach is used to algorithmically generate simulation domains. The developed mechanical and thermal model is applied in a large simulation study. The study includes statistical volume elements of the graphite microstructures classes GG-15 and IA2 to IA5, with 10 v.-%, 11 v.-% and 12 v.-% graphite, respectively, for a temperature range from 20 °C to 750 °C. Homogenized macroscopic quantities such as the Young's moduli, Poisson's ratios, yield strengths and thermal conductivities are predicted for the different microstructure classes by applying simulation and data analysis tools of the research data infrastructure Kadi4Mat.

Accurate treatment planning in radiotherapy essentially decreases secondary damage to healthy tissue surrounding the tumor. Due to plans to use a direct, highly collimated, narrow beam with high intensity to treat small area tumors, researchers have studied microbeam radiation therapy extensively. Using a synchrotron beam as the radiation source may help to limit secondary damage, but treatment planning using computerized simulations and dosimetry is still necessary to achieve optimal results. For this purpose, PDA-gel dosimeters were developed and their sensitivity around a 150 keV induced synchrotron X-ray radiation beam was examined via Monte Carlo simulations using the EGS5 code system. The microbeam development is now at the animal study stage. In this study, we simulate the irradiation of a rat's brain. The simulation results obtained spectra for two types of PDA-gel dosimeters that were compared with the spectrum obtained in a modelized brain tumor of a rat. Additionally, percentage depth dose curves were calculated for the brain tissue and the two gels. Correction equations for the dosimeters were obtained from the dose-difference plots. For further references, these equations can be used to calculate the actual dose in a brain tumor in a rat. The Monte Carlo simulations demonstrate that PDA-gel dosimeters can be used as a reference technique in planning treatment using synchrotron irradiations and in other medical treatment planning methods.

The Covid-19 pandemic has resulted in the closure of schools at every level, globally, forcing education to move online. Meeting the needs of students online for Science Lab classes, in particular, is a challenge since the physical labs are not available to the teachers or students. OLabs is a virtual Science Lab providing a complete learning environment of theory, experimental procedures, videos, animations, simulations, and assessments that capture real lab experiences with the relevant pedagogy. This study looks at the acquisition and behaviors of users, on the OLabs platform, during pre and Covid-19 times. Using Google Analytics, we observe that, during the pandemic time, users increasingly adopted OLabs as a new learning pedagogy for performing experiments as indicated by parameters like the number of users; the number of unique pages viewed per session; time spent on viewing content; bounce rate; and preference for content types such as theory, simulations, videos, and animations.

We addressed the frequent occurrence of mixed-chain lipids in biological membranes and their impact on membrane structure by studying several chain-asymmetric phosphatidylcholines and the highly asymmetric milk sphingomyelin. Specifically, we report trans-membrane structures of the corresponding fluid lamellar phases using small-angle X-ray and neutron scattering, which were jointly analyzed in terms of a membrane composition-specific model, including a headgroup hydration shell. Focusing on terminal methyl groups at the bilayer center we found a linear relation between hydrocarbon chain length mismatch and the methyl-overlap for phosphatidylcholines, and a non-negligible impact of the glycerol backbone-tilting, letting the sn1-chain penetrate deeper into the opposing leaflet by half a CH2 group. That is, penetration-depth differences due to the ester-linked hydrocarbons at the glycerol backbone, reported previously for gel phase structures also extend to the physiological more relevant fluid phase, but are significantly reduced. Moreover, milk sphingomyelin was found to follow the same linear relationship suggesting a similar tilt of the sphingosine backbone. Complementary performed molecular dynamics simulations revealed that there is always a part of the lipid tails bending back, even if there is a high interdigitation with the opposing chains. This suggests that hydrocarbon chain interdigitation plays only a minor role in transbilayer coupling. For both cases of adaption to chain length mismatch, chain-asymmetry has a large impact on hydrocarbon chain ordering, inducing disorder in the longer of the two hydrocarbons.

Fires are complex multi-physics problems that span wide spatial scale ranges. Capturing this complexity in computationally affordable numerical simulations for process studies and “outer-loop” techniques (e.g., optimization and uncertainty quantification) is a fundamental challenge in reacting flow research. Further complications arise for propagating fires where a priori knowledge of the fire spread rate and direction is typically not available. In such cases, static mesh refinement at all possible fire locations is a computationally inefficient approach to bridging the wide range of spatial scales relevant to fire behavior. In the present study, we address this challenge by incorporating adaptive mesh refinement (AMR) in fireFoam, an OpenFOAM solver for simulations of complex fire phenomena involving pyrolyzing solid surfaces. The AMR functionality in the extended solver, called fireDyMFoam, is load balanced, models gas, solid, and liquid phases, and allows us to dynamically track regions of interest, thus avoiding inefficient over-resolution of areas far from a propagating flame. We demonstrate the AMR capability and computational efficiency for fire spread on vertical panels, showing that the AMR solver reproduces results obtained using much larger statically refined meshes, but at a substantially reduced computational cost. We then leverage the computational efficiency of the AMR solver to demonstrate an optimization framework for fire suppression based on the open-source Dakota toolkit.

The mean flow and turbulence statistics of the flow through a simplified urban environment, which is an active research area in order to improve the knowledge of turbulent flow in cities, is investigated. This is useful for civil engineering, pedestrian comfort and for health concerns caused by pollutant spreading. In this work, we provide analysis of the turbulence statistics obtained from well-resolved large-eddy simulations (LES). A detailed analysis of this database reveals the impact of the geometry of the urban array on the flow characteristics and provides for a good description of the turbulent features of the flow within a simplified urban environment. The most prominent features of this complex flow include coherent vortical structures such as the so-called arch vortex, the horseshoe vortex and the roof vortex. These structures of the flow have been identified by an analysis of the turbulence statistics. The influence of the geometry of the urban environment (and particularly the street width and the building height) on the overall flow behavior have also been studied. Finally, the well-resolved LES results were compared with the experimental database from Monnier et al. to discuss differences and similarities between the respective urban configurations.

Background: Colorectal cancer is considered the third most fetal among all type of cancer. Spleen tyrosine kinase (SYK) is a non-receptor type tyrosine-protein that plays crucial role in signaling mediated via immune receptor. We adopted an onco-informatics analysis to evaluate the SYK expression and prognostic value of SYK in colorectal cancer, and identification of potential phytochemicals which may inhibit overexpression of SYK protein as well as minimized colorectal cancer. Materials & Methods: Differential expression of SYK gene was analyzed using the several transcriptomic databases including Oncomine, UALCAN, GENT2 and GEPIA2. The server, cBioPortal was used to analyze mutation and copy number alterations whereas GENT2, GEPIA, OncoLnc and PrognoScan were employed to examine the survival rate. A protein-protein interaction network of SYK and co-expressed genes of SYK was conducted via GeneMANIA. Considering SYK gene encoding protein as drug target, selected phytochemicals were assessed by molecular docking using PyRx 0.8 packages. YASARA molecular dynamics simulators were applied for the post validation of the molecular docking data. Results: We have observed significant overexpression of mRNA expression levels of SYK gene colorectal adenocarcinoma (COAD) samples compared with normal tissues. Significant methylation level and various genetic alterations are assembled in SYK gene which can lead to the development of colorectal cancer. As a result, lower level of SYK expression was related to the more chances of patients’ survival by which all the outcomes from the multiple bioinformatics platforms and web resources have demonstrated the significant evidences that the SYK kinsase can possess as a potential biomarker for the treatment of colorectal cancer. Here, aromatic phytochemicals namely, Kaempferol and Glabridin targeting SYK showed more stability compared to controls and may be useful for the treatment of colorectal cancer. Conclusion: Our study showed dysregulated expression of SYK in colorectal cancer and potentiality to act as a biomarker for the prognosis of CRC. Moreover, we have shown phytochemicals (Kaempferol and Glabridin) target SYK as potential treatment strategies and drug repositioning potentiality in colorectal cancer.

ND1 subunit possesses the majority of the inhibitor binding domain of the human MRC-I. This is an attractive target for the search for new inhibitors that seek mitochondrial dysfunction. It is known, from in vitro experiments, some metabolites from Annona muricata called acetogenins have important biological activities such as anticancer, antiparasitic, and insecticide. Previous studies propose an inhibitory activity of bovine MRC-I by bis-THF acetogenins such as annocatacin B, however, there are few studies on its inhibitory effect on human MRC-I. In this work, we evaluate the molecular and energetic affinity of the annocatacin B molecule with the human ND1 subunit in order to elucidate its potential capacity to be a good inhibitor of this subunit. For this purpose, QM optimizations, MD simulations and MM/PBSA analysis were performed. As a control to compare our outcomes, the molecule rotenone, which is a known MRC-I inhibitor, was chosen. Our results show that annocatacin B has a greater affinity for the ND1 structure, its size and folding were probably the main characteristics that contributed to stabilize the molecular complex. Furthermore, the MM/PBSA calculations showed a 35% stronger BFE compared to the rotenone complex. Detailed analysis of the BFE shows that the aliphatic chains of annocatacin B play a key role in molecular coupling by distributing favorable interactions throughout the major part of the ND1 structure. These results are consistent with experimental studies that mention that acetogenins may be good inhibitors of MRC-I.

The objective of this study was to correlate the binding of drugs on a very popular nanoparticulate polymeric matrix; PLGA nanoparticles with their main constitutional, electronic and physico-chemical descriptors. Gaussian Processes (GPs) was the artificial intelligence machine learning method that was utilized to fulfil this task. The method could successfully model the results where optimum values of the investigated descriptors of the loaded drugs were deduced. A percentage bias of 12.68 % ± 2.1 was obtained in predicting the binding energies of a group of test drugs. As a conclusion, GPs could successfully model the drugs-PLGA interactions associated with a good predicting power. The GPs-predicted binding energies (ΔG) can easily be projected to the drugs loading as was previously proven. Adopting the “Pharmaceutics Informatics” approach can save the pharmaceutical industry and the drug delivery scientists a lot of exerted resources, efforts and time.

The anisotropy in the CMBR detected by the COBE satellite has sprouted the research and theories of the void that got created, after being washed away by a parallel universe after its collision. This details of the roadmap to the parallel universe, that are previously been entangled, but now, separated, with the concept of 2-time dimensions as a time curve of containing the closed curves embedded on the surface area, thereby time running backward in orientation in the parallel universe, along with the perspective of eternal inflation and divided subspaces giving birth to twin universes are provided here. This time curve being responsible for creating an exponentiality of time frames, growing in layers, giving us the perception of the confabulations being an indication of the previously connected worlds.

In the current work, in continuation of our recent research [1] we synthesized and studied new chimeric compounds comprising the ribosome-targeting antibiotic chloramphenicol (CHL) and the membrane-penetrating cation triphenylphosphonium (TPP) connected by alkyl linkers of different lengths. Using various biochemical assays, we showed that these CAM-Cn-TPP compounds bind to the bacterial ribosome, inhibit protein synthesis in vitro and in vivo in a way similar to that of the parent CHL, and significantly decrease membrane potential. Similar to CAM-C4-TPP, the mode of action of CAM-C10-TPP and CAM-C14-TPP on bacterial ribosomes differ from that of CHL. By simulating the dynamics of complexes of CAM-Cn-TPP with bacterial ribosomes, we have proposed a possible explanation for the specificity of the action of these analogs on the translation process. CAM-C10-TPP and CAM-C14-TPP stronger inhibit the growth of the Gram-positive bacteria in comparison to the CHL and suppress some strains of CHL-resistant bacteria. Thus, we have shown that TPP derivatives of CHL are dual-acting compounds that target the ribosomes and the cellular membranes of bacteria. The TPP fragment of CAM-Cn-TPP compounds contributes to the inhibitory effect on bacteria. Moreover, since the mitochondria of eukaryotic cells have qualities similar to those of their prokaryotic ancestors, we demonstrate the possibility of targeting chemoresistant cancer cells with these compounds.