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.

Knowledge of the interaction between inorganic and organic phosphates with soil minerals is vital for improving the soil P fertility. To achieve an in-depth understanding we combined adsorption experiments and hybrid ab initio molecular dynamics simulations to analyze the adsorption of common phosphates, i.e. orthophosphate (OP), glycerolphosphate (GP) and inositolhexaphosphate (IHP), onto the 100 surface plane of goethite. Experimental adsorption data per mol P-molecule basis fitted to the Freundlich model show the adsorption strength increases in the order GP < OP < IHP, and IHP adsorption being saturated faster followed by GP and OP. Modeling results show that OP and GP form stable monodentate (M) and binuclear bidentate (B) motifs with B being more stable than M, whereas IHP forms stable M and 3M motifs. Interfacial water plays an important role through hydrogen bonds and proton transfers with OP/GP/IHP and goethite. It also controls the binding motifs of phosphates with goethite. Combining both experimental and modeling results, we propose that the B motif dominates for OP, whereas GP forms M and IHP forms a combination of M and 3M motifs. The joint approach plausibly explains why IHP is the predominant organically bound P form in soil. This study could be considered as a preliminary step for further studies for understanding the mechanisms of how microbes and plants overcome the strong IHP–mineral binding to implement the phosphate groups into their metabolism.

The non-symmetrical collapse of an empty cylindrical cavity is modelled using Smoothed Particle Hydrodynamics. The presence of a nearby surface produces an anisotropic pressure field generating a high velocity jet that hits the surface. The collapse follows a different dynamic based to the initial distance between the centre of the cavity and the surface. When the distance is greater than the cavity radius (detached cavity) the surface is hit by travelling shock waves. When the distance is less than the cavity radius (attached cavity) the surface is directly hit by the jet and later by other shock waves generated in the last stages of the of the collapse. The results show that the surface is hit by a stronger shock when distance between the centre of the cavity and the surface is zero while showing more complex double peaks behaviour for other distances.

Tsunami modeling and simulation has changed in the past few years more than it had in decades, especially so with respect to coastal inundation. Among other things, this change is supported by the approaching era of exa-scale computing, whether via GPU or more likely forms of hybrid computing whose presence is growing across the geosciences. For reasons identified across this review, exa-scale computing efforts will impact the on-shore, highly turbulent r\'egime to higher degree than the 2D shallow water equations used to model tsunami propagation in the open ocean. This short review describes the different approaches to tsunami modeling from generation to impact and underlines the limits of each model based on the flow r\'egime. Moreover, from the perspective of a future comprehensive multi-scale modeling infrastructure to simulate a full tsunami, we underline the current challenges associated with this approach and review the few efforts that are currently underway to achieve this goal. A table of existing tsunami software packages is provided along with an open Github repository to allow developers and model users to update the table with additional models as they are published and help with model discoverability.

Thermal shape memory polymers (SMPs) find increasing applications in biology and medicine due to their promising potential for improved biocompatibility. In such applications, the inevitable penetration of small molecules from the ambient fluid into the polymer influences the shape recovery process and often leads to a reduction of the temperature, at which shape recovery takes place. We show here via molecular dynamics simulations that the size of additive molecules plays a key role for this process. While the effect of concentration on the recovery rate is monotonic in the investigated range, a non-monotonic dependence on the size of additive molecules emerges at temperatures close to the glass transition. This work thus identifies the additives’ size to be a qualitatively novel parameter for switching the recovery process in polymer-based shape memory materials.

Metal nanoparticles are used to modify/enhance the properties of a polymer matrix for a broad range of applications in bio-nanotechnology. Here, we study the properties of polymer/gold nanoparticle (NP) nanocomposites through atomistic molecular dynamics, MD, simulations. We probe the structural, conformational and dynamical properties of polymer chains at the vicinity of a gold (Au) NP and a functionalized (core/shell) Au NP, and compare them against the behavior of bulk PE. The bare Au NPs were constructed via a systematic methodology starting from ab-initio calculations and an atomistic Wulff construction algorithm resulting in the crystal shape with the minimum surface energy. For the functionalized NPs the interactions between gold atoms and chemically adsorbed functional groups change their shape. As a model polymer matrix we consider polyethylene of different molecular lengths, from the oligomer to unentangled Rouse like systems. By computing the different properties the concept of the interface, and the interphase as well, in polymer nanocomposites with metal NPs are critically examined. Results concerning polymer density profiles, bond order parameter, segmental and terminal dynamics show clearly that the size of the interface / interphase, depends on the actual property under study. In addition, the anchored polymeric chains change the behavior/properties, and especially the chain density profile and the dynamics, of the polymer chain at the vicinity of the Au NP.

Three body systems in which one of the bodies is ejected without escaping the binary system have previously been studied in various restricted forms. However, none of these studies dwells on the problem in a general setting. Thus, to study this phenomenon qualitatively, we try to expand this problem's scope to unequal mass systems and generalize them by considering various configurations of fixed initial points with precisely calculated initial velocities, some zero velocity models and some optimized models. We will see the use of terminology similar to the previous studies done in this domain but incorporate different analytical and evaluation methods.

Remotely Piloted Aircraft Systems (RPAS) are increasingly becoming relevant actors flying through the airspace and will assume much more importance in the future perspective. In order to allow their safe integration with manned conventional traffic in non-segregated airspaces, in accordance with the overall Air Traffic Management (ATM) paradigm, specific enabling technologies are needed. As well known, among the enabling technologies identified as crucial for RPAS integration into the overall ATM system, the Detect and Avoid (DAA) technology is fundamental. In the meantime, to support extended surveillance, the universal introduction on-board of aircraft of cooperative Automatic Dependent Surveillance – Broadcast (ADS-B) is increasingly implemented, having the potential to allow coverage of the whole airspace also in remote areas not usually covered by conventional radar surveillance. In this paper, the experimental results are presented and discussed that have been obtained through the real-time validation, with hardware and human in the loop (RTS-HIL) simulations, of an automatic ADS-B based Separation Assurance and Collision Avoidance System aimed to support RPAS automatic operations as well as remote pilot decision making. In the paper, after an introductory outline of the Concept of Operations (ConOps) of the system and of its architectural organization, while also providing basic information about the main system functionalities, the description is reported of the tests that have been carried out and the obtained results are described and discussed, in order to emphasize the performances and limitations of the proposed system. In particular, not only the quantitative performances obtained are reported and commented but also the feedbacks received by the pilots in order to improve the system are described, for instance in terms of preferred typology of conflict resolution manoeuver elaborated by the system.

Understanding the flow in urban environments is an increasingly relevant problem due to its significant impact on air quality and thermal effects in cities worldwide. In this review we provide an overview of efforts based on experiments and simulations to gain insight into this complex physical phenomenon. We highlight the relevance of coherent structures in urban flows, which are responsible for the pollutant-dispersion and thermal fields in the city. We also suggest a more widespread use of data-driven methods to characterize flow structures as a way to further understand the dynamics of urban flows, with the aim of tackling the important sustainability challenges associated to them.

Solid state sensors having timing capabilities are becoming an absolute need in particle tracking techniques of future experiments at colliders. In this sense, silicon sensors having 3D structure are becoming an interesting solution, due to their intrinsic speed and radiation resistance. A characteristics of such devices is the strict dependence of their performance on their geometric structure, which can be widely optimised by design, thus requiring suitable tools for an accurate modeling of their behaviour. This paper illustrates the development, performance and use of the TCoDe simulator, specifically dedicated to the fast simulation of carrier transportation phenomena in solid state sensors. Some examples of its effectiveness in the design and analysis of 3D sensors is also given.

We prepared heterogeneous alumina-silicate glasses by consolidating nanoparticles using molecular dynamics simulations. Consolidated glasses from either low alumina content alumina-silicate glasses or high alumina content alumina-silicate glasses show significantly improved ductility around consolidation pressure of ~3 GPa. The introduced structural heterogeneities, namely over-coordinated network formers and their neighboring oxygen atoms, are identified as plasticity carriers due to their high rearrangement propensity. In addition, consolidated oxide glass from both 23.4Al₂O₃76.6SiO₂ and 73.1Al₂O₃26.9SiO₂ nanoparticles show improved flow strength (up to 1 GPa) due to the introduction of chemical heterogeneities. Last but not least, apparent hardening behavior appears upon cold work in consolidated glasses, with an increase of yield strength from ~3.3 GPa to ~6.4 GPa. This method is a big advancement toward ultra-strong and ultra-tough glasses by breaking the structure, composition and size limitations in traditional melt-quench process.

Motivated by the way animals react in nature, we introduce a fully-connected neural-network model, which incorporates the external pattern presented to the system as a fundamental tool of the recognition process. In this new scenario, in the absence of this external field, memories are not attractors inside basins of attraction, as in usual attractor neural networks, although basins may be created according to the external pattern, thus allowing storing a much larger number of memories. The key point consists in calibrating the influence of the external pattern such as to cancel the noise generated by those memories not correlated with the external pattern.We illustrate how this proposal works by including this new contribution in the standard Hopfield model, showing a significant increase in its recognition capacity (typically by a factor $10^{2}$). As an additional feature of this model, we show its ability to react promptly to changes in the external environment, a crucial attribute of living beings. This procedure can be applied to a wide variety of neural-network models to increase considerably their recognition and reaction capabilities.

The asymmetry in the dynamics of an electro-pneumatic actuating device consisting of an electro-pneumatic transducer and a single-action pneumatic actuator was unexpectedly found experimentally. This asymmetry manifests in response to large step excitations. The dynamic asymmetry effect is understood as a change in the shape of the response of an actuator depending on the direction of the actuators stem movement. The questions appears: How to explain this effect? Does this phenomenon reflect thermodynamic air processes? Is it connected with air-to-mechanical energy conversion? Together, six working hypotheses explaining this effect were formulated. The asymmetry was studied in detail using analytical and simulation modeling, as well as experimental research. In this respect, a nonlinear analytical model was developed, tuned, and later solved using simulations. The simulation model was verified based on the experiment data. In addition, the problem of the efficiency in the energy conversion of a single-action actuator was discussed and, in result, the maximum theoretical energy efficiency was determined. Subsequently, all six working hypotheses were verified. Finally, the hypothesis explaining asymmetry as an effect of the different thermodynamic air processes in both actuator’s stem travel directions was confirmed.

The application of instrumented indentation to assess material properties like Young’s modulus and micro-hardness has become a standard method. In recent developments, indentation experiments and simulations have been combined to inverse methods, from which further material parameters as yield strength, work hardening rate, and tensile strength can be determined. In this work, an inverse method is introduced by which material parameters for cyclic plasticity, i.e. kinematic hardening parameters, can be determined. To accomplish this, cyclic Vickers indentation experiments are combined with finite element simulations of the indentation with unknown material properties, which are then determined by inverse analysis. To validate the proposed method, these parameters are subsequently applied to predict the uniaxial stress-strain response of a material with success. The method has been validated successfully for a quenched and tempered martensitic steel and for technically pure copper, where an excellent agreement between measured and predicted cyclic stress-strain-curves has been achieved. Hence, the proposed inverse method based on cyclic nanoindentation, as a quasi-non-destructive method, could complement or even substitute the resource-intensive conventional fatigue testing in the future for some applications.

Fractional differential mathematical model unfolding the dynamics of the COVID-19 pandemic in India is presented and explored in this paper. The purpose of this study is to estimate the future outbreak of disease and potential control strategies using mathematical models in India as a whole country as well as in some of the states of the country. This model is calibrated based on reported cases of infections over the month of April 2020 in India. We have used iterative fractional complex transform method to find approximate solutions of the model having modified Riemann Liouville fractional differential operator. We have also carried out a comparative analysis between actual and estimated cumulative cases graphically, moreover, most sensitive parameters for basic reproduction number$(R_0)$ are computed and their effect on transmission dynamics of COVID-19 pandemic is investigated in detail.

The emergence of SARS/MERS drug resistant COVID-19 with high transmission and mortality has recently been declared a deadly pandemic causing economic chaos and significant health problems. Like all coronaviruses, SARS-CoV-2 is a large virus that has many druggable components within its proteome. In this study, we focused on repurposing approved and investigational drugs by identifying potential drugs that are predicted to effectively inhibit critical enzymes within SARS-CoV-2. We shortlisted seven target proteins with enzymatic activities known to be essential at different stages of the virus life cycle. For virtual screening, the energy minimization of a crystal structure or modeled protein was carried out using Protein Preparation Wizard (Schrödinger LLC, 2020-1). Following active site selection based on data mining and COACH predictions, we performed a high-throughput virtual screen of drugs (n=5903) that are already approved by worldwide regulatory bodies including the FDA, using the ZINC database. Screening was performed against viral targets using three sequential docking modes (i.e. HTVS, SP and XP). Our in-silico virtual screening identified ~290 potential drugs based on the criteria of energy, docking parameters, ligand and binding site strain and score. Drugs specific to each target protein were further analyzed for binding free energy perturbation by molecular mechanics (prime MM-GBSA) and pruning the hits to the top 32 candidates. A top lead from each target group was further subjected to molecular dynamics simulation (MDS) using the Desmond module to validate the efficacy of the screening pipeline. All of the simulated hit-target complexes were predicted to strongly interact and with highly stable binding. Thus, we have identified a number of approved and investigational drugs with high likelihood of inhibiting a variety of key SARS-CoV-2 proteins. Follow-up studies will continue to identify inhibitors suitable for combination therapy based on drug-drug synergy to thwart resistance. In addition, the screening hits that we have identified provide excellent probes for understanding the binding properties of the active sites of all seven targets, further enabling us to derive consensus molecules through computer-aided drug design (CADD). While infections are expanding at a rampant pace, it must be recognized that resistance will grow commensurately through either genetic shift and/or genetic drift to all small molecule drugs identified. Vaccines should provide a more permanent solution through prevention, but resistivity is still a possible scenario. Nevertheless, a persistent multi-target drug development program is essential to curb this ongoing pandemic and to keep reemergence in check.

Since the first case of 2019 novel coronavirus disease (COVID-19) detected on Jan 30, 2020, in India, the number of cases rapidly increased to 3819 cases including 106 deaths as of 5 April 2020. Taking this into account, in the present work, we are studying a Bats-Hosts-Reservoir-People transmission fractional-order COVID-19 model for simulating the potential transmission with the thought of individual social response and control measures by the government. The real data available about infectious cases from $14^{th}$ March to $26^{th}$ March 2020 is analysed and accordingly various parameters of the model are estimated or fitted. The Picard successive approximation technique and Banach's fixed point theory have been used for verification of the existence and stability criteria of the model. Numerical computations are done utilizing the iterative Laplace transform method. In the end, we illustrate the obtained results graphically. The purpose of this study is to estimate the effectiveness of preventive measures, predicting future outbreaks and potential control strategies using the mathematical model.

The SARS-CoV-2 was confirmed to cause the regional outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China. The 3C-like protease (3CL^pro), an essential enzyme for viral replication, is a valid target to compacts SARS-CoV and MERS-CoV. In this research, an integrated library consisting of 1000 compounds from Asinex Focused Covalent (AFCL) library and 16 FDA-approved protease inhibitors were screened against SARS-CoV-2 3CL^pro. Top compounds with significant docking scores and making stable interactions with catalytic dyad residues were obtained. The screening results in identification of compound 621 from AFCL library as well as Paritaprevir and Simeprevir from FDA-approved protease inhibitors as potential inhibitors of SARS-CoV-2 3CL^pro. The mechanism and dynamic stability of binding between the identified compounds and SARS-CoV-2 3CL^pro were characterized using 50 nanoseconds (ns) molecular dynamic (MD) simulation approach. The identified compounds are potential inhibitors worthy of further development as SARS-CoV-2 3CLpro inhibitors/drugs. Importantly, the identified FDA-approved therapeutics could be ready for clinical trials to treat infected patients and help to curb the COVID-19.

Chiroptical responses have been an essential tool over the last decades for chemical structural elucidation due to their exceptional sensitivity to geometry and intermolecular interactions. In recent times, there has been an increasing interest for the search of more efficient sensing by the rational design of tailored chiroptical systems. In this Review article, advances on chiroptical systems towards their implementation in sensing applications are summarized. Strategies to generate chiroptical responses are illustrated. Theoretical approaches to assist in the design of these systems are discussed. Development of efficient chiroptical reporters in different states of matter, essential for the implementation in sensing devises, is reviewed. In the last part, remarkable examples of chiroptical sensing applications are highlighted.

We study in this paper the time evolution of stock markets using a statistical physics approach. We consider an ensemble of agents who sell or buy a good according to several factors acting on them: the majority of the neighbors, the market ambiance, the variation of the price and some specific measure applied at a given time. Each agent is represented by a spin having a number of discrete states q or continuous states, describing the tendency of the agent for buying or selling. The market ambiance is represented by a parameter T which plays the role of the temperature in physics: low T corresponds to a calm market, high T to a turbulent one. We show that there is a critical value of T, say T_c, where strong fluctuations between individual states lead to a disordered situation in which there is no majority: the numbers of sellers and buyers are equal, namely the market clearing. The specific measure, by the government or by economic organisms, is parameterized by $H$ applied on the market at the time t₁ and removed at the time t₂. We have used Monte Carlo simulations to study the time evolution of the price as functions of those parameters. In particular we show that the price strongly fluctuates near T_c and there exists a critical value H_c above which the boosting effect remains after H is removed. Our model replicates the stylized facts in finance (time-independent price variation), volatility clustering (time-dependent dynamics) and persistent effect of a temporary shock. The second party of the paper deals with the price variation using a time-dependent mean-field theory. By supposing that the sellers and the buyers belong to two distinct communities with their characteristics different in both intra-group and inter-group interactions, we find the price oscillation with time. Results are shown and discussed.

This study reports a general scenario for the out-of-equilibrium features of collapsing polymeric architectures. We use molecular dynamics simulations to characterize the coarsening kinetics, in bad solvent, for several macromolecular systems with an increasing degree of structural complexity. In particular, we focus on: flexible and semiflexible polymer chains, star polymers with 3 and 12 arms, and microgels with both ordered and disordered networks. Starting from a powerful analogy with critical phenomena, we construct a density field representation that removes fast fluctuations and provides a consistent characterization of the domain growth. Our results indicate that the coarsening kinetics presents a scaling behaviour that is independent of the solvent quality parameter, in analogy to time-temperature superposition principle. Interestingly, the domain growth in time follows a power-law behaviour that is approximately independent of the architecture for all the flexible systems; while it is steeper for the semiflexible chains. Nevertheless, the fractal nature of the dense regions emerging during the collapse exhibits the same scaling behaviour for all the macromolecules. This, suggests that the faster growing length scale in the semiflexible chains originates just from a faster mass diffusion along the chain contour, induced by the local stiffness. The decay of the dynamic correlations displays scaling behavior with the growing length scale of the system, which is a characteristic signature in coarsening phenomena.

In this paper, the columnar supramolecular aggregates of photosensitive star-shaped azobenzenes with benzene-1,3,5-tricarboxamide core and azobenzene arms are analysed theoretically applying a combination of computer simulation techniques. Without a light stimulus, the trans-stars build one-dimensional columns of stacked molecules during the first stage of the noncovalent association. These columnar aggregates represent the structural elements of more complex experimentally observed morphologies -- fibers, spheres, gels and others. Upon UV light exposure, the azobenzene arms isomerise from thermodynamically stable planar trans- to a metastable kinked cis-state influencing the aggregate morphology. Here, we determine the most favourable mutual orientations of the \textit{trans}-stars in the stack in terms of (i) the pi-pi distance between the cores lengthwise the aggregate, (ii) the star slipped displacements and (iii) the rotation promoting the helical twist and chirality of the aggregate by calculating the binding energy diagrams using density functional theory. The model predictions are further compared with available experimental data. The intermolecular forces responsible for the stability of the stacks made of trans-azobenzene stars in crystals are quantified using Hirshfeld surface analysis. Finally, to characterize the self-assembly mechanism of such stars in solution, we calculate the hydrogen bond lengths, the normalized dipole moment and the binding energies as the functions of the columnar length using molecular dynamics trajectories, and conclude about the cooperative nature of this process.

Due to an increase of the monocrystalline PV systems installations, for a drive towards the sustainable smart cities in the hot arid developing country such as Pakistan, pose challenges of the performance and degradation issues. Monocrystalline PV module efficiencies are declining and damaging under the continuous exposure to higher surface day-time temperatures in the different parts of the country. A MATLAB simulations were performed based on the validated mathematical approach. This paper investigates the hot arid surface temperature impacts on the performance of PV modules during the summer and winter seasons in Pakistan. The investigations are performed examining the power generating efficiency of the PV system. This paper also investigates the influence of installations of PV-system in the North, South, East and West regions of Pakistan. It was examined that the northern areas of Pakistan are more suitable for maintaining the long-term durability of the PV system. Investigations are performed for the peak summer and peak winter days. During summer months, cooling strategies have to be implemented to overcome the heating effects whilst reducing degradation effect on installed PV-system.

Histone Lysine Specific Demethylase 1 (LSD1) is overexpressed in many cancers and become a new target for anticancer drugs. In recent years, the small molecule inhibitors with various structures targeting LSD1 have been reported. Here we report the binding interaction modes of a series of thieno[3,2-b]pyrrole-5-carboxamides LSD1 inhibitors using molecular docking, three dimensional quantitative structure-activity relationship (3D-QSAR). Comparative molecular field analysis (CoMFA q²=0.783, r²=0.944, r²_pred=0.851) and Comparative molecular similarity indices analysis (CoMSIA q²=0.728, r²=0.982, r²_pred=0.814) were used to establish 3D-QSAR models, which had good verification and prediction capabilities. Based on the contour maps and the information of molecular docking, 8 novel small molecules were designed in silico, among which compounds D4, D5 and D8 with high predictive activity were subjected to further molecular dynamics simulations (MD), and their possible binding modes were explored. It was found that Asn535 plays a crucial role in stabilizing the inhibitors. Furthermore, the ADME and bioavailability prediction for D4, D5 and D8 were carried out. The results would provide valuable guidance for designing new reversible LSD1 inhibitors in the future.

The effect of river fronts on oil slick transport has been demonstrated using high resolution forcing models and a fully fledged oil drift model, OpenOil. The model system is used to simulate the 2010 DeepWater Horizon oil spill. Metocean forcing data are taken from the GoM-HYCOM 1/50° ocean model with realistic river input and ECMWF global forecast products of wind and wave parameters with 1/8° resolution. The simulations are initialized from satellite observations of the surface oil patch. OpenOil includes most of the relevant processes, such as emulsification, evaporation, wave entrainment, stranding and droplet formation. The model takes account of the actual oil type and properties, using the ADIOS oil weathering database of NOAA. The effect of using a newly developed parameterization for oil droplet size distribution is studied and compared to a traditional algorithm. Although the algorithms provide different distributions for a single wave breaking event, it is found that the net difference after long simulations is negligible, indicating that the outcome is robust regarding the choice of parameterization. That indicates that the wave entrainment, vertical mixing and re-surfacing mechanisms that are part of OpenOil are more important for determining the final droplet size spectrum than the spectrum prescribed for individual wave breaking events. In both cases, the size of the droplets controls how much oil is present at the surface and hence are subject to wind and Stokes drift. The effect of removing river outflow in the ocean model is investigated in order to showcase effects of river induced fronts on oil spreading. A consistent effect on the amount and location of stranded oil is found, and considerable impact of river induced fronts is seen on the location of the surface oil patch. During a case with large river outflow (May 20-27, 2010), the total amount of stranded oil is reduced by about 50% in the simulation with no river input. The results compares well with satellite observations of the surface oil patch.

A ducted photovoltaic façade (DPV) unit Studied using experimental Prototype and simulated in a full scale Computational Fluid Dynamics CFD Model. The Study comes in two parts; This is Part I with the title detailed above and Part II titled ‘A Ducted Photovoltaic Façade Unit with Buoyancy Cooling: Part II CFD Simulation’.. The process adopted in the experimental study is replicated in the simulation Part. The aim was to optimize the duct width behind the solar cells to allow for maximum buoyancy-driven cooling for the cells during operation. Duct widths from 5 to 50 cm were tested in a Proto-type. A duct width of 45 cm had the maximum calculated heat removed from the duct; however, the lowest cell-operating temperature was reported for duct width of 50 cm. It was found that the DT between ducts' inlets and outlets range from 5.47 °C to 12.32 °C for duct widths of 5–50 cm, respectively. The ducted system enhanced module efficiency by 12.69% by reducing PV temperature by 27 °C from 100°C to 73 °C. The maximum calculated heat recovered from the ducted PV system is 422 W. This is 47.98% from the incident radiation in the test. Total summation of heat recovered and power enhanced by the ducted system is 61.67%.

As the energy efficiency demands for future buildings become increasingly stringent, preliminary assessments of energy consumption are mandatory. These are possible only through numerical simulations, whose reliability crucially depends on boundary conditions. We therefore investigate their role in numerical estimates for the usage of geothermal energy, performing annual simulations of transient heat transfer for a building employing a geothermal heat pump plant and energy piles. Starting from actual measurements, we solve the heat equations in 2D and 3D using COMSOL Multiphysics and IDA-ICE, and discover a negligible impact of the multiregional ground surface boundary conditions. Moreover, we verify that the thermal mass of the soil medium induces a small vertical temperature gradient on the piles surface. We also find a roughly constant temperature on each horizontal cross-section, with nearly identical values if the average temperature is integrated over the full plane or evaluated at one single point. Calculating the yearly heating need for an entire building we then show that the chosen upper boundary condition affects the energy balance dramatically. Using directly the pipes’ outlet temperature induces a 54% overestimation of the heat flux, while the exact ground surface temperature above the piles reduces the error to 0.03%.

The Particle-In-Cell (PIC) method has been developed in order to investigate microscopic phenomena, and with the advances of computing power, newly developed codes have been used for several fields such as astrophysical, magnetospheric, and solar plasmas. PIC applications have grown extensively with large computing powers available on supercomputers such as Pleiades and Blue Waters in the US. For astrophysical plasma research PIC methods have been utilized for several topics such as reconnection, pulsar dynamics, non-relativistic shocks, relativistic shocks, relativistic jets, etc. PIC simulations of relativistic jets have been reviewed with the emphasis on the physics involved in the simulations. This review summarizes PIC simulations, starting with the Weibel instability in slab models of jets, and then focuses on global jet evolution in helical magnetic field geometry. In particular we address kinetic Kelvin-Helmholtz instabilities and mushroom instabilities.

The description of protein disordered states is important for understanding protein folding mechanisms and their functions. In this short review, we briefly describe a simulation approach to modeling disordered protein interactions and unfolded states of globular proteins. It is based on the CABS coarse-grained protein model that uses a Monte Carlo (MC) sampling scheme and a knowledge-based statistical force field. We review several case studies showing that description of protein disordered states resulting from CABS simulations is consistent with experimental data. The case studies comprise investigations of protein-peptide binding and protein folding processes. The CABS model has been recently made available as the simulation engine of multiscale modeling tools enabling studies of protein-peptide docking and protein flexibility. Those tools offer customization of the modeling process, driving the conformational search using distance restraints, reconstruction of selected models to all-atom resolution and studies of large protein systems in a reasonable computational time. Therefore, CABS can be combined in integrative modeling pipelines incorporating experimental data and other modeling tools of various resolution.

Heat emitters constitute the primary devices used in space heating and cover a fundamental role in the energy efficient use of buildings. In the search for an optimized design, heating devices should be compared with a benchmark emitter with maximum heat emission efficiency. However, such an ideal heater still needs to be defined. In this paper we perform an analysis of heat transfer in a European reference room, considering room side effects of thermal radiation and computing the induced operative temperature both analytically and numerically. By means of functional optimization, we analyse trends such as the variation of operative temperature with radiator panel dimensions, finding optimal configurations. In order to make our definitions as general as possible, we address panel radiators, convectors, underfloor (UFH) and ceiling heater. We obtain analytical formulas for the operative temperature induced by panel radiators and identify the 10-type as our ideal radiator, while the UFH provides the best performance overall. Regarding specifically UFH and ceiling heaters, we find optimal sizes that identify the according ideal emitters. The analytical method and quantitative results reported in this paper can be generalized and adopted in most studies concerning the efficiency of different heat emitter types in building enclosures.

The tsscds method, recently developed in our group, discovers chemical reaction mechanisms with minimal human intervention. It employs accelerated molecular dynamics, spectral graph theory, statistical rate theory and stochastic simulations to uncover chemical reaction paths and to solve the kinetics at the experimental conditions. In the present review, its application to solve mechanistic/kinetics problems in different research areas will be presented. Examples will be given of reactions involved in photodissociation dynamics, mass spectrometry, combustion chemistry and organometallic catalysis. Some planned improvements will also be described.

Molecular dynamics simulation is currently the theoretical technique eligible to simulate a wide range of systems from soft condensed matter to biological systems. However, of the excellent results that the technique has arrogated, this approach remains computationally expensive, but with the emergence of the new supercomputing technologies bases on graphics processing units graphical processing units-based systems GPUs, the perspective has changed. The GPUs allow performing large and complex simulations at a significantly reduced time. In this work, we present recent innovations in the acceleration of molecular dynamics in GPUs to simulate non-Hamiltonian systems. In particular, we show the performance of measure-preserving geometric integrator in the canonical ensemble, that is, at constant temperature. We provide a validation and performance evaluation of the code by calculating the thermodynamic properties of a Lennard-Jones fluid. Our results are in excellent agreement with reported data reported from literature, which were calculated with CPUs. The scope and limitations for performing simulations of high-throughput MD under rigorous statistical thermodynamics in the canonical ensemble are discussed and analyzed.

This paper presents the latest developments in microCT, both globally and locally, for supporting the additive manufacturing industry. There are a number of recently developed capabilities which are especially relevant to the non-destructive quality inspection of additive manufactured parts; and also for advanced process optimization. These new capabilities are all locally available but not yet utilized to their full potential, most likely due to a lack of knowledge of these capabilities. The aim of this paper is therefore to fill this gap and provide an overview of these latest capabilities, showcasing numerous local examples.

Bell type inequalities are proven using oversimplified probabilistic models and/or counterfactual definiteness (CFD). If setting-dependent variables describing measuring instruments are correctly introduced none of these inequalities may be proven. In spite of this a belief in a mysterious quantum nonlocality is not fading. Computer simulations of Bell tests allow studying different scenarios how the experimental data might have been created. They allow also to generate outcomes of various counterfactual experiments such as repeated or simultaneous measurements performed in different settings on the same ‘’ photon-pair” etc. They allow reinforcing or relaxing CFD- compliance and /or to study the impact of various “photon identification procedures” mimicking those used in real experiments. Using a specific setting- dependent identification procedure data samples consistent with quantum predictions may be generated. It reflects an active role of instruments during the measurement process. Each setting dependent data samples are consistent with specific setting –dependent probabilistic models which may not be deduced using non-contextual local realistic or stochastic hidden variables. In this paper we discuss the results of these simulations. Since the data samples are generated in a locally causal way, these simulations provide additional strong arguments for closing the door on quantum nonlocality

FRAP technique have been used for decades to measure movements of molecules in 2D. Data obtained by FRAP experiments in cell plasma membranes are assumed to be described through means of two parameters, a diffusion coefficient D (as defined in a pure Brownian model) and a mobile fraction M. Nevertheless, it has also been shown that recoveries can be nicely fit using anomalous sub-diffusion. FRAP at variable radii has been developed using the Brownian diffusion model to access geometrical characteristics of the surrounding landscape of the molecule. Here we performed numerical simulations of continuous time random walk (CTRW) anomalous subdiffusion and interpreted them in the context of variable radii FRAP. These simulations were compared to experimental data obtained at variable radii on living cells using the PH domain of the membrane binding protein EFA6 (exchange factor for ARF6, a small G protein). This protein domain is an excellent candidate to explore the structure of the interface between cytosol and plasma membrane in cells. By direct comparison of our numerical simulations to the experiments, we show that this protein does not exhibit anomalous diffusion in BHK cells. The non Brownian PH-EFA6 dynamics observed here is more related to spatial heterogeneities such as cytoskeleton fences effects.

Transient analysis of gas flow in pipeline was studied. Finite Element Method based on ANSYS FLOTRAN was used to account for changes in pressure, temperature and flow rate. Compressibility factor function of temperature and pressure was considered. For non-isothermal transient results, the pressure and the flowrate gave wave propagation as a result of slow transients created by demand condition at the outlet end of custody transfer. Results obtained were in agreement with the demand restrictions at the outlet end of custody transfer indicating that the predictions are accurate and reliable. The results demonstrated that the Finite Element Method gave accurate prediction of pressure, temperature and flowrate in transient gas studies. For steady state non-isothermal model, results showed that the magnitude of the average pressure drop was higher when pressure was predicted with constant compressibility factor, but the same average pressure drop was reduced when the pressure was predicted with variable compressibility factor, z. Since compressibility factor is a function of temperature and pressure, the above findings signifies that in the case when gas temperature does not stabilize, the prediction of pressure with isothermal model and constant compressibility factor will lead to significant errors.

Silicates are among the most abundant and important inorganic materials, not only in the Earth’s crust but also in the interstellar medium in the form of micro-/nano-particles or embedded in the matrices of comets, meteorites and other asteroidal bodies. Although the crystalline phases of silicates are indeed present in Nature, amorphous forms are also highly abundant. Here we report a theoretical investigation of the structural, dielectric and vibrational properties of the amorphous bulk for forsterite (Mg₂SiO₄) as a silicate test case by a combined approach of classical molecular dynamics (MD) simulations for structure evolution, and periodic quantum mechanical DFT calculations for electronic structure analysis. Using classical MD based on an empirical partial charge rigid ionic model within a melt-quenching scheme at different temperatures performed with the GULP 4.0 code amorphous bulk structures for Mg₂SiO₄ were generated using as initial guess the crystalline phase. This has been done for bulks with three different unit cell sizes adopting a super-cell approach; i.e., 1×1×2, 2×1×2 and 2×2×2. The radial distribution functions indicated a good degree of amorphisation of the structures. Periodic B3LYP-geometry optimizations performed with the CRYSTAL14 code on the generated amorphous systems were used to analyze their structure, to calculate their high frequency dielectric constants (ε_∞), and to simulate the IR, Raman and reflectance spectra, which were compared with the experimental and theoretical crystalline Mg₂SiO₄. The most significant changes of the physico-chemical properties of the amorphous systems compared to the crystalline ones are presented and discussed (e.g., larger deviations in the bond distances and angles, broadening of the IR bands, etc.), which are consistent with their disordered nature. It is also shown that by increasing the unit cell size the bulk structures present larger degree of amorphisation.

The classical Rotational Isomeric State (RIS) model, originally proposed by Flory, has been used to rationalize a wide range of physicochemical properties of neutral polymers. However, many weak polyelectrolytes of interest are able to regulate their charge depending on the conformational state of the bonds. Recently, it has been shown that the RIS model can be coupled with the Site Binding (SB) model, for which the ionizable sites can adopt two states: protonated or deprotonated. The resulting combined scheme, the SBRIS model, allows to analyse ionization and conformational equilibria on the same foot. In the present work this approach is extended to include pH-dependent electrostatic Long Range (LR) interactions, ubiquitous in weak polyelectrolytes at moderate and low ionic strengths. With this aim the original LR interactions are taken into account by defining effective Short Range (SR) and pH-dependent parameters, such as effective microscopic protonation constants and rotational bond energies. The new parameters are systematically calculated using variational methods. The machinery of statistical mechanics for SR interactions, including the powerful and fast transfer matrix methods, can then be applied. The resulting technique, to which we will refer as Local Effective Interaction Parameters (LEIP) method, is illustrated with a minimal model of a flexible linear polyelectrolyte containing only one type of rotating bonds. LEIP reproduces very well the pH dependence of the degree of protonation and bond probabilities obtained by semi-grand canonical Monte Carlo simulations, where LR interactions are taken explicitly into account. The reduction in the computational time in several orders of magnitude suggests that the LEIP technique could be useful in a range of areas involving linear weak polyelectrolytes, allowing direct fitting of the relevant physical parameters to the experimental quantities.

Purification of biologically-derived therapeutics is a major cost contributor to the production of this rapidly growing class of pharmaceuticals. Monoclonal antibodies comprise a large percentage of these products therefore new antibody purification tools are needed. Small peptides, as opposed to traditional antibody affinity ligands such as Protein A, may have advantages in stability and production costs. Multiple heptapeptides that demonstrate Fc binding behavior that have been identified from a combinatorial peptide library using M13 Phage Display are presented herein. Seven unique peptide sequences of diverse hydrophobicity and charge were identified. All seven peptides showed strong binding to the four major human IgG isotypes, human IgM, as well as binding to canine, rat, and mouse IgG. These seven peptides were also shown to bind human IgG4 from DMEM cell culture media with 5% FCS and 5 g/L ovalbumin present. These peptides may be useful as surface ligands for antibody detection and purification purposes. Molecular docking and classical molecular dynamics (MD) simulations were conducted to elucidate the mechanisms and energetics for the binding of these peptides to the Fc region. The binding site was found to be located between the two glycan chains inside the Fc fragment. Both hydrogen bonding and hydrophobic interactions were found to be crucial for the binding interactions. Excellent agreement for the binding strength was obtained between experimental results and simulations.

The present work is concerned with the study of the generalized Langevin equation and its link to the physical theories of statistical mechanics and scale relativity. It is demonstrated that the form of the coefficients of Langevin equation depend critically on the assumption of continuity of the reconstructed trajectory. This in turn demands for the fluctuations of the diffusion term to be discontinuous in time. This paper further investigates the connection between the scale-relativistic and stochastic mechanics approaches, respectively, with the study of the Burgers equation, which in this case appears as a stochastic geodesic equation. By further demanding time reversibility of the drift the Langevin equation can also describe equivalent quantum-mechanical systems in a path-wise manner. The resulting statistical description obeys the Fokker-Plank equation of the probability density of the differential system, which can be readily estimated from Monte Carlo simulations of the random paths. Based on the Fokker-Plank formalism a new derivation of the transient probability densities is presented. Finally, stochastic simulations are compared to the theoretical results.

Based on a local causal model of the dynamics of curved discrete spacetime, a causal model of quantum field theory in curved discrete spacetime is described. At the elementary level, space(-time) is assumed to consists of interconnected space points. Each space point is connected to a small discrete set of neighbor space points. Density distribution of the space points and the lengths of the space point connections depend on the distance from the gravitational sources. This leads to curved spacetime in accordance with general relativity. Dynamics of spacetime (i.e., the emergence of space and the propagation of space changes) dynamically assigns "in-connections" and "out-connections" to the affected space points. Emergence and propagation of quantum fields (including particles) are mapped to the emergence and propagation of space changes by utilizing identical paths of in/out-connections. Compatibility with standard quantum field theory (QFT) requests the adjustment of the QFT techniques (e.g., Feynman diagrams, Feynman rules, creation/annihilation operators), which typically apply to three in/out connections, to n > 3 in/out connections. In addition, QFT computation in position space has to be adapted to a curved discrete space-time.

Based on a local causal model of the dynamics of curved discrete spacetime, a causal model of quantum field theory in curved discrete spacetime is described. At the elementary level, space(-time) is assumed to consists of interconnected space points. Each space point is connected to a small discrete set of neighbor space points. Density distribution of the space points and the lengths of the space point connections depend on the distance from the gravitational sources. This leads to curved spacetime in accordance with general relativity. Dynamics of spacetime (i.e., the emergence of space and the propagation of space changes) dynamically assigns "in-connections" and "out-connections" to the affected space points. Emergence and propagation of quantum fields (including particles) are mapped to the emergence and propagation of space changes by utilizing identical paths of in/out-connections. Compatibility with standard quantum field theory (QFT) requests the adjustment of the QFT techniques (e.g., Feynman diagrams, Feynman rules, creation/annihilation operators), which typically apply to three in/out connections, to n > 3 in/out connections. In addition, QFT computation in position space has to be adapted to a curved discrete space-time.

Meta-aminobenzoic acid, an important model system in the study of polymorphism and crystallization of active pharmaceutical ingredients, exist in water in both the nonionic (mABA) and zwitterionic (mABA^±) forms. However, the constituent molecules of the polymorph that crystallizes from aqueous solutions are zwitterionic. This study reports atomistic simulations of the events surrounding the early stage of crystal nucleation of meta-aminobenzoic acid from aqueous solutions. Ab initio molecular dynamics was used to simulate the hydration of mABA± and mABA, and to quantify the interaction of these molecules with the surrounding water molecules. Density functional theory calculations were conducted to determine the low-lying energy conformers of meta-aminobenzoic acid dimers and compute the Gibbs free energies in water of nonionic, (mABA)₂, zwitterionic, (mABA^±)₂ and nonionic-zwitterionic, (mABA)(mABA^±), species. Classical molecular dynamics simulations of mixed mABA–mABA^± aqueous solutions were carried out to examine the aggregation of meta-aminobenzoic acid. According to these simulations the selective crystallization of the polymorph which constituent molecules are zwitterionic is driven by the formation of zwitterionic dimers in solution, which are thermodynamically more stable than (mABA)₂ and (mABA)(mABA^±) pairs. This work represents a paradigm of the role of molecular processes during the early stages of crystal nucleation in affecting polymorph selection during crystallization from solution.

This study presents results of the sediment yield Watershed of Ribeirão do Pinhal, in the city of Limeira, São Paulo, conducted under three different scenarios of the land use: 1 – land use in 2008, 2 – with reforested protection areas, 3 – the increase sugarcane's areas over grassland and citrus areas. The Soil and Water Assessment Tool (SWAT) was used as a hydro-sedimentological modeling tool to simulate these scenarios. This watershed was divided into five sub-watersheds according to the prevalent use, and adjustments were made in soils database parameters and cultures that are in SWAT, to adapt it to the Brazilian reality. Was used climatological data of eight years (2007-2014) for this modeling. Different sediment yield could be noted in the different types of land use, sub-watersheds and scenarios. The uses that presented higher sediment yield, in ascending order, were: natural vegetation, sugarcane, citrus, annual crop e grassland. Sub-watershed number 2 had the highest sediment yield (~10Mg.ha^-1), while the sub-watershed 5, the lowest (5.51Mg.ha^-1). This remained in the three scenarios. Overall, scenario 2 had the lowest sediment yield (7.74Mg.ha^-1). Scenario 1 had 8.37 Mg.ha^-1 and scenario 3, 8.58Mg.ha^-1. SWAT was considered efficient to simulate the sediment yield by scenarios and by use, combining different thematic and tabular data when performing the necessary adjustments on their original database.

Multi-step ahead streamflow forecasting is of practical interest for the operation of hydropower reservoirs. We provide generalized results on the error evolution in multi-step ahead forecasting by conducting several large-scale experiments based on simulations. We also present a multiple-case study using monthly time series of streamflow. Our findings suggest that some forecasting methods are more useful than others. However, the errors computed at each time step of a forecast horizon within a specific case study strongly depend on the case examined and can be either small or large, regardless of the forecasting method used and the time step of interest.

Numerical models widely used for hydrocarbon phase behavior and compositional flow simulations are based on assumption of thermodynamic equilibrium. However, it is not uncommon for oil and gas-condensate reservoirs to exhibit essentially non-equilibrium phase behavior, e.g., in the processes of secondary recovery after pressure depletion below saturation pressure, or during gas injection, or for condensate evaporation at low pressures. In many cases the ability to match field data with equilibrium model depends on simulation scale. The only method to account for non-equilibrium phase behavior adopted by the majority of flow simulators is the option of limited rate of gas dissolution (condensate evaporation) in black oil models. For compositional simulations no practical yet thermodynamically consistent method has been presented so far except for some upscaling techniques in gas injection problems. Previously reported academic non-equilibrium formulations have a common drawback of doubling the number of flow equations and unknowns compared to the equilibrium formulation. In the paper a unified thermodynamically-consistent formulation for compositional flow simulations with non-equilibrium phase behavior model is presented. Same formulation and a special scale-up technique can be used for upscaling of an equilibrium or non-equilibrium model to a coarse-scale non-equilibrium model. A number of test cases for real oil and gas-condensate mixtures are given. Model implementation specifics in a flow simulator are discussed and illustrated with test simulations. A non-equilibrium constant volume depletion algorithm is presented to simulate condensate recovery at low pressures in gas-condensate reservoirs. Results of satisfactory model matching to field data are reported and discussed.

The dynamic behaviour of a machine tool (MT) directly influences the machining performances. The adoption of lightweight structures may reduce the effects of undesired vibrations and increasing the workpiece quality. This paper aims to present and compare a set of hybrid materials that may be excellent candidate to fabricate the MT moving parts. The selected materials have high dynamic characteristics and capacity to damp mechanical vibrations. In this way, starting by the kinematic model of a milling machine that highlights the main critical factors, this study paper evaluates a number of prototypes made of Al Foam sandwiches (AFS), Al Corrugated sandwiches (ACS) and materials reinforced by carbon fibres (CFRP). A set of prototypes has been fabricated, represented the Z-axis ram of a commercial milling machine. The static and dynamical properties have been evaluated by using both FE simulations and experimental tests. The obtained results show that the proposed structures may be a valid alternative to the conventional materials of MT moving parts, increasing machining performances. In particular, the AFS prototype highlighted a damping coefficient that is 20 times greater than a conventional ram (e.g. steel). The CFRP structure is able to satisfy the machining requirements with a reduced weight of 48.5%, while the ACS prototype showed a good trade-off between stiffness and damping.

We explore the possibility of using the external regions of galaxy clusters to measure their mass accretion rate (MAR). The main goal is to provide a method to observationally investigate the growth of structures on the nonlinear scales of galaxy clusters. We derive the MAR by using the mass profile beyond the splashback radius, evaluating the mass of a spherical shell and the time it takes to fall in. The infall velocity of the shell is extracted from N-body simulations. The average MAR returned by our prescription in the redshift range z=[0, 2] is within 20-40% of the average MAR derived from the merger trees of dark matter haloes in the reference N-body simulations. Our result suggests that the external regions of galaxy clusters can be used to measure the mean MAR of a sample of clusters.

In the study of relativistic jets one of the key open questions is their interaction with the environment on the microscopic level. Here, we study the initial evolution of both electron–proton (e^- - p⁺) and electron–positron (e^±) relativistic jets containing helical magnetic fields, focusing on their interaction with an ambient plasma. We have performed simulations of "global" jets containing helical magnetic fields in order to examine how helical magnetic fields affect kinetic instabilities such as the Weibel instability, the kinetic Kelvin-Helmholtz instability (kKHI) and the Mushroom instability (MI). In our initial simulation study these kinetic instabilities are suppressed and new types of instabilities can grow. In the e^- - p⁺ jet simulation recollimation-like instability occurs and jet electrons are strongly perturbed. In the e^± jet simulation a recollimation-like instability occurs at early times followed by a kinetic instability and the general structure is similar to a simulation without helical magnetic field. Simulations using much larger systems are required in order to thoroughly follow the evolution of global jets containing helical magnetic fields.