The aim of this paper is to attempt to understand why the popular academic and policy field of promoting, studying and evangelising “entrepreneurship” should have been associated with great success but, in the past twenty years or more in many advanced economies, so much failure. From the US to lesser and developing countries, emerging economies and the European Union, entrepreneurship, especially in regard to start-ups and particularly high-tech start-ups have been in constant more or less recent decline. This is seldom registered in the mainstream literature where a positive and benign profile is generally presented. The paper examines this phenomenon, ties it partly with the “productivity paradox” and seeks tentative hypotheses in relation to the apparent illusions if not delusions regarding “entrepreneurship”.

HIV-1 assembly is a complex mechanism taking place at the plasma membrane of the host cell. It requires nice spatial and temporal coordination to end up with a full immature virus. Researchers have extensively studied HIV-1 assembly molecular mechanism during the past decades, in order to dissect the respective roles of viral proteins, viral genome and host cell factors. Nevertheless, the time course of the process has been observed in living cells only a decade ago. The very recent revolution of optical microscopy, combining high speed and high spatial resolution now permit to study assemblies and their consequences at the single molecule level within (living) cells. In this review, after a short description of these new approaches, we will show how HIV-1 assembly in cells has been revisited using these advanced super resolution microscopy techniques and how much it could make a bridge in studying assembly from the single molecule to the host cell.

Utility perceived by individuals is believed to be different from the utility experienced by that individual. System dynamicists implicitly categorize this phenomenon as a form of bounded rationality and traditionally employ a simple smoothing function to capture it. We challenge this generalization by testing it against an alternative formulation of utility perception that is suggested by modern theories of behavioral economics. In particular, the traditional smoothing formulation is compared with the peak-end rule in a simple theoretical model as well as in a medium-size model of electronic health record implementation. Experimentation with the models reveals that the way utility perception is formulated is important and might affect behavior and policy implications of system dynamics models.

The coordination planning between land use and transportation system is an important premise of solving urban transportation problems and realizing land use integration. This study investigates the interactive and feedback relationship between land use and transportation system from the perspective of access management. By integrating the land use and traffic data from Las Vegas Metropolitan area with the system dynamics model, the causal relationship and causal loop diagrams (CLDs) are introduced to analyze the cause-and-effect relationship and quantitative relationship between the factors of the combined system of land use and transportation, and then sub-models partition and system simulation are performed. The systems dynamics model is established by analyzing the relationship between a series of access management techniques, traffic characteristics, and land use features. The results show that system dynamics model can be used as an effective alternative to model the symbiosis relationship of land use and transportation system for urban planning and construction.

The molecular dynamics simulation has been used to investigate the structural and transport properties of (Ba_0.5-xSr_x)La_0.5InO_3-δ (x=0, 0.1, 0.2) oxygen-ion conductor. The previous studies reported that the ionic conductivity of Ba-doped LaInO3 decreases because Ba dopant forms narrow oxygen path in the lattice, which could hinder the diffusion of oxygen ion. In this study, we reveal the mechanism to improve the ionic conductivity by Ba and Sr co-doping on La site in LaInO3 perovskite oxide. The results show that the ionic conductivity of (Ba_0.5-xSr_x)La_0.5InO_3-δ increases with increasing numbers of Sr ions, which oxygen diffusion paths including Sr ion have larger critical radius than Ba ions. The RDF calculations showed the heights of peak in composition including Sr ions is lower and broaden, so oxygen ions moved easily into other oxygen sites.

Stratified Taylor Couette Flow (STCF) undergoes transient growth. Recent studies have shown that there exists transient amplification in the linear regime of counter-rotating STCF. It is reported that as Gr increases, the maximum amplification factor ($G_0$) initially decays before it eventually starts growing after reaching a certain critical value Gr$_{c}$. Assuming other parameters of the model are kept constant, the value Gr$_{c}$ changes with respect to different speed ratios of the cylinders. The observed decay/growth pattern of $G_0$ is attributed to the interplay between the induced shear and buoyancy. In this study, the mechanism that triggers this observed pattern is investigated. The kinetic budget of the optimal transient perturbation is analysed numerically to simulate the interaction of the shear production (SP), buoyancy production (BP) and other energy components that contributes to the total optimal transient kinetic energy. These contributions affect the total energy by influencing the perturbation to extract kinetic energy (KE) from the mean flow. The decay of $G_0$ resulted from the positive amplification of both BP and SP, while the growth is attributed to the negative and positive amplification of BP and SP, respectively. The optimal SP is positively amplified, implying that there is the possibility of constant linear growth. These findings agree with the linear growth rate for increasing values of Gr.

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 main objective of this work is to study the effects of carbon nanotubes (CNT) on the strength and electrical properties of cement mortar. Molecular dynamic simulations (MDS) were carried out for the mechanical and electrical properties of the cementitious composite and the associated mechanisms. To model the atomic structure of the Calcium-Silicate-Hydrates (C-S-H) gel, tobermorite 11Å was chosen. Single-walled carbon nanotubes (SWCNTs) embedded in tobermorite structure were tested numerically. In particular, the effect of the concentration of CNT in cement paste was studied. An innovative experiment of electrical characterization of a cementitious composite of carbon nanotubes has been developed.

Experimental test facilities are generally characterised using linear transfer functions to relate the wavemaker forcing amplitude to wave elevation at a probe located in the wavetank. Second and third order correction methods are becoming available but are limited to certain ranges of waves in their applicability. Artificial intelligence has been shown to be a suitable tool to find even highly nonlinear functional relationships. This paper reports on a numerical wavetank implemented using the OpenFOAM software package which is characterised using artificial intelligence. The aim of the research is to train neural networks to represent non-linear transfer functions mapping a desired surface-elevation time-trace at a probe to the wavemaker input required to create it. These first results already demonstrate the viability of the approach and the suitability of a single setup to find solutions over a wide range of sea states and wave characteristics.

Let f : V → V be a Cohomological Expanding Mapping¹ of a smooth complex compact homogeneous manifold with $ dim_{\mathbb{C}}(\Vc)=k \ge 1$ and Kodaira Dimension $\leq 0$. We study the dynamics of such mapping from a probabilistic point of view, that is, we describe the asymptotic behavior of the orbit $ O_{h} (x) = \{h^{n} (x), n \in \mathbb{N} \quad \mbox{or}\quad \mathbb{Z}\}$ of a generic point. Using pluripotential methods, we have constructed in our previous paper \cite{Armand4} a natural invariant canonical probability measure of maximal Cohomological Entropy $ \nu_{h} $ such that ${\chi_{2l}^{-m}} (h^m)^\ast \Omega \to \nu_h \qquad \mbox{as} \quad m\to\infty$ for each smooth probability measure $\Omega $ in $\Vc$ . We have also studied the main stochastic properties of $ \nu_{h}$ and have shown that $ \nu_{h}$ is a smooth equilibrium measure , ergodic, mixing, K-mixing, exponential-mixing. In this paper we are interested on equidistribution problems and we show in particular that $ \nu_{h}$ reflects a property of equidistribution of periodic points by setting out the Third and Fourth Main Results in our study. Finally we conjecture that $$\nu_h:=T_l^+ \wedge T_{k-l}^-,$$ $$\dim_\HH(\nu_h)= \Psi h_{\chi}(h) , $$ $$\dim_\HH( \mbox{Supp} T_l^+) \geq 2(k-l) + \frac{\log \chi_{2l}}{\psi_l},$$ $$|\langle \nu_m^x-\nu_h,\zeta\rangle|\leq M \Big[1+\log^+{1\over D(x,\Tc)}\Big]^{\beta/2}\|\zeta\|_{\Cc^\beta} \gamma^{-\beta m/2}$$ and $$|\langle \nu_m^x-\nu_h,\zeta\rangle|\leq M \Big[1 +\log^+{1\over D(x,E_\gamma)}\Big]^{\beta/2}\|\zeta\|_{\Cc^\beta} \gamma^{-\beta m/2}.$$

Let $f:V\rightarrow V $ be a Cohomological Expanding Mapping¹ of a smooth complex compact homogeneous manifold with dim_C(V) = k ≥ 1 and Kodaira Dimension $\leq 0$. We study the dynamics of such mapping from a probabilistic point of view, that is, we describe the asymptotic behavior of the orbit $ O_{f} (x) = \{f^{n} (x), n \in \mathbb{N} \quad \mbox{or}\quad \mathbb{Z}\}$ of a generic point. Using pluripotential methods, we construct a natural invariant canonical probability measure of maximum Cohomological Entropy $ \mu_{f} $ such that ${\chi_{2l}^{-m}} (f^m)^\ast \Omega \to \mu_f \qquad \mbox{as} \quad m\to\infty$ for each smooth probability measure $\Omega $ on V . Then we study the main stochastic properties of $ \mu_{f}$ and show that $ \mu_{f}$ is a measure of equilibrium, smooth, ergodic, mixing, K-mixing, exponential-mixing and the unique measure with maximum Cohomological Entropy. We also conjectured that $\mu_f:=T_l^+ \wedge T_{k-l}^-$, $\dim_\H(\mu_f)= \Psi h_{\chi}(f) $ and $\dim_\H( \mbox{Supp} T_l^+) \geq 2(k-l) + \frac{\log \chi_{2l}}{\psi_l}.$

The combination of wet-lab experimental data on multi-site combinatorial mutations and machine learning is an innovative method in protein engineering. In this study, we present an improved innovative sequence–activity relationship (innov'SAR) methodology based on novel descriptors and digital signal processing (DSP) to construct a predictive model. In this improved approach, 21 experimental (R)-selective amine transaminases from Aspergillus terreus (AT-ATA) were used as an input to predict higher thermostability than that predicted using the existing data. We successfully improved the determination coefficient (R2) of the model from 0.66 to 0.92. In addition, root mean square deviation (RMSD) and root mean square fluctuation (RMSF) were estimated and conformation analysis based on molecular dynamics simulations was performed to verify the enhanced thermal stability of the screened mutants. The improved innov'SAR algorithm enhanced the predictive accuracy, suggesting a method for modifying the stability of AT-ATA, which may help in directed evolutionary screening and open up new avenues for protein engineering.

: Arboviruses transmitted by Aedes aegypti and Ae. albopictus have been introduced to Florida on many occasions. Infrequently, these introductions lead to sporadic local transmission and, more rarely, sustained local transmission. Both mosquito species are present in Florida, with spatio-temporal variation in population composition. We developed a 2-vector compartmental, deterministic model to investigate factors influencing Chikungunya virus (CHIKV) establishment. The model includes a non-linear, temperature-dependent mosquito mortality function based on minimum mortality in a central temperature region. Latin Hypercube sampling was used to generate parameter sets used to simulate transmission dynamics, following the introduction of one infected human. The analysis was repeated for 3 values of the mortality function central temperature. Mean annual temperature was consistently important in the likelihood of epidemics, and epidemics increased as the central temperature increased. Ae. albopictus recruitment was influential at the lowest central temperature while Ae. aegypti recruitment was influential at higher central temperatures. Our results indicate that the likelihood of CHIKV establishment may vary, but overall Florida is permissive for introductions. Model outcomes were sensitive to the specifics of mosquito mortality. Mosquito biology parameters are variable, and improved understanding of this variation will improve our ability to predict the outcome of introductions.

COVID-19 appeared as an infectious disease of global health emergency and the highest public health concern of 21st century for this world due to its high-speed of spread across the globe. The disease started as one single case to a cluster of cases in Wuhan, China (Dec 2019) and within few months with its continuous upsurge of cases spreading globally which has created enormous threat and tension across the global Public health care field. Most significantly to share the fact that, this disease caused high level of Risk Group mortality, high morbidity, health care services burden, panic anxiety, mental trauma and tension, social and economic insecurity, which also collectively surfaced by diverse range of social reaction and political pressure across the world. Also with the appearance of new and unknown pathogenesis of the disease has created the most and significant attention and concern for the scientific community and political leaders as well. The disease also varies much with its pattern of virus, sign, symptoms, characteristics including its epidemiological and public health response (like prevention strategy, diagnoses, case management, treatment pattern) across the countries. However, this variance is comparatively less rather even more in commonality while it comes to basic public health prevention interventions like frequent hand washing, wearing face mask, maintaining social/physical distancing (2 - 6 meter in between), individual isolation and community quarantine for suspected exposure and lockdown in community areas where cases are identified. These are with the most commonly practiced public health interventions to deal with this disease in majority of the epicenters across countries. Also with the progress of the disease with its diverse categorical appearance of sign symptoms which are uniquely portraying this disease is more of a kind of COVID-19 syndrome than as COVID-19. Moreover, various factors including socio economic status, health status, population dynamics, health system and infrastructure, health behavioral pattern, nutrition and food habit and access to information and knowledge made this viral disease one of the historically counted on expensive disease of the modern world to fight for. Specially to mention here, the case fatality rate distinctively vary with the population dynamics and the health system infrastructure and ability factors which have already created clear evidence as explained in this paper how these factors are uniquely distinguished and different from country to country. Apart from the contextual differences, the various kind of ongoing preventive measures (like prevention, diagnosis and treatment) learnt every day from the emerging characteristics and pattern of this viral disease which are most commonly practiced across countries with a variance. According to the Public health prevention practice and interventions, the total world is connected and learning from each other’s public health experiences to fight for the virus. However, the world communities are eagerly waiting to see the result and outcome of the ongoing therapeutics and vaccine trial initiated in several countries, the people of the world are quite optimistic and hopeful that, global scientific community will be able to invent some miraculous and magic solution in upcoming months which ultimately will free the world from this most terrifying COVID-19 pandemic of 21st century.

In this paper we develop from first principles a unique law pertaining to the flow of fluids through closed conduits. This law, which we call “Quinn’s Law”, may be described as follows: When fluids are forced to flow through closed conduits under the driving force of a pressure gradient, there is a linear relationship between the normalized dimensionless pressure gradient, P_Q, and the normalized dimensionless fluid current, C_Q. The relationship is expressed mathematically as: P_Q = k₁ +k₂C_Q. This linear relationship remains the same whether the conduit is filled with or devoid of solid obstacles. The law differentiates, however, between a packed and an empty conduit by virtue of the tortuosity of the fluid path, which is seamlessly accommodated within the normalization framework of the law itself. When movement of the fluid is very close to being at rest, i.e., very slow, this relationship has the unique minimum constant value of k₁, and as the fluid acceleration increases, it varies with a slope of k₂ as a function of normalized fluid current. Quinn’s Law is validated herein by applying it to the data from published classical studies of measured permeability in both packed and empty conduits, as well as to the data generated by home grown experiments performed in the author’s own laboratory.

Modeling brain dynamics to better understand and control complex behaviors underlying various cognitive brain functions are of interests to engineers, mathematicians, and physicists from the last several decades. With a motivation of developing computationally efficient models of brain dynamics to use in designing control-theoretic neurostimulation strategies, we have developed a novel data-driven approach in a long short-term memory (LSTM) neural network architecture to predict the temporal dynamics of complex systems over an extended long time-horizon in future. In contrast to recent LSTM-based dynamical modeling approaches that make use of multi-layer perceptrons or linear combination layers as output layers, our architecture uses a single fully connected output layer and reversed-order sequence-to-sequence mapping to improve short time-horizon prediction accuracy and to make multi-timestep predictions of dynamical behaviors. We demonstrate the efficacy of our approach in reconstructing the regular spiking to bursting dynamics exhibited by an experimentally-validated 9-dimensional Hodgkin-Huxley model of hippocampal CA1 pyramidal neurons. Through simulations, we show that our LSTM neural network can predict the multi-time scale temporal dynamics underlying various spiking patterns with reasonable accuracy. Moreover, our results show that the predictions improve with increasing predictive time-horizon in the multi-timestep deep LSTM neural network.

Electrostatic interactions have a determining role in conformational and dynamic behavior of polyelectrolyte molecules [1]. In this study, anionic polyelectrolyte molecules, poly(glutamic acid) (PGA) and poly(aspartic acid) (PASA), in water solution with the most commonly used K+ or Na+ counterions were investigated using atomistic molecular dynamics (MD) simulations. Seven common force fields, AMBER99SB-ILDN, AMBER14SB, AMBER-FB15, CHARMM22*, CHARMM27, CHARMM36m and OPLS-AA/L, both with their native parameters and with the non-bonded fix (NBFIX) and electronic continuum corrections (ECC) to were studied. These corrections have bene introduced to correct for the problem of overbinding of ions to the charged groups of polyelectrolytes. Physical properties, such as molecular sizes, local structure and dynamics, were studied using two types of common counterions, potassium and sodium. The results show that in some cases, the macroion size and dynamics depend strongly on the models (parameters) for the counterions due to strong overbinding of ions and charged side chain groups. The local structures and dynamics are more sensitive on dihedral angle parameterization resulting in a preference for defined monomer conformations amd the type of correction used.

Most fully developed galaxies have vivid spiral structure, but the formation and evolution of spiral structure is still a mystery that is not fully understood in astrophysics. We find that the currently used equations of galactic dynamics contain some unreasonable components. In this paper, the following three working assumptions are introduced to simplify the galactic structural equations. 1. In the research of large-scale structure, the retarded potential of the gravitational field should be taken into account. The propagating time of the gravitational field from center to border is longer than the revolution periods of the stars near the center of galaxy. Newton's gravitational potential is unreasonable for such case, and the weak field and low velocity approximation of Einstein's field equation should be adopted. 2. The stars in a fully developed galaxy should be zero-pressure and inviscid fluid, and the equation of motion is different from that of ordinary continuum mechanics. Stars move along geodesics. 3. The structure of the galaxy is only related to the total mass density distribution. The equation of state of dark halo is different from that of ordinary luminous interstellar matter, so their trajectories are also very different. Dark halo and ordinary matter in galaxy are automatically separated. The total mass density distribution can be presupposed according to the observation data, and then it can be determined by comparing the solution of the equations with the observed data. These assumptions and treatments are supported by theory and observation. The variables of the equations of simplified galactic dynamics are separated from each other, and the equations are well-posed and can be solved according to a definite procedure. Therefore, this simplified dynamic equation system provides a more reasonable and practical framework for the further study of galactic structure, and can solve many practical problems. Besides, it is closely related to the study of dark energy and dark matter.

I present an experimental paradigm to explore the interpersonal dynamics generating a collective mind. I hypothesized that collective organization is based on dual interpersonal modes: (1) symmetrical and (2) anti‑symmetrical. I specified the geometric topology of these modes by detecting the spatiotemporal patterns that embed cooperative agents in a three‑dimensional matrix. I found that the symmetrical mode is executed automatically and without guidance. Conversely, the anti‑symmetrical mode required explicit direction and recruited attention for execution. I demonstrate that self‑other mirror‑symmetry stabilized group dynamics, enabled fast and efficient symmetrical imitation that optimized information transmission, whereas anti‑symmetrical imitation was comparatively slow, inefficient, and unstable. I determined that the anti‑symmetrical mode spontaneously transitioned to the symmetrical mode under perturbations. Crucially, this renormalization mechanism never transitioned from symmetrical to anti‑symmetrical. These self-organizing dynamics speak to interpersonal symmetry‑breaking. In the present work, spontaneous group choice mandated that agents synchronize cooperative cycles in symmetrical space under internal or external perturbations. I provide examples to illustrate that this self-regulating pullback attractor manifests in invertebrates and vertebrates alike. I conclude by suggesting that inter‑agent symmetry provides the social stability manifold through which attention-driven interactions enable intrapersonal and interpersonal change.

Zinc finger proteins (ZFP) play important roles in cellular processes. The DNA binding region of ZFP consists of 3 zinc finger DNA binding domains connected by amino acid linkers, the sequence TGQKP connects ZF1 and ZF2, and TGEKP connects ZF2 with ZF3. Linkers act to tune the zinc finger protein in the right position to bind its DNA target, the type of amino acid residues and length of linkers reflect on ZF1-ZF2-ZF3 interactions and contribute to the search and recognition process of ZF protein to its DNA target. Linker mutations and the affinity of the resulting mutants to specific and nonspecific DNA targets were studied by MD simulations and MM_GB(PB)SA. The affinity of mutants to DNA varied with type and position of amino acid residue. Mutation of K in TGQKP resulted in loss in affinity due to the loss of positive K interaction with phosphates, mutation of G showed loss in affinity to DNA, WT protein and all linker mutants showed loss in affinity to a nonspecific DNA target, this finding confirms previous reports which interpreted this loss in affinity as due to ZF1 having an anchoring role, and ZF3 playing an explorer role in the binding mechanism. The change in ZFP-DNA affinity with linker mutations is discussed in view of protein structure and role of linker residues in binding.

Asymmetric lithium salts, such as Lithium (difluoromethanesulfonyl)(trifluoromethanesulfonyl)imide (LiDFTFSI), have been demonstrated to surpass traditional symmetric lithium salts with improved Li+ conductivity and the capacity to generate stable solid electrolyte interphase (SEI) while maintaining compatibility with aluminum (Al0) current collector. However, the intrinsic reductive mechanism through which LiDFTFSI influences battery performance remains unclear and under debate. Herein, the detailed SEI reactions of LiDFTFSI-based electrolytes were investigated by combining density functional theory and molecular dynamics, aiming to clarify the formation process and atomic structure of SEI. Our results show that asymmetric DFTFSI– weakens the interaction between carbonate solvents and Li+, and substantially alter the solvation structure, exhibiting a well-balanced coordination capacity to bis(trifluoromethanesulfonyl)imide (TFSI–). Nanoseconds hybrid molecular dynamics simulation further reveals that the preferential decomposition of LiDFTFSI produces sufficient LiF and Li2O to facilitate a robust SEI. Moreover, the abundant F– generated from LiDFTFSI decomposition accumulates on the Al surface and subsequently combines with Al3+ from the current collector to form AlF3, potentially inhibiting corrosion of the current collector. Overall, these findings elucidate how LiDFTFSI regulates the solvation sheath and SEI structure, advancing the development of high-performance electrolytes compatible with current collector.

Matrix Metaloproteinase-2 (MMP-2) is an extracellular Zn²⁺ protease specific to type I and IV collagens. Its expression is associated with several inflammatory, degenerative, and malignant diseases. Conformational properties, domain movements, and interactions between MMP-2 and its associated metal ions were characterized using a 1.0 µs molecular dynamics simulation. Dihedral principle component analysis revealed 10 families of conformations with the greatest degree of variability occurring in the link region connecting the catalytic and hemopexin domains. Dynamics cross correlation analysis indicated domain movements corresponding to opening and closing of the hemopexin domain in relation to the fibronectin and catalytic domains facilitated by the link region. Interaction energies were calculated using the MMPBSA-interaction entropy analysis method and revealed strong binding energies for the catalytic Zn²⁺ ion 1, Ca²⁺ ion 1, and Ca²⁺ ion 3 with significant conformational stability at the binding sites of Zn²⁺ ion 1 and Ca²⁺ ion 1. Ca²⁺ ion 2 diffuses freely away from its crystallographically defined binding site. Zn²⁺ ion 2 plays a minor role in conformational stability of the catalytic domain while Ca²⁺ ion 3 is strongly attracted to the highly electronegative sidechains of the Asp residues around the central β-sheet core of the hemopexin domain.

A computational simulation of a PT6A gas turbine engine operating at off-design conditions is described in the present article. The model consists of a 0-dimensional thermo-fluidic description of the engine by applying the mass, linear momentum, angular momentum, and energy balances in each engine's component. The transient behavior of the engine is simulated for different blends of the original JET-A1 fuel with bio-diesel. Simulated thermodynamic variables of the air at each engine's component, as well as some performance parameters correspond to the reported experimental measurements. The numerical results also demonstrate the ability of the computational simulation to predict acceptable fuel blends, such that the efficiency of the engine is maximized and its structural integrity is maintained.

The present study shows a methodology for analyzing and designing a cylindrical packed-bed reactor considering stationary and dynamic models. The design comprises the reactor's stationary and dynamic governing differential equations for mass and heat transfer under multi-dimensional approaches. The results included simulation of concentration, temperature, and reaction rate profiles via the 1-D and 2-D differential equations solution with FlexPDE software. The analysis was complemented with a scaled 3-D dynamic model implemented in COMSOL Multiphysics. Both FlexPDE and COMSOL Multiphysics relied on the finite element technique to solve the governing differential equations. The simulated concentration and temperature profiles from both FlexPDE and COMSOL models were compared to experimental data gathered from literature (specifically from a Fischer-Tropsch process to produce low-molecular-weight hydrocarbons in a configuration of cylindrical packed-bed reactors). Simulated concentration and temperature profiles from the 2-dimensional dynamic model and the COMSOL model were in good agreement with the trend observed in experimental data. Finally, the predicted reaction rate profiles from the COMSOL model and the 2-dimensional dynamic model followed the temperature trend, thus reflecting the temperature dependence of the reaction.

We performed for the first time to our knowledge fully ab initio molecular dynamics simulations of additive tribochemistry in boundary lubrication conditions. We consider an organophosphourus additive that has been experimentally shown to reduce friction in steel-on-steel sliding contacts thanks to the tribologically-induced formation of an iron phosphide tribofilm. The simulations allow us to observe in real time the molecular dissociation at the sliding iron interface under pressure and to understand the mechanism of iron phosphide formation. We discuss the role played by the mechanical stress by comparing the activation times for molecular dissociation observed in the tribological simulations at different applied loads with that expected on the basis of the dissociation barrier.

This paper numerically investigates a 3D mesh independency study of a straight blade horizontal axis tidal turbine modelled using Computational Fluid Dynamics (CFD). The solution was produced by employing two turbulence models, the standard k-ε model and Shear Stress Transport (SST) in ANSYS CFX. Three parameters were investigated: mesh resolution, turbulence model, and power coefficient in the initial CFD, analysis. It was found that the mesh resolution and the turbulence model affect the power coefficient results. The power coefficients obtained from the standard k-ε model are 15% to 20% lower than the accuracy of the SST model. It can also be demonstrated that the torque coefficient increases with the increasing Tip Speed Ratio (TSR), but drops drastically after TSR = 5 and k-ε model failing to capture the non-linearity in the torque coefficient with the increasing TSR.

In order to perceive the behavior presented by the multiphase chemical reactors, the ant colony optimization algorithm was combined with computational fluid dynamics (CFD) data. This intelligent algorithm creates a probabilistic technique for computing flow and it can predict various levels of three-dimensional bubble column reactor (BCR). This artificial ant algorithm is mimicking real ant behavior. This method can anticipate the flow characteristics in the reactor using almost 30 % of the whole data in the domain. Following discovering the suitable parameters, the method is used for predicting the points not being simulated with CFD, which represent mesh refinement of Ant colony method. In addition, it is possible to anticipate the bubble-column reactors in the absence of numerical results or training of exact values of evaluated data. The major benefits include reduced computational costs and time savings. The results show a great agreement between ant colony prediction and CFD outputs in different sections of the BCR. The combination of ant colony system and neural network framework can provide the smart structure to estimate biological and nature physics base phenomena. The ant colony optimization algorithm (ACO) framework based on ant behavior can solve all local mathematical answers throughout 3D bubble column reactor. The integration of all local answers can provide the overall solution in the reactor for different characteristics. This new overview of modelling can illustrate new sight into biological behavior in nature.

The buildup dynamics of diode-pumped passively mode-locked solid-state laser is thoroughly explored by the real-time measurement with temporal sampling rate up to 40 GHz. A concise cavity is developed to ensure the transient dynamics purely arising from the gain medium and saturable absorber. Experimental results reveal that the laser output in the buildup process exhibits numerous passively Q-switched pulses followed with a damped relaxation oscillation prior to the stable mode locking. Furthermore, it is confirmed that the laser output has already displayed single clean mode-locked pulses inside the first several Q-switched envelopes before stepping into the stage of relaxation oscillation. The present real-time exploration is expected to provide important information for practical applications with temporal modulation of the pump intensity.

The airborne inoculum of Fusarium circinatum, the fungal pathogen causing Pine Pitch Canker (PPC), is one of the main means of spread of the disease in forest stands and forest nurseries. Since this world-wide known pathogen was introduced in Europe, its biology in this newly infected area still remains scarcely known. To shed more light on this topic, we set an experiment on a naturally PPC infected forest of Monterey pine in Galicia (NW Spain) with the following two goals: (i) to describe the seasonal spore dispersal pattern during one year of regular sampling and (ii) to assess the spatial spore dispersal pattern around the infested plot. Portable rotating arm spore traps were used and complemented with meteorological measurements. The abundance of F. circinatum spores in the samples was evaluated by quantitative PCR (qPCR) with hydrolysis probe. The results showed almost permanent occurrence of the air inoculum throughout the whole year, being detected in 27 of the 30 samplings. No clear temporal trends were observed, but higher air inoculum was favoured by previous lower air temperatures and lower leaf wetness. Conversely, neither rainfall nor air humidity seemed to have any significant importance. The spatial spread of the inoculum was noted to be successful up to a distance of 1000 m in the wind direction, even with winds of just 5 m s^-1. Our study shows that rotating arm spore traps combined with qPCR may be an efficient tool for F. circinatum detection.

We used population reconstruction techniques to assess for the first time the population dynamics of a seagrass, Cymodocea nodosa, exposed to long-term elevated CO₂ near three volcanic seeps and compare them with reference sites away from the seeps. Under high CO₂, the density of shoots and of individuals (apical shoots), and the vertical and horizontal elongation and production rates, were higher. Nitrogen effects on rhizome elongation and production rates and on biomass, were stronger than CO₂ as these were highest at the location where the availability of nitrogen was highest. At the seep where the availability of CO₂ was highest and nitrogen lowest, density of shoots and individuals were highest, probably due to CO₂ effects on shoot differentiation and induced reproductive output, respectively. In all three seeps there was higher short- and long-term recruitment and growth rates around zero, indicating that elevated CO₂ increases the turnover of C. nodosa shoots.

Background: Understanding the factors that influence the market entry, exit, and stability of community pharmacies (i.e., market dynamics) is important for stakeholders ranging from patients to health policymakers and small business owners to large corporate institutions. The purpose of this article is to provide an update to a 15-year ecological comparison for the market dynamics of Minnesota community pharmacies from 2002 to 2017 [1]. Objectives: The first objective was to update the 15-year study [1] by describing the market dynamics of community pharmacies for each county in the state of Minnesota every five years over a 20-year period (i.e., 2002-2022). The second objective was to update the 15-year study by describing the number and proportion of community pharmacies for each county in the state of Minnesota every five years over a 20-year period (i.e., 2002-2022) by (1) ‘Business Organization Structure’ and (2) ‘Pharmacy Type.’ The third and fourth objectives were new for the 2022 study. In response to evolutionary trends in the pharmacy market, objective three described the number of Minnesota licensed pharmacies located in-state and out-of-state between 2002 and 2022. Objective four described the primary type of service provided by licensed pharmacies categorized as out-of-state in 2002 and in 2022. Methods: Data were obtained from the Minnesota Board of Pharmacy, US Census Bureau, and Minnesota State Demographic Center for 2002, 2007, 2012, 2017, and 2022. Descriptive statistics were used to tabulate and summarize the findings and test associations between study variables. Results: Over the 20-year study period, the total number of community pharmacies in Minnesota remained steady. Findings for 2022 were similar to those for 2017 regarding the effects of population density and metropolitan designation on the market dynamics of community pharmacies and regarding the organizational structures and types of pharmacies. The findings revealed significant growth in the number of proportion of pharmacies licensed in Minnesota that were located out-of-state. In 2002, there were 283 of these pharmacies (19% of the total). By 2022, this grew to 960 (46% of the total). Over that 20-year period, the number of mail order and medical supply service pharmacies rose from 196 to 413. The number of specialty pharmacy distributors rose from 37 to 230 and the number of compounding pharmacies rose from 33 to 202. Discussion: The findings confirmed the shift over the past 20 years from traditional retail convenience models to healthcare access models based on population health metrics. National scalability was another detected shift in order to have profitable margins for some services and was feasible due to advances in technologies. Conclusion: The findings showed that community pharmacy distribution in Minnesota’s 87 counties shifted between 2002 and 2022 from traditional retail convenience models to healthcare access models based on population health metrics and to nationally scalable models based on economic pressures. This signals the need for not only new approaches for tracking community pharmacy market dynamics but also adjustments by community pharmacies to remain relevant in a new environment of patient care services.

The adsorption of proteins on polymer is widely used in biosensors. Here, molecular dynamics (MD) simulation was used to study the immobilization of angiotensin converting enzyme II (ACE2) with six initial orientations proposed on polystyrene (PS) at the ambient conditions of pH (4.5, 6, 7, 8, 9.5) and NaCl (0.01, 0.05, 0.1, 0.15, 0.2, 0.25 M). ACE2 immobilization under favorable ambient conditions was characterized by minimum distance (short), settlement time (fast), interaction energy (substantial) and protein configuration (stable). ACE2 orientations proposed in 0.15M NaCl were respectively preferable to (90, 0, 0), (0, 0, 0) and (0, 270, 0), (180, 0, 0) and (0, 90, 0), (90, 0, 0) at pH 4.5, 6, 7, 9.5. ACE2 immobilization was further evaluated at pH 7 by optimizing NaCl concentration. Its proposed orientations of (i) (0, 270, 0), (ii) (0, 0, 0) and (90, 0, 0), and (iii) (0, 90, 0) and (90, 0, 0) were preferable in 0.05, 0.1 and 0.2 M NaCl, respectively. The great significance of cubic-orientation settlement mode provides tangible improvement for the microfabrication of biochips for rapid diagnosis of severe acute respiratory syndrome coronavirus II (SARS-CoV-2).

In this research, the computational fluid dynamic (CFD) approach that has been used in wind power generation field was applied for the solution of the problems of local strong wind areas in railway fields, and the mechanism of wind generation was discussed. At the same time, the affectivity of the application of computational fluid dynamic approach to railway field was discussed. The problem of local wind that occurs on the railway line in winter was taken up in this research. A computational simulation for the prediction of wind conditions by LES was implemented and it was clarified that the local strong wind area is mainly caused by separated flows originating from the small‐scale terrain positioned at its upstream (at approximately 180.0 m above sea level). Meanwhile, the effects of the size of calculation area and spatial grid resolution on the result of calculation and the effect of atmospheric stability were also discussed. It was clarified that when the air flow characteristic of the separated flow originating from the small‐scale terrain (at altitude of approximately 180.0 m) targeted in this research is reproduced at high accuracy by computational simulation of wind conditions, approximately 10.0 m of spatial resolution of computational grid in horizontal direction is required. As a result of the computational simulation of wind conditions of stably stratified flow (Fr = 1.0), lee waves were excited at the downstream of the terrain over time. As a result, the reverse‐flow region lying behind the terrain that had been observed at a neutral time was inhibited. Consequently, local strong wind area was generated at the downstream of the terrain and the strong wind area passing through the observation mast was observed. By investigating the speed increasing rate of local strong wind area induced at the time of stable stratification, it was found that the wind was approximately 1.2 times stronger than what was generated at a neutral time.

Molecular dynamics(MD) simulations are carried out to characterize the mechanicalproperties and failure behavior of van der Waals heterostructures composed ofgraphene and hexagonal boron nitride(hBN) single layer sheets. The graphene–hBNand hBN–graphene–hBN heterostructures simulations are carried out under tensileand shear deformation. Accordingly, stress versus strain curves of each systemare plotted and various properties of heterostructures, namely elastic modulusand shear modulus as well as failure stress and failure strain, are evaluatedand compared with one another as well as with the pristine graphene and hBNsheets. Subsequently, the failure mechanism/characterization of each sheet in theheterostructures is described. Alternatively, the elastic and shear modulus of eachheterostructure are computed by means of rule of mixture(ROM) which are in goodagreement with results that are obtained from MD simulations.

In this age of mass media and, in particular, social media-driven perception of reality, coupling disease and prophylactic opinion dynamics models can provide better insights into disease evolution than using a disease model alone. We develop in this work two disease-opinion dynamics models based on the epidemiology of the new coronavirus disease (COVID-19) and the availability or not of imperfect vaccines. We assume that susceptibility to infection decreases with the level of prophylactic attitude (personal hygiene, social distancing), and changes in prophylactic attitudes of susceptible individuals occur in response to perceived disease prevalence and vaccination coverage and efficacy in the population. We derive and discuss the disease-free equilibriums and reproduction numbers in the introduced models. We further assess the impacts of the distribution of opinions at disease introduction, the ability to detect presymptomatic, asymptomatic and symptomatic positive COVID-19 cases, the behavioural responses to the outbreak and the introduction of vaccination, and the effects of distortions of disease prevalence by public policy and mass media on disease dynamics. The insights highlighted from the proposed models are expected to make informative contributions to public policy in a context of opinion fluxes in response to perceived disease prevalence.

Regeneration is crucial for forest continuity in natural and managed stands. Analyzing intra-annual dynamics improves the understanding between growth and climate, identifying survival thresholds. The objective was to determine microclimate constraints (rainfall, air and soil temperatures) over Nothofagus antarctica regeneration growing at closed, open, and edge forests in Patagonia. We measured stand characteristics (forest structure, understory, soil properties, animal use), microclimate, and daily growth of regeneration using dendrometers (n = 6) during two growing seasons. We found significant differences in the studied variables (e.g. overstory, light, soil, understory, animal use). These changes defined microclimate across overstory gradient (e.g. soil moisture), influencing the daily growth across seasons (lag, exponential, stationary). Rainfall influenced more than temperature. Daily growth in closed forests indicating shrinkage (-0.0082 mm day-1 without rain, and -0.0008 mm day-1 with 0.0-0.2 mm day-1 rainfall), while above 0.2 mm day-1 rainfall, growth always increased. Open forests presented shrinkage during days without rain (-0.0051 mm day-1), showing positive growths according rainfall. Edge forests always presented positive daily growths. The resilience of regeneration under these changed conditions was related with overstory. Main outputs indicated that regeneration was vulnerable during non-rainy days, suggesting the needs of long-term monitoring to develop better silvicultural proposals.

The hyper-arid environment is characterized by high inter-annual climatic fluctuations. The yearly average rainfall can change substantially for several years, forming wet or dry sub-periods. Observing rainfall trends over a sub-period can lead to a false perception of a change in the trend but may in fact represent a periodic cycle when examined on a larger time scale. We aimed to better characterize the rainfall regime prevailing in the hyper-arid Arava Valley (Israel/Jordan), and to examine the response of vegetation to annual rainfall. We hypothesized that annual and perennial vegetation would respond differently to wet and dry sub-periods, and that grazing activities will impact vegetation growth. We used a time series of monthly rainfall, from which we calculated Standard Precipitation Index (SPI), and calculated proxies of perennial and annual vegetation over the last four decades using Landsat-derived Normalized Difference Vegetation Index (NDVI). We found no clear trend in rainfall amounts during this period, however we did identify wet and dry sub-periods which were statistically distinct in rain and in vegetation patterns from each other. The highest levels of correlation between rainfall and the NDVI derived proxies were found when examining average rainfall over a period of two- three years for the annual vegetation and over four years for perennial vegetation. Using the Mann-Kendall test, we identified a time lag of two to four years, with the proxies of annual vegetation responding faster than the proxies of perennial vegetation, to shifts between wet and dry sub-period. In addition, we found a consistent difference between natural vegetation cover in Jordan (grazed) and Israel (non-grazed), favoring the development of natural vegetation on the Israeli side. We conclude that integrating between long-term remote sensing satellite imagery and climatic records revealed the greater resilience of perennial vegetation in the hyper-arid region to climatic fluctuation, and enabled us to identify the vegetation’s sensitivity to anthropogenic impact.

Plant life-long organogenesis involves sequential, time and tissue specific expression of developmental genes. This requires activities of Polycomb Group (PcG) and trithorax Group complexes, respectively responsible for repressive Histone 3 trimethylation at lysine 27 (H3K27me3) and activation-related H3K4me3. However, the genome-wide dynamics in histone modifications that occur during developmental processes have remained elusive. Here, we report the distributions of H3K27me3 and H3K4me3 along with transcriptional changes, in a developmental series including Arabidopsis leaf and three stages of flower development. We found that chromatin mark levels are highly dynamic over the time series on nearly half of all Arabidopsis genes. Moreover, during early flower morphogenesis, changes in H3K4me3 prime over changes in H3K27me3 and quantitatively correlate with transcription changes, while H3K27me3 changes occur after prolonged expression changes. Notably, early activation of PcG target genes is dominated by increases in H3K4me3 while H3K27me3 remains present at the locus. Our results reveal H3K4me3 as greater predictor over H3K27me3 for transcription dynamics, unveil unexpected chromatin mechanisms at gene activation and underline the relevance of tissue-specific temporal epigenomics.

This research paper presents a comprehensive study on the gasification of wheat straw pellets in a 10-kW fixed bed gasifier through a combination of Computational Fluid Dynamics (CFD) simulation and experimental validation. The developed 2D CFD model in ANSYS meshing simulates the gasification process in ANSYS Fluent software. The investigation evaluates key parameters such as equivalence ratio, higher heating value, and temperature distribution within the gasifier to enhance syngas production efficiency. The simulated results exhibit a noteworthy agreement with experimental data obtained from gasification. The impact of the equivalence ratio on gas production and lower heating value (LHV) is systematically explored, revealing that an equivalence ratio of 0.35 is optimal for syngas production. The resulting producer gas composition at this optimum condition includes CO (~27.67%), CH4 (~3.29%), CO2 (~11.09%), H2 (~11.09%), and N2 (~51%). The study further investigates the positive influence of reactor temperature on increasing syngas quantity while considering the uneven shape of the reactor and various thermal reactions affecting temperature, static pressure, velocity, and density. The findings contribute valuable insights to improve the efficiency of fixed-bed gasifiers, offering essential information on performance parameters for sustainable and optimized syngas production.

In every agricultural setting, weed seeds can be found in every cubic centimeter of soil. Weed seeds, as a valuable trait underlying the fate of weed populations, exhibit differing levels of seed dormancy, ensuring their survival under uncertain conditions. Seed dormancy is considered as an innate mechanism that constrains germination under suitable conditions that would otherwise stimulate germination of non-dormant seeds. This work provides new insight into changes in germination patterns along the dormant to nondormancy continuum in seeds with physiological dormancy. Notable findings are: (1) germination synchrony can act as a new parameter that quantitatively describes dormancy patterns and subsequently weed population dynamics, (2) germination synchrony is dynamic, suggesting that the more dormancy decreases, the more synchrony is obtainable, (3) after-ripening and stratification can function as a synchronizing agent that regulates germination behavior. Brassica napus showed the most synchronous germination with the value of 3.14, while lower level of germination asynchrony was for Sinapis arvensis, with the asynchrony value of 2.25. After-ripening and stratification can act as a synchronizing factor through decreasing asynchrony level and increasing synchrony. Weed establish a firm relationship between dormancy cycling and germination synchrony patterns, ensuring their survival and reproductive strategies. By germinating in synchrony, which is accompanied by cycling mechanisms, weeds have more opportunities to persist. The synchrony model used in the present study predicts germination behavior and synchrony along the dormant to nondormancy continuum in weed seeds with physiological dormancy, suggesting a useful method for quantification of germination strategies and weed population dynamics.

Self-organized criticality (SOC) is a universal mechanism for self-sustained critical behavior in large-scale systems evolving outside equilibrium. Our report explores a tentative link between SOC and Lagrangian field theory, with the long-term goal of bridging the gap between complex dynamics and the non-perturbative behavior of quantum fields.

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.

Human NAD(P)H:quinone oxidoreductase 1 (NQO1) is a multi-functional protein whose alteration is associated with cancer, Parkinson´s and Alzheimer´s diseases. NQO1 displays a remarkable functional chemistry, capable of binding different functional ligands that modulate its activity, stability and interaction with proteins and nucleic acids. Our understanding on this functional chemistry is limited by the difficulty of obtaining structural and dynamic information on many of these states. Herein, we have used hydrogen/deuterium exchange monitored by mass-spectrometry (HDXMS) to investigate the structural dynamics of NQO1 in three ligation states: without ligands (NQO1apo), with FAD (NQO1holo) and with FAD and the inhibitor dicoumarol (NQO1dic). We show that NQO1apo has a minimally stable folded core holding the protein dimer and with FAD and dicoumarol ligand binding sites populating binding non-competent conformations. Binding of FAD significantly decreases protein dynamics and stabilizes the FAD and dicoumarol binding sites as well as the monomer:monomer interface. Dicoumarol binding further stabilizes all three functional sites, a result not previously anticipated by available crystallographic models. Our work provides an experimental perspective into the communication of stability effects through the NQO1 dimer, valuable to understand at the molecular level the effects of disease-associated variants, post-translation modifications and ligand binding cooperativity in NQO1.

User-generated passwords often pose a security risk in authentication systems. However, providing a comparative substitute poses a challenge, given the common tradeoff between security and user experience. This paper integrates cryptographic methods (both asymmetric and symmetric), steganography, and a combination of physiological and behavioral biometrics to construct a prototype for a passwordless authentication system. We demonstrate the feasibility of scalable passwordless authentication while maintaining a balance between usability and security. We employed threat modeling techniques to pinpoint the security prerequisites for the system, along with choosing appropriate cryptographic protocols. In addition, a comparative analysis is conducted, examining the security impacts of the proposed system in contrast to that of traditional password-based systems. Results from the prototype indicate that authentication is possible within a timeframe similar to passwords (within 2 seconds), without imposing additional hardware costs on users to enhance security or compromising usability. Given the scalable nature of the system design and the elimination of shared secrets, the financial and efficiency burdens associated with password resets are alleviated. Furthermore, the risk of breaches is mitigated, as there is no longer a need to store passwords and/or their hashes. Differing from prior research, our study presents a pragmatic design and prototype that deserves consideration as a viable alternative for both password-based and passwordless authentication systems.

The article proposes an amendment to the relativistic continuum mechanics which introduces the relationship between density tensors and the curvature of spacetime. The resulting formulation of a symmetric stress-energy tensor for a system with an electromagnetic field, leads to the solution of Einstein Field Equations indicating a relationship between the electromagnetic field tensor and the metric tensor. In this EFE solution, the cosmological constant is related to the invariant of the electromagnetic field tensor, and additional pulls appear, dependent on the vacuum energy contained in the system. In flat Minkowski spacetime, the vanishing four-divergence of the proposed stress-energy tensor expresses relativistic Cauchy's momentum equation, leading to the emergence of force densities which can be developed and parameterized to obtain known interactions. Transformation equations were also obtained between spacetime with fields and forces, and a curved spacetime reproducing the motion resulting from the fields under consideration, which allows for the extension of the solution with new fields.

Turbulent flow is the first and fundamental physical phenomena to evaluate when optimising cost and reducing emissions from an Anode Baking Furnace (ABF). Gas flow patterns, velocity field, pressure drop, shear stress, and turbulent dissipation rate variables are the main operational parameters to be optimised, considering a specific geometry. Computational Fluid Dynamics (CFD) allows simulating physical phenomena using numerical methods with computer resources. In particular, the finite element method is one of the most used methods to solve the flow equations. This method requires a discretisation of the geometry of the ABF, called mesh. Hence, mesh is the main input to the finite element method. A suitable mesh for applying a discretisation method determines whether the problem can be simulated or not. Generating an appropriate mesh remains a challenge to perform accurate simulations. In this work, a comparison between meshes generated using two mesh generation tools is presented. Results of different study cases are included.

Bimetallic nanoparticles are of interest since they lead to many interesting electrical, chemical, catalytic, and optical properties. They are particularly important in the field of catalysis since they show superior catalytic properties than their monometallic counterparts. The structures of bimetallic nanoparticles depend mainly on the synthesis conditions and the miscibility of the two components. In this work, PdPt alloyed-bimetallic nanoparticles (NPs) were synthesized through the polyol method, and characterized using spherical aberration (Cs) corrected scanning transmission electron microscopy (STEM). High-angle annular dark-field (HAADF)-STEM images of bimetallic nanoparticles were obtained. The contrast of images shows that nanoparticles have an alloy structure with an average size of 8.2 nm. Together with the characterization of nanoparticles, a systematic molecular dynamics simulations study, focused on the structural stability and atomic surface segregation trends in 923-atom PdPt alloyed-bimetallic NPs was carried out.

By employing the stochastic extension of the Madelung quantum-hydrodynamic description within a discrete methodology, we establish a solution using the path integral approach to explore the progression of quantum states' superposition. This investigation aims to understand the eventual establishment of a stable end-state configuration amid the backdrop of gravitational background fluctuations. The model identifies the circumstances that lead to a limited range of interaction for the quantum potential, allowing for the emergence of sizeable, classically described macroscopic phenomena. The theory unveils the lowest achievable level of uncertainty in an open quantum system and investigate its congruence with the localized behaviors of macroscopic classical systems. The study examines agreements and differences with decoherence theory and the Copenhagen interpretation of quantum mechanics, and evaluates the impact of wave function decay on the measurement process.

The genetic code conceals a ‘code within the codons’, which hints at biophysical interactions between amino acids and their cognate nucleotides. But research over decades has failed to corroborate systematic biophysical interactions across the code. Using molecular dynamics simulations and NMR, we have analysed interactions between the 20 standard proteinogenic amino acids and four RNA mononucleotides in three charge states. Our simulations show that 50% of amino acids bind best with their anticodonic middle base in the -1 charge state common to the backbone of RNA, while 95% of amino acids interact most strongly with at least one of their codonic or anticodonic bases. Preference for the cognate anticodonic middle base was greater than 99% of randomized assignments. We verify a selection of our results using NMR, and highlight challenges with both techniques for interrogating large numbers of weak interactions. Finally, we extend our simulations to a range of amino acids and dinucleotides, and corroborate similar preferences for cognate nucleotides. Despite some discrepancies between the predicted patterns and those observed in biology, the existence of weak stereochemical interactions means that random RNA sequences could template non-random peptides. This offers a compelling explanation for the emergence of genetic information in biology.

It has been more than a year since the first case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was found. This coronavirus has infected more than 110 million people worldwide by the end of February, 2021, and several virulent as well as more spreadable mutant forms of SARS-CoV-2 have emerged subsequently. In the latter group, three variants B.1.1.7, B.1.351, and P1 lineages, have been reported. Using computer simulation, the present paper investigates the structural differences between the wild type SARS-CoV-2 spike protein and its Asn501Tyr (N501Y) mutant variant. Time-based structural changes between the receptor binding domains of these two species are also examined. The N501Y mutation is common to all the three aforesaid mutant variants.

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.

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.

Electrowetting – induced detachment of droplets from solid surfaces is important for numerous applications in the fields of heat transfer and fluid mechanics. The forced oscillations of droplets on solid surfaces and their ability to detach are studied. In this study the process is efficiently simulated by implementing a powerful methodology developed by our team. Our results agree with experiments, showing that optimal detachment, in terms of actuation energy, is achieved when the application of voltage is synchronized with the spreading time of the droplet. Under these conditions, the droplet oscillates with a period close to that of a mirrored Rayleigh droplet. The relation between the droplet’s oscillation period and its physical properties is examined. During voltage-droplet synchronization, the droplet’s ability to detach depends mostly on its contact angle, its viscosity, and the applied voltage. An energy analysis is also conducted, revealing how energy is supplied to the droplet by electrowetting-induced detachment.

G protein-coupled receptors (GPCRs) play a key role in many cellular signaling mechanisms, and must select among multiple coupling possibilities in a ligand-specific manner in order to carry out a myriad of functions in diverse cellular contexts. Much has been learned about the molecular mechanisms of ligand-GPCR complexes from Molecular Dynamics (MD) simulations. However, to explore ligand-specific differences in the response of a GPCR to diverse ligands, as is required to understand ligand bias and functional selectivity, necessitates creating very large amounts of data from the needed large-scale simulations. This becomes a Big Data problem for the high dimensionality analysis of the accumulated trajectories. Here we describe a new machine learning (ML) approach to the problem that is based on transforming the analysis of GPCR function-related, ligand-specific differences encoded in the MD simulation trajectories into a representation recognizable by state-of-the-art deep learning object recognition technology. We illustrate this method by applying it to recognize the pharmacological classification of ligands bound to the 5-HT2A and D2 subtypes of class A GPCRs from the serotonin and dopamine families. The ML-based approach is shown to perform the classification task with high accuracy, and we identify the molecular determinants of the classifications in the context of GPCR structure and function. This study builds a framework for the efficient computational analysis of MD Big Data collected for the purpose of understanding ligand-specific GPCR activity.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is pandemic. Prevention and control strategies require an improved understanding of SARS-CoV-2 dynamics. We did a rapid review of the literature on SARS-CoV-2 viral dynamics with a focus on infective dose. We sought comparisons of SARS-CoV-2 with other respiratory viruses including SARS-CoV-1 and MERS-CoV. We examined laboratory animal, and human studies. The literature on infective dose, transmission, and routes of exposure was limited specially in humans, and varying endpoints were used for measurement of infection. We propose the minimum infective dose of COVID-19 in humans, is higher than 100 particles, possibly slightly lower than the 700 particles estimated for H1N1 influenza. Despite variability in animal studies, there was some evidence that increased dose at exposure correlated with higher viral load clinically, and severer symptoms. Higher viral load measures did not reflect COVID-19 severity. Aerosol transmission seemed to raise the risk of more severe respiratory complications in animals. An accurate quantitative estimate of the infective dose of SARS-CoV-2 in humans is not currently feasible and needs further research. Further work is also required on the relationship between routes of transmission, infective dose, co-infection, and outcomes.

In the course of SARS-CoV-2 infection, the 3CL or nsp5 protease plays a pivotal role as the most important viral protease required for the maturation of viral proteins during host infection. Herein, we simulated for 500 ns 3CLproWT, 3CLproH41A, , 3CLproBeta, and 3CLproOmicron, in complex with the substrates nsp 4|5 and nsp 5|6. Our results show that mutations in the 3CLpro present in the SARS-CoV-2 variant of concerns (VOCs) did not lead to significant conformational changes or changes in substrate binding affinities. However, significantly high cleavage rates for the boundary between nsp4 and nsp5 were obtained for 3CLproBeta and 3CLproOmicron and may play a key role in the viral replication and virus fitness gain. Our molecular dynamics data suggest that the cleavage rate of nsp4|5 may be related to the increased amount of viral load observed for these VOCs, releasing more nsp4 than other non-structural proteins. Based on our hydrogen bonding analyses, we also discovered that Gly143 and Glu166 are key residues in substrate recognition, suggesting that these residues may be incorporated as pharmacophoric centers for Beta and Omicron variants in drug design. Our results suggest that Gly143 and Glu166 are essential residues to interact with Gln6 of the different substrates and, therefore, are potential broad-spectrum pharmacophoric centers of SARS-CoV-2 3CLpro.

The mechanical properties of α-chitin and chitosan biocomposite are investigated due to their broad range of potential applications in bioengineering, materials science, and environmental technology. Employing molecular dynamics (MD), and stress-strain analyses, this study comprehensively investigates biopolymers mechanical response and anisotropic mechanical behavior under uniaxial tensile loading conditions in an aqueous environment. Our computational models were validated against existing experimental data, showing high degrees of correspondence. Uniaxial tensile tests revealed that α-chitin exhibits a remarkable ultimate tensile strength (UTS) of 10.07 GPa in the crystalline chain direction (y-axis) at a high strain rate of 0.636, compared to a significantly lower UTS of 2.78 GPa in the perpendicular direction (x-axis) at a lower strain rate of 0.066. The biocomposite nanostructure, encompassing randomly distributed chitosan, reduced stiffness, maintaining remarkable flexibility as α-chitin, with a UTS of 5.03 GPa in the y-axis and 2.34 GPa in the x-axis. Further, the directional elastic modules for α-chitin were calculated as 51.76 GPa and 39.76 GPa in the x and y directions, respectively. In contrast, these values for the α-chitin-chitosan biocomposite were estimated as 31.66 GPa and 26.00 GPa, respectively. The findings provide valuable insights into the distinct mechanical properties of α-chitin and chitosan biocomposite, making a substantial contribution to optimizing these materials for specialized applications.

The four-way reversing valve is a key component determining whether a heat pump air conditioning system can work. Studying the four-way reversing valve is of great significance for improving the performance of the heat pump air conditioning system. In this paper, the control equation of the sliding block movement process is constructed to simulate the reversing process of the four-way reversing valve in fluid mechanics, and a detailed study is carried out from the sliding block speed, sliding block acceleration, sliding block force, refrigerant leakage, and other aspects. Research has shown that optimizing the structure of the slider can greatly improve the working performance of the four-way reversing valve. Increasing the height of the slider not only improves the pressure relief ability of the four-way reversing valve and prevents the slider from being damaged by high-pressure gas impact, but also reduces the leakage of refrigerant during the directional process; When reducing the length of the slider, although it will improve the pressure relief capacity of the four-way reversing valve, it also increases the amount of refrigerant leakage. The research results provide a theoretical basis and improvement direction for designers to improve the performance of four-way reversing valves.

This study aims to determine the optimal configuration (position and operation duration) for wall mounted mechanical mixers based on the comparison of three-dimensional computational fluid dynamics (CFD) modelling results and physical data collected from the treatment plant. A three-dimensional model of anoxic zone 1, 2 and 3 of Northern Wastewater Treatment Plant (WWTP) located at Cairns Regional Council, Cairns, Queensland, Australia was developed and validated. The model was used to simulate the flow pattern of the WWTP and the simulation results are in good agreement with the physical data varying between 0% to 15% in key locations. The anoxic zones were subject to velocities less than the desired 0.3 metres per second however results for suspended solids concentration indicate that good mixing is being achieved. Results for suspended solids concentrations suggest that the anoxic zones are towards the upper limits recommended by literature for specific power dissipation. The duration for operation of mechanical mixers was investigated and identified that the duration could be reduced from 900 seconds down to 150 seconds. Alternative mixer positioning was also investigated and identified positioning which would increase the average flow velocity with decreased duration (150 seconds). The study identified that Council may achieve savings of $24,000 per year through optimisation of the mechanical mixers.

Coronavirus disease 2019 (COVID-19) is an emerging infectious disease that was first reported in Wuhan, China and has subsequently spread worldwide. In the absence of any antiviral or immunomodulatory therapies, the disease is spreading at an alarming rate. 5 to 10% of recovered patients in Wuhan test positive again; this suggest that for controlling COVID-19, vaccines may be better option than drugs. A clinical trial to evaluate an anti-COVID-19 vaccine has started recently. However, its efficacy and potency have to be evaluated and validated. As an alternative, we are presenting a first-of-its-kind, designed multi-peptide subunit based epitope vaccine against COVID-19. The vaccine construct comprise an adjuvant, CTL, HTL, and B-cell epitopes joined by linkers. The vaccine is non-toxic, non-allergenic, thermostable and immunogenic with the capability to elicit a humoral and cell-mediated immune response. The findings are validated with high-end computation-based methods. This unique vaccine is made up of 33 highly antigenic epitopes from three proteins that have a prominent role in host receptor recognition, viral entry, and pathogenicity. We advocate this vaccine must be synthesized and tested urgently as public health priority.

Short-term (hours) biological and biogeochemical processes cannot be fully captured by the current suite of polar-orbiting satellite ocean color sensors, as their temporal resolution is limited to potentially one clear image per day. Geostationary sensors, such as the Geostationary Ocean Color Imager (GOCI) from the Republic of Korea, allow the study of these short-term processes because their geostationary orbits permit the collection of multiple images throughout each day. To assess the capability to detect changes in water properties caused by these processes, however, requires an understaning of the uncertainties introduced by the instrument and/or geophysical retrieval algorithms. This work presents a study of the variability during the day over a water region of low-productivity with the assumption that only small changes in the water properties occur during the day over the area of study. The complete GOCI mission data were processed using the SeaDAS/l2gen package. Filtering criteria were applied to assure the quality of the data. Relative differences with respect to the midday value were calculated for each hourly observation of the day. Also, the influence of the solar zenith angle in the retrieval of remote sensing reflectances and derived products was analyzed. We determined that the uncertainties in water-leaving “remote-sensing” reflectance ($R_\text{rs}$) for the 412, 443, 490, 555, 660 and 680 nm bands on GOCI are 8.05$\times10^{-4}$, 5.49$\times10^{-4}$, 4.48$\times10^{-4}$, 2.51$\times10^{-4}$, 8.83$\times10^{-5}$, and 1.36$\times10^{-4}$ sr$^{-1}$, respectively, and 1.09$\times10^{-2}$ mg m$^{-3}$ for the chlorophyll-a concentration (Chl-{\it a}), 2.09$\times10^{-3}$ m$^{-1}$ for the absorption coefficient of chromophoric dissolved organic matter at 412 nm ($a_{\text{g}}(412)$), and 3.7 mg m$^{-3}$ for particulate organic carbon (POC). We consider these to be the floor values for detectable changes in the water properties due to biological, physical or chemical processes.

This work is an addition to the previously developed two-dimensional model of the shock-plasma interaction extending it into the third dimension. The model allows tracing the evolution of the state of the hypersonic flow and the shock front refracted at a thermal discontinuity. The advantages of using the spherical coordinate system for this type of the problems include more transparency in interpreting the solution and a shortened calculation procedure, because all the changes to the front become reduced to one distortion component only. Although the vorticity generation triggered at the interface is the consequence of the refraction and tied to the steep changes of the front, it is shown here that it is not because of an instant parameter jump at the interface due to refraction itself.

Discrete-time architectures offer a distinct advantage over their continuous counterparts, as they can be seamlessly implemented on embedded hardware without the necessity for discretization processes. Yet, because of the difficulty of ensuring Lyapunov difference expressions, their designs, which are based on quadratic Lyapunov-based frameworks, are highly complex. As a result, various existing continuous-time results using adaptive control methods to deal with system uncertainties and coupled dynamics in agents of a multiagent system cannot be directly applied to the discrete-time context. Furthermore, compared to their continuous-time equivalent, discrete-time information exchange based on periodic time intervals is more practical in the control of multiagent systems. In this paper, we first introduce a discrete-time adaptive control architecture designed for uncertain scalar multiagent systems without coupled dynamics as a preliminary result. We then introduce another discrete-time adaptive control approach for uncertain multiagent systems in the presence of coupled dynamics. Our approach incorporates observer dynamics to manage unmeasurable coupled dynamics, along with a user-assigned Laplacian matrix to induce cooperative behaviors among multiple agents. Our solution includes Lyapunov analysis with logarithmic and quadratic Lyapunov functions for guaranteeing asymptotic stability with both controllers. To demonstrate the effectiveness of the proposed control architectures, we provide an illustrative example.

In an era characterized by the ever-shifting landscapes of the digital realm, this paper intricately examines the interplay between digital culture, cultural dynamics, and beliefs in academia. Utilizing insights from cutting-edge language models, the study uncovers nuanced cultural expressions among Arts and Sciences students navigating the digital domain. Employing qualitative methods including interviews, observations, in-depth literature reviews, and thematic analysis, findings highlight digital interactions' transformative impact on cultural narratives and the potential of digital ethnography as a lens for understanding intricate cultural phenomena. This research enriches digital ethnography and cultural dynamics, offering fresh perspectives on the symbiotic relationship between digital culture and traditional beliefs, underscored by data from a maximum purposeful sampling of thirty (30) participants. Overall, this exploration emphasizes digital culture's dynamic role in shaping and reflecting cultural convictions, contributing to the understanding of cultural dynamics and evolving digital ethnography in the academic landscape.

Using LSMS-ISA panel data, we analyzed determinants of diversification into Rural Non-Farm Enterprises (RNFEs) and dynamics of the sector by studying the transition between farming and both low- and high-return RNFEs. We found that diversification into RNFE is determined by household characteristics mainly age and gender of the household head, whereas initial capital endowments such as assets, human capital, land and livestock significantly affect level of participation than entry into RNFE. Furthermore, analysing dynamics of RNFE separately for the youth and matured households, our study finds that continuous participation in RNFE is higher among the youth than among matured households. Similarly, initial capital endowments mainly educational level and access to credit are important factors for the youth to transit to high return RNFE, implying that entrepreneurial skills development and access to finance that enhance investments and gradual accumulation of capital are vital for the youth to benefit from RNFEs. Moreover, shocks that affect agricultural productivity are significant in increasing the probability of transition out of high-return RNFE signifying the need for social protection measures to ensure growth of RNFEs.

Equine metabolic syndrome (EMS) is a major health threat in veterinary endocrinology medicine worldwide, and there is growing interest in utilizing molecular agents for modulation of hepatocyte function for potential clinical applications with recent studies showing promising results in the inhibition of PTP1B on adipose-derived stromal cells. In this study, we investigated the effects of MSI-1436 on equine hepatic progenitor cells (HPCs) in terms of their proliferative activity, glucose uptake, and mitochondrial morphogenesis under lipotoxic condition. Our study found that MSI-1436 promotes the entry of HPCs in the cell cycle and rescues them from palmitate-induced apoptosis by regulating mitochondrial dynamics and biogenesis. MSI-1436 also increases glucose uptake and protects HPCs from palmitate-induced stress by reorganizing the morphological architecture of the cells. Additionally, our findings suggest that MSI-1436 enhances the 2-NBDG internalization by increasing the expression of SIRT1, which is associated with liver insulin sensitivity, and promotes mitochondrial dynamics by modulating their number and morphotype through PINK1, MFN1, and MFN2 increased expression. Our study provides evidence that MSI-1436 has a positive impact on equine hepatic progenitor cells, indicating its potential therapeutic value in the treatment of EMS and insulin dysregulation.

We propose Reduced Collatz Conjecture that is equivalent to Collatz Conjecture, which states that every positive integer can return to an integer less than it, instead of 1. Reduced Collatz Conjecture should be easier because some properties are presented in reduced dynamics, rather than in original dynamics (e.g., ratio and period). Reduced dynamics is a computation sequence from starting integer to the first integer less than it, and original dynamics is a computation sequence from starting integer to 1. Reduced dynamics is a component of original dynamics. We denote dynamics of x as a sequence of either computations in terms of ``I'' that represents (3*x+1)/2 and ``O'' that represents x/2. Here 3*x+1 and x/2 are combined together, because 3*x+1 is always even and followed by x/2. We formally prove that all positive integers are partitioned into two halves and either presents ``I'' or ``O'' in next ongoing computation. More specifically, (1) if any positive integer x that is i module $2^t$ (i is an odd integer) is given, then the first t computations (each one is either ``I'' or ``O'' corresponding to whether current integer is odd or even) will be identical with that of i. (2) If current integer after t computations (in terms of ``I'' or ``O'') is less than x, then reduced dynamics of x is available. Otherwise, the residue class of x (namely, i module $2^t$) can be partitioned into two halves (namely, i module $2^{t+1}$ and $i+2^t$ module $2^{t+1}$), and either half presents ``I'' or ``O'' in intermediately forthcoming (t+1)-th computation.

The higher-order interactions in complex systems are gaining attention. Extending the classic bounded confidence model where an agent’s opinion update is the average opinion of its peers, this paper proposes a higher-order version of the bounded confidence model. Each agent organizes a group opinion discussion among its peers. Then, the discussion’s result influences all participants’ opinions. Since an agent is also the peer of its peers, the agent actually participates in multiple group discussions. We assume the agent’s opinion update is the average over multiple group discussions. The opinion dynamics rules can be arbitrary in each discussion. In this work, we experiment with two discussion rules: centralized and decentralized. We show that the centralized rule is equivalent to the classic bounded confidence model. The decentralized rule, however, can promote opinion consensus. In need of modeling specific real-life scenarios, the higher-order bounded confidence is convenient to combine with other higher-order dynamics, from the contagion process to evolutionary dynamics.

We study the deterministic dynamics of N point particles moving at constant speed in a 2D table made of two polygonal urns connected by an active rectangular channel, which applies a feedback-control on the particles, inverting the horizontal component of their velocities, when their number in the channel exceeds a fixed threshold. Such a bounce--back mechanism is non-dissipative: it preserves volumes in phase space. An additional passive channel closes the billiard table forming a circuit in which a stationary current may flow. Under specific constraints on the geometry and on the initial conditions, the large N limit allows nonequilibrium phase transitions between homogeneous and inhomogeneous phases. The role of ergodicity in making a probabilistic theory applicable is discussed both for rational and irrational urns. The theoretical predictions are compared with the numerical simulation results. Connections with the dynamics of feedback-controlled biological systems are highlighted.

Complex colloidal fluids, depending on particulates’ shapes and packing fractions, may have a wide range of shear thinning and thickening behaviors. A particular interesting way to transition between different types of such behavior is by infusing functional complex particles that can be manufactured using modern techicques such as 3D printing. In this paper, we display 2D molecular dynamics simulations of such fluids with infused star-shaped functional particles, with variable leg length and number of legs, as they are infused in a non-interacting, coarse-grained fluid. We vary the packing fraction (ϕ) of the system, and for each different system we apply shear with various strain rate that turns the fluid into a jammed state and rise the apparent viscosity of fluid. We demonstrate the dependence of viscosity with the particles’ packing fraction. We show the role of shape and design dependence of the functional particles towards the transition to a shear thickening fluid .

Overexpression of BRF2, a selective subunit of RNA polymerase III, has been shown to be crucial in the development of several types of cancers, including breast cancer and lung squamous cell carcinoma . Predominately, BRF2 acts as a central redox-sensing transcription factor (TF) and is involved in rescuing oxidative stress (OS) -induced apoptosis. Here, we showed a novel link between BRF2 and DNA damage response. Due to the lack of BRF2 specific inhibitors, through virtual and molecular dynamics screening, we identified potential drug candidates that interfere with BRF2-TATA-binding Protein (TBP)-DNA complex interactions based on binding energy, intermolecular, and torsional energy parameters. We experimentally tested Bexarotene as a potential BRF2 inhibitor. We found that Bexarotene (Bex) treatment resulted in a dramatic decline in oxidative stress (Tert-butylhydroquinone (tBHQ))-induced levels of BRF2 and consequently, lead to a decrease in cellular proliferation of cancer cells which may in part be due to drug pretreatment induced reduction of ROS generated by the oxidizing agent. Our data thus, provide the first experimental evidence that BRF2 is a novel player in DNA damage response pathway and Bexarotene can be used as a potential inhibitor to treat cancers with the specific elevation of oxidative stress.

The PI3K/mTOR signalling pathway plays a central role in the governing of cell growth, survival and metabolism. As such, it must integrate and decode information from both external and internal sources to guide efficient decision-making by the cell. To facilitate this, the pathway have evolved an intricate web of complex regulatory mechanisms and elaborate crosstalk with neighbouring signalling pathways, making it a highly non-linear system. Here, we describe the mechanistic biological details that underpin these regulatory mechanisms, covering a multitude of negative and positive feedback loops, feed-forward loops, competing protein interactions, and crosstalk with major signalling pathways. Further, we highlight the non-linear and dynamic network behaviours that arise from these regulations, uncovered through both computational and experimental studies. Given the pivotal role of the PI3K/mTOR network in cellular homeostasis and its frequent dysregulation in pathologies including cancer and diabetes, a coherent and systems-level understanding of the complex regulation and consequential dynamic signalling behaviours within this network is imperative for advancing biology and development of new therapeutic approaches.

To sample from complex, high-dimensional distributions, one may choose algorithms based on the Hybrid Monte Carlo (HMC) method. HMC-based algorithms generate nonlocal moves alleviating diffusive behavior. Here, I build on an already defined HMC framework, Hybrid Monte Carlo on Hilbert spaces [A. Beskos, F.J. Pinski, J.-M. Sanz-Serna and A.M. Stuart, Stoch. Proc. Applic. 121, 2201 - 2230 (2011); doi:10.1016/j.spa.2011.06.003] that provides finite-dimensional approximations of measures π which have density with respect to a Gaussian measure on an infinite-dimensional Hilbert (path) space. In all HMC algorithms, one has some freedom to choose the mass operator. The novel feature of the algorithm described in this article lies in the choice of this operator. This new choice defines a Markov Chain Monte Carlo (MCMC) method which is well defined on the Hilbert space itself. As before, the algorithm described herein uses an enlarged phase space Π having the target π as a marginal, together with a Hamiltonian flow that preserves Π. In the previous method, the phase space π was augmented with Brownian bridges. With the new choice for the mass operator, π is augmented with Ornstein-Uhlenbeck (OU) bridges. The covariance of Brownian bridges grows with its length, which has negative effects on the Metropolis-Hasting acceptance rate. This contrasts with the covariance of OU bridges which is independent of the path length. The ingredients of the new algorithm include the definition of the mass operator, the equations for the Hamiltonian flow, the (approximate) numerical integration of the evolution equations, and finally the Metropolis-Hastings acceptance rule. Taken together, these constitute a robust method for sampling the target distribution in an almost dimension-free manner. The behavior of this novel algorithm is demonstrated by computer experiments for a particle moving in two dimensions, between two free-energy basins separated by an entropic barrier.

The discovery of a growing number of exoplanets and even extrasolar systems supports the scientific consensus that it is possible to find other signs of life in the universe. The present work proposes for the first time, an explicit mechanism inspired by the dynamics of biological dispersion, widely used in ecology and epidemiology, to study the dispersion of biogenic units, interpreted as complex organic molecules, between rocky or water exoplanets (habitats) located inside star clusters. The results of the dynamic simulation suggest that for clusters with populations lower than 4 M+/ly³ it is not possible to obtain biogenic worlds after 5 Gyr. Above this population size, biogenic dispersion seems to follow a power law, the larger the density of worlds lesser will be the impact rate (β ) value to obtain at least one viable biogenic Carrier habitat after 5 Gyr. Finally, when we investigate scenarios by varying β, a well-defined set of density intervals can be defined in accordance to its characteristic β value, suggesting that biogenic dispersion has a behavior of “minimal infective dose” of “minimal biogenic effective” events by interval i.e. once this dose has been achieved, doesn’t matter if additional biogenic impact events occur on the habitat.

Persistent, non-explosive passive degassing is a common characteristic of active volcanoes. Distinct periodic components in measurable parameters of gas release have been widely identified over timescales ranging from seconds to months. The development and implementation of high temporal resolution gas measurement techniques now enables the robust quantification of high frequency processes operating on timescales comparable to those detectable in geophysical datasets. This review presents an overview of the current state of understanding regarding periodic volcanic degassing, and evaluates the methods available for detecting periodicity, e.g., autocorrelation, variations of the Fast Fourier Transform (FFT), and the continuous wavelet transform (CWT). Periodicities in volcanic degassing from published studies are summarised and statistically analysed, together with analyses of literature-derived datasets where periodicity had not previously been investigated. Finally, an overview of current knowledge on drivers of periodicity is presented and discussed in the framework of four main generating categories, including: (1) non-volcanic (e.g., atmospheric or tidally generated); (2) gas-driven, shallow conduit processes; (3) magma movement, intermediate to shallow storage zone; and (4) deep magmatic processes.

The establishment and spread of exotic species is a contemporary major concern. Alien species may become invasive in their new habitat, leading to both/either environmental and/or economic impacts. I briefly reviewed the literature in the last decade about the relationship of exotic species and native communities. I identified that professionals usually approach the subject in two main points of view: (1) researchers tend to point out the impacts of alien species on entire communities, evaluating if the relationship is positive, negative or neutral; (2) they focus on the eco-evolutionary processes involved in the introductions, the dynamics of invasion, and individual study cases. When evaluating the response of introductions to entire communities, evidence seems to be ambiguous and may support positive, negative or neutral relationship, especially depending on the scale approached. The unique eco-evolutionary pathways of each introduction may be a great shortcoming in the searching for generalities. On the other hand, advances have been made in understanding the dynamics of invasion on different lineages through a more selective/individualized approach. I suggest that the dynamics of invasion might be studied through a perspective in which different eco-evolutionary processes, levels of organization (from gene to entire communities), the history of the organism(s) and time are taken into account. Individual cases might be compared in attempt to understand how the relationship exotic and native works and in the search for generalities.

This paper aims to show that sustainable behavior by firms may be impaired by regulatory restrictions. We challenge the assumption that regulation aimed at curbing greenhouse gas emissions (GHG) on the form of a target to meet the Country’s GHG emissions commitments will promote sustainable corporations. We argue that, in fact, such regulation may impair sustainability practices because it creates unintended consequences. This paper tackles the efficiency of the institutional framework chosen through the lenses of the analytical themes of fit, scale and interplay, then we use a systems dynamic approach to represent how regulation in the arenas of energy efficiency and GHG emissions reduction may withhold competitive business outcomes and corporate sustainability schemes. We exemplify and simulate a single regulation scheme and found that as a result of the institutional scheme chosen, the system is dominated by negative feedback processes resulting in lesser outcomes that would be better tackled by firms not being subject to the restrictions imposed by the regulation.

Remanufacturing is a viable option to extend the useful life of an end-of-use product or its parts, ensuring sustainable competitive advantages under the current global economic climate. Challenges typical to remanufacturing still persist, despite its many benefits. According to the European Remanufacturing Network a key challenge is lack of accurate, timely and consistent product knowledge as highlighted in a 2015 survey of 188 European remanufacturers. With more data being produced by electric and hybrid vehicles, this adds to the information complexity challenge already experienced in remanufacturing. Therefore, it is difficult to implement real-time and accurate remanufacturing for the shop floor; there are no papers that focus on this within an electric and hybrid vehicle environment. To address this problem this paper attempts to (1) identify the required parameters/ variables needed for fuel cell remanufacturing by means of interviews (2) rank the variables by Pareto analysis (3) develop a casual loop diagram for the identified parameters/ variables to visualise its impact on remanufacturing (4) model a simple stock and flow diagram to simulate and understand data and information-driven schemes in remanufacturing.

We consider a random dynamical system arising in a model of associative memory. This system can be seen as a small (stochastic and deterministic) perturbation of a determinstic system having two weak attractors which are destroyed after the perturbation. We show, with a computer aided proof, that the system has a kind of chaotic itineracy. Typical orbits are globally chaotic, while they spend relatively long time visiting attractor's ruins.

Due to poor ventilation conditions in the tunnel, if gas pipeline leaks, the consequence of the accident will be more serious. Therefore, before the emergency repair, gas in the tunnel needs to be excharged so as not to explode during the repair process. Therefore, it is necessary to study the ventilation of gas in the tunnel. Based on the computational fluid dynamics (CFD) theory and taking the Yanyingshan tunnel section of China-Myanmar pipeline as an example, this paper uses Fluent software to establish the leakage model of the gas pipeline and fan model in the tunnel and analyzes the influence of different fan locations and number of fans on gas concentration. It can be concluded that: (1) the use of press-in method makes it more efficient to discharge gas out of the tunnel. (2) In order to make ventilation efficient, the fan should be arranged in a higher position and needs to be at a distance from the top of the tunnel. (3) Parallel use of two fans has better ventilation effect than single fan.

Copper demand for a country's copper industry has a greater pull effect. China's copper consumption in 2015 has accounted for 50% of the world. The scientific forecast of China's copper demands trend is also an important basis for analyzing its future environmental impact. This paper assumes that China's economy will be developing high, medium and low scenarios, and forecasts economic and social indicators such as total GDP, population and per capita GDP in China from 2016 to 2030. Then, predicted the demand of copper resources in China from 2016 to 2030 by the combination of system dynamics model, vector autoregressive moving average model and inverted U-type empirical model. The results show that: (1) in 2020, 2025 and 2030, China's refined copper demand will be 13 Mt, 15 Mt and 15.5 Mt. (2) China's copper demand growth slowed down significantly from 2016-2030. (3) 2025-2030, China's copper resource demand is stable, into the platform of demand growth, the highest peak value in 2027 will be 15.5 Mt. (4) 2030 years later, China's copper resource demand will enter a slow decline.

The main purpose of this study was to determine the size and direction of the seasonal dynamics of organic carbon (Сmicro) and nitrogen (Nmicro) biomass of microorganisms and microbial index (Cmicro : Corg) of natural and agrocenoses with their different uses. Field research methods involved taking of soil samples in 0-10-, 10-20- and 20-40 сm layers. Under laboratory conditions, the content of total soil carbon was determined by dry oxygen combustion on a Vario EL III analyzer (Elementar Analyzensysteme, Hanau, Germany). The carbon content of microbial biomass (Сmicro) was determined by chloroform fumigation extraction method (CFE). To freshly taken soil samples (2 hours) and soil samples after their 24-hour fumigation with chloroform vapors, 0.5 M K2SO4 was added to extract biomass lysis products of soil microorganisms. The content of organic carbon and nitrogen in the biomass of microorganisms in the obtained filtrates was determined on the Elementar Liqui TOC II, Analyzensysteme GmbH, Germany. The carbon content of microbial biomass was calculated from the difference between carbon in fumigated and control samples using a factor of 0,45 - for carbon and 0,54 – for nitrogen. The microbial index of soils was determined by the ratio between the carbon of microorganisms and the total organic carbon of the soil – Cmicro : Corg • 100 (%). Average values and confidence intervals were determined for each defined indicator. The Bonferoni method was used to correct the errors of multiple comparative samples of a one-way ANOVA analyze. K. Pearson’s linear correlation analysis was used to establish the relationships between the dynamics of carbon biomass of microorganisms and organic carbon of the soil during the growing season. Our research has shown the dynamics of Сmicro, Nmicro, Сmicro : Nmicro and Cmicro : Corg during the growing season. Analysis of the box plot showed the largest amplitude of Сmicro changes in the upper 0-10 cm layer of izogumusol. The smallest difference in the quartile range (IQR0,25-0,75) was for no-till and overhang (Ab) in the upper 0-10-, no-till (NT) and fallow (F) - in the layer 10-20- and plowing (CT) - in a layer of 20-40 cm. The content of organic carbon biomass of microorganisms in the upper layer of izogumusol at the beginning of the growing season had the highest values of Ab (577,79  1,64 mg/kg), NT (485,43  1,97 mg/kg) and CT (470,43  0,77 mg/kg), the smallest - for F (370,15  2,18 mg/kg). The content of Nmicro during this period decreased from Ab to Comb (combined tillage), NT, CT, Rot (rotary tillage), RT (reduced (ridge) tillage) and F, respectively. In the 20-40 cm layer, the highest values of Сmicro and Nmicro were observed in mid-July. The lowest values of Сmicro and Nmicro and the largest – Сmicro : Nmicro were found in late August for all variants and layers of the study. The dynamics of the microbial index resembled the trends of Сmicro and Nmicro. The largest share of Smicro in Sorghum during the growing season, on average was: - Ab (1,82  1,85 %) and NT (1,66  1,52 %) - in the layer 0-10-, - Ab (1,23  1,27 %) and NT (1,29  1,32 %) - in the layer 10-20- and - Ab (1,19  1,09 %) and F (1,11  1,077 %) - in a layer of 20-40 cm. Different use of izogumusol affected the amplitude of seasonal changes of Сmicro and Nmicro and did not affect on their direction. The maximum content of Сmicro and Nmicro was observed at the beginning of the growing season - in a layer of 0-10 cm and in mid-July - in a layer of 20-40 cm, the minimum - at the end of the summer period. During this period, the widest ratio of Сmicro : Nmicro was for F and CT - in the layer 0-20 cm and CT and Rot - in the layer 20-40 cm. The Pearson’s correlation coefficient between Сmicro and Corg increased from the upper 0-10- to the lower 20-40 cm layer of izogumusol. "Strong" and "high" negative correlations have been established between Сmicro and Corg, but no pattern has been found between the correlation coefficient and tillage technologies.

Alzheimer's disease (AD) is a progressive neurodegenerative brain disorder. One of the important therapeutic approaches of AD is the inhibition of β‐site APP cleaving enzyme‐1 (BACE1). This enzyme plays a central role in the synthesis of the pathogenic β-amyloid peptides (Aβ) in Alzheimer's disease. A group of potent BACE1 inhibitors with known x-ray structures (PDB ID 5i3X, 5i3Y, 5iE1, 5i3V, 5i3W, 4LC7, 3TPP) were studied by molecular dynamics simulation and binding energy calculation employing MM_GB(PB)SA. The calculated binding energies gave Kd values 0.139 µM, 1.39 nM, 4.39 mM, 24.3 nM, 1.39 mM, 29.13 mM and 193.07 nM, respectively. These inhibitors showed potent inhibitory activities in enzymatic and cell assays. The Kd values were compared with experimental values, the structures were discussed in view of the energy contributions to binding. Drug likeness of these inhibitors is also discussed. Accommodation of ligands in the catalytic site of BACE1 is discussed depending on the type of fragment involved in each structure. Molecular dynamics (MD) simulations and energy studies were used to explore the recognition of the selected BACE1 inhibitors by Asp 32, Asp228 and the hydrophobic flap. The results show that selective BACE1 inhibition may be due to the formation of strong electrostatic interactions with Asp32 and Asp228 and a large number of hydrogen bonds, π-π and Van der Waals interactions with the amino acid residues located inside the catalytic cavity. Interactions with the ligands show a similar binding mode with BACE1. These results help to rationalize the design of selective BACE1 inhibitors.

Current progress in the prediction of mechanical behavior of solids requires understanding of spatiotemporal complexity of plastic flow caused by self-organization of crystal defects. It may be particularly important in hexagonal materials because of their strong anisotropy and combination of different mechanisms of plasticity, such as dislocation glide and twinning. These materials often display complex behavior even on the macroscopic scale of deformation curves, e.g., a peculiar three-stage elastoplastic transition, the origin of which is a matter of debates. The present work is devoted to a multiscale study of plastic flow in α-Ti, based on simultaneous recording of deformation curves, 1D local strain field, and acoustic emission (AE). It is found that the average AE activity also reveals three-stage behavior, but in a qualitatively different way depending on the crystallographic orientation of the sample axis. On the finer scale, the statistical analysis of AE events and local strain rates testifies to an avalanche-like character of dislocation processes, reflected in power-law probability distribution functions. The results are discussed from the viewpoint of collective dislocation dynamics and are confronted to predictions of a recent micromechanical model of Ti strain hardening.

In this study, cotton fabric reinforced phenolic resin (CPF) composites were modified by adding four two-dimensional fillers: graphitic carbon nitride (g-C3N4), graphite (Gr), molybdenum disulfide (MoS2), and hexagonal boron nitride (h-BN). The tribological properties of these modified materials were investigated under dry friction and water lubrication conditions. CPF/ Gr composite exhibits significantly better tribological performance than the other three fillers modified CPF composites under dry friction, with a 24% reduction in friction coefficient and a 78% reduction in wear rate compared to unmodified CPF composite. Under water lubrication conditions, all four fillers did not significantly alter the friction coefficient of the CPF composite. However, except for an excessive amount of Gr, the other three fillers can reduce the wear rate. Particularly, in the case of 10% MoS2 content, the wear rate decreased by 56%. Scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) were employed for the analysis of the morphology and composition of the transfer films. Additionally, molecular dynamics (MD) simulations were conducted to investigate the adsorption effects of Gr, MoS2, and PF on the counterpart surface under both dry friction and water lubrication conditions. The difference in the adsorption capacity of Gr and MoS2 on the counterpart, as well as the resulting formation of transfer films, accounts for the variation in tribological behavior between CPF/Gr and CPF/MoS2 composites. By combining the lubrication properties of MoS2 and Gr under dry friction and water lubrication conditions, using them as co-fillers can achieve a synergistic lubrication effect.

The accelerated pace with which new diagnostic possibilities are produced and the budget re-strictions of the healthcare sector require that the decision-making process of acquiring new technologies becomes systematic in nature. There are some methodologies such as the Health Technology Assessment (HTA) that encompasses technological domains, clinical effectiveness, patient safety, organizational and financial aspects, among others. However, these methods do not contemplate the learning curve (LC) which is a differential factor in operator-dependent technologies. An assessment model was conceived based on the assessment domains of the AdHopHTA project with the addition of LC. The model was validated and calibrated through System Dynamics (SD) and using as case study the assessment of Point-of-care Ultrasound (POCUS) equipment in dengue screening. The model helped identify the influence of the LC and patient demand on the income and costs for the healthcare system regarding dengue screening as well as the cost-benefit indicator. The control charts LC-CUSUM and CUSUM are graphic tools to intuitively assess the learning curve which can be used for real-time monitoring once students reach a certain skill level.

The JC polyomavirus virus (JCPyV) affects more than 80% of the human population in their early life stage. It mainly affects immunocompromised individuals where virus replication in oligodendrocytes and astrocytes may lead to fatal progressive multifocal encephalopathy (PML). Virus protein 1 (VP1) is one of the major structural proteins of the viral capsid, responsible for keeping the virus alive in the gastrointestinal and urinary tracts. VP1 is often targeted for antiviral drug and vaccine development. Similarly, this study implied immunoinformatics and molecular dynamics simulation-based approaches to design a multi-epitope subunit vaccine targeting JCPyV. The VP1 protein epitopic sequences, which are highly conserved, were used to build the vaccine. This designed vaccine includes two adjuvants, five HTL epitopes, six CTL epitopes, and two linear BCL epitopes to stimulate cellular, humoral, and innate immune responses against JCPyV. Furthermore, molecular docking and molecular dynamics simulation (100ns) studies were used to examine the interaction and stability of the vaccine protein with TLR4. Trajectory analysis showed that the vaccine and TLR4 receptor form a stable complex with the vaccine protein. Overall, this study contributed to the path of vaccine development against JCPyV and may prevent PML from happening. However, this study needs experimental validation to conclude our findings.

Lipid mesophases are being intensively studied as potential candidates for drug-delivery purposes. Extensive experimental characterization has unveiled a wide palette of release features depending on the nature of the host lipids and of the guest molecule, as well as on the environmental conditions. However, only few simulation works have addressed the matter, which hampers a solid rationalization of the richness of outcomes observed in experiments. Particularly, to date there are no theoretical works addressing the impact of hydropathy on the transport of a molecule within lipid mesophases, despite the significant fraction of hydrophobic molecules among currently-available drugs. Similarly, the high heterogeneity of water mobility in the nanoscopic channels within lipid mesophases has also been neglected. To fill this gap, we introduce here a minimal model to account for these features in a lamellar geometry, and systematically study the role played by hydropathy and water-mobility heterogeneity by Brownian-dynamics simulations. We unveil a fine interplay between the presence of free-energy barriers, the affinity of the drug for the lipids, and the reduced mobility of water in determining the net molecular transport. More in general, our work is an instance of how multiscale simulations can be fruitfully employed to assist experiments in release systems based on lipid mesophases.

Consumer products contain the chemical substances that threaten human health. The modeling methods and experimental methods have been used to estimate the inhalation exposure concentration by the consumer products. The model and measurement methods have the spatial property problem and time/cost consuming problem, respectively. For solving the problems due to the conventional methodology, this study performed the feasibility of applying CFD for evaluation of inhalation exposure by comparing the experiment results and the zero-dimensional results with CFD results. To calculate the aerosol concentration, the CFD was performed by combined the 3D Reynolds averaged Navier Stoke’s equation and discrete phased model using ANSYS FLUENT. As a result of comparing the three methodologies performed under the same simulation/experimental conditions, we found the zero-dimensional spray model shows approximately 5 times underestimated inhalation exposure concentration when compared with the CFD results and measurement results in near field. Also, the results of the measured concentration of aerosols at five locations and the CFD results at the same location were compared to show the possibility of evaluating inhalation exposure at various locations using CFD instead of experimental method. The CFD results according to measurement positions can predict rationally the measurement results with low error. In conclusion, in the field of exposure science, a guideline for exposure evaluation using CFD was found that complements the shortcomings of the conventional methodology, the zero-dimensional spray model and measurement method.

For condensed systems, the incorporation of quantum chemical solvent effects into molecular dynamics simulations has been a major concern. To this end, quantum mechanical/molecular mechanical (QM/MM) techniques are popular and powerful options to treat gigantic systems. However, they cannot be directly applied because of temporal and spatial discontinuity problems. To overcome these problems, in a previous study, we proposed a corrective QM/MM method, size-consistent multipartitioning (SCMP) QM/MM, and successfully demonstrated that, using SCMP, it is possible to perform stable molecular dynamics simulations by effectively taking into account solvent quantum chemical effects. The SCMP method is characterized by two original features: size-consistency of a QM region among all QM/MM partitioning and partitioning update. However, in our previous study, the performance was not fully elicited compared to the theoretical upper bound, and the optimal partitioning update protocol and parameters were not fully verified. To elicit the potential performance, in the present study, we simplified the theoretical framework and modified the partitioning protocol.

Various distance metrics and their induced norms are employed in the quantitative modeling of evolutionary dynamics. Minimization of these distance metrics when applied to evolutionary optimization are hypothesized to result in different outcomes. Here, we apply the different distance metrics to the evolutionary trait dynamics brought about by the interaction between two competing species infected by parasites (exploiters). We present deterministic cases showing the distinctive selection outcomes under the Manhattan, Euclidean and Chebyshev norms. Specifically, we show how they differ in the time of convergence to the desired optima (e.g., no disease), and in the egalitarian sharing of carrying capacity between the competing species. However, when randomness is introduced to the population dynamics of parasites and to the trait dynamics of the competing species, the distinctive characteristics of the outcomes under the three norms become indistinguishable. Our results provide theoretical cases when evolutionary dynamics using different distance metrics exhibit similar outcomes.

Atomic force microscopes are used, beside their principal function as surface imaging tools, in surface manipulation and measurement of interfacial properties. In particular, they can be modified to measure lateral friction forces that occur during the sliding of the tip against the underlying substrate. However, the shape, size, and deformation of the tips profoundly affect the measurements in a manner that is difficult to predict. In this work, we investigate the contribution of these effect to the magnitude of the lateral forces during sliding. The surface substrate is chosen to be few-layer AB-stacked graphene surface whereas the tip is initially constructed from face-centered cubic gold. In order to separate the effect of deformation from shape, rigid tips of three different shapes were considered first, namely a cone, a pyramid and a hemisphere. The shape was seen to dictate all aspects of the interface during sliding, from temperature dependence to stick-slip behavior. Deformation was investigated next by comparing a rigid hemispherical tip to one of identical shape and size but with all but the top three layers of atoms free to move. The deformation, as also verified by an indentation analysis, occurs by means of the lower layers collapsing on the upper ones, thereby increasing the contact area. This collapse mitigates the friction force and decreases it with respect to the rigid tip for the same vertical distance. Finally, the size effect is studied by means of calculating the friction forces for a much larger hemispherical tip whose atoms are free to move. In this case, the deformation is found to be much smaller but the stick-slip behavior is much more clearly seen.

Identifying or authenticating a computer user are necessary steps to keep systems secure on the network and to prevent fraudulent users from accessing accounts. Keystroke dynamics authentication can be used as an additional authentication method. Keystroke dynamics involves in-depth analysis of how you type on the keyboard, analysis of how long a key is pressed or the time between two consecutive keys. This field has seen a continuous growth in scientific research. In the last five years alone, about 10,000 scientific researches in this field have been published. One of the main problems facing researchers is the small number of public data sets that include how users type on the keyboard. This paper aims to provide researchers with a data set that includes how to type free text on the keyboard by 80 users. The data were collected in a single session via a web platform. The dataset contains 410,633 key-events collected in a total time interval of almost 24 hours. In similar research, most datasets are with texts written by users in English. The language in which the users wrote for this research is Romanian. This paper also provides an extensive analysis of the data set collected and presents relevant information for the analysis of the data set in future research.

Streptococcus mutans is well known for having virulence factors associated with its cariogenic role, such as glucosyltransferases, which have been used as targets for the virtual screening of molecules with inhibitory capacity. The Antigen I/II of S. mutans is involved in the adhesion to the surface of the tooth and the bacterial co-aggregation in the biofilm formation, despite that, this protein has not been used as a target in a virtual strategy search for inhibitors. In this study we identified in silico and evaluated in vitro molecules with adhesion inhibitory potential on S. mutans Ag I/II. A virtual screening of 883,551 molecules was conducted, cytotoxicity analysis on fibroblast cells, S. mutans adhesion studies, scanning electron microscopy analysis for bacterial integrity, and molecular dynamics simulation were also performed. We have found three molecules (ZI-187, ZI-939, ZI-906) that were not cytotoxic and inhibited the adhesion of S. mutans to polystyrene microplates. Molecular dynamic simulation by 300 nanoseconds showed stability of the interaction between ZI-187 and Ag I/II (PDB: 3IPK). This work provides three new molecules that targets Ag I/II and have the capacity to inhibit in vitro the S. mutans adhesion on polystyrene microplates and provides a new computational line for the search and selection of safe inhibitory molecules against different pathogens.

One of the principal hallmarks of Alzheimer’s disease (AD) is related to the aggregation of amyloid-β fibrils in an insoluble form in the brain, also known as amyloidosis. Therefore, a prominent therapeutic strategy against AD consists either in blocking the amyloid aggregation and/or destroying the already formed aggregates. Natural products have shown significant therapeutic potential as amyloid inhibitors from in vitro studies as well as in vivo animal tests. In this study, the interaction of five natural biophenols (curcumin, dopamine, (-)-Epigallocatechin-3-gallate, Quercetin, and Rosmarinic acid) with the amyloid-β(1-40) fibrils has been studied through computational simulations. The results allowed the identification and characterization of the different binding modalities of each compounds and their consequences on fibril dynamics and aggregation. It emerges that the lateral aggregation of the fibrils is strongly influenced by the intercalation of the ligands, which modulate the double-layered structure stability.

The intricate architecture of dendritic arborization is fundamental to the formation and functionality of neural networks, serving as the primary site for synaptic integration and signal propagation. This study presents a pioneering computational model that simulates dendritic growth dynamics, employing exponential and logarithmic scaling over an extended developmental period of 720 days. This model offers a valuable tool for investigating the implications of diverse dendritic growth patterns on neural development, synaptic connectivity, and ultimately, cognitive functions. The computational framework incorporates biologically plausible parameters, allowing for the systematic exploration of dendritic branching patterns and their potential impact on neuronal information processing. By simulating exponential and logarithmic growth scales, the model captures the inherent complexity and diversity of dendritic morphologies observed in various neuronal populations across different brain regions. The findings from this study hold significant implications for our understanding of neural circuit assembly, synaptic integration, and the potential functional consequences of aberrant dendritic growth patterns observed in neurodevelopmental disorders. Furthermore, the model's ability to simulate extended developmental trajectories over a prolonged period of 720 days offers insights into the dynamic interplay between dendritic growth and synaptic pruning, which is crucial for the refinement and optimization of neural networks.

The seasonal and vertical spatial variation characteristics of total N, NH4+—N and NO3-—N in the soil in Picea mongolica forest at different stand ages were studied. The results showed that: (1) NH4+ —N in the soil in Picea mongolica forest was positively correlated with sample date, soil NO3-—N and forest age (P <0.05), and negatively correlated with soil depth (P < 0.01). NO3-—N in the soil in Picea mongolica forest was negatively correlated with sample date and forest age (P < 0.05), and significantly negatively correlated with soil depth (P < 0.01); (2) the content of NH4+—N is greater than that of NO3-—N in each soil layer of Picea mongolica forest at three forest ages. The correlation analysis showed which had an impact on the content of NH4+—N and NO3-—N in the soil in Picea mongolica forest. The content was lower in February and November, and higher in May and August；(3) The contents of total N, NH4+—N and NO3-—N in the soil of Picea mongolica forest in the three forest ages increased with the depth of soil layer (0-50cm), and showed an overall downward trend. The contents of NH4+—N in the soil layer of young forest (0-10cm, 10-20cm and 20-30cm, 30-40cm and 40-50cm) were significantly different (P＜0.05), and the contents of NO3-—N were also significantly different (P＜0.05), while their contents of middle-aged forest and near mature forest increased with the depth of soil layer, There was no significant difference in the content of NH4+—N; (4) The content of NH4+—N in the soil in Picea mongolica forest generally showed the following change trend near mature forest > middle-aged forest > young forest. The change trend of soil NO3-—N content is consistent with that of the content of NH4+—N in the soil in Picea mongolica forest.

This paper deals with the characteristics of the cyclone separator from the Lagrangian perspective to design important dependent variables, develops a neural network model for predicting the separation performance parameter, and compares the predictive performance between the traditional surrogate model and the neural network model. In order to design the important parameters of the cyclone separator based on the particle separation theory, the force acting until the particles are separated was calculated using the Lagrangian-based CFD methodology. As a result, it was proved that the centrifugal force and drag acting on the critical diameter having a separation efficiency of 50% were similar, and the particle separation phenomenon in the cyclone occurred from the critical diameter, and it was set as an important dependent variable. For developing a critical diameter prediction model based on machine learning and multiple regression methods, Unsteady-RANS analyzes according to shape dimensions were performed. The input design variables for predicting the critical diameter were selected as four geometry parameters that affect the turbulent flow inside the cyclone. As a result of comparing the model prediction performances, the ML model showed the 32.5 % of improvement rate of R2 compared to the traditional MLR considering the nonlinear relationship between the cyclone design variable and the critical diameter. The proposed techniques have proven to be fast and practical tools for cyclone design.

Quantum loops are processes that constitute quantum objects. In the causal model of quantum loops and quantum objects presented here, the nonlinear processes involve the elementary units of spacetime and the associated elementary units of quantum fields. As such, quantum loop processes are the sources of gravitational fields (i.e., spacetime curvature) and of the quantum objects wave function. The model may be viewed as a derivative of loop quantum gravity, spin networks and causal dynamical triangulation, although significant deviations to these theories exist. The causal model of quantum loops is based on a causal model of spacetime dynamics where space(-time) consists of interconnected space points, each of which is connected to a small number of neighboring space points. The curvature of spacetime is expressed by the density of these space points and by the arrangement of the connections between them. The quantum loop emerges in a nonlinear collective behavioral process from a collection of space points that carry energy and quantum field attributes.

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.