Energy Minimization Method Research Articles

In silico annotation of a hypothetical protein from Listeria monocytogenes EGD-e unfolds a toxin protein of the type II secretion system.

The gram-positive bacterium Listeria monocytogenes is an important foodborne intracellular pathogen that is widespread in the environment. The functions of hypothetical proteins (HP) from various pathogenic bacteria have been successfully annotated using a variety of bioinformatics strategies. In this study, a HP Imo0888 (NP_464414.1) from the Listeria monocytogenes EGD-e strain was annotated using several bioinformatics tools. Various techniques, including CELLO, PSORTb, and SOSUIGramN, identified the candidate protein as cytoplasmic. Domain and motif analysis revealed that the target protein is a PemK/MazFlike toxin protein of the type II toxin-antitoxin system (TAS) which was consistent with BLASTp analysis. Through secondary structure analysis, we found the random coil to be the most frequent. The Alpha Fold 2 Protein Structure Prediction Database was used to determine the three-dimensional (3D) structure of the HP using the template structure of a type II TAS PemK/MazF family toxin protein (DB ID_AFDB: A0A4B9HQB9) with 99.1% sequence identity. Various quality evaluation tools, such as PROCHECK, ERRAT, Verify 3D, and QMEAN were used to validate the 3D structure. Following the YASARA energy minimization method, the target protein's 3D structure became more stable. The active site of the developed 3D structure was determined by the CASTp server. Most pathogens that harbor TAS create a crucial risk to human health. Our aim to annotate the HP Imo088 found in Listeria could offer a chance to understand bacterial pathogenicity and identify a number of potential targets for drug development.

A Predictive Model of Capillary Forces and Contact Diameters between Two Plates Based on Artificial Neural Network.

Many efforts have been devoted to the forecasting of the capillary force generated by capillary adsorption between solids, which is fundamental and essential in the fields of micro-object manipulation and particle wetting. In this paper, an artificial neural network (ANN) model optimized by a genetic algorithm (GA-ANN) was proposed to predict the capillary force and contact diameter of the liquid bridge between two plates. The mean square error (MSE) and correlation coefficient (R2) were employed to evaluate the prediction accuracy of the GA-ANN model, theoretical solution method of the Young-Laplace equation and simulation approach based on the minimum energy method. The results showed that the values of MSE of capillary force and contact diameter using GA-ANN were 10.3 and 0.0001, respectively. The values of R2 were 0.9989 and 0.9977 for capillary force and contact diameter in regression analysis, respectively, demonstrating the accuracy of the proposed predictive model. The sensitivity analysis was conducted to investigate the influence of input parameters, including liquid volume and separation distance, on the capillary force and contact diameter. The liquid volume and separation distance played dominant roles in affecting the capillary force and contact diameter.

Superadditivity and Convex Optimization for Globally Optimal Cell Segmentation Using Deformable Shape Models.

Cell nuclei segmentation is challenging due to shape variation and closely clustered or partially overlapping objects. Most previous methods are not globally optimal, limited to elliptical models, or are computationally expensive. In this work, we introduce a globally optimal approach based on deformable shape models and global energy minimization for cell nuclei segmentation and cluster splitting. We propose an implicit parameterization of deformable shape models and show that it leads to a convex energy. Convex energy minimization yields the global solution independently of the initialization, is fast, and robust. To jointly perform cell nuclei segmentation and cluster splitting, we developed a novel iterative global energy minimization method, which leverages the inherent property of superadditivity of the convex energy. This property exploits the lower bound of the energy of the union of the models and improves the computational efficiency. Our method provably determines a solution close to global optimality. In addition, we derive a closed-form solution of the proposed global minimization based on the superadditivity property for non-clustered cell nuclei. We evaluated our method using fluorescence microscopy images of five different cell types comprising various challenges, and performed a quantitative comparison with previous methods. Our method achieved state-of-the-art or improved performance.

Modeling and Thermodynamic Studies of γ-Valerolactone Production from Bio-derived Methyl Levulinate.

The exploitation of biomass to reduce the dependency on fossil fuels represents a challenge that needs to be solved as soon as possible. Nowadays, one of the most fashionable processes is γ-valerolactone (GVL) production from bio-derived methyl levulinate (ML). Deep understanding of the thermodynamic aspects involved in this process is key for a successful outcome, but detailed studies are missing in the existing literature. A thermodynamic study of the reaction of γ-valerolactone (GVL) production from bio-derived methyl levulinate (ML) is performed by the Gibbs free energy minimization method. The effect of various reaction conditions (temperature, concentration, flow rate) and the implication of possible intermediates and byproducts are assessed. Conversion and selectivity are calculated from the simulation of the ML hydrogenation using isopropanol as the hydrogen donor under continuous flow conditions. Significant increases in GVL selectivity can be achieved under dry conditions, keeping the high conversion. Comparison between theoretical and experimental results from a previous article discloses the effect of using 5%RuTiO2 catalysts, which increases the selectivity from 3-40% to 41-98%. Enthalpy and Gibbs free energy of the reactions at issue are also calculated from models using Barin equations according to Aspen Physical Property System parameters.

Three-dimensional soil slope dynamic stability assessment using minimum potential energy approach

This study introduces a new stability analysis method of 3D slopes under the earthquake forces by combining the minimum potential energy method with pseudo-dynamic method. A new formulation for 3D slope stability analysis is given by introducing the elastic module and Poisson ratio. The minimum potential energy approach is used to directly obtain the stress state on failure surface, and the displacement direction where the potential energy of slope reaches the minimum is regarded as the movement direction of landslide mass. The determination of critical failure surface under earthquake forces and the associated safety factor (SF) are resolved using the genetic algorithm. The performance of the developed approach for evaluating slope stability is demonstrated with four cases. The influences of seismic forces and Poisson ratio on the slope stability are investigated, and the results show that Poisson ratio is insensitive to the accuracy of the proposed method, while the horizontal earthquake force has a greater impact on slope stability than the vertical earthquake force. The effects of the earthquake forces on the normal stress on failure surface, the sliding direction of landslide mass and the shape of failure surface are also explored. In addition, we discuss the differences between the proposed method and the pseudo-static method.

Analysis modeling and experiment of bionic winding soft actuator inspired by plant tendrils

As a special group of plants, vine plants can be spontaneously fixed with supports by winding or adsorbing. If the vine winding behavior is combined with a soft actuator, it is expected to improve the performance of the soft actuator in unstructured environments. Based on the pneumatic network structure, this study proposes a soft actuator with a symmetrical chamber and capable of winding or bending motion by imitating the winding motion of vine plants. Through the coupling motion of the symmetrical chamber under different or the same pressures, the winding flexibility of imitating vine plants can be better realized. Based on the minimum potential energy method and the constant curvature assumption, combined with the Yeoh model for large deformation of super elastic body, the deformation trajectory model of soft actuator in two states of unilateral winding and bending is constructed. The influence of structural design parameters of soft actuator on winding deformation is analyzed by finite element analysis. Finally, the reliability of the theoretical mathematical model is verified by experiments, the working performance of the software driver is tested, and the possible future applications are demonstrated.

Prediction of Pyrolysis Gas Composition Based on the Gibbs Equation and TGA Analysis

Conventional methods used to determine pyrolysis gas composition are based on chemical kinetics. The mechanism of those reactions is often unknown, which makes the calculations more difficult. Solving complex chemical reactions’ kinetics involving a nonlinear set of equations is CPU time demanding. An alternative approach is based on the Gibbs free energy minimization method. It requires only the initial composition and operation parameters as the input data, for example, temperature and pressure. In this paper, the method for calculating the pyrolytic gas composition from biogenic fuels has been presented, and the thermogravimetric experimental results have been adopted to determine the total gas yield. The studied problem has been reduced to the optimization method with the use of the Lagrange multipliers. This solution procedure is advantageous since it does not require knowledge of the reaction mechanism. The obtained results are in good agreement with experimental data, demonstrating the usefulness of the proposed method.

Assessment of the groundwater for household and drinking purposes in central Kazakhstan

Water resources, including potable water availability, are complicated issues in many Kazakhstan regions. Central Kazakhstan region is one such region, which requires the proper support in the water supply. Most of the Kazakhstan regions had been using mostly surface water, however, with the limitation of the surface water, the groundwater resources have been used more intensively during the last decades. At the same time, the groundwater chemical composition plays a decisive role for categorization as the potable water. Within this research work the chemical composition of groundwater formation features in the arid conditions of Kazakhstan are presented. The regional hydrogeochemical field works were carried out to establish the patterns of fresh and brackish groundwater formation. In the arid conditions of Kazakhstan, the two main factors influencing the chemical compositions were investigated, including: a) the water-rock interaction for mountain-folded areas, and b) water-soil-gas interaction and evaporative concentration (water evaporation and salts accumulation) for flat areas. The physical and chemical modeling by the Gibbs free energy minimization method, which is based on the thermodynamics laws, were provided to analyze processes of these two main factors influencing the chemical compositions. The results of these analyses, for the a) mountain-folded areas, we found that with the growth of gypsum (1.2%) in the rock, the content of sulfate compounds in water increases tenfold. In the fractured rocks of mountain-folded areas with free access to atmospheric air (open system), waters are enriched with oxygen and carbon dioxide. At the same time, the cationic composition of waters is determined by the lithological composition of the rocks. The sodium cations predominate in granite massifs. Calcium is predominant in enriched calcium minerals. Bicarbonate anions predominate in the anionic component with weak mineralization. For the b) flat areas, as mineralization increases due to the interaction of water-soil-gas and evaporative concentration, the chemical composition changes. The changes occur from sulfate to chloride in anions and from calcium to sodium in cations. These two main factors pattern a-b influencing the chemical compositions were also observed in the bigger regional hydrogeochemical studies, mountain-folded with connected flat areas. Waters are predominantly fresh bicarbonate calcium-sodium in the feeding zones of the mountain-folded areas originally. With water movement down to the flat areas, the mineralization increases. The water's mineralization increases and becomes more sulfate to chloride. The hydrogeochemical zonings are traced. This study is applicable for forecasting, searching the fresh and slightly brackish waters, which could be suitable for domestic water supply.

Transport Coefficients of H2–Cu/Al2O3 Plasma Mixtures Considering Solid and Liquid Status

Obtaining the plasma transport coefficients of the mixed system of arc-extinguishing medium and erosion product is the precondition of numerical simulation of erosion–diffusion in an arc chamber. In this article, the minimum Gibbs free energy method was used to calculate the composition of the H2–Cu/Al2O3 system, including solid and liquid copper (aluminum oxide), because copper and aluminum oxide are commonly used as electrode and ceramic materials in hydrogen dc contactors, respectively. The transport coefficients of H2–Cu/Al2O3 system and the phase transition of erosion products provide the basis for the subsequent simulation of erosion–diffusion of electrode and arc chamber in the H2 plasma. Results revealed that: 1) in the low-temperature range, copper (aluminum oxide) mainly exists in the form of a solid or a liquid state, resulting in the transport coefficients of the H2–Cu/Al2O3 system consistent with that of the H2 system; 2) as temperature increases, the copper (aluminum oxide) undergoes gasification (sublimation–decomposition) reaction that exists in a gaseous state and begins to affect the transport properties of the H2–Cu/Al2O3 system; in particular, the proportion of copper (aluminum oxide) has the most significant effect on viscosity; and 3) as the temperature continues to rise, atoms and molecules in the H2–Cu/Al2O3 system are completely ionized and the proportion of copper (aluminum oxide) has little effect on the transport properties (except electrical conductivity) of the H2–Cu/Al2O3 system. Finally, the transport coefficients of H2–Cu/Al2O3 plasma mixtures are reliable enough, in engineering application aspect, to be applied for simulation of erosion–diffusion in hydrogen dc contactors.

Study of the Thermodynamic Properties of Thermal Plasmas of Fluoroalkylamine-Air Mixtures

Knowledge of thermodynamic properties as well as parameters such as energy density and power flow isimportant for modeling thermal plasmas of fluoroalkylamine-air mixtures. In this paper, these thermodynamic properties of fluoroalkylamine-air mixture plasmas are calculated in a temperature range of 500 K to 20,000 K at atmospheric pressure and local thermodynamic equilibrium (LTE). The Gibbs free energy minimization method is used to determine the chemical equilibrium compositions of the plasmas that are needed to calculate the thermodynamic properties. These thermodynamic properties are then used to calculate the energy density and power flow of these plasmas. The variation of the energy density is related to the variations of the density and mass enthalpy. We notice that, this energy density increases with the percentage of air in the mixture for temperatures higher than 7000 K. The power flow, which depends also on density, enthalpy mass and sound speed, increases with the percentage of air in the same temperature range. Energy density and power flow results show that increasing air percentage in the mixture can be more interesting for damaging gaseous chemical species such as CF2, CO, HCN, and HF appearing at low temperatures with high concentrations.

A finite element method to calculate geometrically necessary dislocation density: Accounting for orientation discontinuities in polycrystals

Strain gradients have been used to link various microscale deformation phenomena to the mechanical response of a polycrystalline material, revealing sub-crystal deformation structures. The strain gradients are computed in terms of the orientation gradients and then converted to geometrically necessary dislocation densities, a quantity considered important to explain flow stress and strain hardening behaviour. In this study, a unique method has been developed to compute the orientation gradients by finite element method while enforcing orientation continuity inside the grains and allowing sharp gradients at the grain boundaries by a global minimization approach. The method is showcased on an exemplar electron backscatter diffraction datasets of a stainless type of steel. The energy minimization method (Demir et al., 2009) reveals geometrically necessary dislocation densities that are an order of magnitude lower than those calculated using the widely accepted Least-Squares minimization approach (Arsenlis et al., 1999). The proposed approach successfully eliminates sharp orientation gradients at grain boundaries, removing the artificially high dislocation densities near orientation discontinuities that is characteristic to the finite difference-based approaches.

The Impact of Thermochemical Exhaust Energy Recovery Using Ethanol-Gasoline Blend on Gasoline Direct Injection Engine Performance

Thermochemical exhaust energy recovery in a modern gasoline direct injection engine is investigated using ethanol-gasoline blend (E25) and gasoline, as base fuel. The primary objectives of this research are focused on reducing carbonaceous emissions as well as improving thermal efficiency and fuel economy in combustion engines. These are consistent with the global commitment to lessen carbon emissions and meet environmental regulations and agreements.The possibility of hydrogen production through catalytic reforming of mentioned fuels using actual exhaust composition is investigated on full-scale Rh (Rhodium)—Pt (Platinum) catalysts. ANSYS-Chemkin is utilized for thermodynamic equilibrium analyses based on the Gibbs energy minimization method to explore the key reaction pathways for E25 reforming. Main reforming parameters including steam to carbon molar ratios and reforming temperatures are selected to investigate the feasibility of ethanol-gasoline blend reforming as well as to identify the reformate composition and evaluate the whole process efficiency. The results revealed that the presence of ethanol in reforming fuel mixture facilitates endothermic reactions and improves hydrogen-rich mixture, particularly at high engine load conditions where maximum heat recovery is obtained. Furthermore, E25 fuel reforming helped achieving up to 16% greater CO2 compared to gasoline fuel reforming under the same engine condition. Overall, the experimental results of full-scale reforming tests using E25 can be accredited for effective implementation of the reforming technique in practical application.

Thermodynamic assessment of hydrothermal combustion assisted fossil fuel in-situ gasification in the context of sustainable development

Developing countries cannot get rid of the fate of relying on fossil energy development in the short term, so the low-carbon transformation must be carried out in the development process to achieve the goal of net zero emissions. This work proposed a novel hydrothermal combustion assisted fossil fuel in-situ gasification (HC-ISG) system combining renewable energy, supercritical hydrothermal combustion technology and supercritical water gasification technology. The system has the advantages of high thermal efficiency, high hydrogen yield, carbon dioxide utilization and storage, and landfill of hazardous waste. Firstly, based on the concept of energy grade, the effects of renewable energy and auxiliary fuel on the characteristics of energy grade change in HC-ISG system is studied. Then, the Gibbs free energy minimization method is conducted to discuss the effects of fossil fuels, oxidants, sub- and supercritical water on the key parameters of the system. The results indicated that for HC-ISG system, the energy grade and input amount of renewable energy have the optimal values. Compared with coke and methane, the system with methanol as an auxiliary fuel for hydrothermal combustion owned better the matching between energy quantity and energy grade. Moreover, increasing the reaction temperature could reduce the exergy destruction of the system and increase the energy grade change of the input energy. When the combustion coefficient was 0.2–0.3, the molar fraction of H2 reached the maximum value. When fossil fuel with high carbon content was used, the maximum H2 yield could reach 89.4 mol/kg, and the carbon emission was 3.9 kg CO2/kg H2, so the HC-ISG system could produce clean hydrogen. The system proposed in this study may provide a promising method for efficient and low-carbon in-situ conversion of fossil energy to hydrogen production.

Deformation and Springback Behavior of Sheet Metal With Convex-Shaped Surfaces in Heat-Assisted Incremental Bending Process Based on Minimum Energy Method

Abstract Three-dimensional sheet metal forming is one of the biggest challenges in the shipbuilding industry. The forming quality of the traditionally applied line heating method depends entirely on the skills of the technicians. Moreover, this approach is inefficient and error-prone. This calls for a need to develop new forming technologies that are easy to control and more efficient. In this paper, a novel forming method called heat-assisted incremental bending is presented. The minimum energy loading path of bidirectional curvature sheet along the direction of Gaussian curvature is adapted to deform the sheet metals with a convex shape surface. Besides, the auxiliary heating method and the auxiliary supporting are exclusively included in the forming process to improve the formability and accuracy. In this study, the convex-shaped sheet metal with large curvature is obtained along the two loading trajectories in two principal curvature directions, respectively. Results proved that using the minimum energy loading trajectory and including the auxiliary supports and heating can reduce the forming force to the greatest extent and effectively reduce the number of stamping points, thus improving the sheet metal forming efficiency and forming accuracy.

General Injection Transformer Turn Ratio Design Method and Hybrid Harmonic Reduction Methods for Series-Connected Multipulse Rectifiers

To simplify the complex calculation process of the optimal injection transformer turn ratio, a minimum error energy method is proposed in this article. According to the structure of multipulse rectifiers, the injection waveform when the rectifier without harmonics is analyzed, and the relationship between the input voltage and the injection voltage is studied. According to the relationship, the minimum error energy method is researched. To prove the accuracy of the minimum error energy method and improve the harmonic suppression ability of multipulse rectifiers, an improvable hybrid harmonic suppression method is proposed. Based on the structure of the proposed hybrid method, the optimal injection transformer turn ratio is calculated, respectively, by the minimum THD of input voltages and the minimum error energy method. The results show that the proposed minimum error energy method accurately solves the optimal turn ratio of the injection transformer with reduced computation. The proposed harmonic reduction method effectively suppresses the harmonics of the input side, which is suitable for high-power quality requirements.

Integration of Light Curve Brightness Information and Layered Discriminative Constrained Energy Minimization for Automatic Binary Asteroid Detection

Binary asteroid exploration is an important research focus in the areas of deep space exploration and space informatics because of its unique scientific value in analyzing the structure and gravitational dynamic properties of asteroids, as well as the origin and evolution of celestial bodies in the solar system. Remote photometric observations can reveal the key characteristics of binary asteroids that differ from other kinds of asteroids, especially unary asteroids, and provide an efficient and convenient way to discover binary asteroids. However, the automatic binary asteroid detection problem by advanced machine learning methodology remains unresolved when handing complex asteroid photometric data. For this problem, this article proposes to simulate unary and binary asteroid systems using cellinoid and oblate sphere shape models and generate the corresponding light curve brightness information with different asteroid physical parameters. Then, a benchmark unary and binary asteroid light curve dataset is constructed. Afterward, a layered discriminative constrained energy minimization (LDCEM) method is developed to train a binary asteroid detector in a layered learning manner by enlarging the response differences between the light curve data of unary and binary asteroids such that the two common kinds of asteroids can be well distinguished. The experimental results on the simulated asteroid light curve data, as well as the real observed asteroid light curve data, show that the proposed LDCEM method can yield promising binary asteroid detection performance in comparison with some representative detection methods.

Study on micro crack propagation mechanism of ferrite–pearlite gas transmission pipeline steel with lamellar structure

The deformation and failure characteristics of pipeline steel depend on its atomic structure and microstructure. Based on the serial multi-scale analysis technology, the ferrite/cementite (α-Fe/Fe3C) lamellar atomic structure with Bagaryatskii orientation relationship is established. In order to obtain the experimental sample of the lowest energy state, The step-by-step relaxation method of conjugate gradient energy minimization and constant temperature and constant pressure relaxation under NPT conditions is carried out, and the energy state and atomic structure of the relaxed samples are analyzed. For the models of different cementite terminal plane structures, the tension displacement curves on the propagation path of mode I central through crack are extracted respectively, combined with the bilinear cohesion zone model, The cohesion parameters at the atomic scale are successfully transferred from bottom to top to the macro and micro scales. By simulating the reaction force and displacement response law at the loading point, the critical fracture toughness of each terminal interface of ferrite–pearlite pipeline steel at different scales is calculated, which provides a reliable path for exploring the micro mechanism of macro cracking behavior of pipeline steel.

Investigation on minimum uncut chip thickness and size effect in micro milling of glow discharge polymer (GDP)

Glow discharge polymer (GDP) is used as the ablator material in inertial confinement fusion (ICF) applications. Its machining surface quality and geometric accuracy directly affect its high energy performance. Minimum uncut chip thickness (MUCT) and size effect are the keys to obtain higher surface quality during micro cutting. In this work, a hybrid analytical model of MUCT using cutting forces and effective rake angle based on minimum energy method (Model A), and micro milling experiment are applied to determine the MUCT of GDP. Furthermore, a specific cutting energy-based model (Model B), considering the mechanical properties, strain evolution, and tool geometry, is established to verify model A. Additionally, the material removal mechanism and size effect are also studied. It is found that the MUCT value of GDP determined by model A is between 0.268 and 0.532 μm, and the normalized MUCT value is between 0.148 and 0.295. These results are verified by the specific cutting energy obtained from model B. It is also proved that model B could preliminarily evaluate the MUCT value of GDP without conducting milling experiment. Moreover, below the MUCT threshold, the severe size effect and ploughing effect cause nonlinearly increase of specific cutting energy, and the random variation of cutting force and surface roughness. When the ratio of feed per tooth to cutting edge radius is larger than 0.61, the size effect could be ignored since the cutting mode is shearing.

A successive substitution approach with embedded phase stability for simultaneous chemical and phase equilibrium calculations

We propose a nested Gibbs energy minimization method for simultaneous chemical and phase equilibrium calculations, relying on a new formulation of the Lagrange multiplier based inner sub-problem with fixed activity coefficients. Using a sufficient condition for global optimality with fixed activity coefficients equivalent in this case to the tangent plane distance criterion, we describe two equivalent algorithms, a combinatorial and a complementarity based one, allowing to robustly solve this new sub-problem always incorporating all phases. The outer-loop of the global successive substitution reactive flash then only consists in updating the values of the activity coefficients from the non necessarily normalized species fractions for all phases calculated by the inner sub-problem. Numerical experiments from the literature illustrate the correct behavior of the proposed approach.

Atomistically-informed continuum modeling and isogeometric analysis of 2D materials over holey substrates

This work develops, discretizes, and validates a continuum model of a molybdenum disulfide (MoS2) monolayer interacting with a periodic holey silicon nitride (Si3N4) substrate via van der Waals (vdW) forces. The MoS2 layer is modeled as a geometrically nonlinear Kirchhoff–Love shell, and vdW forces are modeled by a Lennard-Jones (LJ) potential, simplified using approximations for a smooth substrate topography. Both the shell model and LJ interactions include novel extensions informed by close comparison with fully-atomistic calculations. The material parameters of the shell model are calibrated by comparing small-strain tensile and bending tests with atomistic simulations. This model is efficiently discretized using isogeometric analysis (IGA) for the shell structure and a pseudo-time continuation method for energy minimization. The IGA shell model is validated against fully-atomistic calculations for several benchmark problems with different substrate geometries. Agreement with atomistic results depends on geometric nonlinearity in some cases, but a simple isotropic St.Venant–Kirchhoff model is found to be sufficient to represent material behavior. We find that the IGA discretization of the continuum model has a much lower computational cost than atomistic simulations, and expect that it will enable efficient design space exploration in strain engineering applications. This is demonstrated by studying the dependence of strain and curvature in MoS2 over a holey substrate as a function of the hole spacing on scales inaccessible to atomistic calculations. The results show an unexpected qualitative change in the deformation pattern below a critical hole separation.