Minimum Free Energy Method Research Articles

A novel coupled algorithm for Studying the performance characteristics of water ramjet in the flight of supercavitating vehicle

When a supercavitating vehicle performs a flight, the water ramjet of the vehicle exploits the water in the surrounding environment as an oxidiser and is inevitably affected by the vehicle motions. In this study, the characteristics of the performance change in a water ramjet were investigated when a supercavitating vehicle performs a flight to gain more insights into the design of underwater power systems. Given the principle of independent cross-section expansion of cavities, a longitudinal ventilated supercavity model was built to predict the development of a ventilated cavity and its interaction with the body. A thermal calculation model was developed based on the minimum free energy method to calculate the performance parameters of water ramjets. A novel coupling algorithm was proposed based on the aforementioned model to integrate the motion of a supercavitating vehicle with the operation of a water ramjet. The integration described above was achieved by linking the water intake and body motion and calculating the performance change characteristics of the water ramjet during the flight of the supercavitating vehicle. The operating characteristics of the water ramjet with changes in the designed water-fuel ratios were investigated to provide a basis for exploring the unperturbed flight of the vehicle, depth regulation, and underwater environmental changes. The thrust of the water ramjet is less affected by external factors, and its performance feedback tends to exacerbate external disturbances at a designed water-fuel ratio lower than the optimal water-fuel ratio. A water ramjet with a designed water-fuel ratio higher than the optimal water-fuel ratio has a rapid response time, adaptive thrust, and stable combustion chamber pressure. External disturbances slightly affected the thrust and combustion chamber pressure of the water ramjet when the designed water-fuel ratio was equal to the optimal water-fuel ratio. The results of this study provide technical support for optimising the design of water ramjet.

Liquid chemical looping gasification of biomass: Thermodynamic analysis on cellulose

Liquid chemical looping technology is an innovation of chemical looping conversion technology. Using liquid metal oxide as the oxygen carrier during gasification process could prolong the service life of oxygen carrier and improve the process efficiency. In this paper, based on Gibbs minimum free energy method, the thermodynamic characteristics of biomass liquid chemical looping gasification were studied. Cellulose and lignin, the main components of biomass, were taken as the research objects. Bismuth oxide and antimony oxide were selected as liquid oxygen carriers. The results showed that when the temperature increased from 600 °C to 900 °C, the output of H 2 and CO in the products of cellulose gasification increased from 0.5 and 0.3 kmol to 1.3 and 2.6 kmol respectively. Different ratios of oxygen carriers to gasification raw materials had the best molar ratio. The addition of steam in the system was beneficial to the increase of H 2 content and the increase of H 2 /CO molar ratio. Bi 2 O 3 and Sb 2 O 3 with different mass ratios were used as mixed oxygen carriers. The simulation results showed that the gasification temperature of biomass with different mixed oxygen carriers had the same equilibrium trend products. It could be seen from the results of product distribution that the influence of the mixing ratio of Bi 2 O 3 and Sb 2 O 3 on gas product distribution could be neglected. These results could provide simulation reference and data basis for subsequent research on liquid chemical looping gasification.

Thermodynamic Study on Reduction of Iron Oxides by H2 + CO + CH4 + N2 Mixture at 900 °C

The reduction gas used in the gas-based direct reduction iron-making process contains CH4 in different concentrations, which has an important effect on the gas and heat needed for the reduction of iron oxide. To investigate the influence of CH4 on gas utilization rate and heat needed at 900 °C, the initial conditions are set as H2% + CO% = 90, CH4% + N2% = 10, gas pressure 1–9 atm, and 0.5 mol Fe2O3, and the equilibrium state composition is calculated using the minimum free energy method. The utilization rate of total gas can be improved, and gas demand can be decreased by increasing CH4 concentration or H2 concentration or reducing gas pressure. For the production of per ton of Fe from 25 °C to 900 °C, 6.08–7.29 m3 of reduction gas, and 7.338–8.952 MJ of gas sensible heat can be saved by increasing 1 m3 CH4, while 10.959–11.189 MJ of reaction heat is increased. Compared with 3390.828–3865.760 MJ of the total heat of per ton of Fe for the reduction by H2 + CO, 2.174–3.703 MJ of total heat is increased by increasing 1 m3 CH4, and the increase ratio is 0.065–0.096%. This study is helpful to improve the gas efficiency and lower the pursuit of higher concentration of H2 + CO in reduction gas.

Thermal Behaviors and Their Correlations of Mg(BH4)2-Contained Explosives

ABSTRACTIn order to explore the effect of metal hydride on energetic materials’ thermal behaviors and their correlations, we studied the heats of combustion and detonation of RDX, TNT, and Mg(BH4)2-containing explosives both theoretically and experimentally. The results showed that Mg(BH4)2 can significantly improve the energy of explosive. As the mass fraction of Mg(BH4)2 increases, the combustion heat of composite explosives increases gradually, while the combustion efficiency decreases. When its mass fraction is about 30%, the theoretical heats of detonation of RDX/Mg(BH4)2 and TNT/Mg(BH4)2 reach maximum, which are 7418.47 and 7032.46 kJ/kg, respectively. When we compared the errors between calculation and experimental values, we found that L-C method is more accurate in calculating oxygen-enriched and oxygen-balanced explosives, and that minimum free energy method is more suitable for seriously negative oxygen-balanced explosive. For single explosive, there are three kinds of relationships between heat of combustion and detonation according to the oxygen balance. For Mg(BH4)2-containing explosives, the relationship is in accordance with Boltzmann function.

Influences of pH and CO2 on the formation of Metasilicate mineral water in Changbai Mountain, Northeast China

Mineral dissolution reactions actively participate in controlling the composition of mineral water. In this study, water soluble, acidic–alkaline and carbonated solution experiments were designed, and mineral reaction mechanisms were researched using chemical kinetics and the minimum free-energy method. The results showed that the release of metasilicate was controlled by pH, CO2, and rock characteristics. In the water soluble experiment, the release process of metasilicate in powdered rocks reached equilibrium after 40 days, while metasilicate in solid rocks took 170 days. The release process of metasilicate in solid rocks satisfied an asymptotic model, while in powdered rocks it accorded with the Stanford reaction kinetic model. In the acidic–alkaline experiment, metasilicate was released earlier under acidic conditions (2.46 < pH < 7) than under alkaline conditions (7 < pH < 10.61). The release process of metasilicate under acidic conditions reached equilibrium in 40 days, compared with 60 days for alkaline conditions. The addition of CO2 to the water solution was beneficial to the formation of metasilicate. Under neutral pH conditions, the reaction barely occurred. Under alkaline conditions, metasilicate was produced by the hydrolysis of metasilicate minerals. Under acidic and additional CO2 conditions, metasilicate formation was mainly via the reaction of H+, CO2, and metasilicate minerals. From these results, we concluded that the metasilicate mineral water from the Changbai Mountains, Jingyu County, is generated by a combination of the hydrolysis of metasilicate minerals and the reaction of H+, CO2, and metasilicate minerals. These results can contribute to a better development and protection of the mineral water resources in the Changbai Mountains.

Phylogenetic reconstruction of endophytic fungal isolates using internal transcribed spacer 2 (ITS2) region.

Endophytic fungi are inhabitants of plants, living most part of their lifecycle asymptomatically which mainly confer protection and ecological advantages to the host plant. In this present study, 48 endophytic fungi were isolated from the leaves of three medicinal plants and characterized based on ITS2 sequence – secondary structure analysis. ITS2 secondary structures were elucidated with minimum free energy method (MFOLD version 3.1) and consensus structure of each genus was generated by 4SALE. ProfDistS was used to generate ITS2 sequence structure based phylogenetic tree respectively. Our elucidated isolates were belonging to Ascomycetes family, representing 5 orders and 6 genera. Colletotrichum/Glomerella spp., Diaporthae/Phomopsis spp., and Alternaria spp., were predominantly observed while Cochliobolus sp., Cladosporium sp., and Emericella sp., were represented by singletons. The constructed phylogenetic tree has well resolved monophyletic groups with >50% bootstrap value support. Secondary structures based fungal systematics improves not only the stability; it also increases the precision of phylogenetic inference. Above ITS2 based phylogenetic analysis was performed for our 48 isolates along with sequences of known ex-types taken from GenBank which confirms the efficiency of the proposed method. Further, we propose it as superlative marker for reconstructing phylogenetic relationships at different taxonomic levels due to their lesser length.

Wild-type and molten globular chorismate mutase achieve comparable catalytic rates using very different enthalpy/entropy compensations

The origin of the catalytic power of enzymes with a meta-stable native state, e.g. molten globular state, is an unsolved challenging issue in biochemistry. To help understand the possible differences between this special class of enzymes and the typical ones, we report here computer simulations of the catalysis of both the well-folded wild-type and the molten globular mutant of chorismate mutase. Using the ab initio quantum mechanical/molecular mechanical minimum free-energy path method, we determined the height of reaction barriers that are in good agreement with experimental measurements. Enzyme-substrate interactions were analyzed in detail to identify factors contributing to catalysis. Computed angular order parameters of backbone N-H bonds and side-chain methyl groups suggested site-specific, non-uniform rigidity changes of the enzymes during catalysis. The change of conformational entropy from the ground state to the transition state revealed distinctly contrasting entropy/enthalpy compensations in the dimeric wild-type enzyme and its molten globular monomeric variant. A unique catalytic strategy was suggested for enzymes that are natively molten globules: some may possess large conformational flexibility to provide strong electrostatic interactions to stabilize the transition state of the substrate and compensate for the entropy loss in the transition state. The equilibrium conformational dynamics in the reactant state were analyzed to quantify their contributions to the structural transitions enzymes needed to reach the transition states. The results suggest that large-scale conformational dynamics make important catalytic contributions to sampling conformational regions in favor of binding the transition state of substrate.

Viral IRES Prediction System - a Web Server for Prediction of the IRES Secondary Structure In Silico

The internal ribosomal entry site (IRES) functions as cap-independent translation initiation sites in eukaryotic cells. IRES elements have been applied as useful tools for bi-cistronic expression vectors. Current RNA structure prediction programs are unable to predict precisely the potential IRES element. We have designed a viral IRES prediction system (VIPS) to perform the IRES secondary structure prediction. In order to obtain better results for the IRES prediction, the VIPS can evaluate and predict for all four different groups of IRESs with a higher accuracy. RNA secondary structure prediction, comparison, and pseudoknot prediction programs were implemented to form the three-stage procedure for the VIPS. The backbone of VIPS includes: the RNAL fold program, aimed to predict local RNA secondary structures by minimum free energy method; the RNA Align program, intended to compare predicted structures; and pknotsRG program, used to calculate the pseudoknot structure. VIPS was evaluated by using UTR database, IRES database and Virus database, and the accuracy rate of VIPS was assessed as 98.53%, 90.80%, 82.36% and 80.41% for IRES groups 1, 2, 3, and 4, respectively. This advance useful search approach for IRES structures will facilitate IRES related studies. The VIPS on-line website service is available at http://140.135.61.250/vips/.

New Heuristic Algorithm of RNA Structure Prediction Including Pseudoknots

Computational models and methods for predicting secondary structure of RNA sequence are in demand. Based on MFE principle and the relative stability of the n-stems in RNA molecules, Minimum Free Energy method is adopted widely to predict RNA secondary structure. An improved heuristic algorithm is presented to predict RNA pseudoknotted structure, and it can compute arbitrary pseudoknots. The algorithm requires O(n 3 ) time and O(n 2 ) space. This algorithm not only reduces the time complexity to O(n 3 ), but also widens the maximum length of the RNA sequence. The preliminary experimental test on the RNA families in PseudoBase shows that the algorithm is more effective than the existing algorithms.

Research on the TNT Equivalence of Aluminized Explosive

Aluminum as an important fuel component has been widely used in the field of arms and ammunition. The Determination of TNT equivalent of aluminized explosive, focused on the experimental study, is still lack of numerical calculation study. It is one of the main factors on safety research, so that effective measures should be taken to determine the TNT equivalence of aluminized explosive. In previous studies, the determination of TNT equivalence of aluminized explosive is mainly based on experimental study. But the affection to its explosive heat due to different ratio of aluminum powder is neglected in experiment researches. Based on the minimum free energy method, this paper programmed composition with Matlab. The equilibrium products of aluminized explosive detonation were calculated. The TNT equivalence of aluminized explosive with different ratio was determined. The results show that for the same mass of aluminized explosive, the higher mass fraction of aluminum powder was, the higher thermal damage to the environment was.

Characteristics of NEPE Propellant with Ammonium Dinitramide (ADN)

The theoretical performances of NEPE (nitrate ester plasticized polyether) propellant with and without ADN were calculated with minimum free energy method. The burning characteristics and the thermal decomposition of propellants were determined by nickel chromium wire method and TG- DTG, respectively. The SEM of NEPE propellants and the mechanical sensitivity were also detected. The results show that the specific impulse and the adiabatic flame temperature are increase with an increase in the content of ADN oxidizer. The burning rate and pressure exponent of propellant with a change of pat content of ADN can be boosted higher than those of the AP formulations.

Autocatalytic intramolecular isopeptide bond formation in gram-positive bacterial pili: a QM/MM simulation.

Many gram-positive pathogens possess external pili or fimbriae with which they adhere to host cells during the infection process. Unusual dual intramolecular isopeptide bonds between Asn and Lys side chains within the N-terminal and C-terminal domains of the pilus subunits have been observed initially in the Streptococcus pyogenes pilin subunit Spy0128 and subsequently in GBS52 from Streptococcus agalactiae, in the BcpA major pilin of Bacillus cereus and in the RrgB pilin of Streptococcus pneumoniae, among others. Within each pilin subunit, intramolecular isopeptide bonds serve to stabilize the protein. These bonds provide a means to withstand large external mechanical forces, as well as possibly assisting in supporting a conformation favored for pilin subunit polymerization via sortase transpeptidases. Genome-wide analyses of pili-containing gram-positive bacteria are known or suspected to contain isopeptide bonds in pilin subunits. For the autocatalytic formation of isopeptide cross-links, a conservation of three amino acids including Asn, Lys, and a catalytically important acidic Glu (or Asp) residue are responsible. However, the chemical mechanism of how isopeptide bonds form within pilin remains poorly understood. Although it is possible that several mechanistic paths could lead to isopeptide bond formation in pili, the requirement of a conserved glutamate and highly organized positioning of residues within the hydrophobic environment of the active site were found in numerous pilin crystal structures such as Spy0128 and RrgB. This suggests a mechanism involving direct coupling of lysine side chain amine to the asparagine carboxamide mediated by critical acid/base or hydrogen bonding interactions with the catalytic glutamate residue. From this mechanistic perspective, we used the QM/MM minimum free-energy path method to examine the reaction details of forming the isopeptide bonds with Spy0128 as a model pilin, specifically focusing on the role of the glutamate in catalysis. It was determined that the reaction mechanism likely consists of two major steps: the nucleophilic attack on Cγ by nitrogen in the unprotonated Lys ε-amino group and, then two concerted proton transfers occur during the formation of the intramolecular isopeptide bond to subsequently release ammonia. More importantly, within the dual active sites of Spy0128, Glu(117), and Glu(258) residues function as crucial catalysts for each isopeptide bond formation, respectively, by relaying two proton transfers. This work also suggests that domain-domain interactions within Spy0128 may modulate the reactivity of residues within each active site. Our results may hopefully shed light on the molecular mechanisms of pilin biogenesis in gram-positive bacteria.

IRSS: a web-based tool for automatic layout and analysis of IRES secondary structure prediction and searching system in silico

BackgroundInternal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for bi-cistronic expression vectors. Most existing RNA structure prediction programs are unable to deal with IRES elements.ResultsWe designed an IRES search system, named IRSS, to obtain better results for IRES prediction. RNA secondary structure prediction and comparison software programs were implemented to construct our two-stage strategy for the IRSS. Two software programs formed the backbone of IRSS: the RNAL fold program, used to predict local RNA secondary structures by minimum free energy method; and the RNA Align program, used to compare predicted structures. After complete viral genome database search, the IRSS have low error rate and up to 72.3% sensitivity in appropriated parameters.ConclusionIRSS is freely available at this website . In addition, all source codes, precompiled binaries, examples and documentations are downloadable for local execution. This new search approach for IRES elements will provide a useful research tool on IRES related studies.

Two-Dimensional Spectral Estimation by Free Energy Minimization

Kiernan, P., Two-Dimensional Spectral Estimation by Free Energy Minimization,Digital Signal Processing6 (1996), 160–168.We present a high-resolution 2-D minimum free energy (MFE) spectral estimation technique which is a 2-D extension of the MFE spectral estimation method. We demonstrate the performance of the technique for spectral estimation of closely spaced 2-D sinusoids in white Gaussian noise. Results from our tests on the effect of signal processing temperature illustrate that our method provides accurate low model order autoregressive spectral estimation. The method provides superior spectral estimation with similar computational burden to that achieved with the Levinson algorithm for a number of cases involving sinusoids in white noise at various signal-to-noise ratio (SNR) levels. An example is provided. The method is faster than the modified covariance method (MCV). An example is given from a number of cases involving two closely spaced sinusoids at low SNR, where MFE estimates are as well resolved as MCV estimates. MFE models may also be used for correlation extension and for field modeling and synthesis. We indicate possible extensions to the MFE method for computational efficiency improvement, a priori temperature determination, and the use of higher-order statistics.

High resolution two-dimensional minimum free energy AR spectral estimation

We extend the minimum free energy (MFE) parameter estimation method to 2-D fields. This 2-D MFE method may be used to determine autoregressive (AR) model parameters for spectral estimation of 2-D fields. It may also be used to provide AR models for texture synthesis. The performance of the technique for closely spaced sinusoids in white noise is demonstrated by numerical example. Better results can be achieved than with the multidimensional Levinson algorithm.

Two-dimensional AR spectral estimation using a two-dimensional minimum free energy method

We present a 2-D extension of the minimum free energy (MFE) autoregressive parameter and spectral estimation technique. MFE can outperform the multidimensional Levinson algorithm producing superior spectral estimation of 2-D sinusoids in white Gaussian noise. MFE spectral estimates are found to be comparable to modified covariance method estimates. MFE also outperforms the conventional Fourier method for closely spaced sinusoids at low signal-to-noise ratio and low data set size.

A minimum free-energy hybrid algorithm for 2-D spectral estimation

A separable quasi 2-D spectral estimation algorithm is presented. This hybrid algorithm combines the 1-D minimum free-energy method with the 1-D periodogram. The algorithm reduces to the corresponding maximum entropy hybrid spectral estimator in some cases. The minimum free-energy hybrid algorithm is preferable to the maximum entropy version when the estimated autocorrelation sequence is not extendable or when the signal-to-noise ratio is low. A simulation helps illustrate this point.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Recursive autoregressive spectral estimation by minimization of the free energy

A digital signal processing technique applicable to power spectrum estimation, designated as the minimum free energy method, is described. With no a priori model assumption and no attempt to extract special features such as sinusoids, one can obtain high resolution even with high noise contamination of the measured signal. The technique is demonstrated by modification of the Burg recursive method of spectral analysis. A recursive minimum free energy method in which the reflection coefficient is chosen at each step is proposed for minimizing the free energy (the Burg energy measure minus the product of a temperature and an information entropy). The method produces a spectral estimator more impervious to high noise contamination than the Burg method and diminishes the Burg tendency to produce spurious peaks.< <ETX xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">&gt;</ETX>

Minimum-free-energy method of spectral estimation: autocorrelation-sequence approach

A new method of parametric spectral estimation, which is called minimum-free-energy (MFE) estimation, is introduced. The MFE method produces a generic theoretic estimation model that is particularly relevant to signal-analysis problems that suffer from incomplete and/or noisy data. In the general MFE formulation, the objective function is defined as a linear combination of a mean-square-error-energy expression and a signal entropy expression. This objective function form is analogous to a free-energy function in statistical thermodynamics. The negative coefficient of the entropy term is represented by an effective signal-processing temperature that drives noise-induced fluctuations in the statistical model. The model parameters that characterize the spectrum are determined commensurate with a minimum of the objective function. The mathematical details and solution methods are developed for a specific embodiment of the MFE method, called the MFE-ACS method, in which the error energy is defined as the window-weighted sum of the absolute square of the difference between the initial and final estimated values of the autocorrelation sequence. The order of the autocorrelation sequence used corresponds to the parametric model order for the spectral estimation procedure. Simulations for a variety of narrow-band and broadband test signals and combinations thereof are presented. These simulations are performed for a variety of signal-to-noise-ratio (SNR) scenarios. The MFE algorithms have a broad application domain because they are not restricted to narrow-band sources as are the signal–noise-subspace algorithms. The MFE-ACS algorithm is shown to compare quite favorably with the signal-subspace Tufts–Kumaresan noise-reduced modified-covariance algorithm for closely separated narrow-band sources in the low-SNR regime (∼10 dB).

Minimum energy analysis of membrane deformation applied to pipet aspiration and surface adhesion of red blood cells

An experimental procedure is demonstrated which can be used to determine the interfacial free energy density for red cell membrane adhesion and membrane elastic properties. The experiment involves micropipet aspiration of a flaccid red blood cell and manipulation of the cell proximal to a surface where adhesion occurs. A minimum free energy method is developed to model the equilibrium contour of unsupported membrane regions and to evaluate the partial derivatives of the total free energy, which correspond to the micropipet suction force and the interfacial free energy density of adhesion. It is shown that the bending elasticity of the red cell membrane does not contribute significantly to the pressure required to aspirate a flaccid red cell. Based on experimental evidence, the upper bound for the bending or curvature elastic modulus of the red cell membranes is 10-12 ergs (dyn-cm). Analysis of the adhesion experiment shows that interfacial free energy densities for red cell adhesion can be measured from a lower limit of 10-4 ergs/cm2 to an upper limit established by the membrane tension for lysis of 5-10 ergs/cm2.