Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics.Force spectroscopy experiments by optical tweezers and atomic force microscopy have m...Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics.Force spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling geometry.However,the equilibrium folding and unfolding dynamics at constant forces has not been reported.Here,using stable magnetic tweezers,we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N-and C-termini.From the obtained force-dependent transition rates,a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy,transition state barrier height and position,which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.展开更多
We build a double quantum-dot system with Coulomb coupling and aim at studying connections among the entropy production,free energy,and information flow.By utilizing concepts in stochastic thermodynamics and graph the...We build a double quantum-dot system with Coulomb coupling and aim at studying connections among the entropy production,free energy,and information flow.By utilizing concepts in stochastic thermodynamics and graph theory analysis,Clausius and nonequilibrium free energy inequalities are built to interpret local second law of thermodynamics for subsystems.A fundamental set of cycle fluxes and affinities is identified to decompose two inequalities by using Schnakenberg's network theory.Results show that the thermodynamic irreversibility has energy-related and information-related contributions.A global cycle associated with the feedback-induced information flow would pump electrons against the bias voltage,which implements a Maxwell demon.展开更多
Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simul...Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins.The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge)were investigated.Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding,peptide capping has the largest influence on the predicted free energy of binding.Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.展开更多
The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa an...The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa and choosingappropriate reaction coordinae, a reasonable free energy dinram is constructed and thercorganhaion energy for the product state is calculated.展开更多
The theory of phase transitions is one of the branches of statistical physics in which smoothness and continuity play an important role. In fact, phase transitions are characterized mathematically by the degree of non...The theory of phase transitions is one of the branches of statistical physics in which smoothness and continuity play an important role. In fact, phase transitions are characterized mathematically by the degree of non-analyticity of the thermodynamic potentials associated with the given system. In this paper, we propose a method that is not based on cluster expansions for computing the higher derivatives of the free energy and estimating the error between the finite and infinite volume free energy in certain continuum gas models. Our approach is suitable for a direct proof of the analyticity of the pressure or free energy in certain models of Kac-type. The methods known up to now strongly rely on the validity of the cluster expansion. An extension of the method to classical lattice gas models is also discussed.展开更多
Online monitoring and diagnosis of production processes face great challenges due to the nonlinearity and multivariate of complex industrial processes.Traditional process monitoring methods employ kernel function or m...Online monitoring and diagnosis of production processes face great challenges due to the nonlinearity and multivariate of complex industrial processes.Traditional process monitoring methods employ kernel function or multilayer neural networks to solve the nonlinear mapping problem of data.However,the above methods increase the model complexity and are not interpretable,leading to difficulties in subsequent fault recognition/diagnosis/location.A process monitoring and diagnosis method based on the free energy of Gaussian-Bernoulli restricted Boltzmann machine(GBRBM-FE)was proposed.Firstly,a GBRBM network was established to make the probability distribution of the reconstructed data as close as possible to the probability distribution of the raw data.On this basis,the weights and biases in GBRBM network were used to construct F statistics,which represents the free energy of the sample.The smaller the energy of the sample is,the more normal the sample is.Therefore,F statistics can be used to monitor the production process.To diagnose fault variables,the F statistic for each sample was decomposed to obtain the Fv statistic for each variable.By analyzing the deviation degree between the corresponding variables of abnormal samples and normal samples,the cause of process abnormalities can be accurately located.The application of converter steelmaking process demonstrates that the proposed method outperforms the traditional methods,in terms of fault monitoring and diagnosis performance.展开更多
The purpose of this study is to develop a standard methodology for measuring the surface free energy (SFE),and its component parts of bamboo fiber materials.The current methods was reviewed to determine the surface te...The purpose of this study is to develop a standard methodology for measuring the surface free energy (SFE),and its component parts of bamboo fiber materials.The current methods was reviewed to determine the surface tension of natural fibers and the disadvantages of techniques used were discussed.Although numerous techniques have been employed to characterize surface tension of natural fibers,it seems that the credibility of results obtained may often be dubious.In this paper,critical surface tension estimates were obtained from computer aided machine vision based measurement.Data were then analyzed by the least squares method to estimate the components of SFE.SFE was estimated by least squares analysis and also by Schultz' method.By using the Fowkes method the polar and disperse fractions of the surface free energy of bamboo fiber materials can be obtained.Strictly speaking,this method is based on a combination of the knowledge of Fowkes theory. SFE is desirable when adhesion is required,and it avoids some of the limitations of existing studies which has been proposed.The calculation steps described in this research are only intended to explain the methods.The results show that the method that only determines SFE as a single parameter may be unable to differentiate adequately between bamboo fiber materials,but it is feasible and very efficient.In order to obtain the maximum performance from the computer aided machine vision based measurement instruments,this measurement should be recommended and kept available for reference.展开更多
β-β″-Al_2O_3 precursor powder was successfully prepared by a solid-phase sintering method with Li_2CO_3,Na_2CO_3 (as the sources of Li_2O and Na_2O, respectively) and α-Al_2O_3 powder as the raw materials. The pre...β-β″-Al_2O_3 precursor powder was successfully prepared by a solid-phase sintering method with Li_2CO_3,Na_2CO_3 (as the sources of Li_2O and Na_2O, respectively) and α-Al_2O_3 powder as the raw materials. The precursor was characterized by X-ray diffraction (XRD) and scan-ning electron microscope (SEM). The results indicate that the amount of Na_2O in the raw materials has a great effect on the formation of β″-Al_2O_3 in the β-β″-Al_2O_3 precursor.When Na_2O content is 10 wt%,the content of β″-Al_2O_3 phase reaches the maximum value of 86.24 wt% in the precursor. The β-β〃-Al_2O_3 ceramic was prepared from β-β″-Al_2O_3 precursor powder by isostatic pressing and burying sintering process. The conductive property of the β-β″-Al_2O_3 ceramic was examined by electrochemical impedance spectroscopy (EIS)method, and the density was measured by the Archimedes method. The results reveal that when 10 wt% Na_2O was added, the sample exhibits the best performance with the lowest resistivity of 4.51 Ω·cm and the highest density of 3.25 g·cm^(-3). A solid electrolyte battery of Pt|SnO_2, Na_2SnO_31|β-β″-Al_2O_3|Na-CrO_2, Cr_2O_3|Pt was assembled by the β-β″-Al_2O_3 elec-trolyte tube to measure the open potential of the resulting battery, and the formation free energy of sodium stannate was calculated. In the temperature range of 1273-773 K,the relationship between formation free energy of sodium stannate and temperature was generated as follows:ΔG_(Na_2SnO_3)~0= —1040.83 + 0.2221T± 7.54.展开更多
Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds,which is a topic of high interest in organic and medicinal ch...Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds,which is a topic of high interest in organic and medicinal chemistry.However,most approaches cannot efficiently predict the potency level of candidates after scaffold hopping.Herein,we identified potent PDE5 inhibitors with a novel scaffold via a free energy perturbation(FEP)-guided scaffold-hopping strategy,and FEP shows great advantages to precisely predict the theoretical binding potenciesΔGFEPbetween ligands and their target,which were more consistent with the experimental binding potenciesΔGEXP(the mean absolute deviations|ΔGFEP-ΔGEXP|<2 kcal/mol)than thoseΔGMM-PBSAorΔGMM-GBSApredicted by the MM-PBSA or MM-GBSA method.Lead L12 had an IC_(50) of 8.7 nmol/L and exhibited a different binding pattern in its crystal structure with PDE5 from the famous starting drug tadalafil.Our work provides the first report via the FEPguided scaffold hopping strategy for potent inhibitor discovery with a novel scaffold,implying that it will have a variety of future applications in rational molecular design and drug discovery.展开更多
Protein folding,stability,and function are usually in-fluenced by pH.And free energy plays a fundamental role in analysis of such pH-dependent properties.Elec-trostatics-based theoretical framework using dielectric so...Protein folding,stability,and function are usually in-fluenced by pH.And free energy plays a fundamental role in analysis of such pH-dependent properties.Elec-trostatics-based theoretical framework using dielectric solvent continuum model and solving Poisson-Boltzm-ann equation numerically has been shown to be very successful in understanding the pH-dependent proper-ties.However,in this approach the exact computation of pH-dependent free energy becomes impractical for proteins possessing more than several tens of ioni-zable sites(e.g.>30),because exact evaluation of the partition function requires a summation over a vast number of possible protonation microstates.Here we present a method which computes the free energy us-ing the average energy and the protonation probabili-ties of ionizable sites obtained by the well-established Monte Carlo sampling procedure.The key feature is to calculate the entropy by using the protonation prob-abilities.We used this method to examine a well-studied protein(lysozyme)and produced results which agree very well with the exact calculations.Applications to the optimum pH of maximal stability of proteins and pro-tein-DNA interactions have also resulted in good agreement with experimental data.These examples recommend our method for application to the elucidation of the pH-dependent properties of proteins.展开更多
The surface free energy of a biomaterial plays an important role in the early stages of cell-biomaterial interactions,profoundly influencing protein adsorption,interfacial water accessibility,and cell attachment on th...The surface free energy of a biomaterial plays an important role in the early stages of cell-biomaterial interactions,profoundly influencing protein adsorption,interfacial water accessibility,and cell attachment on the biomaterial surface.Although multiple approaches have been developed to engineer the surface free energy of biomaterials,systematically tuning their surface free energy without altering other physicochemical properties remains challenging.In this study,we constructed an array of chemically-equivalent surfaces with comparable apparent roughness through assembly of gold nanoparticles adopting various geometrically-distinct shapes but all capped with the same surface ligand,(1-hexadecyl)trimethylammonium chloride,on cell culture substrates.We found that bone marrow stem cells exhibited distinct osteogenic differentiation behaviours when interacting with different types of substrates comprising shape-controlled gold nanoparticles.Our results reveal that bone marrow stem cells are capable of sensing differences in the nanoscale topographical features,which underscores the role of the surface free energy of nanostructured biomaterials in regulating cell responses.The study was approved by Institutional Animal Care and Use Committee,School of Medicine,University of South Carolina.展开更多
Thermochromic wood is a kind of new functional materials. It is significant for thermochromic wood development to study surface free energy. Samples of Chinese white poplar were colored using thermochromic agent thoug...Thermochromic wood is a kind of new functional materials. It is significant for thermochromic wood development to study surface free energy. Samples of Chinese white poplar were colored using thermochromic agent though the method of ultrasonic impregnation and its surface free energy was investigated in the experiment. The results showed that the surface free energy for untreated, black-red, orange-yellow and blue thermochromic wood was 40.25, 29.85, 28.30 and 21.05 mN/m, respectively. The FTIR results showed that both the type and the number of function groups resulted in the change of free energy for untreated and thermochromic wood.展开更多
We present a new theoretical method for efficient calculation of free energy of liquid. This interaction entropy method allows one to compute entropy and free energy of liquid from standard single step MD(molecular dy...We present a new theoretical method for efficient calculation of free energy of liquid. This interaction entropy method allows one to compute entropy and free energy of liquid from standard single step MD(molecular dynamics) simulation directly in liquid state without the need to perform MD simulations at many intermediate states as required in thermodynamic integration or free energy perturbation methods. In this new approach, one only needs to evaluate the interaction energy of a single(fixed) liquid molecule with the rest of liquid molecules as a function of time from a standard MD simulation of liquid and the fluctuation of distribution of this interaction energy is then used to calculate the interaction entropy of the liquid. Explicit theoretical derivation of this interaction entropy approach is provided and numerical calculations for the benchmark liquid water system were carried out using three different water models. Numerical analysis of the result was performed and comparison of the computational result with experimental data and other theoretical results were provided. Excellent agreement of calculated free energies with the experimental data using TIP4 P model is obtained for liquid water.展开更多
The regression model for octanol/water partition coefficients ( K ow ), is founded with only two molecular descriptors available through quantum chemical calculations: solvation free energy (Δ G S ), and solvent acce...The regression model for octanol/water partition coefficients ( K ow ), is founded with only two molecular descriptors available through quantum chemical calculations: solvation free energy (Δ G S ), and solvent accessible surface area (SASA). For the properties of 47 organic compounds from 17 types, the model gives a correction coefficient (adjusted for degrees of freedom) of 0 959 and a standard error of 0 277 log unit. It is a suitable way to predict the partition properties that are related to solute solvent interactions in the water phase.展开更多
We focus on the distribution and free energy of a wormlike polymer confined between two parallel hard walls.The variation in the distribution and free energy of the wormlike chain as the spacing between the walls decr...We focus on the distribution and free energy of a wormlike polymer confined between two parallel hard walls.The variation in the distribution and free energy of the wormlike chain as the spacing between the walls decreases(or as the total contour length of the wormlike chain increases or as the persistence length of the chain increases)is simulated.The main reason for these changes is a degradation of the long wormlike chain into a Gaussian long chain under weak confinement.展开更多
The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)gained tremendous attention due to its high infectivity and pathogenicity.The 3-chymotrypsin-like hydrolase protease(Mpro)of SARS-CoV-2 has been proven to...The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)gained tremendous attention due to its high infectivity and pathogenicity.The 3-chymotrypsin-like hydrolase protease(Mpro)of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity.To better identify the drugs with potential in treating coronavirus disease 2019(COVID-19)caused by SARS-CoV-2 and according to the crystal structure of Mpro,we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials.As a result,9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2.Consequently,molecular dynamics(MD)simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro.The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes.Based on the binding free energy calculated by using MM/PBSA,Lopiravir,an inhibitor of human immunodeficiency virus(HIV)protease,is under investigation for the treatment of COVID-19 in combination with ritionavir,and it might inhibit Mpro effectively.Moreover,Ombitasvir,an inhibitor for non-structural protein 5 A of hepatitis C virus(HCV),has good inhibitory potency for Mpro.It is notable that the GS-6620 has a binding free energy,with respect to binding Mpro,comparable to that of ombitasvir.Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19,and that GS-6620 has good anti-SARS-CoV-2 activity.展开更多
As an important building block for the synthesis of angiotensin-converting enzyme inhibitors,ethyl(R)-2-hy-droxyl-4-phenylbutanoate[(R)-HPBE]has attracted increasing attention.The key to industrial biosynthesis of(R)-...As an important building block for the synthesis of angiotensin-converting enzyme inhibitors,ethyl(R)-2-hy-droxyl-4-phenylbutanoate[(R)-HPBE]has attracted increasing attention.The key to industrial biosynthesis of(R)-HPBE is a biocatalyst that efficiently reduces ethyl 2-oxo-4-phenylbutanoate(OPBE)with high R-enantiose-lectivity.This paper proposed a strategy for identifying key residues involved in enantioselectivity control based on per-residue free energy decomposition and sequence conservatism analysis.Using this strategy,4 noncon-servative sites with high energy contribution to binding of OPBE were chosen as engineering targets,generating variant Mu27 with 99%conversion and 98%(R)ee value at substrate loading of up to 500 mmol/L.MD simu-lations suggested the higher stability and formation probability of Mu27-OPBEproR prereaction state as key rea-sons for the excellent R-enantioselectivity of Mu27 towards OPBE.The success in this study provides a viable approach for rational design of alcohol dehydrogenases with high enantioselectivity towards unnatural substrates.展开更多
In this paper,it is shown that for stable,steady state operation of devices typical of microwave and millimeter wave electronics,no negative differential capacitance is possible with conventional thinking.However,it m...In this paper,it is shown that for stable,steady state operation of devices typical of microwave and millimeter wave electronics,no negative differential capacitance is possible with conventional thinking.However,it may be possible,with strain engineering of materials,to obtain some if not all elements of the differential capacitance tensor which are negative.Rigorous derivations are provided based upon analyzing the physics using thermodynamic phenomenological free energy.It should be emphasized that,even with strain engineering,and possible discovery of some negative capacitive elements,stable operation will not be obtained because the thermodynamics precludes it.展开更多
PrBa_(0.5)Sr_(0.5)Co_(1.5)Fe_(0.5)O_(5+δ)(PrBSCF) has attracted much research interest as a potential triple ionic and electronic conductor(TIEC) electrode for protonic ceramic fuel cells(PCFCs). The chemical formula...PrBa_(0.5)Sr_(0.5)Co_(1.5)Fe_(0.5)O_(5+δ)(PrBSCF) has attracted much research interest as a potential triple ionic and electronic conductor(TIEC) electrode for protonic ceramic fuel cells(PCFCs). The chemical formula for Pr BSCF is AA'B_(2)O_(5+δ), with Pr(A-site) and Ba/Sr(A'-site) alternately stacked along the c-axis. Due to these structural features, the bulk oxygen ion diffusivity is significantly enhanced through the disorder-free channels in the PrO layer;thus, the A site cations(lanthanide ions) play a pivotal role in determining the overall electrochemical properties of layered perovskites. Consequently, previous research has predominantly focused on the electrical properties and oxygen bulk/surface kinetics of Ln cation effects,whereas the hydration properties for PCFC systems remain unidentified. Here, we thoroughly examined the proton uptake behavior and thermodynamic parameters for the hydration reaction to conclusively determine the changes in the electrochemical performances depending on LnBa_(0.5)Sr_(0.5)Co_(1.5)Fe_(0.5)O_(5+δ)(LnBSCF,Ln=Pr, Nd, and Gd) cathodes. At 500 ℃, the quantitative proton concentration of PrBSCF was 2.04 mol% and progressively decreased as the Ln cation size decreased. Similarly, the Gibbs free energy indicated that less energy was required for the formation of protonic defects in the order of Pr BSCF < Nd BSCF < Gd BSCF. To elucidate the close relationship between hydration properties and electrochemical performances in LnBSCF cathodes, PCFC single cell measurements and analysis of the distribution of relaxation time were further investigated.展开更多
The thermodynamical properties of MgCl2 in KCI-MgCl2-LiCl molten electrolytes containing MgCl2 below 0.5 （mole fraction, the same below） have been determined from the interchange energies of two binary systems KCI-M...The thermodynamical properties of MgCl2 in KCI-MgCl2-LiCl molten electrolytes containing MgCl2 below 0.5 （mole fraction, the same below） have been determined from the interchange energies of two binary systems KCI-MgCl2 and LiCI-MgCl2, by means of a model on the assumptions that the electrolytes in the solution are treated as independent particles instead of their ion forms and the interchange energy between the component pair KCI-LiCl is ignored when compared with those of component pairs KCl-MgCl2 and MgCl2-LiCl. The interchange energies, wKCl-MgCl2 and wMgcCl2-Licl, are obtained as-70000 and -13800 J.mol-1, from the corresponding binary solutions, respectively.展开更多
基金the National Natural Science Foundation of China(Grant Nos.11874309 and 11474237)the 111 Project(Grant No.B16029)。
文摘Src SH3 protein domain is a typical two-state protein which has been confirmed by research of denaturant-induced unfolding dynamics.Force spectroscopy experiments by optical tweezers and atomic force microscopy have measured the force-dependent unfolding rates with different kinds of pulling geometry.However,the equilibrium folding and unfolding dynamics at constant forces has not been reported.Here,using stable magnetic tweezers,we performed equilibrium folding and unfolding dynamic measurement and force-jump measurement of src SH3 domain with tethering points at its N-and C-termini.From the obtained force-dependent transition rates,a detailed two-state free energy landscape of src SH3 protein is constructed with quantitative information of folding free energy,transition state barrier height and position,which exemplifies the capability of magnetic tweezers to study protein folding and unfolding dynamics.
基金Project supported by the National Natural Science Foundation(Grant No.11805159)the First Batch of National First-class Undergraduate Courses of China(2020)+1 种基金the Natural Science Foundation of Fujian Province,China(Grant No.2019J05003)Teaching Research Program of Thermodynamics and Statistical Physics in the Institution of Higher Education of China(2019).
文摘We build a double quantum-dot system with Coulomb coupling and aim at studying connections among the entropy production,free energy,and information flow.By utilizing concepts in stochastic thermodynamics and graph theory analysis,Clausius and nonequilibrium free energy inequalities are built to interpret local second law of thermodynamics for subsystems.A fundamental set of cycle fluxes and affinities is identified to decompose two inequalities by using Schnakenberg's network theory.Results show that the thermodynamic irreversibility has energy-related and information-related contributions.A global cycle associated with the feedback-induced information flow would pump electrons against the bias voltage,which implements a Maxwell demon.
基金the State Key Laboratory of Phytochemistry and Plant Resources in West China,Kunming Institute of Botany,Chinese Academy of Sciences(P2013-ZZ05).
文摘Coiled-coils are well known protein–protein interaction motifs,with the leucine zipper region of activator protein-1(AP-1)consisting of the c-Jun and c-Fos proteins being a typical example.Molecular dynamics(MD)simulations using the MM/GBSA method have been used to predict the free energy of interaction of these proteins.The influence of force field polarisation and capping on the predicted free energy of binding of complexes with different electrostatic environments(net charge)were investigated.Although both force field polarisation and peptide capping are important for the prediction of the absolute free energy of binding,peptide capping has the largest influence on the predicted free energy of binding.Polarisable simulations appear better suited to determine structural properties of the complexes of these proteins while non-polarisable simulations seem to give better predictions of the associated free energies of binding.
文摘The microscopic moleeular theory for electron transfer in a model solvent ishahr developed. The nonlinear response of the solvent molecules is be computedquanitatively in a new way. Adopting computer simulation daa and choosingappropriate reaction coordinae, a reasonable free energy dinram is constructed and thercorganhaion energy for the product state is calculated.
文摘The theory of phase transitions is one of the branches of statistical physics in which smoothness and continuity play an important role. In fact, phase transitions are characterized mathematically by the degree of non-analyticity of the thermodynamic potentials associated with the given system. In this paper, we propose a method that is not based on cluster expansions for computing the higher derivatives of the free energy and estimating the error between the finite and infinite volume free energy in certain continuum gas models. Our approach is suitable for a direct proof of the analyticity of the pressure or free energy in certain models of Kac-type. The methods known up to now strongly rely on the validity of the cluster expansion. An extension of the method to classical lattice gas models is also discussed.
基金the financial support from the National Key R&D Program of China(Grant No.2020YFA0405700).
文摘Online monitoring and diagnosis of production processes face great challenges due to the nonlinearity and multivariate of complex industrial processes.Traditional process monitoring methods employ kernel function or multilayer neural networks to solve the nonlinear mapping problem of data.However,the above methods increase the model complexity and are not interpretable,leading to difficulties in subsequent fault recognition/diagnosis/location.A process monitoring and diagnosis method based on the free energy of Gaussian-Bernoulli restricted Boltzmann machine(GBRBM-FE)was proposed.Firstly,a GBRBM network was established to make the probability distribution of the reconstructed data as close as possible to the probability distribution of the raw data.On this basis,the weights and biases in GBRBM network were used to construct F statistics,which represents the free energy of the sample.The smaller the energy of the sample is,the more normal the sample is.Therefore,F statistics can be used to monitor the production process.To diagnose fault variables,the F statistic for each sample was decomposed to obtain the Fv statistic for each variable.By analyzing the deviation degree between the corresponding variables of abnormal samples and normal samples,the cause of process abnormalities can be accurately located.The application of converter steelmaking process demonstrates that the proposed method outperforms the traditional methods,in terms of fault monitoring and diagnosis performance.
基金the National Natural Science Foundation of China(No.31101085)the Scientific Research and Development Foundation for Start-up Projects of Zhejiang Agriculture and Forestry University (No.2034020044)
文摘The purpose of this study is to develop a standard methodology for measuring the surface free energy (SFE),and its component parts of bamboo fiber materials.The current methods was reviewed to determine the surface tension of natural fibers and the disadvantages of techniques used were discussed.Although numerous techniques have been employed to characterize surface tension of natural fibers,it seems that the credibility of results obtained may often be dubious.In this paper,critical surface tension estimates were obtained from computer aided machine vision based measurement.Data were then analyzed by the least squares method to estimate the components of SFE.SFE was estimated by least squares analysis and also by Schultz' method.By using the Fowkes method the polar and disperse fractions of the surface free energy of bamboo fiber materials can be obtained.Strictly speaking,this method is based on a combination of the knowledge of Fowkes theory. SFE is desirable when adhesion is required,and it avoids some of the limitations of existing studies which has been proposed.The calculation steps described in this research are only intended to explain the methods.The results show that the method that only determines SFE as a single parameter may be unable to differentiate adequately between bamboo fiber materials,but it is feasible and very efficient.In order to obtain the maximum performance from the computer aided machine vision based measurement instruments,this measurement should be recommended and kept available for reference.
基金financially supported by the National Natural Science Foundation of China (No.51234009)
文摘β-β″-Al_2O_3 precursor powder was successfully prepared by a solid-phase sintering method with Li_2CO_3,Na_2CO_3 (as the sources of Li_2O and Na_2O, respectively) and α-Al_2O_3 powder as the raw materials. The precursor was characterized by X-ray diffraction (XRD) and scan-ning electron microscope (SEM). The results indicate that the amount of Na_2O in the raw materials has a great effect on the formation of β″-Al_2O_3 in the β-β″-Al_2O_3 precursor.When Na_2O content is 10 wt%,the content of β″-Al_2O_3 phase reaches the maximum value of 86.24 wt% in the precursor. The β-β〃-Al_2O_3 ceramic was prepared from β-β″-Al_2O_3 precursor powder by isostatic pressing and burying sintering process. The conductive property of the β-β″-Al_2O_3 ceramic was examined by electrochemical impedance spectroscopy (EIS)method, and the density was measured by the Archimedes method. The results reveal that when 10 wt% Na_2O was added, the sample exhibits the best performance with the lowest resistivity of 4.51 Ω·cm and the highest density of 3.25 g·cm^(-3). A solid electrolyte battery of Pt|SnO_2, Na_2SnO_31|β-β″-Al_2O_3|Na-CrO_2, Cr_2O_3|Pt was assembled by the β-β″-Al_2O_3 elec-trolyte tube to measure the open potential of the resulting battery, and the formation free energy of sodium stannate was calculated. In the temperature range of 1273-773 K,the relationship between formation free energy of sodium stannate and temperature was generated as follows:ΔG_(Na_2SnO_3)~0= —1040.83 + 0.2221T± 7.54.
基金supported by Natural Science Foundation of China(21877134,81872727,22077143,21702238,82003576,and 81703341)Guangzhou Science and Technology Project(The People’s Livelihood Programs for Science and Technology,201803010075,China)+1 种基金Science Foundation of Guangzhou City(201904020023,China)Fundamental Research Funds for Hainan University(KYQD(ZR)-21031,China)。
文摘Scaffold hopping refers to computer-aided screening for active compounds with different structures against the same receptor to enrich privileged scaffolds,which is a topic of high interest in organic and medicinal chemistry.However,most approaches cannot efficiently predict the potency level of candidates after scaffold hopping.Herein,we identified potent PDE5 inhibitors with a novel scaffold via a free energy perturbation(FEP)-guided scaffold-hopping strategy,and FEP shows great advantages to precisely predict the theoretical binding potenciesΔGFEPbetween ligands and their target,which were more consistent with the experimental binding potenciesΔGEXP(the mean absolute deviations|ΔGFEP-ΔGEXP|<2 kcal/mol)than thoseΔGMM-PBSAorΔGMM-GBSApredicted by the MM-PBSA or MM-GBSA method.Lead L12 had an IC_(50) of 8.7 nmol/L and exhibited a different binding pattern in its crystal structure with PDE5 from the famous starting drug tadalafil.Our work provides the first report via the FEPguided scaffold hopping strategy for potent inhibitor discovery with a novel scaffold,implying that it will have a variety of future applications in rational molecular design and drug discovery.
基金This study was supported in part by grants from the National Natural Sci-ence Foundation of China(Grant No.30570406)the HI-tech Re-search and Development Program of China(Grant No.2008AA02Z311)the Shanghai Leading Academic Discipline Project(B111).
文摘Protein folding,stability,and function are usually in-fluenced by pH.And free energy plays a fundamental role in analysis of such pH-dependent properties.Elec-trostatics-based theoretical framework using dielectric solvent continuum model and solving Poisson-Boltzm-ann equation numerically has been shown to be very successful in understanding the pH-dependent proper-ties.However,in this approach the exact computation of pH-dependent free energy becomes impractical for proteins possessing more than several tens of ioni-zable sites(e.g.>30),because exact evaluation of the partition function requires a summation over a vast number of possible protonation microstates.Here we present a method which computes the free energy us-ing the average energy and the protonation probabili-ties of ionizable sites obtained by the well-established Monte Carlo sampling procedure.The key feature is to calculate the entropy by using the protonation prob-abilities.We used this method to examine a well-studied protein(lysozyme)and produced results which agree very well with the exact calculations.Applications to the optimum pH of maximal stability of proteins and pro-tein-DNA interactions have also resulted in good agreement with experimental data.These examples recommend our method for application to the elucidation of the pH-dependent properties of proteins.
基金supported by National Science Foundation(NSF)and South Carolina Experimental Program to Stimulate Competitive Research and Institutional Development Awards(SC EPSCoR/IDeA)Program under NSF Award#OIA-1655740.
文摘The surface free energy of a biomaterial plays an important role in the early stages of cell-biomaterial interactions,profoundly influencing protein adsorption,interfacial water accessibility,and cell attachment on the biomaterial surface.Although multiple approaches have been developed to engineer the surface free energy of biomaterials,systematically tuning their surface free energy without altering other physicochemical properties remains challenging.In this study,we constructed an array of chemically-equivalent surfaces with comparable apparent roughness through assembly of gold nanoparticles adopting various geometrically-distinct shapes but all capped with the same surface ligand,(1-hexadecyl)trimethylammonium chloride,on cell culture substrates.We found that bone marrow stem cells exhibited distinct osteogenic differentiation behaviours when interacting with different types of substrates comprising shape-controlled gold nanoparticles.Our results reveal that bone marrow stem cells are capable of sensing differences in the nanoscale topographical features,which underscores the role of the surface free energy of nanostructured biomaterials in regulating cell responses.The study was approved by Institutional Animal Care and Use Committee,School of Medicine,University of South Carolina.
基金supported by "the 11th Five-year Plan" National Science and Technology support project " the Value-added and Processing Technology of Furniture and Decoration Materials" (Grant No. 2006BAD18B06)
文摘Thermochromic wood is a kind of new functional materials. It is significant for thermochromic wood development to study surface free energy. Samples of Chinese white poplar were colored using thermochromic agent though the method of ultrasonic impregnation and its surface free energy was investigated in the experiment. The results showed that the surface free energy for untreated, black-red, orange-yellow and blue thermochromic wood was 40.25, 29.85, 28.30 and 21.05 mN/m, respectively. The FTIR results showed that both the type and the number of function groups resulted in the change of free energy for untreated and thermochromic wood.
基金supported by the National Natural Science Foundation of China (21603144, 21433004)Ministry of Science and Technology of China (2016YFA0501700)+1 种基金NYU Global Seed Grant, Shanghai Putuo District (2014-A-02)Shanghai Sailing Program (2016YF1408400)
文摘We present a new theoretical method for efficient calculation of free energy of liquid. This interaction entropy method allows one to compute entropy and free energy of liquid from standard single step MD(molecular dynamics) simulation directly in liquid state without the need to perform MD simulations at many intermediate states as required in thermodynamic integration or free energy perturbation methods. In this new approach, one only needs to evaluate the interaction energy of a single(fixed) liquid molecule with the rest of liquid molecules as a function of time from a standard MD simulation of liquid and the fluctuation of distribution of this interaction energy is then used to calculate the interaction entropy of the liquid. Explicit theoretical derivation of this interaction entropy approach is provided and numerical calculations for the benchmark liquid water system were carried out using three different water models. Numerical analysis of the result was performed and comparison of the computational result with experimental data and other theoretical results were provided. Excellent agreement of calculated free energies with the experimental data using TIP4 P model is obtained for liquid water.
基金TheNationalNaturalScienceFoundationofChina (No .2 9837180 )andtheResearchFoundationfortheDoctoralProgramofHigherEducationofChi
文摘The regression model for octanol/water partition coefficients ( K ow ), is founded with only two molecular descriptors available through quantum chemical calculations: solvation free energy (Δ G S ), and solvent accessible surface area (SASA). For the properties of 47 organic compounds from 17 types, the model gives a correction coefficient (adjusted for degrees of freedom) of 0 959 and a standard error of 0 277 log unit. It is a suitable way to predict the partition properties that are related to solute solvent interactions in the water phase.
基金partly supported by the National Natural Science Foundation of China (Nos.11471046 and 11971002)
文摘We focus on the distribution and free energy of a wormlike polymer confined between two parallel hard walls.The variation in the distribution and free energy of the wormlike chain as the spacing between the walls decreases(or as the total contour length of the wormlike chain increases or as the persistence length of the chain increases)is simulated.The main reason for these changes is a degradation of the long wormlike chain into a Gaussian long chain under weak confinement.
基金supported by the National Natural Science Foundation of China(31400667)Chongqing Municipal Education Commission Science and Technology Research Project(KJZD-K201801102)+2 种基金Chongqing Research Program of Basic Research and Frontier Technology(cstc2018jcyj AX0683)Opening Foundation of State Key Laboratory of Silkworm Genome Biology(sklsgb1819-2)Computational support from the Information Center of Chongqing University of Technology。
文摘The severe acute respiratory syndrome coronavirus 2(SARS-CoV-2)gained tremendous attention due to its high infectivity and pathogenicity.The 3-chymotrypsin-like hydrolase protease(Mpro)of SARS-CoV-2 has been proven to be an important target for anti-SARS-CoV-2 activity.To better identify the drugs with potential in treating coronavirus disease 2019(COVID-19)caused by SARS-CoV-2 and according to the crystal structure of Mpro,we conducted a virtual screening of FDA-approved drugs and chemical agents that have entered clinical trials.As a result,9 drug candidates with therapeutic potential for the treatment of COVID-19 and with good docking scores were identified to target SARS-CoV-2.Consequently,molecular dynamics(MD)simulation was performed to explore the dynamic interactions between the predicted drugs and Mpro.The binding mode during MD simulation showed that hydrogen bonding and hydrophobic interactions played an important role in the binding processes.Based on the binding free energy calculated by using MM/PBSA,Lopiravir,an inhibitor of human immunodeficiency virus(HIV)protease,is under investigation for the treatment of COVID-19 in combination with ritionavir,and it might inhibit Mpro effectively.Moreover,Ombitasvir,an inhibitor for non-structural protein 5 A of hepatitis C virus(HCV),has good inhibitory potency for Mpro.It is notable that the GS-6620 has a binding free energy,with respect to binding Mpro,comparable to that of ombitasvir.Our study suggests that ombitasvir and lopinavir are good drug candidates for the treatment of COVID-19,and that GS-6620 has good anti-SARS-CoV-2 activity.
基金This study is financially supported by the National Key Research and Development Program of China(No.2018YFA0901800 to H.Yu and L.Ye)Zhejiang Provincial Natural Science Foundation of China(No.LY18B060001 to L.Ye and No.LZ20B060002 to H.Yu)Natural Science Foundation of China(No.21776244 to H.Yu).We are grateful to the constructive suggestions from academician Fen-Er Chen(Department of Chemistry,Fudan University,Shanghai,China)and the support of Discovery Studio software from Fuzhou University platform.
文摘As an important building block for the synthesis of angiotensin-converting enzyme inhibitors,ethyl(R)-2-hy-droxyl-4-phenylbutanoate[(R)-HPBE]has attracted increasing attention.The key to industrial biosynthesis of(R)-HPBE is a biocatalyst that efficiently reduces ethyl 2-oxo-4-phenylbutanoate(OPBE)with high R-enantiose-lectivity.This paper proposed a strategy for identifying key residues involved in enantioselectivity control based on per-residue free energy decomposition and sequence conservatism analysis.Using this strategy,4 noncon-servative sites with high energy contribution to binding of OPBE were chosen as engineering targets,generating variant Mu27 with 99%conversion and 98%(R)ee value at substrate loading of up to 500 mmol/L.MD simu-lations suggested the higher stability and formation probability of Mu27-OPBEproR prereaction state as key rea-sons for the excellent R-enantioselectivity of Mu27 towards OPBE.The success in this study provides a viable approach for rational design of alcohol dehydrogenases with high enantioselectivity towards unnatural substrates.
文摘In this paper,it is shown that for stable,steady state operation of devices typical of microwave and millimeter wave electronics,no negative differential capacitance is possible with conventional thinking.However,it may be possible,with strain engineering of materials,to obtain some if not all elements of the differential capacitance tensor which are negative.Rigorous derivations are provided based upon analyzing the physics using thermodynamic phenomenological free energy.It should be emphasized that,even with strain engineering,and possible discovery of some negative capacitive elements,stable operation will not be obtained because the thermodynamics precludes it.
基金supported by the National Research Foundation (NRF) grant funded by the Korea government (NRF2022R1C1C1007619, NRF-2021M3H4A1A01002921, NRF2021M3I3A1084292)supported by the KIST Institutional Program (Project No. 2E32592-23-069)。
文摘PrBa_(0.5)Sr_(0.5)Co_(1.5)Fe_(0.5)O_(5+δ)(PrBSCF) has attracted much research interest as a potential triple ionic and electronic conductor(TIEC) electrode for protonic ceramic fuel cells(PCFCs). The chemical formula for Pr BSCF is AA'B_(2)O_(5+δ), with Pr(A-site) and Ba/Sr(A'-site) alternately stacked along the c-axis. Due to these structural features, the bulk oxygen ion diffusivity is significantly enhanced through the disorder-free channels in the PrO layer;thus, the A site cations(lanthanide ions) play a pivotal role in determining the overall electrochemical properties of layered perovskites. Consequently, previous research has predominantly focused on the electrical properties and oxygen bulk/surface kinetics of Ln cation effects,whereas the hydration properties for PCFC systems remain unidentified. Here, we thoroughly examined the proton uptake behavior and thermodynamic parameters for the hydration reaction to conclusively determine the changes in the electrochemical performances depending on LnBa_(0.5)Sr_(0.5)Co_(1.5)Fe_(0.5)O_(5+δ)(LnBSCF,Ln=Pr, Nd, and Gd) cathodes. At 500 ℃, the quantitative proton concentration of PrBSCF was 2.04 mol% and progressively decreased as the Ln cation size decreased. Similarly, the Gibbs free energy indicated that less energy was required for the formation of protonic defects in the order of Pr BSCF < Nd BSCF < Gd BSCF. To elucidate the close relationship between hydration properties and electrochemical performances in LnBSCF cathodes, PCFC single cell measurements and analysis of the distribution of relaxation time were further investigated.
基金National Natural Science Foundation of China!No.59774028
文摘The thermodynamical properties of MgCl2 in KCI-MgCl2-LiCl molten electrolytes containing MgCl2 below 0.5 （mole fraction, the same below） have been determined from the interchange energies of two binary systems KCI-MgCl2 and LiCI-MgCl2, by means of a model on the assumptions that the electrolytes in the solution are treated as independent particles instead of their ion forms and the interchange energy between the component pair KCI-LiCl is ignored when compared with those of component pairs KCl-MgCl2 and MgCl2-LiCl. The interchange energies, wKCl-MgCl2 and wMgcCl2-Licl, are obtained as-70000 and -13800 J.mol-1, from the corresponding binary solutions, respectively.
