Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search ...Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti- cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.展开更多
Deep learning methods have been shown to be effective in representing ground-state wavefunctions of quantum many-body systems,however the existing approaches cannot be easily used for non-square like or large systems....Deep learning methods have been shown to be effective in representing ground-state wavefunctions of quantum many-body systems,however the existing approaches cannot be easily used for non-square like or large systems.Here.we propose a variational ansatz based on the graph attention network(GAT)which learns distributed latent representations and can be used on non-square lattices.展开更多
High volumetric power density （VPD） is the basis for the commercial success of micro-tubular solid oxide fuel cells （mtSOFCs）. To find maximal VPD （MVPD） for anode-supported mtSOFC （as-mtSOFC）, the effects of ...High volumetric power density （VPD） is the basis for the commercial success of micro-tubular solid oxide fuel cells （mtSOFCs）. To find maximal VPD （MVPD） for anode-supported mtSOFC （as-mtSOFC）, the effects of geometric parameters on VPD are analyzed and the anode thickness, tan, and the cathode length, lea, are identified as the key design parameters. Thermo-fluid electrochemical models were built to examine the dependence of the electrical output on the cell parameters. The multiphysics model is validated by reproducing the experimental I-V curves with no adjustable parameters. The optimal lea and the corresponding MVPDs are then determined by the multiphysics model for 20 combinations of rin, the inner tube radius, and tan. And all these optimization are made at 1073.15 K. The results show that： （i） significant performance improvement may be achieved by geometry optimization, （ii） the seemingly high MVPD of 11 and 14 W/cm^3 can be easily realized for as-mtSOFC with single- and double-terminal anode current collection, respectively. Moreover, the variation of the area specific power density with/cac（2 mm, 40 mm） is determined for three representative （tin, tan） combinations. Besides, it is demonstrated that the current output of mtSOFC with proper geometric parameters is comparable to that of planar SOFC.展开更多
The conformations for leucine （Leu） hydrated with one to three water molecules, Leu-（H2O）n （n=1-3）, were carefully searched by considering the trial structures generated by all possible combinations of rotamers ...The conformations for leucine （Leu） hydrated with one to three water molecules, Leu-（H2O）n （n=1-3）, were carefully searched by considering the trial structures generated by all possible combinations of rotamers of Leu combined with all likely hydration modes. The structures were optimized at the BHandHLYP/6-31＋G^＊ level and the single point energies were calculated at the BHandHLYP/6-311＋＋G^＊＊ level. Good correspondence between the conformations of Leu-（H2O）n and bare Leu is found, showing that the conformations of Leu-（H2O）n may be efficiently and reliably determined by the hydration of Leu conformers. The simulated IR spectra of canonical and zwitterionic conformers of Leu-（H2O）n are compared with the experimental result of Leu in aqueous solution. The IR spectrum of zwitterionic Leu- （H2O）3 provides the best description of the experiment. The result demonstrates that the IR spectrum of solute in solution may be simulated by the solute hydrated with an adequate number of water molecules in the gas phase.展开更多
An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential ener...An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface （PES） of OlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G＊, BHandHLYP/6-31G＊ and BHandHLYP/6-311＋＋G＊＊ in order to reliably find the low energy conformations. The eonformational energies were finally determined with the methods of BHandHLYP, cam- B3LYP, B97D, and MP2 using the basis set of 6-311＋＋G（3df,3pd）. The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.展开更多
A multiphysics model for a production scale planar solid oxide fuel cell （SOFC） stack is important for the SOFC technology, but usually requires an unpractical amount of computing resource. The major cause for the h...A multiphysics model for a production scale planar solid oxide fuel cell （SOFC） stack is important for the SOFC technology, but usually requires an unpractical amount of computing resource. The major cause for the huge computing resource requirement is identified as the need to solve the cathode O2 transport and the associated electrochemistry. To overcome the technical obstacle, an analytical model for solving the O2 transport and its coupling with the electrochemistry is derived. The analytical model is used to greatly reduce the numerical mesh complexity of a multiphysics model. Numerical test shows that the analytical approximation is highly accurate and stable. A multiphysics numerical modeling tool taking advantage of the analytical solution is then developed through Fluent@. The numerical efficiency and stability of this modeling tool are further demonstrated by simulating a 30- cell stack with a production scale cell size. Detailed information about the stack performance is revealed and briefly discussed. The multiphysics modeling tool can be used to guide the stack design and select the operating parameters.展开更多
There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help th...There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five repre- sentative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conforma- tional energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311＋＋G（d,p） are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomoleeules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase展开更多
文摘Systematic search of the potential energy surface of tetrapeptide glycine-phenylalanine- glycine-glycine （GFGG） in gas phase is conducted by a combination of PM3, HF and BHandHLYP methods. The conformational search method is described in detail. The relative electronic energies, zero point vibrational energies, dipole moments, rotational constants, vertical ionization energies and the temperature dependent conformational distributions for a number of important conformers are obtained. The structural characteristics of these conformers are analyzed and it is found that the entropic effect is a dominating factor in determining the relative stabilities of the conformers. The measurements of dipole moments and some characteristic IR mode are shown to be effective approaches to verify the theoreti- cal prediction. The structures of the low energy GFGG conformers are also analyzed in their connection with the secondary structures of proteins. Similarity between the local structures of low energy GFGG conformers and the α-helix is discussed and many β- and γ-turn local structures in GFGG conformers are found.
基金supported by the National Natural Science Foundation of China(Grant Nos.12374017 and 12074362)the Innovation Program for Quantum Science and Technology(Grant No.2021ZD0303303)。
文摘Deep learning methods have been shown to be effective in representing ground-state wavefunctions of quantum many-body systems,however the existing approaches cannot be easily used for non-square like or large systems.Here.we propose a variational ansatz based on the graph attention network(GAT)which learns distributed latent representations and can be used on non-square lattices.
基金This work was supported by the National Natural Science Foundation of China （No.11374272 and No.11574284） and the Collaborative Innovation Center of Suzhou Nano Science and Technology.
文摘High volumetric power density （VPD） is the basis for the commercial success of micro-tubular solid oxide fuel cells （mtSOFCs）. To find maximal VPD （MVPD） for anode-supported mtSOFC （as-mtSOFC）, the effects of geometric parameters on VPD are analyzed and the anode thickness, tan, and the cathode length, lea, are identified as the key design parameters. Thermo-fluid electrochemical models were built to examine the dependence of the electrical output on the cell parameters. The multiphysics model is validated by reproducing the experimental I-V curves with no adjustable parameters. The optimal lea and the corresponding MVPDs are then determined by the multiphysics model for 20 combinations of rin, the inner tube radius, and tan. And all these optimization are made at 1073.15 K. The results show that： （i） significant performance improvement may be achieved by geometry optimization, （ii） the seemingly high MVPD of 11 and 14 W/cm^3 can be easily realized for as-mtSOFC with single- and double-terminal anode current collection, respectively. Moreover, the variation of the area specific power density with/cac（2 mm, 40 mm） is determined for three representative （tin, tan） combinations. Besides, it is demonstrated that the current output of mtSOFC with proper geometric parameters is comparable to that of planar SOFC.
基金V. ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China （No.11074233） the National Basic Research Program of China （No.2012CB215405）, and the Specialized Research Fund for the Doctoral Program of Higher Education （No.20113402110038）.
文摘The conformations for leucine （Leu） hydrated with one to three water molecules, Leu-（H2O）n （n=1-3）, were carefully searched by considering the trial structures generated by all possible combinations of rotamers of Leu combined with all likely hydration modes. The structures were optimized at the BHandHLYP/6-31＋G^＊ level and the single point energies were calculated at the BHandHLYP/6-311＋＋G^＊＊ level. Good correspondence between the conformations of Leu-（H2O）n and bare Leu is found, showing that the conformations of Leu-（H2O）n may be efficiently and reliably determined by the hydration of Leu conformers. The simulated IR spectra of canonical and zwitterionic conformers of Leu-（H2O）n are compared with the experimental result of Leu in aqueous solution. The IR spectrum of zwitterionic Leu- （H2O）3 provides the best description of the experiment. The result demonstrates that the IR spectrum of solute in solution may be simulated by the solute hydrated with an adequate number of water molecules in the gas phase.
基金This work was supported by the National Natu- ral Science Foundation of China （No.11374272） and the Specialized Research Fund for the Doctoral Pro- gram of Higher Education （No.20113402110038 and No.20123402110064）.
文摘An extensive computational study on the conformations of gaseous dipeptide glycine- arginine, GlyArg, has been performed. A large number of trail structures were generated by systematically sampling the potential energy surface （PES） of OlyArg. The trial structures were successively optimized with the methods of PM3, HF/3-21G＊, BHandHLYP/6-31G＊ and BHandHLYP/6-311＋＋G＊＊ in order to reliably find the low energy conformations. The eonformational energies were finally determined with the methods of BHandHLYP, cam- B3LYP, B97D, and MP2 using the basis set of 6-311＋＋G（3df,3pd）. The results establish firmly that gaseous GlyArg exists primarily in its canonical form, in sharp contrast with ArgGly that adopts the zwitterionic form. Important data such as the rotational constants, dipole moments, vertical ionization energies, temperature distributions and IR spectra of the low energy conformers are represented for the understanding of the future experiments. Moreover, considering the global minima of all amino acids and many dipeptides, combined with the hydrophobicities of amino acids, a model predicting whether the global minimum configuration of a dipeptide is canonical or zwitterionic is developed.
基金This work is supported the National Natural Science Foundation of China （No. 11374272 and No. 11574284）, the National Basic Research Program of China （No.2012CB215405） and Collaborative Innovation Center of Suzhou Nano Science and Technology are gratefully acknowledged.
文摘A multiphysics model for a production scale planar solid oxide fuel cell （SOFC） stack is important for the SOFC technology, but usually requires an unpractical amount of computing resource. The major cause for the huge computing resource requirement is identified as the need to solve the cathode O2 transport and the associated electrochemistry. To overcome the technical obstacle, an analytical model for solving the O2 transport and its coupling with the electrochemistry is derived. The analytical model is used to greatly reduce the numerical mesh complexity of a multiphysics model. Numerical test shows that the analytical approximation is highly accurate and stable. A multiphysics numerical modeling tool taking advantage of the analytical solution is then developed through Fluent@. The numerical efficiency and stability of this modeling tool are further demonstrated by simulating a 30- cell stack with a production scale cell size. Detailed information about the stack performance is revealed and briefly discussed. The multiphysics modeling tool can be used to guide the stack design and select the operating parameters.
文摘There is a growing interest in the study of structures and properties of biomolecules in gas phase. Applications of force fields are highly desirable for the computational efficiency of the gas phase study. To help the selection of force fields, the performances of five repre- sentative force fields for gaseous neutral, protonated, deprotonated and capped amino acids are systematically examined and compared. The tested properties include relative conforma- tional energies, energy differences between cis and trans structures, the number and strength of predicted hydrogen bonds, and the quality of the optimized structures. The results of BHandHLYP/6-311＋＋G（d,p） are used as the references. GROMOS53A6 and ENCADS are found to perform poorly for gaseous biomoleeules, while the performance of AMBER99SB, CHARMM27 and OPLSAA/L are comparable when applicable. Considering the general availability of the force field parameters, CHARMM27 is the most recommended, followed by OPLSAA/L, for the study of biomolecules in gas phase
