Elastic behavior of 4-branched star polymer chain with different chain length N adsorbed on attractive surface is investigated using steered molecular dynamics （SMD） simulation method based on the united-atom （UA）...Elastic behavior of 4-branched star polymer chain with different chain length N adsorbed on attractive surface is investigated using steered molecular dynamics （SMD） simulation method based on the united-atom （UA） model for branched alkanes. The simulation is realized by pulling up the chain via a linear spring with a constant velocity v = 0.005 nm/ps. At the beginning, the chain lies extensionally on adsorbed surface and suffers continuous deformations during the tensile process. Statistical parameters as mean-square radii of gyration 〈S2〉xy, 〈S2〉z, shape factor 〈δ〉, describing the conformational changes, sectional density 〈den〉 which gives the states of the chain, and average surface attractive energy 〈Ua〉, average total energy 〈U〉, average force 〈f〉 probed by the spring, which characterize the thermodynamic properties, are calculated in the stimulant process. Remarkably, distinguishing from the case in linear chains that there only exists one long plateau in the curve of 〈f 〉, the force plateau in our study for star chains is multiple, denoting different steps of desorption, and this agrees well with the experimental results in essence. We find during the tensile process, there are three characteristic distances Zc, Zt and Z0 from the attractive surface, and these values vary with N. When Z = Zc, the chain is stripped from the surface, but due to the form of wall-monomer interaction, the surface retains weak influence on the chain till Z = Zc. From Z = Zt, parameters 〈Ua〉, 〈U〉 and 〈f〉 respectively reach a stable value, while the shape and the size of the chain still need adjustments after Zt till Zo to reach their equilibrium states. Specifically, for short chain of N = 41, Zt and Z0 are incorporated. These results may help us to deepen the knowledge about the elastic behavior of adsorbed star polymer chains.展开更多
In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-e...In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.展开更多
During aircraft ground steering,the nose landing gear(NLG)tires of large transport aircraft often experience excessive lateral loads,leading to sideslip.This compromises steering safety and accelerates tire wear.To ad...During aircraft ground steering,the nose landing gear(NLG)tires of large transport aircraft often experience excessive lateral loads,leading to sideslip.This compromises steering safety and accelerates tire wear.To address this issue,the rear landing gear is typically designed to steer in coordination with the nose wheels,reducing sideslip and improving maneuverability.This study examines how structural parameters and weight distribution affect the performance of coordinated steering in landing gear design for large transport aircraft.Using the C-5 transport aircraft as a case study,we develop a multi-wheel ground steering dynamics model,incorporating the main landing gear(MLG)deflection.A ground handling dynamics model is also established to evaluate the benefits of coordinated steering for rear MLG during steering.Additionally,the study analyzes the impact of structural parameters such as stiffness and damping on the steering performance of the C-5.It further investigates the effects of weight distribution,including the center-of-gravity(CG)height,the longitudinal CG position,and the mass asymmetry.Results show that when the C-5 employs coordinated steering for rear MLG,the lateral friction coefficients of the NLG tires decrease by 22%,24%,26%,and 27%.The steering radius is reduced by 29.7%,and the NLG steering moment decreases by 19%,significantly enhancing maneuverability.Therefore,in the design of landing gear for large transport aircraft,coordinated MLG steering,along with optimal structural and CG position parameters,should be primary design objectives.These results provide theoretical guidance for the design of multi-wheel landing gear systems in large transport aircraft.展开更多
The giant muscle protein titin known for its mechanical stability serves as an ideal model for developing protein-based biomaterials.However,practical applications are hindered by challenges such as low expression yie...The giant muscle protein titin known for its mechanical stability serves as an ideal model for developing protein-based biomaterials.However,practical applications are hindered by challenges such as low expression yields,poor solubility,and limited thermal stability.In this study,we combined artificial intelligence(AI)tools—ProteinMPNN and Alpha-Fold2—with human insights and steered molecular dynamics(SMD)simulations to redesign the titin Ig domain.This approach generated thousands of novel sequences,preserving structural features essential for mechanical stability.Six de novo proteins were experimentally validated,all demonstrating mechanical and kinetic stability comparable to the natural I27 domain at the 100 pN level.Notably,these proteins exhibited significantly improved physical properties,with up to a fivefold increase in expression yield and enhanced solubility.Circular dichroism and atomic force microscopy-based single molecule force spectroscopy(AFM-SMFS)confirmed proper folding and mechanical stability,while thermal stability was retained or improved in some designs.Control experiments with unguided random designs,which yielded negative results,underscored the critical role of integrating AI tools with domain-specific knowledge for functional outcomes.Our findings highlight the transformative potential of integrating AI-driven design with human expertise and computational simulations,enabling the development of mechanically robust proteins for applications in bioengineering and biomaterials science.展开更多
The crystal structure of Ig81 domain confirms that the domain folds into a compactβ-sandwich,but with an evanescent BC-loop at the N-terminus.It is not clear whether the divergent BC-loop has an effect on the stabili...The crystal structure of Ig81 domain confirms that the domain folds into a compactβ-sandwich,but with an evanescent BC-loop at the N-terminus.It is not clear whether the divergent BC-loop has an effect on the stability of the shear topology formed by two of parallel A and Gβ-strands.In this paper,two Cαatoms in A and Gβ-strands were selected as two stress points,and the domains were stretched in opposite directions as a speed of 2.5×10-4 nm·ps-1.Under the same stretching conditions,100 steered molecular dynamics(SMD)runs were performed.The free energy of Ig81 was constructed as a function of the increasing distance between the two stress points using the Jarzynski's equality.For comparison,the free energy profile of the Ig27 domain was reconstructed with same method.The results show that the work done to unfold Ig81 is greater than the work done to unfold Ig27,and that the folding barrier of Ig81 is lower than that of Ig27.This suggests that the presence of the distinctive long BC-loop increases the sta-bility of the shear topology,thereby improving the mechanical strength of the protein.展开更多
This work was focused on the model-based design method of two-axis four-actuator(TAFA) fast steering mirror system(FSM), in order to improve the design efficiency. The structure and operation principle commonality of ...This work was focused on the model-based design method of two-axis four-actuator(TAFA) fast steering mirror system(FSM), in order to improve the design efficiency. The structure and operation principle commonality of normal TAFA FSM were investigated. Based on the structure and the commonality, the conditions of single-axis idea, high-frequency resonance and coupling were modeled gradually. Combining these models, a holonomic system model was established to reflect and predict the performance of TAFA FSM. A model-based design method was proposed based on the holonomic system model. The design flow and design concept of the method were described. In accordance with the method, a TAFA FSM was designed. Simulations and experiments of the FSM were done, and the results of them were compared. The compared results indicate that the holonomic system model can well reflect and predict the performance of TAFA FSM. The bandwidth of TAFA FSM is more than 250 Hz; adjust time is less than 15 ms;overshoot is less than 8%; position accuracy is better than 10 μrad; the FSM prototype can satisfy the requirements.展开更多
基金supported by the National Natural Science Foundation of China(Nos.20904047,10947104).
文摘Elastic behavior of 4-branched star polymer chain with different chain length N adsorbed on attractive surface is investigated using steered molecular dynamics （SMD） simulation method based on the united-atom （UA） model for branched alkanes. The simulation is realized by pulling up the chain via a linear spring with a constant velocity v = 0.005 nm/ps. At the beginning, the chain lies extensionally on adsorbed surface and suffers continuous deformations during the tensile process. Statistical parameters as mean-square radii of gyration 〈S2〉xy, 〈S2〉z, shape factor 〈δ〉, describing the conformational changes, sectional density 〈den〉 which gives the states of the chain, and average surface attractive energy 〈Ua〉, average total energy 〈U〉, average force 〈f〉 probed by the spring, which characterize the thermodynamic properties, are calculated in the stimulant process. Remarkably, distinguishing from the case in linear chains that there only exists one long plateau in the curve of 〈f 〉, the force plateau in our study for star chains is multiple, denoting different steps of desorption, and this agrees well with the experimental results in essence. We find during the tensile process, there are three characteristic distances Zc, Zt and Z0 from the attractive surface, and these values vary with N. When Z = Zc, the chain is stripped from the surface, but due to the form of wall-monomer interaction, the surface retains weak influence on the chain till Z = Zc. From Z = Zt, parameters 〈Ua〉, 〈U〉 and 〈f〉 respectively reach a stable value, while the shape and the size of the chain still need adjustments after Zt till Zo to reach their equilibrium states. Specifically, for short chain of N = 41, Zt and Z0 are incorporated. These results may help us to deepen the knowledge about the elastic behavior of adsorbed star polymer chains.
基金Project supported by the National Natural Science Foundation of China (Grant Nos 20274040,20574052 and 20774066)the Program for New Century Excellent Talents in University,China (Grant No NCET-05-0538)the Natural Science Foundation of Zhejiang Province,China (Grant No R404047)
文摘In this paper the influence of a knot on the structure of a polymethylene （PM） strand in the tensile process is investigated by using the steered molecular dynamics （SMD） method. The gradual increasing of end-to-end distance, R, results in a tighter knot and a more stretched contour. That the break in a knotted rope almost invariably occurs at a point just outside the ＇entrance＇ to the knot, which has been shown in a good many experiments, is further theoretically verified in this paper through the calculation of some structural and thermodynamic parameters. Moreover, it is found that the analyses on bond length, torsion angle and strain energy can facilitate to the study of the localization and the size of a knot in the tensile process. The symmetries of torsion angles, bond lengths and bond angles in the knot result in the whole symmetry of the knot in microstructure, thereby adapting itself to the strain applied. Additionally, the statistical property of the force-dependent average knot size illuminates in detail the change in size of a knot with force f, and therefore the minimum size of the knot in the restriction of the potentials considered in this work for a PM chain is deduced. At the same time, the difference in response to uniaxial strain, between a knotted PM strand and an unknotted one is also investigated. The force-extension profile is easily obtained from the simulation. As expected, for a given f, the knotted chain has an R significantly smaller than that of an unknotted polymer. However, the scaled difference becomes less pronounced for larger values of N, and the results for longer chains approach those of the unknotted chains.
基金supported in part by the Fundamental Research Funds for the Central Universi-ties(No.NP2022416)the Aeronautical Science Founda-tion of China(No.2022Z029052001).
文摘During aircraft ground steering,the nose landing gear(NLG)tires of large transport aircraft often experience excessive lateral loads,leading to sideslip.This compromises steering safety and accelerates tire wear.To address this issue,the rear landing gear is typically designed to steer in coordination with the nose wheels,reducing sideslip and improving maneuverability.This study examines how structural parameters and weight distribution affect the performance of coordinated steering in landing gear design for large transport aircraft.Using the C-5 transport aircraft as a case study,we develop a multi-wheel ground steering dynamics model,incorporating the main landing gear(MLG)deflection.A ground handling dynamics model is also established to evaluate the benefits of coordinated steering for rear MLG during steering.Additionally,the study analyzes the impact of structural parameters such as stiffness and damping on the steering performance of the C-5.It further investigates the effects of weight distribution,including the center-of-gravity(CG)height,the longitudinal CG position,and the mass asymmetry.Results show that when the C-5 employs coordinated steering for rear MLG,the lateral friction coefficients of the NLG tires decrease by 22%,24%,26%,and 27%.The steering radius is reduced by 29.7%,and the NLG steering moment decreases by 19%,significantly enhancing maneuverability.Therefore,in the design of landing gear for large transport aircraft,coordinated MLG steering,along with optimal structural and CG position parameters,should be primary design objectives.These results provide theoretical guidance for the design of multi-wheel landing gear systems in large transport aircraft.
基金the funding support from the National Natural Science Foundation of China(grant nos.22222703 and 22477058)the Natural Science Foundation of Jiangsu Province,China(grant no.BK20202004)the Fundamental Research Funds for the Central Universities,China(grant no.020514380335).
文摘The giant muscle protein titin known for its mechanical stability serves as an ideal model for developing protein-based biomaterials.However,practical applications are hindered by challenges such as low expression yields,poor solubility,and limited thermal stability.In this study,we combined artificial intelligence(AI)tools—ProteinMPNN and Alpha-Fold2—with human insights and steered molecular dynamics(SMD)simulations to redesign the titin Ig domain.This approach generated thousands of novel sequences,preserving structural features essential for mechanical stability.Six de novo proteins were experimentally validated,all demonstrating mechanical and kinetic stability comparable to the natural I27 domain at the 100 pN level.Notably,these proteins exhibited significantly improved physical properties,with up to a fivefold increase in expression yield and enhanced solubility.Circular dichroism and atomic force microscopy-based single molecule force spectroscopy(AFM-SMFS)confirmed proper folding and mechanical stability,while thermal stability was retained or improved in some designs.Control experiments with unguided random designs,which yielded negative results,underscored the critical role of integrating AI tools with domain-specific knowledge for functional outcomes.Our findings highlight the transformative potential of integrating AI-driven design with human expertise and computational simulations,enabling the development of mechanically robust proteins for applications in bioengineering and biomaterials science.
基金supported by Natural Science Foundation of Shandong Province(ZR2021QD126)。
文摘The crystal structure of Ig81 domain confirms that the domain folds into a compactβ-sandwich,but with an evanescent BC-loop at the N-terminus.It is not clear whether the divergent BC-loop has an effect on the stability of the shear topology formed by two of parallel A and Gβ-strands.In this paper,two Cαatoms in A and Gβ-strands were selected as two stress points,and the domains were stretched in opposite directions as a speed of 2.5×10-4 nm·ps-1.Under the same stretching conditions,100 steered molecular dynamics(SMD)runs were performed.The free energy of Ig81 was constructed as a function of the increasing distance between the two stress points using the Jarzynski's equality.For comparison,the free energy profile of the Ig27 domain was reconstructed with same method.The results show that the work done to unfold Ig81 is greater than the work done to unfold Ig27,and that the folding barrier of Ig81 is lower than that of Ig27.This suggests that the presence of the distinctive long BC-loop increases the sta-bility of the shear topology,thereby improving the mechanical strength of the protein.
基金Projects(51135009)supported by the National Natural Science Foundation of China
文摘This work was focused on the model-based design method of two-axis four-actuator(TAFA) fast steering mirror system(FSM), in order to improve the design efficiency. The structure and operation principle commonality of normal TAFA FSM were investigated. Based on the structure and the commonality, the conditions of single-axis idea, high-frequency resonance and coupling were modeled gradually. Combining these models, a holonomic system model was established to reflect and predict the performance of TAFA FSM. A model-based design method was proposed based on the holonomic system model. The design flow and design concept of the method were described. In accordance with the method, a TAFA FSM was designed. Simulations and experiments of the FSM were done, and the results of them were compared. The compared results indicate that the holonomic system model can well reflect and predict the performance of TAFA FSM. The bandwidth of TAFA FSM is more than 250 Hz; adjust time is less than 15 ms;overshoot is less than 8%; position accuracy is better than 10 μrad; the FSM prototype can satisfy the requirements.
