In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the re...In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.展开更多
Determining the similarity degree between process models was very important for their management,reuse,and analysis.Current approaches either focused on process model's structural aspect,or had inefficiency or imp...Determining the similarity degree between process models was very important for their management,reuse,and analysis.Current approaches either focused on process model's structural aspect,or had inefficiency or imprecision in behavioral similarity.Aiming at these problems,a novel similarity measure which extended an existing method named Transition Adjacent Relation(TAR) with improved precision and efficiency named TAR * was proposed.The ability of measuring similarity was extended by eliminating the duplicate tasks without impacting the behaviors.For precision,TARs was classified into repeatable and unrepeatable ones to identify whether a TAR was involved in a loop.Two new kinds of TARs were added,one related to the invisible tasks after the source place and before sink place,and the other representing implicit dependencies.For efficiency,all TARs based on unfolding instead of its reach ability graph of a labeled Petri net were calculated to avoid state space explosion.Experiments on artificial and real-world process models showed the effectiveness and efficiency of the proposed method.展开更多
Ultra-large plate forgings are foundation of heavy machinery,but many parts of the type cannot be made by conventional technologies due to the characters of extreme manufacturing in terms of size and quality requireme...Ultra-large plate forgings are foundation of heavy machinery,but many parts of the type cannot be made by conventional technologies due to the characters of extreme manufacturing in terms of size and quality requirements.This paper introduced a systematically method called cylinder unfolding method(CUM)for producing large plate forgings,by using a serial of operations including“splitting”,“unfolding”,and“flattening”of a thick cylinder obtained from saddle forging.The technological route of CUM was presented in detail with an example of plate forging with the horizontal sizes of 6100 mm and thickness of 300 mm.The deformation features of saddle forging for fabricating transitional cylinders were analyzed,and then the subsequent handling steps including splitting,unfolding and flattening of the cylinder,as well as the auxiliary processing,were addressed.The practice proved that CUM can provide an efficient way for manufacturing ultra-large plate forgings and meet the strict requirements in geometry and mechanical performance,without highly increasing the investments of forming equipment and tooling.展开更多
To tackle the challenges of intractable parameter tun-ing,significant computational expenditure and imprecise model-driven sparse-based direction of arrival(DOA)estimation with array error(AE),this paper proposes a de...To tackle the challenges of intractable parameter tun-ing,significant computational expenditure and imprecise model-driven sparse-based direction of arrival(DOA)estimation with array error(AE),this paper proposes a deep unfolded amplitude-phase error self-calibration network.Firstly,a sparse-based DOA model with an array convex error restriction is established,which gets resolved via an alternating iterative minimization(AIM)algo-rithm.The algorithm is then unrolled to a deep network known as AE-AIM Network(AE-AIM-Net),where all parameters are opti-mized through multi-task learning using the constructed com-plete dataset.The results of the simulation and theoretical analy-sis suggest that the proposed unfolded network achieves lower computational costs compared to typical sparse recovery meth-ods.Furthermore,it maintains excellent estimation performance even in the presence of array magnitude-phase errors.展开更多
At the vascular injury sites,the ultra-large (UL) multimeric von willebrand Factor (VWF) is released in response to physiological and pathophysiological stimuli,and mediates platelet adhesion,aggregation,and cross-lin...At the vascular injury sites,the ultra-large (UL) multimeric von willebrand Factor (VWF) is released in response to physiological and pathophysiological stimuli,and mediates platelet adhesion,aggregation,and cross-linking to maintain hemostasis.This UL-VWF is specifically cleaved by ADAMTS13(A Disintegrin And Metalloprotease with a ThromboSpondintype-1 motif,member 13)to prevent microvascular thrombosis.Each VWF monomer consists of five types of repeat domains in the order of D1-D2-D’-D3-A1-A2-A3-D4-C1-C2-C3-C4-C5-C6-CK,in which the A2 domain contains the ADAMTS13cleavage site(Tyr1605-Met1606),exposure of which requires mechanical or chemical stimuli.Under flows,fluid shear stress regulates VWF degradation and size distribution through opening the A2 domain and exposing its cleavage site for ADAMTS13.VWF A2 domain contains a C-terminal vicinal disulfide bond,a calcium binding sites,and a flexibleα4-less-loop.These unique structure features together make A2 more sensitive to mechanical signal than other VWF A subdomains,i.e.A1 and A3 domains.It is believed that A2 is first bound with and then cleaved by ADAMTS13,together with force-induced conformation transformation.To reveal molecular basis of this two-step model of VWF hydrolyzation by ADAMTS13,we here examined stretch-induced unfolding processes of VWF A2 domain in more detail by Steered molecular dynamics(SMD)simulations,with the use of crystal structure of VWF A2(PDB ID 3GXB),and observed that there were multiple quasi-stable conformations of stretched A2 until itsβ4-strand and a3-helix were pulled away the central hydrophobic core and the cleavage sites were fully accessible to solvent.Our MD simulation data showed that,in unfolding,at first,the cleavage site residue Tyr1605 was exposed partially and binding sites for Spacer domain of ADAMTS13 were exposed to a high level whenα6-helix was separated from A2 body;then,withβ6-strand and a5-helix been pulled away,the binding sites for Cysrich domain of ADAMTS13 was exposed completely while the exposure degree of Tyr1605 was not improved;further,separation ofβ5-strand andα4-less-loop made Tyr1605 and Met1606 and the respective binding sites for ADAMTS13 Spacer domain,Cys-rich domain,and Disintegrin-like domain be fully exposed to reach the optimal catalytic state;lastly,withβ4-strand separation,the cleavage sites and binding sites all were overstretched,leading to mismatch of ADAMTS13 and A2 conformation especially in the binding sites.This conformational mismatch may cause reduction of ADAMTS13 hydrolysis efficiency.Furthermore,the data of SMD simulations under constant forces demonstrated that,the stretched A2 conformation had different quasi-stable states,which all had the better mechanical stability within simulation time of 100 ns;and the conformational transformation from one state to another must overcome their respective potential barriers.The hydrolysis efficiency should depend on each state of the stretched A2 conformation,because of the exclusive matched-degree of A2 and ADMATS13.This computer prediction on the mechanical stability and multi-states of stretched A2 provides a novel insight into the mechano-chemical regulation on cleavage of A2 by ADAMTS13.It would be helpful for design of related drug targeting the binding sites on A2 and exosites on ADAMTS13 for the treatment of patients with acquired TTP.展开更多
文摘In this study,circular dichroism(CD)and molecular dynamics(MD)simulation were used to investigate the thermal unfolding pathway of staphylococcal enterotoxin B(SEB)at temperatures of 298–371 and 298–500 K,and the relationship between the experimental and simulation results were explored.Our computational findings on the secondary structure of SEB showed that at room temperature,the CD spectroscopic results were highly consistent with the MD results.Moreover,under heating conditions,the changing trends of helix,sheet and random coil obtained by CD spectral fitting were highly consistent with those obtained by MD.In order to gain a deeper understanding of the thermal stability mechanism of SEB,the MD trajectories were analyzed in terms of root mean square deviation(RMSD),secondary structure assignment(SSA),radius of gyration(R_(g)),free energy surfaces(FES),solvent-accessible surface area(SASA),hydrogen bonds and salt bridges.The results showed that at low heating temperature,domain Ⅰ without loops(omitting the mobile loop region)mainly relied on hydrophobic interaction to maintain its thermal stability,whereas the thermal stability of domain Ⅱ was mainly controlled by salt bridges and hydrogen bonds.Under high heating temperature conditions,the hydrophobic interactions in domain Ⅰ without loops were destroyed and the secondary structure was almost completely lost,while domain Ⅱ could still rely on salt bridges as molecular staples to barely maintain the stability of the secondary structure.These results help us to understand the thermodynamic and kinetic mechanisms that maintain the thermal stability of SEB at the molecular level,and provide a direction for establishing safer and more effective food sterilization processes.
基金Project supported by the National Science Foundation,China(No.61003099)the National Basic Research Program,China(No.2009CB320700)
文摘Determining the similarity degree between process models was very important for their management,reuse,and analysis.Current approaches either focused on process model's structural aspect,or had inefficiency or imprecision in behavioral similarity.Aiming at these problems,a novel similarity measure which extended an existing method named Transition Adjacent Relation(TAR) with improved precision and efficiency named TAR * was proposed.The ability of measuring similarity was extended by eliminating the duplicate tasks without impacting the behaviors.For precision,TARs was classified into repeatable and unrepeatable ones to identify whether a TAR was involved in a loop.Two new kinds of TARs were added,one related to the invisible tasks after the source place and before sink place,and the other representing implicit dependencies.For efficiency,all TARs based on unfolding instead of its reach ability graph of a labeled Petri net were calculated to avoid state space explosion.Experiments on artificial and real-world process models showed the effectiveness and efficiency of the proposed method.
基金Project(cstc2018jcyjAX0159)supported by the Natural Science Foundation of Chongqing,ChinaProject(51575066)supported by the National Natural Science Foundation of China。
文摘Ultra-large plate forgings are foundation of heavy machinery,but many parts of the type cannot be made by conventional technologies due to the characters of extreme manufacturing in terms of size and quality requirements.This paper introduced a systematically method called cylinder unfolding method(CUM)for producing large plate forgings,by using a serial of operations including“splitting”,“unfolding”,and“flattening”of a thick cylinder obtained from saddle forging.The technological route of CUM was presented in detail with an example of plate forging with the horizontal sizes of 6100 mm and thickness of 300 mm.The deformation features of saddle forging for fabricating transitional cylinders were analyzed,and then the subsequent handling steps including splitting,unfolding and flattening of the cylinder,as well as the auxiliary processing,were addressed.The practice proved that CUM can provide an efficient way for manufacturing ultra-large plate forgings and meet the strict requirements in geometry and mechanical performance,without highly increasing the investments of forming equipment and tooling.
基金supported by the National Natural Science Foundation of China(62301598).
文摘To tackle the challenges of intractable parameter tun-ing,significant computational expenditure and imprecise model-driven sparse-based direction of arrival(DOA)estimation with array error(AE),this paper proposes a deep unfolded amplitude-phase error self-calibration network.Firstly,a sparse-based DOA model with an array convex error restriction is established,which gets resolved via an alternating iterative minimization(AIM)algo-rithm.The algorithm is then unrolled to a deep network known as AE-AIM Network(AE-AIM-Net),where all parameters are opti-mized through multi-task learning using the constructed com-plete dataset.The results of the simulation and theoretical analy-sis suggest that the proposed unfolded network achieves lower computational costs compared to typical sparse recovery meth-ods.Furthermore,it maintains excellent estimation performance even in the presence of array magnitude-phase errors.
基金supported by National Natural Science Foundation of China Grants 11672109 ( to Y. F.) and 11432006 ( to J. W.)
文摘At the vascular injury sites,the ultra-large (UL) multimeric von willebrand Factor (VWF) is released in response to physiological and pathophysiological stimuli,and mediates platelet adhesion,aggregation,and cross-linking to maintain hemostasis.This UL-VWF is specifically cleaved by ADAMTS13(A Disintegrin And Metalloprotease with a ThromboSpondintype-1 motif,member 13)to prevent microvascular thrombosis.Each VWF monomer consists of five types of repeat domains in the order of D1-D2-D’-D3-A1-A2-A3-D4-C1-C2-C3-C4-C5-C6-CK,in which the A2 domain contains the ADAMTS13cleavage site(Tyr1605-Met1606),exposure of which requires mechanical or chemical stimuli.Under flows,fluid shear stress regulates VWF degradation and size distribution through opening the A2 domain and exposing its cleavage site for ADAMTS13.VWF A2 domain contains a C-terminal vicinal disulfide bond,a calcium binding sites,and a flexibleα4-less-loop.These unique structure features together make A2 more sensitive to mechanical signal than other VWF A subdomains,i.e.A1 and A3 domains.It is believed that A2 is first bound with and then cleaved by ADAMTS13,together with force-induced conformation transformation.To reveal molecular basis of this two-step model of VWF hydrolyzation by ADAMTS13,we here examined stretch-induced unfolding processes of VWF A2 domain in more detail by Steered molecular dynamics(SMD)simulations,with the use of crystal structure of VWF A2(PDB ID 3GXB),and observed that there were multiple quasi-stable conformations of stretched A2 until itsβ4-strand and a3-helix were pulled away the central hydrophobic core and the cleavage sites were fully accessible to solvent.Our MD simulation data showed that,in unfolding,at first,the cleavage site residue Tyr1605 was exposed partially and binding sites for Spacer domain of ADAMTS13 were exposed to a high level whenα6-helix was separated from A2 body;then,withβ6-strand and a5-helix been pulled away,the binding sites for Cysrich domain of ADAMTS13 was exposed completely while the exposure degree of Tyr1605 was not improved;further,separation ofβ5-strand andα4-less-loop made Tyr1605 and Met1606 and the respective binding sites for ADAMTS13 Spacer domain,Cys-rich domain,and Disintegrin-like domain be fully exposed to reach the optimal catalytic state;lastly,withβ4-strand separation,the cleavage sites and binding sites all were overstretched,leading to mismatch of ADAMTS13 and A2 conformation especially in the binding sites.This conformational mismatch may cause reduction of ADAMTS13 hydrolysis efficiency.Furthermore,the data of SMD simulations under constant forces demonstrated that,the stretched A2 conformation had different quasi-stable states,which all had the better mechanical stability within simulation time of 100 ns;and the conformational transformation from one state to another must overcome their respective potential barriers.The hydrolysis efficiency should depend on each state of the stretched A2 conformation,because of the exclusive matched-degree of A2 and ADMATS13.This computer prediction on the mechanical stability and multi-states of stretched A2 provides a novel insight into the mechano-chemical regulation on cleavage of A2 by ADAMTS13.It would be helpful for design of related drug targeting the binding sites on A2 and exosites on ADAMTS13 for the treatment of patients with acquired TTP.
