Flasher origami pattern has been widely utilized to improve the stowage efficiency of deployable structures.Nevertheless,flasher origami cannot be folded fully flat,and they still have great potential for optimization...Flasher origami pattern has been widely utilized to improve the stowage efficiency of deployable structures.Nevertheless,flasher origami cannot be folded fully flat,and they still have great potential for optimization in terms of storage volume and folding creases.In this paper,a flat foldable equiangular spiral folding pattern inspired by the sunflower disk is introduced.Then,a parametric design method for this equiangular spiral crease diagram is introduced in detail.Subsequently,a kinematic model of the equiangular spiral folding pattern is established based on the kinematic equivalence between rigid origami and spherical linkages.A simulation of the developed model demonstrates that the equiangular spiral folding pattern can be folded flat.Using the folded ratio as an evaluation index,the calculated results and experiments show that the equiangular spiral crease pattern can yield fewer creases and improve stowage efficiency in comparison to flasher origami pattern.Equiangular spiral folding pattern can save a considerable amount of space and provide a new approach to spatially deployable structures.展开更多
The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segm...The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of α-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a β-strand. And peptlde P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a β-folding structure to that with an α-helical one.展开更多
Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structur...Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.展开更多
Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model...Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of m RNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by m RNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.展开更多
Based on the first-order shear deformation theory,a 3-node co-rotational triangular finite element formulation is developed for large deformation modeling of non-smooth,folded and multi-shell laminated composite struc...Based on the first-order shear deformation theory,a 3-node co-rotational triangular finite element formulation is developed for large deformation modeling of non-smooth,folded and multi-shell laminated composite structures.The two smaller components of the mid-surface normal vector of shell at a node are defined as nodal rotational variables in the co-rotational local coordinate system.In the global coordinate system,two smaller components of one vector,together with the smallest or second smallest component of another vector,of an orthogonal triad at a node on a non-smooth intersection of plates and/or shells are defined as rotational variables,whereas the two smaller components of the mid-surface normal vector at a node on the smooth part of the plate or shell(away from non-smooth intersections)are defined as rotational variables.All these vectorial rotational variables can be updated in an additive manner during an incremental solution procedure,and thus improve the computational efficiency in the nonlinear solution of these composite shell structures.Due to the commutativity of all nodal variables in calculating of the second derivatives of the local nodal variables with respect to global nodal variables,and the second derivatives of the strain energy functional with respect to local nodal variables,symmetric tangent stiffness matrices in local and global coordinate systems are obtained.To overcome shear locking,the assumed transverse shear strains obtained from the line-integration approach are employed.The reliability and computational accuracy of the present 3-node triangular shell finite element are verified through modeling two patch tests,several smooth and non-smooth laminated composite shells undergoing large displacements and large rotations.展开更多
An idea to develop a family of cellular cores for sandwich panels using a technology of prepreg folding is presented. Polar folded quadra structures are regarded as a geometric basis for these cores whose standard fra...An idea to develop a family of cellular cores for sandwich panels using a technology of prepreg folding is presented. Polar folded quadra structures are regarded as a geometric basis for these cores whose standard frag ment has lhe fourlh degree of axial symmelry. The classification of the polar strucluresaredeseribedanda method of various quadra slrueture synthesis is developed. A possibilily to provide high strength of lhe structure due m preservation of faces reinforcement pattern is presented. Arrangemen! of the plane core on a bi curvature surface is also introduced. Besides, provision of isotropyof the core in two or three directions are described. Finally, exam ples of cellular folded cores manufaclured from basalt reinforced plaslic are demonslrated.展开更多
One of the long-standing controversial arguments in protein folding is Levinthal＇s paradox. We have recently proposed a new nucleation hypothesis and shown that the nucleation residues are the most conserved sequence...One of the long-standing controversial arguments in protein folding is Levinthal＇s paradox. We have recently proposed a new nucleation hypothesis and shown that the nucleation residues are the most conserved sequences in protein. To avoid the complicated effect of tertiary interactions, we limit our search for structural codes to the nucleation residues. Starting with the hypotheses of secondary structure nucleation and conservation of residues important for folding, we have analysed 762 folds classified as unique by SCOP. Segments of 17 residues around the top 20% conserved amino acids are analysed, resulting in approximately 100 clusters each for the main secondary structure classes of helix, sheet and coil. Helical clusters have the longest correlation range, coils the shortest （four residues）. Strong specific sequence-structure correlation is observed for coil but not for helix and sheet, suggesting a mapping relationship between the sequence and the structure for coil. We propose that the central sequences in these clusters form ＇structural codes＇, a useful basis set for identifying nucleation sites, protein fragments stable in isolation, and secondary structural patterns in proteins （particularly turns and loops）.展开更多
A structural cross-section constructed across the Zagros Fold-Thrust Belt covering the Abadan Plain, Dezful Embayment, and Izeh Zone applied 2D and 3D seismic data, well data, surface and subsurface geological maps, s...A structural cross-section constructed across the Zagros Fold-Thrust Belt covering the Abadan Plain, Dezful Embayment, and Izeh Zone applied 2D and 3D seismic data, well data, surface and subsurface geological maps, satellite images and field reconnaissance. Besides validation and modification of the cross-section, restoration allows better understanding of the geology, structural style and stratigraphy of the Zagros basin. In the area of interest, the Hormuz basal decollement and the Gachsaran detachment play the most significant roles in the structural style and deformation of the Zagros belt. More complexity is associated with interval decollements such as Triassic evaporites, Albian shales and Eocene marls. A variety of lithotectonic units and detachment surfaces confound any estimation of shortening, which generally decreases with increasing depth. Deformation completely differs in the Abadan Plain, Dezful Embayment and Izeh Zone because of different sedimentation histories and tectonic evolution; gentle and young structures can be interpreted as pre-collisional structures of the Dezful Embayment before the Late Cretaceous. After the Late Cretaceous, the Mountain Front Fault is the main control of sedimentation and deformation in the Zagros Basin, and this completely characterizes fold style and geometry within the Dezful Embayment and the Izeh Zone.展开更多
A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each s...A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial stage.Furthermore,a more realistic formula is used to compute the energy ofmulti-branch loop in the following iteration.Then a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different stems.Finally by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values forparameters.The measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.展开更多
[Background]Traveling-wave tubes(TWTs)are widely applied in radar,imaging,and military systems owing to their excellent amplification characteristics.Miniaturization and integration are critical to the future of TWTs,...[Background]Traveling-wave tubes(TWTs)are widely applied in radar,imaging,and military systems owing to their excellent amplification characteristics.Miniaturization and integration are critical to the future of TWTs,with multi-channel slow-wave structures(SWSs)forming the foundation for their realization in high-power vacuum electronic devices.[Purpose]To provide design insights for multi-channel TWTs and simultaneously enhance their output power,a W-band folded-waveguide TWT with dual electron beams and H-plane power combining was proposed.[Methods]Three-dimensional electromagnetic simulations in CST were conducted to verify the highfrequency characteristics,electric field distribution,and amplification performance of the proposed SWS,thereby confirming the validity of the design.[Results]Results indicate that the designed TWT achieves a transmission bandwidth of 10 GHz.With an electron beam voltage of 17.9 kV and a current of 0.35 A,the output power reaches 450 W at 94 GHz,corresponding to an efficiency of 7.18%and a gain of 23.5 dB.Moreover,under fixed beam voltage and current,the TWT delivers over 200 W output power across 91–99 GHz,with a 3 dB bandwidth of 91–98.5 GHz.The particle voltage distribution after modulation further validates the mode analysis.[Conclusions]These results demonstrate the feasibility of compact dual-beam power-combining structures and provide useful guidance for the design of future multi-channel TWTs.展开更多
The northern Sichuan Basin,spreading in the northern section of the Longmenshan Fault Fold Belt,is characterized by dramatic fluctuations in the surface landforms,development of abdominal faults,and low-quality seismi...The northern Sichuan Basin,spreading in the northern section of the Longmenshan Fault Fold Belt,is characterized by dramatic fluctuations in the surface landforms,development of abdominal faults,and low-quality seismic data,resulting in difficulties in clarifying relevant structures.The key target formation,the Mid-Permian Qixia Fm,is deeply buried with thin reservoirs and high heterogeneity,which brings great challenges to seismic prediction.Under such circumstances,researches have been conducted jointly in terms of seismic data acquisition,processing and interpretation,and finally some relevant seismic survey technologies were developed suitable for surface/underground complex structures.Through surface structural surveys,dynamic deep-well lithologic identification,single-point detector deployment and process optimization,acquisition parameters can be excited.In addition,by using an observation systemwith high-coverage,wide-azimuth and huge-displacement,quality of acquired seismic data can be enhanced dramatically.Seismic imaging technologies for complex structures have been developed to enhance the quality of images for deep formations.These technologies are dominated by microscopic logging-constrained tomography static correction,high-resolution processing with fidelity and amplitude preservation and all-around PSDM in an angular domain.By using high-resolution gravity,magnetic and electric data,details related to geological structures and faults can be identified.In combination with fine seismic data interpretation,structural details and fault features can be verified effectively.Based on forwardmodeling and fine seismic calibration of reservoirs in individualwells,suitable attributes can be identified for predictions related to the distribution of reservoirs.By using all these auxiliary technologies,a large-scale structuralelithologic composite trap with a total area of 1223 km^(2) has been discovered in the NW Sichuan Basin.The Shuangyushi-Jiangyou area as a whole distributes on structural highs.In the areas to the south of Shuangyushi,the Qixia Fm dolomite reservoirs of platform margins are continuously developed.In conclusion,these auxiliary technologies can effectively allow trap identification and thin reservoir prediction in complex structures in the study area.In addition to clarifying the exploration orientation and providing a necessarily technical supports forwell development,these technologies help to accelerate the construction of demonstration projects for the exploration and development of deep marine carbonate formations.展开更多
The design of any antagonist or inhibitor for any enzyme requires the knowledge of structure- function relationship of the protein and the optimum conformational states for maximum and minimum activities. Furthermore,...The design of any antagonist or inhibitor for any enzyme requires the knowledge of structure- function relationship of the protein and the optimum conformational states for maximum and minimum activities. Furthermore, designing of the inhibitors or drugs against an enzyme becomes easier if there is information available about various well characterized intermediate conformation of the molecule. In vivo folding pathway of any recombinant protein is an important parameter for understanding its ability to fold by itself inside the cell, which always dictates the downstream processing for the purification. In the present manuscript we have discussed about the in vivo and in vitro folding, and structure-function relationship of Dihydrofolate reductase enzyme. This is an important enzyme involved in the cell growth and hence inhibition or inactivation of the enzyme may reduce the cell growth. It was observed that the equilibrium unfolding transition of DHFR proceeds through the formation of intermediates having higher exposed surface hydrophobicity, unchanged enzymatic activity and minimum changes in the secondary structural elements. Because of enhanced surface hydrophobicity, and unchanged enzymatic activity, these intermediates could be a nice target for designing drugs against DHFR.展开更多
Fold terminations are key features in the study of compressional fault-related folds. Such terminations could be due to loss of displacement on the thrust fault or/and forming a lateral or oblique ramp. Thus, high-qua...Fold terminations are key features in the study of compressional fault-related folds. Such terminations could be due to loss of displacement on the thrust fault or/and forming a lateral or oblique ramp. Thus, high-quality seismic data would help unambiguously define which mechanism should be responsible for the termination of a given fault-related fold. The Qiongxi and Qiongxinan structures in the Sichuan Basin, China are examples of natural fault-propagation folds that possess a northern termination and a structural saddle between them. The folds/fault geometry and along-strike displacement variations are constrained by the industry 3-D seismic volume. We interpret that the plunge of the fold near the northern termination and the structural saddle are due to the loss of displacement along strike. The fault geometry associated with the northern termination changes from a flat-ramp at the crest of the Qiongxinan structure, where displacement is the greatest, to simply a ramp near the northern tip of the Qiongxi structure, without forming a lateral or oblique ramp. In this study, we also use the drainage pattern, embryonic structure preserved in the crest of the Qiongxinan structure and the assumption that displacement along a fault is proportional to the duration of thrusting to propose a model for the lateral propagation of the Qiongxinan and Qiongxi structures. Specifically, we suggest that the structure first initiated as an isolated fault ramp within brittle units. With increased shortening, the fault grows to link with lower detachments in weaker shale units to create a hybridized fault-propagation fold. Our model suggests a possible explanation for the lateral propagation history of the Qiongxinan and Qiongxi structures, and also provides an alternative approach to confirming the activity of the previous Pingluoba structure in the southwestern Sichuan Basin in the late Cenozoic.展开更多
Seeking for innovative structures with higher mechanical performance is a continuous target in railway vehicle crashworthiness design.In the present study,three types of hexagonal reinforced honeycomb-like structures ...Seeking for innovative structures with higher mechanical performance is a continuous target in railway vehicle crashworthiness design.In the present study,three types of hexagonal reinforced honeycomb-like structures were developed and analyzed subjected to out-of-plane compression,namely triangular honeycomb(TH),double honeycomb(DH)and full inside honeycomb(FH).Theoretical formulas of average force and specific energy absorption(SEA)were constructed based on the energy minimization principle.To validate,corresponding numerical simulations were carried out by explicit finite element method.Good agreement has been observed between them.The results show that all these honeycomb-like structures maintain the same collapsed stages as conventional honeycomb;cell reinforcement can significantly promote the performance,both in the average force and SEA;full inside honeycomb performs better than the general,triangular and double schemes in average force;meanwhile,its SEA is close to that of double scheme;toroidal surface can dissipate higher plastic energy,so more toroidal surfaces should be considered in design of thin-walled structure.These achievements pave a way for designing high-performance cellular energy absorption devices.展开更多
A folding beam-type piezoelectric phononic crystal model is proposed to isolate vibration. Two piezoelectric bimorphs are joined by two masses as a folding structure to comprise each unit cell of the piezoelectric pho...A folding beam-type piezoelectric phononic crystal model is proposed to isolate vibration. Two piezoelectric bimorphs are joined by two masses as a folding structure to comprise each unit cell of the piezoelectric phononic crystal. Each bimorph is connected independently by a resistive-inductive resonant shunting circuit. The folding structure extends the propagation path of elastic waves, while its structure size remains quite small. Propagation of coupled extension-flexural elastic waves is studied by the classical laminated beam theory and transfer matrix method. The theoretical model is further verified with the finite element method(FEM). The effects of geometrical and circuit parameters on the band gaps are analyzed. With only 4 unit cells, the folding beam-type piezoelectric phononic crystal generates two Bragg band gaps of 369 Hz to1 687 Hz and 2 127 Hz to 4 000 Hz. In addition, between these two Bragg band gaps, a locally resonant band gap is induced by resonant shunting circuits. Appropriate circuit parameters are used to join these two Bragg band gaps by the locally resonant band gap.Thus, a low-frequency and broad band gap of 369 Hz to 4 000 Hz is obtained.展开更多
To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a...To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a-helix （seqB： KVFKQYAN）, two -turns （seqA： LNGKTLKG and seqC： YDDATKTF）, and one -strand （seqD： DGEWTYDD）. The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-#s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.展开更多
The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in r...The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromo- some stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 51-（CCCTAA）3CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable inter- mediate state whose nature is yet to be determined. Overall, the unique mechano-chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices.展开更多
The central wavelength of the first Bragg scattering bandgap is approximately twice that of the lattice.Therefore,a low-frequency Bragg scattering bandgap with a small structural dimension for phononic crystals is dif...The central wavelength of the first Bragg scattering bandgap is approximately twice that of the lattice.Therefore,a low-frequency Bragg scattering bandgap with a small structural dimension for phononic crystals is difficult to obtain.In this study,a folded S-type periodic structure is developed to reduce the dimension in the direction of vibration suppression by folding unit cells.According to the foregoing,an improved folded S-type periodic structure with different unit cell arrangements is designed to widen the bandgap frequency range.Energy band diagrams and frequency responses are calculated based on the Bloch theory and using the finite element method.Furthermore,a prototype of the improved folded S-type periodic structure is fabricated using a three-dimensional printing technique,and a vibration experiment is conducted.To verify the vibration reduction performance of the structure,numerical simulation and experimental results are compared.This type of folded periodic structure can effectively reduce dimensions to satisfy the dimension requirements pertaining to the direction of vibration suppression.Hence,the foregoing can aid in promoting the use of elastic bandgap structures in engineering.展开更多
5-（Hydroxymethyl） isophthalic acid （H2HIA） as a novel organic ligand was prepared from 3,5-bis（methoxycarbonyl）benzoic acid by a two-step method. And then, a 3D helical coor- dination polymer with a 3-fold inter...5-（Hydroxymethyl） isophthalic acid （H2HIA） as a novel organic ligand was prepared from 3,5-bis（methoxycarbonyl）benzoic acid by a two-step method. And then, a 3D helical coor- dination polymer with a 3-fold interpenetration structure, namely [Zn1/2（HIA）1/2（DPEE）1/2]n （1）, was hydrothermally synthesized at 160 ℃, using H2HIA ligands to assemble with DPEE ligands and Zn2＋ ions. Complex 1 crystalizes in orthorhombic system, space group Pnna, with a = 8.2118（5）, b = 17.1698（7）, c =14.9922（7） ？, V = 2113.82（18） ？3, μ = 1.194 mm-1, Z = 4 and S = 0.967. Moreover, some physical characteristics of complex 1, such as powder X-ray diffraction （PXRD）, thermogravimetry analyses （TGA） and photoluminescent properties, were also investigated.展开更多
Two fascinating Zn（II）entangled coordination polymers,[Zn（eoba）(bbi)];·nH;O（1）and[Zn（boba）(bbi);];（2）,(bbi=1,1?-（1,4-butanediyl）-bis（imidazole）,H;eoba=4,4?-（ethane-1,2-diyldioxy）-dibenzoic acid,H;...Two fascinating Zn（II）entangled coordination polymers,[Zn（eoba）(bbi)];·nH;O（1）and[Zn（boba）(bbi);];（2）,(bbi=1,1?-（1,4-butanediyl）-bis（imidazole）,H;eoba=4,4?-（ethane-1,2-diyldioxy）-dibenzoic acid,H;boba=4,4?-（butane-1,4-diyldioxy）-dibenzoic acid),were obtained by hydrothermal technology and characterized by elemental analysis,infrared spectrum,thermogravimetric analysis and single-crystal X-ray diffraction.1 is a rare 2D→3D example with a 3-fold parallel interpenetration and polycatenaned architecture.2 features a scarce2D→2D example with a 3-fold parallel interpenetrating network which possesses polyrotaxane and polycatenane characters.Moreover,the luminescent properties of 1 and 2 have been discussed.展开更多
基金supported in part by National Key R&D Program of China(Grant No.2018YFB1304600)CAS Interdisciplinary Innovation Team(Grant No.JCTD-2018-11)the Natural Science Foundation of China(Grant No.51775541).
文摘Flasher origami pattern has been widely utilized to improve the stowage efficiency of deployable structures.Nevertheless,flasher origami cannot be folded fully flat,and they still have great potential for optimization in terms of storage volume and folding creases.In this paper,a flat foldable equiangular spiral folding pattern inspired by the sunflower disk is introduced.Then,a parametric design method for this equiangular spiral crease diagram is introduced in detail.Subsequently,a kinematic model of the equiangular spiral folding pattern is established based on the kinematic equivalence between rigid origami and spherical linkages.A simulation of the developed model demonstrates that the equiangular spiral folding pattern can be folded flat.Using the folded ratio as an evaluation index,the calculated results and experiments show that the equiangular spiral crease pattern can yield fewer creases and improve stowage efficiency in comparison to flasher origami pattern.Equiangular spiral folding pattern can save a considerable amount of space and provide a new approach to spatially deployable structures.
基金Project supported by the National Natural Science Foundation of China （Grant Nos 90103031, 10474041, 90403120 and 10021001）, and the Nonlinear Project （973） of the NSM.
文摘The folding dynamics and structural characteristics of peptides RTKAWNRQLYPEW （P1） and RTKQLYPEW （P2） are investigated by using all-atomic simulation procedure CHARMM in this work. The results show that P1, a segment of an antigen, has a folding motif of α-helix, whereas P2, which is derived by deleting four residues AWNR from peptide P1, prevents the formation of helix and presents a β-strand. And peptlde P1 experiences a more rugged energy landscape than peptide P2. From our results, it is inferred that the antibody CD8 cytolytic T lymphocyte prefers an antigen with a β-folding structure to that with an α-helical one.
文摘Although the advanced 3-dimensional structure measurements provide more and more detailed structures in Protein Data Bank, the simplest 2-dimensional lattice model still looks meaningful because 2-dimensional structures play a complementary role with respect to 3-dimensional structures. In this study, the folding structures of delta-hemolysin and its six variants were studied at 2-dimensional lattice, and their amino acid contacts in folding structures were considered according to HP model with the aid of normalized amino acid hydrophobicity index. The results showed that: 1) either delta-hemolysin or each of its variants could find any of its folding structure in one eighth of 1,129,718,145,924 folding structures because of symmetry, which reduces the time required for folding, 2) the impact of pH on folding structures is varying and associated directly with the amino acid sequence itself, 3) the changes in folding structures of variants appeared different case by case, and 4) the assigning of hydrophobicity index to each amino acid was a way to distinguish folding structures at the same native state. This study can help to understand the structure of delta-hemolysin, and such an analysis can shed lights on NP-problem listed in millennium prize because the HP folding in lattice belongs to a sub-problem of NP-problem.
基金supported by the start-up grant from“Top 100 Talents Program”of Sun Yat-sen University to JRY(50000-31131114)General Program of National Natural Science Foundation of China to JRY(31671320)
文摘Currently many facets of genetic information are illdefined. In particular, how protein folding is genetically regulated has been a long-standing issue for genetics and protein biology. And a generic mechanistic model with supports of genomic data is still lacking. Recent technological advances have enabled much needed genome-wide experiments. While putting the effect of codon optimality on debate, these studies have supplied mounting evidence suggesting a role of m RNA structure in the regulation of protein folding by modulating translational elongation rate. In conjunctions with previous theories, this mechanistic model of protein folding guided by m RNA structure shall expand our understandings of genetic information and offer new insights into various biomedical puzzles.
基金This work was supported by National Natural Science Foundation of China under Grant 11672266.
文摘Based on the first-order shear deformation theory,a 3-node co-rotational triangular finite element formulation is developed for large deformation modeling of non-smooth,folded and multi-shell laminated composite structures.The two smaller components of the mid-surface normal vector of shell at a node are defined as nodal rotational variables in the co-rotational local coordinate system.In the global coordinate system,two smaller components of one vector,together with the smallest or second smallest component of another vector,of an orthogonal triad at a node on a non-smooth intersection of plates and/or shells are defined as rotational variables,whereas the two smaller components of the mid-surface normal vector at a node on the smooth part of the plate or shell(away from non-smooth intersections)are defined as rotational variables.All these vectorial rotational variables can be updated in an additive manner during an incremental solution procedure,and thus improve the computational efficiency in the nonlinear solution of these composite shell structures.Due to the commutativity of all nodal variables in calculating of the second derivatives of the local nodal variables with respect to global nodal variables,and the second derivatives of the strain energy functional with respect to local nodal variables,symmetric tangent stiffness matrices in local and global coordinate systems are obtained.To overcome shear locking,the assumed transverse shear strains obtained from the line-integration approach are employed.The reliability and computational accuracy of the present 3-node triangular shell finite element are verified through modeling two patch tests,several smooth and non-smooth laminated composite shells undergoing large displacements and large rotations.
基金supported by the Ministry of Education and Science of Russian Federation (No.RFMEFI57414X0078)
文摘An idea to develop a family of cellular cores for sandwich panels using a technology of prepreg folding is presented. Polar folded quadra structures are regarded as a geometric basis for these cores whose standard frag ment has lhe fourlh degree of axial symmelry. The classification of the polar strucluresaredeseribedanda method of various quadra slrueture synthesis is developed. A possibilily to provide high strength of lhe structure due m preservation of faces reinforcement pattern is presented. Arrangemen! of the plane core on a bi curvature surface is also introduced. Besides, provision of isotropyof the core in two or three directions are described. Finally, exam ples of cellular folded cores manufaclured from basalt reinforced plaslic are demonslrated.
文摘One of the long-standing controversial arguments in protein folding is Levinthal＇s paradox. We have recently proposed a new nucleation hypothesis and shown that the nucleation residues are the most conserved sequences in protein. To avoid the complicated effect of tertiary interactions, we limit our search for structural codes to the nucleation residues. Starting with the hypotheses of secondary structure nucleation and conservation of residues important for folding, we have analysed 762 folds classified as unique by SCOP. Segments of 17 residues around the top 20% conserved amino acids are analysed, resulting in approximately 100 clusters each for the main secondary structure classes of helix, sheet and coil. Helical clusters have the longest correlation range, coils the shortest （four residues）. Strong specific sequence-structure correlation is observed for coil but not for helix and sheet, suggesting a mapping relationship between the sequence and the structure for coil. We propose that the central sequences in these clusters form ＇structural codes＇, a useful basis set for identifying nucleation sites, protein fragments stable in isolation, and secondary structural patterns in proteins （particularly turns and loops）.
文摘A structural cross-section constructed across the Zagros Fold-Thrust Belt covering the Abadan Plain, Dezful Embayment, and Izeh Zone applied 2D and 3D seismic data, well data, surface and subsurface geological maps, satellite images and field reconnaissance. Besides validation and modification of the cross-section, restoration allows better understanding of the geology, structural style and stratigraphy of the Zagros basin. In the area of interest, the Hormuz basal decollement and the Gachsaran detachment play the most significant roles in the structural style and deformation of the Zagros belt. More complexity is associated with interval decollements such as Triassic evaporites, Albian shales and Eocene marls. A variety of lithotectonic units and detachment surfaces confound any estimation of shortening, which generally decreases with increasing depth. Deformation completely differs in the Abadan Plain, Dezful Embayment and Izeh Zone because of different sedimentation histories and tectonic evolution; gentle and young structures can be interpreted as pre-collisional structures of the Dezful Embayment before the Late Cretaceous. After the Late Cretaceous, the Mountain Front Fault is the main control of sedimentation and deformation in the Zagros Basin, and this completely characterizes fold style and geometry within the Dezful Embayment and the Izeh Zone.
基金supported by the National Natural Science Foundation of China(Grant No.60971089)the Specialized Research Foundation for the Doctoral Program of Higher Education of China(Grant No.20070183057)
文摘A new method for simulating the folding pathway of RNA secondary structure using the modified ant colony algorithmis proposed.For a given RNA sequence,the set of all possible stems is obtained and the energy of each stem iscalculated and stored at the initial stage.Furthermore,a more realistic formula is used to compute the energy ofmulti-branch loop in the following iteration.Then a folding pathway is simulated,including such processes as constructionof the heuristic information,the rule of initializing the pheromone,the mechanism of choosing the initial andnext stem and the strategy of updating the pheromone between two different stems.Finally by testing RNA sequences withknown secondary structures from the public databases,we analyze the experimental data to select appropriate values forparameters.The measure indexes show that our procedure is more consistent with phylogenetically proven structures thansoftware RNAstructure sometimes and more effective than the standard Genetic Algorithm.
基金National Key Research and Development Program of China(2022YFF0707602)National Natural Science Foundation of China(62471097,62471115,62471101)National Natural Science Foundation of Sichuan(2025ZNSFSC0537)。
文摘[Background]Traveling-wave tubes(TWTs)are widely applied in radar,imaging,and military systems owing to their excellent amplification characteristics.Miniaturization and integration are critical to the future of TWTs,with multi-channel slow-wave structures(SWSs)forming the foundation for their realization in high-power vacuum electronic devices.[Purpose]To provide design insights for multi-channel TWTs and simultaneously enhance their output power,a W-band folded-waveguide TWT with dual electron beams and H-plane power combining was proposed.[Methods]Three-dimensional electromagnetic simulations in CST were conducted to verify the highfrequency characteristics,electric field distribution,and amplification performance of the proposed SWS,thereby confirming the validity of the design.[Results]Results indicate that the designed TWT achieves a transmission bandwidth of 10 GHz.With an electron beam voltage of 17.9 kV and a current of 0.35 A,the output power reaches 450 W at 94 GHz,corresponding to an efficiency of 7.18%and a gain of 23.5 dB.Moreover,under fixed beam voltage and current,the TWT delivers over 200 W output power across 91–99 GHz,with a 3 dB bandwidth of 91–98.5 GHz.The particle voltage distribution after modulation further validates the mode analysis.[Conclusions]These results demonstrate the feasibility of compact dual-beam power-combining structures and provide useful guidance for the design of future multi-channel TWTs.
基金Project supported by the National Major Science and Technology Project“Development of Large Oil/Gas Fields and Coalbed Methane”(No.2016ZX05004-005&2016ZX05007-004)the CNPC Major Science and Technology Project“Research and application of key technologies for maintaining gas productivity of 30 billion cubic meters in Southwest Oil and Gas Fields”(No.2016E-06,2016E-0602,2016E-0603&2016E-0604).
文摘The northern Sichuan Basin,spreading in the northern section of the Longmenshan Fault Fold Belt,is characterized by dramatic fluctuations in the surface landforms,development of abdominal faults,and low-quality seismic data,resulting in difficulties in clarifying relevant structures.The key target formation,the Mid-Permian Qixia Fm,is deeply buried with thin reservoirs and high heterogeneity,which brings great challenges to seismic prediction.Under such circumstances,researches have been conducted jointly in terms of seismic data acquisition,processing and interpretation,and finally some relevant seismic survey technologies were developed suitable for surface/underground complex structures.Through surface structural surveys,dynamic deep-well lithologic identification,single-point detector deployment and process optimization,acquisition parameters can be excited.In addition,by using an observation systemwith high-coverage,wide-azimuth and huge-displacement,quality of acquired seismic data can be enhanced dramatically.Seismic imaging technologies for complex structures have been developed to enhance the quality of images for deep formations.These technologies are dominated by microscopic logging-constrained tomography static correction,high-resolution processing with fidelity and amplitude preservation and all-around PSDM in an angular domain.By using high-resolution gravity,magnetic and electric data,details related to geological structures and faults can be identified.In combination with fine seismic data interpretation,structural details and fault features can be verified effectively.Based on forwardmodeling and fine seismic calibration of reservoirs in individualwells,suitable attributes can be identified for predictions related to the distribution of reservoirs.By using all these auxiliary technologies,a large-scale structuralelithologic composite trap with a total area of 1223 km^(2) has been discovered in the NW Sichuan Basin.The Shuangyushi-Jiangyou area as a whole distributes on structural highs.In the areas to the south of Shuangyushi,the Qixia Fm dolomite reservoirs of platform margins are continuously developed.In conclusion,these auxiliary technologies can effectively allow trap identification and thin reservoir prediction in complex structures in the study area.In addition to clarifying the exploration orientation and providing a necessarily technical supports forwell development,these technologies help to accelerate the construction of demonstration projects for the exploration and development of deep marine carbonate formations.
文摘The design of any antagonist or inhibitor for any enzyme requires the knowledge of structure- function relationship of the protein and the optimum conformational states for maximum and minimum activities. Furthermore, designing of the inhibitors or drugs against an enzyme becomes easier if there is information available about various well characterized intermediate conformation of the molecule. In vivo folding pathway of any recombinant protein is an important parameter for understanding its ability to fold by itself inside the cell, which always dictates the downstream processing for the purification. In the present manuscript we have discussed about the in vivo and in vitro folding, and structure-function relationship of Dihydrofolate reductase enzyme. This is an important enzyme involved in the cell growth and hence inhibition or inactivation of the enzyme may reduce the cell growth. It was observed that the equilibrium unfolding transition of DHFR proceeds through the formation of intermediates having higher exposed surface hydrophobicity, unchanged enzymatic activity and minimum changes in the secondary structural elements. Because of enhanced surface hydrophobicity, and unchanged enzymatic activity, these intermediates could be a nice target for designing drugs against DHFR.
基金supported by grants from the 973 program of China(Grant No.2008CB425702)the National Science Foundation of China(Grant No.40672132).
文摘Fold terminations are key features in the study of compressional fault-related folds. Such terminations could be due to loss of displacement on the thrust fault or/and forming a lateral or oblique ramp. Thus, high-quality seismic data would help unambiguously define which mechanism should be responsible for the termination of a given fault-related fold. The Qiongxi and Qiongxinan structures in the Sichuan Basin, China are examples of natural fault-propagation folds that possess a northern termination and a structural saddle between them. The folds/fault geometry and along-strike displacement variations are constrained by the industry 3-D seismic volume. We interpret that the plunge of the fold near the northern termination and the structural saddle are due to the loss of displacement along strike. The fault geometry associated with the northern termination changes from a flat-ramp at the crest of the Qiongxinan structure, where displacement is the greatest, to simply a ramp near the northern tip of the Qiongxi structure, without forming a lateral or oblique ramp. In this study, we also use the drainage pattern, embryonic structure preserved in the crest of the Qiongxinan structure and the assumption that displacement along a fault is proportional to the duration of thrusting to propose a model for the lateral propagation of the Qiongxinan and Qiongxi structures. Specifically, we suggest that the structure first initiated as an isolated fault ramp within brittle units. With increased shortening, the fault grows to link with lower detachments in weaker shale units to create a hybridized fault-propagation fold. Our model suggests a possible explanation for the lateral propagation history of the Qiongxinan and Qiongxi structures, and also provides an alternative approach to confirming the activity of the previous Pingluoba structure in the southwestern Sichuan Basin in the late Cenozoic.
基金Projects(51875581,51505502)supported by the National Natural Science Foundation of ChinaProjects(2017M620358,2018T110707)supported by China Postdoctoral Science FoundationProject(kq1905057)supported by the Training Program for Excellent Young Innovators of Changsha,China
文摘Seeking for innovative structures with higher mechanical performance is a continuous target in railway vehicle crashworthiness design.In the present study,three types of hexagonal reinforced honeycomb-like structures were developed and analyzed subjected to out-of-plane compression,namely triangular honeycomb(TH),double honeycomb(DH)and full inside honeycomb(FH).Theoretical formulas of average force and specific energy absorption(SEA)were constructed based on the energy minimization principle.To validate,corresponding numerical simulations were carried out by explicit finite element method.Good agreement has been observed between them.The results show that all these honeycomb-like structures maintain the same collapsed stages as conventional honeycomb;cell reinforcement can significantly promote the performance,both in the average force and SEA;full inside honeycomb performs better than the general,triangular and double schemes in average force;meanwhile,its SEA is close to that of double scheme;toroidal surface can dissipate higher plastic energy,so more toroidal surfaces should be considered in design of thin-walled structure.These achievements pave a way for designing high-performance cellular energy absorption devices.
基金Project supported by the National Natural Science Foundation of China(Nos.11272126,51435006,and 51121002)the Fundamental Research Funds for the Central Universities(Nos.HUST:2016JCTD114 and HUST:2015TS121)
文摘A folding beam-type piezoelectric phononic crystal model is proposed to isolate vibration. Two piezoelectric bimorphs are joined by two masses as a folding structure to comprise each unit cell of the piezoelectric phononic crystal. Each bimorph is connected independently by a resistive-inductive resonant shunting circuit. The folding structure extends the propagation path of elastic waves, while its structure size remains quite small. Propagation of coupled extension-flexural elastic waves is studied by the classical laminated beam theory and transfer matrix method. The theoretical model is further verified with the finite element method(FEM). The effects of geometrical and circuit parameters on the band gaps are analyzed. With only 4 unit cells, the folding beam-type piezoelectric phononic crystal generates two Bragg band gaps of 369 Hz to1 687 Hz and 2 127 Hz to 4 000 Hz. In addition, between these two Bragg band gaps, a locally resonant band gap is induced by resonant shunting circuits. Appropriate circuit parameters are used to join these two Bragg band gaps by the locally resonant band gap.Thus, a low-frequency and broad band gap of 369 Hz to 4 000 Hz is obtained.
基金Supported by the National Basic Research Program of China under Grant No.2013CB932804the National Natural Science Foundation of China under Grant No.11421063the CAS Biophysics Interdisciplinary Innovation Team Project
文摘To understand how the stabilities of key nuclei fragments affect protein folding dynamics, we simulate by molecular dynamics （MD） simulation in aqueous solution four fragments cut out of a protein G, including one a-helix （seqB： KVFKQYAN）, two -turns （seqA： LNGKTLKG and seqC： YDDATKTF）, and one -strand （seqD： DGEWTYDD）. The Markov State Model clustering method combined with the coarse-grained conformation letters method are employed to analyze the data sampled from 2-#s equilibrium MD simulation trajectories. We find that seqA and seqB have more stable structures than their native structures which become metastable when cut out of the protein structure. As expected, seqD alone is flexible and does not have a stable structure. Throughout our simulations, the native structure of seqC is stable but cannot be reached if starting from a structure other than the native one, implying a funnel-shape free energy landscape of seqC in aqueous solution. All the above results suggest that different nuclei have different formation dynamics during protein folding, which may have a major contribution to the hierarchy of protein folding dynamics.
基金supported by Grants from the National Research Foundation through the Mechanobiology Institute Singapore and the Ministry of Education of Singapore(Grant No.MOE2012-T3-1-001)[to Yan J]the National Basic Research Program of China(Grant No.2013CB932800)+1 种基金the Major Research Plan of the National Natural Science Foundation of China(Grant Nos.91027046 and 91027045)the Fundamental Research Funds for the Central Universities(Grant No.2013121005)
文摘The DNA i-motif is a quadruplex structure formed in tandem cytosine-rich sequences in slightly acidic conditions. Besides being considered as a building block of DNA nano-devices, it may also play potential roles in regulating chromo- some stability and gene transcriptions. The stability of i-motif is crucial for these functions. In this work, we investigated the mechanical stability of a single i-motif formed in the human telomeric sequence 51-（CCCTAA）3CCC, which revealed a novel pH and loading rate-dependent bimodal unfolding force distribution. Although the cause of the bimodal unfolding force species is not clear, we proposed a phenomenological model involving a direct unfolding favored at lower loading rate or higher pH value, which is subject to competition with another unfolding pathway through a mechanically stable inter- mediate state whose nature is yet to be determined. Overall, the unique mechano-chemical responses of i-motif-provide a new perspective to its stability, which may be useful to guide designing new i-motif-based DNA mechanical nano-devices.
基金supported by the National Natural Science Foundation of China(Nos.12072086,12211540384 and 11761131006)the Fundamental Research Funds for the Central Universities(No.3072022CF0203).
文摘The central wavelength of the first Bragg scattering bandgap is approximately twice that of the lattice.Therefore,a low-frequency Bragg scattering bandgap with a small structural dimension for phononic crystals is difficult to obtain.In this study,a folded S-type periodic structure is developed to reduce the dimension in the direction of vibration suppression by folding unit cells.According to the foregoing,an improved folded S-type periodic structure with different unit cell arrangements is designed to widen the bandgap frequency range.Energy band diagrams and frequency responses are calculated based on the Bloch theory and using the finite element method.Furthermore,a prototype of the improved folded S-type periodic structure is fabricated using a three-dimensional printing technique,and a vibration experiment is conducted.To verify the vibration reduction performance of the structure,numerical simulation and experimental results are compared.This type of folded periodic structure can effectively reduce dimensions to satisfy the dimension requirements pertaining to the direction of vibration suppression.Hence,the foregoing can aid in promoting the use of elastic bandgap structures in engineering.
基金supported by the Natural Science Foundation of Guizhou Province(20122344)125 program of Guizhou Education Department(2012015)the Doctoral Scientific Fund of Zunyi Normal College(2012BSJJ12)
文摘5-（Hydroxymethyl） isophthalic acid （H2HIA） as a novel organic ligand was prepared from 3,5-bis（methoxycarbonyl）benzoic acid by a two-step method. And then, a 3D helical coor- dination polymer with a 3-fold interpenetration structure, namely [Zn1/2（HIA）1/2（DPEE）1/2]n （1）, was hydrothermally synthesized at 160 ℃, using H2HIA ligands to assemble with DPEE ligands and Zn2＋ ions. Complex 1 crystalizes in orthorhombic system, space group Pnna, with a = 8.2118（5）, b = 17.1698（7）, c =14.9922（7） ？, V = 2113.82（18） ？3, μ = 1.194 mm-1, Z = 4 and S = 0.967. Moreover, some physical characteristics of complex 1, such as powder X-ray diffraction （PXRD）, thermogravimetry analyses （TGA） and photoluminescent properties, were also investigated.
基金Supported by the Science and Technology Development plan of Jilin Province(20150520006JH)Science and Technology Research Project of Education Department of Jilin province(2016219,JJKH20180776KJ)Science and Technology Development plan of Siping City(2013055)
文摘Two fascinating Zn（II）entangled coordination polymers,[Zn（eoba）(bbi)];·nH;O（1）and[Zn（boba）(bbi);];（2）,(bbi=1,1?-（1,4-butanediyl）-bis（imidazole）,H;eoba=4,4?-（ethane-1,2-diyldioxy）-dibenzoic acid,H;boba=4,4?-（butane-1,4-diyldioxy）-dibenzoic acid),were obtained by hydrothermal technology and characterized by elemental analysis,infrared spectrum,thermogravimetric analysis and single-crystal X-ray diffraction.1 is a rare 2D→3D example with a 3-fold parallel interpenetration and polycatenaned architecture.2 features a scarce2D→2D example with a 3-fold parallel interpenetrating network which possesses polyrotaxane and polycatenane characters.Moreover,the luminescent properties of 1 and 2 have been discussed.
