In this paper, molecular orientation behavior of polymethylene chains was investigated on the basis of considering long\|distance interactions by using the enumeration calculation method and the rotational isomeric st...In this paper, molecular orientation behavior of polymethylene chains was investigated on the basis of considering long\|distance interactions by using the enumeration calculation method and the rotational isomeric state(RIS) model. The chain lengths are from \%N\%=12 to \%N=\%24, and the Lennord\|Jennes potential was adopted in the non\|local interaction calculations. The molecular orientation function(Legendre polynomial) may be well expressed as\$\$<P\-2(ζ)>/(λ\+2-λ\+\{-1\})=a(λ\+2-λ\+\{-1\})+b\$\$here\% a\% and\% b\% only depend on the chain length, and decrease with the increase of chain length, especially for \%b\%. In the meantime, we also calculate the Helmholtz free energy change in the process of tensile deformation. Comparisons with Gaussian chains are made, and our results are close to those obtained from the Roe and Krigbaum theory.展开更多
The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics sinmla...The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics sinmlations. The power-law scaling of the translocation time T with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be T - N^a with the exponent a varying from a = 0.71 for relatively short chains to a = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α= 1.27 for the transloeation of double-strand DNA. The distribution of translocation time D（τ） is close to a Gaussian function for duration time τ 〈 τp and follows a falling exponential function for duration time T 〉 wp. For closed knotted polymers, the scaling exponent a is 1.27 for small field force （F = 5） and 1.38 for large field force （F = 10）. The distribution of translocation time D（τ） remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.展开更多
The phase behaviours of diblock copolymers under cylindrical confinement are studied in two-dimensional space by using the self-consistent field theory. Several phase parameters are adjusted to investigate the cylindr...The phase behaviours of diblock copolymers under cylindrical confinement are studied in two-dimensional space by using the self-consistent field theory. Several phase parameters are adjusted to investigate the cylindrical-confinement-induced phase behaviours of diblock copolymers. A series of lamella-cylinder mixture phases, such as the mixture of broken-lamellae and cylinders and the mixture of square-lamellae and cylinders, are observed by varying the phase parameters, in which the behaviours of these mixture phases are discussed in the corresponding phase diagrams. Furthermore, the free energies of these mixture phases are investigated to illustrate their evolution processes. Our results are compared with the available observations from the experiments and simulations respectively, and they are in good agreement and provide an insight into the phase behaviours under cylindrical confinement.展开更多
The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is adde...The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.展开更多
The phase behaviour of a single polyethylene chain is studied by using molecular dynamics simulations. A free chain and a chain with fixing one end are considered here, since the atomic force microscope （AFM） tip ca...The phase behaviour of a single polyethylene chain is studied by using molecular dynamics simulations. A free chain and a chain with fixing one end are considered here, since the atomic force microscope （AFM） tip can play a significant role in polymer crystallization in experiment. For a free chain, it is confirmed in our calculation that the polymer chain exhibits an extended coil state at high temperatures, collapses into a condensed state at low temperatures, i.e. the coil-to-globule transition that is determined by a high temperature shoulder of the heat capacity curve, and an additional liquid-to-solid transition that is described by a low temperature peak of the same heat curve. These results accord with previous studies of square-well chains and Lennard-Jones homopolymers. However, when one of the end monomers of the same chain is fixed the results become very different, and the chain cannot reach an extended coil-like state as a free chain does at high temperatures, i.e. there exists no coil-to-globule-like transition. These results may provide some insights into the influence of AFM tip when it is used to study the phase behaviour of polymer chains. If the interaction force between AFM tip and polymer monomers is strong, some monomers or one of them can be seen as being fixed by the tip, which is similar to our simulation model, and it is also found that AFM tip could induce polymer crystallization.展开更多
Transport of passive particles induced by chiral-active particles in microchannel is investigated by using the overdamped Langevin dynamics simulation in a two-dimensional model system. Due to the chirality of active ...Transport of passive particles induced by chiral-active particles in microchannel is investigated by using the overdamped Langevin dynamics simulation in a two-dimensional model system. Due to the chirality of active particles and special structure of microchannel, effective ratchet transport of passive particles is achieved. Effective transport of passive particles depends on the width of microchannel（d）, the density（ρ）, and the angular velocity（ω） of chiral-active particles.There exist optimal parameters for d and ω at which the transport efficiency for passive particles takes its maximal value.This investigation can help us understand the necessity of active motion for living systems to maintain a number of vital processes such as materials transport inside cells and the foraging dynamics of mobile organisms.展开更多
Using molecular dynamics simulations and atomic force microscopy （AFM）, we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic ...Using molecular dynamics simulations and atomic force microscopy （AFM）, we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transi- tions of DNA are also experimentally observed in mixing spermidine with X-phage DNA at different concentrations of NaCl/MgCl2 solutions.展开更多
The surface-induced effect on the morphologies of lamella-forming diblock copolymers in nanorod arrays is studied by using the self-consistent field theory. In the simulation study, a rich variety of novel morphologie...The surface-induced effect on the morphologies of lamella-forming diblock copolymers in nanorod arrays is studied by using the self-consistent field theory. In the simulation study, a rich variety of novel morphologies are observed by variations in the strength of the surface field for the diblock copolymers. Different surface-field-induced effects are examined for the diblock copolymers in the arrays with distinct preferential surfaces. It is observed that the majority-block preferential surfaces have more obvious induced effects than those of minority-block preferential surfaces. The strong surface fields exhibit different behaviours from those observed in the weak surface fields, by which the morphologies possess cylindrical symmetries. Results from this research deepen the knowledge of surface-induced effects in a confinement system, which may aid the fabrication of polymer-based na^omaterials.展开更多
The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the res...The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond （S2）/（Nb2） and the shape factor （（δ＊） depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity Cv, and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.展开更多
The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories o...The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobieity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of/3 sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.展开更多
The composition and residue-residue interactions of knotted proteins, compared with those of other proteins, can provide considerable insight into the driver of the knots in proteins. In this paper, we calculate the p...The composition and residue-residue interactions of knotted proteins, compared with those of other proteins, can provide considerable insight into the driver of the knots in proteins. In this paper, we calculate the probabilities of 20 amino acids in 273 knotted entries from the Protein Data Bank （PDB）. The collection of 273 entries contains all knotted structures in the PDB, and it is not a subset. With an appropriate value of Re, the numbers of all residue residue contacts are counted in all 273 knotted structures. To make an accurate comparison, we count up to 9000 other entries from the PDB as well, and these entries spread over all sorts. In knotted structures, Leu occupies a maximal proportion of 9.62% among all 20 amino acids, and Leu, Phe, Trp, Gly, His, Gln, Asp, Lys and Pro may all play a more important role. Also, we analyse the effects of amino acid residues on the long-range contacts. We observe a larger average number of long-range contacts in the knotted structures than that in other ones, implying their important role in achieving the knots. Accordingly, the average number of short-range contacts becomes small when the structure becomes knotted because it depends mainly on the short-haul sequence of amino acids to form the short-range contact. In addition, the shape distribution of knotted proteins and the contrast with the other proteins are also presented. A comparison shows that the knots may make structures more globular because the average shape factor is 0.059 for the knotted proteins, which is only about 1/3 of the average shape factor for the other proteins.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
Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel.A novel helix-like structure is found to form during the simulation.Moreover,the det...Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel.A novel helix-like structure is found to form during the simulation.Moreover,the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated.We find that the structure is not a perfect helix,but a bundle of elliptical turns.In addition,we conduct a statistical analysis for the chain monomer distribution along the radial direction.This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent.展开更多
文摘In this paper, molecular orientation behavior of polymethylene chains was investigated on the basis of considering long\|distance interactions by using the enumeration calculation method and the rotational isomeric state(RIS) model. The chain lengths are from \%N\%=12 to \%N=\%24, and the Lennord\|Jennes potential was adopted in the non\|local interaction calculations. The molecular orientation function(Legendre polynomial) may be well expressed as\$\$<P\-2(ζ)>/(λ\+2-λ\+\{-1\})=a(λ\+2-λ\+\{-1\})+b\$\$here\% a\% and\% b\% only depend on the chain length, and decrease with the increase of chain length, especially for \%b\%. In the meantime, we also calculate the Helmholtz free energy change in the process of tensile deformation. Comparisons with Gaussian chains are made, and our results are close to those obtained from the Roe and Krigbaum theory.
基金Project supported by the National Natural Science Foundation of China (Grant Nos. 20574052, 20774066, 20974081 and 20934004)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. Y4090098)
文摘The dynamic behaviours of the translocations of closed circular polymers and closed knotted polymers through a nanopore, under the driving of an applied field, are studied by three-dimensional Langevin dynamics sinmlations. The power-law scaling of the translocation time T with the chain length N and the distribution of translocation time are investigated separately. For closed circular polymers, a crossover scaling of translocation time with chain length is found to be T - N^a with the exponent a varying from a = 0.71 for relatively short chains to a = 1.29 for longer chains under driving force F = 5. The scaling behaviour for longer chains is in good agreement with experimental results, in which the exponent α= 1.27 for the transloeation of double-strand DNA. The distribution of translocation time D（τ） is close to a Gaussian function for duration time τ 〈 τp and follows a falling exponential function for duration time T 〉 wp. For closed knotted polymers, the scaling exponent a is 1.27 for small field force （F = 5） and 1.38 for large field force （F = 10）. The distribution of translocation time D（τ） remarkably features two peaks appearing in the case of large driving force. The interesting result of multiple peaks can conduce to the understanding of the influence of the number of strands of polymers in the pore at the same time on translocation dynamic process and scaling property.
基金supported by the National Natural Science Foundation of China (Grant Nos. 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 Nos. R404047, Y4090174, and Y405553)
文摘The phase behaviours of diblock copolymers under cylindrical confinement are studied in two-dimensional space by using the self-consistent field theory. Several phase parameters are adjusted to investigate the cylindrical-confinement-induced phase behaviours of diblock copolymers. A series of lamella-cylinder mixture phases, such as the mixture of broken-lamellae and cylinders and the mixture of square-lamellae and cylinders, are observed by varying the phase parameters, in which the behaviours of these mixture phases are discussed in the corresponding phase diagrams. Furthermore, the free energies of these mixture phases are investigated to illustrate their evolution processes. Our results are compared with the available observations from the experiments and simulations respectively, and they are in good agreement and provide an insight into the phase behaviours under cylindrical confinement.
基金supported by the National Natural Science Foundation of China (Grant Nos. 20974081, 20934004, 21174131, and 21104060)the Zhejiang Provincial Natural Science Foundation of China (Grant No. Y4110357)
文摘The condensation of DNA induced by spermine is studied by atomic force microscopy （AFM） and molecular dynamics （MD） simulation in this paper. In our experiments, an equivalent amount of multivalent cations is added to the DNA solutions in different numbers of steps, and we find that the process of DNA condensation strongly depends on the speed of adding cations. That is, the slower the spermine cations are added, the slower the DNA aggregates. The MD and steered molecular dynamics （SMD） simulation results agree well with the experimental results, and the simulation data also show that the more steps of adding multivalent cations there are, the more compact the condensed DNA structure will be. This investigation can help us to control DNA condensation and understand the complicated structures of DNA--cation complexes.
基金Project supported by the National Natural Science Foundation of China (Grant Nos 20574052 and 20774066)the Program for New Century Excellent Talents in University (Grant No NCET-05-0538)the Natural Science Foundation of Zhejiang Province (Grant No R404047)
文摘The phase behaviour of a single polyethylene chain is studied by using molecular dynamics simulations. A free chain and a chain with fixing one end are considered here, since the atomic force microscope （AFM） tip can play a significant role in polymer crystallization in experiment. For a free chain, it is confirmed in our calculation that the polymer chain exhibits an extended coil state at high temperatures, collapses into a condensed state at low temperatures, i.e. the coil-to-globule transition that is determined by a high temperature shoulder of the heat capacity curve, and an additional liquid-to-solid transition that is described by a low temperature peak of the same heat curve. These results accord with previous studies of square-well chains and Lennard-Jones homopolymers. However, when one of the end monomers of the same chain is fixed the results become very different, and the chain cannot reach an extended coil-like state as a free chain does at high temperatures, i.e. there exists no coil-to-globule-like transition. These results may provide some insights into the influence of AFM tip when it is used to study the phase behaviour of polymer chains. If the interaction force between AFM tip and polymer monomers is strong, some monomers or one of them can be seen as being fixed by the tip, which is similar to our simulation model, and it is also found that AFM tip could induce polymer crystallization.
基金supported by the National Natural Science Foundation of China(Grant Nos.21374102,21674096,and 21674082)
文摘Transport of passive particles induced by chiral-active particles in microchannel is investigated by using the overdamped Langevin dynamics simulation in a two-dimensional model system. Due to the chirality of active particles and special structure of microchannel, effective ratchet transport of passive particles is achieved. Effective transport of passive particles depends on the width of microchannel（d）, the density（ρ）, and the angular velocity（ω） of chiral-active particles.There exist optimal parameters for d and ω at which the transport efficiency for passive particles takes its maximal value.This investigation can help us understand the necessity of active motion for living systems to maintain a number of vital processes such as materials transport inside cells and the foraging dynamics of mobile organisms.
基金supported by the National Natural Science Foundation of China(Grant No.31340026)the Natural Science Foundation of Zhejiang Province,China(Grant Nos.Z13F20019 and LQ12E01003)the Science and Technology Project of Zhejiang Science and Technology Department,China(Grant No.2014C31147)
文摘Using molecular dynamics simulations and atomic force microscopy （AFM）, we study the decondensation process of DNA chains induced by multivalent cations at high salt concentrations in the presence of short cationic chains in solutions. The typical simulation conformations of DNA chains with varying salt concentrations for multivalent cations imply that the concentration of salt cations and the valence of multivalent cations have a strong influence on the process of DNA decondensation. The DNA chains are condensed in the absence of salt or at low salt concentrations, and the compacted conformations of DNA chains become loose when a number of cations and anions are added into the solution. It is explicitly demonstrated that cations can overcompensate the bare charge of the DNA chains and weaken the attraction interactions between the DNA chains and short cationic chains at high salt concentrations. The condensation-decondensation transi- tions of DNA are also experimentally observed in mixing spermidine with X-phage DNA at different concentrations of NaCl/MgCl2 solutions.
基金Project supported by the National Natural Science Foundation of China (Grant Nos.20374050,20934004,21074096,50773072,and 90403022)the Outstanding Youth Fund of China (Grant No.20525416)+3 种基金the National Basic Research Program of China(Grant No.2005CB623800)Program for New Century Excellent Talents in University (Grant No.NCET-05-0538)the Natural Science Foundation of Zhejiang Province (Grant Nos.Y4090174 and Y6100033)the Science Technology Development Plan of Wenzhou City,China (Grant No.H20080041)
文摘The surface-induced effect on the morphologies of lamella-forming diblock copolymers in nanorod arrays is studied by using the self-consistent field theory. In the simulation study, a rich variety of novel morphologies are observed by variations in the strength of the surface field for the diblock copolymers. Different surface-field-induced effects are examined for the diblock copolymers in the arrays with distinct preferential surfaces. It is observed that the majority-block preferential surfaces have more obvious induced effects than those of minority-block preferential surfaces. The strong surface fields exhibit different behaviours from those observed in the weak surface fields, by which the morphologies possess cylindrical symmetries. Results from this research deepen the knowledge of surface-induced effects in a confinement system, which may aid the fabrication of polymer-based na^omaterials.
基金supported by the National Natural Science Foundation of China (Grant Nos. 20574052,20774066,20974081,and 20934004)the Program for New Century Excellent Talents in University of the Ministry of Education of China (Grant No. NCET-05-0538)the Ph.D. Program Foundation of the Ministry of Education of China (Grant No. 20090101110002)
文摘The phase behaviour of polyethylene knotted ring chains is investigated by using molecular dynamics simulations. In this paper, we focus on the collapse of the polyethylene knotted ring chain, and also present the results of linear and ring chains for comparison. At high temperatures, a fully extensive knot structure is observed. The mean-square radius of gyration per bond （S2）/（Nb2） and the shape factor （（δ＊） depend on not only the chain length but also the knot type. With temperature decreasing, chain collapse is observed, and the collapse temperature decreases with the chain length increasing. The actual collapse transition can be determined by the specific heat capacity Cv, and the knotted ring chain undergoes gas-liquid-solid-like transition directly. The phase transition of a knotted ring chain is only one-stage collapse, which is different from the polyethylene linear and ring chains. This investigation can provide some insights into the statistical properties of knotted polymer chains.
基金Project supported by the National Natural Science Foundation of China (Grant No 10747160)SRF for ROCS, SEM (Grant No [2008]890)
文摘The character of forming long-range contacts affects the three-dimensional structure of globular proteins deeply. As the different ability to form long-range contacts between 20 types of amino acids and 4 categories of globular proteins, the statistical properties are thoroughly discussed in this paper. Two parameters NC and ND are defined to confine the valid residues in detail. The relationship between hydrophobieity scales and valid residue percentage of each amino acid is given in the present work and the linear functions are shown in our statistical results. It is concluded that the hydrophobicity scale defined by chemical derivatives of the amino acids and nonpolar phase of large unilamellar vesicle membranes is the most effective technique to characterise the hydrophobic behavior of amino acid residues. Meanwhile, residue percentage Pi and sequential residue length Li of a certain protein i are calculated under different conditions. The statistical results show that the average value of Pi as well as Li of all-α proteins has a minimum among these 4 classes of globular proteins, indicating that all-α proteins are hardly capable of forming long-range contacts one by one along their linear amino acid sequences. All-β proteins have a higher tendency to construct long-range contacts along their primary sequences related to the secondary configurations, i.e. parallel and anti-parallel configurations of/3 sheets. The investigation of the interior properties of globular proteins give us the connection between the three-dimensional structure and its primary sequence data or secondary configurations, and help us to understand the structure of protein and its folding process well.
基金Project supported by the National Natural Science Foundation of China (Grant Nos 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The composition and residue-residue interactions of knotted proteins, compared with those of other proteins, can provide considerable insight into the driver of the knots in proteins. In this paper, we calculate the probabilities of 20 amino acids in 273 knotted entries from the Protein Data Bank （PDB）. The collection of 273 entries contains all knotted structures in the PDB, and it is not a subset. With an appropriate value of Re, the numbers of all residue residue contacts are counted in all 273 knotted structures. To make an accurate comparison, we count up to 9000 other entries from the PDB as well, and these entries spread over all sorts. In knotted structures, Leu occupies a maximal proportion of 9.62% among all 20 amino acids, and Leu, Phe, Trp, Gly, His, Gln, Asp, Lys and Pro may all play a more important role. Also, we analyse the effects of amino acid residues on the long-range contacts. We observe a larger average number of long-range contacts in the knotted structures than that in other ones, implying their important role in achieving the knots. Accordingly, the average number of short-range contacts becomes small when the structure becomes knotted because it depends mainly on the short-haul sequence of amino acids to form the short-range contact. In addition, the shape distribution of knotted proteins and the contrast with the other proteins are also presented. A comparison shows that the knots may make structures more globular because the average shape factor is 0.059 for the knotted proteins, which is only about 1/3 of the average shape factor for the other proteins.
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Project supported by the National Natural Science Foundation of China(Grant Nos.11504033 and 11404290)the General Research Fund of Hong Kong Research Council of China(Grant No.15301014)
文摘Molecular dynamics method is used to study the conformation behavior of a semi-flexible polymer chain confined in a cylinder channel.A novel helix-like structure is found to form during the simulation.Moreover,the detailed characteristic parameters and formation probability of these helix-like structures under moderate conditions are investigated.We find that the structure is not a perfect helix,but a bundle of elliptical turns.In addition,we conduct a statistical analysis for the chain monomer distribution along the radial direction.This research contributes to our understanding of the microscopic conformation of polymer chains in confined environments filled with a solvent.
