Molecular dynamics simulations were performed to investigate the sliding dynamics of a small charged ring chain along rigid cyclic diblock polyelectrolyte in catenane immersed in salt solution.We found that both the m...Molecular dynamics simulations were performed to investigate the sliding dynamics of a small charged ring chain along rigid cyclic diblock polyelectrolyte in catenane immersed in salt solution.We found that both the mean-square displacement g_(3)(t)and diffusion coefficient D of ring are influenced by the salt type,electrostatic interaction strength A and salt concentration cs.D first decreases and then increases as A increases when Ais not large.At large A,D decreases with an increase in A owing to the polyelectrolyte charge reversal caused by the aggregation of ions near it.Meanwhile,g_(3)(t)exhibited intermediate oscillating behavior at moderate A in monovalent cation salt solution.The sliding dynamics of ring can be attributed to the free energy landscape for diffusion.According to the potential of mean force(PMF)of ring chain,we found that our simulation results agreed well with the theoretical results of Lifson-Jackson formula.This study can provide a practical model for the diffusion of charged particles in different dielectric and periodic media,and provides a new perspective for regulating the sliding dynamics of mechanically interlocked molecules in electrolyte solutions.展开更多
In this paper, we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo, Schulten, and Schulten formula with the probability distribution P（r） based on 375 prote...In this paper, we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo, Schulten, and Schulten formula with the probability distribution P（r） based on 375 proteins from PDB （Protein Data Bank）. The probability distribution for residue pair in proteins is different from the Gaussian distribution, especially for short distance between two residues in proteins. The rate of contact formation in the interior of protein is discussed as a function of distance n （=｜j -i｜） between two residues, and it decreases monotonically with n and follows the scaling relationship of k ∝ n^-γ with γ= 1.43 for the contact radius a = 0.40 nm and γ=1.05 for a = 0.50 nm. The diffusion coefficient for the relative diffusion of two residues in the interior of proteins is estimated as D = 6.4 × 10^-6 cm^2/s, which is close to the result that is found for monomer diffusion.展开更多
A two-dimensional binary driven disk system embedded by impermeable tilted plates is investigated through nonequilibrium computer simulations. It is well known that a binary disk system in which two particle species a...A two-dimensional binary driven disk system embedded by impermeable tilted plates is investigated through nonequilibrium computer simulations. It is well known that a binary disk system in which two particle species are driven in opposite directions exhibits jammed, phase separated, disordered, and laning states. The presence of tilted plates can not only advance the formation of laning phase, but also effectively stabilize laning phase by suppressing massively drifting behavior perpendicular to the driving force. The lane width distribution can be controlled easily by the interplate distance. The collective behavior of driven particles in laning phase is guided by the funnel-shaped confinements constituted by the neighboring tilted plates. Our results provide the important clues for investigating the mechanism of laning formation in driven system.展开更多
Langevin dynamics simulations are employed to explore the effects of chain stiffness and electrostatic interaction(EI) on the conformational behavior of a circular semiflexible polyelectrolyte(CSPE) in presence of tri...Langevin dynamics simulations are employed to explore the effects of chain stiffness and electrostatic interaction(EI) on the conformational behavior of a circular semiflexible polyelectrolyte(CSPE) in presence of trivalent counterions.We investigate the effect of bending energy b and the dimensionless Bjerrum length A on the conformational behavior of the CSPE with a fixed chain length.The competition among the EIs,chain stiffness and entropy of the system leads to rich conformations for the CSPE.As the b is less than or equal to 50,The shape of the CSPE changes from a oblate ring to a rod at small A,then to a toroid at intermediate A,and finally to a globule at very large A.However,the globular conformation is not observed for large b.In addition,we find that the number of torus ring increases with A increase,while decreases with b increase.This study should be helpful in gaining insight into the conformational behaviour of charged biopolymer.展开更多
It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimens...It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p（r） of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p（r） of short two-dimensional compact polymers chains may consist of two parts, i.e. p（r） = p1（r） ＋ p2（r）, where p1（r） and p2（r） are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k（N）∝ N^-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H （hydrophobic） residues in the sequences of compact chains and the energy parameters of ^εНН、 ^εНН and ^εpp. Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.展开更多
The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels （left channel, middle channel, and right channel, respectively） is investi...The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels （left channel, middle channel, and right channel, respectively） is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f （f〉0） versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observed with the elastic force f〈0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the transloeation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the component translocation time is not the same for different channels can be presented.展开更多
基金supported by the National Natural Science Foundation of China(Nos.22173080,22403062,and22363005)the Jiangxi Provincial Natural Science Foundation(No.20202BABL203015)。
文摘Molecular dynamics simulations were performed to investigate the sliding dynamics of a small charged ring chain along rigid cyclic diblock polyelectrolyte in catenane immersed in salt solution.We found that both the mean-square displacement g_(3)(t)and diffusion coefficient D of ring are influenced by the salt type,electrostatic interaction strength A and salt concentration cs.D first decreases and then increases as A increases when Ais not large.At large A,D decreases with an increase in A owing to the polyelectrolyte charge reversal caused by the aggregation of ions near it.Meanwhile,g_(3)(t)exhibited intermediate oscillating behavior at moderate A in monovalent cation salt solution.The sliding dynamics of ring can be attributed to the free energy landscape for diffusion.According to the potential of mean force(PMF)of ring chain,we found that our simulation results agreed well with the theoretical results of Lifson-Jackson formula.This study can provide a practical model for the diffusion of charged particles in different dielectric and periodic media,and provides a new perspective for regulating the sliding dynamics of mechanically interlocked molecules in electrolyte solutions.
基金This research was financially supported by the National Natural Science Foundation of China (No. 20574052)Program for New Century Excellent Talents in University,and Natural Science Foundation of Zhejiang Province (No. R404047)
文摘In this paper, we estimate the rate of contact formation between two residues in the interior of the proteins using the Szabo, Schulten, and Schulten formula with the probability distribution P（r） based on 375 proteins from PDB （Protein Data Bank）. The probability distribution for residue pair in proteins is different from the Gaussian distribution, especially for short distance between two residues in proteins. The rate of contact formation in the interior of protein is discussed as a function of distance n （=｜j -i｜） between two residues, and it decreases monotonically with n and follows the scaling relationship of k ∝ n^-γ with γ= 1.43 for the contact radius a = 0.40 nm and γ=1.05 for a = 0.50 nm. The diffusion coefficient for the relative diffusion of two residues in the interior of proteins is estimated as D = 6.4 × 10^-6 cm^2/s, which is close to the result that is found for monomer diffusion.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.21873082,21674082,and 21674096)the Natural Science Foundation of Zhejiang Province,China(Grant No.LY19B040006)
文摘A two-dimensional binary driven disk system embedded by impermeable tilted plates is investigated through nonequilibrium computer simulations. It is well known that a binary disk system in which two particle species are driven in opposite directions exhibits jammed, phase separated, disordered, and laning states. The presence of tilted plates can not only advance the formation of laning phase, but also effectively stabilize laning phase by suppressing massively drifting behavior perpendicular to the driving force. The lane width distribution can be controlled easily by the interplate distance. The collective behavior of driven particles in laning phase is guided by the funnel-shaped confinements constituted by the neighboring tilted plates. Our results provide the important clues for investigating the mechanism of laning formation in driven system.
基金financially supported by the National Natural Science Foundation of China (Nos. 21863003, 22173080, 21873082, 21674096 and 61762048)the Jiangxi Provincial Natural Science Foundation (No.20202BABL203015)。
文摘Langevin dynamics simulations are employed to explore the effects of chain stiffness and electrostatic interaction(EI) on the conformational behavior of a circular semiflexible polyelectrolyte(CSPE) in presence of trivalent counterions.We investigate the effect of bending energy b and the dimensionless Bjerrum length A on the conformational behavior of the CSPE with a fixed chain length.The competition among the EIs,chain stiffness and entropy of the system leads to rich conformations for the CSPE.As the b is less than or equal to 50,The shape of the CSPE changes from a oblate ring to a rod at small A,then to a toroid at intermediate A,and finally to a globule at very large A.However,the globular conformation is not observed for large b.In addition,we find that the number of torus ring increases with A increase,while decreases with b increase.This study should be helpful in gaining insight into the conformational behaviour of charged biopolymer.
基金This research was financially supported by the National Natural Science Foundation of China(Nos.20174036,20274074,20574052)the Natural Science Foundation of Zhejiang Province(No.R404047).
文摘It is important to know the rate of intra-molecular contact formation in proteins in order to understand how proteins fold clearly. Here we investigate the rate of intra-molecular contact formation in short two-dimensional compact polymer chains by calculating the probability distribution p（r） of end-to-end distance r using the enumeration calculation method and HP model on two-dimensional square lattice. The probability distribution of end-to-end distance p（r） of short two-dimensional compact polymers chains may consist of two parts, i.e. p（r） = p1（r） ＋ p2（r）, where p1（r） and p2（r） are different for small r. The rate of contact formation decreases monotonically with the number of bonds N, and the rate approximately conforms to the scaling relation of k（N）∝ N^-α. Here the value of α increases with the contact radius a and it also depends on the percentage of H （hydrophobic） residues in the sequences of compact chains and the energy parameters of ^εНН、 ^εНН and ^εpp. Some comparisons of theoretical predictions with experimental results are also made. This investigation may help us to understand the protein folding.
基金ACKNOWLEDGMENTS This work was supported by the National Natural Science Foundation of China （No.20574052 and No.20774066）, the Program for New Century Excellent Talents in University （NCET-05-0538）, and the Natural Science Foundation of Zhejiang Province （No.R404047）.
文摘The elastic behavior of a single chain transporting through complex channel which can be seen as the combination of three different channels （left channel, middle channel, and right channel, respectively） is investigated using the new pruned-enriched Rosenbluth method with importance sampling. The elastic force during the translocation process is calculated. At the entrance into the middle channel, there is the first plateau in the curve of the elastic force f （f〉0） versus x, here x represents the position of the first monomer along the x-axis direction. When the first monomer moves to a certain position, a second plateau is observed with the elastic force f〈0, which represents spontaneous translocation. The free energy difference between the subchain in the right channel and the subchain in the left channel may drive the transloeation. The influence of chain length and width of the left and right channels on the translocation process are also investigated. From the simulation results, more detailed explanations for the reason why the component translocation time is not the same for different channels can be presented.
