Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium visc...Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders. By contrast, the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders. Notably, the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44. We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.展开更多
Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional （3D） Langevin dynamics simulations, we investigate adsorption behaviors of m...Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional （3D） Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration Rg and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of Rg with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional （2D） and a 3D chain, while it is slightly collapsed subsequently.展开更多
In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The tempo...In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The temporal stabilities of particle is simulated. The influence of the duration, repetition period and delay time between pulses on stability is discussed.展开更多
Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics ...Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation [J. Chem. Phys. 147, 184104 （2017）] in principle exists in other types of stochastic thermostats as well. The recommended ＂middle＂ scheme [J. Chem. Phys. 147, 034109 （2017）] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation thermostatting processes with molecular is proposed for understanding efficient stochastic dynamics.展开更多
基金Supported by the China Postdoctoral Science Foundation(2015M581998)the Fundamental Research Funds for the Central Universities of China(WK2060200020)
基金This work is supported by the Fundamental Research Funds for the Central Universities of China （No.WK2060200020） and the China Postdoctoral Science Foundation （No.2015M581998）.
文摘Using 3D Langevin dynamics simulations, we investigate the effects of the shape of crowders on the dynamics of a polymer chain closure. The chain closure in spherical crowders is dominated by the increased medium viscosity so that it gets slower with the increasing volume fraction of crowders. By contrast, the dynamics of chain closure becomes very complicated with increasing volume fraction of crowders in spherocylindrical crowders. Notably, the mean closure time is found to have a dramatic decrease at a range of volume fraction of crowders 0.36-0.44. We then elucidate that an isotropic to nematic transition of spherocylindrical crowders at this range of volume fraction of crowders is responsible for the unexpected dramatic decrease in the mean closure time.
文摘Multivalent polymer chains exhibit excellent prospect in biomedical applications by serving as therapeutic agents. Using three-dimensional （3D） Langevin dynamics simulations, we investigate adsorption behaviors of multivalent polymer chains to a surface with receptors. Multivalent polymer chains display superselective adsorption. Furthermore, the range of density of surface receptors at which a multivalent polymer chain displays a superselective behavior, narrows down for chains with higher density of ligands. Meanwhile, the optimal density of surface receptors where the highest superselectivity is achieved, decreases with increasing the density of ligands. Then, the conformational properties of bound multivalent chains are studied systematically. Interestingly, we find that the equilibrium radius of gyration Rg and its horizontal component have a maximum as a function of the density of surface receptors. The scaling exponents of Rg with the length of chain suggest that with increasing the density of surface receptors., the conformations of a bound multivalent polymer chain first fall in between those of a two-dimensional （2D） and a 3D chain, while it is slightly collapsed subsequently.
文摘In this article, the dynamical process of the dielectric particle in the optical tweezer using the counter-propagating Gaussian pulses is investigated by the Langevin equation concerning the Brownian motion. The temporal stabilities of particle is simulated. The influence of the duration, repetition period and delay time between pulses on stability is discussed.
文摘Molecular dynamics with the stochastic process provides a convenient way to compute structural and thermodynamic properties of chemical, biological, and materials systems. It is demonstrated that the virtual dynamics case that we proposed for the Langevin equation [J. Chem. Phys. 147, 184104 （2017）] in principle exists in other types of stochastic thermostats as well. The recommended ＂middle＂ scheme [J. Chem. Phys. 147, 034109 （2017）] of the Andersen thermostat is investigated as an example. As shown by both analytic and numerical results, while the real and virtual dynamics cases approach the same plateau of the characteristic correlation time in the high collision frequency limit, the accuracy and efficiency of sampling are relatively insensitive to the value of the collision frequency in a broad range. After we compare the behaviors of the Andersen thermostat to those of Langevin dynamics, a heuristic schematic representation thermostatting processes with molecular is proposed for understanding efficient stochastic dynamics.
