Recently Hari Shroff and his collaborators[Nano Letters 5(2005)]developed a nanoscopic force sensor,but the force which they measured in their single molecular experiment was much lower than the theoretical critical v...Recently Hari Shroff and his collaborators[Nano Letters 5(2005)]developed a nanoscopic force sensor,but the force which they measured in their single molecular experiment was much lower than the theoretical critical value.In order to fix this problem,we investigate the micromechanics of dsDNA based on the worm-like chain model and flexible hinge model by using Monte Carlo algorithm.The simulation results not only address Hari Shroff’s experiment difficulty reasonably,but also provide strong support for flexible hinge mechanism put forward recently by Yan and Marko[Phys.Rev.Lett.93(2004)].展开更多
Parallel tempering simulation is widely used in enhanced sampling of systems with complex energy surfaces.We hereby introduce generalized canonical ensemble(GCE)instead of the usual canonical ensemble into the paralle...Parallel tempering simulation is widely used in enhanced sampling of systems with complex energy surfaces.We hereby introduce generalized canonical ensemble(GCE)instead of the usual canonical ensemble into the parallel tempering to further improve abilities of the simulation technique.GCE utilizes an adapted weight function to obtain a unimodal energy distribution even in phase-coexisting region and then the parallel tempering on GCE yields the steady swap acceptance rates(SARs)instead of the fluctuated SARs in that on canonical ensemble.With the steady SARs,we can facilitate assign the parameters of the parallel tempering simulation to more efficiently reach equilibrium among different phases.We illustrate the parallel tempering simulation on GCE in the phase-coexisting region of 2-dimensional Potts model,a benchmark system for new simulation method developing.The result indicates that the new parallel tempering method is more efficient to estimate statistical quantities(i.e.,to sample the conformational space)than the normal parallel tempering,specially in phase-coexisting regions of larger systems.展开更多
The energetic optimization problem,e.g.,searching for the optimal switching protocol of certain system parameters to minimize the input work,has been extensively studied by stochastic thermodynamics.In this work,we st...The energetic optimization problem,e.g.,searching for the optimal switching protocol of certain system parameters to minimize the input work,has been extensively studied by stochastic thermodynamics.In this work,we study this problem numerically using iterative dynamic programming.The model systems under investigation are toy actuators consisting of spring-linked beads with loading force imposed on both ending beads.For the simplest case,i.e.,a one-spring actuator driven by tuning the stiffness of the spring,we compare the optimal control protocol of the stiffness for both the overdamped and the underdamped situations,and discuss how inertial effects alter the irreversibility of the driven process and thus modify the optimal protocol.Then,we study the systems with multiple degrees of freedom by constructing oligomer actuators,in which the harmonic interaction between the two ending beads is tuned externally.With the same rated output work,actuators of different constructions demand different minimal input work,reflecting the influence of the internal degrees of freedom on the performance of the actuators.展开更多
基金This research was supported by the Young Investigator Award received by Yan in 2006 and the Foundation for the Visiting PhD Candidate of the Chinese Academy of Science received by Liu in 2006Liu is also supported by the Innovation Foundation for Graduate Students of Guizhou University(2007022).
文摘Recently Hari Shroff and his collaborators[Nano Letters 5(2005)]developed a nanoscopic force sensor,but the force which they measured in their single molecular experiment was much lower than the theoretical critical value.In order to fix this problem,we investigate the micromechanics of dsDNA based on the worm-like chain model and flexible hinge model by using Monte Carlo algorithm.The simulation results not only address Hari Shroff’s experiment difficulty reasonably,but also provide strong support for flexible hinge mechanism put forward recently by Yan and Marko[Phys.Rev.Lett.93(2004)].
文摘Parallel tempering simulation is widely used in enhanced sampling of systems with complex energy surfaces.We hereby introduce generalized canonical ensemble(GCE)instead of the usual canonical ensemble into the parallel tempering to further improve abilities of the simulation technique.GCE utilizes an adapted weight function to obtain a unimodal energy distribution even in phase-coexisting region and then the parallel tempering on GCE yields the steady swap acceptance rates(SARs)instead of the fluctuated SARs in that on canonical ensemble.With the steady SARs,we can facilitate assign the parameters of the parallel tempering simulation to more efficiently reach equilibrium among different phases.We illustrate the parallel tempering simulation on GCE in the phase-coexisting region of 2-dimensional Potts model,a benchmark system for new simulation method developing.The result indicates that the new parallel tempering method is more efficient to estimate statistical quantities(i.e.,to sample the conformational space)than the normal parallel tempering,specially in phase-coexisting regions of larger systems.
文摘The energetic optimization problem,e.g.,searching for the optimal switching protocol of certain system parameters to minimize the input work,has been extensively studied by stochastic thermodynamics.In this work,we study this problem numerically using iterative dynamic programming.The model systems under investigation are toy actuators consisting of spring-linked beads with loading force imposed on both ending beads.For the simplest case,i.e.,a one-spring actuator driven by tuning the stiffness of the spring,we compare the optimal control protocol of the stiffness for both the overdamped and the underdamped situations,and discuss how inertial effects alter the irreversibility of the driven process and thus modify the optimal protocol.Then,we study the systems with multiple degrees of freedom by constructing oligomer actuators,in which the harmonic interaction between the two ending beads is tuned externally.With the same rated output work,actuators of different constructions demand different minimal input work,reflecting the influence of the internal degrees of freedom on the performance of the actuators.
