In recent years, a new fundamental equation of nonequilibrium statistical physics was proposed in place of the Liouville equation. That is the anomalous Langevin equation in (?) space or its equivalent Liouville diffu...In recent years, a new fundamental equation of nonequilibrium statistical physics was proposed in place of the Liouville equation. That is the anomalous Langevin equation in (?) space or its equivalent Liouville diffusion equation of time-reversal asymmetry. This equation reflects that the form of motion of particles in statistical thermody-namic systems has the drift-diffusion duality and the law of motion of statistical thermodynamics is stochastic in essence, but does not obey the Newton equation of motion, though it is also constrained by dynamics. The stochastic diffusion of the particles is the microscopic origin of macroscopic irre-versibility. Starting from this equation, the BBGKY diffusion equation hierarchy was presented, the hydrodynamic equations, such as the generalized Navier-Stokes equation, the mass drift-diffusion equation and the thermal conductivity equation have been derived succinctly. The unified description of all three level equations of microscopic, kinetic and hydrodynamic展开更多
A two-dimensional single-mode laser model with cross-correlations between the real and imaginary parts of the quantum noise as well as the pump noise is investigated.The general closed form of the laser intensity Lang...A two-dimensional single-mode laser model with cross-correlations between the real and imaginary parts of the quantum noise as well as the pump noise is investigated.The general closed form of the laser intensity Langevin equation(GILE)is obtained under a stable locked phase resulting from the cross-correlationλ_(q) between the real and imaginary parts of the quantum noise.Because of the presence of a new term containingλ_(q),we can unify the two opposite intensity Langevin equations which correspond to the two special cases for|λ_(q)|→0 and|λ_(q)|→1 in the GILE.It is expected that the transient and stationary properties of the laser model can be changed qualitatively whenλ_(q) varies.展开更多
The biasing fluctuation model with a colored noise is presented to study the directional stepping motion of the molecular motor. The expression of probability current is obtained in the adiabatic approximation. The fo...The biasing fluctuation model with a colored noise is presented to study the directional stepping motion of the molecular motor. The expression of probability current is obtained in the adiabatic approximation. The force velocity relation and the stepping motion for motor are simulated by Monte Carlo method.展开更多
Some derivations based on the anomalous Langevin equation in Liouville space (i.e. Γ space) or its equivalent Liouville diffusion equation of time reversal asymmetry are presented. The time rate of change, the balanc...Some derivations based on the anomalous Langevin equation in Liouville space (i.e. Γ space) or its equivalent Liouville diffusion equation of time reversal asymmetry are presented. The time rate of change, the balance equation, the entropy flow, the entropy production and the law of entropy increase of Gibbs nonequilibrium entropy and Boltzmann nonequilibrium entropy are rigorously derived and presented here. Furthermore, a nonlinear evolution equation of Gibbs nonequilibrium entropy density and Boltzmann nonequilibrium entropy density is first derived. The evolution equation shows that the change of nonequilibrium entropy density originates from not only drift, but also typical diffusion and inherent source production. Contrary to conventional knowledge, the entropy production density σ ≥0 everywhere for all the inhomogeneous systems far from equilibrium cannot be proved. Conversely, σ may be negative in some local space of such systems.展开更多
In order to study the influence of the shell effects on the formation and fission of superheavy elements, we applied multidimensional Langevin equations. The evaporation residue cross sections have been calculated for...In order to study the influence of the shell effects on the formation and fission of superheavy elements, we applied multidimensional Langevin equations. The evaporation residue cross sections have been calculated for 3n, 4n, and 5n evaporation channels using three(K = 0)-and four(K ≠ 0)-dimensional Langevin equations. Calculations were done for ^(48)Ca + ^(238)U and ^(48)Ca + ^(244)Pu hot fusion reactions with 3n, An evaporation channels and ^(70)Zn+ ^(208)Pb, and ^(54)Cr + ^(209)Bi cold fusion reactions with In and 2n evaporation channels. The calculations were performed for An and 5n evaporation channels of the ^(26)Mg+ ^(238)U reaction, as well. Our results show that with increasing dimension of Langevin equations the residue cross section increases, whereas the fission cross section decreases. The obtained results with four-dimensional Langevin and considering shell effects are in better agreement with experimental data in comparison with three-and four-dimensional Langevin equations without shell effects.展开更多
The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a...The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a tensioned polymer in different spatial constraints.The polymer accommodating a knot was tethered to two macrospheres to block the unravelling of the knot.As a result,the curves for the diffusion coefficients of the knot with different bending stiffness as a function of the tension in different spatial constraints were obtained.In the space without constraints or with weak constraints,the corresponding curves for the knot with relatively large bending stiffness exhibited two turnover behaviours.On the contrary,for the knot with relatively small bending stiffness,the diffusion coefficients were monotonically reduced with increasing tension.However,in a space with strong constraints,all the curves showed one turnover behaviour regardless of the bending stiffness.The turnover behaviours divided the curves into different regimes,and the dominant diffusion mechanisms in the regimes,namely,knot-region breathing,self-reptation,and internal friction,were clearly identified.The effective friction coefficientsξof the knots with 3_(1),4_(1),5_(1) and 5_(2) types as a function of the knot size N at a fixed tension were well fitted by the relationξ∝N.The effective friction coefficients of the knots at relatively large tension f>3 sharply increased with the knot complexity,which is not dependent on the spatial constraints.By contrast,the values of these coefficients at relatively small tension f≤3 were remarkably dependent on the spatial constraints.Our work not only provides valuable simulation results to assist the understanding of the diffusion of DNA knot,but also highlights the single-molecule design for the manipulation of DNA knots in future.展开更多
Langevin simulation of the particles multi-passing over the saddle point is proposed to calculate thermal fission rate. Due to finite friction and the corresponding thermal fluctuation, a backstreaming exists in the p...Langevin simulation of the particles multi-passing over the saddle point is proposed to calculate thermal fission rate. Due to finite friction and the corresponding thermal fluctuation, a backstreaming exists in the process of the particle descent from the saddle to the scission. This leads to that the diffusion behind the saddle point has influence upon the stationary flow across the saddle point. A dynamical correction factor, as a ratio of the flows of multi- and first-overpassing the saddle point, is evaluated analytically. The results show that the fission rate calculated by the particles multi-passing over the saddle point is lower than the one calculated by the particle firstly passing over the saddle point, and the former approaches the results at the scission point.展开更多
Ultrasonic motors have the merits of high ratio of torque to volume, high positioning precision, intrinsic holding torque, etc., compared to the conventional electromagnetic motors. There have been several potential a...Ultrasonic motors have the merits of high ratio of torque to volume, high positioning precision, intrinsic holding torque, etc., compared to the conventional electromagnetic motors. There have been several potential applications for this type of motor in aerospace exploration, but bearings and bonding mechanism of the piezoelectric ring in the motors limit the performance of them in the space operation conditions. It is known that the Langevin type transducer has excel- lent energy efficiency and reliability. Hence using the Langevin type transducer in ultrasonic motors may improve the reliability of piezoelectric motors for space applications. In this study, a novel in-plane mode rotary ultrasonic motor is designed, fabricated, and characterized. The proposed motor operates in in-plane vibration mode which is excited by four Langevin-type bending vibra- tors separately placed around a ring-shaped stator. Two tapered rotors are assembled to the inner ring of the stator and clamped together by a screw nut. In order to make the motor more stable and convenient to fix, a thin cylindrical support is placed under the stator ring. Due to its no-bearing structure and Langevin transducer excitation, the prototype ultrasonic motor may operate well in aeronautic and astronautic environments.展开更多
In this paper the author presents an overview on his own research works. More than ten years ago, we proposed a new fundamental equation of nonequilibrium statistical physics in place of the present Liouville equation...In this paper the author presents an overview on his own research works. More than ten years ago, we proposed a new fundamental equation of nonequilibrium statistical physics in place of the present Liouville equation. That is the stochastic velocity type’s Langevin equation in 6N dimensional phase space or its equivalent Liouville diffusion equation. This equation is time-reversed asymmetrical. It shows that the form of motion of particles in statistical thermodynamic systems has the drift-diffusion duality, and the law of motion of statistical thermodynamics is expressed by a superposition of both the law of dynamics and the stochastic velocity and possesses both determinism and probability. Hence it is different from the law of motion of particles in dynamical systems. The stochastic diffusion motion of the particles is the microscopic origin of macroscopic irreversibility. Starting from this fundamental equation the BBGKY diffusion equation hierarchy, the Boltzmann collision diffusion equation, the hydrodynamic equations such as the mass drift-diffusion equation, the Navier-Stokes equation and the thermal conductivity equation have been derived and presented here. What is more important, we first constructed a nonlinear evolution equation of nonequilibrium entropy density in 6N, 6 and 3 dimensional phase space, predicted the existence of entropy diffusion. This entropy evolution equation plays a leading role in nonequilibrium entropy theory, it reveals that the time rate of change of nonequilibrium entropy density originates together from its drift, diffusion and production in space. From this evolution equation, we presented a formula for entropy production rate (i.e. the law of entropy increase) in 6N and 6 dimensional phase space, proved that internal attractive force in nonequilibrium system can result in entropy decrease while internal repulsive force leads to another entropy increase, and derived a common expression for this entropy decrease rate or another entropy increase rate, obtained a theoretica展开更多
A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as...A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.展开更多
Stochastic modeling of biochemical reactions taking place at the cellular level has become the subject of intense research in recent years. Molecular interactions in a single cell exhibit random fluctuations. These fl...Stochastic modeling of biochemical reactions taking place at the cellular level has become the subject of intense research in recent years. Molecular interactions in a single cell exhibit random fluctuations. These fluctuations may be significant when small populations of some reacting species are present and then a stochastic description of the cellular dynamics is required. Often, the biochemically reacting systems encountered in applications consist of many species interacting through many reaction channels. Also, the dynamics of such systems is typically non-linear and presents multiple time-scales. Consequently, the stochastic mathematical models of biochemical systems can be quite complex and their analysis challenging. In this paper, we present a method to reduce a stochastic continuous model of well-stirred biochemical systems, the Chemical Langevin Equation, while preserving the overall behavior of the system. Several tests of our method on models of practical interest gave excellent results.展开更多
Recent developments in the measurement of radioactive gases in passive diffusion motivate the analysis of Brownian motion of decaying particles, a subject that has received little previous attention. This paper report...Recent developments in the measurement of radioactive gases in passive diffusion motivate the analysis of Brownian motion of decaying particles, a subject that has received little previous attention. This paper reports the derivation and solution of equations comparable to the Fokker-Planck and Langevin equations for one-dimensional diffusion and decay of unstable particles. In marked contrast to the case of stable particles, the two equations are not equivalent, but provide different information regarding the same stochastic process. The differences arise because Brownian motion with particle decay is not a continuous process. The discontinuity is readily apparent in the computer-simulated trajectories of the Langevin equation that incorporate both a Wiener process for displacement fluctuations and a Bernoulli process for random decay. This paper also reports the derivation of the mean time of first passage of the decaying particle to absorbing boundaries. Here, too, particle decay can lead to an outcome markedly different from that for stable particles. In particular, the first-passage time of the decaying particle is always finite, whereas the time for a stable particle to reach a single absorbing boundary is theoretically infinite due to the heavy tail of the inverse Gaussian density. The methodology developed in this paper should prove useful in the investigation of radioactive gases, aerosols of radioactive atoms, dust particles to which adhere radioactive ions, as well as diffusing gases and liquids of unstable molecules.展开更多
Based on a stochastic mesoscopic model, the influence of internal noise on the oscillatory kinetics of the catalytic oxidation of CO on nm-sized palladium particles is studied, using the chemical Langevin equations, P...Based on a stochastic mesoscopic model, the influence of internal noise on the oscillatory kinetics of the catalytic oxidation of CO on nm-sized palladium particles is studied, using the chemical Langevin equations, Poisson approximation algorithm, and exact stochastic simulation algorithm. The reaction rate oscillations are of stochastic nature due to considerable internal noise in such mesoscopic systems. It is found that the performance of the stochastic oscillations undergoes a maximum with the variation of internal noise level for a given CO partial pressure, which demonstrates the occurrence of internal noise stochastic resonance. This phe-nomenon implies that optimal internal noise would favor the reaction rate oscillation of CO oxi-dation on nm particles. Such a phenomenon is robust to the change of external parameters, such as CO pressures.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 Master equation is considered the gold standard for modeling the stochastic mechanisms of gene regulation in molecular detail, but it is too complex to solve exactly in most cases, so approximation and simulation ...The Master equation is considered the gold standard for modeling the stochastic mechanisms of gene regulation in molecular detail, but it is too complex to solve exactly in most cases, so approximation and simulation methods are essential. However, there is still a lack of consensus about the best way to carry these out. To help clarify the situation, we review Master equation models of gene regulation, theoretical approximations based on an expansion method due to N.G. van Kampen and R. Kubo, and simulation algorithms due to D.T. Gillespie and P. Langevin. Expansion of the Master equation shows that for systems with a single stable steady-state, the stochastic model reduces to a deterministic model in a first-order approximation. Additional theory, also due to van Kampen, describes the asymptotic behavior of multistable systems. To support and illustrate the theory and provide further insight into the complex behavior of multistable systems, we perform a detailed simulation study comparing the various approximation and simulation methods applied to synthetic gene regulatory systems with various qualitative characteristics. The simulation studies show that for large stochastic systems with a single steady-state, deterministic models are quite accurate, since the probability distribution of the solution has a single peak tracking the deterministic trajectory whose variance is inversely proportional to the system size. In multistable stochastic systems, large fluctuations can cause individual trajectories to escape from the domain of attraction of one steady-state and be attracted to another, so the system eventually reaches a multimodal probability distribution in which all stable steady- states are represented proportional to their relative stability. However, since the escape time scales exponentially with system size, this process can take a very long time in large systems.展开更多
Langevin dynamical simulations are performed to determine the bulk modulus in twodimensional(2D) dusty plasmas from uniform periodic radial compressions. The bulk modulus is calculated directly from its physical defin...Langevin dynamical simulations are performed to determine the bulk modulus in twodimensional(2D) dusty plasmas from uniform periodic radial compressions. The bulk modulus is calculated directly from its physical definition of the ratio of the internal pressure/stress to the volume strain. Under various conditions, the bulk moduli obtained agree with the previous theoretical derivations from completely different approaches. It is found that the bulk moduli of2D Yukawa solids and liquids are almost independent of the system temperature and the external compressional frequency.展开更多
Inspired by the eccentricity design of self-driven disks,we propose a computational model to study the remarkable behavior of this kind of active matter via Langevin dynamics simulations.We pay attention to the effect...Inspired by the eccentricity design of self-driven disks,we propose a computational model to study the remarkable behavior of this kind of active matter via Langevin dynamics simulations.We pay attention to the effect of rotational friction coefficient and rotational noise on the phase behavior.A homogeneous system without rotational noise exhibits a sharp discontinuous transition of orientational order from an isotropic to a polar state with the increase of rotational friction coefficient.When there is rotational noise,the transition becomes continuous.The formation of polar state originates from the effective alignment effect due to the mutual coupling of the positional and orientational degrees of freedom of each disk.The rotational noise could weaken the alignment effect and cause the large spatial density inhomogeneity,while the translational noise homogenizes the system.Our model makes further conceptual progress on how the microscopic interaction among self-driven agents yields effective alignment.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
Efficient numerical algorithm for stochastic differential equation has been an important object in the research of statistical physics and mathematics for a long time.In this work we study the highly accurate numerica...Efficient numerical algorithm for stochastic differential equation has been an important object in the research of statistical physics and mathematics for a long time.In this work we study the highly accurate numerical algorithm for the overdamped Langevin equation.In particular,our interest is in the behaviour of the numerical schemes for solving the overdamped Langevin equation in the harmonic system.Based on the large friction limit of the underdamped Langevin dynamic scheme,three algorithms for overdamped Langevin equation are obtained.We derive the explicit expression of the stationary distribution of each algorithm by analysing the discrete time trajectory for both one-dimensional case and multi-dimensional case.The accuracy of the stationary distribution of each algorithm is illustrated by comparing with the exact Boltzmann distribution.Our results demonstrate that the“BAOA-limit”algorithm generates an accurate distribution of the harmonic system in a canonical ensemble,within a stable range of time interval.The other algorithms do not produce the exact distribution of the harmonic system.展开更多
Considering that thermodynamic irreversibility, the principle of entropy increase and hydrodynamic equations cannot be derived rigorously and in a unified way from the Liouville equations, the anomalous Langevin equat...Considering that thermodynamic irreversibility, the principle of entropy increase and hydrodynamic equations cannot be derived rigorously and in a unified way from the Liouville equations, the anomalous Langevin equation in Liouville space or its equivalent generalized Liouville equation is proposed as a basic equation of statistical physics. This equation reflects the fact that the law of motion of statistical thermodynamics is stochastic, but not deterministic. From that the nonequilibrium entropy, the principle of entropy increase, the theorem of minimum entropy production and the BBGKY diffusion equation hierarchy have been derived. The hydrodynamic equations, such as the generalized Navier-Stokes equation and the mass drift-diffusion equation, etc. have been derived from the BBGKY diffusion equation hierarchy. This equation has the same equilibrium solution as that of the Liouville equation. All these are unified and rigorous without adding any extra assumption. But it is difficult to prove that the entropy production density a can never be negative everywhere for all the isolated inhomogeneous systems far from equilibrium.展开更多
文摘In recent years, a new fundamental equation of nonequilibrium statistical physics was proposed in place of the Liouville equation. That is the anomalous Langevin equation in (?) space or its equivalent Liouville diffusion equation of time-reversal asymmetry. This equation reflects that the form of motion of particles in statistical thermody-namic systems has the drift-diffusion duality and the law of motion of statistical thermodynamics is stochastic in essence, but does not obey the Newton equation of motion, though it is also constrained by dynamics. The stochastic diffusion of the particles is the microscopic origin of macroscopic irre-versibility. Starting from this equation, the BBGKY diffusion equation hierarchy was presented, the hydrodynamic equations, such as the generalized Navier-Stokes equation, the mass drift-diffusion equation and the thermal conductivity equation have been derived succinctly. The unified description of all three level equations of microscopic, kinetic and hydrodynamic
基金Supported by the National Natural Science Foundation of China under Grant No.19975020.
文摘A two-dimensional single-mode laser model with cross-correlations between the real and imaginary parts of the quantum noise as well as the pump noise is investigated.The general closed form of the laser intensity Langevin equation(GILE)is obtained under a stable locked phase resulting from the cross-correlationλ_(q) between the real and imaginary parts of the quantum noise.Because of the presence of a new term containingλ_(q),we can unify the two opposite intensity Langevin equations which correspond to the two special cases for|λ_(q)|→0 and|λ_(q)|→1 in the GILE.It is expected that the transient and stationary properties of the laser model can be changed qualitatively whenλ_(q) varies.
文摘The biasing fluctuation model with a colored noise is presented to study the directional stepping motion of the molecular motor. The expression of probability current is obtained in the adiabatic approximation. The force velocity relation and the stepping motion for motor are simulated by Monte Carlo method.
文摘Some derivations based on the anomalous Langevin equation in Liouville space (i.e. Γ space) or its equivalent Liouville diffusion equation of time reversal asymmetry are presented. The time rate of change, the balance equation, the entropy flow, the entropy production and the law of entropy increase of Gibbs nonequilibrium entropy and Boltzmann nonequilibrium entropy are rigorously derived and presented here. Furthermore, a nonlinear evolution equation of Gibbs nonequilibrium entropy density and Boltzmann nonequilibrium entropy density is first derived. The evolution equation shows that the change of nonequilibrium entropy density originates from not only drift, but also typical diffusion and inherent source production. Contrary to conventional knowledge, the entropy production density σ ≥0 everywhere for all the inhomogeneous systems far from equilibrium cannot be proved. Conversely, σ may be negative in some local space of such systems.
文摘In order to study the influence of the shell effects on the formation and fission of superheavy elements, we applied multidimensional Langevin equations. The evaporation residue cross sections have been calculated for 3n, 4n, and 5n evaporation channels using three(K = 0)-and four(K ≠ 0)-dimensional Langevin equations. Calculations were done for ^(48)Ca + ^(238)U and ^(48)Ca + ^(244)Pu hot fusion reactions with 3n, An evaporation channels and ^(70)Zn+ ^(208)Pb, and ^(54)Cr + ^(209)Bi cold fusion reactions with In and 2n evaporation channels. The calculations were performed for An and 5n evaporation channels of the ^(26)Mg+ ^(238)U reaction, as well. Our results show that with increasing dimension of Langevin equations the residue cross section increases, whereas the fission cross section decreases. The obtained results with four-dimensional Langevin and considering shell effects are in better agreement with experimental data in comparison with three-and four-dimensional Langevin equations without shell effects.
基金The National Natural Science Foundation of China under Grant Nos.11864006, 11874309, 12164007, and 12204118
文摘The knots frequently occur in biopolymer and their diffusion plays an active role in the gene regulation.In this work,Langevin dynamics simulations were carried out to detect the diffusion behaviours of a knot along a tensioned polymer in different spatial constraints.The polymer accommodating a knot was tethered to two macrospheres to block the unravelling of the knot.As a result,the curves for the diffusion coefficients of the knot with different bending stiffness as a function of the tension in different spatial constraints were obtained.In the space without constraints or with weak constraints,the corresponding curves for the knot with relatively large bending stiffness exhibited two turnover behaviours.On the contrary,for the knot with relatively small bending stiffness,the diffusion coefficients were monotonically reduced with increasing tension.However,in a space with strong constraints,all the curves showed one turnover behaviour regardless of the bending stiffness.The turnover behaviours divided the curves into different regimes,and the dominant diffusion mechanisms in the regimes,namely,knot-region breathing,self-reptation,and internal friction,were clearly identified.The effective friction coefficientsξof the knots with 3_(1),4_(1),5_(1) and 5_(2) types as a function of the knot size N at a fixed tension were well fitted by the relationξ∝N.The effective friction coefficients of the knots at relatively large tension f>3 sharply increased with the knot complexity,which is not dependent on the spatial constraints.By contrast,the values of these coefficients at relatively small tension f≤3 were remarkably dependent on the spatial constraints.Our work not only provides valuable simulation results to assist the understanding of the diffusion of DNA knot,but also highlights the single-molecule design for the manipulation of DNA knots in future.
基金The project supported by National Natural Science Foundation of China under Grant Nos.10075007 and 10235020
文摘Langevin simulation of the particles multi-passing over the saddle point is proposed to calculate thermal fission rate. Due to finite friction and the corresponding thermal fluctuation, a backstreaming exists in the process of the particle descent from the saddle to the scission. This leads to that the diffusion behind the saddle point has influence upon the stationary flow across the saddle point. A dynamical correction factor, as a ratio of the flows of multi- and first-overpassing the saddle point, is evaluated analytically. The results show that the fission rate calculated by the particles multi-passing over the saddle point is lower than the one calculated by the particle firstly passing over the saddle point, and the former approaches the results at the scission point.
基金supported by the National Natural Science Foundation of China (Nos. 51205203, 51275228, 51075212, and 91123020)Nanjing University of Aeronautics and Astronautics (Nos. 56YAH12015, 56XZA12044, and S0896-013)+1 种基金Innovation and Entrepreneurship Program of Jiangsu, the 111 Project (No. B12021)PAPD
文摘Ultrasonic motors have the merits of high ratio of torque to volume, high positioning precision, intrinsic holding torque, etc., compared to the conventional electromagnetic motors. There have been several potential applications for this type of motor in aerospace exploration, but bearings and bonding mechanism of the piezoelectric ring in the motors limit the performance of them in the space operation conditions. It is known that the Langevin type transducer has excel- lent energy efficiency and reliability. Hence using the Langevin type transducer in ultrasonic motors may improve the reliability of piezoelectric motors for space applications. In this study, a novel in-plane mode rotary ultrasonic motor is designed, fabricated, and characterized. The proposed motor operates in in-plane vibration mode which is excited by four Langevin-type bending vibra- tors separately placed around a ring-shaped stator. Two tapered rotors are assembled to the inner ring of the stator and clamped together by a screw nut. In order to make the motor more stable and convenient to fix, a thin cylindrical support is placed under the stator ring. Due to its no-bearing structure and Langevin transducer excitation, the prototype ultrasonic motor may operate well in aeronautic and astronautic environments.
文摘In this paper the author presents an overview on his own research works. More than ten years ago, we proposed a new fundamental equation of nonequilibrium statistical physics in place of the present Liouville equation. That is the stochastic velocity type’s Langevin equation in 6N dimensional phase space or its equivalent Liouville diffusion equation. This equation is time-reversed asymmetrical. It shows that the form of motion of particles in statistical thermodynamic systems has the drift-diffusion duality, and the law of motion of statistical thermodynamics is expressed by a superposition of both the law of dynamics and the stochastic velocity and possesses both determinism and probability. Hence it is different from the law of motion of particles in dynamical systems. The stochastic diffusion motion of the particles is the microscopic origin of macroscopic irreversibility. Starting from this fundamental equation the BBGKY diffusion equation hierarchy, the Boltzmann collision diffusion equation, the hydrodynamic equations such as the mass drift-diffusion equation, the Navier-Stokes equation and the thermal conductivity equation have been derived and presented here. What is more important, we first constructed a nonlinear evolution equation of nonequilibrium entropy density in 6N, 6 and 3 dimensional phase space, predicted the existence of entropy diffusion. This entropy evolution equation plays a leading role in nonequilibrium entropy theory, it reveals that the time rate of change of nonequilibrium entropy density originates together from its drift, diffusion and production in space. From this evolution equation, we presented a formula for entropy production rate (i.e. the law of entropy increase) in 6N and 6 dimensional phase space, proved that internal attractive force in nonequilibrium system can result in entropy decrease while internal repulsive force leads to another entropy increase, and derived a common expression for this entropy decrease rate or another entropy increase rate, obtained a theoretica
文摘A new simulation approach to incorporate hydration force into generalized Langevin dynamics (GLD) is developed in this note. The hydration force determined by the boundary element method (BEM) is taken into account as the mean force terms of solvent including Coulombic interactions with the induced surface charge and the surface pressure of solvent. The exponential model is taken for the friction kernel. A simulation study has been performed on the cyclic undecapeptide cyclosporin A (CPA). The results obtained from the new method (GLDBEM) have been analyzed and compared with that obtained from the molecular dynamics (MD) simulation and the conventional stochastic dynamics (SD) simulation. We have found that the results obtained from GLDBEM show the obvious improvement over the SD simulation technique in the study of molecular structure and dynamic properties.
文摘Stochastic modeling of biochemical reactions taking place at the cellular level has become the subject of intense research in recent years. Molecular interactions in a single cell exhibit random fluctuations. These fluctuations may be significant when small populations of some reacting species are present and then a stochastic description of the cellular dynamics is required. Often, the biochemically reacting systems encountered in applications consist of many species interacting through many reaction channels. Also, the dynamics of such systems is typically non-linear and presents multiple time-scales. Consequently, the stochastic mathematical models of biochemical systems can be quite complex and their analysis challenging. In this paper, we present a method to reduce a stochastic continuous model of well-stirred biochemical systems, the Chemical Langevin Equation, while preserving the overall behavior of the system. Several tests of our method on models of practical interest gave excellent results.
文摘Recent developments in the measurement of radioactive gases in passive diffusion motivate the analysis of Brownian motion of decaying particles, a subject that has received little previous attention. This paper reports the derivation and solution of equations comparable to the Fokker-Planck and Langevin equations for one-dimensional diffusion and decay of unstable particles. In marked contrast to the case of stable particles, the two equations are not equivalent, but provide different information regarding the same stochastic process. The differences arise because Brownian motion with particle decay is not a continuous process. The discontinuity is readily apparent in the computer-simulated trajectories of the Langevin equation that incorporate both a Wiener process for displacement fluctuations and a Bernoulli process for random decay. This paper also reports the derivation of the mean time of first passage of the decaying particle to absorbing boundaries. Here, too, particle decay can lead to an outcome markedly different from that for stable particles. In particular, the first-passage time of the decaying particle is always finite, whereas the time for a stable particle to reach a single absorbing boundary is theoretically infinite due to the heavy tail of the inverse Gaussian density. The methodology developed in this paper should prove useful in the investigation of radioactive gases, aerosols of radioactive atoms, dust particles to which adhere radioactive ions, as well as diffusing gases and liquids of unstable molecules.
基金the National Natural Science Foundation of China(Grant Nos.20203017&20433050).
文摘Based on a stochastic mesoscopic model, the influence of internal noise on the oscillatory kinetics of the catalytic oxidation of CO on nm-sized palladium particles is studied, using the chemical Langevin equations, Poisson approximation algorithm, and exact stochastic simulation algorithm. The reaction rate oscillations are of stochastic nature due to considerable internal noise in such mesoscopic systems. It is found that the performance of the stochastic oscillations undergoes a maximum with the variation of internal noise level for a given CO partial pressure, which demonstrates the occurrence of internal noise stochastic resonance. This phe-nomenon implies that optimal internal noise would favor the reaction rate oscillation of CO oxi-dation on nm particles. Such a phenomenon is robust to the change of external parameters, such as CO pressures.
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.
文摘The Master equation is considered the gold standard for modeling the stochastic mechanisms of gene regulation in molecular detail, but it is too complex to solve exactly in most cases, so approximation and simulation methods are essential. However, there is still a lack of consensus about the best way to carry these out. To help clarify the situation, we review Master equation models of gene regulation, theoretical approximations based on an expansion method due to N.G. van Kampen and R. Kubo, and simulation algorithms due to D.T. Gillespie and P. Langevin. Expansion of the Master equation shows that for systems with a single stable steady-state, the stochastic model reduces to a deterministic model in a first-order approximation. Additional theory, also due to van Kampen, describes the asymptotic behavior of multistable systems. To support and illustrate the theory and provide further insight into the complex behavior of multistable systems, we perform a detailed simulation study comparing the various approximation and simulation methods applied to synthetic gene regulatory systems with various qualitative characteristics. The simulation studies show that for large stochastic systems with a single steady-state, deterministic models are quite accurate, since the probability distribution of the solution has a single peak tracking the deterministic trajectory whose variance is inversely proportional to the system size. In multistable stochastic systems, large fluctuations can cause individual trajectories to escape from the domain of attraction of one steady-state and be attracted to another, so the system eventually reaches a multimodal probability distribution in which all stable steady- states are represented proportional to their relative stability. However, since the escape time scales exponentially with system size, this process can take a very long time in large systems.
基金supported by National Natural Science Foundation of China(Nos.12175159 and 11875199)the 1000 Youth Talents Plan,startup funds from Soochow Universitythe Priority Academic Program Development(PAPD)of Jiangsu Higher Education Institutions。
文摘Langevin dynamical simulations are performed to determine the bulk modulus in twodimensional(2D) dusty plasmas from uniform periodic radial compressions. The bulk modulus is calculated directly from its physical definition of the ratio of the internal pressure/stress to the volume strain. Under various conditions, the bulk moduli obtained agree with the previous theoretical derivations from completely different approaches. It is found that the bulk moduli of2D Yukawa solids and liquids are almost independent of the system temperature and the external compressional frequency.
基金Project supported by the National Natural Science Foundation of China(Grant Nos.21674078,21774091,and 21574096).
文摘Inspired by the eccentricity design of self-driven disks,we propose a computational model to study the remarkable behavior of this kind of active matter via Langevin dynamics simulations.We pay attention to the effect of rotational friction coefficient and rotational noise on the phase behavior.A homogeneous system without rotational noise exhibits a sharp discontinuous transition of orientational order from an isotropic to a polar state with the increase of rotational friction coefficient.When there is rotational noise,the transition becomes continuous.The formation of polar state originates from the effective alignment effect due to the mutual coupling of the positional and orientational degrees of freedom of each disk.The rotational noise could weaken the alignment effect and cause the large spatial density inhomogeneity,while the translational noise homogenizes the system.Our model makes further conceptual progress on how the microscopic interaction among self-driven agents yields effective alignment.
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Project supported by the Basic and Applied Basic Research Foundation of Guangdong Province,China(Grant No.2021A1515010328)the Key-Area Research and Development Program of Guangdong Province,China(Grant No.2020B010183001)the National Natural Science Foundation of China(Grant No.12074126)。
文摘Efficient numerical algorithm for stochastic differential equation has been an important object in the research of statistical physics and mathematics for a long time.In this work we study the highly accurate numerical algorithm for the overdamped Langevin equation.In particular,our interest is in the behaviour of the numerical schemes for solving the overdamped Langevin equation in the harmonic system.Based on the large friction limit of the underdamped Langevin dynamic scheme,three algorithms for overdamped Langevin equation are obtained.We derive the explicit expression of the stationary distribution of each algorithm by analysing the discrete time trajectory for both one-dimensional case and multi-dimensional case.The accuracy of the stationary distribution of each algorithm is illustrated by comparing with the exact Boltzmann distribution.Our results demonstrate that the“BAOA-limit”algorithm generates an accurate distribution of the harmonic system in a canonical ensemble,within a stable range of time interval.The other algorithms do not produce the exact distribution of the harmonic system.
文摘Considering that thermodynamic irreversibility, the principle of entropy increase and hydrodynamic equations cannot be derived rigorously and in a unified way from the Liouville equations, the anomalous Langevin equation in Liouville space or its equivalent generalized Liouville equation is proposed as a basic equation of statistical physics. This equation reflects the fact that the law of motion of statistical thermodynamics is stochastic, but not deterministic. From that the nonequilibrium entropy, the principle of entropy increase, the theorem of minimum entropy production and the BBGKY diffusion equation hierarchy have been derived. The hydrodynamic equations, such as the generalized Navier-Stokes equation and the mass drift-diffusion equation, etc. have been derived from the BBGKY diffusion equation hierarchy. This equation has the same equilibrium solution as that of the Liouville equation. All these are unified and rigorous without adding any extra assumption. But it is difficult to prove that the entropy production density a can never be negative everywhere for all the isolated inhomogeneous systems far from equilibrium.
