arXiv subjects

Ping Ao

Publications and source records attributed to Ping Ao.

At least 37 records · Page 2Linked to original sources

arXiv2012

Exact Mapping Noisy van der Pol Type Oscillator onto Quasi-symplectic Dynamics

We find exact mappings for a class of limit cycle systems with noise onto quasi-symplectic dynamics, including a van der Pol type oscillator. A dual role potential function is obtained as a component of the quasi-symplectic dynamics. Based on a stochastic interpretation different from the traditional Ito's and Stratonovich's, we show the corresponding steady state distribution is the familiar Boltzmann-Gibbs type for arbitrary noise strength. The result provides a new angle for understanding processes without detailed balance and can be verified by experiments.

cond-mat.stat-mech↗

arXiv2012

Non-fixation in infinite potential

Under the effects of strong genetic drift, it is highly probable to observe gene fixation or loss in a population, shown by divergent probability density functions, or infinite adaptive peaks on a landscape. It is then interesting to ask what such infinite peaks imply, with or without combining other biological factors (e.g. mutation and selection). We study the stochastic escape time from the generated infinite adaptive peaks, and show that Kramers' classical escape formula can be extended to the non-Gaussian distribution cases. The constructed landscape provides a global description for system's middle and long term behaviors, breaking the constraints in previous methods.

q-bio.PE↗

arXiv2012

Relation of a New Interpretation of Stochastic Differential Equations to Ito Process

Stochastic differential equations (SDE) are widely used in modeling stochastic dynamics in literature. However, SDE alone is not enough to determine a unique process. A specified interpretation for stochastic integration is needed. Different interpretations specify different dynamics. Recently, a new interpretation of SDE is put forward by one of us. This interpretation has a built-in Boltzmann-Gibbs distribution and shows the existence of potential function for general processes, which reveals both local and global dynamics. Despite its powerful property, its relation with classical ones in arbitrary dimension remains obscure. In this paper, we will clarify such connection and derive the concise relation between the new interpretation and Ito process. We point out that the derived relation is experimentally testable.

math-ph↗

arXiv2012

Beyond Itô versus Stratonovich

Recently, a novel framework to handle stochastic processes has emerged from a series of studies in biology, showing situations beyond 'Itô versus Stratonovich'. Its internal consistency can be demonstrated via the zero mass limit of a generalized Klein-Kramers equation. Moreover, the connection to other integrations becomes evident: the obtained Fokker-Planck equation defines a new type of stochastic calculus that in general differs from the α-type interpretation. A unique advantage of this new approach is a natural correspondence between stochastic and deterministic dynamics, which is useful or may even be essential in practice. The core of the framework is a transformation from the usual Langevin equation to a form that contains a potential function with two additional dynamical matrices, which reveals an underlying symplectic structure. The framework has a direct physical meaning and a straightforward experimental realization. A recent experiment has offered a first empirical validation of this new stochastic integration.

cond-mat.stat-mech↗

arXiv2012

Absorbing Phenomena and Escaping Time for Muller's Ratchet in Adaptive Landscape

Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist, a process often described as Muller's ratchet with the absorbing phenomenon. The key to understand this absorbing phenomenon is to characterize the decaying time of the fittest class of the population. Adaptive landscape introduced by Wright, a re-emerging powerful concept in systems biology, is used as a tool to describe biological processes. To our knowledge, the dynamical behaviors for Muller's ratchet over the full parameter regimes are not studied from the point of the adaptive landscape. And the characterization of the absorbing phenomenon is not yet quantitatively obtained without extraneous assumptions as well. Results: We describe the dynamical behavior of the population exposed to Muller's ratchet in all parameters regimes by adaptive landscape. The adaptive landscape has rich structures such as finite and infinite potential, real and imaginary fixed points. We give the formula about the single click time with finite and infinite potential. And we find the single click time increases with selection rates and population size increasing, decreases with mutation rates increasing. These results provide a new understanding of infinite potential. We analytically demonstrate the adaptive and unadaptive states for the whole parameters regimes. Interesting issues about the parameters regions with the imaginary fixed points is demonstrated. This can help understand the biological meaning of the critical points such as the intersection points of regimes. Most importantly, we find that the absorbing phenomenon is characterized by the adaptive landscape and the single click time without any extraneous assumptions. These results suggest a graphical and quantitative framework to study the absorbing phenomenon.

q-bio.PE↗

arXiv2012

Potential Function in a Continuous Dissipative Chaotic System: Decomposition Scheme and Role of Strange Attractor

In this paper, we demonstrate, first in literature known to us, that potential functions can be constructed in continuous dissipative chaotic systems and can be used to reveal their dynamical properties. To attain this aim, a Lorenz-like system is proposed and rigorously proved chaotic for exemplified analysis. We explicitly construct a potential function monotonically decreasing along the system's dynamics, revealing the structure of the chaotic strange attractor. The potential function can have different forms of construction. We also decompose the dynamical system to explain for the different origins of chaotic attractor and strange attractor. Consequently, reasons for the existence of both chaotic nonstrange attractors and nonchaotic strange attractors are clearly discussed within current decomposition framework.

nlin.CD↗

arXiv2012

Flow Decomposition Reveals Dynamical Structure of Markov Process

Markov process is widely applied in almost all aspects of literature, especially important for understanding non-equilibrium processes. We introduce a decomposition to general Markov process in this paper. This decomposition decomposes the process into 3 independent parts: stationary distribution, symmetric detailed-balance part and anti-symmetric breaking detailed-balance part. This complete decomposition captures the steady state as well as the dynamics of the process, providing an elegant perspective for construction or analyzing problems. In light of the decomposition, a unique definition of relative entropy is found to formally separate the effect of detailed-balance part and breaking detailed-balance part. We find that the relative Gini entropy production introduced in the paper is not affected by the non-detailed balance part of the process. This property do not holds for other entropy definition in general discrete case.

math-ph↗

arXiv2012

Zero Mass Limit and Its Experimental Test

J. M. Sancho [Phys. Rev. E 84, 062102 (2011)] analyzed two stochastic interpretations on a recent experiment [Phys. Rev. Lett. 104, 170602 (2010)] of Brownian colloidal particles. The author asserted that the stochastic interpretation "obtained by simply setting the acceleration equal to zero" should not be taken and that the zero-mass limit interpretation of the experimental data would not be physically correct. In this Comment we show that Sancho's analysis is incomplete in that it pre-excludes zero mass limit and hence his assertions are incorrect. Our reasoning will be both mathematical and physical.

physics.data-an↗

arXiv2011

Kinetics of Muller's Ratchet from Adaptive Landscape Viewpoint

Background: The accumulation of deleterious mutations of a population directly contributes to the fate as to how long the population would exist. Muller's ratchet provides a quantitative framework to study the effect of accumulation. Adaptive landscape as a powerful concept in system biology provides a handle to describe complex and rare biological events. In this article we study the evolutionary process of a population exposed to Muller's ratchet from the new viewpoint of adaptive landscape which allows us estimate the single click of the ratchet starting with an intuitive understanding. Methods: We describe how Wright-Fisher process maps to Muller's ratchet. We analytically construct adaptive landscape from general diffusion equation. It shows that the construction is dynamical and the adaptive landscape is independent of the existence and normalization of the stationary distribution. We generalize the application of diffusion model from adaptive landscape viewpoint. Results: We develop a novel method to describe the dynamical behavior of the population exposed to Muller's ratchet, and analytically derive the decaying time of the fittest class of populations as a mean first passage time. Most importantly, we describe the absorption phenomenon by adaptive landscape, where the stationary distribution is non-normalizable. These results suggest the method may be used to understand the mechanism of populations evolution and describe the biological processes quantitatively.

q-bio.PE↗

arXiv2011

Nonequilibrium Steady State Driven by a Nonlinear Drift Force

We investigate the properties of the nonequilibrium steady state for the stochastic system driven by a nonlinear drift force and influenced by noises which are not identically and independently distributed. The nonequilibrium steady state (NESS) current results from a residual part of the drift force which is not cancelled by the diffusive action of noises. From our previous study for the linear drift force the NESS current was found to circulate on the equiprobability surface with the maximum at a stable fixed point of the drift force. For the nonlinear drift force, we use the perturbation theory with respect to the cubic and quartic coefficients of the drift force. We find an interesting potential landscape picture where the probability maximum shifts from the fixed point of the drift force and, furthermore, the NESS current has a nontrivial circulation which flows off the equiprobability surface and has various centers not located at the probability maximum. The theoretical result is well confirmed by the computer simulation.

cond-mat.stat-mech↗

arXiv2010

Constructive Proof of Global Lyapunov Function as Potential Function

We provide a constructive proof on the equivalence of two fundamental concepts: the global Lyapunov function in engineering and the potential function in physics, establishing a bridge between these distinct fields. This result suggests new approaches on the significant unsolved problem namely to construct Lyapunov functions for general nonlinear systems through the analogy with existing methods on potential functions. In addition, we show another connection that the Lyapunov equation is a reduced form of the generalized Einstein relation for linear systems.

nlin.CD↗

arXiv2006

Nonequilibrium Approach to Bloch-Peierls-Berry Dynamics

We examine the Bloch-Peierls-Berry dynamics under a classical nonequilibrium dynamical formulation. In this formulation all coordinates in phase space formed by the position and crystal momentum space are treated on equal footing. Explicitly demonstrations of the no (naive) Liouville theorem and of the validity of Darboux theorem are given. The explicit equilibrium distribution function is obtained. The similarities and differences to previous approaches are discussed. Our results confirm the richness of the Bloch-Peierls-Berry dynamics.

physics.class-ph↗

arXiv2005

Structure of Stochastic Dynamics near Fixed Points

We analyze the structure of stochastic dynamics near either a stable or unstable fixed point, where force can be approximated by linearization. We find that a cost function that determines a Boltzmann-like stationary distribution can always be defined near it. Such a stationary distribution does not need to satisfy the usual detailed balance condition, but might have instead a divergence-free probability current. In the linear case the force can be split into two parts, one of which gives detailed balance with the diffusive motion, while the other induces cyclic motion on surfaces of constant cost function. Using the Jordan transformation for the force matrix, we find an explicit construction of the cost function. We discuss singularities of the transformation and their consequences for the stationary distribution. This Boltzmann-like distribution may be not unique, and nonlinear effects and boundary conditions may change the distribution and induce additional currents even in the neighborhood of a fixed point.

cond-mat.stat-mech↗

arXiv2004

Phase slip in a superfluid Fermi gas near a Feshbach resonance

In this paper, we study the properties of a phase slip in a superfluid Fermi gas near a Feshbach resonance. The phase slip can be generated by the phase imprinting method. Below the superfluid transition temperature, it appears as a dip in the density profile, and becomes more pronounced when the temperature is lowered. Therefore the phase slip can provide a direct evidence of the superfluid state. The condensation energy of the superfluid state can be extracted from the density profile of the phase slip, due to the unitary properties of the Fermi gas near the resonance. The width of the phase slip is proportional to the square root of the difference between the transition temperature and the temperature. The signature of the phase slip in the density profile becomes more robust across the BCS-BEC crossover.

cond-mat.other↗

arXiv2004

Effective Vortex Mass from Microscopic Theory

We calculate the effective mass of a single quantized vortex in the BCS superconductor at finite temperature. Based on effective action approach, we arrive at the effective mass of a vortex as integral of the spectral function $J(ω)$ divided by $ω^3$ over frequency. The spectral function is given in terms of the quantum-mechanical transition elements of the gradient of the Hamiltonian between two Bogoliubov-deGennes (BdG) eigenstates. Based on self-consistent numerical diagonalization of the BdG equation we find that the effective mass per unit length of vortex at zero temperature is of order $m (k_f ξ_0)^2$ ($k_f$=Fermi momentum, $ξ_0$=coherence length), essentially equaling the electron mass displaced within the coherence length from the vortex core. Transitions between the core states are responsible for most of the mass. The mass reaches a maximum value at $T\approx 0.5 T_c$ and decreases continuously to zero at $T_c$.

cond-mat.supr-con↗

arXiv1997

Berry Phase and Dissipation of Topological Singularities

We outline a path integral derivation of both the transverse force, the Berry phase, and friction for a vortex from the microscopic fermionic superfluid theory. The derivation manifests transparently the mutual independence of the Berry phase and dissipative terms in the effective vortex action.

cond-mat↗

arXiv1997

Quantized Vortices in Superfluids and Superconductors

We give a general review of recent developments in the theory of vortices in superfluids and superconductors, discussing why the dynamics of vortices is important, and why some key results are still controversial. We discuss work that we have done on the dynamics of quantized vortices in a superfluid. Despite the fact that this problem has been recognized as important for forty years, there is still a lot of controversy about the forces on and masses of quantized vortices. We think that one can get unambiguous answers by considering a broken symmetry state that consists of one vortex in an infinite ideal system. We argue for a Magnus force that is proportional to the superfluid density, and we find that the effective mass density of a vortex in a neutral superfluid is divergent at low frequencies. We have generalized some of the results for a neutral superfluid to a charged system.

cond-mat↗

arXiv1996

Tunneling with the Lorentz Force and the Friction

We present a semiclassical study of a transport process, the tunneling, in the presence of a magnetic field and a dissipative environment. We have found that the problem can be mapped onto an effective one-dimensional one, and the tunneling rate is strongly affected by the magnetic field, such as a complete suppression by a large parallel magnetic field, an example of the dynamical localization. In such case a small perpendicular component of the field, or the dissipation, can enhance the tunneling rate. In the small parallel field and finite temperatures the tunneling rate is finite. Explicit expressions will be presented in those cases. If viewing the tunneling in the presence of a magnetic field as a dissipative tunneling process, by varying the magnetic field and the potential one can obtain the dissipative spectral function between the subohmic $s =0$ and the superohmic $s = \infty$. In combination with a real dissipative spectral function, the effect of the magnetic field can map the spectral function from $s $ to $2-s$, with $s>2$ mapping to $ s = 0$, revealing a dual symmetry between the friction and the Lorentz force. Two cases relevant to experiments, the edge state tunneling in a Hall bar and the tunneling near the dynamical localization will be discussed in detail.

cond-mat↗