arXiv subjects

Hao Ge

Publications and source records attributed to Hao Ge.

At least 55 records · Page 3Linked to original sources

arXiv2017

A Parameter-Free Learning Automaton Scheme

For a learning automaton, a proper configuration of its learning parameters, which are crucial for the automaton's performance, is relatively difficult due to the necessity of a manual parameter tuning before real applications. To ensure a stable and reliable performance in stochastic environments, parameter tuning can be a time-consuming and interaction-costing procedure in the field of LA. Especially, it is a fatal limitation for LA-based applications where the interactions with environments are expensive. In this paper, we propose a parameter-free learning automaton scheme to avoid parameter tuning by a Bayesian inference method. In contrast to existing schemes where the parameters should be carefully tuned according to the environment, the performance of this scheme is not sensitive to external environments because a set of parameters can be consistently applied to various environments, which dramatically reduce the difficulty of applying a learning automaton to an unknown stochastic environment. A rigorous proof of $ε$-optimality for the proposed scheme is provided and numeric experiments are carried out on benchmark environments to verify its effectiveness. The results show that, without any parameter tuning cost, the proposed parameter-free learning automaton (PFLA) can achieve a competitive performance compared with other well-tuned schemes and outperform untuned schemes on consistency of performance.

cs.LG↗

arXiv2017

Zone folding induced topological insulators in phononic crystals

This letter investigates a flow-free, pseudospin-based acoustic topological insulator. Zone folding, a strategy originated from photonic crystal, is used to form double Dirac cones in phononic crystal. The lattice symmetry of the phononic crystal is broken by tuning the size of the center "atom" of the unit cell in order to open the nontrivial topological gap. Robust sound one-way propagation is demonstrated both numerically and experimentally. This study provides a flexible approach for realizing acoustic topological insulators, which are promising for applications such as noise control and waveguide design.

cond-mat.mes-hall↗

arXiv2017

Cycle symmetry, limit theorems, and fluctuation theorems for diffusion processes on the circle

Cyclic structure and dynamics are of great interest in both the fields of stochastic processes and nonequilibrium statistical physics. In this paper, we find a new symmetry of the Brownian motion named as the quasi-time-reversal invariance. It turns out that such an invariance of the Brownian motion is the key to prove the cycle symmetry for diffusion processes on the circle, which says that the distributions of the forming times of the forward and backward cycles, given that the corresponding cycle is formed earlier than the other, are exactly the same. With the aid of the cycle symmetry, we prove the strong law of large numbers, functional central limit theorem, and large deviation principle for the sample circulations and net circulations of diffusion processes on the circle. The cycle symmetry is further applied to obtain various types of fluctuation theorems for the sample circulations, net circulation, and entropy production rate.

math.PR↗

arXiv2016

Nonequilibrium steady state of biochemical cycle kinetics under non-isothermal conditions

Nonequilibrium steady state of isothermal biochemical cycle kinetics has been extensively studied, but much less investigated under non-isothermal conditions. However, once the heat exchange between subsystems is rather slow, the isothermal assumption of the whole system meets great challenge, which is indeed the case inside many kinds of living organisms. Here we generalize the nonequilibrium steady-state theory of isothermal biochemical cycle kinetics, in the master-equation models, to the situation in which the temperatures of subsystems can be far from uniform. We first obtain a new thermodynamic relation between the chemical reaction rates and thermodynamic potentials under such a non-isothermal circumstances, which immediately implies simply applying the isothermal transition-state rate formula for each chemical reaction in terms of only the reactants' temperature, is not thermodynamically consistent. Therefore, we mathematically derive several revised reaction-rate formulas which not only obey the new thermodynamic relation but also approximate the exact reaction rate better than the rate formula under isothermal condition. The new thermodynamic relation also predicts that in the transporter system with different temperatures inside and outside the membrane, the net flux of the transported molecules can possibly even go against the temperature gradient in the absence of the chemical driving force.

physics.chem-ph↗

arXiv2016

Mathematical Formalism of Nonequilibrium Thermodynamics for Nonlinear Chemical Reaction Systems with General Rate Law

This paper studies a mathematical formalism of nonequilibrium thermodynamics for chemical reaction models with $N$ species, $M$ reactions, and general rate law. We establish a mathematical basis for J. W. Gibbs' macroscopic chemical thermodynamics under G. N. Lewis' kinetic law of entire equilibrium (detailed balance in nonlinear chemistry kinetics). In doing so, the equilibrium thermodynamics is then naturally generalized to nonequilibrium settings without detailed balance. The kinetic models are represented by a Markovian jumping process. A generalized macroscopic chemical free energy function and its associated balance equation with nonnegative source and sink are the major discoveries. The proof is based on the large deviation principle of this type of Markov processes. A general fluctuation dissipation theorem for stochastic reaction kinetics is also proved. The mathematical theory illustrates how a novel macroscopic dynamic law can emerges from the mesoscopic kinetics in a multi-scale system.

math-ph↗

arXiv2016

Nonequilibrium Thermodynamic Formalism of Nonlinear Chemical Reaction Systems with Waage-Guldberg's Law of Mass Action

Macroscopic entropy production $σ^{(tot)}$ in the general nonlinear isothermal chemical reaction system with mass action kinetics is decomposed into a free energy dissipation and a house-keeping heat: $σ^{(tot)}=σ^{(fd)}+σ^{(hk)}$; $σ^{(fd)}=-\rd A/\rd t$, where $A$ is a generalized free energy function. This yields a novel nonequilibrium free energy balance equation $\rd A/\rd t=-σ^{(tot)}+σ^{(hk)}$, which is on a par with celebrated entropy balance equation $\rd S/\rd t=σ^{(tot)}+η^{(ex)}$ where $η^{(ex)}$ is the rate of entropy exchange with the environment.For kinetic systems with complex balance, $σ^{(fd)}$ and $σ^{(hk)}$ are the macroscopic limits of stochastic free energy dissipation and house-keeping heat, which are both nonnegative, in the Delbrück-Gillespie description of the stochastic chemical kinetics.Therefore, we show that a full kinetic and thermodynamic theory of chemical reaction systems that transcends mesoscopic and macroscopic levels emerges.

physics.chem-ph↗

arXiv2016

Mesoscopic Kinetic Basis of Macroscopic Chemical Thermodynamics: A Mathematical Theory

From a mathematical model that describes a complex chemical kinetic system of $N$ species and $M$ elementrary reactions in a rapidly stirred vessel of size $V$ as a Markov process, we show that a macroscopic chemical thermodynamics emerges as $V\rightarrow\infty$. The theory is applicable to linear and nonlinear reactions, closed systems reaching chemical equilibrium, or open, driven systems approaching to nonequilibrium steady states. A generalized mesoscopic free energy gives rise to a macroscopic chemical energy function $φ^{ss}(\vx)$ where $\vx=(x_1,\cdots,x_N)$ are the concentrations of the $N$ chemical species. The macroscopic chemical dynamics $\vx(t)$ satisfies two emergent laws: (1) $(\rd/\rd t)φ^{ss}[\vx(t)]\le 0$, and (2)$(\rd/\rd t)φ^{ss}[\vx(t)]=\text{cmf}(\vx)-σ(\vx)$ where entropy production rate $σ\ge 0$ represents the sink for the chemical energy, and chemical motive force $\text{cmf}\ge 0$ is non-zero if the system is driven under a sustained nonequilibrium chemostat. For systems with detailed balance $\text{cmf}=0$, and if one assumes the law of mass action,$φ^{ss}(\vx)$ is precisely the Gibbs' function $\sum_{i=1}^N x_i\big[μ_i^o+\ln x_i\big]$ for ideal solutions. For a class of kinetic systems called complex balanced, which include many nonlinear systems as well as many simple open, driven chemical systems, the $φ^{ss}(\vx)$, with global minimum at $\vx^*$, has the generic form $\sum_{i=1}^N x_i\big[\ln(x_i/x_i^*)-x_i+x_i^*\big]$,which has been known in chemical kinetic literature.Macroscopic emergent "laws" are independent of the details of the underlying kinetics. This theory provides a concrete example from chemistry showing how a dynamic macroscopic law can emerge from the kinetics at a level below.

physics.chem-ph↗

arXiv2015

Acoustic topological insulator and robust one-way sound transport

Discovery of novel topological orders of condensed matters is of a significant interest in both fundamental and applied physics due to the associated quantum conductance behaviors and unique symmetry-protected backscattering-immune propagation against defects, which inspired similar fantastic effects in classical waves system, leading to the revolution of the manipulation of wave propagation. To date, however, only few theoretical models were proposed to realize acoustic topological states. Here, we theoretically and experimentally demonstrate a two dimensional acoustic topological insulators with acoustic analogue of quantum spin Hall Effect. Due to the band inversion mechanism near the double Dirac cones, acoustic one-way pseudospin dependent propagating edge states, corresponding to spin-plus and spin-minus, can be observed at the interface between two graphene-like acoustic crystals. We have also experimentally verified the associated topological immunity of such one-way edge states against the different lattice defects and disorders, which can always lead to inherent propagation loss and noise. We show that this unique acoustic topological phenomenon can offer a new promising application platform for the design of novel acoustic devices, such as one-way sound isolators, acoustic mode switchers, splitters, filters etc.

cond-mat.mes-hall↗

arXiv2015

Stochastic robustness and relative stability of multiple pathways in biological networks

Multiple dynamic pathways always exist in biological networks, but their robustness against internal fluctuations and relative stability have not been well recognized and carefully analyzed yet. Here we try to address these issues through an illustrative example, namely the Siah-1/beta-catenin/p14/19 ARF loop of protein p53 dynamics. Its deterministic Boolean network model predicts that two parallel pathways with comparable magnitudes of attractive basins should exist after the protein p53 is activated when a cell becomes harmfully disturbed. Once the low but non-neglectable intrinsic fluctuations are incorporated into the model, we show that a phase transition phenomenon is emerged: in one parameter region the probability weights of the normal pathway, reported in experimental literature, are comparable with the other pathway which is seemingly abnormal with the unknown functions, whereas, in some other parameter regions, the probability weight of the abnormal pathway can even dominate and become globally attractive. The theory of exponentially perturbed Markov chains is applied and further generalized in order to quantitatively explain such a phase transition phenomenon, in which the nonequilibrium "activation energy barriers" along each transiting trajectory between the parallel pathways and the number of "optimal transition paths" play a central part. Our theory can also determine how the transition time and the number of optimal transition paths between the parallel pathways depend on each interaction's strength, and help to identify those possibly more crucial interactions in the biological network.

q-bio.MN↗

arXiv2015

Macroscopic fluxes and local reciprocal relation in second-order stochastic processes far from equilibrium

Stochastic process is an essential tool for the investigation of the physical and life sciences at nanoscale. In the first-order stochastic processes widely used in chemistry and biology, only the flux of mass rather than that of heat can be well defined. Here we investigate the two macroscopic fluxes in second-order stochastic processes driven by position-dependent forces and temperature gradient. We prove that the thermodynamic equilibrium defined through the vanishing of macroscopic fluxes is equivalent to that defined via time reversibility at mesoscopic scale. In the small noise limit, we find that the entropy production rate, which has previously been defined by the mesoscopic irreversible fluxes on the phase space, matches the classic macroscopic expression as the sum of the products of macroscopic fluxes and their associated thermodynamic forces. Further we show that the two pairs of forces and fluxes in such a limit follow a linear phenomenonical relation and the associated scalar coefficients always satisfy the reciprocal relation for both transient and steady states. The scalar coefficient is proportional to the square of local temperature divided by the local frictional coefficient and originated from the second moment of velocity distribution along each dimension. This result suggests the very close connection between Soret effect (thermal diffusion) and Dufour effect at nano scale even far from equilibrium.

cond-mat.stat-mech↗

arXiv2015

Time reversibility and nonequilibrium thermodynamics of second-order stochastic processes

Nonequilibrium thermodynamics of a general second-order stochastic system is investigated. We prove that at steady state, under inversion of velocities, the condition of time-reversibility over the phase space is equivalent to the antisymmetry of spatial flux and the symmetry of velocity flux. Then we show that the condition of time-reversibility alone could not always guarantee the Maxwell-Boltzmann distribution. Comparing the two conditions together, we found that the frictional force naturally emerges as the unique odd term of the total force at thermodynamic equilibrium, and is followed by the Einstein relation. The two conditions respectively correspond to two previously reported different entropy production rates. In case that the external force is only position-dependent, the two entropy production rates become one. We prove that such an entropy production rate can be decomposed into two nonnegative terms, expressed respectively by the conditional mean and variance of the thermodynamic force associated with the irreversible velocity flux at any given spatial coordinate. In the small inertia limit, the former term becomes the entropy production rate of the overdamped dynamics; while the anomalous entropy production rate originated from the latter term. Furthermore, regarding the connection between the First Law and Second Law, we found that in the steady state of such a limit, the anomalous entropy production rate is also the leading order of the Boltzmann-factor weighted difference between the spatial heat dissipation densities of the underdamped and overdamped dynamics, while their unweighted difference always tends to vanish.

cond-mat.stat-mech↗

arXiv2015

Stochastic phenotype transition of a single cell in an intermediate region of gene-state switching

Multiple phenotypic states often arise in a single cell with different gene-expression states that undergo transcription regulation with positive feedback. Recent experiments have shown that at least in E. coli, the gene state switching can be neither extremely slow nor exceedingly rapid as many previous theoretical treatments assumed. Rather it is in the intermediate region which is difficult to handle mathematically.Under this condition, from a full chemical-master-equation description we derive a model in which the protein copy-number, for a given gene state, follow a deterministic mean-field description while the protein synthesis rates fluctuate due to stochastic gene-state switching. The simplified kinetics yields a nonequilibrium landscape function, which, similar to the energy function for equilibrium fluctuation, provides the leading orders of fluctuations around each phenotypic state, as well as the transition rates between the two phenotypic states. This rate formula is analogous to Kramers theory for chemical reactions. The resulting behaviors are significantly different from the two limiting cases studied previously.

q-bio.MN↗

arXiv2015

The Large Deviation Principle and Steady-state Fluctuation Theorem for the Entropy Production Rate of a Stochastic Process in Magnetic Fields

Fluctuation theorem is one of the major achievements in the field of nonequilibrium statistical mechanics during the past two decades. Steady-state fluctuation theorem of sample entropy production rate in terms of large deviation principle for diffusion processes have not been rigorously proved yet due to technical difficulties. Here we give a proof for the steady-state fluctuation theorem of a diffusion process in magnetic fields, with explicit expressions of the free energy function and rate function. The proof is based on the Karhunen-Loéve expansion of complex-valued Ornstein-Uhlenbeck process.

math.PR↗

arXiv2013

Dissipation, Generalized Free Energy, and a Self-consistent Nonequilibrium Thermodynamics of Chemically Driven Open Subsystems

Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe". It remains a question what the minimally required description for the surrounding of such an open driven system is, so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system, or in a quasi-steady state (QSS) with an excess amount of ATP, ADP, and Pi. We introduce the key notion of {\em minimal work} that is needed, $W_{min}$, for the external regenerating system to sustain a NESS ({\em e.g.}, maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the Second Law in terms of a same positive entropy production rate. The difference between the heat dissipation of a NESS and its corresponding QSS is exactly the $W_{min}$. This provides a justification for introducing an {\em ideal external regenerating system} and yields a {\em free energy balance equation} between the net free energy input $F_{in}$ and total dissipation $F_{dis}$ in an NESS: $F_{in}$ consists of chemical input minus mechanical output; $F_{dis}$ consists of dissipative heat; and the amount of useful energy becoming heat is the NESS entropy production. Furthermore, we show that for non-stationary systems, the $F_{dis}$ and $F_{in}$ correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics, and identify a relative entropy $H$ as a generalized free energy.

cond-mat.stat-mech↗

arXiv2012

One-Dimensional Birth-Death Process and Delbrück-Gillespie Theory of Mesoscopic Nonlinear Chemical Reactions

As a mathematical theory for the stochasstic, nonlinear dynamics of individuals within a population, Delbrück-Gillespie process (DGP) $n(t)\in\mathbb{Z}^N$, is a birth-death system with state-dependent rates which contain the system size $V$ as a natural parameter. For large $V$, it is intimately related to an autonomous, nonlinear ordinary differential equation as well as a diffusion process. For nonlinear dynamical systems with multiple attractors, the quasi-stationary and stationary behavior of such a birth-death process can be underestood in terms of a separation of time scales by a $T^*\sim e^{αV}$ $(α>0)$: a relatively fast, intra-basin diffusion for $t\ll T^*$ and a much slower inter-basin Markov jump process for $t\gg T^*$. In the present paper for one-dimensional systems, we study both stationary behavior ($t=\infty$) in terms of invariant distribution $p_n^{ss}(V)$, and finite time dynamics in terms of the mean first passsage time (MFPT) $T_{n_1\rightarrow n_2}(V)$. We obtain an asymptotic expression of MFPT in terms of the "stochastic potential" $Φ(x,V)=-(1/V)\ln p^{ss}_{xV}(V)$. We show in general no continuous diffusion process can provide asymptotically accurate representations for both the MFPT and the $p_n^{ss}(V)$ for a DGP. When $n_1$ and $n_2$ belong to two different basins of attraction, the MFPT yields the $T^*(V)$ in terms of $Φ(x,V)\approx ϕ_0(x)+(1/V)ϕ_1(x)$. For systems with a saddle-node bifurcation and catastrophe, discontinuous "phase transition" emerges, which can be characterized by $Φ(x,V)$ in the limit of $V\rightarrow\infty$. In terms of time scale separation, the relation between deterministic, local nonlinear bifurcations and stochastic global phase transition is discussed. The one-dimensional theory is a pedagogic first step toward a general theory of DGP.

math.DS↗

arXiv2012

Analytical Mechanics in Stochastic Dynamics: Most Probable Path, Large-Deviation Rate Function and Hamilton-Jacobi Equation

Analytical (rational) mechanics is the mathematical structure of Newtonian deterministic dynamics developed by D'Alembert, Langrange, Hamilton, Jacobi, and many other luminaries of applied mathematics. Diffusion as a stochastic process of an overdamped individual particle immersed in a fluid, initiated by Einstein, Smoluchowski, Langevin and Wiener, has no momentum since its path is nowhere differentiable. In this exposition, we illustrate how analytical mechanics arises in stochastic dynamics from a randomly perturbed ordinary differential equation $dX_t=b(X_t)dt+εdW_t$ where $W_t$ is a Brownian motion. In the limit of vanishingly small $ε$, the solution to the stochastic differential equation other than $\dot{x}=b(x)$ are all rare events. However, conditioned on an occurence of such an event, the most probable trajectory of the stochastic motion is the solution to Lagrangian mechanics with $\mathcal{L}=\|\dot{q}-b(q)\|^2/4$ and Hamiltonian equations with $H(p,q)=\|p\|^2+b(q)\cdot p$. Hamiltonian conservation law implies that the most probable trajectory for a "rare" event has a uniform "excess kinetic energy" along its path. Rare events can also be characterized by the principle of large deviations which expresses the probability density function for $X_t$ as $f(x,t)=e^{-u(x,t)/ε}$, where $u(x,t)$ is called a large-deviation rate function which satisfies the corresponding Hamilton-Jacobi equation. An irreversible diffusion process with $\nabla\times b\neq 0$ corresponds to a Newtonian system with a Lorentz force $\ddot{q}=(\nabla\times b)\times \dot{q}+1/2\nabla\|b\|^2$. The connection between stochastic motion and analytical mechanics can be explored in terms of various techniques of applied mathematics, for example, singular perturbations, viscosity solutions, and integrable systems.

math-ph↗

arXiv2012

Landscapes of Non-gradient Dynamics Without Detailed Balance: Stable Limit Cycles and Multiple Attractors

Landscape is one of the key notions in literature on biological processes and physics of complex systems with both deterministic and stochastic dynamics. The large deviation theory (LDT) provides a possible mathematical basis for the scientists' intuition. In terms of Freidlin-Wentzell's LDT, we discuss explicitly two issues in singularly perturbed stationary diffusion processes arisen from nonlinear differential equations: (1) For a process whose corresponding ordinary differential equation has a stable limit cycle, the stationary solution exhibits a clear separation of time scales: an exponential terms and an algebraic prefactor. The large deviation rate function attains its minimum zero on the entire stable limit cycle, while the leading term of the prefactor is inversely proportional to the velocity of the non-uniform periodic oscillation on the cycle. (2) For dynamics with multiple stable fixed points and saddles, there is in general a breakdown of detailed balance among the corresponding attractors. Two landscapes, a local and a global, arise in LDT, and a Markov jumping process with cycle flux emerges in the low-noise limit. A local landscape is pertinent to the transition rates between neighboring stable fixed points; and the global landscape defines a nonequilibrium steady state. There would be nondifferentiable points in the latter for a stationary dynamics with cycle flux. LDT serving as the mathematical foundation for emergent landscapes deserves further investigations.

math-ph↗

arXiv2012

Mesoscopic Biochemical Basis of Isogenetic Inheritance and Canalization: Stochasticity, Nonlinearity, and Emergent Landscape

Biochemical reaction systems in mesoscopic volume, under sustained environmental chemical gradient(s), can have multiple stochastic attractors. Two distinct mechanisms are known for their origins: ($a$) Stochastic single-molecule events, such as gene expression, with slow gene on-off dynamics; and ($b$) nonlinear networks with feedbacks. These two mechanisms yield different volume dependence for the sojourn time of an attractor. As in the classic Arrhenius theory for temperature dependent transition rates, a landscape perspective provides a natural framework for the system's behavior. However, due to the nonequilibrium nature of the open chemical systems, the landscape, and the attractors it represents, are all themselves {\em emergent properties} of complex, mesoscopic dynamics. In terms of the landscape, we show a generalization of Kramers' approach is possible to provide a rate theory. The emergence of attractors is a form of self-organization in the mesoscopic system; stochastic attractors in biochemical systems such as gene regulation and cellular signaling are naturally inheritable via cell division. Delbrück-Gillespie's mesoscopic reaction system theory, therefore, provides a biochemical basis for spontaneous isogenetic switching and canalization.

q-bio.SC↗