Mutation accumulation in growing asexual lineages

The stochastic loss of entire classes of individuals bearing the fewest number of mutations-a process known as Muller's ratchet-is studied in asexual populations growing unconstrained from a single founder. In the neutral regime, where mutations have zero effect on fitness, we derive a recursion equation for the probability distribution of the minimum number of mutations carried by individuals in the least-loaded class, and obtain an explicit condition for the halting of the ratchet. Next, we consider the case of deleterious mutations, and show that weak selection can actually accelerate the ratchet beyond that achieved for the neutral regime. This effect is transitory, however, as our results suggest that even weak purifying selection will eventually lead to the complete cessation of the ratchet. These results may have important implications for problems in biology and the medical sciences.     

Speed of adaptation in structured populations

Adaptation of populations takes place with the occurrence and subsequent fixation of mutations that confer some selective advantage to the individuals which acquire it. For this reason, the study of the process of fixation of advantageous mutations has a long history in the population genetics literature. Particularly, the previous investigations aimed to find out the main evolutionary forces affecting the strength of natural selection in the populations. In the current work, we investigate the dynamics of fixation of beneficial mutations in a subdivided population. The subpopulations (demes) can exchange migrants among their neighbors, in a migration network which is assumed to have either a random graph or a scale-free topology. We have observed that the migration rate drastically affects the dynamics of mutation fixation, despite of the fact that the probability of fixation is invariant on the migration rate, accordingly to Maruyama's conjecture. In addition, we have noticed a topological dependence of the adaptive evolution of the population when clonal interference becomes effective.     

Adaptation of asexual populations in correlated environments

We introduce two computational models of subdivided populations of asexual organisms which present variability in selection pressure. In both models one can handle the level of environmental correlation among the subpopulations (demes), which is dependent on the length of the shortest path between the demes. This work mainly addresses how environmental heterogeneity can affect the rate at beneficial mutations fixes in a structured population, and the conditions under which clonal interference becomes significant. Although the fixation probability of beneficial mutations is roughly the same as in a panmitic population and so does not depend on the level of correlation among the demes, the simulation results show that fixation rates may be strongly influenced by environmental variability. Based on our simulations we conclude that an increased variability in selection leads to a smaller fixation rate. The effect of environmental heterogeneity on the adaptive process is enhanced as the flow of organisms between subpopulations is reduced. In extreme scenarios, the fixation rate decreases as the rate of beneficial mutations rises.     

Population turnover and adaptation in heterogeneous environments

We study adaptive dynamics in a structured population model of asexual individuals which takes into account environmental heterogeneity among the subpopulations. The key purpose of the present work is to address how population turnovers, i.e. extinction events followed by recolonization, affect the rate of fixation of advantageous mutations. This model is a generalization of our previous model to address the interplay between environmental correlation and evolutionary forces on the adaptive process. The incorporation of population turnovers into the model enables us to make a direct correspondence between the model and host-parasite dynamics (epidemiological models). Strikingly, contrary to the intuitive and usual deleterious effect associated to extinction events, it is observed that population turnovers can in fact speed up adaptation as heterogeneity rises. On the other side, in nearly homogeneous population turnovers have a neutral effect on fixation rates, but a detrimental outcome is also achieved when extinction events become very common. In resume, population turnover outcomes on fixation rates of advantageous mutations are strongly influenced by the selective correlation among the subpopulations (demes).     

The effect of spatial structure in adaptive evolution

We study the dynamics of adaptation in a spatially structured population. The model assumes local competition for replication, where each organism interacts only with its nearest neighbors and is inspired by experimental methods that can be used to study the process of adaptive evolution in microbes. In such experiments microbial populations are grown on petri dishes and allowed to adapt by serial passage. We compare the rate of adaptation in a structured population where the structure is maintained intact to those where movement of individuals can occur. We observe that the rate of adaptive evolution is higher and the mean effect of fixed beneficial mutations is lower in intact structures than in structures with mixing.     

Transport and dynamical properties of inertial ratchets

In this paper we discuss the dynamics and transport properties of a massive particle in a ratchet type potential immersed in a dissipative environment. The directional currents and characteristics of the motion are studied as the specific frictional coefficient varies, finding that the stationary regime is strongly dependent on this parameter. The maximal Lyapunov exponent and the current show large fluctuations and inversions, therefore for some range of the control parameter, this inertial ratchet could originate a mass separation device. Also an exploration of the effect of a random force on the system is performed.     

Adaptive walks and extreme value theory

We study biological evolution in a high-dimensional genotype space in the regime of rare mutations and strong selection. The population performs an uphill walk which terminates at local fitness maxima. Assigning fitness randomly to genotypes, we show that the mean walk length is logarithmic in the number of initially available beneficial mutations, with a prefactor determined by the tail of the fitness distribution. This result is derived analytically in a simplified setting where the mutational neighborhood is fixed during the adaptive process, and confirmed by numerical simulations.     

Charging ratchets: Coulomb blockade and rectification

Discrete ratchets describe directed motion of a ‘reaction coordinate’ through a cycle of states in response to some varying external parameter. Such systems, in the simple, history-independent case, are described by a Markov process which in turn leads to a master equation with a transition matrix. Thus the ratchet property is reduced to a characteristic of the parameter-dependent symmetry of matrices. In the standard model of tunneling through a set of quantum dots in the Coulomb-blockade regime, a master equation is also used to describe the evolution through states in ‘dot-occupancy space’, leading to transport of electrons from a source to a drain. The symmetry of the transition matrix in this case is also a function of external parameters, notably the applied gate voltages and source–drain voltage, as well as depending on the configuration of dots and their tunnel couplings. We show that rectification and other ratchet behavior is a common feature of tunneling transport in the Coulomb-blockade regime. We also show that specific arrangements of dots and their tunnel couplings can be designed to enhance the ratchet effect. Finally, we show that the strong rectification of Coulomb-blockaded systems results from the reduction in phase space accessible to the system as it traverses the states in the reaction cycle. Received: 16 October 2001 / Accepted: 14 January 2002 / Published online: 22 April 2002     

Quantum ratchets and quantum heat pumps

Quantum ratchets are Brownian motors in which the quantum dynamics of particles induces qualitatively new behavior. We review a series of experiments in which asymmetric semiconductor devices of sub-micron dimensions are used to study quantum ratchets for electrons. In rocked quantum-dot ratchets electron-wave interference is used to create a non-linear voltage response, leading to a ratchet effect. The direction of the net ratchet current in this type of device can be sensitively controlled by changing one of the following experimental variables: a small external magnetic field, the amplitude of the rocking force, or the Fermi energy. We also describe a tunneling ratchet in which the current direction depends on temperature. In our discussion of the tunneling ratchet we distinguish between three contributions to the non-linear current–voltage characteristics that lead to the ratchet effect: thermal excitation over energy barriers, tunneling through barriers, and wave reflection from barriers. Finally, we discuss the operation of adiabatically rocked tunneling ratchets as heat pumps. Received: 8 February 2002 / Accepted: 11 February 2002 / Published online: 22 April 2002     

Rectification in Luttinger liquids

We investigate the rectification of an ac bias in Luttinger liquids in the presence of an asymmetric potential (the ratchet effect). We show that a strong repulsive electron interaction enhances the ratchet current in comparison with Fermi-liquid systems, and the dc I-V curve is strongly asymmetric in the low-voltage regime even for a weak asymmetric potential. At higher voltages the ratchet current exhibits an oscillatory voltage dependence.     

Thermal convection in a rotating layer of a magnetic fluid

We consider Brownian particles with the ability to take up energy from the environment, to store it in an internal depot, and to convert internal energy into kinetic energy of motion. Provided a supercritical supply of energy, these particles are able to move in a “high velocity” or active mode, which allows them to move also against the gradient of an external potential. We investigate the critical energetic conditions of this self-driven motion for the case of a linear potential and a ratchet potential. In the latter case, we are able to find two different critical conversion rates for the internal energy, which describe the onset of a directed net current into the two different directions. The results of computer simulations are confirmed by analytical expressions for the critical parameters and the average velocity of the net current. Further, we investigate the influence of the asymmetry of the ratchet potential on the net current and estimate a critical value for the asymmetry in order to obtain a positive or negative net current. Received 20 September 1999     

Transport reversal in a delayed feedback ratchet

Feedback flashing ratchets are thermal rectifiers that use information on the state of the system to operate the switching on and off of a periodic potential. They can induce directed transport even with symmetric potentials thanks to the asymmetry of the feedback protocol. We investigate here the dynamics of a feedback flashing ratchet when the asymmetry of the ratchet potential and of the feedback protocol favor transport in opposite directions. The introduction of a time delay in the control strategy allows one to nontrivially tune the relative relevance of the competing asymmetries leading to an interesting dynamics. We show that the competition between the asymmetries leads to a current reversal for large delays. For small ensembles of particles current reversal appears as the consequence of the emergence of an open-loop like dynamical regime, while for large ensembles of particles it can be understood as a consequence of the stabilization of quasiperiodic solutions. We also comment on the experimental feasibility of these feedback ratchets and their potential applications.     

Dynamics of matter-wave solitons in a ratchet potential

We study the dynamics of bright solitons formed in a Bose-Einstein condensate with attractive atomic interactions perturbed by a weak bichromatic optical lattice potential. The lattice depth is a biperiodic function of time with a zero mean, which realizes a flashing ratchet for matter-wave solitons. We find that the average velocity of a soliton and the soliton current induced by the ratchet depend on the number of atoms in the soliton. As a consequence, soliton transport can be induced through scattering of different solitons. In the regime when matter-wave solitons are narrow compared to the lattice period the dynamics is well described by the effective Hamiltonian theory.     

Active Brownian motion models and applications to ratchets

We give an overview over recent studies on the model of Active Brownian Motion (ABM) coupled to reservoirs providing free energy which may be converted into kinetic energy of motion. First, we present an introduction to a general concept of active Brownian particles which are capable to take up energy from the source and transform part of it in order to perform various activities. In the second part of our presentation we consider applications of ABM to ratchet systems with different forms of differentiable potentials. Both analytical and numerical evaluations are discussed for three cases of sinusoidal, staircaselike and Mateos ratchet potentials, also with the additional loads modelled by tilted potential structure. In addition, stochastic character of the kinetics is investigated by considering perturbation by Gaussian white noise which is shown to be responsible for driving the directionality of the asymptotic flux in the ratchet. This stochastically driven directionality effect is visualized as a strong nonmonotonic dependence of the statistics of the right versus left trajectories of motion leading to a net current of particles. Possible applications of the ratchet systems to molecular motors are also briefly discussed.     

Theoretical study of a membrane channel gated by ATP

We study channel transport across biomembranes. We propose a model that couples the diffusive dynamics with the gating process via a two-state ratchet mechanism. This gating process is governed by ATP binding and hydrolysis, and the process exhibits Michaelis-Menten enzymatic kinetics. The particle flow and permeability of the channel are studied both analytically and numerically in the steady-state regime, while working between fixed concentrations. The results are compared with simpler models and with experimental data. Also, a simulation framework, that allows high flexibility in parameter exploration, is introduced.     

Information and maximum power in a feedback controlled Brownian ratchet

Closed-loop or feedback controlled ratchets are Brownian motors that operate using information about the state of the system. For these ratchets, we compute the power output and we investigate its relation with the information used in the feedback control. We get analytical expressions for one-particle and few-particle flashing ratchets, and we find that the maximum power output has an upper bound proportional to the information. In addition, we show that the increase of the power output that results from changing the optimal open-loop ratchet to a closed-loop ratchet also has an upper bound that is linear in the information.     

Temporal and dimensional effects in evolutionary graph theory

The spread in time of a mutation through a population is studied analytically and computationally in fully connected networks and on spatial lattices. The time t* for a favorable mutation to dominate scales with the population size N as N(D+1)/D in D-dimensional hypercubic lattices and as NlnN in fully-connected graphs. It is shown that the surface of the interface between mutants and nonmutants is crucial in predicting the dynamics of the system. Network topology has a significant effect on the equilibrium fitness of a simple population model incorporating multiple mutations and sexual reproduction.     

Molecular evolution under fitness fluctuations

Molecular evolution is a stochastic process governed by fitness, mutations, and reproductive fluctuations in a population. Here, we study evolution where fitness itself is stochastic, with random switches in the direction of selection at individual genomic loci. As the correlation time of these fluctuations becomes larger than the diffusion time of mutations within the population, fitness changes from an annealed to a quenched random variable. We show that the rate of evolution has its maximum in the crossover regime, where both time scales are comparable. Adaptive evolution emerges in the quenched fitness regime (evidence for such fitness fluctuations has recently been found in genomic data). The joint statistical theory of reproductive and fitness fluctuations establishes a conceptual connection between evolutionary genetics and statistical physics of disordered systems.     

二维耦合定向输运模型研究

建立了外部驱动力及噪声作用下的二维耦合定向输运模型, 其中的一个维度上为周期性分段棘齿势, 另一垂直维度上为周期性对称非棘齿势, 外部驱动力及噪声加在周期对称非棘齿势方向上, 而棘齿势方向不加任何驱动, 采用非平衡统计及非线性动力学理论研究了过阻尼情况下耦合系统在两个维度上的输运性质. 结果显示, 棘齿势与非棘齿势方向均可产生定向输运, 其中棘齿势方向的系统平均速度对耦合强度、噪声强度、驱动力强度及粒子数目均有明显的依赖性, 合适的耦合强度、噪声强度、驱动力强度或粒子数目下均可产生最大输运速度. 而非棘齿势方向的系统平均速度受非棘齿势势垒高度影响显著, 但随耦合强度、驱动力强度、驱动力初相位差及粒子数目的变化均出现波动现象, 表现出平均速度对这些参量的依赖性较弱.     

Entropy in quantum ratchet for a delta-kicked model

We investigate the evolution of Shannon entropy in quantum ratchet effect for a delta-kicked model, where a particle with initial momentum zero is periodically kicked by an asymmetric potential. It is shown that the evolution of Shannon entropy of the particle can remarkably reflect whether quantum resonance emerges and gives rise to ratchet current or not. Furthermore, for different kinds of quantum resonances, low-order or high-order quantum resonances, the evolutions of the entropy are quite different.