Biased diffusion in confined media: Test of the Fick-Jacobs approximation and validity criteria

We study biased, diffusive transport of Brownian particles through narrow, spatially periodic structures in which the motion is constrained in lateral directions. The problem is analyzed under the perspective of the Fick-Jacobs equation which accounts for the effect of the lateral confinement by introducing an entropic barrier in a one dimensional diffusion. The validity of this approximation, being based on the assumption of an instantaneous equilibration of the particle distribution in the cross-section of the structure, is analyzed by comparing the different time scales that characterize the problem. A validity criterion is established in terms of the shape of the structure and of the applied force. It is analytically corroborated and verified by numerical simulations that the critical value of the force up to which this description holds true scales as the square of the periodicity of the structure. The criterion can be visualized by means of a diagram representing the regions where the Fick-Jacobs description becomes inaccurate in terms of the scaled force versus the periodicity of the structure.Comment: 20 pages, 7 figure

Deformed Jarzynski Equality

The well-known Jarzynski equality, often written in the form $e^{-\beta\Delta F}=\langle e^{-\beta W}\rangle$, provides a non-equilibrium means to measure the free energy difference $\Delta F$ of a system at the same inverse temperature $\beta$ based on an ensemble average of non-equilibrium work $W$. The accuracy of Jarzynski's measurement scheme was known to be determined by the variance of exponential work, denoted as ${\rm var}\left(e^{-\beta W}\right)$. However, it was recently found that ${\rm var}\left(e^{-\beta W}\right)$ can systematically diverge in both classical and quantum cases. Such divergence will necessarily pose a challenge in the applications of Jarzynski equality because it may dramatically reduce the efficiency in determining $\Delta F$. In this work, we present a deformed Jarzynski equality for both classical and quantum non-equilibrium statistics, in efforts to reuse experimental data that already suffers from a diverging ${\rm var}\left(e^{-\beta W}\right)$. The main feature of our deformed Jarzynski equality is that it connects free energies at different temperatures and it may still work efficiently subject to a diverging ${\rm var}\left(e^{-\beta W}\right)$. The conditions for applying our deformed Jarzynski equality may be met in experimental and computational situations. If so, then there is no need to redesign experimental or simulation methods. Furthermore, using the deformed Jarzynski equality, we exemplify the distinct behaviors of classical and quantum work fluctuations for the case of a time-dependent driven harmonic oscillator dynamics and provide insights into the essential performance differences between classical and quantum Jarzynski equalities.Comment: 24 pages, 1 figure, accepted version to appear in Entropy (Special Issue on "Quantum Thermodynamics"

Comment on "Coherent Ratchets in Driven Bose-Einstein Condensates"

C. E. Creffield and F. Sols (Phys. Rev. Lett. 103, 200601 (2009)) recently reported finite, directed time-averaged ratchet current, for a noninteracting quantum particle in a periodic potential even when time-reversal symmetry holds. As we explain in this Comment, this result is incorrect, that is, time-reversal symmetry implies a vanishing current.Comment: revised versio

Dynamics of magnetization coupled to a thermal bath of elastic modes

We study the dynamics of magnetization coupled to a thermal bath of elastic modes using a system plus reservoir approach with realistic magnetoelastic coupling. After integrating out the elastic modes we obtain a self-contained equation for the dynamics of the magnetization. We find explicit expressions for the memory friction kernel and hence, {\em via} the Fluctuation-Dissipation Theorem, for the spectral density of the magnetization thermal fluctuations. For magnetic samples in which the single domain approximation is valid, we derive an equation for the dynamics of the uniform mode. Finally we apply this equation to study the dynamics of the uniform magnetization mode in insulating ferromagnetic thin films. As experimental consequences we find that the fluctuation correlation time is of the order of the ratio between the film thickness, $h$, and the speed of sound in the magnet and that the line-width of the ferromagnetic resonance peak should scale as $B_1^2h$ where $B_1$ is the magnetoelastic coupling constant.Comment: Revised version as appeared in print. 12 pages 9 figure

Viscosity Dependence of the Folding Rates of Proteins

The viscosity dependence of the folding rates for four sequences (the native state of three sequences is a beta-sheet, while the fourth forms an alpha-helix) is calculated for off-lattice models of proteins. Assuming that the dynamics is given by the Langevin equation we show that the folding rates increase linearly at low viscosities \eta, decrease as 1/\eta at large \eta and have a maximum at intermediate values. The Kramers theory of barrier crossing provides a quantitative fit of the numerical results. By mapping the simulation results to real proteins we estimate that for optimized sequences the time scale for forming a four turn \alpha-helix topology is about 500 nanoseconds, whereas the time scale for forming a beta-sheet topology is about 10 microseconds.Comment: 14 pages, Latex, 3 figures. One figure is also available at http://www.glue.umd.edu/~klimov/seq_I_H.html, to be published in Physical Review Letter

Thermal conductivity of one-dimensional lattices with self-consistent heat baths: a heuristic derivation

We derive the thermal conductivities of one-dimensional harmonic and anharmonic lattices with self-consistent heat baths (BRV lattice) from the Single-Mode Relaxation Time (SMRT) approximation. For harmonic lattice, we obtain the same result as previous works. However, our approach is heuristic and reveals phonon picture explicitly within the heat transport process. The results for harmonic and anharmonic lattices are compared with numerical calculations from Green-Kubo formula. The consistency between derivation and simulation strongly supports that effective (renormalized) phonons are energy carriers in anharmonic lattices although there exist some other excitations such as solitons and breathers.Comment: 4 pages, 3 figures. accepted for publication in JPS

Star clusters dynamics in a laboratory: electrons in an ultracold plasma

Electrons in a spherical ultracold quasineutral plasma at temperature in the Kelvin range can be created by laser excitation of an ultra-cold laser cooled atomic cloud. The dynamical behavior of the electrons is similar to the one described by conventional models of stars clusters dynamics. The single mass component, the spherical symmetry and no stars evolution are here accurate assumptions. The analog of binary stars formations in the cluster case is three-body recombination in Rydberg atoms in the plasma case with the same Heggie's law: soft binaries get softer and hard binaries get harder. We demonstrate that the evolution of such an ultracold plasma is dominated by Fokker-Planck kinetics equations formally identical to the ones controlling the evolution of a stars cluster. The Virial theorem leads to a link between the plasma temperature and the ions and electrons numbers. The Fokker-Planck equation is approximate using gaseous and fluid models. We found that the electrons are in a Kramers-Michie-King's type quasi-equilibrium distribution as stars in clusters. Knowing the electron distribution and using forced fast electron extraction we are able to determine the plasma temperature knowing the trapping potential depth.Comment: Submitted to MNRA

Mean first-passage times of non-Markovian random walkers in confinement

The first-passage time (FPT), defined as the time a random walker takes to reach a target point in a confining domain, is a key quantity in the theory of stochastic processes. Its importance comes from its crucial role to quantify the efficiency of processes as varied as diffusion-limited reactions, target search processes or spreading of diseases. Most methods to determine the FPT properties in confined domains have been limited to Markovian (memoryless) processes. However, as soon as the random walker interacts with its environment, memory effects can not be neglected. Examples of non Markovian dynamics include single-file diffusion in narrow channels or the motion of a tracer particle either attached to a polymeric chain or diffusing in simple or complex fluids such as nematics \cite{turiv2013effect}, dense soft colloids or viscoelastic solution. Here, we introduce an analytical approach to calculate, in the limit of a large confining volume, the mean FPT of a Gaussian non-Markovian random walker to a target point. The non-Markovian features of the dynamics are encompassed by determining the statistical properties of the trajectory of the random walker in the future of the first-passage event, which are shown to govern the FPT kinetics.This analysis is applicable to a broad range of stochastic processes, possibly correlated at long-times. Our theoretical predictions are confirmed by numerical simulations for several examples of non-Markovian processes including the emblematic case of the Fractional Brownian Motion in one or higher dimensions. These results show, on the basis of Gaussian processes, the importance of memory effects in first-passage statistics of non-Markovian random walkers in confinement.Comment: Submitted version. Supplementary Information can be found on the Nature website : http://www.nature.com/nature/journal/v534/n7607/full/nature18272.htm

Polarons as Nucleation Droplets in Non-Degenerate Polymers

We present a study of the nucleation mechanism that allows the decay of the metastable phase (trans-cisoid) to the stable phase (cis-transoid) in quasi one-dimensional non-degenerate polymers within the continuum electron-phonon model. The electron-phonon configurations that lead to the decay, i.e. the critical droplets (or transition state), are identified as polarons of the metastable phase. We obtain an estimate for the decay rate via thermal activation within a range of parameters consistent with experimental values for the gap of the cis-configuration. It is pointed out that, upon doping, the activation barriers of the excited states are quite smaller and the decay rate is greatly enhanced. Typical activation energies for electron or hole polarons are $\approx 0.1$ eV and the typical size for a critical droplet (polaron) is about $20 \AA$. Decay via quantum nucleation is also studied and it is found that the crossover temperature between quantum nucleation and thermal activation is of order $T_c \leq 40 ^oK$. Metastable configurations of non-degenerate polymers may provide examples for mesoscopic quantum tunneling.Comment: REVTEX 3.0, 28 PAGES, 3 FIGURES AVAILABLE UPON REQUEST, PITT 94-0

Vacuum decay in quantum field theory

We study the contribution to vacuum decay in field theory due to the interaction between the long and short-wavelength modes of the field. The field model considered consists of a scalar field of mass $M$ with a cubic term in the potential. The dynamics of the long-wavelength modes becomes diffusive in this interaction. The diffusive behaviour is described by the reduced Wigner function that characterizes the state of the long-wavelength modes. This function is obtained from the whole Wigner function by integration of the degrees of freedom of the short-wavelength modes. The dynamical equation for the reduced Wigner function becomes a kind of Fokker-Planck equation which is solved with suitable boundary conditions enforcing an initial metastable vacuum state trapped in the potential well. As a result a finite activation rate is found, even at zero temperature, for the formation of true vacuum bubbles of size $M^{-1}$. This effect makes a substantial contribution to the total decay rate.Comment: 27 pages, RevTeX, 1 figure (uses epsf.sty