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Biomedical subjects

J Klafter

Publications and source records attributed to J Klafter.

At least 19 recordsLinked to original sources
PubMed2002

Ballistic flights and random diffusion as building blocks for Hamiltonian kinetics.

We propose a kinetic approach to transport in Hamiltonian systems with a mixed phase space. The approach is based on the decomposition of the dynamical picture into two contributions: (a) ballistic flights, and (b) random diffusion. The kinetic scheme leads to a stochastic process with statistical properties which are similar to those produced by the original Hamiltonian. We show that our approach helps in obtaining an insight into several properties of Hamiltonian kinetics such as anomalous diffusion, chaos-assisted population exchange, and current rectification. In particular, the chaos-assisted exchange offers a classical counterpart for the recently reported chaos-assisted tunneling.

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PubMed2002

Manipulation of dynamical systems by symmetry breaking.

We propose an approach to manipulate and control transport in Hamiltonian systems which are characterized by a mixed phase space. The approach is based on symmetry breaking of the phase space structure by applying a zero-mean periodic force for a finite duration of time. This induces time and space reversal asymmetry, which modifies the internal dynamics of the system and leads to directed transport. It is shown that our strategy allows to perform manipulations both with individual particles and with statistical ensembles of particles.

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PubMed2001

Confined molecules under shear: from a microscopic description to phenomenology.

A coarse grained two-state model is derived starting from a molecular dynamics description of a molecular system under shear. This model captures the main features of the response of a confined system under shear, and generalizes the phenomenological Tomlinson model for the response of a driven system. The derivation is based on the solution of coupled microscopic equations using a mean field approximation. The two-state model agrees well with the direct numerical solution and offers a practical approach to investigate the response of sheared systems under a broad range of parameters.

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PubMed2001

Do strange kinetics imply unusual thermodynamics?

We introduce a fractional Fokker-Planck equation (FFPE) for Lévy flights in the presence of an external field. The equation is derived within the framework of the subordination of random processes which leads to Lévy flights. It is shown that the coexistence of anomalous transport and a potential displays a regular exponential relaxation toward the Boltzmann equilibrium distribution. The properties of the Lévy-flight FFPE derived here are compared with earlier findings for a subdiffusive FFPE. The latter is characterized by a nonexponential Mittag-Leffler relaxation to the Boltzmann distribution. In both cases, which describe strange kinetics, the Boltzmann equilibrium is reached, and modifications of the Boltzmann thermodynamics are not required.

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PubMed2000

Molecular motor that never steps backwards.

We investigate the dynamics of a classical particle in a one-dimensional two-wave potential composed of two periodic potentials that are time independent and of the same amplitude and periodicity. One of the periodic potentials is externally driven and performs a translational motion with respect to the other. It is shown that, if one of the potentials is of the ratchet type, translation of the potential in a given direction leads to motion of the particle in the same direction, whereas translation in the opposite direction leaves the particle localized at its original location. Moreover, even if the translation is random, but still has a finite velocity, an efficient directed transport of the particle occurs.

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PubMed2000

Strong anomaly in diffusion generated by iterated maps.

We investigate the diffusion generated deterministically by periodic iterated maps that are defined by x(t+1) = x(t)+ax(z)(t)exp[-(b/x(t))(z-1)], z>1. It is shown that the obtained mean squared displacement grows asymptotically as sigma(2)(t) approximately ln (1/(z-1))(t) and that the corresponding propagator decays exponentially with the scaling variable |x|/square root of (sigma(2)(t))]. This strong diffusional anomaly stems from the anomalously broad distribution of waiting times in the corresponding random walk process and leads to a behavior obtained for diffusion in the presence of random local fields. A scaling approach is introduced which connects the explicit form of the maps to the mean squared displacement.

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PubMed2000

Atomic scale engines: cars and wheels.

We introduce a new approach to build microscopic engines on the atomic scale that move translationally or rotationally and can perform useful functions such as the pulling of a cargo. Characteristic of these engines is the possibility to determine dynamically the directionality of the motion. The approach is based on the transformation of the fed energy to directed motion through a dynamical competition between the intrinsic lengths of the moving object and the supporting carrier.

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PubMed2000

One-dimensional stochastic Levy-lorentz gas

We introduce a Levy-Lorentz gas in which a light particle is scattered by static point scatterers arranged on a line. We investigate the case where the intervals between scatterers xi(i) are independent random variables identically distributed according to the probability density function &mgr;(xi) approximately xi(-(1+gamma)). We show that under certain conditions the mean square displacement of the particle obeys >/=Ct3-gamma for 1<gamma<2. This behavior is compatible with a renewal Levy walk scheme. We discuss the importance of rare events in the proper characterization of the diffusion process.

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PubMed2000

From continuous time random walks to the fractional fokker-planck equation

We generalize the continuous time random walk (CTRW) to include the effect of space dependent jump probabilities. When the mean waiting time diverges we derive a fractional Fokker-Planck equation (FFPE). This equation describes anomalous diffusion in an external force field and close to thermal equilibrium. We discuss the domain of validity of the fractional kinetic equation. For the force free case we compare between the CTRW solution and that of the FFPE.

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PubMed2000

Generalized model for dynamic percolation

We study the dynamics of a carrier, which performs a biased motion under the influence of an external field E-->, in an environment which is modeled by dynamic percolation and created by hard-core particles. The particles move randomly on a simple cubic lattice, constrained by hard-core exclusion, and they spontaneously annihilate and reappear at some prescribed rates. We determine the density profiles of the "environment" particles, as seen from the stationary moving carrier, and calculate its terminal velocity V(c) as the function of the applied field and other system parameters. For sufficiently small driving forces the force exerted on the carrier by the "environment" particles shows a viscouslike behavior. An analog Stokes formula for such dynamic percolative environments and the corresponding friction coefficient are derived. We show that the density profile of the environment particles is strongly inhomogeneous: In front of the stationary moving carrier the density is higher than the average density rho(s), while past the carrier the local density is lower than rho(s).

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PubMed1999

Hierarchies and logarithmic oscillations in the temporal relaxation patterns of proteins and other complex systems.

Logarithmic oscillations superimposed on the temporal relaxation patterns of complex systems are considered from the standpoint of their hierarchical origin. We propose that a closer examination of experimental data should reveal logarithmic oscillations in systems that are characterized by a hierarchical structure of their dynamical degrees of freedom. On that footing, a new methodology of data analysis is proposed that may prove important for the dynamics of protein folding and of conformational fluctuations in proteins in which the relevant time scales of the dynamical evolution underlying the relaxation kinetics can be deduced from these oscillations.

Protein Conformation↗
PubMed1999

Escape from a fluctuating system: a master equation and trapping approach.

We present a general solution for the mean exit time in a system with on-site fluctuations between two configurations described by a master equation. The coupled configurations represent a spatially discretized version of an escape over a fluctuating barrier [C. R. Doering and J. C. Gadoua, Phys. Rev. Lett. 69, 2318 (1992)], and passage through modulating channels. Based on the general properties of the mean exit time, we obtain a simple solution for a coupled "birth" and "death" case that exhibits resonant activation. Within this exactly solvable model we derive analytically the optimal fluctuating rate, which is sensitive to the initial condition and scales as 1/n, where n is the system size. Our approach unifies a number of escape problems and points towards the generality of resonant activation.

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PubMed1999

Sorting single events: mean arrival times of N random walkers.

Using a scaling approach we investigate the first passage time < mu(1,N)(r)> for the first out of N identical independently diffusing particles in ordered and disordered structures. For Euclidean spaces we obtain < mu(1,N)(r)> in terms of a series in (ln N)(-1), independent of dimension. In the case of disordered ramified fractals < mu(1,N)(r)> is expressed in terms of a series in (ln N)((1-d(l)(w))), where d(l)(w) describes how the mean topological distance evolves with time t. We propose a scaling behavior for the related quantity S(N)(t), the number of distinct sites visited by N particles. We verify our predictions by numerical simulations.

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