Quantum Charge Transport and Conformational Dynamics of Macromolecules

We study the dynamics of quantum excitations inside macromolecules which can undergo conformational transitions. In the first part of the paper, we use the path integral formalism to rigorously derive a set of coupled equations of motion which simultaneously describe the molecular and quantum transport dynamics, and obey the fluctuation/dissipation relationship. We also introduce an algorithm which yields the most probable molecular and quantum transport pathways in rare, thermally-activated reactions. In the second part of the paper, we apply this formalism to simulate the propagation of a charge during the collapse of a polymer from an initial stretched conformation to a final globular state. We find that the charge dynamics is quenched when the chain reaches a molten globule state. Using random matrix theory we show that this transition is due to an increase of quantum localization driven by dynamical disorder.Comment: 11 pages, 2 figure

Conservation law of operator current in open quantum systems

We derive a fundamental conservation law of operator current for master equations describing reduced quantum systems. If this law is broken, the temporal integral of the current operator of an arbitrary system observable does not yield in general the change of that observable in the evolution. We study Lindblad-type master equations as examples and prove that the application of the secular approximation during their derivation results in a violation of the conservation law. We show that generally any violation of the law leads to artificial corrections to the complete quantum dynamics, thus questioning the accuracy of the particular master equation.Comment: 5 pages, final versio

Adaptive Resolution Molecular Dynamics Simulation: Changing the Degrees of Freedom on the Fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular dynamics (MD) simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecule's atomic and coarse-grained level of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, the other containing only one particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The coarse-grained and the atomistically resolved systems have the same statistical properties at the same physical conditions.Comment: 17 pages, 11 figures, 5 table

Exact Results for the One-Dimensional Self-Organized Critical Forest-Fire Model

We present the analytic solution of the self-organized critical (SOC) forest-fire model in one dimension proving SOC in systems without conservation laws by analytic means. Under the condition that the system is in the steady state and very close to the critical point, we calculate the probability that a string of $n$ neighboring sites is occupied by a given configuration of trees. The critical exponent describing the size distribution of forest clusters is exactly $\tau = 2$ and does not change under certain changes of the model rules. Computer simulations confirm the analytic results.Comment: 12 pages REVTEX, 2 figures upon request, dro/93/

Relaxation kinetics of biological dimer adsorption models

We discuss the relaxation kinetics of a one-dimensional dimer adsorption model as recently proposed for the binding of biological dimers like kinesin on microtubules. The non-equilibrium dynamics shows several regimes: irreversible adsorption on short time scales, an intermediate plateau followed by a power-law regime and finally exponential relaxation towards equilibrium. In all four regimes we give analytical solutions. The algebraic decay and the scaling behaviour can be explained by mapping onto a simple reaction-diffusion model. We show that there are several possibilities to define the autocorrelation function and that they all asymptotically show exponential decay, however with different time constants. Our findings remain valid if there is an attractive interaction between bound dimers.Comment: REVTeX, 6 pages, 5 figures; to appear in Europhys. Letters; a Java applet showing the simulation is accessible at http://www.ph.tum.de/~avilfan/rela

Non-Markovian dynamics for bipartite systems

We analyze the appearance of non-Markovian effects in the dynamics of a bipartite system coupled to a reservoir, which can be described within a class of non-Markovian equations given by a generalized Lindblad structure. A novel master equation, which we term quantum Bloch-Boltzmann equation, is derived, describing both motional and internal states of a test particle in a quantum framework. When due to the preparation of the system or to decoherence effects one of the two degrees of freedom is amenable to a classical treatment and not resolved in the final measurement, though relevant for the interaction with the reservoir, non-Markovian behaviors such as stretched exponential or power law decay of coherences can be put into evidence.Comment: published version, 15 pages, revtex, no figure

Investigating Biological Matter with Theoretical Nuclear Physics Methods

The internal dynamics of strongly interacting systems and that of biomolecules such as proteins display several important analogies, despite the huge difference in their characteristic energy and length scales. For example, in all such systems, collective excitations, cooperative transitions and phase transitions emerge as the result of the interplay of strong correlations with quantum or thermal fluctuations. In view of such an observation, some theoretical methods initially developed in the context of theoretical nuclear physics have been adapted to investigate the dynamics of biomolecules. In this talk, we review some of our recent studies performed along this direction. In particular, we discuss how the path integral formulation of the molecular dynamics allows to overcome some of the long-standing problems and limitations which emerge when simulating the protein folding dynamics at the atomistic level of detail.Comment: Prepared for the proceedings of the "XII Meeting on the Problems of Theoretical Nuclear Physics" (Cortona11

Critical sound attenuation in a diluted Ising system

The field-theoretic description of dynamical critical effects of the influence of disorder on acoustic anomalies near the temperature of the second-order phase transition is considered for three-dimensional Ising-like systems. Calculations of the sound attenuation in pure and dilute Ising-like systems near the critical point are presented. The dynamical scaling function for the critical attenuation coefficient is calculated. The influence of quenched disorder on the asymptotic behaviour of the critical ultrasonic anomalies is discussed.Comment: 12 RevTeX pages, 4 figure

Crossover from Percolation to Self-Organized Criticality

We include immunity against fire as a new parameter into the self-organized critical forest-fire model. When the immunity assumes a critical value, clusters of burnt trees are identical to percolation clusters of random bond percolation. As long as the immunity is below its critical value, the asymptotic critical exponents are those of the original self-organized critical model, i.e. the system performs a crossover from percolation to self-organized criticality. We present a scaling theory and computer simulation results.Comment: 4 pages Revtex, two figures included, to be published in PR