Universal Markovian reduction of Brownian particle dynamics

Non-Markovian processes can often be turned Markovian by enlarging the set of variables. Here we show, by an explicit construction, how this can be done for the dynamics of a Brownian particle obeying the generalized Langevin equation. Given an arbitrary bath spectral density $J_{0}$, we introduce an orthogonal transformation of the bath variables into effective modes, leading stepwise to a semi-infinite chain with nearest-neighbor interactions. The transformation is uniquely determined by $J_{0}$ and defines a sequence $\{J_{n}\}_{n\in\mathbb{N}}$ of residual spectral densities describing the interaction of the terminal chain mode, at each step, with the remaining bath. We derive a simple, one-term recurrence relation for this sequence, and show that its limit is the quasi-Ohmic expression provided by the Rubin model of dissipation. Numerical calculations show that, irrespective of the details of $J_{0}$, convergence is fast enough to be useful in practice for an effective Markovian reduction of quantum dissipative dynamics

Non-Markovian reduced dynamics of ultrafast charge transfer at an oligothiophene–fullerene heterojunction

We extend our recent quantum dynamical study of the exciton dissociation and charge transfer at an oligothiophene-fullerene heterojunction interface (Tamura et al., 2012) [6] by investigating the process using the non-perturbative hierarchical equations of motion (HEOM) approach. Based upon an effective mode reconstruction of the spectral density the effect of temperature on the charge transfer is studied using reduced density matrices. It was found that the temperature had little effect on the charge transfer and a coherent dynamics persists over the first few tens of femtoseconds, indicating that the primary charge transfer step proceeds by an activationless pathway

Quantum dynamics of hydrogen atoms on graphene. I. System-bath modeling

An accurate system-bath model to investigate the quantum dynamics of hydrogen atoms chemisorbed on graphene is presented. The system comprises a hydrogen atom and the carbon atom from graphene that forms the covalent bond, and it is described by a previously developed 4D potential energy surface based on density functional theory ab initio data. The bath describes the rest of the carbon lattice and is obtained from an empirical force field through inversion of a classical equilibrium correlation function describing the hydrogen motion. By construction, model building easily accommodates improvements coming from the use of higher level electronic structure theory for the system. Further, it is well suited to a determination of the system-environment coupling by means of ab initio molecular dynamics. This paper details the system-bath modeling and shows its application to the quantum dynamics of vibrational relaxation of a chemisorbed hydrogen atom, which is here investigated at T = 0 K with the help of the multi-configuration time-dependent Hartree method. Paper II deals with the sticking dynamics

Single Molecule Fluorescence Image Patterns Linked to Dipole Orientation and Axial Position: Application to Myosin Cross-Bridges in Muscle Fibers

Photoactivatable fluorescent probes developed specifically for single molecule detection extend advantages of single molecule imaging to high probe density regions of cells and tissues. They perform in the native biomolecule environment and have been used to detect both probe position and orientation.Fluorescence emission from a single photoactivated probe captured in an oil immersion, high numerical aperture objective, produces a spatial pattern on the detector that is a linear combination of 6 independent and distinct spatial basis patterns with weighting coefficients specifying emission dipole orientation. Basis patterns are tabulated for single photoactivated probes labeling myosin cross-bridges in a permeabilized muscle fiber undergoing total internal reflection illumination. Emitter proximity to the glass/aqueous interface at the coverslip implies the dipole near-field and dipole power normalization are significant affecters of the basis patterns. Other characteristics of the basis patterns are contributed by field polarization rotation with transmission through the microscope optics and refraction by the filter set. Pattern recognition utilized the generalized linear model, maximum likelihood fitting, for Poisson distributed uncertainties. This fitting method is more appropriate for treating low signal level photon counting data than χ(2) minimization.Results indicate that emission dipole orientation is measurable from the intensity image except for the ambiguity under dipole inversion. The advantage over an alternative method comparing two measured polarized emission intensities using an analyzing polarizer is that information in the intensity spatial distribution provides more constraints on fitted parameters and a single image provides all the information needed. Axial distance dependence in the emission pattern is also exploited to measure relative probe position near focus. Single molecule images from axial scanning fitted simultaneously boost orientation and axial resolution in simulation

RNA secondary structure design

We consider the inverse-folding problem for RNA secondary structures: for a given (pseudo-knot-free) secondary structure find a sequence that has that structure as its ground state. If such a sequence exists, the structure is called designable. We implemented a branch-and-bound algorithm that is able to do an exhaustive search within the sequence space, i.e., gives an exact answer whether such a sequence exists. The bound required by the branch-and-bound algorithm are calculated by a dynamic programming algorithm. We consider different alphabet sizes and an ensemble of random structures, which we want to design. We find that for two letters almost none of these structures are designable. The designability improves for the three-letter case, but still a significant fraction of structures is undesignable. This changes when we look at the natural four-letter case with two pairs of complementary bases: undesignable structures are the exception, although they still exist. Finally, we also study the relation between designability and the algorithmic complexity of the branch-and-bound algorithm. Within the ensemble of structures, a high average degree of undesignability is correlated to a long time to prove that a given structure is (un-)designable. In the four-letter case, where the designability is high everywhere, the algorithmic complexity is highest in the region of naturally occurring RNA.Comment: 11 pages, 10 figure

Book Reviews

BOOK REVIEWS The Assembly Line by Robert Linhart - Reviewed by MIKE PARKER The Crisis In Social Security: Economic and Political Origins by Carolyn L. Weaver - Reviewed by GARY FREEMAN The Political Econany of Aging: The State, Private Power and Social Welfare by laura Katz Olson - Reviewed by MARTIN B. TRACY The Other Side of Organizing: Resolving the Personal Dilemmas and Political Demands of Daily Practice by Steve Burghardt - Reviewed by MICHAEL REISCH The Radical Future of Liberal Feminism by Zillah Eisenstein - Reviewed by KATHRYN B. WARD Setting National Priorities: The 1983 Budget edited by Joseph A. Peobmand Crisis In the Public Sector edited by Union for Radical Political Economics - Reviewed by STEVE BUR(HARDT Alcohol and the Family by Jim Oxford and Judith Harwin - Reviewed by PATRICIA MORGA

Development and test results of a readout chip for the GERDA experiment

This paper describes the F-CSA104 architecture and its measurement results. The F-CSA104 is for γ spectroscopy with Ge detectors. It is a low noise, fully integrated, four channel XFAB 0.6μm CMOS technology ASIC, that has been developed for the GERDA experiment. Each channel contains a charge sensitive preamplifier (CSA) followed by a 11.7MHz differential line driver. It has been particularly designed to operate in liquid argon (T = 87K/-186°C) and to have a measuring sensitivity of 660e- with an ENC of 110e-, after offline filtering with 10μs shaping, when connected to a 30pF load. Special techniques are used to improve the SNR such as a large input PMOS FET, an integrated 500MΩ CSA feedback resistor and a noise degeneration drain resistor