Phase-space geometry of the generalized Langevin equation

The generalized Langevin equation is widely used to model the influence of a heat bath upon a reactive system. This equation will here be studied from a geometric point of view. A dynamical phase space that represents all possible states of the system will be constructed, the generalized Langevin equation will be formally rewritten as a pair of coupled ordinary differential equations, and the fundamental geometric structures in phase space will be described. It will be shown that the phase space itself and its geometric structure depend critically on the preparation of the system: A system that is assumed to have been in existence for ever has a larger phase space with a simpler structure than a system that is prepared at a finite time. These differences persist even in the long-time limit, where one might expect the details of preparation to become irrelevant

Reaction rate calculation with time-dependent invariant manifolds

The identification of trajectories that contribute to the reaction rate is the crucial dynamical ingredient in any classical chemical reactivity calculation. This problem often requires a full scale numerical simulation of the dynamics, in particular if the reactive system is exposed to the influence of a heat bath. As an efficient alternative, we propose here to compute invariant surfaces in the phase space of the reactive system that separate reactive from nonreactive trajectories. The location of these invariant manifolds depends both on time and on the realization of the driving force exerted by the bath. These manifolds allow the identification of reactive trajectories simply from their initial conditions, without the need of any further simulation. In this paper, we show how these invariant manifolds can be calculated, and used in a formally exact reaction rate calculation based on perturbation theory for any multidimensional potential coupled to a noisy environment

Finite size effects on transport coefficients for models of atomic wires coupled to phonons

We consider models of quasi-1-d, planar atomic wires consisting of several, laterally coupled rows of atoms, with mutually non-interacting electrons. This electronic wire system is coupled to phonons, corresponding, e.g., to some substrate. We aim at computing diffusion coefficients in dependence on the wire widths and the lateral coupling. To this end we firstly construct a numerically manageable linear collision term for the dynamics of the electronic occupation numbers by following a certain projection operator approach. By means of this collision term we set up a linear Boltzmann equation. A formula for extracting diffusion coefficients from such Boltzmann equations is given. We find in the regime of a few atomic rows and intermediate lateral coupling a significant and non-trivial dependence of the diffusion coefficient on both, the width and the lateral coupling. These results, in principle, suggest the possible applicability of such atomic wires as electronic devices, such as, e.g., switches.Comment: 9 pages, 5 figures, accepted for publication in Eur. Phys. J.

Quantitative performance characterization of three-dimensional noncontact fluorescence molecular tomography

© 2016 The Authors.Fluorescent proteins and dyes are routine tools for biological research to describe the behavior of genes, proteins, and cells, as well as more complex physiological dynamics such as vessel permeability and pharmacokinetics. The use of these probes in whole body in vivo imaging would allow extending the range and scope of current biomedical applications and would be of great interest. In order to comply with a wide variety of application demands, in vivo imaging platform requirements span from wide spectral coverage to precise quantification capabilities. Fluorescence molecular tomography (FMT) detects and reconstructs in three dimensions the distribution of a fluorophore in vivo. Noncontact FMT allows fast scanning of an excitation source and noninvasive measurement of emitted fluorescent light using a virtual array detector operating in free space. Here, a rigorous process is defined that fully characterizes the performance of a custom-built horizontal noncontact FMT setup. Dynamic range, sensitivity, and quantitative accuracy across the visible spectrum were evaluated using fluorophores with emissions between 520 and 660 nm. These results demonstrate that high-performance quantitative three-dimensional visible light FMT allowed the detection of challenging mesenteric lymph nodes in vivo and the comparison of spectrally distinct fluorescent reporters in cell culture

The reconstruction of causal networks in physiology

We systematically compare strengths and weaknesses of two methods that can be used to quantify causal links between time series: Granger-causality and Bivariate Phase Rectified Signal Averaging (BPRSA). While a statistical test method for Granger-causality has already been established, we show that BPRSA causality can also be probed with existing statistical tests. Our results indicate that more data or stronger interactions are required for the BPRSA method than for the Granger-causality method to detect an existing link. Furthermore, the Granger-causality method can distinguish direct causal links from indirect links as well as links that arise from a common source, while BPRSA cannot. However, in contrast to Granger-causality, BPRSA is suited for the analysis of non-stationary data. We demonstrate the practicability of the Granger-causality method by applying it to polysomnography data from sleep laboratories. An algorithm is presented, which addresses the stationarity condition of Granger-causality by splitting non-stationary data into shorter segments until they pass a stationarity test. We reconstruct causal networks of heart rate, breathing rate, and EEG amplitude from young healthy subjects, elderly healthy subjects, and subjects with obstructive sleep apnea, a condition that leads to disruption of normal respiration during sleep. These networks exhibit differences not only between different sleep stages, but also between young and elderly healthy subjects on the one hand and subjects with sleep apnea on the other hand. Among these differences are 1) weaker interactions in all groups between heart rate, breathing rate and EEG amplitude during deep sleep, compared to light and REM sleep, 2) a stronger causal link from heart rate to breathing rate but disturbances in respiratory sinus arrhythmia (breathing to heart rate coupling) in subjects with sleep apnea, 3) a stronger causal link from EEG amplitude to breathing rate during REM sleep in subjects with sleep apnea. The Granger-causality method, although initially developed for econometric purposes, can provide a quantitative, testable measure for causality in physiological networks

Projet de conversion et d'unification des titres des Series B. C. & D. de la Dette Ottomane

Taha Toros Arşivi, Dosya No: 71-Duyun-u Umumiyeİstanbul Kalkınma Ajansı (TR10/14/YEN/0033) İstanbul Development Agency (TR10/14/YEN/0033

Heparin and air filters reduce embolic events caused by intra-arterial cerebral angiography - A prospective, randomized trial

Background-Intra-arterial cerebral angiography is associated with a low risk for neurological complications, but clinically silent ischemic events after angiography have been seen in a substantial number of patients.Methods and Results-In a prospective study, diffusion-weighted magnetic resonance imaging (DW-MRI) before and after intra-arterial cerebral angiography and transcranial Doppler sonography during angiography were used to evaluate the frequency of cerebral embolism. One hundred fifty diagnostic cerebral angiographies were randomized into 50 procedures, each using conventional angiographic technique, or systemic heparin treatment throughout the procedure, or air filters between the catheter and both the contrast medium syringe and the catheter flushing. There was no neurological complication during or after angiography. Overall, DW-MRI revealed 26 new ischemic lesions in 17 patients (11%). In the control group, 11 patients showed a total of 18 lesions. In the heparin group, 3 patients showed a total of 4 lesions. In the air filter group, 3 patients exhibited a total of 4 lesions. The reduced incidence of ischemic events in the heparin and air filter groups compared with the control group was significantly different (P=0.002). Transcranial Doppler sonography demonstrated a large number of microembolic signals that was significantly lower in the air filter group compared with the heparin and control groups (P=0.01), which did not differ from each other.Conclusions-Air filters and heparin both reduce the incidence of silent ischemic events detected by DW-MRI after intra-arterial cerebral angiography and can potentially lower clinically overt ischemic complications. This may apply to any intra-arterial angiographic procedure

An empirical study of aspect-oriented metrics

Metrics for aspect-oriented software have been proposed and used to investigate the benefits and the disadvantages of crosscutting concerns modularisation. Some of these metrics have not been rigorously defined nor analytically evaluated. Also, there are few empirical data showing typical values of these metrics in aspect-oriented software. In this paper, we provide rigorous definitions, usage guidelines, analytical evaluation, and empirical data from ten open source projects, determining the value of six metrics for aspect-oriented software (lines of code, weighted operations in module, depth of inheritance tree, number of children, crosscutting degree of an aspect, and coupling on advice execution). We discuss how each of these metrics can be used to identify shortcomings in existing aspect-oriented software. (C) 2012 Elsevier B.V. All rights reserved.CNPq [140046/06-2]; Project CNPQ-PROSUL [490478/06-9]; Capes-Grices [2051-05-2]; FAPERGS [10/0470-1]; FCT MCTESinfo:eu-repo/semantics/publishedVersio

The Transition State in a Noisy Environment

Transition State Theory overestimates reaction rates in solution because conventional dividing surfaces between reagents and products are crossed many times by the same reactive trajectory. We describe a recipe for constructing a time-dependent dividing surface free of such recrossings in the presence of noise. The no-recrossing limit of Transition State Theory thus becomes generally available for the description of reactions in a fluctuating environment

Transient fluctuation theorem in closed quantum systems

Our point of departure are the unitary dynamics of closed quantum systems as generated from the Schr\"odinger equation. We focus on a class of quantum models that typically exhibit roughly exponential relaxation of some observable within this framework. Furthermore, we focus on pure state evolutions. An entropy in accord with Jaynes principle is defined on the basis of the quantum expectation value of the above observable. It is demonstrated that the resulting deterministic entropy dynamics are in a sense in accord with a transient fluctuation theorem. Moreover, we demonstrate that the dynamics of the expectation value are describable in terms of an Ornstein-Uhlenbeck process. These findings are demonstrated numerically and supported by analytical considerations based on quantum typicality.Comment: 5 pages, 6 figure