Exploring the performance of spatial stochastic simulation algorithms

Since the publication of Gillespie’s direct method, diverse methods have been developed to improve the performance of stochastic simulation methods and to enter the spatial realm. In this paper we discuss a spatial τ-leaping variant (Sτ) that extends the basic leap method. Sτ takes reaction and both outgoing and incoming diffusion events into account when calculating a leap candidate. A performance analysis shall reveal details on the achieved success in balancing speed and accuracy in comparison to other methods. However, performance analysis of spatial stochastic algorithms requires significant effort — it is crucial to choose suitable (benchmark) models and to carefully define model and simulation setups that take problem and simulation design spaces into account.     

Polyelectrolyte-compression forces between spherical DNA brushes

Optical tweezers are employed to measure the forces of interaction within a single pair of DNA-grafted colloids, dependent on the molecular weight of the DNA chains, and the concentration and valence of the surrounding ionic medium. The resulting forces are short range and set in as the surface-to-surface distance between the colloidal cores reaches the value of the brush height. The measured force-distance relation is analyzed by means of a theoretical treatment that quantitatively describes the effects of compression of the chains on the surface of the opposite-lying colloid. Quantitative agreement with the experiment is obtained for all parameter combinations.     

Improved laser-induced forward transfer of organic semiconductor thin films by reducing the environmental pressure and controlling the substrate–substrate gap width

Laser-induced forward transfer (LIFT) has been investigated for bilayer transfer material systems: silver/organic film (Alq₃ or PFO). The LIFT process uses an intermediate dynamic release layer of a triazene polymer. This study focuses on the effect of introducing a controlled donor–receiver substrate gap distance and the effect of doing the transfer at reduced air pressures, whilst varying the fluence up to ∼200 mJ/cm². The gap between ‘in-contact’ substrates has been measured to be a minimum of 2–3 μm. A linear variation in the gap width from ‘in contact’ to 40 μm has been achieved by adding a spacer at one side of the substrate–substrate sandwich. At atmospheric pressure, very little transfer is achieved for Alq₃, although PFO shows some signs of successful doughnut transfer (with a large hole in the middle) in a narrow fluence range, at gaps greater than 20 μm. For the transfer of Ag/PFO bilayers at atmospheric pressure, the addition of a PFO layer onto the receiver substrate improved the transfer enormously at smaller gaps and higher fluences. However, the best transfer results were obtained at reduced pressures where a 100% transfer success rate is obtained within a certain fluence window. The quality of the pixel morphology at less than 100 mbar is much higher than at atmospheric pressure, particularly when the gap width is less than 20 μm. These results show the promise of LIFT for industrial deposition processes where a gap between the substrates will improve the throughput.     

Comparing closed quotient in children singers' voices as measured by high-speed-imaging, electroglottography, and inverse filtering

The closed quotient, i.e., the ratio between the closed phase and the period, is commonly studied in voice research. However, the term may refer to measures derived from different methods, such as inverse filtering, electroglottography or high-speed digital imaging (HSDI). This investigation compares closed quotient data measured by these three methods in two boy singers. Each singer produced sustained tones on two different pitches and a glissando. Audio, electroglottographic signal (EGG), and HSDI were recorded simultaneously. The audio signal was inverse filtered by means of the decap program; the closed phase was defined as the flat minimum portion of the flow glottogram. Glottal area was automatically measured in the high speed images by the built-in camera software, and the closed phase was defined as the flat minimum portion of the area-signal. The EGG-signal was analyzed in four different ways using the matlab open quotient interface. The closed quotient data taken from the EGG were found to be considerably higher than those obtained from inverse filtering. Also, substantial differences were found between the closed quotient derived from HSDI and those derived from inverse filtering. The findings illustrate the importance of distinguishing between these quotients.     

The decoupling of damped linear systems in free or forced vibration

The purpose of this paper is to extend classical modal analysis to decouple any viscously damped linear system in non-oscillatory free vibration or in forced vibration. Based upon an exposition of how exponential decay in a system can be regarded as imaginary oscillations, the concept of damped modes of imaginary vibration is introduced. By phase synchronization of these real and physically excitable modes, a time-varying transformation is constructed to decouple non-oscillatory free vibration. When time drifts caused by viscous damping and by external excitation are both accounted for, a time-varying decoupling transformation for forced vibration is derived. The decoupling procedure devised herein reduces to classical modal analysis for systems that are undamped or classically damped. This paper constitutes the second and final part of a solution to the “classical decoupling problem.” Together with an earlier paper, a general methodology that requires only the solution of a quadratic eigenvalue problem is developed to decouple any damped linear system.     

Cross-approximate entropy of cortical local field potentials quantifies effects of anesthesia - a pilot study in rats

Background

Anesthetics dose-dependently shift electroencephalographic (EEG) activity towards high-amplitude, slow rhythms, indicative of a synchronization of neuronal activity in thalamocortical networks. Additionally, they uncouple brain areas in higher (gamma) frequency ranges possibly underlying conscious perception. It is currently thought that both effects may impair brain function by impeding proper information exchange between cortical areas. But what happens at the local network level? Local networks with strong excitatory interconnections may be more resilient towards global changes in brain rhythms, but depend heavily on locally projecting, inhibitory interneurons. As anesthetics bias cortical networks towards inhibition, we hypothesized that they may cause excessive synchrony and compromise information processing already on a small spatial scale. Using a recently introduced measure of signal independence, cross-approximate entropy (XApEn), we investigated to what degree anesthetics synchronized local cortical network activity. We recorded local field potentials (LFP) from the somatosensory cortex of three rats chronically implanted with multielectrode arrays and compared activity patterns under control (awake state) with those at increasing concentrations of isoflurane, enflurane and halothane.

Results

Cortical LFP signals were more synchronous, as expressed by XApEn, in the presence of anesthetics. Specifically, XApEn was a monotonously declining function of anesthetic concentration. Isoflurane and enflurane were indistinguishable; at a concentration of 1 MAC (the minimum alveolar concentration required to suppress movement in response to noxious stimuli in 50% of subjects) both volatile agents reduced XApEn by about 70%, whereas halothane was less potent (50% reduction).

Conclusions

The results suggest that anesthetics strongly diminish the independence of operation of local cortical neuronal populations, and that the quantification of these effects in terms of XApEn has a similar discriminatory power as changes of spontaneous action potential rates. Thus, XApEn of field potentials recorded from local cortical networks provides valuable information on the anesthetic state of the brain.