Weakly nonlinear rheology of transiently crosslinked biopolymer gels

Recent experimental investigations have revealed a non-Maxwellian absorption pattern in the rheological spectra of actin gels, which was interpreted in terms of transient bonds. Here we examine the consequences of reversible crosslinking on the apparent linear spectra of biopolymer solutions theoretically. For a schematic model consisting of a reversibly crosslinked power-law fluid we obtain a simple analytical prediction for the position of the absorption peak, which is backed up by a numerical evaluation of the inelastic glassy wormlike chain model. This establishes bond breaking as a nonlinear non-equilibrium effect that can already be significant for very small driving amplitudes. Our results may be useful for inferring binding affinities and reaction rates of biochemical crosslinkers from rheological measurements of {\it in-vitro} reconstituted cytoskeletal gels

Photoacoustics Modelling using Amplitude Mode Expansion Method in a Multiscale T-cell Resonator

The photoacoustic (PA) effect consisting of the generation of an acoustic signal based on the absorption of light has already demonstrated its potential for various spectroscopic applications for both gaseous and solid samples. The signal produced during photoacoustic spectroscopy (PAS) measurement is, however, usually weak and needs to be amplified. This is achieved by using a photoacoustic cell resonator where acoustic resonances are utilized to significantly boost the signal. Therefore, a PA resonator has a significant role in PAS measurement set-ups. When designing or optimizing a new PA resonator, numerical methods are generally used to simulate the photoacoustic signal generation. In this paper, the amplitude mode expansion (AME) method is presented as a quick and accurate simulation tool. The method is used to simulate the photoacoustic signal in a multi-scale T-cell resonator over a wide frequency range. The AME method is based on eigenmode expansion and introduction of losses by quality factors. The AME simulation results are compared and analyzed against the results from the viscothermal method. Reasonably good agreement is obtained between the two methods. However, small frequency shifts in the resonances of the AME method are noted. The shifts are attributed to the location of the dominant mode within the T-cell. The viscothermal method is considered the most accurate method for simulating the photoacoustic signal in small resonators. However, it is computationally very demanding. The AME method provides a much faster simulation alternative. This is particularly useful in the design and optimization of photoacoustic resonators where numerical methods are preferred over experimental measurements due to their speed and low cost.Comment: Comsol Conference 201

Inelastic mechanics of sticky biopolymer networks

We propose a physical model for the nonlinear inelastic mechanics of sticky biopolymer networks with potential applications to inelastic cell mechanics. It consists of a minimal extension of the glassy wormlike chain (Gwlc) model, which has recently been highly successful as a quantitative mathematical description of the viscoelastic properties of biopolymer networks and cells. To extend its scope to nonequilibrium situations, where the thermodynamic state variables may evolve dynamically, the Gwlc is furnished with an explicit representation of the kinetics of breaking and reforming sticky bonds. In spite of its simplicity, the model exhibits many experimentally established nontrivial features such as power-law rheology, stress stiffening, fluidization and cyclic softening effects

Extending ASSL: Making UML Metamodel-based Workflows executable

ASSL is a language that enables UML developers to test and certify UML and OCL models [5]. Snapshots of system states are semi-automatically created and main parts of the UML action semantics is implemented by the language. Its interpreter is the well-known UML modeling tool USE. The article proposes a number of language extensions to ASSL. These include (sub ) procedure calls and pre- and postcondition checks on entering and exiting of operations using OCL. The paper motivates the need for these extensions as well as their usage and development along the problem of metamodel-based execution of workflow models. Executable workflow models, driven by ASSL procedures, are introduced in detail to present the usage of ASSL and our extensions

Comparison of tree species diversity, deadwood volume and regeneration of managed and old-growth Oriental beech (Fagus orientalis L.) forests in Eastern Georgia

Abstract Main stand characteristics and tree species composition were studied in managed and old-growth Oriental beech (Fagus orientalis L.) forests in eastern Georgia (Caucasus). Oriental beech dominates both the regeneration layer and the upper story in old-growth forest. In managed forests, Caucasian hornbeam (Carpinus orientalis) and Oriental beech co-dominate the tree layer as well as the regeneration layer. Tree species diversity and deadwood proportion are higher in managed forests than in old-growth forests. However, the absolute deadwood proportion is similar in both studied forest types. Hence, deadwood proportion is not a suitable indicator to assess the naturalness or management intensity of forests in the study area. The observed proportions of Caucasian hornbeam in managed forests raise concerns about the sustainable use of beechwood in the long term. Harvesting hornbeam and smaller removals of beech are recommended to maintain the uneven-aged forest ecosystem, with Oriental beech as the dominant tree species. The established long-term study plots are important to observe and improve future stand development and forest management

Efficiency and contribution of strategies for finding randomized controlled trials: a case study from a systematic review on therapeutic interventions of chronic depression

Background. Identifying all existing evidence is a crucial aspect in conducting systematic reviews. Since the retrieval of electronic database searches alone is limited, guidelines recommend the use of addi- tional search strategies. The aim of this investigation was to assess the efficiency and contribution of additional search strategies for identifying randomized controlled trials in conducting a systematic review on interventions after performing a sensitive electronic database search. Design and Methods. Seven electronic databases, 3 journals and 11 systematic reviews were searched. All first authors of the included studies were contacted; citation tracking and a search in clinical trial registers were performed. A priori defined evaluation criteria were calculated for each search strategy. Results. A total of 358 full-text articles were identified; 50 studies were included in the systematic review, wherefrom 84.0% (42) were acquired by the sensitive electronic database search and 16.0% (8) through additional search strategies. Screening reference lists of related systematic reviews was the most beneficial additional search strategy, with an efficiency of 31.3% (5) and a contribution of 10.0% (5/50), whereas hand-searching and author contacts contributed two and one additional studies, respectively. Citation tracking and searching clinical trial registers did not lead to any further inclusion of primary studies. Conclusions. Based on our findings, hand-searching contents of relevant journals and screening reference lists of related systematic reviews may be helpful additional strategies to identify an extensive body of evidence. In case of limited resources, a sensitive electronic database search may constitute an appropriate alternative for identifying relevant trials