Microscale Mechanics of Plug-and-Play In Vitro Cytoskeleton Networks

This chapter describes recent techniques that have been developed to reconstitute and characterize well-controlled, tunable networks of actin and microtubules outside of cells. It describes optical tweezers microrheology techniques to characterize the linear and nonlinear mechanics of these plug-and-play in vitro networks from the molecular-level to mesoscopic scales. It also details fluorescence microscopy and single-molecule tracking methods to determine macromolecular transport properties and stress propagation through cytoskeleton networks. Throughout the chapter the intriguing results that this body of work has revealed are highlighted—including how the macromolecular constituents of cytoskeleton networks map to their signature responses to stress or strain; and the elegant couplings between network structure, macromolecular mobility, and stress response that cytoskeleton networks exhibit

A Multicanonical Molecular Dynamics Study on a Simple Bead-Spring Model for Protein Folding

We have performed a multicanonical molecular dynamics simulation on a simple model protein.We have studied a model protein composed of charged, hydrophobic, and neutral spherical bead monomers.Since the hydrophobic interaction is considered to significantly affect protein folding, we particularly focus on the competition between effects of the Coulomb interaction and the hydrophobic interaction. We found that the transition which occurs upon decreasing the temperature is markedly affected by the change in both parameters and forms of the hydrophobic potential function, and the transition changes from first order to second order, when the Coulomb interaction becomes weaker.Comment: 7 pages, 6 postscript figures, To appear in J.Phys.Soc.Jpn. Vol.70 No.

Re-evaluation of cosmic ray cutoff terminology

The study of cosmic ray access to locations inside the geomagnetic field has evolved in a manner that has led to some misunderstanding and misapplication of the terminology originally developed to describe particle access. This paper presents what is believed to be a useful set of definitions for cosmic ray cutoff terminology for use in theoretical and experimental cosmic ray studies

Protein folding mediated by solvation: water expelling and formation of the hydrophobic core occurs after the structure collapse

The interplay between structure-search of the native structure and desolvation in protein folding has been explored using a minimalist model. These results support a folding mechanism where most of the structural formation of the protein is achieved before water is expelled from the hydrophobic core. This view integrates water expulsion effects into the funnel energy landscape theory of protein folding. Comparisons to experimental results are shown for the SH3 protein. After the folding transition, a near-native intermediate with partially solvated hydrophobic core is found. This transition is followed by a final step that cooperatively squeezes out water molecules from the partially hydrated protein core.Comment: Proceedings of the National Academy of Science, 2002, Vol.99. 685-69

Timescales of spike-train correlation for neural oscillators with common drive

We examine the effect of the phase-resetting curve (PRC) on the transfer of correlated input signals into correlated output spikes in a class of neural models receiving noisy, super-threshold stimulation. We use linear response theory to approximate the spike correlation coefficient in terms of moments of the associated exit time problem, and contrast the results for Type I vs. Type II models and across the different timescales over which spike correlations can be assessed. We find that, on long timescales, Type I oscillators transfer correlations much more efficiently than Type II oscillators. On short timescales this trend reverses, with the relative efficiency switching at a timescale that depends on the mean and standard deviation of input currents. This switch occurs over timescales that could be exploited by downstream circuits

Fostering online learning at the workplace : a scheme to identify and analyse collaboration processes in asynchronous discussions

Research has shown that providing participants with high‐quality learning material is not sufficient to help them profit most from online education. The level of interaction among participants is another key determinant for learning outcomes. However, merely proposing interaction does not automatically lead to fruitful discussion and collaboration. Specifically, social presence and facilitation activities add value to online discussions. In Murphy's collaboration framework, social presence represents the basis of successful online collaboration from which more reflective discussions and co‐construction can evolve. In this paper, an adjusted version of this framework was applied in a workplace learning context. The content analysis of 1170 comments in an online course for careers practitioners of a public employment service showed that the extended framework generated deeper insights into the dynamics of online discussions. The results show that involvement in collaborative learning at the workplace was supported by a high social presence and influenced by course topic and tasks. Facilitation played an important role in creating a sympathetic sense of community and stimulating co‐creation processes

Motif Statistics and Spike Correlations in Neuronal Networks

Motifs are patterns of subgraphs of complex networks. We studied the impact of such patterns of connectivity on the level of correlated, or synchronized, spiking activity among pairs of cells in a recurrent network model of integrate and fire neurons. For a range of network architectures, we find that the pairwise correlation coefficients, averaged across the network, can be closely approximated using only three statistics of network connectivity. These are the overall network connection probability and the frequencies of two second-order motifs: diverging motifs, in which one cell provides input to two others, and chain motifs, in which two cells are connected via a third intermediary cell. Specifically, the prevalence of diverging and chain motifs tends to increase correlation. Our method is based on linear response theory, which enables us to express spiking statistics using linear algebra, and a resumming technique, which extrapolates from second order motifs to predict the overall effect of coupling on network correlation. Our motif-based results seek to isolate the effect of network architecture perturbatively from a known network state

Hygrothermal effects and moisture kinetics in a bio-based multi-layered wall:Experimental and numerical studies

International audienceA bio-based multi-layered reference wall has been developed within the framework of the European ISOBIO project. One of the key points of this project was to be able to perform proper simulations of the hygrothermal transfers occurring inside such walls. Previous published investigations, also performed in the framework of this project, have demonstrated that the classic assumption of instantaneous equilibrium between local relative humidity and water content according to the sorption isotherm is not relevant for bio-based porous materials, where, in practice, a rather slow kinetics of sorption occurs. The theoretical background developed in this previous study is used here to determine the kinetic constants of the bio-based construction materials and to perform 1D hygrothermal simulations. The kinetics constants are determined thanks to a 1D cylindrical tool based on the local kinetics approach, validated against several experiments of sorption. Then, heat and hygric transfers recorded on a demonstrator building (The HIVE, Wroughton, UK) are analyzed and are simulated using two modeling tools: TMC based on the Künzel approach and TMCKIN based on the local kinetic approach. From the simulations, the local kinetics improves the small timescale RH dynamics. The comparison with measurements performed in the demonstrator confirms the relevance of the local kinetics approach