Platform economy: (dis-) embeddedness processes in urban spaces

Digital platforms, understood as multi-sided matchmakers, have amassed huge power, reimagining the role of consumers, producers, and even ownership. They increasingly dictate the way the economy and urban life is organized. Yet, despite their influential and far-reaching role in shaping our economic as well as sociocultural world, our understanding of their embeddedness, namely how their activities are embedded in systems of social and societal relationships and how they conceptualize their main functions and actions in relation to their wider setting, remains rudimentary. Consequently, the purpose of this frontier paper is threefold. Firstly, it reveals the need to discuss and evaluate (dis-)embedding processes in platform urbanism in order to understand the underlying dynamics of platform power and urban transformation. Secondly, it aims to reveal the main reasons in regard to the difficulties in pinpointing digital platforms embeddedness. Thirdly, it seeks to propose future research unravelling the (dis-)embeddedness of the platform economy.This paper argues for three main reasons namely unawareness, unaccountability and non-transparency of digital platforms that drive the lack of embeddedness and reaffirms platform power. This is mainly based on the configuration of new commodities, platforms’ strategic avoidance of labour protections and other regulatory frameworks as well as platforms’ secrecy in which they operate. This frontier paper argues that transferring the concept of embeddedness to the platform economy might serve as a valuable tool to understand and pinpoint essential dynamics and relationships at play, therefore proposing embeddedness as a basis for future research on the platform economy. It strongly argues that a more detailed understanding is urgently needed, in order to be able to understand, accompany and actively influence the development of the platform economy in regulatory terms.

Essential Loop Dynamics Modulates Catalytic Activity in α-Chymotrypsin

Conformational dynamics of macromolecules including enzymes are essential for their function. The present work reports the role of essential dynamics in alpha-chymotrypsin (CHT) which correlates with its catalytic activity. Detailed optical spectroscopy and classical molecular dynamics (MD) simulation were used to study thermal stability, catalytic activity and dynamical flexibility of the enzyme. The study of the enzyme kinetics reveals an optimum catalytic efficiency at 308K. Polarization gated fluorescence anisotropy with 8-anilino-1-napthelene sulfonate (ANS) have indicated increasing flexibility of the enzyme with an increase in temperature. Examination of the structure of CHT reveal the presence of five loop regions (LRs) around the catalytic S1 pocket. MD simulations have indicated that flexibility increases concurrently with temperature which decreases beyond optimum temperature. Principal component analysis (PCA) of the eigenvectors manifests essential dynamics and gatekeeping role of the five LRs surrounding the catalytic pocket which controls the enzyme activity.

JEDi: java essential dynamics inspector — a molecular trajectory analysis toolkit

Background Principal component analysis (PCA) is commonly applied to the atomic trajectories of biopolymers to extract essential dynamics that describe biologically relevant motions. Although application of PCA is straightforward, specialized software to facilitate workflows and analysis of molecular dynamics simulation data to fully harness the power of PCA is lacking. The Java Essential Dynamics inspector (JEDi) software is a major upgrade from the previous JED software. Results Employing multi-threading, JEDi features a user-friendly interface to control rapid workflows for interrogating conformational motions of biopolymers at various spatial resolutions and within subregions, including multiple chain proteins. JEDi has options for Cartesian-based coordinates (cPCA) and internal distance pair coordinates (dpPCA) to construct covariance (Q), correlation (R), and partial correlation (P) matrices. Shrinkage and outlier thresholding are implemented for the accurate estimation of covariance. The effect of rare events is quantified using outlier and inlier filters. Applying sparsity thresholds in statistical models identifies latent correlated motions. Within a hierarchical approach, small-scale atomic motion is first calculated with a separate local cPCA calculation per residue to obtain eigenresidues. Then PCA on the eigenresidues yields rapid and accurate description of large-scale motions. Local cPCA on all residue pairs creates a map of all residue-residue dynamical couplings. Additionally, kernel PCA is implemented. JEDi output gives high quality PNG images by default, with options for text files that include aligned coordinates, several metrics that quantify mobility, PCA modes with their eigenvalues, and displacement vector projections onto the top principal modes. JEDi provides PyMol scripts together with PDB files to visualize individual cPCA modes and the essential dynamics occurring within user-selected time scales. Subspace comparisons performed on the most relevant eigenvectors using several statistical metrics quantify similarity/overlap of high dimensional vector spaces. Free energy landscapes are available for both cPCA and dpPCA. Conclusion JEDi is a convenient toolkit that applies best practices in multivariate statistics for comparative studies on the essential dynamics of similar biopolymers. JEDi helps identify functional mechanisms through many integrated tools and visual aids for inspecting and quantifying similarity/differences in mobility and dynamic correlations.