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Molecular dynamics simulations play an increasingly important role in the rational design of (nano)-materials and in the study of biomacromolecules. However, generating input files and realistic starting coordinates for these simulations is a major bottleneck, especially for high throughput protocols and for complex multi-component systems. To eliminate this bottleneck, we present the polyply software suite that leverages 1) a multi-scale graph matching algorithm designed to generate parameters quickly and for arbitrarily complex polymeric topologies, and 2) a generic multi-scale random walk protocol capable of setting up complex systems efficiently and independent of the target force-field or model resolution. We benchmark quality and performance of the approach by creating melt simulations of six different polymers using two force-fields with different resolution. We further demonstrate the power of our approach by setting up a multi lamellar microphase-separated block copolymer system for next generation batteries, and by generating a liquid-liquid phase separated polyethylene oxide-dextran system inside a lipid vesicle, featuring both branching and molecular weight distribution of the dextran component.
The MechElastic Python package evaluates the mechanical and elastic properties of bulk and 2D materials using the elastic coefficient matrix ($C_{ij}$) obtained from any ab-initio density-functional theory (DFT) code. The current version of this pack
Qudi is a general, modular, multi-operating system suite written in Python 3 for controlling laboratory experiments. It provides a structured environment by separating functionality into hardware abstraction, experiment logic and user interface layer
The development of science-based categorization strategies for regulatory purposes is not a simple task. It requires understanding the needs and capacity of a wide variety of stakeholders and should consider the potential risks and unintended consequ
Metal nano-aerogels combine a large surface area, a high structural stability, and a high catalytic activity towards a variety of chemical reactions. The performance of such nanostructures is underpinned by the atomic-level distribution of their cons
Structural heterogeneity of amorphous solids present difficult challenges that stymie the prediction of plastic events, which are intimately connected to their mechanical behavior. Based on a perturbation analysis of the potential energy landscape, w