TeachOpenCADD: a teaching platform for computer-aided drug design using open source packages and data

Owing to the increase in freely available software and data for cheminformatics and structural bioinformatics, research for computer-aided drug design (CADD) is more and more built on modular, reproducible, and easy-to-share pipelines. While documentation for such tools is available, there are only a few freely accessible examples that teach the underlying concepts focused on CADD, especially addressing users new to the field. Here, we present TeachOpenCADD, a teaching platform developed by students for students, using open source compound and protein data as well as basic and CADD-related Python packages. We provide interactive Jupyter notebooks for central CADD topics, integrating theoretical background and practical code. TeachOpenCADD is freely available on GitHub: https://github.com/volkamerlab/TeachOpenCAD

Probing Ultrafast Dynamics with Time-resolved Multi-dimensional Coincidence Imaging: Butadiene

Time-resolved coincidence imaging of photoelectrons and photoions represents the most complete experimental measurement of ultrafast excited state dynamics, a multi-dimensional measurement for a multi-dimensional problem. Here we present the experimental data from recent coincidence imaging experiments, undertaken with the aim of gaining insight into the complex ultrafast excited-state dynamics of 1,3-butadiene initiated by absorption of 200 nm light. We discuss photoion and photoelectron mappings of increasing dimensionality, and focus particularly on the time-resolved photoelectron angular distributions (TRPADs), expected to be a sensitive probe of the electronic evolution of the excited state and to provide significant information beyond the time-resolved photoelectron spectrum (TRPES). Complex temporal behaviour is observed in the TRPADs, revealing their sensitivity to the dynamics while also emphasising the difficulty of interpretation of these complex observables. From the experimental data some details of the wavepacket dynamics are discerned relatively directly, and we make some tentative comparisons with existing ab initio calculations in order to gain deeper insight into the experimental measurements; finally, we sketch out some considerations for taking this comparison further in order to bridge the gap between experiment and theory.Comment: 18 pages, 10 figures. Pre-print of JMO submissio

Archaeology and virtual acoustics. A pan flute from ancient Egypt

This paper presents the early developments of a recently started research project, aimed at studying from a multidisciplinary perspective an exceptionally well preserved ancient pan flute. A brief discussion of the history and iconography of pan flutes is provided, with a focus on Classical Greece. Then a set of non-invasive analyses are presented, which are based on 3D scanning andmaterials chemistry, and are the starting point to inspect the geometry, construction, age and geographical origin of the instrument. Based on the available measurements, a preliminary analysis of the instrument tuning is provided, which is also informed with elements of theory of ancient Greek music. Finally, the paper presents current work aimed at realizing an interactive museum installation that recreates a virtual flute and allows intuitive access to all these research facets

A bibliometric analysis of the Journal of Molecular Graphics and Modelling

This paper reviews the articles published in Volumes 2-24 of the Journal of Molecular Graphics and Modelling (formerly the Journal of Molecular Graphics), focusing on the changes that have occurred in the subject over the years, and on the most productive and most cited authors and institutions. The most cited papers are those describing systems or algorithms, but the proportion of these types of article is decreasing as more applications of molecular graphics and molecular modelling are reported

Stratospheric General Circulation with Chemistry Model (SGCCM)

In the past two years constituent transport and chemistry experiments have been performed using both simple single constituent models and more complex reservoir species models. Winds for these experiments have been taken from the data assimilation effort, Stratospheric Data Analysis System (STRATAN)