lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025PUCHIK means 'balloon' in Armenian, which is home for Hrach and is also a well-suited name for the nanoscale objects that we hope to facilitate the understanding of with this code. 10/10 000
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025The efforts of so many people have resulted in numerous manuscripts being published in close succession. Hrach Ishkhanyan & Alejandro Santana Bonilla did all of the hard work in this case. 9/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025If you wish to listen to a podcast summarising our manuscript, then here is a link: bit.ly/3QcUY2F. 8/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025PUCHIK also assists in linking MD simulation data to experimental data by providing accurate definitions of nanoparticle shapes, which are needed for modelling neutron scattering experiments. The code is freely available here: bit.ly/4hYh7Oi. 7/10bit.lyGitHub - hrachishkhanyan/PUCHIK at alpha_shapesContribute to hrachishkhanyan/PUCHIK development by creating an account on GitHub. 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025PUCHIK is built for computational efficiency using SciPy, MDAnalysis, and Cython, and is designed to be user-friendly and modular. 6/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025PUCHIK can be used to analyse each aggregate separately in simulated systems with multiple nanoparticles. In particle, this software provides accurate descriptions of aspherical nanoparticles, which are poorly characterised by methods employed in our PySoftK software. 5/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025By accurately accounting for the location of the interface of the aggregate, one can also accurately determine the amount of molecular cargo solubilised within the nanoparticles (e.g. small molecule or peptide therapeutic or any other desirable molecular cargo). 4/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025The software enables the calculation of key properties, such as densities of (and therefore the internal structure) the molecules which are found within the nanoparticle and in its local environment, nanoparticle volume and surface area. 3/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025PUCHIK employs both convex hulls and alpha shapes to define the nanoparticle interface, allowing for a detailed representation of solid, hollow, and mesoporous nanoparticles. This is crucial as surface effects are dominant in nanoparticle functionality. 2/10 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 13/02/2025Our latest manuscript to be published introduces PUCHIK (bit.ly/3QeqbT4), a novel & efficient Python package designed for the analysis of molecular dynamics simulations of nanoparticles, w/ a focus on accurately describing the interfaces of aspherical nanoparticles. 1/10 111
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025Thanks to the amazing Alejandro Santana-Bonilla , Rob Ziolek & Raquel López-Ríos de Castro for doing all of the hard work! 7/7 000
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025The code and tutorials can be found via the PySoftK website: bit.ly/3CXXML3 ... If you want to here a podcast summarising the latest in PySoftK then here is a link: bit.ly/3WUJSmT 6/7bit.lyWelcome to PySoftK’s documentation! — PySoftK 1.0.1 documentation 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025PySoftK v1.0 provides an automated approach to investigate interfaces in soft matter systems, interactions that govern structure within soft matter, and soft matter self-assembly, and will help to accelerate the computer-aided design of new materials. 5/7 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025Finally, it has some basic tools for calculating the radius of gyration and eccentricity of self-assembled structures. 4/7 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025Also there is a tool that correctly accounts for periodic boundary conditions when analysing self-assembled structures, even if these structures are larger than 1/2 of the simulation box (this is not possible with any other tool & allows accurate analyses of these structures) 3/7 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025The software now includes tools that can quantify the self-assembly of molecules, analyse the interfaces of nanoparticles (spherical & sphere-like), investigate molecular interactions like ring stacking, solvation and intermolecular contacts. 2/7 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 11/02/2025Our latest manuscript presents the most recent tools available in the PySoftK software package (bit.ly/4jQps8i). PySoftK now helps scientists analyse molecular simulations of soft materials, w/ tools for analysing interfaces, molecular interactions, & self-assembly 1/7bit.lyAutomated Analysis of Soft Matter Interfaces, Interactions, and Self-Assembly with PySoftKMolecular dynamics simulations have become essential tools in the study of soft matter and biological macromolecules. The large amount of high-dimensional data associated with such simulations does n... 111
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 10/02/2025This is another nice manuscript which has resulted from my continued collaboration with Max Ryadnov (NPL) & Bart Hoogenboom (@ucl.ac.uk). If you are interested in listening to a podcast summarising the paper then here you go: bit.ly/41aueGv 3/3 000
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 10/02/2025This process, which we observed using advanced imaging and molecular dynamics simulations, is similar to how some other antimicrobial agents work and offers a potential new approach to fighting drug-resistant bacteria. 2/3 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 10/02/2025Our latest manuscript has been published in Langmuir: bit.ly/4hMNBuy. In this manuscript we show that thanatin, a naturally occurring antimicrobial peptide, punches holes & disrupts bacterial membranes through multiple mechanisms, causing them to break apart 1/3 111
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 29/01/2025@kingsnmes.bsky.social @kingslsm.bsky.social 000
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 29/01/2025I generated a NotebookLM podcast summarising the paper, to listen - here is a link: bit.ly/3PWshqy. This was a great collaboration w/ Anabella Gaspar & Megan Bester from Pretoria & @profjamesmason.bsky.social w/ Rosalind Van Wyk doing all the hard work & Miruna Serian supporting on the MD. 100
lorenzlab1.bsky.social @lorenzlab1.bsky.social · 29/01/2025Our latest manuscript is now available in Biochemistry @acs.org (bit.ly/3Ct1PSm) In it we show that C-terminal amidation of an antimicrobial peptide increases its conformational flexibility, which improves membrane penetration, leads to faster bacterial killing & better selectivity for pathogens. 174
