Evaluating The Friction Of Rotary Joints In Molecular Machines

Howard Lovy’s name came across my calendar (happy birthday!) and Josh Hall published a fresh post to “Where is my Flying Car?” – seems like a perfect time to post an everything-new-is-still-new-for-the-first-time-type update.

Published way back in 2017 in Molecular Systems Design & Engineering; reportedly one of the most-read Q3 2017 articles to boot. Also my first foray into arxiv territory for those limited in their journal access (arxiv.org/abs/1701.08202).

Tad Hogg*a Matthew S. Moses*b and Damian G. Allis*c

a. Institute for Molecular Manufacturing, Palo Alto, USA
b. Independent Consultant, Lafayette, USA
c. Department of Chemistry, Syracuse University, Syracuse, USA

Abstract: A computationally-efficient method for evaluating friction in molecular rotary bearings is presented. This method estimates drag from fluctuations in molecular dynamics simulations via the fluctuation–dissipation theorem. This is effective even for simulation times short compared to a bearing’s energy damping time and for rotation speeds comparable to or below typical thermal values. We apply this method to two molecular rotary bearings of similar size at 300 K: previously studied nested (9,9)/(14,14) double-walled carbon nanotubes and a hypothetical rotary joint consisting of single acetylenic bonds in a rigid diamondoid housing. The acetylenic joint has a rotational frictional drag coefficient of 2 × 10^-35 kg m2 s^-1. The friction for the nested nanotubes is 120 times larger, comparable to values reported by previous studies. This fluctuation-based method could evaluate dissipation in a variety of molecular systems with similarly rigid and symmetric bearings.

Mol. Syst. Des. Eng., 2017, 2, 235-252 (10.1039/C7ME00021A, direct link)

Free Astronomy Magazine – September-October 2018 Issue Available For Reading And Download

Above: ESA’s Mars Express has used radar signals bounced through underground layers of ice to identify a pond of water buried below the surface. This image shows an example radar profile for one of 29 orbits over the 200 x 200 km study region in the south polar region of Mars. The bright horizontal feature at the top corresponds to the icy surface of Mars. Layers of the south polar layered deposits – layers of ice and dust – are seen to a depth of about 1.5 km. Below is a base layer that in some areas is even much brighter than the surface reflections, while in other places is rather diffuse. The brightest reflections from the base layer – close to the centre of this image – are centred around 193°E/81°S in all intersecting orbits, outlining a well-defined, 20 km wide subsurface anomaly that is interpreted as a pond of liquid water. Image Credit: ESA/NASA/JPL/ASI/Univ. Rome; R. Orosei et al 2018.

The September-October issue of Free Astronomy Magazine has been up for a few weeks now and I hope you were already aware of that from the CNY Observers post about the same.

I’m also pleased to report a promotion from contributing translator to contributing author this month with the publication of the cover story “A Possible Subglacial Lake On Mars.” For the local record, a PDF of the article (with cover and edition TOC) is available for direct download at 5FAM2018_dgallis.pdf and I can now say that my work has been published in over three languages (four, to be exact, including English, Spanish, French, and Italian).

Please download, read, and pass along. Also, check out the many back issues at www.astropublishing.com

astropublishing.com/5FAM2018/ | Direct PDF

Click the Table of Contents image below for a full-size view.

Conversion Of DFTB Parameter Sets From dftb.org For Use In Gaussian 09 And Gaussian 16 – Errors And Fixes

Addressing the conversion of the 3ob-3-1, matsci-0-3, mio-1-1, and pbc-0-3 parameter sets (with fixes transferable to others).

While there is some information available online about converting dftb.org Slater-Koster (.skf) files for use in Gaussian 09/16, the simple procedures you might see for set A might not work for set B because of subtle formatting issues between the different sets.

As is often the case, some of the issues below would not have been confirmed/remedied without the kind assistance of feedback from Gaussian Technical Support. Also as usual for this site, error messages are provided for each stage of the conversion process for relevant parameter sets, with the searches for these errors likely being the way you found this page in the first place.

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