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Jan Jensen
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Reviews of Solvation Energy Predictions Using The SMD Solvation Method and Semiempirical Electronic Structure Methods" Journal of Chemical Physics
Really late posting this. The paper is already in press. Here are the reviews for the record. Reviewer #1 Evaluations: Recommendation: Revision New Potential Energy Surface: No Reviewer #1 (Comments to the Author): In this contribution, the authors report a...
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Computational Chemistry Highlight: August issue
The August issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it i...
Computational Chemistry Highlight: August issue
Computational Chemistry Highlight: August issue
molecularmodelingbasics.blogspot.com
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Assigning bond orders
This last week I've been working off and on changing the way xyz2mol.py assigns bond orders. xyx2mol is an implementation of this paper and works by first assigning connectivity and then increasing the bond order between atoms with unsatisfied valences. As ...
Assigning bond orders
Assigning bond orders
proteinsandwavefunctions.blogspot.com
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A Density Functional Tight Binding Layer for Deep Learning of Chemical Hamiltonians
Haichen Li, Christopher Collins, Matteus Tanha, Geoffrey J. Gordon, David J. Yaron (2018) Highlighted by Jan Jensen There are increasingly many papers on predicting the molecular energy and other properties using machine learning (ML). Most, if not all, use...
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Dealing with nitrogen inversion and racemic mixtures in conformational searches
If you restrict conformational search to rotateable bonds you won't sample three areas of conformational space: ring conformations, unassigned chiral centers, and nitrogen inversion. Here I address the two latter issues. Some molecules are made as racemic m...
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Comparison of genetic algorithm and Monte Carlo tree search for logP optimisation
What have I done? 1. Inspired by this and this study I have implemented graph-based crossover and mutation algorithms and hooked then up to a basic genetic algorithm (GA). "Graph-based" means I'm modifying the molecules by changing/adding atoms and bonds (u...
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Computational Chemistry Highlight: July issue
The July issue of  Computational Chemistry Highlights  is out. CCH is an  overlay journal  that identifies the most important papers in computational and theoretical chemistry published in the last 1-2 years. CCH is not affiliated with any publisher: it is ...
Computational Chemistry Highlight: July issue
Computational Chemistry Highlight: July issue
molecularmodelingbasics.blogspot.com
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Error-Controlled Exploration of Chemical Reaction Networks with Gaussian Processes
Gregor N. Simm and Markus Reiher (2018) Highlighted by  Jan Jensen See if you recognise this scenario: you benchmark a cheap method against an accurate, but expensive, method for a set of molecules and get a mean error that you can use to correct the result...
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Making random molecules one atom at a time
I'm trying to make my own version of  ChemTS , which uses a recurrent neural network to generate molecules (SMILES string) and Monte Carlo tree search to optimise their properties. This post is about some very recent preliminary (i.e. possibly wrong ) resul...
Making random molecules one atom at a time
Making random molecules one atom at a time
proteinsandwavefunctions.blogspot.com
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Comparing a Monte Carlo tree search and a genetic algorithm for conformational search
I've been playing around with this Monte Carlo tree search (MCTS) code  (if you need a short intro to MCTS click here ). I want to learn how to use MCTS to optimise molecular properties so to get started I modified the code to minimise a very simple energy ...
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