Daniel Zuckerman
@DMZuckermanLab
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Computational biophysicist specializing in statistical mechanics methods applied to a wide range of molecular and cellular systems.
Joined June 2021
Having trouble visualizing your data from WESTPA? Try WEDAP! A user-friendly plotting package from @darianyang and @ltchong (1/4) https://t.co/yofj2KDidD
pubs.acs.org
Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great interest in software tools that streamline the generat...
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The Theory and Comp subgroup from Biophysical Society has an early and a mid-career award, apply before August 1! please RT https://t.co/6VSGln7CvG
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Bayesian inference is vital to interpreting experimental data. Learn the relationship of BI to statistical mechanics including important nuances, and get a ‘sampling’ of modern Monte Carlo methods for BI. https://t.co/NxP49PiDxi
pubs.acs.org
On the one hand, much of computational chemistry is concerned with “bottom-up” calculations which elucidate observable behavior starting from exact or approximated physical laws, a paradigm exempli...
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Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in Rates | Journal of the American Chemical Society @ltchong @PittChem @PittTweet #Azide #Clock #PropellerCrawling #Mechanism #Rates
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A recent news article in Nature described increasing numbers of editors mass resigning from for-profit journals, a symptom of misalignment of incentives between publishers’ demand for growth and profits, and the academics’ priority of quality, depth: https://t.co/2k6Mn7HHLg 1/n
nature.com
Nature - Editorial rebellions seem to be on the rise, as researchers seek more control over scholarly communication.
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Awesome postdoc position alert!! Despite, or because of, being Twitter-less, Ed Lyman is a great mentor, scientist, and human being. Interested in membrane proteins, simulations, machine learning, physics, evolution, bioinformatics?? Apply! Check out below 👇👇👇
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New blog post up, on why @livecomsj matters! https://t.co/haW797tELF We're seeing some conventional journals adopting some of our ideas, so it's worth taking a moment to reflect. #compchem
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Nonequilibrium physics rules the world. Here are eight chapters introducing key aspects of nonequilibrium biophysics illustrated with simple examples. https://t.co/ICZQ4u4ZI9
osf.io
An online book consisting of linked preprint chapters, added and updated as they are available. The book covers the essentials of nonequilibrium science with a special focus on biochemical and...
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Register now for the free WESTPA Workshop @Pitt_Chemistry, June 20-21. Explore rare event simulations like protein folding, ligand binding, & chemical reactions with our open-source software. Perfect for those using AMBER, NAMD, GROMACS, etc. Reg info: https://t.co/JeQwUMDAIq
docs.google.com
Please join us for this year's WESTPA workshop at the University of Pittsburgh, June 20-21, 2024. We will be celebrating the 10th anniversary of WESTPA! WESTPA is an open-source, highly-scalable...
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And we also have a new suite of tutorials for getting started with the BioSimSpace framework for interoperable biomolecular simulations; this comes with a big set of example notebooks. https://t.co/bQPCZ91s3X
#compchem
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We have a new tutorial out, on absolute binding free energy calculation via a NAMD-based approach, SAFEP. https://t.co/ltVkg8H3bQ
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Possibly of interest to folks in the chemistry publishing/open access area. Does anyone know how download numbers for more traditional journals compare? Personally I haven't seen these types of stats except for preprints, where these seem to compare favorably, but I'm curious.
LiveCoMS article views & downloads are trending up! Here are some stats we just noticed, including total downloads per article. To us, these look like encouraging numbers! #compchem
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Nominate an outstanding early or mid-career scientist for an award from the Theory & Computation subgroup of the @BiophysicalSoc . https://t.co/rqTq89OiEb
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Great opportunity to expand your skillset and impact!
Looking to do an exciting postdoctoral fellowship in the beautiful Pacific NorthWest? Accepting applications now. Research Training Program: T32 in Integrated Training in Quantitative and Experimental Cancer Systems Biology (ICSB) | OHSU
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We have a new issue out! This includes our first "version 2" article, an updated and expanded article dealing with a new version of the WESTPA enhanced sampling package: https://t.co/7xUaQs8a4p Issue: https://t.co/gBvRY7BiC0
#compchem
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Statistical mechanics - equil and noneq - can enhance sampling and data analysis. Microscopic mechanisms can be inferred from simple experimental data. Learn how, in one of the most beautiful parts of the world. Postdoc/student, email your suitable background, project ideas.
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Important effort here. How can trainees avoid common (and less common) mistakes?
Have you ever been through a long and meticulous scientific effort to generate a piece of data and been disappointed about its fate of being under-appreciated/otherwise unpublishable? @SJFan48552412, @tugbaoztrk, and I came together to launch the Learning Curve Initiative (LCI)!
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Our editorial on MD simulations presents a checklist for reporting and assessing simulation data and data #reproducibility as a guideline for publishing high quality computational work in the journal: https://t.co/eJomB7u8EJ by @lyna_yunluo @jungjin
nature.com
Communications Biology - We present a checklist to improve the reliability and reproducibility of molecular dynamics simulations and related methods.
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The Cell, Developmental & Cancer Biology Summer Research Internship at @OHSUKnight is an opportunity for undergraduates to immerse themselves in research with @OHSUKnight faculty. Learn more and apply to join us today: https://t.co/vVkprksFM5
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OHSU has a great post-bac program for PEERs - "Persons Excluded because of their Ethnicity or Race". One year of paid, mentored research! Please spread the word to folks who might benefit. https://t.co/yj4KrfjXzv
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