@DMZuckermanLab

Computational biophysicist specializing in statistical mechanics methods applied to a wide range of molecular and cellular systems.

Joined June 2021
  • Tweets83
  • Following58
  • Followers897
1Media
Having trouble visualizing your data from WESTPA? Try WEDAP! A user-friendly plotting package from @darianyang and @ltchong (1/4) pubs.acs.org/doi/10.1021/acs…

WEDAP: A Python Package for Streamlined Plotting of Molecular Simulation Data

Abstract. Given the growing interest in path sampling methods for extending the time scales of molecular dynamics (MD) simulations, there has been great in

pubs.acs.org
1
13
36
2,129
Daniel Zuckerman retweeted
Margaret Johnson@Mejohnson8111 Jul 2024
The Theory and Comp subgroup from Biophysical Society has an early and a mid-career award, apply before August 1! please RT biophysics.org/awards-fundin…
8
12
2,489
Daniel Zuckerman retweeted
Lillian Chong@ltchong2 May 2024
It's finally out! Outstanding work by @atbogetti @mczwier using @WestpaSoftware @ambermdprog
J. Am. Chem. Soc.@J_A_C_S1 May 2024
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 pubs.acs.org/doi/10.1021/jac…

Revisiting Textbook Azide-Clock Reactions: A “Propeller-Crawling” Mechanism Explains Differences in...

Abstract. An ongoing challenge to chemists is the analysis of pathways and kinetics for chemical reactions in solution, including transient structures betw

pubs.acs.org
6
24
3,161
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: nature.com/articles/d41586-0… 1/n
7
7
1
20
2,975
Daniel Zuckerman retweeted
Ilya Levental@LeventalLab26 Mar 2024
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 👇👇👇
13
2
31
5,218
New blog post up, on why @livecomsj matters! livecomsjournal.org/index.ph… We're seeing some conventional journals adopting some of our ideas, so it's worth taking a moment to reflect. #compchem
5
8
1,564
Daniel Zuckerman retweeted
MolSSI@MolSSI_NSF7 Feb 2024
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: forms.gle/6gJF6jJ72iexbDTq8

Registration for WESTPA workshop - CLOSED

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...

docs.google.com
14
38
3,595
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. livecomsjournal.org/index.ph… #compchem
An example network of relative free energy calculations set up with BioSimSpace

ALT An example network of relative free energy calculations set up with BioSimSpace

10
22
2,635
We have a new tutorial out, on absolute binding free energy calculation via a NAMD-based approach, SAFEP. livecomsjournal.org/index.ph…
A thermodynamic cycle for binding free energy calculation

ALT A thermodynamic cycle for binding free energy calculation

27
3
102
8,199
Daniel Zuckerman retweeted
David Mobley@davidlmobley14 Dec 2023
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.
Living Journal of Computational Molecular Science@livecomsj14 Dec 2023
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
File downloads over the last year for LiveCoMS

ALT File downloads over the last year for LiveCoMS

Cumulative abstract and download statistics for some LiveCoMS articles

ALT Cumulative abstract and download statistics for some LiveCoMS articles

Cumulative downloads and abstract views for other LiveCoMS articles

ALT Cumulative downloads and abstract views for other LiveCoMS articles

2
2
1,370
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: livecomsjournal.org/index.ph… Issue: livecomsjournal.org/index.ph… #compchem
A stylized graphic of some atoms and molecules in a molecular system, along with some water.

ALT A stylized graphic of some atoms and molecules in a molecular system, along with some water.

16
1
42
8,673
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: nature.com/articles/s42003-0… by @lyna_yunluo @jungjin

Reliability and reproducibility checklist for molecular dynamics simulations

Communications Biology - We present a checklist to improve the reliability and reproducibility of molecular dynamics simulations and related methods.

nature.com
1
27
1
43
6,513
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: spr.ly/6012MLdae
A group photo from CDCB-KCI interns inside the Knight Cancer Research Building in 2022.

ALT A group photo from CDCB-KCI interns inside the Knight Cancer Research Building in 2022.

5
7
We have a new paper out, on polymer prep and simulation -- "Introduction to in silico synthesis of polymers via PySIMM". This is in our Tutorials category. livecomsjournal.org/index.ph… #compchem
A figure of a schematic representation of part of a polymer

ALT A figure of a schematic representation of part of a polymer

3
10
Phenomenal hands-on paid research opportunity for undergraduates. Join us in beautiful Portland OR
OHSU Knight Cancer Institute@OHSUKnight21 Nov 2022
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: spr.ly/6011MLdtt
A group photo from CDCB-KCI interns inside the Knight Cancer Research Building in 2022.

ALT A group photo from CDCB-KCI interns inside the Knight Cancer Research Building in 2022.

3
1
3
Academy Report Affirms Emergence of Biological Physics academic.oup.com/bioscience/… @EMSLscience @sciencePNNL @ApsDbio #biologicalphysics

Academy Report Affirms Emergence of Biological Physics

On 15 March 2022, William Bialek gave a talk to some 200 people at a business meeting of the American Physical Society's (APS) Division of Biological Physi

academic.oup.com
4
2
14
Came across this yesterday while at Rockefeller, should be required reading for anyone in a PhD or supervising PhDs! @CurrentBiology @betenoire1 Wish I had seen it sooner!
10
117
44
537
Highlighting more @livecomsj editorial board members: George Shields @ProfShields is interested in editing articles from the Predominately Undergraduate Institution (PUI) community. LiveCoMS has training-oriented article categories, making this a good fit. @ChemCUR @MERCURY_NSF
3
4
Daniel Zuckerman retweeted
emekdemir@emekdemir19 Sep 2022
1 year ago CausalPath algorithm, developed by one and only @ozgunbabur received desk rejections from some of the leading systems biology journals. Reason? a thinly veiled - " I think this is gonna hurt our IF" argument. In one year it received 31 citations.
emekdemir@emekdemir14 May 2021
You observe correlations in (phospho)proteomic data--and you often ask: What do we know about these two proteins? Easy for just two--how about hundreds? What if you have time series? You need help. Who you wanna call? CausalPath! A 🧵 👇: @ozgunbabur @JoePlatelet @sandercbio
1
2
18
Working on binding free energy calculations? Interested in preparing calculations, assessing performance, analyzing results, or assessing a study which did so? Check out our new best practices guide! livecomsjournal.org/index.ph… #compchem Thanks to @ppxasjsm , @jchodera and others!
Correlation plots of binding free energy calculations

ALT Correlation plots of binding free energy calculations

1
32
5
146
Load more