Xinqiang Ding

Assistant Professor of Chemistry, Tufts University

[Xinqiang Ding @xinqiang_ding]

Delighted to share our new work: "Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles". https://t.co/qjokbPszEo

[Xinqiang Ding @xinqiang_ding]

@PaulRobustelli Congratulations! An ideal paper for our lab's journal club, because we could directly ask the first author all our questions.

[Yu-Shan Lin @Yu_Shan_Lin]

Dept of Chem at @TuftsUniversity  is hiring a TT faculty member at the rank of Assoc Prof, or at the rank of Assist Prof w/ a clear potential for promotion to Assoc Prof in <3 yrs, in any area of chemistry related to human health! https://t.co/L0ylhI8ovv

[Xinqiang Ding @xinqiang_ding]

It is based on the BayesMBAR method we developed recently. The Bayesian framework used in BayesMBAR allows us to naturally couple multiple BayesMBAR calculations using cycles in a perturbation graph. It uses the cycle information to provides more accurate free energy estimates.

[Xinqiang Ding @xinqiang_ding]

Delighted to share our new work: "Principled Approach for Computing Free Energy on Perturbation Graphs with Cycles". https://t.co/qjokbPszEo

[Xinqiang Ding @xinqiang_ding]

It is now published on JPCB. https://t.co/m7wx9SqZqM

[Xinqiang Ding @xinqiang_ding]

Excited to share a new manuscript: "Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting". Here we optimize force fields to match experiments by matching reweighted ensembles. https://t.co/5X7irEKgcD

[Rosana Collepardo @rcollepardo]

We are hiring postdocs at @Cambridge_Uni

Join our diverse and inclusive team and help us understand chromatin phase transitions with multiscale simulations: https://t.co/8N0Hfdu6dA

Friends please RT! Sorry if I've missed your posts, haven't been using X

[Xinqiang Ding @xinqiang_ding]

@clarkkd25 Congratulations, Kevin!

[Xinqiang Ding @xinqiang_ding]

Excited to share a new manuscript: "Optimizing Force Fields with Experimental Data Using Ensemble Reweighting and Potential Contrasting". Here we optimize force fields to match experiments by matching reweighted ensembles. https://t.co/5X7irEKgcD

[Alberto Perez @Al__Perez]

we are looking for a #compchem postdoc to work on an NIH funded project to characterize BET proteins, the complexes it forms, and identifying new viral and host PPIs. Someone with expertise in MD, python, ML, and a passion to solve biological puzzles is a great fit! Pls RT

[Michael J. Robertson @BiophysicsGuy]

We’re hiring postdocs and a lab tech! Experimental & computational people welcome; come learn about GPCRs, cryoEM, MD/FEP, drug discovery, method development and more! Feel free to DM me for more info.
https://t.co/Um99mQKvZ5 https://t.co/RywVLPE24H

Please RT!

[Xinqiang Ding @xinqiang_ding]

To solve the BayesMBAR model and automatically optimize hyperparameters, we employed several computational techniques including variational inference, the reparameterization trick and the NUTS sampler. The code is here https://t.co/7NSXVK4FRo. More docs and examples will follow.

[Xinqiang Ding @xinqiang_ding]

The BayesMBAR paper is published on @JCIM_JCTC. It is a Bayesian generalization of the MBAR method for computing free energy. It offers (1) better uncertainty estimate and (2) the ability to incorporate prior knowledge to improve free energy estimate. https://t.co/gM6OnSf1ab

[Xinqiang Ding @xinqiang_ding]

I am excited to share the first manuscript from the Ding lab: "Bayesian Multistate Bennett Acceptance Ratio Methods". For those who know MBAR, the title says it all. https://t.co/EjmpcWJ2Di

[Xinqiang Ding @xinqiang_ding]

For example, we show that it can use the prior knowledge that the free energy surface over a collective variable is smooth to improve free energy estimates.

[Xinqiang Ding @xinqiang_ding]

@tiwarylab My lab is actively looking for postdocs. Please let Ziyue reach out to me if he is interested.

[Bin Zhang @binzmit]

Our paper just appeared online at ACS Cen Sci! Really impressed with the journal's efficiency. https://t.co/DB7jas9803

[Xinqiang Ding @xinqiang_ding]

@WeiTseHsu @Michael_Shirts @aichecomsef Congratulations!

[Xinqiang Ding @xinqiang_ding]

@tiwarylab @JCIM_JCTC Thanks! Absolutely, I like the journal a lot!