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Studying Molecular mechanisms of protein functions using MD simulations
What is MD and why it is powerful to study protein structure-function relationship? Read more
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About me Read more
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Successfully Defended My Doctoral Thesis
After spending five years or so doing computational biophysics research in Prof. Jianhan Chen's lab, I have successfully completed my PhD dissertation defense and officially become a PhD in computational biophysics. 
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Won the 2nd place research presentation in the 2024 annual Chemistry ResearchFest event
After finishing my 3-month internship at Merck, I attended the annual ResearchFest event held by the Chemistry department of UMass Amherst. I was selected as one of four presenters in this event to represent research in the department. I won the second place for the presentation and was awarded the Dr. Paul Hatheway Terry Endowment Award as first-runner up 
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Published Paper: Targeting TRP Channels: Recent Advances in Structure, Ligand Binding and Molecular Mechanisms
In this short review, we summarize recent progresses toward understanding the structural basis of TRP channel function, as well as potential ligand binding sites that could be targeted for therapeutics. 
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Published Paper: Hydrophobic gating in bundle crossing channels
Transmembrane ion channels frequently regulate ion permeation by forming bundle crossing of the pore-lining helices when deactivated. The resulting physical constriction is believed to serve as the de facto gate that imposes the major free energy barrier to ion permeation. Intriguingly, many ion channels also contain highly hydrophobic inner pores enclosed by bundle crossing, which can undergo spontaneous dewetting and give rise to a “vapor barrier” to block ion flow even in the absence of physical constriction. Using atomistic simulations, we show that hydrophobic gating and bundle-crossing mechanisms co-exist and complement one another in the human TRPV4 channel. In particular, a single hydrophilic mutation in the lower pore can increase pore hydration and reduce the ion permeation free energy barrier by about half without affecting the bundle crossing. We believe that hydrophobic gating may play a key role in other bundle-crossing ion channels with hydrophobic inner pores. 
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Jian passed ORP exam and is now a Ph.D candidate!
The original research proposal (ORP) is an exam designed to test the ability of graduate students to identify significant scientific questions, to develop research proposals based on rationalized and well-reasoned hypotheses, and, most importantly, to successfully defend the proposal. 
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Received CBI Fellowship
CBI program (Chemistry-Biology Interface) is a highly competitive UMass-funded and NIH-funded fellowship, aiming to train students from different backgrounds to advance scientific research “at the interface of chemistry and biology”. 
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Presenting in the Poster Session of the 2022 BPS Annual Meeting
The Biophysical Society (BPS) annual meeting is held by the international biophysics society, aiming at leading, disseminating, and advancing knowledge in biophysics. 
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Jian’s arrival at U.S.
After a year-long remote study in China, I finally arrived in the U.S. and met with Chen lab members! 
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hobbies
Puerto Rico
A trip to Puerto Rico
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Mount Lafayette
Hiking to the Mount Lafayette with friends from UMass Amherst.
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Riverview Hiking
Hiking to the Northfield Mountain Reservoir with a friend.
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publications
Paper Title Number 1
This paper is about the number 1. The number 2 is left for future work. Read more
Recommended citation: Your Name, You. (2009). "Paper Title Number 1." Journal 1. 1(1). http://academicpages.github.io/files/paper1.pdf
Paper Title Number 2
This paper is about the number 2. The number 3 is left for future work. Read more
Recommended citation: Your Name, You. (2010). "Paper Title Number 2." Journal 1. 1(2). http://academicpages.github.io/files/paper2.pdf
Paper Title Number 3
This paper is about the number 3. The number 4 is left for future work. Read more
Recommended citation: Your Name, You. (2015). "Paper Title Number 3." Journal 1. 1(3). http://academicpages.github.io/files/paper3.pdf
research
Prediction of infectivity-enhancing mutations of the SARS-CoV-2 spike protein
In silico affinity maturation identifies single point mutations on the SARS-CoV-2 RBD that can enhance binding to the hACE2 receptor, with 6 out of 9 predictions confirmed by SPR assay. 
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TMEM16F: Activation Mechanism and Dual Ion/Lipid Permeation Pathways
How does TMEM16F open its pore to conduct both ions and lipids? 
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AI-powered modeling for generative ensembles
How do we generate conformational ensembles of proteins using generative AI models? 
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TRPV4: Gating Mechanisms and Lipid Regulation
Dissecting hydrophobic gating and PIP2-mediated regulation in the TRPV4 ion channel using atomistic simulations. 
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Dynamic Domain Interactions Encode CheA Autophosphorylation Mechanisms
Coarse-grained simulations reveal how the phosphorylatable P1 domain docks onto the kinase P4 domain in multiple productive and nonproductive modes to regulate CheA autophosphorylation. 
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Physics-Informed Deep Learning for Protein Variant Effect Prediction
Incorporating biophysical features into deep learning overcomes extrapolation failures in protein sequence-function modeling. 
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resources
Contact analysis
Contact frequency analysis and visualization for MD simulation trajectories Read more
Secondary structure analysis using DSSP
use the STRIDE algorithm to assign helix, sheet and coil to protein structures or trajectories Read more
Secondary structure analysis using STRIDE in VMD
use the STRIDE algorithm to assign helix, sheet and coil to protein structures or trajectories Read more
Intrinsically disordered protein trajectory analysis
This is a short tutorial of analyzing IDP (intrinsically disordered protein) trajectories. Prerequisites are the psf file (structural file) of your IDP system and the corresponding xtc (trajectory file). Read more
Important VMD tricks
In this article, I want to include some VMD tricks based on my personal experience. VMD provides an official documentation, which can be found here: VMD-documentation. Readers are suggested to refer to the VMD User’s Guide for more detailed information. Read more
Markov State Models for biomolecule conformational transitions sampled from MD
MD simulations allow us to characterize protein structure, dynamics and function in the all-atom and femto-second spatiotemporal resolution. However, interpreting data of high dimensionality, such as MD, to infer the inherent transitions between different metastable conformational states, can be tricky. Markov state model (MSM) provides a generally accepted, state-of-the-art dynamics analysis method. Read more
Machine Learning Basics
Contact frequency analysis and visualization for MD simulation trajectories Read more
Matplotlib practices
Obsidian Practices
Conda environment settings
This is a tutorial to:
- download and install conda – the environment and package management tool
- build a conda environment for computational biophysicist
Quick Gnuplot tricks
Define your own line style
# example
set style line 1 lc rgb "#8b0000" lw 2
set style line 2 lc -1 pt 7 ps 0.9