Puerto Rico
A trip to Puerto Rico
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Posts by Collection
hobbies
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Mountain Lyfayette
Hiking to the Mountain 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 virus S (spike) protein
which mutations can enhance the affinity to the cell receptor and thus present challenges for vaccine and antibody development? 
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TMEM16F: an ion channel can scramble lipids
How can an ion channel transport lipid through the membrane bilayer? 
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TRPV4: a thermosensitive non-selective cation channel
Which domain is the thermo-sensor of TRPV4? What is the mechanism behind the thermo-sensitivity of TRPV4? 
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Al-powered modeling for generative ensembles
How do we generate conformational ensembles of proteins using generative Al models 
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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
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 STRIED 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
Machine Learning basis
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