Logan Thrasher Collins

CTO at Conduit, synthetic biologist, science fiction author, and PhD candidate in biomedical engineering
https://logancollinsblog.com/
 Esther Kim  Hi Esther! Yes, I'm here 🙂 
It seems that we share a passion for synthetic biology! I think we already know each other from FB?
That's great! I've followed some of the Bathe lab's work and it looks really exciting. I have not worked in DNA origami directly, but I'd like to get involved at some point, especially in manufacturing strategies. Your work sounds exceptionally interesting and I want to hear more! 

My background is in synthetic biology. Currently, I'm doing gene therapy research in the Curiel lab at Washington University in St. Louis. I am also the CTO at a startup where I am leading a computational project on COVID-19. I have strong interests in nanobiotechnology and in biomanufacturing as well. 

I'd love to connect and chat about research!
 Bradley William English  Hi, glad to hear that you enjoyed my website! 

I certainly agree that it is importantly to target aging as the root cause of other diseases and to increase human healthspan in general. 

As to specific approaches for aging research, I'm really excited about spatial -omics technologies. Spatial transcriptomics, imaging mass spectrometry, mapping of 3d chromatin organization, etc. I think that these technologies (in combination with machine learning for extracting insights) have huge potential for mining sufficient data and knowledge to construct reasonably predictive models of complex biological phenomena. This will be important for developing treatments that can mitigate the aging process.

I'm also really excited about how next-generation gene therapies will allow for genetic and epigenetic perturbations which mitigate aging. (One of my own areas of research is in combining synthetic biology with gene therapy, so this area is near and dear to me).
Hi Aoi! That depends on the area of computational biology you would like to explore. 

For an introduction to protein biophysics, I would recommend the book "Protein Actions Principles and Modeling", which is available on libgen here: https://libgen.is/book/index.php?md5=52E0B9AF0D28A83F051C33E832048019

Of potential interest is that I made some notes on a few sections of the Protein Actions book: https://logancollinsblog.com/2020/07/26/introduction-to-the-physical-chemistry-of-protein-folding/

For molecular dynamics, I would recommend trying to install GROMACS and then going through some of these tutorials: http://www.mdtutorials.com/gmx/
You also will want to install VMD (Visual Molecular Dynamics, an excellent GUI and visualizer for computational biology in general) and play with it:
https://www.ks.uiuc.edu/Research/vmd/

For computational neuroscience, I would recommend installing the Python version of NEURON and playing around with coding some simple models of neurons and networks. I would also recommend taking a look at the free textbook and lectures on this website: https://neuronaldynamics.epfl.ch/

For general biology learning, here is a list of textbooks to browse: https://logancollinsblog.com/2020/11/27/want-to-learn-biology-recommended-texts-from-beginner-to-advanced/

You might also be interested in trying to figure out the Rosetta suite from the Baker lab. I've wanted to explore that myself, but I've had some difficulties with installation. Please do let me know if you find a good route :)