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Dancing DNA Revealed in High-Res HPC Simulations

Using the highest-resolution images of a single DNA molecule captured to date, researchers in the U.K. discovered that coiled strands of genetic material twist and writhe while crammed in a cell.

Using the highest-resolution images of a single DNA molecule captured to date, researchers in the U.K. discovered that coiled strands of genetic material twist and writhe while crammed in a cell.

This previously unobserved movement was simulated on GPU-based systems including JADE, a University of Oxford supercomputer made up of NVIDIA DGX systems. Published in Nature Communications, this research could improve scientists’ understanding of DNA mechanics and inform the development of genetic therapies and diagnostics. 

“GPUs have massively changed the capabilities of biomolecular simulation,” said Sarah Harris, associate professor at the University of Leeds and a researcher on the project, a collaboration among multiple universities. 

By pairing high-resolution atomic force microscopy with HPC simulations, the team created the first videos of twisted DNA molecules called minicircles — where both ends of the molecule join together in a loop. Prior research suggests these minicircles might be markers of health, ageing, and disease. 

Using the GPU-accelerated AMBER package, the researchers were able to model DNA structure with state-of-the-art force fields based on highly accurate quantum mechanical simulations. The dynamics of the molecular simulations were visualized with VMD, which was also used to confirm the presence of hydrogen bonding interactions in the coiled DNA structure.

Adding a twist to a strand of DNA, the researchers found, made the molecules more dynamic, displaying dance-like moves that might help the DNA bind to other molecules. 

The minicircle simulations “are extremely exciting because they show, with remarkable detail, how wrinkled, bubbled, kinked, denatured, and strangely shaped they are, which we hope to be able to control someday,” said Professor Lynn Zechiedrich from Baylor College of Medicine, who provided the DNA minicircles for the study.  

The combination of microscopy images and simulation enabled the researchers to see not just the DNA’s double-helix structure, but the position of each atom within the loop, which contains between 250 and 340 base pairs. 

Read the full Nature Communications paper here

Categories
Misc

Model within a model?

How can I take two feature vectors as outputs from two inputs, store them, and compare a feature vector from a third input to the first feature vectors within one model? End result is dataset C is 80% similar to dataset A 20% to dataset B, etc.

submitted by /u/BestUCanIsGoodEnough
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Misc

Why my Model has a low MAE and low R2 score at the same time?

https://stackoverflow.com/questions/66363862/why-my-model-has-a-low-mae-and-low-r2-score-at-the-same-time

submitted by /u/notm3llo
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Misc

Help with debugging

Help with debugging
submitted by /u/iWatchBlack
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Misc

New TensorBoard Integration in VS Code

New TensorBoard Integration in VS Code

In the latest update of VS Code last week, they added support for TensorBoard integration in VS Code. Just wanted to share with everyone!

https://preview.redd.it/lg64jrhqhij61.png?width=2556&format=png&auto=webp&s=1afe8944a278356a3eafbc98039424b62069c505

To launch tensorboard, just open the command palette in VS Code and search for the command “Launch TensorBoard”

https://preview.redd.it/g96z1lxxhij61.png?width=1064&format=png&auto=webp&s=cc1f0bc16bd9141796e88b6fea4878141bbe74c2

It looks like VS Code will automatically look for your TensorBoard log files within your directory.

submitted by /u/evilcubed
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Categories
Misc

Help with debugging

Help with debugging
submitted by /u/iWatchBlack
[visit reddit] [comments]
Categories
Misc

New TensorBoard Integration in VS Code

New TensorBoard Integration in VS Code

In the latest update of VS Code last week, they added support for TensorBoard integration in VS Code. Just wanted to share with everyone!

https://preview.redd.it/lg64jrhqhij61.png?width=2556&format=png&auto=webp&s=1afe8944a278356a3eafbc98039424b62069c505

To launch tensorboard, just open the command palette in VS Code and search for the command “Launch TensorBoard”

https://preview.redd.it/g96z1lxxhij61.png?width=1064&format=png&auto=webp&s=cc1f0bc16bd9141796e88b6fea4878141bbe74c2

It looks like VS Code will automatically look for your TensorBoard log files within your directory.

submitted by /u/evilcubed
[visit reddit] [comments]

Categories
Misc

Help with debugging

Help with debugging
submitted by /u/iWatchBlack
[visit reddit] [comments]
Categories
Misc

New TensorBoard Integration in VS Code

New TensorBoard Integration in VS Code

In the latest update of VS Code last week, they added support for TensorBoard integration in VS Code. Just wanted to share with everyone!

https://preview.redd.it/lg64jrhqhij61.png?width=2556&format=png&auto=webp&s=1afe8944a278356a3eafbc98039424b62069c505

To launch tensorboard, just open the command palette in VS Code and search for the command “Launch TensorBoard”

https://preview.redd.it/g96z1lxxhij61.png?width=1064&format=png&auto=webp&s=cc1f0bc16bd9141796e88b6fea4878141bbe74c2

It looks like VS Code will automatically look for your TensorBoard log files within your directory.

submitted by /u/evilcubed
[visit reddit] [comments]

Categories
Misc

Help with debugging

Help with debugging
submitted by /u/iWatchBlack
[visit reddit] [comments]