What this section is for

Insights collects perspectives, observations, and practical reflections on molecular modeling and computational chemistry methods. Article sources live in src/content/insights-en/; contributions are welcome through GitHub Pull Request.

Each article is a single .mdx file. The YAML frontmatter at the top carries the metadata (title, author, date, avatar); the body is plain Markdown, with the option to embed Astro components when needed.

Tables

SystemAtomsA100 (ns/day)H100 (ns/day)
1UBQ18,000320540
2OOB95,000110175
4XCN220,0004878

Formulas

Inline math: the potential energy decomposes into a bonded term UbondU_{\text{bond}} and a non-bonded term UnbU_{\text{nb}}, i.e. U=Ubond+UnbU = U_{\text{bond}} + U_{\text{nb}}.

Block math:

ULJ(r)=4ε[(σr)12−(σr)6]U_{\text{LJ}}(r) = 4\varepsilon\left[\left(\frac{\sigma}{r}\right)^{12} - \left(\frac{\sigma}{r}\right)^{6}\right] Fi=−∇iU(r1,…,rN)F_i = -\nabla_i U(\mathbf{r}_1, \dots, \mathbf{r}_N)

Code

#include <iostream>

int main() {
    std::cout << "Hello, SPONGE!" << std::endl;
    return 0;
}

Mermaid Diagrams

flowchart LR
  A["Prepare system"] --> B["Choose model"]
  B --> C["Run simulation"]
  C --> D["Analyze results"]

Images

A schematic of the 1UBQ1 protein commonly used in SPONGE, as an example:

1UBQ structure

Interactive structure

The 1UBQ1 structure below is rendered with Mol*23. Drag to rotate, scroll to zoom, click a residue to see more information:

How to contribute

  1. Fork spongemm/spongemm_cn
  2. Create a new .mdx file under src/content/insights-en/
  3. Fill in the frontmatter and body, then preview locally with npm run dev
  4. Open a Pull Request; once merged, it ships with the next deploy

Footnotes

  1. Vijay-Kumar S, Bugg CE, Cook WJ. Structure of ubiquitin refined at 1.8 Å resolution. J Mol Biol. 1987;194(3):531–544. doi:10.1016/0022-2836(87)90679-6 ↩ ↩2

  2. Sehnal D, Bittrich S, Deshpande M, et al. Mol* Viewer: modern web app for 3D visualization and analysis of large biomolecular structures. Nucleic Acids Research. 2021;49(W1):W431–W437. doi:10.1093/nar/gkab314 ↩

  3. Mol* Viewer official website. https://molstar.org/ ↩