template.qmd

---
title: What a title!
date: today
date-format: long
author:
  - name: Jane Doe
    url: https://example.com
    orcid: 0000-0000-0000-0000
    affiliations:
      - id: some-inst
        name: Institute for Cool Things
        url: https://example.com
      - id: some-uni
        name: University of Awesome Research
        url: https://example.com
    email: corresponding email
  - name: John Doe
    affiliations:
      - ref: some-inst
github: https://github.com/quarto-journals/
repo: biophysical-journal
format:
  bj-pdf:
    classoption:
      - twocolumn
colorlinks: true
link-citations: true
keep-tex: true
abstract: |
  TODO
  Look at all the cool stuff we found out!
sigstatement: |
  TODO
  This is very important, because...
  Each manuscript must also have a statement of significance or no more than 120 words.
license: CC BY
keywords:
  - Research
  - Cool Stuff
citation:
  type: article
  citation-key: citationKeyNumber
  status: draft
bibliography: references.bib
---

# Introduction

This template is based on the Overleaf template provided by the Biphysical Journal:
<https://www.overleaf.com/articles/biophysical%E2%80%90journaltemplate/pxxcptphxdhv>
Your introduction goes here!
Some examples of commonly used commands and features are listed below, to help you get started.
Leave a blank line between blocks of text to start a new paragraph.
Abbreviations should be defined in the text at first mention.

We are using quarto [@quarto].

Please also take note of the `\section*{...}` titles in this template:
they are the required sections in a regular research Article manuscript.

In particular, the main text of regular Articles and Computational Tools manuscripts must be structured with the following sections:
**Introduction**, **Materials and Methods**, **Results**, **Discussion
(or Results and Discussion)**, **Conclusion**.

Theoretical manuscripts may include just a **Methods** section and do not require **Materials**.

No particular organization structure is required for Letters.

If your manuscript is accepted, the Biophysical production team will re-format the references for publication.
*It is not necessary to format the reference list yourself to mirror the final published form.*

# Materials and Methods

Capitalize trade names and give manufacturers' full names and addresses
(city and state).

## Sectioning commands

Lorem ipsum dolor sit amet, qui minim labore adipisicing minim sint cillum sint consectetur cupidatat.

# Results

See @tbl-numbers.

LaTeX is great at typesetting mathematics:

Let $X_1, X_2, \ldots, X_n$ be a sequence of independent and identically
distributed random variables with $\text{E}[X_i] = \mu$ and
$\text{Var}[X_i] = \sigma^2 < \infty$, and let
$$
S_n = \frac{X_1 + X_2 + \cdots + X_n}{n}
      = \frac{1}{n}\sum_{i}^{n} X_i
$${#eq-clt}
denote their mean.
Then as $n$ approaches infinity, the random variables $\sqrt{n}(S_n - \mu)$ converge
in distribution to a normal $\mathcal{N}(0, \sigma^2)$.
Thus concludes the explanation about @eq-clt.

You can make lists with automatic numbering ...

1.  Like this,
2.  and like this.

...or bullet points ...

-   Like this,
-   and like this.

...or with words and descriptions ...

Word

:   Definition

Concept

:   Explanation

Idea

:   Text

An example quotation:

> Lorem ipsum dolor sit amet, consectetur adipiscing elit, sed do
> eiusmod tempor incididunt ut labore et dolore magna aliqua. Ut enim ad
> minim veniam, quis nostrud exercitation ullamco laboris nisi ut
> aliquip ex ea commodo consequat.

## Figures and Tables

Here is a table (or not, this is LaTeX, so it will put it wherever it wants. "Here" is very relative...).

|Thing   | Value  |
|:-------|-------:|
|A 42    |      18|
|B 15    |      18|
|C 34    |      17|
|D 99    |      24|

: Look, numbers! {#tbl-numbers}

# Discussion

Lorem ipsum dolor sit amet, qui minim labore adipisicing minim sint cillum sint consectetur cupidatat.

# Conclusion

Sed ut perspiciatis unde omnis iste natus error sit voluptatem
accusantium doloremque laudantium, totam rem aperiam, eaque ipsa quae ab
illo inventore veritatis et quasi architecto beatae vitae dicta sunt
explicabo.

# Author Contributions

Author1 designed the research. Author2 carried out all simulations,
analyzed the data. Author1 and Author2 wrote the article.

# Declaration of Interest

The authors declare no competing interests.

# Acknowledgments

We thank G. Harrison, B. Harper, and J. Doe for their help.

# References

:::{#refs}
:::

# Supplementary Material

An online supplement to this article can be found by visiting BJ Online
at <http://www.biophysj.org>.