add the files

Makefile

+paper.tex:
+	pandoc -s --filter pandoc-fignos --filter pandoc-citeproc --filter pandoc-crossref --natbib paper.md -o paper.tex --bibliography paper.bib --template revtex.template
+
+paper.pdf: paper.tex
+	pdflatex paper.tex
+	bibtex paper
+	pdflatex paper.tex

environment.yml

+name: revtex-markdown-paper
+
+channels:
+- conda-forge
+
+dependencies:
+  - python
+  - pandoc
+  - pandoc-crossref
+  - pip:
+    - pandoc-fignos

paper.bib

+@article{nijholt2016orbital,
+  title={Orbital effect of magnetic field on the Majorana phase diagram},
+  author={Nijholt, Bas and Akhmerov, Anton R},
+  journal={Physical Review B},
+  volume={93},
+  number={23},
+  pages={235434},
+  year={2016},
+  publisher={APS}
+}

paper.md

+---
+title:  'Great and certainly not overstated contribution to the literature'
+journal: 'Journal of Good Research'
+author:
+- name: Bas Nijholt
+  affiliation:
+    - TU Delft
+    - Station Q
+  email: bas@nijho.lt
+- name: Anton Akhmerov
+  affiliation:
+    - TU Delft
+  email: i@antonakhmerov.org
+abstract: |
+  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. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+bibliography: references.bib
+acknowledgements: |
+  We'd like to thank ...
+contribution: |
+  B.N. created the template with input from J.W.
+  A.A. is a place holder.
+  All authors looked at the manuscript.
+...
+
+# Introduction
+
+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. Duis aute irure dolor in reprehenderit in voluptate velit esse cillum dolore eu fugiat nulla pariatur. Excepteur sint occaecat cupidatat non proident, sunt in culpa qui officia deserunt mollit anim id est laborum.
+
+Some [red text **which supports** markdown.]{.red}
+
+
+<!---
+Comments look like this and do not show up in the PDF
+-->
+
+References are cited as [@nijholt2016orbital].
+
+# Methods
+
+Footnotes can be entered using this code[^1].
+
+[^1]: a footnote
+
+Figures are included like this.
+
+![This is gonna be the caption.](pics/dummy.pdf){#fig:dummy}
+
+And referenced from here as Fig. @fig:dummy.
+
+Complex tables can use standard LaTeX code as this one.
+
+Equations can be used inline $y=\beta_0 + \beta_1 x + \epsilon$ or as usual $$f(x)=\frac{1}{x}$${#eq:example_eq} and referenced with [@eq:example_eq].
+
+
+<!---
+Table in LaTeX format because of fancy formatting
+-->
+
+\begin{table}[ht]
+\centering
+\caption{Probability to observe Bayes Factors of a certain magnitude or above for the used sample-size of $N=60$ assuming the original and the null-hypothesis.}
+\begin{tabular}{llrrr}
+  & & \multicolumn{3}{l}{$P(\text{BF}\ge\theta)$}\\
+  Hypothesis & BF Type & $\theta=3$ & $\theta=10$ & $\theta=20$ \\
+  \hline
+  $d\sim \mathcal{N}(1.57, 0.51)$ & JZS BF$_{10}$ & 0.98 & 0.97 & 0.96 \\
+     & Replication BF$_{10}$ & 0.98 & 0.96 & 0.96 \\
+     & Meta-Analysis BF$_{10}$ & 0.99 & 0.99 & 0.99 \\\cline{2-5}
+    $d=0$ & JZS BF$_{01}$ & 0.81 & 0.00 & 0.00 \\
+   & Replication BF$_{01}$ & 0.98 & 0.95 & 0.91 \\
+     & Meta-Analysis BF$_{01}$ & 0.63 & 0.27 & 0.06 \\
+   \hline
+\end{tabular}
+\label{tab:probbf}
+\end{table}
+
+# Results
+
+# Discussion
+
+# References

revtex.template

+\documentclass[english, twocolumn, 10pt, aps, superscriptaddress, floatfix, prb, citeautoscript]{revtex4-1}
+\pdfoutput=1
+\usepackage[utf8]{inputenc}
+\usepackage[T1]{fontenc}
+\usepackage{verbatim}
+\usepackage{units}
+\usepackage{mathtools}
+\usepackage{amsmath}
+\usepackage{amssymb}
+\usepackage{graphicx}
+\usepackage{wasysym}
+\usepackage{layouts}
+\usepackage{siunitx}
+\usepackage{bm}
+\usepackage{xcolor}
+\usepackage[colorlinks, citecolor={blue!50!black}, urlcolor={blue!50!black}, linkcolor={red!50!black}]{hyperref}
+\usepackage{bookmark}
+\usepackage{tabularx}
+\usepackage{microtype}
+\usepackage{babel}
+\hypersetup{pdfauthor={$for(author)$$author.name$$sep$, $endfor$},pdftitle={$if(title)$$title$$endif$}}
+
+\setcounter{secnumdepth}{4}
+\setcounter{tocdepth}{4}
+
+\DeclareMathOperator{\e}{e}
+\DeclareMathOperator{\de}{d\!}
+\DeclareMathOperator{\Tr}{Tr}
+\DeclareMathOperator{\diag}{diag}
+\DeclareMathOperator{\Res}{Res}
+\DeclareMathOperator{\sgn}{sgn}
+\DeclareMathOperator{\Pf}{Pf}
+\DeclareMathOperator{\Det}{Det}
+\DeclareMathOperator{\rank}{rank}
+\DeclareMathOperator{\im}{Im}
+\DeclareMathOperator{\re}{Re}
+\newcommand{\kx}{k_x}
+\newcommand{\ky}{k_y}
+\newcommand{\meff}{m_\text{eff}}
+
+\renewcommand{\comment}[2]{#2}
+% Uncomment the following line for paragraph descriptions to appear in the file.
+\renewcommand{\comment}{\paragraph}
+
+\DeclarePairedDelimiter\abs{\lvert}{\rvert}
+\DeclarePairedDelimiter\norm{\lVert}{\rVert}
+
+\makeatletter
+\let\oldabs\abs
+\def\abs{\@ifstar{\oldabs}{\oldabs*}}
+\let\oldnorm\norm
+\def\norm{\@ifstar{\oldnorm}{\oldnorm*}}
+\makeatother
+
+\newcommand{\ev}[1]{\langle#1\rangle}
+\newcommand{\bra}[1]{\langle#1|}
+\newcommand{\ket}[1]{|#1\rangle}
+\newcommand{\bracket}[2]{\langle#1|#2\rangle}
+
+\newcolumntype{L}[1]{>{\raggedright\arraybackslash}p{#1}}
+\newcolumntype{C}[1]{>{\centering\arraybackslash}p{#1}}
+\newcolumntype{R}[1]{>{\raggedleft\arraybackslash}p{#1}}
+
+% workaround for https://github.com/jgm/pandoc/issues/2392#issuecomment-140114736
+\renewcommand{\citep}{\cite}
+
+\begin{document}
+
+\title{$if(title)$$title$$endif$}
+
+$for(author)$
+$if(author.name)$
+\author{$author.name$}
+\email[Electronic address: ]{$author.email$}
+$for(author.affiliation)$
+\affiliation{$author.affiliation$}
+$endfor$
+$endif$
+$endfor$
+
+\date{\today}
+
+$if(abstract)$
+\begin{abstract}
+$abstract$
+\end{abstract}
+$endif$
+
+\flushbottom
+\maketitle
+
+$body$
+
+$if(acknowledgements)$
+\section*{Acknowledgements}
+$acknowledgements$
+$endif$
+
+$if(contribution)$
+\section*{Author contributions statement}
+$contribution$
+$endif$
+
+$if(additionalinformation)$
+\section*{Additional information}
+$additionalinformation$
+$additionalinformation$
+$endif$
+
+\bibliographystyle{apsrev4-1}
+\bibliography{$bibliography$}
+
+\end{document}