\documentclass[12pt,a4paper,twoside]{report}
%\documentclass[12pt,a4paper,twoside,draft]{report}
%\usepackage{mathptmx}  % times font!!
\usepackage[english]{babel}
\usepackage{amssymb,amsmath}  % various mathematical symbols
\usepackage{textcomp}
\usepackage{color,setspace,calc,hyperref,verbatim}
%\hypersetup{colorlinks=true, citecolor=blue, linkcolor=blue, filecolor=blue,urlcolor=blue}
\hypersetup{colorlinks=true, citecolor=black, linkcolor=black, filecolor=black,urlcolor=black}

%%packages to be used to print on landscape and 2 pages per sheet
%  \usepackage{pgfpages}
%  \pgfpagesuselayout{2 on 1}[a4paper,landscape]
%%%%%%%%%%%%%%%%%%%%%%%%%%
%+++++++++++++++++++++++++++++++
\usepackage[small,bf]{caption}
\renewcommand{\captionfont}{\small\sffamily}

\usepackage{graphicx,rotating,subfigure} 
\graphicspath{{pics/eps/}}

\usepackage[super,comma,sort&compress]{natbib}
\bibliographystyle{biophysj}

%This says that we want a minimum margin of 2cm on the left and right plus a binding offset of 1cm on the appropriate side and to allocate the remaining space horizontally for text. We want to have 22cm of text vertically on the page, and to balance the remaining space for the header and footer using the default ratio.
%\usepackage[includeheadfoot,bindingoffset=1cm,textheight=22cm,hdivide={2cm,*,2cm},vdivide={1cm,*,1cm}]{geometry}
\usepackage[bindingoffset=1cm,hdivide={2cm,*,2cm},vdivide={*,22cm,*},includehead]{geometry}
\setlength{\headheight}{1cm}

\usepackage{fancyhdr}
\pagestyle{fancy}
\fancyhf{} % clear all fields
\fancyhead[HEL]{{\slshape\thepage}}
\fancyhead[HER]{{\slshape\leftmark}}
\fancyhead[HOR]{{\slshape\thepage}}
\fancyhead[HOL]{{\slshape\rightmark}}
\renewcommand{\chaptermark}[1]{\markboth{\uppercase{\chaptername}\ \thechapter.\ #1}{}}
\renewcommand{\sectionmark}[1]{\markright{\thesection.\ #1}}

\hyphenpenalty=5000
\tolerance=1000
% just to show also subsubsection in the table of content
\setcounter{tocdepth}{4}
\setcounter{secnumdepth}{4}
%to leave the space at the end of the page rather than between paragraphs
\raggedbottom
\renewcommand{\topfraction}{0.85}
\renewcommand{\textfraction}{0.1}
\renewcommand{\floatpagefraction}{0.80}

%#####%%%%%%and so it begins%%%%%%%%%%%%%%%%%%%%%%%%%%%%
\begin{document}
 \onehalfspacing
\include{initpages}
\clearpage
\pagenumbering{roman}
 \tableofcontents
\cleardoublepage
\pagenumbering{arabic}
%%%%#####CHAPTERS STARTS HERE##########
\include{intro}
\cleardoublepage
\include{methods}
\cleardoublepage
\include{bulkphase}
\cleardoublepage
\include{replica}
\cleardoublepage
\include{surface}
\cleardoublepage
\addcontentsline{toc}{chapter}{Summary}
\pagestyle{myheadings}
\markboth{Summary}{Summary}
\include{summary}
\cleardoublepage
%%%%%%%%%##################################
\addcontentsline{toc}{chapter}{Bibliography}
\pagestyle{myheadings}
\markboth{Bibliography}{Bibliography}
\bibliography{thesis}
\end{document}
