BiblioInfo.tex

% Filling in this bibliographic information facilitates the
% processing of this document.
% Insert linebreaks if necessary
% The abstract page is not generated by default. The reason for this is that it
% will be generated by the unit for Publishing and Graphic sevices from the metadata 
% template ("Spikningsmallen"). If you want to include the abstract page generated from this template,
% please edit the \frontmatterMonograph or \frontmatterCS command at the en of this file
%. Because of this, some of the bibliografic data on this page will not be used.

% Abstract and titelpage
\newcommand{\authorSurname}{Maia} % Your surname
\newcommand{\authorFirstName}{Filipe} % Your given name
\newcommand{\authorFirstInitial}{RNC} % Initial of given name
\newcommand{\authorEmail}{filipe@xray.bmc.uu.se} % Your e-mail address
\newcommand{\dissertationTitle}{Ultrafast Coherent X-ray Diffractive Nanoimaging} % The title of the dissertation
\newcommand{\dissertationSubtitle}{}% The subtitle of the dissertation (if there is any).
\newcommand{\yearOfPublication}{2010} % Year of publication
\newcommand{\placeOfDisputation}{B41, BMC, Husargatan 3, Uppsala} % Place of disputation
\newcommand{\dateOfDisputation}{Friday, May 14, 2010} % Date of disputation (Day, Month, Year)
\newcommand{\timeOfDisputation}{13:15} % Time of disputation (Swedish time format)
\newcommand{\disputationLanguage}{English} % Language the examination will be conducted in.
\newcommand{\numberOfPages}{51} % The page number of the last page
\newcommand{\placeOfPublication}{Uppsala} % The place of publication
\newcommand{\ISBN}{} % The ISBN number of the dissertation.
%\newcommand{\series}{Uppsala Dissertations from the Faculty of Science and
%  Technology} % The title of the series
\newcommand{\series}{Digital Comprehensive Summaries of Uppsala Dissertations from the Faculty of Science and Technology} % The title of the series
\newcommand{\serialNumber}{} % The number in the series.
\newcommand{\keywords}{free-electron laser, X-ray diffraction, Coherent
  Diffractive Imaging, Image Reconstruction, Single Particle Imaging, keyword6,\\ keyword7, keyword8, keyword9, keyword10,...} % Key words separated by comma
\newcommand{\department}{Department of Cell and Molecular Biology} % Name of your department
\newcommand{\departmentaddress}{Box 596, Uppsala University, SE-75124 Uppsala,
Sweden} % Address of your department
\newcommand{\ISSN}{} % (ISSN for Digital comprehensive summaries of Uppsala dissertations from the faculty of science and technology)
\newcommand{\urn}{urn:nbn:se:uu:diva-} % URN number

% List of papers
\newcommand{\listofpapers}
{\cleardoublepage
\pdfbookmark[0]{List of Publications}{LOP}
\chapter*{List of Publications}
\noindent 
\noindent This thesis is based on the following papers, which are referred
to in the text by their Roman numerals.
\vspace{1\baselineskip}

        % It is possible to refer to the published papers using labels in the text.
        % Suggested order
        % Author 1 surname, Author 2 first name initial., Author 1 surname, Author 2 first name
        % initial. etc. (Year of publication) Paper main title.
        % Paper subtitle. Name of journal in italics, volume(number):page rage
        % Example
        
    \begin{romanlist}


      \item
        \label{cowboys}
        Chapman, H.N., Barty, A., Bogan, M.J., Boutet, S., Frank, M., Hau-Riege, S.P.,
        Marchesini, S., Woods, B.W., Bajt, S., Benner, H., London, R.A., Plonjes, E., Kuhlmann,
        M., Treusch, R., Dusterer, S., Tschentscher, T., Schneider, J.R.,
        Spiller, E., Moller, T., Bostedt, C., Hoener, M., Shapiro, D.A.,
        Hodgson, K.O., Van der Spoel, D., Burmeister, F., Bergh, M., Caleman,
        C., Huldt, G., Seibert, M.M., Maia, F.R.N.C., Lee, R.W., Szoke, A.,
        Timneanu, N., Hajdu J. (2006) Femtosecond diffractive imaging with a
        soft-X-ray free-electron laser. {\em Nature Physics}, 2(12):839-843

    \item
      \label{melting}
      van der Spoel, D., Maia, F.R.N.C., Caleman, C. (2008), Structural studies of
      melting on the picosecond time scale. {\em Physical Chemistry Chemical
        Physics},10(42):6344-6349

    \item 
      \label{music}
      Ravasio, A., Gauthier, D., Maia, F.R.N.C., Billon, M., Caumes, J.P.,
      Garzella, D., Geleoc, M., Gobert, O., Hergott, J.F., Pena, A.M., Perez,
      H., Carre, B., Bourhis, E., Gierak, J., Madouri, A., Mailly, D., Schiedt,
      B., Fajardo, M., Gautier, J., Zeitoun, P., Bucksbaum, P.H., Hajdu, J.,
      Merdji, H. (2009) Single-Shot Diffractive Imaging with a Table-Top
      Femtosecond Soft X-Ray Laser-Harmonics Source. {\em Physical Review
        Letters}, 103:028104

    \item 
      \label{dynamics}
      Maia, F.R.N.C., Ekeberg, T., T\^{i}mneanu, N., van der Spoel, D., Hajdu,
      J. (2009) Structural variability and the incoherent addition of scattered
      intensities in single-particle diffraction. {\em Physical Review E}, 80:031905
      
    \item 
      \label{hawk}
      Maia, F.R.N.C.,  Ekeberg, T., van der Spoel, D., Hajdu, J. (2010)
      Hawk: the image reconstruction package for coherent X-ray diffractive
      imaging. {\em Submitted for publication}
\end{romanlist}

\vspace{1\baselineskip} \noindent {\small Reprints were made with permission from
the publishers.}

\clearpage 

\noindent {\LARGE Supporting Publications}

\vspace{1cm}

\begin{romanlist}
  \setcounter{romanlistc}{5}
\item Bergh, M., Huldt, G., T\^{i}mneanu, N., Maia, F.R.N.C., Hajdu, J. (2008)
  Feasibility of imaging living cells at subnanometer resolutions by ultrafast
  X-ray diffraction. {\em Quarterly Reviews of Biophysics}, 41(3-4):181-204
  \label{QRB}
\item Bogan, M.J., Benner, W.H., Boutet, S., Rohner, U., Frank, M., Barty, A.,
  Seibert, M.M., Maia, F., Marchesini, S., Bajt, S., Woods, B., Riot, V.,
  Hau-Riege, S.P., Svenda, M., Marklund, E., Spiller, E., Hajdu, J., Chapman,
  H.N. (2008) Single particle X-ray diffractive imaging. {\em Nano Letters},
  8(1):310-316
  \label{nano}
\end{romanlist}
}


% Dedication. Dedication is optional. You can enter whatever feels right and use the fonts and images you like as long as they are embedded in the document. The suggested format does not have to be used.
\newcommand{\dedication}%
{\cleardoublepage
\thispagestyle{empty}
\vspace*{\stretch{3}}
\begin{flushright}
		
{\fontfamily{pzc}\Large\selectfont\emph{to my grandparents...}}

\end{flushright}
\vspace*{\stretch{1}}} % 

% Frontmatter commands
% Halftitle page for monographs
\newcommand{\halftitlepage}{%
\thispagestyle{empty}
\begin{center}
	ACTA UNIVERSITATIS UPSALIENSIS

	\emph{\series{}}
	
	\serialNumber
\end{center}
\cleardoublepage}

% Title page for monographs
\newcommand{\thetitlepage}%
{\thispagestyle{empty}
\vspace*{40mm}
\begin{center}
\Large \authorFirstName{} \authorSurname{}

\vspace{6mm}

\Huge{ \dissertationTitle{}}

\vspace{6mm}

\fontsize{14}{16}\fontshape{it}\selectfont\dissertationSubtitle{}			
\end{center}
\begin{figure}[b]
\begin{center}
\ifpdf
\includegraphics{UU_logo_pc_sv_42}
\else
\includegraphics{UU_logo_pc_sv_42.eps}
\fi
\end{center}
\end{figure}}

% Abstract. This is optional. 
\newcommand{\thesisabstract}{%
\begin{abstract}{%
	\newpage
	\thispagestyle{empty}
    \fontsize{9}{11}\selectfont
    \noindent
    \begin{flushleft}{\nohyphens
    Dissertation at Uppsala University to be publicly examined in \placeOfDisputation{}, \dateOfDisputation{} at \timeOfDisputation{}
    for the Degree of Doctor of Philosophy. The examination will be conducted in \disputationLanguage{}}\end{flushleft}

    \noindent\textbf{Abstract}
    \vspace{-9pt}
    \begin{flushleft}{\nohyphens\noindent\authorSurname{}, \authorFirstInitial{}. \yearOfPublication{}.
    \dissertationTitle{}. \dissertationSubtitle{}. Acta Universitatis
    Upsaliensis. \emph{\series{}} \serialNumber{}. \numberOfPages{}~pp.
    \placeOfPublication{}. ISBN~\ISBN{}}\end{flushleft}

% Type your abstracttext here. Remove the latin text. Try to not type more than 300 words.
\noindent 
% The advent of X-ray lasers provides the scientific community with a
% new kind of instrument that is many orders of magnitude brigther, faster and
% more coherent that existing X-ray light sources. Such revolutionary  change is
% almost certain to be accompanied by a range of new experiments that were
% previously unfeasible.

% One important class of such experiments is ultrafast coherent X-ray diffractive
% imaging (CXDI). In such an experiment an extremely bright and very fast X-ray pulse is
% focused on a sample. The sample is quickly vaporized, but not before scattering
% sufficient light for a diffraction pattern to be recorded. The pattern can then
% be phased and the structure of the undamaged sample recovered.

% This thesis presents the results of some of the first ultrafast X-ray diffractive imaging experiments
% are presented. It combines experiments made using both linear accelerator-driven
% free-electron lasers, and optically driven table-top X-ray lasers. It also
% theoretically explores the possibility of investigating phase transitions in
% crystals using X-ray lasers.

% An important problem with ultrafast CXDI of small samples such as proteins is
% that the signal from a measurement is very small, making the pattern
% uninterpretable. So averaging over multiple equivalent samples will be
% necessary. We present a numerical investigation of the problems introduced when
% the samples are not exactly identical and propose some tentative solutions.

% Hawk, a software package for processing and reconstruction of patterns
% obtained in CXDI experiments is introduced. Currently there is no publicly
% available software for this purpose and we hope Hawk fills this gap. It is
% essential that the rapid progresses in terms of experimental hardware are
% accompanied by equivalent developments on the software side otherwise soon we
% will have much more data that what can be analyzed, and Hawk is released as open
% source with the aspiration of fostering such development.
X-ray lasers are creating unprecedented research opportunities in physics,
chemistry and biology. The peak brightness of these lasers exceeds present
synchrotrons by $10^{10}$, the coherence degeneracy parameters exceed
synchrotrons by $10^9$, and the time resolution is $10^5$ times better. In the
duration of a single flash, the beam focused to a micron-sized spot has the same
power density as all the sunlight hitting the Earth, focused to a millimetre
square. 



Ultrafast coherent X-ray diffractive imaging (CXDI) with X-ray lasers exploits
these unique properties of X-ray lasers to obtain high-resolution structures for
non-crystalline biological (and other) objects. In such an experiment, the
sample is quickly vaporised, but not before sufficient scattered light can be
recorded. The continuous diffraction pattern can then be phased and the
structure of a more or less undamaged sample recovered
% (speed of light vs. speed of a shock wave)
.



This thesis presents results from the first ultrafast X-ray diffractive imaging
experiments with linear accelerator-driven free-electron lasers and from
optically-driven table-top X-ray lasers. It also explores the possibility of
investigating phase transitions in crystals by X-ray lasers. 



An important problem with ultrafast CXDI of small samples such as single protein
molecules is that the signal from a single measurement will be small, requiring
signal enhancement by averaging over multiple equivalent samples. We present a
numerical investigation of the problems, including the case where sample
molecules are not exactly identical, and propose tentative solutions. 



A new software package (HAWK) has been developed for data processing and image
reconstruction. HAWK is the first publicly available software package in this
area, and it is released as an open source software with the aspiration of
fostering the development of this field.

    \vspace{11pt}

    \noindent
    \emph{Keywords: XFEL, Diffractive Imaging, Single Particle Imaging, X-ray
      Diffraction, X-ray laser, Phasing, Nanoimaging, Ultrafast Imaging}\keywords

    \vspace{11pt}

    \noindent
    \emph{\authorFirstName{} \authorSurname{}, \department{}, Uppsala University,
    \departmentaddress{}}

    \vspace{11pt}

    \noindent \copyright{} \authorFirstName{} \authorSurname{}
    \yearOfPublication{}

    \vspace{11pt}
    
    \noindent ISSN \ISSN{}

    \noindent ISBN \ISBN{}

    \noindent \urn{} (http://urn.kb.se/resolve?urn=\urn)}\end{abstract}}

% Title page dummy for Compehensive summaries
\newcommand{\titlepagedummy}%
{\newpage
\newpage\thispagestyle{empty}
{\noindent\LARGE Titlepage}\vspace{84pt}

\noindent This is the title page dummy. This page should be substituted for a real title page. The real title page will be provided by Publishing and Graphic services after having submitted your posting details in DiVA. The DiVA registration form can be found at \\ \href{https://uu.diva-portal.org/dream/}{https://uu.diva-portal.org/dream/}.

\vspace{1em}

\noindent More information about the publishing routines can be found at \\
\href{http://beta.ub.uu.se/pgs}{http://beta.ub.uu.se/pgs}}

%Abstractdummy
\newcommand{\abstractdummy}%
{\newpage\thispagestyle{empty}
{\noindent\LARGE Abstract page}\vspace{84pt}

\noindent This is the abstract dummy. This page should be substituted for real abstract/imprint page. The real abstract page will be provided by Publishing and Graphic services after having submitted your posting details in DiVA. The DiVA registration form can be found at \\ \href{https://uu.diva-portal.org/dream/}{https://uu.diva-portal.org/dream/}.
\vspace{1em}

\noindent More information about the publishing routines can be found at \\
\href{http://beta.ub.uu.se/pgs}{http://beta.ub.uu.se/pgs}}

% Front matter commands
\newcommand{\frontmatterMonograph}%
{\halftitlepage\thetitlepage\abstractdummy\dedication}

\newcommand{\frontmatterCS}%
{\titlepagedummy\abstractdummy\dedication\listofpapers}
%%% Local Variables: 
%%% mode: latex
%%% TeX-master: "Thesis"
%%% End: