From 617926e81e3c073f18bcaf9784a474638f2c4447 Mon Sep 17 00:00:00 2001 From: Blaise Thompson Date: Sun, 1 Apr 2018 16:56:35 -0500 Subject: 2018-04-01 16:56 --- introduction/chapter.tex | 157 ++++++++++++++++++++++++++++++++++++++++++++--- 1 file changed, 147 insertions(+), 10 deletions(-) (limited to 'introduction/chapter.tex') diff --git a/introduction/chapter.tex b/introduction/chapter.tex index 81a6b97..be4572d 100644 --- a/introduction/chapter.tex +++ b/introduction/chapter.tex @@ -1,14 +1,89 @@ -\chapter{Introduction} +\cleardoublepage +\chapter{Introduction} \label{cha:int} -\section{Coherent Multidimensional Spectroscopy} +% TODO: cool quote, if I can think of one... -% Unraveling quantum pathways using optical 3D Fourier-transform spectroscopy doi:10.1038/ncomms2405 +\clearpage -\Gls{CMDS}, \gls{coherent multidimensional spectroscopy} +Coherent multidimensional spectroscopy (CMDS) is a family of experimental strategies capable of +providing unique insights into microscopic material physics. % +It is similar to the more familiar [NMR EXPERIMENTS], although the implementation is different due +to differences between the behavior of nuclear spin states (probed by NMR) and electronic and +vibrational states (probed by CMDS). % +CMDS can resolve couplings between states, and can decongest spectra by taking advantage of +dimensionality and selection rules. % +With the advent of ultrafast lasers, CMDS can resolve dynamics in excited states and the coupling +between them. % -\section{The CMDS Instrument} +CMDS is most often performed in the time domain, where multiple broadband pulses are scanned in +time to collect a multidimensional interferogram. [CITE] % +This technique is fast and robust---it has even been performed on a single shot. [CITE] % +However time-domain CMDS has some fundamental limitations: +\begin{ditemize} + \item The frequency bandwidth must be contained within the excitation pulse---and ultrabroadband + pulses are hard to make and control. [CITE JONAS] + \item A phase-locked local oscillator is required, and preparing a local oscillator for experiments + with unique output colors is challenging. +\end{ditemize} +Scientists in the time-domain CMDS community are taking both of these challenges head-on, pushing +the envelope in excitation pulse bandwidth [CITE 2DWL] and performing two-stage experiments in +which excitation pulses are used to generate a local oscillator in non-resonant media [CITE +ZANNI]. % -From an instrumental perspective, MR-CMDS is a problem of calibration and coordination. % +An alternative strategy is frequency domain ``multi-resonant'' CMDS (MR-CMDS). % +Rather than using a single broadband excitation pulse, MR-CMDS employs a relatively narrow-band +source with a tunable frequency. % +Motorized optical parametric amplifiers (OPAs) are typically used to provide this tunability. % +In MR-CMDS, frequency axes are resolved directly by scanning these motorized OPAs. % +This process is time intensive, and it can be challenging to ensure that the OPAs are well +calibrated and that the experiment is not affected by the motion of crystals and other optics +inside these automated OPAs. % +Despite these challenges, MR-CMDS is an incredibly flexible strategy that can be a very powerful +analytical tool. % +Because MR-CMDS does not require that all frequencies be contained within one broadband source, +there is no theoretical limit to the frequency range that can be resolved in this way. % +MR-CMDS can be homodyne-detected, so experiments with unique output colors are much more +accessible. % +Finally, because the components are more self-contained, MR-CMDS instruments tend to be more +flexable in the kinds of experiments that they can perform. % + +% TODO: boilerplate about the kinds of things that make up an MR-CMDS instrument... OPAs, delays... + +This dissertation contains several projects undertaken to improve the reliability and accessibility +of MR-CMDS. % +While MR-CMDS will never be a single-shot experiment, there are many improvements that can improve +data collection speed. % +Necessary calibration, especially OPA calibration, can be made robust and fully automatic. % +Common artifacts can be addressed through relatively simple modifications in hardware and +software. % +Finally, the complexity that arises from finite pulses with ``marginal'' resolution in frequency +and time can be understood and accounted for through numerical simulation. % +Taken together, these improvements represent a significant improvement in the accessibility of +frequency-domain coherent multidimensional spectroscopy. % + +Due to its diversity and dimensionality, MR-CMDS data is challenging to process and represent. % +The data processing tools that a scientist develops to process one experiment may not work when she +attempts to process an experiment where different experimental variables are explored. % +Historically, this has meant that MR-CMDS practitioners have used custom, one-off data processing +workflows that need to be changed for each particular experiment. % +These changes take time to implement, and can become stumbling blocks or opportunities for +error. % +Even worse, the challenge of designing a new processing workflow may make dissuade scientist from +creatively modifying their experimental strategy, or comparing their data with data taken from +another group. % +This limit to creativity and flexibility defeats one of the main advantages of the MR-CMDS +strategy. % +\autoref{cha:pro} describes a new software package, WrightTools, that greatly simplifies CMDS data +processing. % +WrightTools defines a \emph{universal format} that is capable of representing any CMDS dataset, +regardless of dimensionality or the axes scanned. % +A set of simple functions are used to convert raw data into this universal format. % +Once converted, the data can be manipulated with a set of powerful methods that encompass the +majority of operations needed to process such data. % +Finally, simple tools are defined to quickly and beautifully represent the datasets. % +WrightTools is made to be extended, so it will continue to evolve along with its users. % + +From an instrumental perspective, MR-CMDS is a problem of calibration and coordination. % Within the Wright Group, each of our two main instruments are composed of roughly ten actively moving component hardwares. % Many of these components are purchased directly from vendors such as SpectraPhysics, National @@ -17,8 +92,6 @@ Others are created or heavily modified by graduate students. % The Wright Group has always maintained custom acquisition software packages which control the complex, many-stepped dance that these components must perform to acquire MR-CMDS spectra. % -\section{Scientific Software} - When I joined the Wright Group, I saw that acquisition software was a real barrier to experimental progress and flexibility. % Graduate students had ideas for instrumental enhancements that were infeasible because of the @@ -45,5 +118,69 @@ It offers more fine-grained control of data acquisition and timing, enabling mor algorithms to quickly acquire artifact-free results. % In conjunction with other algorithmic and hardware improvements that I have made, PyCMDS has decreased acquisition times by up to two orders of magnitude. % -A companion software, WrightTools (which I also created), solves some of the processing and -representation challenges of multidimensional data. % \ No newline at end of file + +Like any analytical technique, MR-CMDS is subject to artifacts: features of the data that are +caused by instrumental imperfections or limitations, and do not reflect the intrinsic material +response that is of interest. % +% HOW THE EXPERIMENT WAS DONE, NOT WHAT IT IS HOPING TO MEASURE +For example, M-factors are ... [CITE] and [CITE JONAS PULSE PROPAGATION]. % +Since MR-CMDS is a very active experiment, with many moving motors, an active approach to artifact +correction is particularly appropriate. % +\autoref{cha:act} describes strategies for implementing such corrections. % +Spectral delay correction can be applied to account for the fact that not all output colors arrive +at the same time. % +Dual chopping can correct for scatter and other unwanted processes, ensuring that the observed +signal depends on all of the excitation beams. % +Fibrillation can wash out interference between desired and undesired processes, and is +complementary with chopping. % +Automated poynting correction and power correction can account for non-idealities in OPA +performance. % + +The theory that is used to describe CMDS is typically derived in one of two limits. % +In the impulsive limit, pulses are broad in frequency and short in time compared to material +resonances. % +Resonant responses are impulsive, like a hammer hitting a bell. % +The impulsive limit is particularly well suited for describing time domain experiments. % +In the driven limit, pulses are narrow in frequency and long in time compared to material +response. % +Resonant responses are driven, like a jello dessert sitting on a washing machine. % +The expected spectrum in both of these limits can be computed analytically. [CITE] % +Things get more complicated in the mixed domain, where pulses have similar bandwidth as the +material response. % +Experiments in this domain are a practical necessity as CMDS addresses systems with very fast +dephasing times [CITE]. % +% TODO: cite smallwood and similar somewhere around here +At the same time, the marginal resolution in frequency \emph{and} time that the mixed domain +possess promises huge potential in pathway resolution and decongestion. [CITE JOHN OR ANDREI] % +\autoref{cha:mix} describes the pitfalls and opportunities contained in the mixed domain +approach. % +An intuitive description of mixed-domain experiments is given. % +False signatures of material correlation are discussed, and strategies for resolving true material +correlation are defined. % + +In \hyperref[prt:applications]{Part III: Applications}, three projects in which MR-CMDS was used to +answer chemical questions in materials systems are described. % +These chapters do not directly address improvements to the MR-CMDS methodology, but instead serve +as case studies in the potential of MR-CMDS and the utility of the improvements described in +\autoref{prt:development}. % + +Chapter [...] describes a series of experiments performed on PbSe quantum dots. +PbSe quantum dots are useful because [...] % +We learned [...] % + +Chapter [...] describes an experiment performed on MoS2. +MoS2 is useful because [...] % +We learned [...] % + +Chapter [...] describes an experiment performed on PEDOT:PSS. +useful because... +we learned... + +Despite challenges in software, hardware, and theory MR-CMDS is a crucial tool in the hands of +scientists. % +This dissertation describes several ways to make MR-CMDS more accessible through software and +hardware development. % +PyCMDS has made data collection faster and more artifact-free. % +WrightTools has trivialized data processing, tightening the loop between idea and execution. % +Theory can be used to guide experimental insight in the promising, if challenging, mixed domain. % +Applications of these ideas in three materials are presented. % -- cgit v1.2.3