diff options
| -rw-r--r-- | abstract.tex | 2 | ||||
| -rw-r--r-- | bibliography.bib | 202 | ||||
| -rw-r--r-- | dissertation.tex | 10 | ||||
| -rw-r--r-- | introduction/chapter.tex | 49 | ||||
| -rw-r--r-- | spectroscopy/chapter.tex | 9 | ||||
| -rw-r--r-- | todo.org | 3 |
6 files changed, 192 insertions, 83 deletions
diff --git a/abstract.tex b/abstract.tex index c9c8d9e..64d230f 100644 --- a/abstract.tex +++ b/abstract.tex @@ -16,7 +16,7 @@ This approach has several unique capabilities: \end{denumerate} CMDS can be collected in the frequency or the time domain, and each approach has advantages and -disadvantages. % +disadvantages. \cite{ParkKisam1998a} % Frequency domain ``Multi-resonant'' CMDS (MR-CMDS) requires pulsed ultrafast light sources with tunable output frequencies. % These pulses are directed into a material under investigation. % diff --git a/bibliography.bib b/bibliography.bib index 7133357..f3d001a 100644 --- a/bibliography.bib +++ b/bibliography.bib @@ -1,43 +1,14 @@ -@article{FournierFrederic2009a,
- author = {Frederic Fournier and Rui Guo and Elizabeth M. Gardner and Paul M. Donaldson and
- Christian Loeffeld and Ian R. Gould and Keith R. Willison and David R. Klug},
- title = {Biological and Biomedical Applications of Two-Dimensional Vibrational
- Spectroscopy: Proteomics, Imaging, and Structural Analysis},
- journal = {Accounts of Chemical Research},
- volume = 42,
- number = 9,
- pages = {1322--1331},
- year = 2009,
- doi = {10.1021/ar900074p},
- month = {sep},
- publisher = {American Chemical Society ({ACS})},
-}
-
-@article{OmariAbdoulghafar2012a,
- author = {Abdoulghafar Omari and Iwan Moreels and Francesco Masia and Wolfgang Langbein and
- Paola Borri and Dries Van Thourhout and Pascal Kockaert and Zeger Hens},
- title = {Role of interband and photoinduced absorption in the nonlinear refraction and
- absorption of resonantly excited {PbS} quantum dots around 1550 nm},
- journal = {Physical Review B},
- volume = 85,
- number = 11,
- year = 2012,
- doi = {10.1103/physrevb.85.115318},
- month = {mar},
- publisher = {American Physical Society ({APS})},
-}
-
-@article{SheikBahaeMansoor1990a,
- author = "Sheik-Bahae, M and Said, AA and Wei, T-H and Hagan, DJ and Van Stryland, EW",
- title = "Sensitive measurement of optical nonlinearities using a single beam",
- journal = "IEEE journal of quantum electronics.",
- volume = 26,
- number = 4,
- pages = "760--769",
- year = 1990,
- address = "[New York] :",
- issn = "0018-9197",
- publisher = "Institute of Electrical and Electronics Engineers",
+@article{MurdochKiethM2000a,
+ author = {Keith M. Murdoch and David E. Thompson and Kent A. Meyer and John C. Wright},
+ title = {Modeling Window Contributions to Four-Wave Mixing Spectra and Measurements of
+ Third-Order Optical Susceptibilities},
+ journal = {Appl. Spectrosc.},
+ volume = 54,
+ number = 10,
+ pages = {1495--1505},
+ year = 2000,
+ month = {Oct},
+ publisher = {OSA},
}
@article{AartsmaThijsJ1976a,
@@ -297,7 +268,22 @@ publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
-@article{CarlsonRogerJ1990a,
+@article{CarlsonRogerJohn1989a,
+ author = {Roger J. Carlson and John C. Wright},
+ title = {Absorption and Coherent Interference Effects in Multiply Resonant Four-Wave
+ Mixing Spectroscopy},
+ journal = {Applied Spectroscopy},
+ volume = 43,
+ number = 7,
+ pages = {1195--1208},
+ year = 1989,
+ doi = {10.1366/0003702894203408},
+ url = {https://doi.org/10.1366/0003702894203408},
+ month = {sep},
+ publisher = {{SAGE} Publications},
+}
+
+@article{CarlsonRogerJohn1990a,
author = {Carlson, Roger J. and Wright, John C.},
title = {{Line narrowing in multiresonant third order molecular spectroscopies}},
journal = {Journal of Molecular Spectroscopy},
@@ -310,7 +296,7 @@ month = {sep},
}
-@article{CarlsonRogerJ1990b,
+@article{CarlsonRogerJohn1990b,
author = {Carlson, Roger J and Wright, John C},
title = {{Analysis of vibrational correlations and couplings in the lowest two singlet
states of pentacene by high resolution, fully resonant, coherent four‐wave mixing
@@ -325,7 +311,7 @@ month = {may},
}
-@article{CarlsonRogerJ1990c,
+@article{CarlsonRogerJohn1990c,
author = {Carlson, Roger J and Nguyen, Dinh C and Wright, John C},
title = {{Analysis of vibronic mode coupling in pentacene by fully resonant coherent
four‐wave mixing}},
@@ -339,7 +325,7 @@ month = {feb},
}
-@article{CarlsonRogerJ1991a,
+@article{CarlsonRogerJohn1991a,
author = {Carlson, Roger J. and Wright, John C},
title = {{Enhanced selectivity for spectrochemical measurement by mode selection in fully
resonant nonlinear mixing}},
@@ -388,6 +374,19 @@ publisher = {American Chemical Society ({ACS})},
}
+@article{CerulloGiulio2003a,
+ author = {Giulio Cerullo and Sandro De Silvestri},
+ title = {Ultrafast optical parametric amplifiers},
+ journal = {Review of Scientific Instruments},
+ volume = 74,
+ number = 1,
+ pages = {1--18},
+ year = 2003,
+ doi = {10.1063/1.1523642},
+ month = {jan},
+ publisher = {{AIP} Publishing},
+}
+
@article{ChengJixin2001a,
author = {Cheng, Ji-xin and Volkmer, Andreas and Book, Lewis D and Xie, X Sunney},
title = {An Epi-Detected Coherent Anti-Stokes Raman Scattering (E-CARS) Microscope with
@@ -695,7 +694,6 @@ year = {1998} publisher = {{ACM} Press},
}
-
@article{FourkasJohnT1992a,
author = {Fourkas, John T. and Trebino, Rick and Fayer, M. D.},
title = {{The grating decomposition method: A new approach for understanding
@@ -743,6 +741,21 @@ year = {1998} pmid = 18832166,
}
+@article{FournierFrederic2009a,
+ author = {Frederic Fournier and Rui Guo and Elizabeth M. Gardner and Paul M. Donaldson and
+ Christian Loeffeld and Ian R. Gould and Keith R. Willison and David R. Klug},
+ title = {Biological and Biomedical Applications of Two-Dimensional Vibrational
+ Spectroscopy: Proteomics, Imaging, and Structural Analysis},
+ journal = {Accounts of Chemical Research},
+ volume = 42,
+ number = 9,
+ pages = {1322--1331},
+ year = 2009,
+ doi = {10.1021/ar900074p},
+ month = {sep},
+ publisher = {American Chemical Society ({ACS})},
+}
+
@article{FurutaKoichi2012a,
author = {Furuta, Koichi and Fuyuki, Masanori and Wada, Akihide},
title = {Cross-Term Selective, Two-Pulse Correlation Measurements by Phase-Shifted
@@ -771,6 +784,7 @@ year = {1998} month = {aug},
}
+
@article{GelinMaximF2005a,
author = {Gelin, Maxim F. and Egorova, Dassia and Domcke, Wolfgang},
title = {{Efficient method for the calculation of time- and frequency-resolved four-wave
@@ -877,6 +891,20 @@ year = {1998} publisher = {Institute of Electrical and Electronics Engineers ({IEEE})},
}
+@article{HarelElad2010a,
+ author = {E. Harel and A. F. Fidler and G. S. Engel},
+ title = {Real-time mapping of electronic structure with single-shot two-dimensional
+ electronic spectroscopy},
+ journal = {Proceedings of the National Academy of Sciences},
+ volume = 107,
+ number = 38,
+ pages = {16444--16447},
+ year = 2010,
+ doi = {10.1073/pnas.1007579107},
+ month = {sep},
+ publisher = {Proceedings of the National Academy of Sciences},
+}
+
@article{HarelElad2012a,
author = {Elad Harel and Sara M. Rupich and Richard D. Schaller and Dmitri V. Talapin and
Gregory S. Engel},
@@ -928,6 +956,7 @@ year = {1998} journal = {Science},
doi = {10.1126/science.37.955.610},
}
+
@article{HyblJohnD2001a,
author = {Hybl, John D. and {Albrecht Ferro}, Allison and Jonas, David M.},
title = {{Two-dimensional Fourier transform electronic spectroscopy}},
@@ -987,7 +1016,6 @@ year = {1998} publisher = {Farrar, Straus and Giroux},
isbn = {9780374533557},
}
-
@article{KambhampatiPatanjali2011a,
author = {Patanjali Kambhampati},
title = {Unraveling the Structure and Dynamics of Excitons in
@@ -1001,6 +1029,21 @@ year = {1998} month = {jan},
}
+@article{KearnsNicholasM2017a,
+ author = {Nicholas M. Kearns and Randy D. Mehlenbacher and Andrew C. Jones and Martin T.
+ Zanni},
+ title = {Broadband 2D electronic spectrometer using white light and pulse shaping: noise
+ and signal evaluation at 1 and 100 {kHz}},
+ journal = {Optics Express},
+ volume = 25,
+ number = 7,
+ pages = 7869,
+ year = 2017,
+ doi = {10.1364/oe.25.007869},
+ month = {mar},
+ publisher = {The Optical Society},
+}
+
@article{KimNara2013a,
author = {Nara Kim and Seyoung Kee and Seoung Ho Lee and Byoung Hoon Lee and Yung Ho Kahng
and Yong-Ryun Jo and Bong-Joong Kim and Kwanghee Lee},
@@ -1351,6 +1394,19 @@ year = {1998} month = {oct},
}
+@article{MukamelShaul2009a,
+ author = {Shaul Mukamel and Yoshitaka Tanimura and Peter Hamm},
+ title = {Coherent Multidimensional Optical Spectroscopy},
+ journal = {Accounts of Chemical Research},
+ volume = 42,
+ number = 9,
+ pages = {1207--1209},
+ year = 2009,
+ doi = {10.1021/ar900227m},
+ month = {sep},
+ publisher = {American Chemical Society ({ACS})},
+}
+
@inproceedings{MullerMatthiasM2001a,
author = {M.M. Muller and W.F. Tichy},
title = {Case study: extreme programming in a university environment},
@@ -1410,6 +1466,20 @@ year = {1998} issn = {1521-9615},
}
+@article{OmariAbdoulghafar2012a,
+ author = {Abdoulghafar Omari and Iwan Moreels and Francesco Masia and Wolfgang Langbein and
+ Paola Borri and Dries Van Thourhout and Pascal Kockaert and Zeger Hens},
+ title = {Role of interband and photoinduced absorption in the nonlinear refraction and
+ absorption of resonantly excited {PbS} quantum dots around 1550 nm},
+ journal = {Physical Review B},
+ volume = 85,
+ number = 11,
+ year = 2012,
+ doi = {10.1103/physrevb.85.115318},
+ month = {mar},
+ publisher = {American Physical Society ({APS})},
+}
+
@article{OudarJL1980a,
author = {Oudar, J-L. and Shen, Y. R.},
title = {{Nonlinear spectroscopy by multiresonant four-wave mixing}},
@@ -1784,6 +1854,19 @@ year = {1998} publisher = {Royal Society of Chemistry ({RSC})},
}
+@article{SheikBahaeMansoor1990a,
+ author = "Sheik-Bahae, M and Said, AA and Wei, T-H and Hagan, DJ and Van Stryland, EW",
+ title = "Sensitive measurement of optical nonlinearities using a single beam",
+ journal = "IEEE journal of quantum electronics.",
+ volume = 26,
+ number = 4,
+ pages = "760--769",
+ year = 1990,
+ address = "[New York] :",
+ issn = "0018-9197",
+ publisher = "Institute of Electrical and Electronics Engineers",
+}
+
@article{SimSangwan2013a,
author = {Sangwan Sim and Jusang Park and Jeong-Gyu Song and Chihun In
and Yun-Shik Lee and Hyungjun Kim and Hyunyong Choi},
@@ -2086,7 +2169,6 @@ year = {1998} month = {oct},
}
-
@article{WrightJohnCurtis1997a,
author = {Wright, John C.},
title = {{New selective nonlinear vibrational spectroscopies}},
@@ -2100,6 +2182,7 @@ year = {1998} month = {jun},
}
+
@article{WrightJohnCurtis1997b,
author = {Wright, John C. and Chen, Peter C. and Hamilton, James P. and Zilian, Arne and
Labuda, Mitchell J.},
@@ -2170,6 +2253,20 @@ year = {1998} month = {may},
}
+@article{XiongWei2011a,
+ author = {W. Xiong and J. E. Laaser and R. D. Mehlenbacher and M. T. Zanni},
+ title = {Adding a dimension to the infrared spectra of interfaces using heterodyne
+ detected 2D sum-frequency generation ({HD} 2D {SFG}) spectroscopy},
+ journal = {Proceedings of the National Academy of Sciences},
+ volume = 108,
+ number = 52,
+ pages = {20902--20907},
+ year = 2011,
+ doi = {10.1073/pnas.1115055108},
+ month = {dec},
+ publisher = {Proceedings of the National Academy of Sciences},
+}
+
@article{XuXiaodong2014a,
author = {Xiaodong Xu and Wang Yao and Di Xiao and Tony F. Heinz},
title = {Spin and pseudospins in layered transition metal dichalcogenides},
@@ -2274,6 +2371,17 @@ year = {1998} year = 2000,
}
+@ARTICLE{ZhaoWei2000b,
+ author = {{Zhao}, W. and {Wright}, J.~C.},
+ doi = {10.1103/PhysRevLett.84.1411},
+ journal = {Physical Review Letters},
+ month = feb,
+ pages = {1411-1414},
+ title = "{Doubly Vibrationally Enhanced Four Wave Mixing: The Optical Analog to 2D NMR}",
+ volume = 84,
+ year = 2000,
+}
+
@article{ZhuBairen2014a,
author = {Bairen Zhu and Hualing Zeng and Junfeng Dai and Xiaodong Cui},
title = {The Study of Spin-Valley Coupling in Atomically Thin Group {VI} Transition Metal
diff --git a/dissertation.tex b/dissertation.tex index b1d10fe..29d1821 100644 --- a/dissertation.tex +++ b/dissertation.tex @@ -68,11 +68,11 @@ This dissertation is approved by the following members of the Final Oral Committ \include{software/chapter}
\part{Development} \label{prt:development}
-\include{processing/chapter}
-\include{acquisition/chapter}
-\include{active_correction/chapter}
-\include{opa/chapter}
-\include{mixed_domain/chapter}
+%\include{processing/chapter}
+%\include{acquisition/chapter}
+%\include{active_correction/chapter}
+%\include{opa/chapter}
+%\include{mixed_domain/chapter}
\part{Applications} \label{prt:applications}
%\include{PbSe/chapter}
diff --git a/introduction/chapter.tex b/introduction/chapter.tex index 007b95d..42943a5 100644 --- a/introduction/chapter.tex +++ b/introduction/chapter.tex @@ -19,39 +19,42 @@ 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). %
+It is similar to more familiar multidimensional NMR experiments \cite{ZhaoWei2000b,
+ PakoulevAndreiV2006a}, 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. %
+between them. \cite{RentzepisPM1970a} %
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] %
+time to collect a multidimensional interferogram. \cite{MukamelShaul2009a, GallagherSarahM1998a} %
+This technique is fast and robust---it has even been performed on a single shot.
+\cite{HarelElad2010a} %
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]
+ pulses are hard to make and control. \cite{SpencerAustinP2015a} %
\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]. %
+the envelope in excitation pulse bandwidth \cite{KearnsNicholasM2017a} and performing two-stage
+experiments in which excitation pulses are used to generate a local oscillator in non-resonant
+media \cite{XiongWei2011a}. %
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. %
+Motorized optical parametric amplifiers (OPAs) are typically used to provide this tunability.
+\cite{CerulloGiulio2003a} %
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. %
+analytical tool. \cite{PakoulevAndreiV2009a} %
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
@@ -59,12 +62,10 @@ accessible. % Finally, because the components are more self-contained, MR-CMDS instruments tend to be more
flexible 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. % JCW- NOT SO SURE IT CAN'T BE SINGLE SHOT
+data collection speed. % JCW: NOT SO SURE IT CAN'T BE SINGLE SHOT
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. %
@@ -135,11 +136,13 @@ decreased acquisition times by up to two orders of magnitude. % 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]. %
+% JCW: HOW THE EXPERIMENT WAS DONE, NOT WHAT IT IS HOPING TO MEASURE
+For example, consider absorptive effects \cite{CarlsonRogerJohn1989a}, pulse effects
+\cite{SpencerAustinP2015a}, and window contributions \cite{MurdochKiethM2000a}: all well-known
+artifacts in CMDS. %
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. %
+Chapter \ref{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
@@ -157,15 +160,15 @@ The impulsive limit is particularly well suited for describing time domain exper 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] %
+The expected spectrum in both of these limits can be computed analytically. %
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
+dephasing times. \cite{SmallwoodChristopherL2016a, PerlikVaclav2017a} %
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
+possess promises huge potential in pathway resolution and decongestion.
+\cite{PakoulevAndreiV2009a} %
+Chapter \ref{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
diff --git a/spectroscopy/chapter.tex b/spectroscopy/chapter.tex index a70cd69..b07a407 100644 --- a/spectroscopy/chapter.tex +++ b/spectroscopy/chapter.tex @@ -232,14 +232,9 @@ pulse, and pulses with very large frequency bandwidth (very short in time) becom and control. %
With short, broad pulses:
\begin{ditemize}
- \item Non-resonant signal becomes brighter relative to resonant signal. [CITE]
- \item Pulse distortions become important. [CITE JONAS]
+ \item Non-resonant signal becomes brighter relative to resonant signal. \cite{ChengJixin2001a}
+ \item Pulse distortions become essentially unavoidable. \cite{SpencerAustinP2015a}
\end{ditemize}
-%This epi-CARS paper might have some useful discussion of non-resonant vs resonant for shorter and
-%shorter pulses \cite{ChengJixin2001a}. %
-%An excellent discussion of pulse distortion phenomena in broadband time-domain experiments was
-%published by \textcite{SpencerAustinP2015a}. %
-%See Paul's dissertation
Time domain experiments require a phase-locked, independently controlled local oscillator in order
to collect the interferogram at the heart of such techniques. %
@@ -6,6 +6,9 @@ CLOSED: [2018-04-07 Sat 15:57] * DONE citations :abstract: CLOSED: [2018-04-07 Sat 16:47] +* DONE citations :introduction: + CLOSED: [2018-04-07 Sat 18:19] +* TODO see Paul's dissertation re: loss of resonance advantage with very fast pulses :spectroscopy: * TODO describe spectroscopic instrument :spectroscopy: * TODO incorporate "most software is not peer reviewed" :software: ** see Joppa reference 6 |