the way to the transition state in unimolecular
reactions. Mol Phys 106:433–442
99. Bigwood R, Gruebele M, Leitner DM,
Wolynes PG (1998) The vibrational energy
flow transition in organic molecules: theory
meets experiment. Proc Natl Acad Sci U S A
95:5960–5964
100. Gruebele M (2000) Molecular vibrational
energy flow: a state space approach. Adv
Chem Phys 114:193–261
101. Keshavamurthy S (2013) Scaling perspective
on intramolecular vibrational energy flow:
analogies, insights and challenges. Adv
Chem Phys 153:43–110
102. Manikandan P, Keshavamurthy S (2014)
Dynamical traps lead to the slowing down of
intramolecular vibrational energy flow. Proc
Natl Acad Sci U S A 111:14354–14359
103. Leitner DM (1993) Real-symmetric random
matrix ensembles of Hamiltonians with partial symmetry-breaking. Phys Rev E
48:2536–2546
104. Leitner DM, Cederbaum LS (1994) Some
properties of invariant random-matrix ensembles and their connection to ergodic and
nonergodic Hamiltonian systems. Phys Rev
E 49:114–121
105. Leitner DM, Wolynes PG (1997) Quantization of the stochastic pump model of Arnold
diffusion. Phys Rev Lett 79:55–58
106. Leitner DM, Pandey HD (2015) Quantum
bottlenecks and unidirectional energy flow in
molecules. Ann der Phys 527:601–609
107. Leitner DM, Pandey HD (2015) Asymmetric
energy flow in liquid alkylbenzenes: a computational study. J Chem Phys 143:144301
108. Fujisaki H, Stock G (2008) Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment. J
Chem Phys 129(13):134110
109. Leitner DM (2001) Vibrational energy transfer in helices. Phys Rev Lett 87:188102
110. Leitner DM (2001) Vibrational energy transfer and heat conduction in a one-dimensional
glass. Phys Rev B 64:094201
111. Alicki R, Leitner DM (2015) Size-dependent
accuracy of nanoscale thermometers. J Phys
Chem B 119:9000–9005. https://doi.org/
10.1021/jp508047q
112. Leitner DM (2012) Mode damping rates in a
protein chromophore. Chem Phys Lett
530:102–106
113. Leitner DM, Ko ¨ppel H, Cederbaum LS
(1994) Effects of symmetry breaking on spectra of chaotic Hamiltonian systems. Phys Rev
Lett 73:2970–2973
114. Leitner DM, Ko ¨ppel H, Cederbaum LS
(1996) Statistical properties of molecular
spectra and molecular dynamics: analysis of
their correspondence in NO2 and C2H4+. J
Chem Phys 104:434–443
115. Maisuradze GG, Yu X, Leitner DM (2007)
Normal mode analysis and calculation of the
cooling rates of the chromophore vibrations
during isomerization of photoactive yellow
protein. J Biol Phys Chem 7:25–29
116. Xu Y, Gnanasekaran R, Leitner DM (2013)
The dielectric response to photoexcitation of
GFP: a molecular dynamics study. Chem Phys
Lett 564:78–82
117. Pandey HD, Leitner DM (2018) Small saccharides as a blanket around proteins: a
computational study. J Phys Chem B
122:7277–7285. https://doi.org/10.1021/
acs.jpcb.8b04632
118. Pandey HD, Leitner DM (2017) Influence of
thermalization on thermal conduction
through molecular junctions: computational
study of PEG oligomers. J Chem Phys
147:084701
119. Buldum A, Leitner DM, Ciraci S (1999)
Thermal conduction through a molecule.
Europhys Lett 47:208–212
120. Leitner DM, Matsunaga Y, Li C-B,
Komatsuzaki T, Shojiguchi A, Toda M
(2011) Non-brownian phase space dynamics
of molecules, the nature of their vibrational
states, and non-RRKM kinetics. Adv Chem
Phys 145:83–122
121. Komatsuzaki T, Berry RS, Leitner DM
(2011) Advancing theory for kinetics and
dynamics of complex, many-dimensional systems: clusters and proteins, Adv. chem. phys,
vol 145. Wiley, Hoboken
122. Leitner DM, Wolynes PG (2006) Quantum
theory of enhanced unimolecular reaction
rates below the ergodicity threshold. Chem
Phys 329:163–167
123. Leitner DM, Wolynes PG (1997) Quantum
energy flow during molecular isomerization.
Chem Phys Lett 280:411–418
124. Leitner DM, Levine B, Quenneville J, Martı ´nez TJ, Wolynes PG (2003) Quantum energy
flow and trans-stilbene photoisomerization:
an example of a non-RRKM reaction. J Phys
Chem A 107:10706–10716
125. Leitner DM (1999) Influence of quantum
energy flow and localization on molecular
isomerization in gas and condensed phases.
Int J Quantum Chem 75:523–531
126. Nordholm S (1989) Photoisomerization of
stilbene—a theoretical study of deuteration
Locating and Navigating Energy Transport Networks in Proteins
57
reactions. Mol Phys 106:433–442
99. Bigwood R, Gruebele M, Leitner DM,
Wolynes PG (1998) The vibrational energy
flow transition in organic molecules: theory
meets experiment. Proc Natl Acad Sci U S A
95:5960–5964
100. Gruebele M (2000) Molecular vibrational
energy flow: a state space approach. Adv
Chem Phys 114:193–261
101. Keshavamurthy S (2013) Scaling perspective
on intramolecular vibrational energy flow:
analogies, insights and challenges. Adv
Chem Phys 153:43–110
102. Manikandan P, Keshavamurthy S (2014)
Dynamical traps lead to the slowing down of
intramolecular vibrational energy flow. Proc
Natl Acad Sci U S A 111:14354–14359
103. Leitner DM (1993) Real-symmetric random
matrix ensembles of Hamiltonians with partial symmetry-breaking. Phys Rev E
48:2536–2546
104. Leitner DM, Cederbaum LS (1994) Some
properties of invariant random-matrix ensembles and their connection to ergodic and
nonergodic Hamiltonian systems. Phys Rev
E 49:114–121
105. Leitner DM, Wolynes PG (1997) Quantization of the stochastic pump model of Arnold
diffusion. Phys Rev Lett 79:55–58
106. Leitner DM, Pandey HD (2015) Quantum
bottlenecks and unidirectional energy flow in
molecules. Ann der Phys 527:601–609
107. Leitner DM, Pandey HD (2015) Asymmetric
energy flow in liquid alkylbenzenes: a computational study. J Chem Phys 143:144301
108. Fujisaki H, Stock G (2008) Dynamic treatment of vibrational energy relaxation in a heterogeneous and fluctuating environment. J
Chem Phys 129(13):134110
109. Leitner DM (2001) Vibrational energy transfer in helices. Phys Rev Lett 87:188102
110. Leitner DM (2001) Vibrational energy transfer and heat conduction in a one-dimensional
glass. Phys Rev B 64:094201
111. Alicki R, Leitner DM (2015) Size-dependent
accuracy of nanoscale thermometers. J Phys
Chem B 119:9000–9005. https://doi.org/
10.1021/jp508047q
112. Leitner DM (2012) Mode damping rates in a
protein chromophore. Chem Phys Lett
530:102–106
113. Leitner DM, Ko ¨ppel H, Cederbaum LS
(1994) Effects of symmetry breaking on spectra of chaotic Hamiltonian systems. Phys Rev
Lett 73:2970–2973
114. Leitner DM, Ko ¨ppel H, Cederbaum LS
(1996) Statistical properties of molecular
spectra and molecular dynamics: analysis of
their correspondence in NO2 and C2H4+. J
Chem Phys 104:434–443
115. Maisuradze GG, Yu X, Leitner DM (2007)
Normal mode analysis and calculation of the
cooling rates of the chromophore vibrations
during isomerization of photoactive yellow
protein. J Biol Phys Chem 7:25–29
116. Xu Y, Gnanasekaran R, Leitner DM (2013)
The dielectric response to photoexcitation of
GFP: a molecular dynamics study. Chem Phys
Lett 564:78–82
117. Pandey HD, Leitner DM (2018) Small saccharides as a blanket around proteins: a
computational study. J Phys Chem B
122:7277–7285. https://doi.org/10.1021/
acs.jpcb.8b04632
118. Pandey HD, Leitner DM (2017) Influence of
thermalization on thermal conduction
through molecular junctions: computational
study of PEG oligomers. J Chem Phys
147:084701
119. Buldum A, Leitner DM, Ciraci S (1999)
Thermal conduction through a molecule.
Europhys Lett 47:208–212
120. Leitner DM, Matsunaga Y, Li C-B,
Komatsuzaki T, Shojiguchi A, Toda M
(2011) Non-brownian phase space dynamics
of molecules, the nature of their vibrational
states, and non-RRKM kinetics. Adv Chem
Phys 145:83–122
121. Komatsuzaki T, Berry RS, Leitner DM
(2011) Advancing theory for kinetics and
dynamics of complex, many-dimensional systems: clusters and proteins, Adv. chem. phys,
vol 145. Wiley, Hoboken
122. Leitner DM, Wolynes PG (2006) Quantum
theory of enhanced unimolecular reaction
rates below the ergodicity threshold. Chem
Phys 329:163–167
123. Leitner DM, Wolynes PG (1997) Quantum
energy flow during molecular isomerization.
Chem Phys Lett 280:411–418
124. Leitner DM, Levine B, Quenneville J, Martı ´nez TJ, Wolynes PG (2003) Quantum energy
flow and trans-stilbene photoisomerization:
an example of a non-RRKM reaction. J Phys
Chem A 107:10706–10716
125. Leitner DM (1999) Influence of quantum
energy flow and localization on molecular
isomerization in gas and condensed phases.
Int J Quantum Chem 75:523–531
126. Nordholm S (1989) Photoisomerization of
stilbene—a theoretical study of deuteration
Locating and Navigating Energy Transport Networks in Proteins
57