Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

The Journal of Chemical Physics
Hiroshi FujisakiJohn E Straub

Abstract

Without invoking the Markov approximation, we derive formulas for vibrational energy relaxation (VER) and dephasing for an anharmonic system oscillator using a time-dependent perturbation theory. The system-bath Hamiltonian contains more than the third order coupling terms since we take a normal mode picture as a zeroth order approximation. When we invoke the Markov approximation, our theory reduces to the Maradudin-Fein formula which is used to describe the VER properties of glass and proteins. When the system anharmonicity and the renormalization effect due to the environment vanishes, our formulas reduce to those derived by and Mikami and Okazaki [J. Chem. Phys. 121, 10052 (2004)] invoking the path-integral influence functional method with the second order cumulant expansion. We apply our formulas to VER of the amide I mode of a small amino-acid like molecule, N-methylacetamide, in heavy water.

References

Sep 16, 2000·Physical Review Letters·A XieR H Austin
Oct 21, 2000·Physical Review Letters·K MoritsuguA Kidera
Feb 7, 2002·Proceedings of the National Academy of Sciences of the United States of America·Eran RabaniBruce J Berne
Feb 19, 2002·Chemical Reviews·Pavel Jungwirth, R. Benny Gerber
Aug 2, 2003·Nature·Jenny Hogan
Aug 21, 2004·Proceedings of the National Academy of Sciences of the United States of America·Cathie VentalonManuel Joffre
Mar 16, 2005·Proceedings of the National Academy of Sciences of the United States of America·Hiroshi Fujisaki, John E Straub
Oct 26, 2005·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Hiroshi FujisakiAtushi Tanaka

❮ Previous
Next ❯

Citations

Jun 15, 2007·Proceedings of the National Academy of Sciences of the United States of America·Dmitry V KurochkinIgor V Rubtsov
Jan 15, 2014·Physical Chemistry Chemical Physics : PCCP·Henrike M Müller-Werkmeister, Jens Bredenbeck
Nov 27, 2007·The Journal of Chemical Physics·Arend G DijkstraJasper Knoester
Jan 4, 2007·The Journal of Chemical Physics·Yasuteru ShigetaKimihiko Hirao
Jun 24, 2010·The Journal of Chemical Physics·Valeriy M KasyanenkoIgor V Rubtsov
Dec 3, 2008·The Journal of Chemical Physics·Hiroshi Fujisaki, Gerhard Stock
Mar 25, 2011·The Journal of Chemical Physics·Vincent Pouthier
Mar 19, 2008·The Journal of Chemical Physics·Sri Ram G NaraharisettyIgor V Rubtsov
Feb 28, 2019·Journal of Biological Physics·Tika Ram LamichhaneHari Prasad Lamichhane
Sep 4, 2019·Physical Chemistry Chemical Physics : PCCP·Andrea Amadei, Massimiliano Aschi
Jun 6, 2019·Frontiers in Chemistry·Luisa FerrariStefano Turchini
Mar 5, 2009·Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics·Vincent Pouthier
Sep 17, 2008·The Journal of Physical Chemistry. B·Logan R ChieffoLawrence D Ziegler
Oct 16, 2008·The Journal of Physical Chemistry. a·Edwin L SibertTolga S Gulmen
Feb 7, 2012·The Journal of Physical Chemistry. B·Adolfo BastidaSebastián Fernández-Alberti
Aug 1, 2012·The Journal of Physical Chemistry. B·Gudrun NiehuesMartina Havenith
Jul 26, 2011·Physics of Life Reviews·Xiao-feng Pang
Jul 31, 2012·Chemical Physics·Ayanjeet Ghosh, Robin M Hochstrasser

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.