PERFORM Publications

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Title		Authors	PubMed ID
1	Nonphotochemical Spectral Hole Burning Study of Modified LH2 Complex from em Rbl. acidophilus /em : Do Parts of the Pigment Molecule Affect Small Light-Induced Structural Changes?	Levenberg A; Trempe A; Lujan MA; Picorel R; Zazubovich V;	41802209 PHYSICS
2	Rigorous Quantum-Mechanical Modeling of Tunneling-Based Structural Changes Associated with Line Shifts in Optical Spectroscopy Experiments in Pigment-Protein Complexes	Eng-Michell J; Yi B; Tan X; Garashchuk S; Zazubovich V;	41662623 PHYSICS
3	High-Resolution Frequency-Domain Spectroscopic and Modeling Studies of Photosystem I (PSI), PSI Mutants and PSI Supercomplexes	Zazubovich V; Jankowiak R;	38612659 PHYSICS
4	Identification of Residues Potentially Involved in Optical Shifts in the Water-Soluble Chlorophyll a-Binding Protein through Molecular Dynamics Simulations	Mai M; Zazubovich V; Mansbach RA;	38299975 PHYSICS
5	Frequency-Domain Spectroscopic Study of the Photosystem I Supercomplexes, Isolated IsiA Monomers, and the Intact IsiA Ring	Reinot T; Khmelnitskiy A; Zazubovich V; Toporik H; Mazor Y; Jankowiak R;	36065077 PHYSICS
6	Functional analysis of low-grade glioma genetic variants predicts key target genes and transcription factors.	Manjunath M; Yan J; Youn Y; Drucker KL; Kollmeyer TM; McKinney AM; Zazubovich V; Zhang Y; Costello JF; Eckel-Passow J; Selvin PR; Jenkins RB; Song JS;	33130899 PHYSICS
7	Bound detergent molecules in bacterial reaction centers facilitate detection of tetryl explosive.	Modafferi D, Zazubovich V, Kálmán L	32632533 PHYSICS
8	Evidence of Simultaneous Spectral Hole Burning Involving Two Tiers of the Protein Energy Landscape in Cytochrome b6f.	Shafiei G, Levenberg A, Lujan MA, Picorel R, Zazubovich V	31763829 PHYSICS
9	How Well Does the Hole-Burning Action Spectrum Represent the Site-Distribution Function of the Lowest-Energy State in Photosynthetic Pigment-Protein Complexes?	Zazubovich V, Jankowiak R	31265294 CHEMISTRY
10	Low-temperature protein dynamics of the B800 molecules in the LH2 light-harvesting complex: spectral hole burning study and comparison with single photosynthetic complex spectroscopy.	Grozdanov D, Herascu N, Reinot T, Jankowiak R, Zazubovich V	20166717 PHYSICS
11	Parameters of the protein energy landscapes of several light-harvesting complexes probed via spectral hole growth kinetics measurements.	Herascu N, Najafi M, Amunts A, Pieper J, Irrgang KD, Picorel R, Seibert M, Zazubovich V	21391534 PHYSICS
12	Self-assembly and sensor response of photosynthetic reaction centers on screen-printed electrodes.	Bhalla V, Zazubovich V	22027137 PHYSICS
13	Effects of the distributions of energy or charge transfer rates on spectral hole burning in pigment-protein complexes at low temperatures.	Herascu N, Ahmouda S, Picorel R, Seibert M, Jankowiak R, Zazubovich V	22046956 PHYSICS
14	Spectral hole burning, recovery, and thermocycling in chlorophyll-protein complexes: distributions of barriers on the protein energy landscape.	Najafi M, Herascu N, Seibert M, Picorel R, Jankowiak R, Zazubovich V	22957798 PHYSICS
15	Modeling of various optical spectra in the presence of slow excitation energy transfer in dimers and trimers with weak interpigment coupling: FMO as an example.	Herascu N, Kell A, Acharya K, Jankowiak R, Blankenship RE, Zazubovich V	24506338 PHYSICS
16	On the Controversial Nature of the 825 nm Exciton Band in the FMO Protein Complex.	Kell A, Acharya K, Zazubovich V, Jankowiak R	26269993 PHYSICS
17	Fluorescence line narrowing and Δ-FLN spectra in the presence of excitation energy transfer between weakly coupled chromophores.	Zazubovich V	25369116 PHYSICS
18	Conformational Changes in Pigment-Protein Complexes at Low Temperatures-Spectral Memory and a Possibility of Cooperative Effects.	Najafi M, Herascu N, Shafiei G, Picorel R, Zazubovich V	25985255 PHYSICS
19	Monte Carlo Modeling of Spectral Diffusion Employing Multiwell Protein Energy Landscapes: Application to Pigment-Protein Complexes Involved in Photosynthesis.	Najafi M, Zazubovich V	26020801 PHYSICS
20	On the Conflicting Estimations of Pigment Site Energies in Photosynthetic Complexes: A Case Study of the CP47 Complex.	Reinot T, Chen J, Kell A, Jassas M, Robben KC, Zazubovich V, Jankowiak R	27279733 PHYSICS
21	A simple and efficient method to prepare pure dimers and monomers of the cytochrome b 6 f complex from spinach.	Luján MA, Lorente P, Zazubovich V, Picorel R	28374305 PHYSICS
22	Probing Energy Landscapes of Cytochrome b6f with Spectral Hole Burning: Effects of Deuterated Solvent and Detergent.	Levenberg A, Shafiei G, Lujan MA, Giannacopoulos S, Picorel R, Zazubovich V	28956922 PHYSICS
23	Spectral Hole Burning in Cyanobacterial Photosystem I with P700 in Oxidized and Neutral States.	Herascu N, Hunter MS, Shafiei G, Najafi M, Johnson TW, Fromme P, Zazubovich V	27661089 CHEMBIOCHEM

Title:	Monte Carlo Modeling of Spectral Diffusion Employing Multiwell Protein Energy Landscapes: Application to Pigment-Protein Complexes Involved in Photosynthesis.
Authors:	Najafi M, Zazubovich V
Link:	https://www.ncbi.nlm.nih.gov/pubmed/26020801?dopt=Abstract
Publication:
Keywords:
PMID:	26020801	Category:	J Phys Chem B	Date Added:	2019-06-04
Dept Affiliation:	PHYSICS 1 Department of Physics, Concordia University, Montreal H4B 1R6, Quebec, Canada.

Description:

Monte Carlo Modeling of Spectral Diffusion Employing Multiwell Protein Energy Landscapes: Application to Pigment-Protein Complexes Involved in Photosynthesis.

J Phys Chem B. 2015 Jun 25;119(25):7911-21

Authors: Najafi M, Zazubovich V

Abstract

We are reporting development and initial applications of the light-induced and thermally induced spectral diffusion modeling software, covering nonphotochemical spectral hole burning (NPHB), hole recovery, and single-molecule spectroscopy and involving random generation of the multiwell protein energy landscapes. The model includes tunneling and activated barrier-hopping in both ground and excited states of a protein-chromophore system. Evolution of such a system is predicted by solving the system of rate equations. Using the barrier parameters from the range typical for the energy landscapes of the pigment-protein complexes involved in photosynthesis, we (a) show that realistic cooling of the sample must result in proteins quite far from thermodynamic equilibrium, (b) demonstrate hole evolution in the cases of burning, fixed-temperature recovery and thermocycling that mostly agrees with the experiment and modeling based on the NPHB master equation, and (c) explore the effects of different protein energy landscapes on the antihole shape. Introducing the multiwell energy landscapes and starting the hole burning experiments in realistic nonequilibrium conditions are not sufficient to explain all experimental observations even qualitatively. Therefore, for instance, one is required to invoke the modified NPHB mechanism where a complex interplay of several small conformational changes is poising the energy landscape of the pigment-protein system for downhill tunneling.

PMID: 26020801 [PubMed - indexed for MEDLINE]

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