1
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Romanelli G, Andreani C, Bocedi A, Senesi R. Quantum motion of oxygen and hydrogen in water: Atomic and total kinetic energy across melting from neutron scattering measurements. J Chem Phys 2024; 160:234503. [PMID: 38884402 DOI: 10.1063/5.0211165] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2024] [Accepted: 05/22/2024] [Indexed: 06/18/2024] Open
Abstract
We provide a concurrent measurement of the hydrogen and oxygen nuclear kinetic energies in the water molecule across melting at 270 K in the solid phase and 276 K in the liquid phase. Experimental values are obtained by analyzing the neutron Compton profiles of each atomic species in a deep inelastic neutron scattering experiment. The concurrent measurement of the atom kinetic energy of both hydrogen and oxygen allows the estimate of the total kinetic energy per molecule due to the motion of nuclei, specifically 35.3 ± 0.8 and 34.8 ± 0.8 kJ/mol for the solid and liquid phases, respectively. Such a small difference supports results from ab initio simulations and phenomenological models from the literature on the mechanism of competing quantum effects across the phase change. Despite the experimental uncertainties, the results are consistent with the trend from state-of-the-art computer simulations, whereby the atom and molecule kinetic energies in the liquid phase would be slightly lower than in the solid phase. Moreover, the small change of nuclear kinetic energy across melting can be used to simplify the calculation of neutron-related environmental dose in complex locations, such as high altitude or polar neutron radiation research stations where liquid water and ice are both present: for neutron energies between hundreds of meV and tens of keV, the total scattering cross section per molecule in the two phases can be considered the same, with the macroscopic cross section only depending upon the density changes of water near the melting point.
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Affiliation(s)
- Giovanni Romanelli
- Dipartimento di Fisica and NAST Centre, Università degli Studi di Roma "Tor Vergata," via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Carla Andreani
- Dipartimento di Fisica and NAST Centre, Università degli Studi di Roma "Tor Vergata," via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Alessio Bocedi
- Dipartimento di Scienze e Tecnologie Chimiche and NAST Centre, Università degli Studi di Roma "Tor Vergata," via della Ricerca Scientifica 1, 00133 Rome, Italy
| | - Roberto Senesi
- Dipartimento di Fisica and NAST Centre, Università degli Studi di Roma "Tor Vergata," via della Ricerca Scientifica 1, 00133 Rome, Italy
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2
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Zhang Y, Oberg CP, Hu Y, Xu H, Yan M, Scholes GD, Wang M. Molecular and Supramolecular Materials: From Light-Harvesting to Quantum Information Science and Technology. J Phys Chem Lett 2024:3294-3316. [PMID: 38497707 DOI: 10.1021/acs.jpclett.4c00264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The past two decades have witnessed immense advances in quantum information technology (QIT), benefited by advances in physics, chemistry, biology, and materials science and engineering. It is intriguing to consider whether these diverse molecular and supramolecular structures and materials, partially inspired by quantum effects as observed in sophisticated biological systems such as light-harvesting complexes in photosynthesis and the magnetic compass of migratory birds, might play a role in future QIT. If so, how? Herein, we review materials and specify the relationship between structures and quantum properties, and we identify the challenges and limitations that have restricted the intersection of QIT and chemical materials. Examples are broken down into two categories: materials for quantum sensing where nonclassical function is observed on the molecular scale and systems where nonclassical phenomena are present due to intermolecular interactions. We discuss challenges for materials chemistry and make comparisons to related systems found in nature. We conclude that if chemical materials become relevant for QIT, they will enable quite new kinds of properties and functions.
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Affiliation(s)
- Yipeng Zhang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Catrina P Oberg
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Yue Hu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Hongxue Xu
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Mengwen Yan
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
| | - Gregory D Scholes
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, United States
| | - Mingfeng Wang
- School of Science and Engineering, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P. R. China
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3
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Zarmi Y. High-intensity pulsed-light cultivation of unicellular algae: Photosynthesis continues in the dark. Heliyon 2024; 10:e27224. [PMID: 38495149 PMCID: PMC10943342 DOI: 10.1016/j.heliyon.2024.e27224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 12/15/2023] [Accepted: 02/26/2024] [Indexed: 03/19/2024] Open
Abstract
Experiments have shown that photon exploitation efficiency in unicellular algal biomass production under a pulsed-light regime with a high-photon flux is higher than the efficiency under continuous illumination with the same flux. This observation has been explained theoretically to be a consequence of the improved efficiency of exploitation of photons by Photosystem II (PS II) thanks to the combined effect of photon-absorption statistics, a rate-limiting time scale and the size of the PQ pool. Exploiting the same ideas, it is shown in this paper that, under a pulsed-light regime, there is a pulse-time length, for which the average exploitation efficiency of PS II absorbed photons is maximal. Under ideal conditions, this maximum is close to 100%. The optimal pulse-time length is roughly proportional to the size of the PQ pool, NPQ. This is clearly seen for τ (the average time gap between consecutive photons absorbed by the PS II-Chlorophyll antenna) of the order of 1 ms or less (corresponding to a high photon flux and/or a large photon absorption cross-section area of the antenna) and for small NPQ. The width of the plot of efficiency vs. pulse length around the optimum is then small and the optimal pulse length is well defined. As τ is increased beyond 1 or NPQ becomes large, the width grows, allowing for a broad choice of pulse lengths, for which efficiency is very close to the maximum. These observations open the door to future designs of highly productive bioreactors.
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Affiliation(s)
- Yair Zarmi
- Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, 8499000, Israel
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4
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Mokhtari M, Khoshbakht S, Ziyaei K, Akbari ME, Moravveji SS. New classifications for quantum bioinformatics: Q-bioinformatics, QCt-bioinformatics, QCg-bioinformatics, and QCr-bioinformatics. Brief Bioinform 2024; 25:bbae074. [PMID: 38446742 PMCID: PMC10939336 DOI: 10.1093/bib/bbae074] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Revised: 11/14/2023] [Accepted: 02/07/2021] [Indexed: 03/08/2024] Open
Abstract
Bioinformatics has revolutionized biology and medicine by using computational methods to analyze and interpret biological data. Quantum mechanics has recently emerged as a promising tool for the analysis of biological systems, leading to the development of quantum bioinformatics. This new field employs the principles of quantum mechanics, quantum algorithms, and quantum computing to solve complex problems in molecular biology, drug design, and protein folding. However, the intersection of bioinformatics, biology, and quantum mechanics presents unique challenges. One significant challenge is the possibility of confusion among scientists between quantum bioinformatics and quantum biology, which have similar goals and concepts. Additionally, the diverse calculations in each field make it difficult to establish boundaries and identify purely quantum effects from other factors that may affect biological processes. This review provides an overview of the concepts of quantum biology and quantum mechanics and their intersection in quantum bioinformatics. We examine the challenges and unique features of this field and propose a classification of quantum bioinformatics to promote interdisciplinary collaboration and accelerate progress. By unlocking the full potential of quantum bioinformatics, this review aims to contribute to our understanding of quantum mechanics in biological systems.
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Affiliation(s)
- Majid Mokhtari
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
| | - Samane Khoshbakht
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
- Duke Molecular Physiology Institute, Duke University School of Medicine-Cardiology, Durham, NC, 27701, USA
| | - Kobra Ziyaei
- Department of Fisheries, Faculty of Natural Resources, University of Tehran, Karaj, Iran
| | | | - Sayyed Sajjad Moravveji
- Department of Bioinformatics, Kish International Campus, University of Tehran, Kish Island, Iran
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5
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Civolani A, Stanzione V, Chiofalo ML, Yago Malo J. Engineering Transport via Collisional Noise: A Toolbox for Biology Systems. ENTROPY (BASEL, SWITZERLAND) 2023; 26:20. [PMID: 38248146 PMCID: PMC10814428 DOI: 10.3390/e26010020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/23/2024]
Abstract
The study of noise assisted-transport in quantum systems is essential in a wide range of applications, from near-term NISQ devices to models for quantum biology. Here, we study a generalized XXZ model in the presence of stochastic collision noise, which allows describing environments beyond the standard Markovian formulation. Our analysis through the study of the local magnetization, the inverse participation ratio (IPR) or its generalization, and the inverse ergodicity ratio (IER) showed clear regimes, where the transport rate and coherence time could be controlled by the dissipation in a consistent manner. In addition, when considering various excitations, we characterized the interplay between collisions and system interactions, identifying regimes in which transport was counterintuitively enhanced when increasing the collision rate, even in the case of initially separated excitations. These results constitute an example of an essential building block for the understanding of quantum transport in structured noisy and warm-disordered environments.
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Affiliation(s)
| | | | | | - Jorge Yago Malo
- Dipartimento di Fisica Enrico Fermi, Università di Pisa and INFN, Largo B. Pontecorvo 3, I-56127 Pisa, Italy; (A.C.); (M.L.C.)
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6
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Yago Malo J, Cicchini GM, Morrone MC, Chiofalo ML. Quantum spin models for numerosity perception. PLoS One 2023; 18:e0284610. [PMID: 37098002 PMCID: PMC10128973 DOI: 10.1371/journal.pone.0284610] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 04/04/2023] [Indexed: 04/26/2023] Open
Abstract
Humans share with animals, both vertebrates and invertebrates, the capacity to sense the number of items in their environment already at birth. The pervasiveness of this skill across the animal kingdom suggests that it should emerge in very simple populations of neurons. Current modelling literature, however, has struggled to provide a simple architecture carrying out this task, with most proposals suggesting the emergence of number sense in multi-layered complex neural networks, and typically requiring supervised learning; while simple accumulator models fail to predict Weber's Law, a common trait of human and animal numerosity processing. We present a simple quantum spin model with all-to-all connectivity, where numerosity is encoded in the spectrum after stimulation with a number of transient signals occurring in a random or orderly temporal sequence. We use a paradigmatic simulational approach borrowed from the theory and methods of open quantum systems out of equilibrium, as a possible way to describe information processing in neural systems. Our method is able to capture many of the perceptual characteristics of numerosity in such systems. The frequency components of the magnetization spectra at harmonics of the system's tunneling frequency increase with the number of stimuli presented. The amplitude decoding of each spectrum, performed with an ideal-observer model, reveals that the system follows Weber's law. This contrasts with the well-known failure to reproduce Weber's law with linear system or accumulators models.
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Affiliation(s)
- Jorge Yago Malo
- Department of Physics "Enrico Fermi" and INFN, University of Pisa, Pisa, Italy
| | | | - Maria Concetta Morrone
- Department of Translational Research and of New Surgical and Medical Technologies, University of Pisa and PisaVisionLab, Pisa, Italy
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7
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Li G, Hu Y, Pei S, Meng J, Wang J, Wang J, Yue S, Wang Z, Wang S, Liu X, Weng Y, Peng X, Zhao Q. Excited-state dynamics of all-trans protonated retinal Schiff base in CRABPII-based rhodopsin mimics. Biophys J 2022; 121:4109-4118. [PMID: 36181266 PMCID: PMC9675042 DOI: 10.1016/j.bpj.2022.09.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 09/06/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
The rhodopsin mimic is a chemically synthetized complex with retinyl Schiff base (RSB) formed between protein and the retinal chromophore that can mimic the natural rhodopsin-like protein. The artificial rhodopsin mimic is more stable and designable than the natural protein and hence has wider uses in photon detection devices. The mimic structure RSB, like the case in the actual rhodopsin-like protein, undergoes isomerization and protonation throughout the photoreaction process. As a result, understanding the dynamics of the RSB in the photoreaction process is critical. In this study, the ultrafast transient absorption spectra of three mutants of the cellular retinoic acid-binding protein II-based rhodopsin mimic at acidic environment were recorded, from which the related excited-state dynamics of the all-trans protonated RSB (AT-PRSB) were investigated. The transient fluorescence spectra measurements are used to validate some of the dynamic features. We find that the excited-state dynamics of AT-PRSB in three mutants share a similar pattern that differs significantly from the dynamics of 15-cis PRSB of the rhodopsin mimic in neutral solution. By comparing the dynamics across the three mutants, we discovered that the aromatic residues near the β-ionone ring structure of the retinal may help stabilize the AT-PRSB and hence slow down its isomerization rate. The experimental results provide implications on designing a rhodopsin-like protein with significant infrared fluorescence, which can be particularly useful in the applications in biosensing or bioimaging in deeper tissues.
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Affiliation(s)
- Gaoshang Li
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Yongnan Hu
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Sizhu Pei
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Jiajia Meng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China
| | - Jiayu Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Ju Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
| | - Shuai Yue
- National Center for Nanoscience and Nanotechnology, Beijing, China
| | - Zhuan Wang
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China
| | - Shufeng Wang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, Department of Physics, Peking University, Beijing, China
| | - Xinfeng Liu
- National Center for Nanoscience and Nanotechnology, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Yuxiang Weng
- Beijing National Laboratory for Condensed Matter Physics, Laboratory of Soft Matter Physics, Institute of Physics, Chinese Academy of Sciences, Beijing, China; University of Chinese Academy of Sciences, Beijing, China
| | - Xubiao Peng
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China; Beijing Academy of Quantum Information Sciences, Beijing, China.
| | - Qing Zhao
- Center for Quantum Technology Research, Key Laboratory of Advanced Optoelectronic Quantum Architecture and Measurements (MOE), School of Physics, Beijing Institute of Technology, Beijing, China; Beijing Academy of Quantum Information Sciences, Beijing, China.
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8
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Chakraborty B, Jha R, Kar S, Chattaraj PK. Controlling Tunneling Oscillation and Quantum Localization in an Asymmetric Double-Well Potential: A Bohmian Perspective. J Phys Chem A 2022; 126:4834-4847. [PMID: 35834735 DOI: 10.1021/acs.jpca.2c03049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The roles of spatial symmetry and strength of external time-dependent perturbation on the dynamics of a quantum particle, initially localized in one of the wells of an asymmetric double-well potential are studied using the recently developed techniques incorporating quantum theory of motion and time-dependent Fourier grid Hamiltonian methods. The model used here includes a mimic of the related experimental situations which is considered as a perturbation to the static double-well potential. Analysis of localized and delocalized phase space structures and corresponding time-profile of tunneling probability reveal the recipe toward controlling the tunneling oscillations by modulating the parameters of applied perturbation. A study on a stochastic pulsating potential also reveals the root to the quantum localization, even in moderate field strength.
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Affiliation(s)
- Bhrigu Chakraborty
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Ruchi Jha
- Advanced Technology Development Centre, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
| | - Susmita Kar
- Department of Chemistry, Scottish Church College, Kolkata 700006, India
| | - Pratim Kumar Chattaraj
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India
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9
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Rammler T, Wackenhut F, Zur Oven-Krockhaus S, Rapp J, Forchhammer K, Harter K, Meixner AJ. Strong coupling between an optical microcavity and photosystems in single living cyanobacteria. JOURNAL OF BIOPHOTONICS 2022; 15:e202100136. [PMID: 34761529 DOI: 10.1002/jbio.202100136] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2021] [Revised: 10/15/2021] [Accepted: 11/08/2021] [Indexed: 06/13/2023]
Abstract
The first step in photosynthesis is an extremely efficient energy transfer mechanism that led to the debate to which extent quantum coherence may be involved in the energy transfer between the photosynthetic pigments. In search of such a coherent behavior, we have embedded living cyanobacteria between the parallel mirrors of an optical microresonator irradiated with low intensity white light. As a consequence, we observe vacuum Rabi splitting in the transmission and fluorescence spectra as a result of strong light matter coupling of the chlorophyll a molecules in the photosystems (PSs) and the cavity modes. The Rabi-splitting scales with the number of the PSs chlorophyll a pigments involved in strong coupling indicating a delocalized polaritonic state. Our data provide evidence that a delocalized polaritonic state can be established between the chlorophyll a molecule of the PSs in living cyanobacterial cells at ambient conditions in a microcavity.
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Affiliation(s)
- Tim Rammler
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Frank Wackenhut
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
| | - Sven Zur Oven-Krockhaus
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Johanna Rapp
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Karl Forchhammer
- Interfaculty Institute of Microbiology and Infection Medicine, University of Tübingen, Tübingen, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Alfred J Meixner
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Tübingen, Germany
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10
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Mubeen M, Khalid MA, Mukhtar M, Sumreen P, Gul T, Ul Ain N, Shahrum S, Tabassum M, Ul-Hamid A, Iqbal A. Elucidating the Size-dependent FRET Efficiency in Interfacially Engineered Quantum Dots attached PBSA Sunscreen. Photochem Photobiol 2022; 98:1017-1024. [PMID: 35092012 DOI: 10.1111/php.13599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 01/24/2022] [Indexed: 11/30/2022]
Abstract
Applying sunscreen on human skin provides photoprotection against the harmful ultraviolet (UV) radiation of the sun. Sunscreen absorbs UV radiations and dissipates the absorbed energy through various radiative and non-radiative pathways. The attachment of functionalized quantum dots (QDs) to the sunscreen component is a novel idea to enhance the absorption cross-section of UV radiations. Therefore, the attachment of the sunscreen component to the ligand functionalized biocompatible QDs and the absorbed energy transfer from sunscreen to the QDs could work as a model system to overall improve the efficiency of the sunscreen. This study elucidates the mechanism of size-dependent Förster resonance energy transfer (FRET) efficiency and its rate between 2-phenylbenzimidazole-5-sulfonic acid (PBSA) and mercaptoacetic acid (MAA) functionalized CdS QDs. In the PBSA-QDs dyad, the PBSA (donor) dissipates UV-absorbed energy to the CdS QDs (acceptor). Following excitation at 306 nm, the steady-state photoluminescence (SSPL) and time-resolved photoluminescence (TRPL) techniques measurements demonstrate that both the non-radiative energy transfer efficiency and rate are QDs size-dependent in addition to donor-acceptor distance, and suggest that bigger sized-QDs result in an increase of the FRET efficiency.
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Affiliation(s)
- Muhammad Mubeen
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | | | - Maria Mukhtar
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Poshmal Sumreen
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Tehreem Gul
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Noor Ul Ain
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Saba Shahrum
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Mamoona Tabassum
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
| | - Anwar Ul-Hamid
- Core Research Facilities, King Fahd University of Petroleum & Minerals, Dhahran, 31261, Saudi Arabia
| | - Azhar Iqbal
- Department of Chemistry, Quaid-I-Azam University Islamabad-45320, Pakistan
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11
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Brovarets’ OO, Muradova A, Hovorun DM. Novel horizons of the conformationally-tautomeric transformations of the G·T base pairs: quantum-mechanical investigation. Mol Phys 2022. [DOI: 10.1080/00268976.2022.2026510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Ol’ha O. Brovarets’
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
| | - Alona Muradova
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
| | - Dmytro M. Hovorun
- Department of Molecular and Quantum Biophysics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kyiv, Ukraine
- Department of Molecular Biotechnology and Bioinformatics, Institute of High Technologies, Taras Shevchenko National University of Kyiv, Kyiv, Ukraine
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12
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Cahen D, Pecht I, Sheves M. What Can We Learn from Protein-Based Electron Transport Junctions? J Phys Chem Lett 2021; 12:11598-11603. [PMID: 34852460 PMCID: PMC8647078 DOI: 10.1021/acs.jpclett.1c02446] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Affiliation(s)
- David Cahen
- Weizmann Institute of Science, Rehovot 7610001, Israel
| | - Israel Pecht
- Weizmann Institute of Science, Rehovot 7610001, Israel
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13
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Renger T. Semiclassical Modified Redfield and Generalized Förster Theories of Exciton Relaxation/Transfer in Light-Harvesting Complexes: The Quest for the Principle of Detailed Balance. J Phys Chem B 2021; 125:6406-6416. [PMID: 34126008 PMCID: PMC8237266 DOI: 10.1021/acs.jpcb.1c01479] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
A conceptual problem
of transfer theories that use a semiclassical
description of the electron-vibrational coupling is the neglect of
the correlation between momenta and coordinates of nuclei. In the
Redfield theory of exciton relaxation, this neglect leads to a violation
of the principle of detailed balance; equal “uphill”
and “downhill” transfer rate constants are obtained.
Here, we investigate how this result depends on nuclear reorganization
effects, neglected in Redfield but taken into account in the modified
Redfield theory. These reorganization effects, resulting from a partial
localization of excited states, are found to promote a preferential
“downhill” relaxation of excitation energy. However,
for realistic spectral densities of light-harvesting antennae in photosynthesis,
the reorganization effects are too small to compensate for the missing
coordinate–momentum uncertainty. For weaker excitonic couplings
as they occur between domains of strongly coupled pigments, we find
the principle of detailed balance to be fulfilled in a semiclassical
variant of the generalized Förster theory. A qualitatively
correct description of the transfer is obtained with this theory at
a significantly lower computational cost as with the quantum generalized
Förster theory. Larger deviations between the two theories
are expected for large energy gaps as they occur in complexes with
chemically different pigments.
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Affiliation(s)
- Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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14
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Sordillo LA, Budansky Y, Alfano RR. Photosynthesis on the Ultrafast Time Scale within the Confinements of Quantum Nanostructured Photosystems. Photochem Photobiol 2021; 97:727-731. [PMID: 33521957 DOI: 10.1111/php.13392] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 01/27/2021] [Indexed: 02/03/2023]
Abstract
Fundamental information on the behavior of excited chlorophyll molecules packed within the confinements of nanosized photosystems I and II, following absorption of light, is presented. Using a 100 femtosecond laser with nanojoule (nJ) pulse energy and a one picosecond streak camera, we observed the light emitted from the nanostructured photosystems without oscillations or hops. The fluorescent exponential decay profiles and high efficiency within the nanostructure suggest that light coherently drains out as a unit. This implies that "quantumness" is linked to quantum confinement on the nano scale.
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Affiliation(s)
- Laura A Sordillo
- Institute for Ultrafast Spectroscopy and Lasers, Physics Department, The City College of the City University of New York, New York, NY, USA
| | - Yury Budansky
- Institute for Ultrafast Spectroscopy and Lasers, Physics Department, The City College of the City University of New York, New York, NY, USA
| | - Robert R Alfano
- Institute for Ultrafast Spectroscopy and Lasers, Physics Department, The City College of the City University of New York, New York, NY, USA
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15
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De Silva N, Warnakula T, Gunapala SD, Stockman MI, Premaratne M. Effect of logarithmic perturbations in ohmic like spectral densities in dynamics of electronic excitation using variational polaron transformation approach. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:145304. [PMID: 33503593 DOI: 10.1088/1361-648x/abe078] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Accepted: 01/27/2021] [Indexed: 06/12/2023]
Abstract
Electronic excitation energy transfer is a ubiquitous process that has generated prime research interest since its discovery. Recently developed variational polaron transformation-based second-order master equation is capable of interpolating between Förster and Redfield limits with exceptional accuracy. Forms of spectral density functions studied so far through the variational approach provide theoretical support for various experiments. Recently introduced ohmic like spectral density function that can account for logarithmic perturbations provides generality and exposition to a unique and practical set of environments. In this paper, we exploit the energy transfer dynamics of a two-level system attached to an ohmic like spectral density function with logarithmic perturbations using a variational polaron transformed master equation. Our results demonstrate that even for a relatively large bath coupling strength, quantum coherence effects can be increased by introducing logarithmic perturbations of the order of one and two in super-ohmic environments. Moreover, for particular values of the ohmicity parameter, the effect of logarithmic perturbations is observed to be insignificant for the overall dynamics. In regard to ohmic environments, as logarithmic perturbations increase, damping characteristics of the coherent transient dynamics also increase in general. It is also shown that, having logarithmic perturbations of the order of one in an ohmic environment can result in a less efficient energy transfer for relatively larger system bath coupling strengths.
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Affiliation(s)
- Nisal De Silva
- Advanced Computing and Simulation Laboratory (AχL), Department of Electrical and Computer Systems Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Tharindu Warnakula
- Advanced Computing and Simulation Laboratory (AχL), Department of Electrical and Computer Systems Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - Sarath D Gunapala
- Jet Propulsion Laboratory, California Institute of Technology, Pasadena, CA 91109, United States of America
| | - Mark I Stockman
- Department of Physics and Astronomy, Georgia State University, Atlanta, GA 30303, United States of America
| | - Malin Premaratne
- Advanced Computing and Simulation Laboratory (AχL), Department of Electrical and Computer Systems Engineering, Monash University, Clayton, Victoria 3800, Australia
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16
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Ludeña EV, Tapia O. On interpretations of quantum mechanics and a novel nonrepresentational framework. ADVANCES IN QUANTUM CHEMISTRY 2021. [DOI: 10.1016/bs.aiq.2021.05.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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17
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Chaillet M, Lengauer F, Adolphs J, Müh F, Fokas AS, Cole DJ, Chin AW, Renger T. Static Disorder in Excitation Energies of the Fenna-Matthews-Olson Protein: Structure-Based Theory Meets Experiment. J Phys Chem Lett 2020; 11:10306-10314. [PMID: 33227205 PMCID: PMC7751012 DOI: 10.1021/acs.jpclett.0c03123] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 11/17/2020] [Indexed: 06/11/2023]
Abstract
Inhomogeneous broadening of optical lines of the Fenna-Matthews-Olson (FMO) light-harvesting protein is investigated by combining a Monte Carlo sampling of low-energy conformational substates of the protein with a quantum chemical/electrostatic calculation of local transition energies (site energies) of the pigments. The good agreement between the optical spectra calculated for the inhomogeneous ensemble and the experimental data demonstrates that electrostatics is the dominant contributor to static disorder in site energies. Rotamers of polar amino acid side chains are found to cause bimodal distribution functions of site energy shifts, which can be probed by hole burning and single-molecule spectroscopy. When summing over the large number of contributions, the resulting distribution functions of the site energies become Gaussians, and the correlations in site energy fluctuations at different sites practically average to zero. These results demonstrate that static disorder in the FMO protein is in the realm of the central limit theorem of statistics.
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Affiliation(s)
- Marten
L. Chaillet
- Bijvoet
Centre for Biomolecular Research, University
of Utrecht, Heidelberglaan 8, 3584 CS Utrecht, The Netherlands
| | - Florian Lengauer
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Julian Adolphs
- Leibniz
Institute for Agricultural Engineering and Bioeconomy, Max-Eyth-Allee 100, 14469 Potsdam, Germany
| | - Frank Müh
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Alexander S. Fokas
- TCM
Group, Cavendish Laboratory, 19 J. J. Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Daniel J. Cole
- School
of Natural and Environmental Sciences, Newcastle
University, Newcastle
upon Tyne NE1 7RU, United
Kingdom
| | - Alex W. Chin
- Centre
National de la Recherce Scientifique, Institute des Nanosciences de
Paris, Sorbonne Université, Paris, France
| | - Thomas Renger
- Institute
of Theoretical Physics, Johannes Kepler
University Linz, Altenberger Str. 69, 4040 Linz, Austria
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18
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Klinger A, Lindorfer D, Müh F, Renger T. Normal mode analysis of spectral density of FMO trimers: Intra- and intermonomer energy transfer. J Chem Phys 2020; 153:215103. [PMID: 33291900 DOI: 10.1063/5.0027994] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The intermolecular contribution to the spectral density of the exciton-vibrational coupling of the homotrimeric Fenna-Matthews-Olson (FMO) light-harvesting protein of green sulfur bacteria P. aestuarii is analyzed by combining a normal mode analysis of the protein with the charge density coupling method for the calculation of local transition energies of the pigments. Correlations in site energy fluctuations across the whole FMO trimer are found at low vibrational frequencies. Including, additionally, the high-frequency intrapigment part of the spectral density, extracted from line-narrowing spectra, we study intra- and intermonomer exciton transfer. Whereas the intrapigment part of the spectral density is important for fast intramonomer exciton relaxation, the intermolecular contributions (due to pigment-environment coupling) determine the intermonomer exciton transfer. Neither the variations of the local Huang-Rhys factors nor the correlations in site energy fluctuations have a critical influence on energy transfer. At room temperature, the intermonomer transfer in the FMO protein occurs on a 10 ps time scale, whereas intramonomer exciton equilibration is roughly two orders of magnitude faster. At cryogenic temperatures, intermonomer transfer limits the lifetimes of the lowest exciton band. The lifetimes are found to increase between 20 ps in the center of this band up to 100 ps toward lower energies, which is in very good agreement with the estimates from hole burning data. Interestingly, exciton delocalization in the FMO monomers is found to slow down intermonomer energy transfer, at both physiological and cryogenic temperatures.
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Affiliation(s)
- Alexander Klinger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Dominik Lindorfer
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Frank Müh
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
| | - Thomas Renger
- Institut für Theoretische Physik, Johannes Kepler Universität Linz, Altenberger Str. 69, 4040 Linz, Austria
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19
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Jung KA, Brumer P. Energy transfer under natural incoherent light: Effects of asymmetry on efficiency. J Chem Phys 2020; 153:114102. [PMID: 32962363 DOI: 10.1063/5.0020576] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The non-equilibrium stationary coherences that form in donor-acceptor systems are investigated to determine their relationship to the efficiency of energy transfer to a neighboring reaction center. It is found that the effects of asymmetry in the dimer are generally detrimental to the transfer of energy. Four types of systems are examined, arising from combinations of localized trapping, delocalized (Forster) trapping, eigenstate dephasing, and site basis dephasing. In the cases of site basis dephasing, the interplay between the energy gap of the excited dimer states and the environment is shown to give rise to a turnover effect in the efficiency under weak dimer coupling conditions. Furthermore, the nature of the coherences and associated flux is interpreted in terms of pathway interference effects. In addition, regardless of the cases considered, the ratio of the real part and the imaginary part of the coherences in the energy-eigenbasis tends to a constant value in the steady state limit.
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Affiliation(s)
- Kenneth A Jung
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
| | - Paul Brumer
- Chemical Physics Theory Group, Department of Chemistry, and Center for Quantum Information and Quantum Control, University of Toronto, Toronto, Ontario M5S 3H6, Canada
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20
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Guevara R, Mateos DM, Pérez Velázquez JL. Consciousness as an Emergent Phenomenon: A Tale of Different Levels of Description. ENTROPY (BASEL, SWITZERLAND) 2020; 22:E921. [PMID: 33286690 PMCID: PMC7597170 DOI: 10.3390/e22090921] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Revised: 08/15/2020] [Accepted: 08/19/2020] [Indexed: 01/17/2023]
Abstract
One of the biggest queries in cognitive sciences is the emergence of consciousness from matter. Modern neurobiological theories of consciousness propose that conscious experience is the result of interactions between large-scale neuronal networks in the brain, traditionally described within the realm of classical physics. Here, we propose a generalized connectionist framework in which the emergence of "conscious networks" is not exclusive of large brain areas, but can be identified in subcellular networks exhibiting nontrivial quantum phenomena. The essential feature of such networks is the existence of strong correlations in the system (classical or quantum coherence) and the presence of an optimal point at which the system's complexity and energy dissipation are maximized, whereas free-energy is minimized. This is expressed either by maximization of the information content in large scale functional networks or by achieving optimal efficiency through the quantum Goldilock effect.
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Affiliation(s)
- Ramón Guevara
- Integrative Neuroscience and Cognition Centre (INCC UMR8002), University of Paris and CNRS, 75270 Paris, France
- Department of Physics and Astronomy, University of Padova, 35131 Padova, Italy
| | - Diego M. Mateos
- Department of Science and Technology, Universidad Autónoma de Entre Ríos, Paraná 3100, Argentina;
- Instituto de Matemática Aplicada del Litoral (IMAL-CONICET-UNL), Santa Fe 3000, Argentina
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21
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Quantum transport and utilization of free energy in protein α-helices. ADVANCES IN QUANTUM CHEMISTRY 2020. [DOI: 10.1016/bs.aiq.2020.02.001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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22
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23
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Yang T, Huang L, Xiao C, Chen J, Wang T, Dai D, Lique F, Alexander MH, Sun Z, Zhang DH, Yang X, Neumark DM. Enhanced reactivity of fluorine with para-hydrogen in cold interstellar clouds by resonance-induced quantum tunnelling. Nat Chem 2019; 11:744-749. [DOI: 10.1038/s41557-019-0280-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 05/07/2019] [Indexed: 11/09/2022]
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24
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Li Y, Cohen D, Kottos T. Coherent Wave Propagation in Multimode Systems with Correlated Noise. PHYSICAL REVIEW LETTERS 2019; 122:153903. [PMID: 31050529 DOI: 10.1103/physrevlett.122.153903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Indexed: 06/09/2023]
Abstract
Imperfections in multimode systems lead to mode mixing and interferences between propagating modes. Such disorder is typically characterized by a finite correlation time (in quantum evolution) or correlation length (in paraxial evolution). We show that the long-scale dynamics of an initial excitation that spread in mode space can be tailored by the coherent dynamics on a short scale. In particular we unveil a universal crossover from exponential to power-law ballisticlike decay of the initial mode. Our results have applications to various wave physics frameworks, ranging from multimode fiber optics to quantum dots and quantum biology.
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Affiliation(s)
- Yaxin Li
- Wave Transport in Complex Systems Lab, Physics Department, Wesleyan University, Middletown Connecticut 06459, USA
| | - Doron Cohen
- Department of Physics, Ben-Gurion University of the Negev, Beer-Sheva 84105, Israel
| | - Tsampikos Kottos
- Wave Transport in Complex Systems Lab, Physics Department, Wesleyan University, Middletown Connecticut 06459, USA
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25
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Abstract
The corpus of electron transfer (ET) theory provides considerable power to describe the kinetics and dynamics of electron flow at the nanoscale. How is it, then, that nucleic acid (NA) ET continues to surprise, while protein-mediated ET is relatively free of mechanistic bombshells? I suggest that this difference originates in the distinct electronic energy landscapes for the two classes of reactions. In proteins, the donor/acceptor-to-bridge energy gap is typically several-fold larger than in NAs. NA ET can access tunneling, hopping, and resonant transport among the bases, and fluctuations can enable switching among mechanisms; protein ET is restricted to tunneling among redox active cofactors and, under strongly oxidizing conditions, a few privileged amino acid side chains. This review aims to provide conceptual unity to DNA and protein ET reaction mechanisms. The establishment of a unified mechanistic framework enabled the successful design of NA experiments that switch electronic coherence effects on and off for ET processes on a length scale of multiple nanometers and promises to provide inroads to directing and detecting charge flow in soft-wet matter.
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Affiliation(s)
- David N Beratan
- Department of Chemistry and Department of Physics, Duke University, Durham, North Carolina 27708, USA; .,Department of Biochemistry, Duke University, Durham, North Carolina 27710, USA
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26
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Elucidation of near-resonance vibronic coherence lifetimes by nonadiabatic electronic-vibrational state character mixing. Proc Natl Acad Sci U S A 2018; 116:18263-18268. [PMID: 30093387 DOI: 10.1073/pnas.1701390115] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Recent work suggests that the long-lived coherences observed in both natural and artificial light-harvesting systems (such as the Fenna-Matthews-Olson complex) could be attributed to the mixing of the pigments' electronic and vibrational degrees of freedom. To investigate the underlying mechanism of these long coherence lifetimes, a sophisticated description of interactions between the molecular aggregates and the nonequilibrium fluctuations in the surrounding environment is necessary. This is done by implementing the hierarchical equations of motion approach on model homodimers, a method used in the intermediate coupling regime for many molecular aggregates wherein the nonequilibrium environment phonons play nontrivial roles in exciton dynamics. Here we report a character change in the vibronic states-reflective of property mixing between the electronic and vibrational states-induced by an interplay between system coupling parameters within the exciton-vibrational near-resonance regime. This mixing dictates vital aspects of coherence lifetime; by tracking the degree of mixing, we are able to elucidate the relationship between coherence lifetime and both the electronic energy fluctuation and the vibrational relaxation dephasing pathways.
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27
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Rourk CJ. Ferritin and neuromelanin "quantum dot" array structures in dopamine neurons of the substantia nigra pars compacta and norepinephrine neurons of the locus coeruleus. Biosystems 2018; 171:48-58. [PMID: 30048795 DOI: 10.1016/j.biosystems.2018.07.008] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2018] [Revised: 07/13/2018] [Accepted: 07/22/2018] [Indexed: 01/28/2023]
Abstract
In this review, the author shows that ferritin has documented quantum dot material properties that have been reported in numerous independent studies, and can enable quantum mechanical electron transport over substantial distances. In addition, neuromelanin is a pi-conjugated polymer, and quantum dot/pi-conjugated polymer combinations have been reported in numerous independent studies to facilitate electron transport for solar photovoltaic and other applications. Both ferritin and neuromelanin are present in large quantities in the dopamine neurons of the substantia nigra pars compactaand the norepinephrine neurons of the locus coeruleus. The unique structure of subgroups of these neurons that have a large number of axon branches and synapses may have evolved to take advantage of this electron transport mechanism, if it is present, such as to coordinate conscious action, or for other purposes. Independent clinical and laboratory studies are also reviewed that corroborate this theory of coordinated action in these neuron groups. Research to validate the theory using charge transport measurements, materials characterization, existing fluorescent probe material and reaction time testing is proposed.
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28
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Some Aspects of Nonlinearity and Self-Organization In Biosystems on Examples of Localized Excitations in the DNA Molecule and Generalized Fisher–KPP Model. Symmetry (Basel) 2018. [DOI: 10.3390/sym10030053] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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29
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Karafyllidis IG. Quantum transport in the FMO photosynthetic light-harvesting complex. J Biol Phys 2017; 43:239-245. [PMID: 28378262 DOI: 10.1007/s10867-017-9449-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 03/08/2017] [Indexed: 11/24/2022] Open
Abstract
The very high light-harvesting efficiency of natural photosynthetic systems in conjunction with recent experiments, which showed quantum-coherent energy transfer in photosynthetic complexes, raised questions regarding the presence of non-trivial quantum effects in photosynthesis. Grover quantum search, quantum walks, and entanglement have been investigated as possible effects that lead to this efficiency. Here we explain the near-unit photosynthetic efficiency without invoking non-trivial quantum effects. Instead, we use non-equilibrium Green's functions, a mesoscopic method used to study transport in nano-conductors to compute the transmission function of the Fenna-Matthews-Olson (FMO) complex using an experimentally derived exciton Hamiltonian. The chlorosome antenna and the reaction center play the role of input and output contacts, connected to the FMO complex. We show that there are two channels for which the transmission is almost unity. Our analysis also revealed a dephasing-driven regulation mechanism that maintains the efficiency in the presence of varying dephasing potentials.
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30
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Heres M, Wang Y, Griffin PJ, Gainaru C, Sokolov AP. Proton Conductivity in Phosphoric Acid: The Role of Quantum Effects. PHYSICAL REVIEW LETTERS 2016; 117:156001. [PMID: 27768354 DOI: 10.1103/physrevlett.117.156001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2016] [Indexed: 05/07/2023]
Abstract
Phosphoric acid has one of the highest intrinsic proton conductivities of any known liquids, and the mechanism of this exceptional conductivity remains a puzzle. Our detailed experimental studies discovered a strong isotope effect in the conductivity of phosphoric acids caused by (i) a strong isotope shift of the glass transition temperature and (ii) a significant reduction of the energy barrier by zero-point quantum fluctuations. These results suggest that the high conductivity in phosphoric acids is caused by a very efficient proton transfer mechanism, which is strongly assisted by quantum effects.
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Affiliation(s)
- M Heres
- Department of Chemical and Biomolecular Engineering, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - Y Wang
- Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - P J Griffin
- Department of Materials Science and Engineering, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - C Gainaru
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
| | - A P Sokolov
- Department of Chemistry, University of Tennessee Knoxville, Knoxville, Tennessee 37996, USA
- Chemical Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
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31
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Kumar P, Kumar S, Ghosh S, Pal SK. Femtosecond insights into direct electron injection in dye anchored ZnO QDs following charge transfer excitation. Phys Chem Chem Phys 2016; 18:20672-81. [PMID: 27412034 DOI: 10.1039/c6cp01721e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of the charge transfer (CT) state in interfacial electron transfer in dye-sensitized semiconductor nanocrystals is still poorly understood. To address this problem, femtosecond transient absorption (TA) spectroscopy is used as a probe to investigate the electron injection across a newly synthesized coumarin dye (8-hydroxy-2-oxo-4-phenyl-2 benzo[h]chromene-3-carbonitrile, coded BC5) and ZnO quantum dots (QDs). Steady state and time-resolved spectroscopic measurements reveal that BC5 dye interacts strongly with ZnO QDs in the ground state forming a CT complex. The BC5-ZnO QD complex absorbs more towards red compared to only the dye and QDs, and emits fluorescence due to radiative recombination of photogenerated charges. The formation of charges following the excitation of the CT complex has been demonstrated by observing the signature of dye radical cations and electrons in the conduction band (CB) of the QDs in the TA spectra. The TA signals of these charges grow sharply as a result of ultrafast direct electron injection into the QD. We have monitored the complete dynamics of photogenerated charges by measuring the TA signals of the charges up to a couple of nanoseconds. The injected electrons that are free or shallowly trapped recombine with a time constant of 625 fs, whereas deeply trapped electrons disappear slowly (526 ps) via radiative recombination. Furthermore, theoretical studies based on ab initio calculations have been carried out to complement the experimental findings.
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Affiliation(s)
- Pushpendra Kumar
- School of Basic Sciences and Advanced Material Research Center, Indian Institute of Technology Mandi, Kamand 175005, H.P., India.
| | - Sunil Kumar
- School of Basic Sciences and Advanced Material Research Center, Indian Institute of Technology Mandi, Kamand 175005, H.P., India.
| | - Subrata Ghosh
- School of Basic Sciences and Advanced Material Research Center, Indian Institute of Technology Mandi, Kamand 175005, H.P., India.
| | - Suman Kalyan Pal
- School of Basic Sciences and Advanced Material Research Center, Indian Institute of Technology Mandi, Kamand 175005, H.P., India.
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32
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Butkus V, Dong H, Fleming GR, Abramavicius D, Valkunas L. Disorder-Induced Quantum Beats in Two-Dimensional Spectra of Excitonically Coupled Molecules. J Phys Chem Lett 2016; 7:277-282. [PMID: 26720834 DOI: 10.1021/acs.jpclett.5b02642] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Quantum superposition of molecular electronic states is very fragile because of thermal energy fluctuations and the static conformational disorder induced by the intimate surrounding of constituent molecules of the system. However, the nature of the long-lived quantum beats, observed in time-resolved spectra of molecular aggregates at physiological conditions, is still being debated. We present our study of the conditions when long-lived electronic quantum coherences originating from recently proposed inhomogeneous broadening mechanism are enhanced and reflected in the two-dimensional electronic spectra of the excitonically coupled molecular dimer. We show that depending on the amount of inhomogeneous broadening, the excitonically coupled molecular system can establish long-lived electronic coherences, caused by a disordered subensemble, for which the dephasing due to static energy disorder becomes significantly reduced. On the basis of these considerations, we present explanations for why the electronic or vibrational coherences were or were not observed in a range of recent experiments.
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Affiliation(s)
- Vytautas Butkus
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
| | - Hui Dong
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Graham R Fleming
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Physical Biosciences Division, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Darius Abramavicius
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
| | - Leonas Valkunas
- Department of Theoretical Physics, Faculty of Physics, Vilnius University , Sauletekio 9-III, 10222 Vilnius, Lithuania
- Center for Physical Sciences and Technology, Gostauto 9, 01108 Vilnius, Lithuania
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33
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Craddock TJA, Friesen D, Mane J, Hameroff S, Tuszynski JA. The feasibility of coherent energy transfer in microtubules. J R Soc Interface 2015; 11:20140677. [PMID: 25232047 DOI: 10.1098/rsif.2014.0677] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
It was once purported that biological systems were far too 'warm and wet' to support quantum phenomena mainly owing to thermal effects disrupting quantum coherence. However, recent experimental results and theoretical analyses have shown that thermal energy may assist, rather than disrupt, quantum coherent transport, especially in the 'dry' hydrophobic interiors of biomolecules. Specifically, evidence has been accumulating for the necessary involvement of quantum coherent energy transfer between uniquely arranged chromophores in light harvesting photosynthetic complexes. The 'tubulin' subunit proteins, which comprise microtubules, also possess a distinct architecture of chromophores, namely aromatic amino acids, including tryptophan. The geometry and dipolar properties of these aromatics are similar to those found in photosynthetic units indicating that tubulin may support coherent energy transfer. Tubulin aggregated into microtubule geometric lattices may support such energy transfer, which could be important for biological signalling and communication essential to living processes. Here, we perform a computational investigation of energy transfer between chromophoric amino acids in tubulin via dipole excitations coupled to the surrounding thermal environment. We present the spatial structure and energetic properties of the tryptophan residues in the microtubule constituent protein tubulin. Plausibility arguments for the conditions favouring a quantum mechanism of signal propagation along a microtubule are provided. Overall, we find that coherent energy transfer in tubulin and microtubules is biologically feasible.
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Affiliation(s)
- Travis John Adrian Craddock
- Center for Psychological Studies, Graduate School of Computer and Information Sciences, and College of Osteopathic Medicine, Nova Southeastern University, Ft Lauderdale, FL 33328, USA Institute for Neuro-Immune Medicine, Nova Southeastern University, Ft Lauderdale, FL 33328, USA
| | - Douglas Friesen
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Jonathan Mane
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2
| | - Stuart Hameroff
- Departments of Anesthesiology and Psychology, Center for Consciousness Studies, The University of Arizona Health Sciences Center, Tucson, AZ 210202, USA
| | - Jack A Tuszynski
- Department of Oncology, University of Alberta, Cross Cancer Institute, Edmonton, Alberta, Canada T6G 1Z2 Department of Physics, University of Alberta, Edmonton, Alberta, Canada T6G 2E1
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34
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Venkatasubramanian G. Understanding schizophrenia as a disorder of consciousness: biological correlates and translational implications from quantum theory perspectives. CLINICAL PSYCHOPHARMACOLOGY AND NEUROSCIENCE : THE OFFICIAL SCIENTIFIC JOURNAL OF THE KOREAN COLLEGE OF NEUROPSYCHOPHARMACOLOGY 2015; 13:36-47. [PMID: 25912536 PMCID: PMC4423156 DOI: 10.9758/cpn.2015.13.1.36] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 12/07/2014] [Accepted: 12/08/2014] [Indexed: 11/18/2022]
Abstract
From neurophenomenological perspectives, schizophrenia has been conceptualized as "a disorder with heterogeneous manifestations that can be integrally understood to involve fundamental perturbations in consciousness". While these theoretical constructs based on consciousness facilitate understanding the 'gestalt' of schizophrenia, systematic research to unravel translational implications of these models is warranted. To address this, one needs to begin with exploration of plausible biological underpinnings of "perturbed consciousness" in schizophrenia. In this context, an attractive proposition to understand the biology of consciousness is "the orchestrated object reduction (Orch-OR) theory" which invokes quantum processes in the microtubules of neurons. The Orch-OR model is particularly important for understanding schizophrenia especially due to the shared 'scaffold' of microtubules. The initial sections of this review focus on the compelling evidence to support the view that "schizophrenia is a disorder of consciousness" through critical summary of the studies that have demonstrated self-abnormalities, aberrant time perception as well as dysfunctional intentional binding in this disorder. Subsequently, these findings are linked with 'Orch-OR theory' through the research evidence for aberrant neural oscillations as well as microtubule abnormalities observed in schizophrenia. Further sections emphasize the applicability and translational implications of Orch-OR theory in the context of schizophrenia and elucidate the relevance of quantum biology to understand the origins of this puzzling disorder as "fundamental disturbances in consciousness".
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Affiliation(s)
- Ganesan Venkatasubramanian
- The Schizophrenia Clinic, Department of Psychiatry and Translational Psychiatry Laboratory, Neurobiology Research Centre, National Institute of Mental Health and Neurosciences, Bangalore,
India
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35
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Gillis CG, Jones GA. A Theoretical Investigation into the Effects of Temperature on Spatiotemporal Dynamics of EET in the FMO Complex. J Phys Chem B 2015; 119:4165-74. [DOI: 10.1021/jp509103e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Colm G. Gillis
- School of Chemistry, University of East Anglia, Norwich Research
Park, Norwich, Norfolk NR4 7TJ, United Kingdom
| | - Garth A. Jones
- School of Chemistry, University of East Anglia, Norwich Research
Park, Norwich, Norfolk NR4 7TJ, United Kingdom
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36
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Aly SM, Ahmed GH, Shaheen BS, Sun J, Mohammed OF. Molecular-structure Control of Ultrafast Electron Injection at Cationic Porphyrin-CdTe Quantum Dot Interfaces. J Phys Chem Lett 2015; 6:791-795. [PMID: 26262654 DOI: 10.1021/acs.jpclett.5b00235] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Charge transfer (CT) at donor (D)/acceptor (A) interfaces is central to the functioning of photovoltaic and light-emitting devices. Understanding and controlling this process on the molecular level has been proven to be crucial for optimizing the performance of many energy-challenge relevant devices. Here, we report the experimental observations of controlled on/off ultrafast electron transfer (ET) at cationic porphyrin-CdTe quantum dot (QD) interfaces using femto- and nanosecond broad-band transient absorption (TA) spectroscopy. The time-resolved data demonstrate how one can turn on/off the electron injection from porphyrin to the CdTe QDs. With careful control of the molecular structure, we are able to tune the electron injection at the porphyrin-CdTe QD interface from zero to very efficient and ultrafast. In addition, our data demonstrate that the ET process occurs within our temporal resolution of 120 fs, which is one of the fastest times recorded for organic photovoltaics.
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Affiliation(s)
- Shawkat M Aly
- Solar and Photovoltaics Engineering Research Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Ghada H Ahmed
- Solar and Photovoltaics Engineering Research Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Basamat S Shaheen
- Solar and Photovoltaics Engineering Research Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Jingya Sun
- Solar and Photovoltaics Engineering Research Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
| | - Omar F Mohammed
- Solar and Photovoltaics Engineering Research Center, Division of Physical Sciences and Engineering, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia
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Craddock TJA, Priel A, Tuszynski JA. Keeping time: could quantum beating in microtubules be the basis for the neural synchrony related to consciousness? J Integr Neurosci 2015; 13:293-311. [PMID: 25012713 DOI: 10.1142/s0219635214400019] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
This paper discusses the possibility of quantum coherent oscillations playing a role in neuronal signaling. Consciousness correlates strongly with coherent neural oscillations, however the mechanisms by which neurons synchronize are not fully elucidated. Recent experimental evidence of quantum beats in light-harvesting complexes of plants (LHCII) and bacteria provided a stimulus for seeking similar effects in important structures found in animal cells, especially in neurons. We argue that microtubules (MTs), which play critical roles in all eukaryotic cells, possess structural and functional characteristics that are consistent with quantum coherent excitations in the aromatic groups of their tryptophan residues. Furthermore we outline the consequences of these findings on neuronal processes including the emergence of consciousness.
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Affiliation(s)
- Travis J A Craddock
- Center for Psychological Studies, Graduate School of Computer and Information Sciences, College of Osteophatic Medicine and the Institute for Neuro-Immune Medicine, Nova Southeastern University, Fort Lauderdale, Florida 33314-7796, USA
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Jan L, Fefer D, Košmelj K, Gaberščik A, Jerman I. Geomagnetic and strong static magnetic field effects on growth and chlorophyllafluorescence inLemna minor. Bioelectromagnetics 2015; 36:190-203. [DOI: 10.1002/bem.21898] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2014] [Accepted: 12/26/2014] [Indexed: 11/09/2022]
Affiliation(s)
| | - Dušan Fefer
- Laboratory for Process-Control Technique; Acoustics and Magnetics; Faculty of Electrical Engineering; University of Ljubljana; Ljubljana Slovenia
| | - Katarina Košmelj
- Department of Agronomy; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Alenka Gaberščik
- Department of Biology; Biotechnical Faculty; University of Ljubljana; Ljubljana Slovenia
| | - Igor Jerman
- Bion; Institute for Bioelectromagnetics and New Biology; Ljubljana Slovenia
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39
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Imamoglu A, Whaley KB. Photoactivated biological processes as quantum measurements. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 91:022714. [PMID: 25768538 DOI: 10.1103/physreve.91.022714] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/15/2014] [Indexed: 06/04/2023]
Abstract
We outline a framework for describing photoactivated biological reactions as generalized quantum measurements of external fields, for which the biological system takes on the role of a quantum meter. By using general arguments regarding the Hamiltonian that describes the measurement interaction, we identify the cases where it is essential for a complex chemical or biological system to exhibit nonequilibrium quantum coherent dynamics in order to achieve the requisite functionality. We illustrate the analysis by considering measurement of the solar radiation field in photosynthesis and measurement of the earth's magnetic field in avian magnetoreception.
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Affiliation(s)
- A Imamoglu
- Institute for Quantum Electronics, ETH Zürich, CH-8093 Zürich, Switzerland
| | - K B Whaley
- Berkeley Quantum Information and Computation Center, Department of Chemistry, University of California, Berkeley, California 94720, USA
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40
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Tirandaz A, Ghahramani FT, Shafiee A. Emergence of molecular chirality due to chiral interactions in a biological environment. J Biol Phys 2014; 40:369-86. [PMID: 24996546 DOI: 10.1007/s10867-014-9356-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2014] [Accepted: 05/23/2014] [Indexed: 10/25/2022] Open
Abstract
We explore the interplay between tunneling process and chiral interactions in the discrimination of chiral states for an ensemble of molecules in a biological environment. Each molecule is described by an asymmetric double-well potential and the environment is modeled as a bath of harmonic oscillators. We carefully analyze different time-scales appearing in the resulting master equation at both weak- and strong-coupling limits. The corresponding results are accompanied by a set of coupled differential equations characterizing optical activity of the molecules. We show that, at the weak-coupling limit, chiral interactions prohibit the coherent racemization induced by decoherence effects and thus preserve the initial chiral state. At the strong-coupling limit, considering the memory effects of the environment, Markovian behavior is observed at long times.
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Affiliation(s)
- Arash Tirandaz
- Research Group on Foundations of Quantum Theory and Information, Department of Chemistry, Sharif University of Technology, P.O.Box 11365-9516, Tehran, Iran,
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41
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Jun S, Yang C, Isaji M, Tamiaki H, Kim J, Ihee H. Coherent Oscillations in Chlorosome Elucidated by Two-Dimensional Electronic Spectroscopy. J Phys Chem Lett 2014; 5:1386-1392. [PMID: 26269984 DOI: 10.1021/jz500328w] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Chlorosomes are the most efficient photosynthetic light-harvesting complexes found in nature and consist of many bacteriochlorophyll (BChl) molecules self-assembled into supramolecular aggregates. Here we elucidate the presence and the origin of coherent oscillations in chlorosome at cryogenic temperature using 2D electronic spectroscopy. We observe coherent oscillations of multiple frequencies superimposed on the ultrafast amplitude decay of 2D spectra. Comparison of oscillatory features in the rephasing and nonrephasing 2D spectra suggests that an oscillation of 620 cm(-1) frequency arises from electronic coherence. However, this coherent oscillation can be enhanced by vibronic coupling with intermolecular vibrations of BChl aggregate, and thus it might originate from vibronic coherence rather than pure electronic coherence. Although the 620 cm(-1) oscillation dephases rapidly, the electronic (or vibronic) coherence may still take part in the initial step of energy transfer in chlorosome, which is comparably fast.
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Affiliation(s)
- Sunhong Jun
- †Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- ‡Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Cheolhee Yang
- †Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- ‡Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
| | - Megumi Isaji
- §Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Hitoshi Tamiaki
- §Graduate School of Life Sciences, Ritsumeikan University, Kusatsu, Shiga 525-8577, Japan
| | - Jeongho Kim
- ∥Department of Chemistry, Inha University, Incheon 402-751, Republic of Korea
| | - Hyotcherl Ihee
- †Center for Nanomaterials and Chemical Reactions, Institute for Basic Science (IBS), Daejeon 305-701, Republic of Korea
- ‡Department of Chemistry, KAIST, Daejeon 305-701, Republic of Korea
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Healion D, Zhang Y, Biggs JD, Hua W, Mukamel S. Two-dimensional x-ray correlation spectroscopy of remote core states. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2014; 1:014101. [PMID: 26913804 PMCID: PMC4711603 DOI: 10.1063/1.4833560] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2013] [Accepted: 10/31/2013] [Indexed: 05/19/2023]
Abstract
Nonlinear all-X-ray signals that involve large core-atom separation compared to the X-ray wavelengths may not be described by the dipole approximation since they contain additional phase factors. Expressions for the rotationally averaged 2D X-ray photon echo signals from randomly oriented systems that take this position-dependent phase into account for arbitrary ratio between the core separation and the resonant wavelength are presented. Application is made to the Se K-edge of a selenium dipeptide system.
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Affiliation(s)
- Daniel Healion
- Department of Chemistry, University of California , 450 Rowland Hall, Irvine, California 92697-2025, USA
| | - Yu Zhang
- Department of Chemistry, University of California , 450 Rowland Hall, Irvine, California 92697-2025, USA
| | - Jason D Biggs
- Department of Chemistry, University of California , 450 Rowland Hall, Irvine, California 92697-2025, USA
| | - Weijie Hua
- Department of Chemistry, University of California , 450 Rowland Hall, Irvine, California 92697-2025, USA
| | - Shaul Mukamel
- Department of Chemistry, University of California , 450 Rowland Hall, Irvine, California 92697-2025, USA
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Curutchet C, Novoderezhkin VI, Kongsted J, Muñoz-Losa A, van Grondelle R, Scholes GD, Mennucci B. Energy Flow in the Cryptophyte PE545 Antenna Is Directed by Bilin Pigment Conformation. J Phys Chem B 2012; 117:4263-73. [DOI: 10.1021/jp305033d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Carles Curutchet
- Departament de Fisicoquímica,
Facultat de Farmàcia, Universitat de Barcelona, Av. Joan XXIII s/n, 08028 Barcelona, Spain
| | | | - Jacob Kongsted
- Department
of Physics, Chemistry
and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Aurora Muñoz-Losa
- Dipartimento di Chimica e Chimica
Industriale, Università di Pisa,
via Risorgimento 35, 56126 Pisa, Italy
| | - Rienk van Grondelle
- Department of Physics and Astronomy,
Faculty of Sciences, VU University Amsterdam, Amsterdam, The Netherlands
| | - Gregory D. Scholes
- Department of Chemistry, 80 St. George
Street, Institute for Optical Sciences, and Centre for Quantum Information
and Quantum Control, University of Toronto, Toronto, Ontario, M5S 3H6 Canada
| | - Benedetta Mennucci
- Dipartimento di Chimica e Chimica
Industriale, Università di Pisa,
via Risorgimento 35, 56126 Pisa, Italy
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Plankar M, Brežan S, Jerman I. The principle of coherence in multi-level brain information processing. PROGRESS IN BIOPHYSICS AND MOLECULAR BIOLOGY 2012; 111:8-29. [PMID: 22986048 DOI: 10.1016/j.pbiomolbio.2012.08.006] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Accepted: 08/02/2012] [Indexed: 02/03/2023]
Abstract
Synchronisation has become one of the major scientific tools to explain biological order at many levels of organisation. In systems neuroscience, synchronised subthreshold and suprathreshold oscillatory neuronal activity within and between distributed neuronal assemblies is acknowledged as a fundamental mode of neuronal information processing. Coherent neuronal oscillations correlate with all basic cognitive functions, mediate local and long-range neuronal communication and affect synaptic plasticity. However, it remains unclear how the very fast and complex changes of functional neuronal connectivity necessary for cognition, as mediated by dynamic patterns of neuronal synchrony, could be explained exclusively based on the well-established synaptic mechanisms. A growing body of research indicates that the intraneuronal matrix, composed of cytoskeletal elements and their binding proteins, structurally and functionally connects the synapses within a neuron, modulates neurotransmission and memory consolidation, and is hypothesised to be involved in signal integration via electric signalling due to its charged surface. Theoretical modelling, as well as emerging experimental evidence indicate that neuronal cytoskeleton supports highly cooperative energy transport and information processing based on molecular coherence. We suggest that long-range coherent dynamics within the intra- and extracellular filamentous matrices could establish dynamic ordered states, capable of rapid modulations of functional neuronal connectivity via their interactions with neuronal membranes and synapses. Coherence may thus represent a common denominator of neurophysiological and biophysical approaches to brain information processing, operating at multiple levels of neuronal organisation, from which cognition may emerge as its cardinal manifestation.
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Affiliation(s)
- Matej Plankar
- BION Institute, Stegne 21, 1000 Ljubljana, Slovenia.
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Molecular electronic junction transport: some pathways and some ideas. Top Curr Chem (Cham) 2011. [PMID: 21915776 DOI: 10.1007/128_2011_227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
When a single molecule, or a collection of molecules, is placed between two electrodes and voltage is applied, one has a molecular transport junction. We discuss such junctions, their properties, their description, and some of their applications. The discussion is qualitative rather than quantitative, and focuses on mechanism, structure/function relations, regimes and mechanisms of transport, some molecular regularities, and some substantial challenges facing the field. Because there are many regimes and mechanisms in transport junctions, we will discuss time scales, geometries, and inelastic scattering methods for trying to determine the properties of molecules within these junctions. Finally, we discuss some device applications, some outstanding problems, and some future directions.
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