Publications by authors named "Afsal Manekkathodi"

9 Publications

  • Page 1 of 1

Validating the predictions of murburn model for oxygenic photosynthesis: Analyses of ligand-binding to protein complexes and cross-system comparisons.

J Biomol Struct Dyn 2021 Jul 30:1-33. Epub 2021 Jul 30.

RedOx Lab, Department of Life Sciences, Satyamjayatu: The Science & Ethics Foundation, Palakkad District, Kerala, India.

In this second half of our treatise on oxygenic photosynthesis, we provide support for the murburn model of the light reaction of photosynthesis and ratify key predictions made in the first part. Molecular docking and visualization of various ligands of quinones/quinols (and their derivatives) with PS II/Cytochrome complexes did not support chartered 2e-transport role of quinols. A broad variety of herbicides did not show any affinity/binding-based rationales for inhibition of photosynthesis. We substantiate the proposal that disubstituted phenolics (perceived as protonophores/uncouplers or affinity-based inhibitors in the classical purview) serve as interfacial modulators of diffusible reactive (oxygen) species or DR(O)S. The DRS-based murburn model is evidenced by the identification of multiple ADP-binding sites on the extra-membraneous projection of protein complexes and structure/distribution of the photo/redox catalysts. With a panoramic comparison of the redox metabolic machinery across diverse organellar/cellular systems, we highlight the ubiquitous one-electron murburn facets (cofactors of porphyrin, flavin, FeS, other metal centers and photo/redox active pigments) that enable a facile harnessing of the utility of DRS. In the summative analyses, it is demonstrated that the murburn model of light reaction explains the structures of membrane supercomplexes recently observed in thylakoids and also accounts for several photodynamic experimental observations and evolutionary considerations. , the work provides a new orientation and impetus to photosynthesis research. Communicated by Ramaswamy H. Sarma.
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http://dx.doi.org/10.1080/07391102.2021.1953607DOI Listing
July 2021

Structure-function correlations and system dynamics in oxygenic photosynthesis: classical perspectives and murburn precepts.

J Biomol Struct Dyn 2021 Jul 29:1-27. Epub 2021 Jul 29.

Satyamjayatu: The Science & Ethics Foundation, Kulappully, Kerala, India.

Highlights: Contemporary beliefs on oxygenic photosynthesis are critiqued.Murburn model is suggested as an alternative explanation.In the new model, diffusible reactive species are the main protagonists.All pigments are deemed photo-redox active in the new stochastic mechanism.NADPH synthesis occurs via simple electron transfers, not via elaborate ETC.Oxygenesis is delocalized and not just centered at Mn-Complex.Energetics of murburn proposal for photophosphorylation is provided.The proposal ushers in a paradigm shift in photosynthesis research.
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http://dx.doi.org/10.1080/07391102.2021.1953606DOI Listing
July 2021

Chemiosmotic and murburn explanations for aerobic respiration: Predictive capabilities, structure-function correlations and chemico-physical logic.

Arch Biochem Biophys 2019 11 14;676:108128. Epub 2019 Oct 14.

Institute of Chemical Kinetics and Combustion, Russian Academy of Sciences, St. Institutskaya 3, 630090, Novosibirsk, Russia. Electronic address:

Since mid-1970s, the proton-centric proposal of 'chemiosmosis' became the acclaimed explanation for aerobic respiration. Recently, significant theoretical and experimental evidence were presented for an oxygen-centric 'murburn' mechanism of mitochondrial ATP-synthesis. Herein, we compare the predictive capabilities of the two models with respect to the available information on mitochondrial reaction chemistry and the membrane proteins' structure-function correlations. Next, fundamental queries are addressed on thermodynamics of mitochondrial oxidative phosphorylation (mOxPhos): (1) Can the energy of oxygen reduction be utilized for proton transport? (2) Is the trans-membrane proton differential harness-able as a potential energy capable of doing useful work? and (3) Whether the movement of miniscule amounts of mitochondrial protons could give rise to a potential of ~200 mV and if such an electrical energy could sponsor ATP-synthesis. Further, we explore critically if rotary ATPsynthase activity of Complex V can account for physiological ATP-turnovers. We also answer the question- "What is the role of protons in the oxygen-centric murburn scheme of aerobic respiration?" Finally, it is demonstrated that the murburn reaction model explains the fast kinetics, non-integral stoichiometry and high yield of mOxPhos. Strategies are charted to further demarcate the two explanations' relevance in the cellular physiology of aerobic respiration.
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http://dx.doi.org/10.1016/j.abb.2019.108128DOI Listing
November 2019

Role of carbon nanotube interlayer in enhancing the electron field emission behavior of ultrananocrystalline diamond coated Si-tip arrays.

ACS Appl Mater Interfaces 2015 Apr 31;7(14):7732-40. Epub 2015 Mar 31.

‡Department of Physics, Tamkang University, Tamsui 251, Taiwan, R.O.C.

We improved the electron field emission properties of ultrananocrystalline diamond (UNCD) films grown on Si-tip arrays by using the carbon nanotubes (CNTs) as interlayer and post-treating the films in CH4/Ar/H2 plasma. The use of CNTs interlayer effectively suppresses the presence of amorphous carbon in the diamond-to-Si interface that enhances the transport of electrons from Si, across the interface, to diamond. The post-treatment process results in hybrid-granular-structured diamond (HiD) films via the induction of the coalescence of the ultrasmall grains in these films that enhanced the conductivity of the films. All these factors contribute toward the enhancement of the electron field emission (EFE) process for the HiDCNT/Si-tip emitters, with low turn-on field of E0 = 2.98 V/μm and a large current density of 1.68 mA/cm(2) at an applied field of 5.0 V/μm. The EFE lifetime stability under an operation current of 6.5 μA was improved substantially to τHiD/CNT/Si-tip = 365 min. Interestingly, these HiDCNT/Si-tip materials also show enhanced plasma illumination behavior, as well as improved robustness against plasma ion bombardment when they are used as the cathode for microplasma devices. The study concludes that the use of CNT interlayers not only increase the potential of these materials as good EFE emitters, but also prove themselves to be good microplasma devices with improved performance.
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http://dx.doi.org/10.1021/acsami.5b00844DOI Listing
April 2015

Complete replacement of metal in metal oxide nanowires via atomic diffusion: In/ZnO case study.

Nano Lett 2014 Jun 21;14(6):3241-6. Epub 2014 May 21.

Department of Materials Science and Engineering and §Department of Physics, National Tsing Hua University , Hsinchu 30013, Taiwan.

Atomic diffusion is a fundamental process that dictates material science and engineering. Direct visualization of atomic diffusion process in ultrahigh vacuum in situ TEM could comprehend the fundamental information about metal-semiconductor interface dynamics, phase transitions, and different nanostructure growth phenomenon. Here, we demonstrate the in situ TEM observations of the complete replacement of ZnO nanowire by indium with different growth directions. In situ TEM analyses reveal that the diffusion processes strongly depend and are dominated by the interface dynamics between indium and ZnO. The diffusion exhibited a distinct ledge migration by surface diffusion at [001]-ZnO while continuous migration with slight/no ledges by inner diffusion at [100]-ZnO. The process is explained based on thermodynamic evaluation and growth kinetics. The results present the potential possibilities to completely replace metal-oxide semiconductors with metal nanowires without oxidation and form crystalline metal nanowires with precise epitaxial metal-semiconductor atomic interface. Formation of such single crystalline metal nanowire without oxidation by diffusion to the metal oxide is unique and is crucial in nanodevice performances, which is rather challenging from a manufacturing perspective of 1D nanodevices.
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http://dx.doi.org/10.1021/nl5006228DOI Listing
June 2014

Electric-field control of ferromagnetism in Mn-doped ZnO nanowires.

Nano Lett 2014 5;14(4):1823-9. Epub 2014 Mar 5.

Device Research Laboratory, Department of Electrical Engineering, University of California , Los Angeles, California 90095, United States.

In this Letter, the electric-field control of ferromagnetism was demonstrated in a back-gated Mn-doped ZnO (Mn-ZnO) nanowire (NW) field-effect transistor (FET). The ZnO NWs were synthesized by a thermal evaporation method, and the Mn doping of 1 atom % was subsequently carried out in a MBE system using a gas-phase surface diffusion process. Detailed structural analysis confirmed the single crystallinity of Mn-ZnO NWs and excluded the presence of any precipitates or secondary phases. For the transistor, the field-effect mobility and n-type carrier concentration were estimated to be 0.65 cm(2)/V·s and 6.82 × 10(18) cm(-3), respectively. The magnetic hysteresis curves measured under different temperatures (T = 10-350 K) clearly demonstrate the presence of ferromagnetism above room temperature. It suggests that the effect of quantum confinements in NWs improves Tc, and meanwhile minimizes crystalline defects. The magnetoresistace (MR) of a single Mn-ZnO NW was observed up to 50 K. Most importantly, the gate modulation of the MR ratio was up to 2.5 % at 1.9 K, which implies the electric-field control of ferromagnetism in a single Mn-ZnO NW.
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http://dx.doi.org/10.1021/nl404464qDOI Listing
March 2015

Integrated optical waveguide and photodetector arrays based on comb-like ZnO structures.

Nanoscale 2013 Dec;5(24):12185-91

Department of Material Science and Engineering, National Tsing Hua University, Hsinchu, Taiwan ROC.

On-chip integrations of photonic waveguides and high-performance electrically-driven devices, by combining different active or passive optical components, are imperative towards the advancement of nanophotonic circuitry systems. We experimentally demonstrate the collective optical functionalities of ZnO microstructures towards designing an integrated photonic system by combining the optical waveguiding and detection properties. Comb-like microstructures composed of periodic arrays of smooth, single-crystalline ZnO nanowires are synthesized for these purposes. We demonstrate that ZnO comb structures could be used as optical waveguides, which can manipulate the blue, green, and red laser beams to an interconnected waveguide array. These results are substantiated by extensive investigation of waveguiding properties of single, stacked or crossbar nanowires, and different branched microstructures. These waveguide arrays can be successfully coupled with another ZnO comb-based photodetector and the collective performances of the integrated optical micro-device units are investigated in detail. This study shows that ZnO comb-based optical waveguide arrays have the great potential to be used as a bottom-up strategy for the construction of various miniaturized photonic demultiplexer systems.
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http://dx.doi.org/10.1039/c3nr03735eDOI Listing
December 2013

Electron field emission enhancement of vertically aligned ultrananocrystalline diamond-coated ZnO core-shell heterostructured nanorods.

Small 2014 Jan 29;10(1):179-85. Epub 2013 Jul 29.

Department of Materials Science and Engineering, National Tsing Hua University, Hsin-Chu, Taiwan 300, Republic of China.

Enhanced electron field emission (EFE) behavior of a core-shell heterostructure, where ZnO nanorods (ZNRs) form the core and ultrananocrystalline diamond needles (UNCDNs) form the shell, is reported. EFE properties of ZNR-UNCDN core-shell heterostructures show a high emission current density of 5.5 mA cm(-2) at an applied field of 4.25 V μm(-1) , and a low turn-on field of 2.08 V μm(-1) compared to the 1.67 mA cm(-2) emission current density (at an applied field of 28.7 V μm(-1) ) and 16.6 V μm(-1) turn-on field for bare ZNRs. Such an enhancement in the field emission originates from the unique materials combination, resulting in good electron transport from ZNRs to UNCDNs and efficient field emission of electrons from the UNCDNs. The potential application of these materials is demonstrated by the plasma illumination measurements that lowering the threshold voltage by 160 V confirms the role of ZNR-UNCDN core-shell heterostructures in the enhancement of electron emission.
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http://dx.doi.org/10.1002/smll.201301293DOI Listing
January 2014

Direct growth of aligned zinc oxide nanorods on paper substrates for low-cost flexible electronics.

Adv Mater 2010 Sep;22(36):4059-63

Department of Materials Science and Engineering, National Tsing Hua University, Hsinchu 30043, Taiwan.

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http://dx.doi.org/10.1002/adma.201001289DOI Listing
September 2010
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