A Simple Alternative Approach to Assessing the Fate of Absorbed Light Energy Using Chlorophyll Fluorescence

The distinction is drawn between problems in which single particle motion has physical significance and those in which relative motion between pairs of particles must be considered. Local relative motion is considered from the standpoint of the equation of geodesic deviation, expressed in arbitrary coordinates and in geodesic Fermi coordinates. A simple alternative approach to geodesic deviation using synchronous reference frames is described. Examples of relative motion in the Schwarzschild field and in a gravitational wave are discussed. Criticism of the efficacy of cryogenic cooling to enhance gravitational wave detector sensitivity is shown to be invalid. However, a cautionary note is expressed with regard to the necessity of a local observer to detect deviations from local planeness.

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Optinalysis: A New Approach of Symmetry Detection and Similarity Measurement through a Looking-Glass

10.20944/preprints201905.0295.v2 ◽

2019 ◽

Author(s):

Kabir Bindawa Abdullahi

Keyword(s):

Sequence Comparison ◽

Genomic Sequences ◽

Similarity Measurement ◽

Symmetry Detection ◽

New Approach ◽

Alternative Approach ◽

Simple Alternative ◽

Looking Glass

Optinalysis, as a method of symmetry detection, is a new algorithm that intrametrically (within elements or variables) or intermetrically (between elements or variables) computes and compares two or more univariate or multi-clustered or multivariate sequences as a mirror-like reflection of each other (optics-like manner), hence the name is driven. Optinalysis is based by the principles of reflection and moment about a symmetrical line which detects symmetry that reflects a similarity measurement. This proposed methodology was validated in comparison with Pearson method of skewness detection, and also with some algorithms for pairewise alignment and comparison of genomic sequences (Needle, Stretcher, Water, Matcher) on EMBL-EBI website. A results comparison shows that optinalysis is more advance, more sensitive, more inferential and simple alternative approach of skewness detection and pairewise sequence comparison.

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Shade lichens are characterized by rapid relaxation of non-photochemical quenching on transition to darkness

The Lichenologist ◽

10.1017/s0024282921000323 ◽

2021 ◽

Vol 53 (5) ◽

pp. 409-414

Author(s):

Richard P. Beckett ◽

Farida V. Minibayeva ◽

Kwanele W. G. Mkhize

Keyword(s):

Chlorophyll Fluorescence ◽

Quantum Yield ◽

Light Energy ◽

Photochemical Quenching ◽

Photosynthetic Organisms ◽

Light Levels ◽

Lower Light ◽

Optimal Productivity ◽

Sun And Shade ◽

Non Photochemical Quenching

AbstractNon-photochemical quenching (NPQ) plays an important role in protecting photosynthetic organisms from photoinhibition by dissipating excess light energy as heat. However, excess NPQ can greatly reduce the quantum yield of photosynthesis at lower light levels. Recently, there has been considerable interest in understanding how plants balance NPQ to ensure optimal productivity in environments in which light levels are rapidly changing. In the present study, chlorophyll fluorescence was used to study the induction and relaxation of non-photochemical quenching (NPQ) in the dark and the induction of photosynthesis in ten species of lichens, five sampled from exposed and five sampled from shaded habitats. Here we show that the main difference between sun and shade lichens is the rate at which NPQ relaxes in the dark, rather than the speed that photosynthesis starts upon illumination. During the first two minutes in the dark, NPQ values in the five sun species declined only by an average of 2%, while by contrast, in shade species the average decline was 40%. For lichens growing in microhabitats where light levels are rapidly changing, rapid relaxation of NPQ may enable their photobionts to use the available light most efficiently.

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Optinalysis: A New Approach of Multivariate Analysis through A Looking-Glass

10.20944/preprints201905.0295.v1 ◽

2019 ◽

Author(s):

Kabir Bindawa Abdullahi

Keyword(s):

Multivariate Analysis ◽

T Test ◽

Data Matrix ◽

Data Types ◽

New Approach ◽

Alternative Approach ◽

Simple Alternative ◽

Algorithmic Analysis ◽

Looking Glass ◽

One Way Anova

Optinalysis, as a method of symmetry detection, is a new advanced computational algorithm that intrametrically (within elements) or intermetrically (between elements) computes and compares two or more multivariate sequences in an unclustered or clustered manner as a mirror-like reflection of each other (optics-like manner), hence the name is driven. Optinalysis is based by the principles of reflection and moment about a symmetrical line which detects symmetry that reflects a similarity measurement. Optinalysis is suitable for quantitative and qualitative data types, with or without replications, provided it conform the algorithmic requirements there provided. Optinalysis can be organized for geometrical, geostatistical and statistical analysis in one-way, two-way, or three-way approach. A simulation comparisons shows that Optinalysis is a simple alternative approach of multivariate analysis of sociometric, demographic, socio-demographic, psychometric, ecological, experimental, genomic, nanoparticle and shape morphometric data. Optinalysis of these data matrix shows very similar results or conclusions with some multivariate analysis such as skewness measure, one-way ANOVA, paired t-test, one sample t-test, Tukey’s multiple comparisons, BLAST sequence algorithmic analysis (percentages of identity, similarity, gabs, and positives, and the Needleman-Wunsch score), and Riemannian distance.

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Estimating the timing of HIV infection from unmutated sequences

10.1101/2020.11.28.402271 ◽

2020 ◽

Author(s):

Alec Pankow ◽

Murray Christian ◽

Natalie Smith ◽

Daniel J. Sheward ◽

Ben Murrell

Keyword(s):

Sequence Data ◽

Real Data ◽

Data Curation ◽

Bulk Analysis ◽

Multiple Datasets ◽

Alternative Approach ◽

Simple Alternative ◽

Credible Intervals ◽

Exponential Population Growth ◽

Individual Donor

For HIV, the time since infection can be estimated from sequence data for acutely infected samples. One popular approach relies on the star-like nature of phylogenies generated under exponential population growth, and the resulting Poisson distribution of mutations away from the founding variant. However, real-world complications, such as APOBEC hypermutation and multiple-founder transmission, present a challenge to this approach, requiring data curation to remove these signals before reasonable timing estimates may be obtained. Here we suggest a simple alternative approach that derives the timing estimate not from the entire mutational spectrum but from the proportion of sequences that have no mutations. This can be approximated quickly and is robust to phenomena such as multiple founder transmission and APOBEC hypermutation. Our approach is Bayesian, and we adopt a conjugate prior to obtain closed form posterior distributions at negligible computational expense. Using real data and simulations, we show that this approach provides accurate timing estimates and credible intervals without the inconvenience of data curation and is robust to complicating phenomena that can mislead existing approaches or cause them to fail entirely. For immediate use we provide an implementation via Google Sheets, which offers bulk analysis of multiple datasets, as well as more detailed individual-donor analyses. For inclusion in data processing pipelines we provide implementations in three languages: Julia, R, and Python.

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Micro-Abrasive Blasting—A Novel Approach to Local Silicon and Mold Compound Material Removal

ISTFA 2013: Conference Proceedings from the 39th International Symposium for Testing and Failure Analysis ◽

10.31399/asm.cp.istfa2013p0490 ◽

2013 ◽

Author(s):

Zhenzhou Sun ◽

Alberto Bosio ◽

Luigi Dilillo ◽

Patrick Girard ◽

Aida Todri ◽

...

Keyword(s):

Integrated Circuits ◽

Sample Preparation ◽

Cnc Machining ◽

Novel Approach ◽

Alternative Approach ◽

Computer Numerically Controlled ◽

Simple Alternative ◽

Local Sample ◽

Set Up ◽

Abrasive Blasting

Abstract Post silicon validation techniques on Integrated Circuits (IC) specifically FIB circuit editing require backside sample preparation done by local mold compound and silicon machining. Conventional methods such as Computer Numerically Controlled (CNC) machining and chemical etching preparation platforms are commonly used. This paper will investigate a simple alternative approach to local sample preparation by using micro-abrasive blasting. This approach will display its simple natured set-up along with extremely quick process duration.

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Combining Gas Exchange and Chlorophyll Fluorescence to Assess the Adaptability of Medicinal Plant Aesculus chinensis Compared to Two Imported Aesculus Species

Advanced Materials Research ◽

10.4028/www.scientific.net/amr.726-731.4330 ◽

2013 ◽

Vol 726-731 ◽

pp. 4330-4336

Author(s):

Hai Yan Fu ◽

Fu Qiang Song ◽

Jia Sen Wu ◽

Xiang Shi Kong ◽

Dan Dan Qi

Keyword(s):

Chlorophyll Fluorescence ◽

Electron Transport ◽

Gas Exchange ◽

Tree Species ◽

Light Energy ◽

The Other ◽

Photochemical Quenching ◽

Chlorophyll Fluorescence Parameters ◽

Psii Photochemistry

Analysis of gas exchange and determination of chlorophyll fluorescence parameters in leaves of three tree species including Aesculus chinensis, A. octandra and A. hybrida were conducted under field conditions and then comparison was carried out. The results showed that the light compensation point (LCP) was significantly different among the three tree species, of which the LCP of A. chinensis with 12.53 μmol·m-2·s-1 that of the lowest was notable lower than that of the other two species (36.11 and 46.41 μmol·m-2·s-1respectively). On the other hand, the light saturation point (LSP) of the three tree species also showed remarked different and the LSP of A. chinensis was 1475 μmol·m-2·s-1 which was dramatic higher than that of the other two species respective to 1366.67 and 1025 μmol·m-2·s-1. Beside, the maximum net photosynthetic rate (MNPR) was different too, MNPR of A. chinensis was 9.47μmol CO 2·m-2·s-1which was higher than the other two species (5.91 and 2.30 μmol CO 2·m-2·s-1 respectively), indicating A. chinensis had a higher photosynthetic capacity and stronger utilization ability for light energy. Moreover, the electron transport rate (ETR) of A. chinensis was higher than A. octandra and A. hybrida, the ETR of the former was 55.800 that were 1.33 and 1.44 times of the later two respectively. Quantum yield of PSII photochemistry (ФPSII) in A. chinensis was higher than A. octandra and A. hybrida, the ФPSII of the former was 0.470 that were 1.21 and 1.15 times of the later two respectively. Furthermore, the photochemical quenching (qP) of A. chinensis was 0.975 much higher than A. octandra and A. hybrida respective to 1.10 and 1.10 times of the later two respectively. These three photochemical parameters with dramatic different among the three different tree species suggested A. chinensis had a high activity of electron transport and conversion efficiency for light energy.

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Interplay between LHCSR proteins and state transitions governs the NPQ response in intact cells of Chlamydomonas during light fluctuations.

10.1101/2021.12.31.474662 ◽

2022 ◽

Author(s):

Collin Steen ◽

Adrien Burlacot ◽

Audrey Short ◽

Krishna K. Niyogi ◽

Graham Fleming

Keyword(s):

Chlorophyll Fluorescence ◽

State Transition ◽

Light Harvesting ◽

High Light ◽

Light Energy ◽

State Transitions ◽

Photochemical Quenching ◽

Intact Cells ◽

Fluctuating Light ◽

Light Fluctuations

Photosynthetic organisms use sunlight as the primary energy source to fix CO2. However, in the environment, light energy fluctuates rapidly and often exceeds saturating levels for periods ranging from seconds to hours, which can lead to detrimental effects for cells. Safe dissipation of excess light energy occurs primarily by non-photochemical quenching (NPQ) processes. In the model green microalga Chlamydomonas reinhardtii, photoprotective NPQ is mostly mediated by pH-sensing light-harvesting complex stress-related (LHCSR) proteins and the redistribution of light-harvesting antenna proteins between the photosystems (state transition). Although each component underlying NPQ has been documented, their relative contributions to the dynamic functioning of NPQ under fluctuating light conditions remains unknown. Here, by monitoring NPQ throughout multiple high light-dark cycles with fluctuation periods ranging from 1 to 10 minutes, we show that the dynamics of NPQ depend on the frequency of light fluctuations. Mutants impaired in the accumulation of LHCSRs (npq4, lhcsr1, and npq4lhcsr1) showed significantly less quenching during illumination, demonstrating that LHCSR proteins are responsible for the majority of NPQ during repetitive exposure to high light fluctuations. Activation of NPQ was also observed during the dark phases of light fluctuations, and this was exacerbated in mutants lacking LHCSRs. By analyzing 77K chlorophyll fluorescence spectra and chlorophyll fluorescence lifetimes and yields in a mutant impaired in state transition, we show that this phenomenon arises from state transition. Finally, we quantified the contributions of LHCSRs and state transition to the overall NPQ amplitude and dynamics for all light periods tested and compared those with cell growth under various periods of fluctuating light. These results highlight the dynamic functioning of photoprotection under light fluctuations and open a new way to systematically characterize the photosynthetic response to an ever-changing light environment.

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OPEN PROBLEMS IN THE HYDRODYNAMICAL APPROACH TO RELATIVISTIC HEAVY ION COLLISIONS

International Journal of Modern Physics E ◽

10.1142/s0218301307006265 ◽

2007 ◽

Vol 16 (03) ◽

pp. 763-775 ◽

Cited By ~ 4

Author(s):

T. KODAMA ◽

T. KOIDE ◽

G. S. DENICOL ◽

P. MOTA

Keyword(s):

Heavy Ion Collisions ◽

Heavy Ion ◽

Relativistic Heavy Ion Collisions ◽

Open Problems ◽

Ion Collisions ◽

Alternative Approach ◽

Simple Alternative

We discuss some open problems in hydrodynamical approach to the relativistic heavy ion collisions. In particular, we propose a new, very simple alternative approach to the relativistic dissipative hydrodynamics of Israel and Stewart.

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