Article
Physics, Applied
Shiyun Tang, Wenjiang Tan, Jinhai Si, Jing Li, Yang Yang, Xun Hou
Summary: The article introduces a light intensity-dependent feedback-based wavefront shaping method using a genetic algorithm, which can achieve the desired wavefront shaping faster than the conventional method. By dividing the phase mask into multiple regions and allocating different phase modulation units based on light intensity distribution, the efficiency of wavefront shaping can be significantly improved.
JOURNAL OF APPLIED PHYSICS
(2021)
Article
Environmental Sciences
Haoran Liu, Yuyuan Xie, Thomas J. Browning, Feipeng Xu, Bangqin Huang
Summary: Fast repetition rate fluorometry (FRRf) is a noninvasive tool that allows for studying the physiological status of phytoplankton at high spatial and temporal resolution. In this study, FRRf measurements were carried out in the South China Sea, revealing pronounced diurnal variability of FRRf-derived parameters and the limited impact of cyclonic eddies on surface phytoplankton photophysiology.
FRONTIERS IN MARINE SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Alfonso Garcia, Edgardo Valenzuela, Alejandro Vargas, Ignacio de Godos, Raul Munoz, Meng Wang, Miguel Vital-Jacome, Guillermo Quijano
Summary: A photo-sequencing batch bioreactor (PSBR) was used to treat medium- and low-strength wastewaters, achieving a high removal efficiency of chemical oxygen demand. However, photoinhibition of nitrifying activity occurred under high irradiance conditions. A short settling time promoted the rapid formation of microalgal-bacterial aggregates (MABAs), and simulation of light penetration profiles proved to be a useful tool for identifying photoinhibition of nitrifying activity.
JOURNAL OF CHEMICAL TECHNOLOGY AND BIOTECHNOLOGY
(2023)
Article
Environmental Sciences
Jae-Cheol Lee, Rumi Park, Kyu Seon Yoo, Hyun-Woo Kim
Summary: This study suggests a synergistic system coupling cold plasma and membrane photobioreactor for treating high-turbidity livestock excrements. The integrated system effectively decomposes turbidity and TSS, with microalgal growth directly correlated to these parameters. The role of cold plasma is crucial in achieving the treatment goal for livestock excrements.
Article
Optics
Shu Guo, Richard Stern, Hong Zhang, Lin Pang
Summary: This study developed an accelerated Genetic Algorithm (GA) system based on FPGA and optimized parameters, enabling fast light focusing through scattering media. By manipulating the mutation rate and defining a convergence-efficiency function, the GA was able to converge faster while maintaining applicable light focusing. The system programmed in FPGA achieved light focusing 150 times faster than the PC-based GA, with the potential for further improvement in processing speed.
Article
Marine & Freshwater Biology
Zakia Sultana Juhi, Nur Ain Amani Abdul Mubin, Michelle Glory G. Jonik, Sazlina Salleh, Mahadi Mohammad
Summary: The study examined the effects of high and low light intensities on three coral species, with Turbinaria mesenterina showing rapid adaptive responses to high light, Porites lutea not fully recovering photoprotective responses to both light stresses, and Goniopora cellulosa experiencing rapid declines in photosynthetic yields without any photoacclimation responses.
JOURNAL OF SEA RESEARCH
(2021)
Article
Biotechnology & Applied Microbiology
Catharine Elizabeth Bosman, Robert William McClelland Pott, Steven Martin Bradshaw
Summary: One of the main factors affecting hydrogen production and growth of photofermentative microorganisms is light. This study investigated light distribution in a thermosiphon photobioreactor and evaluated a reflector system for enhancing light distribution. Experimental results showed that the addition of the reflector system increased hydrogen production by 48% and glycerol consumption from 24% to 32%. These findings suggest that the reflector system is a viable option for enhancing light distribution in photobioreactors, leading to increased hydrogen production and glycerol consumption.
JOURNAL OF BIOTECHNOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Zhenzhen Li, Ting Lan, Jiaojiao Zhang, Kunshan Gao, John Beardall, Yaping Wu
Summary: The study revealed that under nitrogen limitation, diatoms exposed to high light and UV radiation showed a significant decrease in photosynthetic pigment and organic nitrogen content, leading to reduced photochemical efficiency and increased nonphotosynthetic quenching. This suggests a higher vulnerability of diatom phytoplankton to the impacts of oceanic global change.
PHOTOCHEMISTRY AND PHOTOBIOLOGY
(2021)
Article
Engineering, Electrical & Electronic
Pasquale Imperatore, Genni Testa, Gianluca Persichetti, Romeo Bernini
Summary: The power coupling between two parallel oriented, equal length light diffusing multimodal optical fibers, coupled through scattering processes, is investigated both theoretically and experimentally. A simple analytical model of the inherent coupling coefficient is developed using a perturbation approach. The results of the model are compared with experimental measurements at three different wavelengths, showing a close agreement. These findings provide a better understanding of the power coupling mechanism and the dependence on the main structural parameters of the two-fiber configuration.
JOURNAL OF LIGHTWAVE TECHNOLOGY
(2022)
Article
Optics
Zhongtao Cheng, Lihong Wang
Summary: A technique called ultrasound-induced field perturbation optical focusing (UFP) is introduced as a more efficient method for achieving noninvasive and addressable optical focusing in scattering media. Compared to conventional methods, UFP leverages brighter zeroth-order photons and can easily be developed into double-shot or single-shot realization for high-speed wavefront shaping. This new approach broadens the horizon of light control in scattering media and provides a flexible mechanism for implementing ultrasound-guided wavefront shaping.
LIGHT-SCIENCE & APPLICATIONS
(2021)
Article
Engineering, Environmental
Wenjia Gu, Emile Theau, Amos W. Anderson, David F. Fletcher, John M. Kavanagh, Dale D. McClure
Summary: In this work, a comprehensive modelling workflow for quantifying photobioreactor performance was developed. The model, validated against experimental data, accurately predicted the flow field and biomass concentration. This work is important for the design and optimization of photobioreactor systems.
CHEMICAL ENGINEERING JOURNAL
(2023)
Article
Engineering, Environmental
Yun Huang, Jintai Wang, Yabo Sun, Weida Zeng, Ao Xia, Xianqing Zhu, Xun Zhu, Qiang Liao
Summary: The use of non-immersed titled zigzag microalgae biofilm proves to be an effective method for purifying digested piggery wastewater by overcoming light attenuation and achieving high removal rates of ammonia nitrogen and total phosphorus.
Article
Chemistry, Multidisciplinary
Serena Lima, Alberto Brucato, Giuseppe Caputo, Luca Schembri, Francesca Scargiali
Summary: By developing a model, researchers were able to predict the growth of microalgae in reactors with different configurations. Furthermore, they found that biomass and lipid content of the microalgae changed under different light intensities and reactor configurations.
APPLIED SCIENCES-BASEL
(2022)
Article
Agricultural Engineering
Panneerselvam Ranganathan, Ashutosh Kumar Pandey, Ranjna Sirohi, Anh Tuan Hoang, Sang-Hyoun Kim
Summary: This study reviews the application of computational flow modelling in photobioreactors and discusses an integrated modelling approach for these reactors. It also reviews intensified systems for improving the performance of photobioreactors. Future considerations include the development of multi-scale modelling methods and low-cost efficient computational frameworks, as well as the use of process intensification techniques to enhance hydrodynamics, mixing, and mass transfer in photobioreactors.
BIORESOURCE TECHNOLOGY
(2022)
Article
Environmental Sciences
Kento Nishi, Shinichi Akizuki, Tatsuki Toda, Tatsushi Matsuyama, Junichi Ida
Summary: This study demonstrates the potential of using light-shielding hydrogel to protect nitrifying bacteria and enable efficient nitrification in a consortium with microalgae under strong light irradiation. The light-shielding hydrogel achieved complete nitrification without nitrite accumulation and had significantly higher nitrification rates compared to other conditions. The findings suggest that this method could be applicable for practical applications in regions with high sunlight intensity.
Article
Mathematics, Applied
Agustin G. Yabo, Jean-Baptiste Caillau, Jean-Luc Gouze, Hidde de Jong, Francis Mairet
Summary: Gaining a better understanding of microbial growth is crucial for scientific research, and self-replicator models based on resource allocation principles have been effective in explaining experimental observations. This study extends a previous model by considering the role of proteins in basic functions and investigates their impact on optimal resource allocation strategies in response to environmental changes. The analysis reveals a globally attractive equilibrium and complex solutions, providing a generalized perspective on microbial growth analysis.
SIAM JOURNAL ON APPLIED DYNAMICAL SYSTEMS
(2022)
Article
Plant Sciences
Anne Pajot, Johann Lavaud, Gregory Carrier, Matthieu Garnier, Bruno Saint-Jean, Noemie Rabilloud, Caroline Baroukh, Jean-Baptiste Berard, Olivier Bernard, Luc Marchal, Elodie Nicolau
Summary: Differences in lhc classification in Chromista were observed. A classification of the lhcf family with specific groups for haptophytes, diatoms, and seaweeds was proposed. Similarity analysis was performed to identify and characterize Fucoxanthin and Chlorophyll a/c-binding Protein (FCP) in the haptophyte microalgae Tisochrysis lutea. The study revealed dynamic changes in lhc gene expression with nitrogen depletion and the exclusive nighttime expression of the lhcx2 gene in T. lutea, suggesting its role in protecting cells from light exposure after prolonged darkness.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Automation & Control Systems
Olivier Bernard, Liu-Di Lu, Julien Salomon
Summary: In this article, the authors investigate a periodic resource allocation problem in a dynamical system, which is applied to a biological system. The goal is to find optimal control strategies to optimize the cost or benefit of the system. The authors illustrate this problem using an industrial biological application and introduce a nonlinear optimization problem and a suboptimal solution to overcome the computational difficulty. Numerical experiments are performed to assess the benefits of optimal strategies in different settings.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2023)
Article
Biochemical Research Methods
Bastien Polizzi, Andrea Fanesi, Filipa Lopes, Magali Ribot, Olivier Bernard
Summary: This article presents a spatial model for the growth of a photosynthetic microalgae biofilm and investigates the biofilm's structural dynamics and the impact of optimal harvesting strategies on its structure.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Engineering, Chemical
Walid Djema, Terence Bayen, Olivier Bernard
Summary: This paper investigates the problem of species separation in minimal time. The evolution of two competing microorganism populations for the same resource is described using the Droop model. The paper focuses on solving an optimal control problem subject to a controlled system with five dimensions. The objective is to select the desired species in minimal time and synthesize an optimal feedback control. The paper provides properties of optimal controls and utilizes the Pontryagin Maximum Principle and a study of singular arcs for analysis. The theoretical results are validated using numerical examples with microalgae and a direct method in optimal control.
Article
Biotechnology & Applied Microbiology
Andrea Fanesi, Thierry Martin, Cyril Breton, Olivier Bernard, Romain Briandet, Filipa Lopes
Summary: Microalgae biofilms have ecological importance and biotechnological potential. However, a comprehensive understanding of their structure and physiology is still lacking. In this study, a novel approach was developed to nondestructively characterize the physiological and structural information of microalgae biofilms. The results showed that the physiology of cells in complex biofilms is more affected, likely due to alterations in local environmental conditions.
BIOTECHNOLOGY AND BIOENGINEERING
(2022)
Article
Microbiology
Francesca Casagli, Olivier Bernard
Summary: High-rate algal-bacterial ponds (HRABP) are considered as an interesting solution to reduce energy demand in wastewater treatment, yet the efficiency is highly influenced by solar fluxes and temperature fluctuations. The temperature patterns and reactor configurations play a crucial role in the biological process of HRABPs.
Article
Ecology
Amin Golpour, Marek Smejkal, Martin Cech, Romulo A. dos Santos, Allan T. Souza, Tomas Juza, Carlos Martinez, Daniel Barton, Mojmir Vasek, Vladislav Drastik, Tomas Kolarik, Lubos Kocvara, Milan Riha, Jiri Peterka, Petr Blabolil
Summary: This study compared the water eDNA targeting fish (wf-eDNA) method with four traditional fish sampling methods to assess the reliability and efficiency of wf-eDNA in evaluating the diversity and composition of freshwater fish communities. The results showed that wf-eDNA was consistent with traditional sampling methods in species detection, but also detected some species that were not detected by traditional methods. The wf-eDNA method was found to be a reliable and complementary approach for biomonitoring and ecosystem management of freshwater fish.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Automation & Control Systems
Frederic Mazenc, Olivier Bernard
Summary: This article presents a simple, necessary, and sufficient condition for a real matrix to be similar to a Metzler matrix of dimension three, and provides a construction method for the transfer matrix. This construction is utilized to design an interval observer for a family of continuous-time systems. The case of limit cycles in the love dynamics is used as an example for the interval observer design.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2022)
Article
Automation & Control Systems
Carlos Martinez, Bruno Assis Pessi, Olivier Bernard
Summary: Zooplankton contamination is a significant constraint in large-scale microalgal cultivation systems, and its development can be controlled by regulating the dilution rate. However, finding the best control strategy for the dilution rate is not straightforward. This study explores the role of dilution rate in controlling zooplankton populations and optimizing biomass productivity. The results suggest that in the long-term operation, the optimal constant dilution rate should ensure the eradication of zooplankton populations.
JOURNAL OF PROCESS CONTROL
(2022)
Article
Green & Sustainable Science & Technology
Francesca Casagli, Olivier Bernard
Summary: Existing mathematical models for outdoor biotechnological processes cannot predict the future dynamics, thus fully predictive models are needed. The FLAME modelling framework integrates biological, heat transfer, and chemical sub-models to forecast outdoor bioprocesses. It provides a powerful tool for controlling and optimizing environmental processes.
JOURNAL OF CLEANER PRODUCTION
(2022)
Article
Marine & Freshwater Biology
Clemence Boucher, Thomas Lacour, Andre Julie, Reveillon Damien, Hansen Per Juel, Mairet Francis
Summary: Many harmful algae have the ability to combine phototrophy and phagotrophy, which may explain their ecological success in suboptimal conditions. This study investigated the effects of phosphorus sufficiency and deficiency on the growth, phagotrophic and lytic activities of the mixotrophic haptophyte Prymnesium parvum. The results showed that the ingestion of organic phosphorus from living prey and/or debris plays a crucial role in P. parvum growth and its ecological success in nutrient-limited environments.
Article
Automation & Control Systems
Terence Bayen, Jerome Coville, Francis Mairet
Summary: In this article, the chemostat system with mutations between species is considered, and the authors aim to globally stabilize the dynamical system around a desired equilibrium point. Auxostat feedback controls are introduced for regulating substrate concentration, and it is proved that they can achieve global stabilization of the closed-loop system. The performance of these controllers is illustrated on an optimal control problem related to maximizing species production over a given time period.
OPTIMAL CONTROL APPLICATIONS & METHODS
(2023)
Article
Biotechnology & Applied Microbiology
David Morgado, Andrea Fanesi, Thierry Martin, Sihem Tebbani, Olivier Bernard, Filipa Lopes
Summary: This study utilized a rotating system to produce the high-value compound astaxanthin using Haematococcus pluvialis biofilms. The effect of nitrogen regime, light intensity, and light history on biofilm traits was assessed, showing that H. pluvialis biofilms follow the classical growth stages of bacterial biofilms and that training the biofilms during the green stage can significantly enhance astaxanthin productivity.
BIOTECHNOLOGY AND BIOENGINEERING
(2023)
Proceedings Paper
Automation & Control Systems
Carlos Martinez, Allan T. Souza, Jan Kubecka
Summary: The removal of planktivorous fish leads to changes in the ecosystem, improving water transparency and reducing the risk of harmful algal blooms. This study presents a generic fish-zooplankton model and identifies conditions for eradicating the fish population through repeated removal. The model considers fish weight, age, and impulsive effects such as reproduction and fish removal, and demonstrates the importance of removing young fish for eradication.
Article
Biology
Iain Hunter, Raz Leib
Summary: Natural movement is related to health, but it is difficult to measure. Existing methods cannot capture the full range of natural movement. Comparing movement across different species helps identify common biomechanical and computational principles. Developing a system to quantify movement in freely moving animals in natural environments and relating it to life quality is crucial. This study proposes a theoretical framework based on movement ability and validates it in Drosophila.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Andy Gardner
Summary: Fisher's geometric model is a useful tool for predicting key properties of Darwinian adaptation, and here it is applied to predict differences between the evolution of altruistic versus nonsocial phenotypes. The results suggest that the effect size maximizing probability of fixation is smaller in the context of altruism and larger in the context of nonsocial phenotypes, leading to lower overall probability of fixation for altruism and higher overall probability of fixation for nonsocial phenotypes.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Thomas F. Pak, Joe Pitt-Francis, Ruth E. Baker
Summary: Cell competition is a process where cells interact in multicellular organisms to determine a winner or loser status, with loser cells being eliminated through programmed cell death. The winner cells then populate the tissue. The outcome of cell competition is context-dependent, as the same cell type can win or lose depending on the competing cell type. This paper proposes a mathematical framework to study the emergence of winner or loser status, highlighting the role of active cell death and identifying the factors that drive cell competition in a cell-based modeling context.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Haruto Tomizuka, Yuuya Tachiki
Summary: Batesian mimicry is a strategy in which palatable prey species resemble unpalatable prey species to avoid predation. The evolution of this mimicry plays a crucial role in protecting the unpalatable species from extinction.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Jason W. Olejarz, Martin A. Nowak
Summary: Gene drive technology shows potential for population control, but its release may have unpredictable consequences. The study suggests that the failure of suppression is a natural outcome, and there are complex dynamics among wild populations.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Hamid Ravaee, Mohammad Hossein Manshaei, Mehran Safayani, Javad Salimi Sartakhti
Summary: Gene expression analysis is valuable for cancer classification and phenotype identification. IP3G, based on Generative Adversarial Networks, enhances gene expression data and discovers phenotypes in an unsupervised manner. By converting gene expression profiles into images and utilizing IP3G, new phenotype profiles can be generated, improving classification accuracy.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Beatrix Rahnsch, Leila Taghizadeh
Summary: This study forecasts the evolution of the COVID-19 pandemic in Germany using a network-based inference method and compares it with other approaches. The results show that the network-inference based approach outperforms other methods in short-to mid-term predictions, even with limited information about the new disease. Furthermore, predictions based on the estimation of the reproduction number in Germany can yield more reliable results with increasing data availability, but still cannot surpass the network-inference based algorithm.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Rongsheng Huang, Qiaojun Situ, Jinzhi Lei
Summary: Maintaining tissue homeostasis requires appropriate regulation of stem cell differentiation. Random inheritance of epigenetic states plays a pivotal role in stem cell differentiation. This computational model provides valuable insights into the intricate mechanism governing stem cell differentiation and cell reprogramming, offering a promising path for enhancing the field of regenerative medicine.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Patrick Vincent N. Lubenia, Eduardo R. Mendoza, Angelyn R. Lao
Summary: This study compares insulin signaling in healthy and type 2 diabetes states using reaction network analysis. The results show similarities and differences between the two conditions, providing insights into the mechanisms of insulin resistance, including the involvement of other complexes, less restrictive interplay between species, and loss of concentration robustness in GLUT4.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Nuverah Mohsin, Heiko Enderling, Renee Brady-Nicholls, Mohammad U. Zahid
Summary: Mathematical modeling is crucial in understanding radiobiology and designing treatment approaches in radiotherapy for cancer. This study compares three tumor volume dynamics models and analyzes the implications of model selection. A new metric, the point of maximum reduction of tumor volume (MRV), is introduced to quantify the impact of radiotherapy. The results emphasize the importance of caution in selecting models of response to radiotherapy due to the artifacts imposed by each model.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
Article
Biology
Armindo Salvador
Summary: Michael Savageau's Biochemical Systems Analysis papers have had a significant impact on Systems Biology, generating core concepts and tools. This article provides a brief summary of these papers and discusses the most relevant developments in Biochemical Systems Theory since their publication.
JOURNAL OF THEORETICAL BIOLOGY
(2024)
