Article
Plant Sciences
Giorgio Perin, Francesca Gambaro, Tomas Morosinotto
Summary: This paper discusses the current knowledge of regulation of photosynthesis and its implications for maximizing microalgae biomass productivity. Fluctuations in light have a negative impact on biomass productivity in large-scale microalgae cultures, thus requiring rapid regulatory mechanisms to respond to sudden changes in light intensity. Microalgae also have the ability to modulate the composition and activity of the photosynthetic apparatus in response to environmental conditions, a response that is also activated in outdoor cultures. Integrating detailed knowledge from large-scale microalgae cultivation is essential for optimizing biomass productivity effectively.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Biotechnology & Applied Microbiology
Nicholas J. Kirchner, Adam Hage, Jose Gomez, Gabriel P. Holbrook
Summary: M. Dek19 is a versatile microalga adapted to low temperatures and light levels, making it suitable for wastewater treatment and biofuel production. It is capable of efficiently removing pollutants from wastewater under cool conditions and exhibits increased photosynthetic capacity and adaptation to lower light penetration and flux.
ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS
(2022)
Article
Marine & Freshwater Biology
Saskia Jurriaans, Mia O. Hoogenboom, Christine Ferrier-Pages
Summary: Contrary to expectations, tropical and temperate coral species exhibited similar performance breadths in photosynthesis and electron transport rates, with thermal optima generally below local average temperature. This suggests that corals have adapted to cope with temperature variation, but current temperatures are pushing the boundaries of coral thermal tolerance.
Article
Energy & Fuels
Jiangyu Zhu, Xiaomiao Tan, Halimatun Saadiah Hafid, Minato Wakisaka
Summary: An environmentally friendly and cost-effective method to improve lipid production in microalgae without sacrificing their growth was established. The potential of syringic acid (SA) and p-coumaric acid (p-CA) in regulating the growth and biosynthesis of valuable metabolites in Euglena gracilis was evaluated. Both phenolic acids treatments improved lipid biosynthesis, making it favorable for biofuel production.
Article
Biochemistry & Molecular Biology
Christopher Holmes, Juan Varas, Sebastian San Martin, Jose Tomas Egana
Summary: This study presents a 3D photosynthetic tumor model composed of human melanoma cells and Chlamydomonas reinhardtii microalgae, which allows for simultaneous study of both cell types. The results show that the two cell types are biocompatible with each other under cell culture conditions, and a 10:1 ratio of microalgae to cells meets the metabolic requirement of the tumor cells, producing sufficient oxygen. This 3D tumor model provides an easy-to-use in vitro resource for analyzing the effects of photosynthetically produced oxygen on a tumor microenvironment, opening up various potential research avenues.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Xuemei Ma, Qiang Liu, Zhidong Zhang, Zewen Zhang, Zeyu Zhou, Yu Jiang, Xuanrui Huang
Summary: The study compared four models in simulating the photosynthetic light response curve of tree crown and found that the MRHM model had the highest fitting accuracy. The light saturation point (LSP) obtained by MRHM was slightly lower than the observed values, while the maximum net photosynthetic rates (P-max) modeled by the four models were close to the measured values.
Article
Biotechnology & Applied Microbiology
Ana Sanchez Zurano, Cintia Gomez Serrano, F. Gabriel Acien-Fernandez, Jose M. Fernandez-Sevilla, Emilio Molina-Grima
Summary: This study highlighted the significant influence of irradiance on microalgae photosynthesis rates, while temperature and pH strongly affected the activities of heterotrophic and nitrifying bacteria. Additionally, dissolved oxygen concentrations above 20 mg/L were found to reduce the photosynthetic rate of microalgae.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Article
Plant Sciences
Sotirios Zerveas, Evangelos Kydonakis, Polychronis Moutidis, Aristeidis Maragkoudakis, Kiriakos Kotzabasis
Summary: The study demonstrates that microalgae can effectively increase oxygen levels in anoxic atmospheres by utilizing high concentrations of CO2 for photosynthesis, promoting growth without stress responses. This survival strategy of microalgae could potentially be used for combating the greenhouse effect and recycling atmospheres on other planets, providing a useful module for (astro)biotechnological applications.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2021)
Article
Mathematics
Abraham Guzman-Palomino, Luciano Aguilera-Vazquez, Hector Hernandez-Escoto, Pedro Martin Garcia-Vite
Summary: This paper delves into the equilibria, stability, and sensitivity of a microalgal growth model developed by Droop (1974) for nutrient-limited batch cultivation. The analysis reveals an infinite number of equilibria in the system depending on the minimal cell quota and initial conditions. Simulation results suggest that the model outputs are more sensitive to variations in the parameters of half saturation constant and minimal cell quota.
Article
Neurosciences
Logan J. Voss, Maxence Plouviez, Nicola Whittle
Summary: This study demonstrated that oxygenation of aCSF by Chlamydomonas reinhardtii can sustain cortical network activity without tissue toxicity. The results suggest that photosynthesis may be a promising mechanism for providing oxygen to rescue ischaemic avascularised brain tissue.
Article
Environmental Sciences
Prima Anugerahanti, Onur Kerimoglu, S. Lan Smith
Summary: The study evaluates different biogeochemical models for phytoplankton growth response, finding that models with fixed stoichiometry are more sensitive to external parameter variations, but the fixed stoichiometry model with photoacclimation can better capture chlorophyll observations when individually tuned. Models with variable C:N ratio perform better in cross-validation experiments, indicating they are more portable.
FRONTIERS IN MARINE SCIENCE
(2021)
Article
Agricultural Engineering
Yen-Cheng Yeh, Tehreem Syed, Gordon Brinitzer, Konstantin Frick, Ulrike Schmid-Staiger, Bernard Haasdonk, Guenter E. M. Tovar, Felix Krujatz, Jonathan Maedler, Leon Urbas
Summary: This study investigates the use of machine learning algorithms in modeling microalgae growth and compares their performance with traditional models. The results show that machine learning models outperform traditional models by utilizing light history as input and have excellent ability in describing the light acclimation effect. Two potential applications of these models, including their use as a biomass soft sensor and development of optimal harvest strategy for outdoor cultivation, are also demonstrated.
BIORESOURCE TECHNOLOGY
(2023)
Article
Plant Sciences
Bin Du, M. K. Shukla, Risheng Ding, Xiaolin Yang, Taisheng Du
Summary: This study demonstrates that injecting elevated CO2 concentration in the greenhouse can improve photosynthetic activity and yield of cherry tomatoes. Inoculation with photosynthetic bacteria can further enhance photosynthetic acclimation and alleviate yield penalties caused by reduced irrigation. This suggests that application of photosynthetic bacteria can potentially improve cherry tomato production.
ENVIRONMENTAL AND EXPERIMENTAL BOTANY
(2022)
Article
Energy & Fuels
Hui Wang, Mingyue Wang, Qi Cheng, Shuaishuai Lv, Xiu Ji
Summary: Under the double carbon goal, distributed generation with inverters will experience explosive growth. Microgrids play an important role in connecting the distributed generation to the main grid, but their instability when switching between grid-connected and islanded modes is exacerbated by the fast response characteristics of power electronics. This study focuses on developing a refined power generation model and a reasonable control strategy, including the addition of a virtual adaptive control loop and frequency signal feedback, to improve the stability and accuracy of the system.
Article
Agricultural Engineering
P. Fernandez del Olmo, F. G. Acien, J. M. Fernandez-Sevilla
Summary: This study uses Computational Fluid Dynamics and a dynamic photosynthesis model to analyze the efficiency of photosynthesis in different sizes and circulation velocities of tubular photobioreactors. The smallest diameters of reactors were found to have sufficient radial mixing for enhancing photosynthesis under optimal light regime, while high circulation velocities in larger diameters increased operating costs without enhancing photosynthetic productivity. The characteristic frequency of the strain (beta) was shown to be crucial for high productivity.
BIORESOURCE TECHNOLOGY
(2022)
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
Immunology
Zoltan Kis, Kyungjae Tak, Dauda Ibrahim, Maria M. Papathanasiou, Benoit Chachuat, Nilay Shah, Cleo Kontoravdi
Summary: This study evaluates and compares the feasibility of three vaccine production platform technologies used during the COVID-19 pandemic, including their production performance, cost, and efficiency. It predicts the cost and resource requirements for manufacturing large-scale vaccine doses and provides important insights and recommendations for policymakers and manufacturers.
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
Computer Science, Interdisciplinary Applications
Tanuj Karia, Claire S. Adjiman, Benoit Chachuat
Summary: This paper revisits the approach of transforming a mixed-integer polynomial program into a mixed-integer quadratically-constrained program, and automates this transformation in a new reformulation engine called CANON. The experimental results demonstrate that the reformulated MIQCPs perform best on the solver GUROBI.
COMPUTERS & CHEMICAL ENGINEERING
(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
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
Computer Science, Interdisciplinary Applications
Ariel Uribe-Rodriguez, Pedro M. Castro, Gonzalo Guillen-Gosalbez, Benoit Chachuat
Summary: This study presents an integrated methodology for optimal short-term planning of integrated refinery-petrochemical complexes (IRPCs) and demonstrates its effectiveness through a full-scale industrial case study. The methodology uses a spatial Lagrangean decomposition to divide the IRPC into multiple subsections, which facilitates the creation of virtual markets for trading crude blends and intermediate petrochemical streams. The results show that decompositions with two or three subsections achieve optimal solutions with small optimality gaps, outperforming global solvers and relaxation strategies.
COMPUTERS & CHEMICAL ENGINEERING
(2023)
Article
Chemistry, Multidisciplinary
Husain A. Baaqel, Andrea Bernardi, Jason P. Hallett, Gonzalo Guillen-Gosalbez, Benoit Chachuat
Summary: This paper presents a systematic methodology for uncertainty quantification in life-cycle assessment (LCA) of early-stage technologies using global sensitivity analysis (GSA). A case study comparing the life-cycle impacts of two dialkylimidazolium ionic liquids is conducted to illustrate the methodology. Failure to account for the foreground process uncertainty alongside the background uncertainty underestimates the predicted variance of the end-point environmental impacts by a factor of two, highlighting the importance of considering both types of uncertainties in LCA.
ACS SUSTAINABLE CHEMISTRY & ENGINEERING
(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)
Article
Chemistry, Multidisciplinary
Kennedy Putra Kusumo, Kamal Kuriyan, Shankarraman Vaidyaraman, Salvador Garcia Munoz, Nilay Shah, Benoit Chachuat
Summary: This article proposes a new method for designing optimal experimental campaigns under model uncertainties and provides a tractable computational framework. The feasibility of this method is demonstrated using a case study with the risk of thermal runaway.
REACTION CHEMISTRY & ENGINEERING
(2022)
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)