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Records with Subject: Biosystems
Showing records 1 to 25 of 51. [First] Page: 1 2 3 Last
An Innovative Agro-Forestry Supply Chain for Residual Biomass: Physicochemical Characterisation of Biochar from Olive and Hazelnut Pellets
Ilaria Zambon, Fabrizio Colosimo, Danilo Monarca, Massimo Cecchini, Francesco Gallucci, Andrea Rosario Proto, Richard Lord, Andrea Colantoni
January 7, 2019 (v1)
Subject: Biosystems
Keywords: biochar, Biomass, hazelnut, olive, soil fertiliser
Concerns about climate change and food productivity have spurred interest in biochar, a form of charred organic material typically used in agriculture to improve soil productivity and as a means of carbon sequestration. An innovative approach in agriculture is the use of agro-forestry waste for the production of soil fertilisers for agricultural purposes and as a source of energy. A common agricultural practice is to burn crop residues in the field to produce ashes that can be used as soil fertilisers. This approach is able to supply plants with certain nutrients, such as Ca, K, Mg, Na, B, S, and Mo. However, the low concentration of N and P in the ashes, together with the occasional presence of heavy metals (Ni, Pb, Cd, Se, Al, etc.), has a negative effect on soil and, therefore, crop productivity. This work describes the opportunity to create an innovative supply chain from agricultural waste biomass. Olive (Olea europaea) and hazelnut (Corylus avellana) pruning residues represent a... [more]
Model for Energy Analysis of Miscanthus Production and Transportation
Alessandro Sopegno, Efthymios Rodias, Dionysis Bochtis, Patrizia Busato, Remigio Berruto, Valter Boero, Claus Sørensen
November 28, 2018 (v1)
Subject: Biosystems
Keywords: Biomass, biomass logistics, operations analysis
A computational tool is developed for the estimation of the energy requirements of Miscanthus x giganteus on individual fields that includes a detailed analysis and account of the involved in-field and transport operations. The tool takes into account all the individual involved in-field and transport operations and provides a detailed analysis on the energy requirements of the components that contribute to the energy input. A basic scenario was implemented to demonstrate the capabilities of the tool. Specifically, the variability of the energy requirements as a function of field area and field-storage distance changes was shown. The field-storage distance highly affects the energy requirements resulting in a variation in the efficiency if energy (output/input ratio) from 15.8 up to 23.7 for the targeted cases. Not only the field-distance highly affects the energy requirements but also the biomass transportation system. Based on the presented example, different transportation systems a... [more]
Cathode Assessment for Maximizing Current Generation in Microbial Fuel Cells Utilizing Bioethanol Effluent as Substrate
Guotao Sun, Anders Thygesen, Anne S. Meyer
November 27, 2018 (v1)
Subject: Biosystems
Keywords: air cathode (AiC), bioethanol effluent, dissolved oxygen cathode (DOC), electrochemical impedance spectroscopy (EIS), ferricyanide cathode (FeC)
Implementation of microbial fuel cells (MFCs) for electricity production requires effective current generation from waste products via robust cathode reduction. Three cathode types using dissolved oxygen cathodes (DOCs), ferricyanide cathodes (FeCs) and air cathodes (AiCs) were therefore assessed using bioethanol effluent, containing 20.5 g/L xylose, 1.8 g/L arabinose and 2.5 g/L propionic acid. In each set-up the anode and cathode had an electrode surface area of 88 cm², which was used for calculation of the current density. Electricity generation was evaluated by quantifying current responses to substrate loading rates and external resistance. At the lowest external resistance of 27 Ω and highest substrate loading rate of 2 g chemical oxygen demand (COD) per L·day, FeC-MFC generated highest average current density (1630 mA/m²) followed by AiC-MFC (802 mA/m²) and DOC-MFC (184 mA/m²). Electrochemical impedance spectroscopy (EIS) was used to determine the impedance of the cathodes. It w... [more]
Assessment of the Variability of Biogas Production from Sugar Beet Silage as Affected by Movement and Loss of the Produced Alcohols and Organic Acids
Ali Heidarzadeh Vazifehkhoran, Jin Mi Triolo, Søren Ugilt Larsen, Kasper Stefanek, Sven G. Sommer
November 27, 2018 (v1)
Subject: Biosystems
Keywords: anaerobic digestion, Beta vulgaris, biomethanation, ensiling, organic components, Renewable and Sustainable Energy
The biochemical methane potential and composition of sugar beet pulp silage were investigated using samples taken from six different depths in both open and closed silos (height 3.6 m). The biochemical methane potential (BMP) of pulp silage in open silos ranged from 337 to 420 normal litre (NL) CH₄/kg volatile solids (VS), while the BMP of pulp silage in closed silos varied between 411 and 451 NL CH₄/kg VS. The biochemical methane potential peaked at a depth of 1.45 m with 420 NL CH₄/kg VS for open silos and 451 NL CH₄/kg VS for closed silos. The ethanol concentration and biochemical methane potential showed the same trend with depth throughout the silos. The energy loss correlated to the loss of volatile solids, and the depths described a linear relationship between them for both the open and closed silos (R² = 0.997 for the open silo and R² = 0.991 for the closed silo). The energy potentials and composition of beet pulp silage were highly stratified and there was a risk that the sila... [more]
Techno-Economic Analysis of Integrating First and Second-Generation Ethanol Production Using Filamentous Fungi: An Industrial Case Study
Karthik Rajendran, Sreevathsava Rajoli, Mohammad J. Taherzadeh
November 27, 2018 (v1)
Subject: Biosystems
Keywords: Ethanol, lignocelluloses, process design, process integration, Technoeconomic Analysis
The 2nd generation plants producing ethanol from lignocelluloses demand risky and high investment costs. This paper presents the energy- and economical evaluations for integrating lignocellulose in current 1st generation dry mill ethanol processes, using filamentous fungi. Dry mills use grains and have mills, liquefactions, saccharifications, fermentation, and distillation to produce ethanol, while their stillage passes centrifugation, and evaporation to recycle the water and dry the cake and evaporated syrup into animal feed. In this work, a bioreactor was considered to cultivate fungi on the stillage either before or after the centrifugation step together with pretreated lignocellulosic wheat bran. The results showed that the integrated 1st and 2nd generation ethanol process requires a capital investment of 77 million USD, which could yield NPV of 162 million USD after 20 years. Compared to the fungal cultivation on thin stillage modified 1st generation process, the integrated proces... [more]
Foliage and Grass as Fuel Pellets⁻Small Scale Combustion of Washed and Mechanically Leached Biomass
Jan Hari Arti Khalsa, Frank Döhling, Florian Berger
November 27, 2018 (v1)
Subject: Biosystems
Keywords: combustion, emission reduction, mechanical leaching, residue biomass, solid biofuel
The high contents of disadvantageous elements contained in non-woody biomass are known to cause problems during small and large scale combustion, typically resulting in a higher risk of slagging, corrosion, and increased emissions. Mechanically leaching the respective elements from the biomass through a sequence of process steps has proven to be a promising solution.The florafuel process used here is comprised of size reduction followed by washing and subsequent mechanical dewatering of the biomass. Densification of the upgraded biomass into standardized pellets (Ø 6mm) enables an application in existing small-scale boilers. The presented combustion trials investigated the performance of pellets made from leached grass, foliage and a mixture of both in two small-scale boilers (<100 kWth) with slightly different technology (moving grate versus water-cooled burner tube) during a 4-h measurement period. Emissions were in accordance with German emissions standards except for NOx (thresh... [more]
Modeling of Production and Quality of Bioethanol Obtained from Sugarcane Fermentation Using Direct Dissolved Sugars Measurements
Borja Velazquez-Marti, Sergio Pérez-Pacheco, Juan Gaibor-Chávez, Paola Wilcaso
November 27, 2018 (v1)
Subject: Biosystems
Keywords: bioenergy, biofuel, developing sectors, kinetics model
Bioethanol production from sugarcane represents an opportunity for urban-agricultural development in small communities of Ecuador. Despite the fact that the industry for bioethanol production from sugarcane in Brazil is fully developed, it is still considered expensive as a small rural business. In order to be able to reduce the costs of monitoring the production process, and avoid the application of expensive sensors, the aim of this research was modeling the kinetics of production of bioethanol based on direct measurements of Brix grades, instead of the concentration of alcohol, during the process of cane juice bio-fermentation with Saccharomyces cerevisiae. This avoids the application of expensive sensors that increase the investment costs. Fermentation experiments with three concentrations of yeast and two temperatures were carried out in a laboratory reactor. In each case Brix grades, amount of ethanol and alcoholic degree were measured. A mathematical model to predict the quality... [more]
Ethanol Production from Sweet Sorghum Juice at High Temperatures Using a Newly Isolated Thermotolerant Yeast Saccharomyces cerevisiae DBKKU Y-53
Sunan Nuanpeng, Sudarat Thanonkeo, Mamoru Yamada, Pornthap Thanonkeo
November 27, 2018 (v1)
Subject: Biosystems
Keywords: gene expression, high temperature fermentation, real-time RT-PCR, Saccharomyces cerevisiae, sweet sorghum, thermotolerant yeast
Ethanol production at elevated temperatures requires high potential thermotolerant ethanol-producing yeast. In this study, nine isolates of thermotolerant yeasts capable of growth and ethanol production at high temperatures were successfully isolated. Among these isolates, the newly isolated thermotolerant yeast strain, which was designated as Saccharomyces cerevisiae DBKKU Y-53, exhibited great potential for ethanol production from sweet sorghum juice (SSJ) at high temperatures. The maximum ethanol concentrations produced by this newly isolated thermotolerant yeast at 37 °C and 40 °C under the optimum cultural condition were 106.82 g·L−1 and 85.01 g·L−1, respectively, which are greater than values reported in the literatures. It should be noted from this study with SSJ at a sugar concentration of 250 g·L−1 and an initial pH of 5.5 without nitrogen supplementation can be used directly as substrate for ethanol production at high temperatures by thermotolerant yeast S. cerevisiae DBKKU Y... [more]
Biochar as Additive in Biogas-Production from Bio-Waste
Daniel Meyer-Kohlstock, Thomas Haupt, Erik Heldt, Nils Heldt, Eckhard Kraft
November 27, 2018 (v1)
Subject: Biosystems
Keywords: anaerobic digestion, bio-waste, biochar, biogas, composting, solid-state fermentation
Previous publications about biochar in anaerobic digestion show encouraging results with regard to increased biogas yields. This work investigates such effects in a solid-state fermentation of bio-waste. Unlike in previous trials, the influence of biochar is tested with a setup that simulates an industrial-scale biogas plant. Both the biogas and the methane yield increased around 5% with a biochar addition of 5%—based on organic dry matter biochar to bio-waste. An addition of 10% increased the yield by around 3%. While scaling effects prohibit a simple transfer of the results to industrial-scale plants, and although the certainty of the results is reduced by the heterogeneity of the bio-waste, further research in this direction seems promising.
Integration of Microalgae-Based Bioenergy Production into a Petrochemical Complex: Techno-Economic Assessment
Ana L. Gonçalves, Maria C. M. Alvim-Ferraz, Fernando G. Martins, Manuel Simões, José C. M. Pires
November 27, 2018 (v1)
Subject: Biosystems
Keywords: algal fuels, bioenergy, Carbon Dioxide Capture, microalgal culture, Renewable and Sustainable Energy, wastewater treatment
The rapid development of modern society has resulted in an increased demand for energy, mainly from fossil fuels. The use of this source of energy has led to the accumulation of carbon dioxide (CO₂) in the atmosphere. In this context, microalgae culturing may be an effective solution to reduce the CO₂ concentration in the atmosphere, since these microorganisms can capture CO₂ and, simultaneously, produce bioenergy. This work consists of a techno-economic assessment of a microalgal production facility integrated in a petrochemical complex, in which established infrastructure allows efficient material and energy transport. Seven different scenarios were considered regarding photosynthetic, lipids extraction and anaerobic digestion efficiencies. This analysis has demonstrated six economically viable scenarios able to: (i) reduce CO₂ emissions from a thermoelectric power plant; (ii) treat domestic wastewaters (which were used as culture medium); and (iii) produce lipids and electrical and... [more]
Quantifying the Impact of Feedstock Quality on the Design of Bioenergy Supply Chain Networks
Krystel K. Castillo-Villar, Hertwin Minor-Popocatl, Erin Webb
November 27, 2018 (v1)
Subject: Biosystems
Keywords: bioenergy, bioethanol, Biomass, logging residues, logistics, Optimization, quality costing, supply chain network design
Logging residues, which refer to the unused portions of trees cut during logging, are important sources of biomass for the emerging biofuel industry and are critical feedstocks for the first-type biofuel facilities (e.g., corn-ethanol facilities). Logging residues are under-utilized sources of biomass for energetic purposes. To support the scaling-up of the bioenergy industry, it is essential to design cost-effective biofuel supply chains that not only minimize costs, but also consider the biomass quality characteristics. The biomass quality is heavily dependent upon the moisture and the ash contents. Ignoring the biomass quality characteristics and its intrinsic costs may yield substantial economic losses that will only be discovered after operations at a biorefinery have begun. This paper proposes a novel bioenergy supply chain network design model that minimizes operational costs and includes the biomass quality-related costs. The proposed model is unique in the sense that it suppor... [more]
Evaluation of Cell Disruption of Chlorella Vulgaris by Pressure-Assisted Ozonation and Ultrasonication
Yuanxing Huang, Shengnan Qin, Daofang Zhang, Liang Li, Yan Mu
November 27, 2018 (v1)
Subject: Biosystems
Keywords: cell disrupture, Chlorella vulgaris (C. vulgaris), pressure-assisted ozonation (PAO), quantitative evaluation, ultrasonication (US)
This study evaluated the effectiveness of pressure-assisted ozonation (PAO) in Chlorella vulgaris (C. vulgaris) cell disruption, and compared the disruption result with that of the ultrasonication (US) by using four quantification indicators: cell counting, ultra violet (UV) absorbance, turbidity and visible light absorbance. It was found that under the condition of 0.8 MPa and 80 cycles, PAO treatment achieved cell rupture of 80.3%, with the power of 1080 W and treatment time of 60 min, US achieved cell rupture of 83.8%. Cell counting was a reliable indicator and applicable to both PAO and US treatments. Turbidity and visible light absorbance gave similar results and featured as the simplest operation. UV absorbance reflected the metabolite release due to cell breakage; however, it was less reproducible when it was applied to quantify the cell rupture by PAO. Its trend indicated that during cell disruption metabolite degradation occurred, especially after significant rupture in the ca... [more]
The Environmental Biorefinery: Using Microalgae to Remediate Wastewater, a Win-Win Paradigm
Florian Delrue, Pablo David Álvarez-Díaz, Sophie Fon-Sing, Gatien Fleury, Jean-François Sassi
November 27, 2018 (v1)
Subject: Biosystems
Keywords: biofuel, bioremediation, microalgae, wastewater treatment, water and nutrient recycling
Microalgae have been shown to be a source of multiple bio-based products ranging from high value molecules to commodities. Along with their potential to produce a large variety of products, microalgae can also be used for the depollution of wastewaters of different origins (urban, industrial, and agricultural). This paper is focused on the importance of harnessing the bioremediation capacity of microalgae to treat wastewaters in order to develop the microalgae industry (especially the microalgae biofuel industry) and to find other alternatives to the classic wastewater treatment processes. The current research on the potential of microalgae to treat a specific wastewater or a targeted pollutant is reviewed and discussed. Then, both strategies of selecting the best microalgae strain to treat a specific wastewater or pollutant and using a natural or an artificial consortium to perform the treatment will be detailed. The process options for treating wastewaters using microalgae will be di... [more]
Potential Biogas Production from Artichoke Byproducts in Sardinia, Italy
Fabio De Menna, Remo Alessio Malagnino, Matteo Vittuari, Giovanni Molari, Giovanna Seddaiu, Paola A. Deligios, Stefania Solinas, Luigi Ledda
November 16, 2018 (v1)
Subject: Biosystems
Keywords: artichoke, biogas, byproducts, Sardinia
The paper aims at evaluating the potential biogas production, both in terms of CH₄ and theoretical energy potential, from globe artichoke agricultural byproducts in Sardinia. Field data about the productivity of byproducts were collected on five artichoke varieties cultivated in Sardinia, to assess the biomethane production of their aboveground non-food parts (excluding the head). Moreover, secondary data from previous studies and surveys at regional scale were collected to evaluate the potential biogas production of the different districts. Fresh globe artichoke residues yielded, on average, 292.2 Nm³·tDOM−1, with dissimilarities among cultivars. Fresh samples were analyzed in two series: (a) wet basis; and (b) wet basis with catalytic enzymes application. Enzymes proved to have some beneficial effects in terms of anticipated biomethane availability. At the regional level, ab. 20 × 10⁶ Nm³ CH₄ could be produced, corresponding to the 60% of current installed capacity. However, district... [more]
Systematic Study of Separators in Air-Breathing Flat-Plate Microbial Fuel Cells—Part 2: Numerical Modeling
Sona Kazemi, Melissa Barazandegan, Madjid Mohseni, Khalid Fatih
November 16, 2018 (v1)
Subject: Biosystems
Keywords: crossover, electrode spacing, flat-plate microbial fuel cell (FPMFC), mixed potential theory, numerical model, passive air-breathing, separator
The separator plays a key role on the performance of passive air-breathing flat-plate MFCs (FPMFC) as it isolates the anaerobic anode from the air-breathing cathode. The goal of the present work was to study the separator characteristics and its effect on the performance of passive air-breathing FPMFCs. This was performed partially through characterization of structure, properties, and performance correlations of eight separators presented in Part 1. Current work (Part 2) presents a numerical model developed based on the mixed potential theory to investigate the sensitivity of the electrode potentials and the power output to the separator characteristics. According to this numerical model, the decreased peak power results from an increase in the mass transfer coefficients of oxygen and ethanol, but mainly increasing mixed potentials at the anode by oxygen crossover. The model also indicates that the peak power is affected by the proton transport number of the separator, which affects t... [more]
A Systematic Study of Separators in Air-Breathing Flat-Plate Microbial Fuel Cells—Part 1: Structure, Properties, and Performance Correlations
Sona Kazemi, Madjid Mohseni, Khalid Fatih
November 16, 2018 (v1)
Subject: Biosystems
Keywords: crossover, electrode spacing, flat-plate microbial fuel cell, passive air-breathing, separator
Passive air-breathing microbial fuel cells (MFCs) are a promising technology for energy recovery from wastewater and their performance is highly dependent on characteristics of the separator that isolates the anaerobic anode from the air-breathing cathode. The goal of the present work is to systematically study the separator characteristics and its effect on the performance of passive air-breathing flat-plate MFCs (FPMFCs). This was performed through characterization of structure, properties, and performance correlations of eight separators in Part 1 of this work. Eight commercial separators were characterized, in non-inoculated and inoculated setups, and were examined in passive air-breathing FPMFCs with different electrode spacing. The results showed a decrease in the peak power density as the oxygen and ethanol mass transfer coefficients in the separators increased, due to the increase of mixed potentials especially at smaller electrode spacing. Increasing the electrode spacing was... [more]
A Viable Electrode Material for Use in Microbial Fuel Cells for Tropical Regions
Felix Offei, Anders Thygesen, Moses Mensah, Kwame Tabbicca, Dinesh Fernando, Irina Petrushina, Geoffrey Daniel
October 23, 2018 (v1)
Subject: Biosystems
Keywords: activated carbon, maximum power density, nanowires, palm kernel shells
Electrode materials are critical for microbial fuel cells (MFC) since they influence the construction and operational costs. This study introduces a simple and efficient electrode material in the form of palm kernel shell activated carbon (AC) obtained in tropical regions. The novel introduction of this material is also targeted at introducing an inexpensive and durable electrode material, which can be produced in rural communities to improve the viability of MFCs. The maximum voltage and power density obtained (under 1000 Ω load) using an H-shaped MFC with AC as both anode and cathode electrode material was 0.66 V and 1.74 W/m³, respectively. The power generated by AC was as high as 86% of the value obtained with the extensively used carbon paper. Scanning electron microscopy and Denaturing Gradient Gel Electrophoresis (DGGE) analysis of AC anode biofilms confirmed that electrogenic bacteria were present on the electrode surface for substrate oxidation and the formation of nanowires.
Enzymatic Biofuel Cells—Fabrication of Enzyme Electrodes
Eileen Hao Yu, Keith Scott
October 17, 2018 (v1)
Subject: Biosystems
Keywords: bioelectronics, biofuel cells, enzyme immobilisation, enzymes, mediator, redox polymer, self-assembled monolayer
Enzyme based bioelectronics have attracted increasing interest in recent years because of their applications on biomedical research and healthcare. They also have broad applications in environmental monitoring, and as the power source for portable electronic devices. In this review, the technology developed for fabrication of enzyme electrodes has been described. Different enzyme immobilisation methods using layered structures with self-assembled monolayers (SAM) and entrapment of enzymes in polymer matrixes have been reviewed. The performances of enzymatic biofuel cells are summarised. Various approaches on further development to overcome the current challenges have been discussed. This innovative technology will have a major impact and benefit medical science and clinical research, healthcare management, energy production from renewable sources.
Prospecting for Oleaginous and Robust Chlorella spp. for Coal-Fired Flue-Gas-Mediated Biodiesel Production
Bohwa Kim, Ramasamy Praveenkumar, Eunji Choi, Kyubock Lee, Sang Goo Jeon, You-Kwan Oh
September 21, 2018 (v1)
Subject: Biosystems
Keywords: biodiesel property, Chlorella, coal-fired flue-gas, mixotrophic cultivation, screening
Prospecting for robust and high-productivity strains is a strategically important step in the microalgal biodiesel process. In this study, 30 local strains of Chlorella were evaluated in photobioreactors for biodiesel production using coal-fired flue-gas. Three strains (M082, M134, and KR-1) were sequentially selected based on cell growth, lipid content, and fatty acid composition under autotrophic and mixotrophic conditions. Under autotrophic conditions, M082 and M134 showed comparable lipid contents (ca. 230 mg FAME [fatty acid methyl esters derived from microalgal lipids]/g cell) and productivities (ca. 40 mg FAME/L·d) versus a reference strain (KR-1) outdoors with actual flue-gas (CO₂, 13%). Interestingly, under mixotrophic conditions, M082 demonstrated, along with maximal lipid content (397 mg FAME/g cell), good tolerance to high temperature (40 °C). Furthermore, the fatty acid methyl esters met important international standards under all of the tested culture conditions. Thus, it... [more]
Dynamic Sequence Specific Constraint-Based Modeling of Cell-Free Protein Synthesis
David Dai, Nicholas Horvath, Jeffrey Varner
August 28, 2018 (v1)
Subject: Biosystems
Keywords: cell-free protein synthesis, dynamic constraint-based modeling, systems biology
Cell-free protein expression has emerged as an important approach in systems and synthetic biology, and a promising technology for personalized point of care medicine. Cell-free systems derived from crude whole cell extracts have shown remarkable utility as a protein synthesis technology. However, if cell-free platforms for on-demand biomanufacturing are to become a reality, the performance limits of these systems must be defined and optimized. Toward this goal, we modeled E. coli cell-free protein expression using a sequence specific dynamic constraint-based approach in which metabolite measurements were directly incorporated into the flux estimation problem. A cell-free metabolic network was constructed by removing growth associated reactions from the iAF1260 reconstruction of K-12 MG1655 E. coli. Sequence specific descriptions of transcription and translation processes were then added to this metabolic network to describe protein production. A linear programming problem was then sol... [more]
The Role of Immune Response in Optimal HIV Treatment Interventions
Hernán Darío Toro-Zapata, Angélica Caicedo-Casso, Sunmi Lee
August 28, 2018 (v1)
Subject: Biosystems
Keywords: anti-retroviral treatment, cytotoxic immune response, HIV transmission dynamics within a host, optimal control theory
A mathematical model for the transmission dynamics of human immunodeficiency virus (HIV) within a host is developed. Our model focuses on the roles of immune response cells or cytotoxic lymphocytes (CTLs). The model includes active and inactive cytotoxic immune cells. The basic reproduction number and the global stability of the virus free equilibrium is carried out. The model is modified to include anti-retroviral treatment interventions and the controlled reproduction number is explored. Their effects on the HIV infection dynamics are investigated. Two different disease stage scenarios are assessed: early-stage and advanced-stage of the disease. Furthermore, optimal control theory is employed to enhance healthy CD4+ T cells, active cytotoxic immune cells and minimize the total cost of anti-retroviral treatment interventions. Two different anti-retroviral treatment interventions (RTI and PI) are incorporated. The results highlight the key roles of cytotoxic immune response in the HIV... [more]
Sequential Parameter Estimation for Mammalian Cell Model Based on In Silico Design of Experiments
Zhenyu Wang, Hana Sheikh, Kyongbum Lee, Christos Georgakis
August 28, 2018 (v1)
Subject: Biosystems
Keywords: Design of Experiments, Mammalian Cell Culture, parameter estimation, Pharmaceutical Processes, sensitivity analysis
Due to the complicated metabolism of mammalian cells, the corresponding dynamic mathematical models usually consist of large sets of differential and algebraic equations with a large number of parameters to be estimated. On the other hand, the measured data for estimating the model parameters are limited. Consequently, the parameter estimates may converge to a local minimum far from the optimal ones, especially when the initial guesses of the parameter values are poor. The methodology presented in this paper provides a systematic way for estimating parameters sequentially that generates better initial guesses for parameter estimation and improves the accuracy of the obtained metabolic model. The model parameters are first classified into four subsets of decreasing importance, based on the sensitivity of the model’s predictions on the parameters’ assumed values. The parameters in the most sensitive subset, typically a small fraction of the total, are estimated first. When estimating the... [more]
Alternatives for Chemical and Biochemical Lignin Valorization: Hot Topics from a Bibliometric Analysis of the Research Published During the 2000⁻2016 Period
Ricardo Abejón, Heriberto Pérez-Acebo, Leonardo Clavijo
August 28, 2018 (v1)
Subject: Biosystems
Keywords: bibliometric analysis, lignin uses, lignin valorization, lignocellulosic biomass, research trends
A complete bibliometric analysis of the Scopus database was performed to identify the research trends related to lignin valorization from 2000 to 2016. The results from this analysis revealed an exponentially increasing number of publications and a high relevance of interdisciplinary collaboration. The simultaneous valorization of the three main components of lignocellulosic biomass (cellulose, hemicellulose, and lignin) has been revealed as a key aspect and optimal pretreatment is required for the subsequent lignin valorization. Research covers the determination of the lignin structure, isolation, and characterization; depolymerization by thermal and thermochemical methods; chemical, biochemical and biological conversion of depolymerized lignin; and lignin applications. Most methods for lignin depolymerization are focused on the selective cleavage of the β-O-4 linkage. Although many depolymerization methods have been developed, depolymerization with sodium hydroxide is the dominant pr... [more]
Modelling and Simulation of Biochemical Processes Using Petri Nets
Safae Cherdal, Salma Mouline
August 28, 2018 (v1)
Subject: Biosystems
Keywords: biochemical processes, diseases, HFPN, metabolic pathway, Methionine cycle, Petri nets, Simulation
Systems composed of many components which interact with each other and lead to unpredictable global behaviour, are considered as complex systems. In a biological context, complex systems represent living systems composed of a large number of interacting elements. In order to study these systems, a precise mathematical modelling was typically used in this context. However, this modelling has limitations in the structural understanding and the behavioural study. In this sense, formal computational modelling is an approach that allows to model and to simulate dynamical properties of these particular systems. In this paper, we use Hybrid Functional Petri Net (HFPN), a Petri net extension dedicated to study and verify biopathways, to model and study the Methionine metabolic pathway. Methionine and its derivatives play significant roles in human bodies. We propose a set of simulations for the purpose of studying and analysing the Methionine pathway’s behaviour. Our simulation results have sh... [more]
Prediction of Metabolite Concentrations, Rate Constants and Post-Translational Regulation Using Maximum Entropy-Based Simulations with Application to Central Metabolism of Neurospora crassa
William R. Cannon, Jeremy D. Zucker, Douglas J. Baxter, Neeraj Kumar, Scott E. Baker, Jennifer M. Hurley, Jay C. Dunlap
July 31, 2018 (v1)
Subject: Biosystems
Keywords: mass action kinetics, maximum entropy production, metabolism, statistical thermodynamics
We report the application of a recently proposed approach for modeling biological systems using a maximum entropy production rate principle in lieu of having in vivo rate constants. The method is applied in four steps: (1) a new ordinary differential equation (ODE) based optimization approach based on Marcelin’s 1910 mass action equation is used to obtain the maximum entropy distribution; (2) the predicted metabolite concentrations are compared to those generally expected from experiments using a loss function from which post-translational regulation of enzymes is inferred; (3) the system is re-optimized with the inferred regulation from which rate constants are determined from the metabolite concentrations and reaction fluxes; and finally (4) a full ODE-based, mass action simulation with rate parameters and allosteric regulation is obtained. From the last step, the power characteristics and resistance of each reaction can be determined. The method is applied to the central metabolism... [more]
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