Predicting biofilm deformation with a viscoelastic phase-field model: Modeling and experimental studies.

Abstract:

:Biofilms commonly develop in flowing aqueous environments, where the flow causes the biofilm to deform. Because biofilm deformation affects the flow regime, and because biofilms behave as complex heterogeneous viscoelastic materials, few models are able to predict biofilm deformation. In this study, a phase-field (PF) continuum model coupled with the Oldroyd-B constitutive equation was developed and used to simulate biofilm deformation. The accuracy of the model was evaluated using two types of biofilms: a synthetic biofilm, made from alginate mixed with bacterial cells, and a Pseudomonas aeruginosa biofilm. Shear rheometry was used to experimentally determine the mechanical parameters for each biofilm, used as inputs for the model. Biofilm deformation under fluid flow was monitored experimentally using optical coherence tomography. The comparison between the experimental and modeling geometries, for selected horizontal cross sections, after fluid-driven deformation was good. The relative errors ranged from 3.2 to 21.1% for the synthetic biofilm and from 9.1 to 11.1% for the P. aeruginosa biofilm. This is the first demonstration of the effectiveness of a viscoelastic PF biofilm model. This model provides an important tool for predicting biofilm viscoelastic deformation. It also can benefit the design and control of biofilms in engineering systems.

journal_name

Biotechnol Bioeng

authors

Li M,Matouš K,Nerenberg R

doi

10.1002/bit.27491

subject

Has Abstract

pub_date

2020-07-13 00:00:00

eissn

0006-3592

issn

1097-0290

pub_type

杂志文章
  • Alteration of bacterial surface electrostatic potential and pH upon adhesion to a solid surface and impacts to cellular bioenergetics.

    abstract::In our previous study [Hong Y, Brown DG (2009) Appl Environ Microbiol 75(8):2346-2353], the adenosine triphosphate (ATP) level of adhered bacteria was observed to be 2-5 times higher than that of planktonic bacteria. Consequently, the proton motive force (Delta p) of adhered bacteria was approximately 15% greater than...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22606

    authors: Hong Y,Brown DG

    更新日期:2010-04-01 00:00:00

  • Efficient production of poly γ-d-glutamic acid from the bloom-forming green macroalgae, Ulva sp., by Bacillus sp. SJ-10.

    abstract::Numerous studies on poly γ-d-glutamicacid (γ-PGA) production have investigated terrestrial renewable sources for reducing production costs, but there are no studies using waste marine resources so far. We aimed to develop a cost-effective production method of γ-d-PGA by Bacillus sp. SJ-10 using green macroalgae (Ulva ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26966

    authors: Kim JH,Lee JM,Jang WJ,Park HD,Kim YO,Kim CH,Kong IS

    更新日期:2019-07-01 00:00:00

  • Diffusion coefficients of glucose and ethanol in cell-free and cell-occupied calcium alginate membranes.

    abstract::The diffusivities of glucose and ethanol in cell-free and cell-occupied membranes of calcium alginate were measured in a diffusion cell. The lag time analysis was used. Diffusivities decreased with increasing alginate concentration and were comparable with those in water for a 2% alginate membrane. Glucose and ethanol...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260280609

    authors: Hannoun BJ,Stephanopoulos G

    更新日期:1986-06-01 00:00:00

  • Bidirectional reporter assay using HAL promoter and TOPFLASH improves specificity in high-throughput screening of Wnt inhibitors.

    abstract::Constitutive activation of Wnt signaling plays an important role in colorectal and liver tumorigenesis. Cell-based assays using synthetic TCF/LEF (T-cell factor/lymphoid enhancer factor) reporters, as readouts of β-catenin/TCF-dependent transcriptional activity, have contributed greatly to the discovery of small molec...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.26394

    authors: Yamaguchi K,Zhu C,Ohsugi T,Yamaguchi Y,Ikenoue T,Furukawa Y

    更新日期:2017-12-01 00:00:00

  • Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.

    abstract::Tissue function is comprised of a complex interplay between biological and physicochemical rate processes. The design of bioreactors for tissue engineering must account for these processes simultaneously in order to obtain a bioreactor that provides a uniform environment for tissue growth and development. In the prese...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19960605)50:5<479::AID-BIT

    authors: Peng CA,Palsson BØ

    更新日期:1996-06-05 00:00:00

  • Kinetics of milk coagulation: II. Kinetics of the secondary phase: micelle flocculation.

    abstract::A kinetic model for the agglomeration of milk micelles following kappa-casein hydrolysis is described. The key features of the model are: (1) the surface potential of casein micelles is sufficient to explain the colloidal stability of the milk system; (2) the reduction in surface potential following kappa-casein hydro...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260290508

    authors: Carlson A,Hill CG Jr,Olson NF

    更新日期:1987-04-01 00:00:00

  • Improved virus purification processes for vaccines and gene therapy.

    abstract::The downstream processing of virus particles for vaccination or gene therapy is becoming a critical bottleneck as upstream titers keep improving. Moreover, the growing pressure to develop cost-efficient processes has brought forward new downstream trains. This review aims at analyzing the state-of-the-art in viral dow...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章,评审

    doi:10.1002/bit.25545

    authors: Nestola P,Peixoto C,Silva RR,Alves PM,Mota JP,Carrondo MJ

    更新日期:2015-05-01 00:00:00

  • Optimizing normoxic conditions in liver devices using enhanced gel matrices.

    abstract::For in vitro liver replacement devices, such as packed bed bioreactors, to maintain the essential functions of the liver, they must at least successfully support hepatocytes, the parenchymal cell of the liver. In vivo, the liver is a major consumer of oxygen. Hence it is unsurprising that the limited transport distanc...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21681

    authors: Niu M,Clemens MG,Coger RN

    更新日期:2008-04-15 00:00:00

  • Theory and applications of unstructured growth models: Kinetic and energetic aspects.

    abstract::Microbial kinetics and energetics are discussed in connection with the formulation of unstructured growth models. The development of microbial energetics and the use of macroscopic methods in the study of microbial growth are briefly evaluated. The general approach to the modelling of microbial growth has been critica...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260251202

    authors: Esener AA,Roels JA,Kossen NW

    更新日期:1983-12-01 00:00:00

  • Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.

    abstract::The increasing accessibility of mass isotopomer data via GC-MS and NMR technology has necessitated the use of a systematic and reliable method to take advantage of such data for flux analysis. Here we applied a nonlinear, optimization-based method to study substrate metabolism in cardiomyocytes using (13)C data from p...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21063

    authors: Vo TD,Palsson BO

    更新日期:2006-12-05 00:00:00

  • Recombinant enterokinase light chain with affinity tag: expression from Saccharomyces cerevisiae and its utilities in fusion protein technology.

    abstract::Enterokinase and recombinant enterokinase light chain (rEK(L)) have been used widely to cleave fusion proteins with the target sequence of (Asp)(4)-Lys. In this work, we show that their utility as a site-specific cleavage agent is compromised by sporadic cleavage at other sites, albeit at low levels. Further degradati...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10082

    authors: Choi SI,Song HW,Moon JW,Seong BL

    更新日期:2001-12-20 00:00:00

  • TGF-beta1 regulation in hepatocyte-NIH3T3 co-culture is important for the enhanced hepatocyte function in 3D microenvironment.

    abstract::Co-culture of hepatocytes or hepatocyte spheroids with the supporting NIH3T3 in a 3D microcapsule formed with a hybrid natural/synthetic matrix has led to enhanced hepatocyte functions. We investigated the mechanism of the functional enhancement in co-culture with respect to the contributions of soluble factors and di...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20372

    authors: Chia SM,Lin PC,Yu H

    更新日期:2005-03-05 00:00:00

  • Continuous acetone-butanol-ethanol (ABE) fermentation using immobilized cells of Clostridium acetobutylicum in a packed bed reactor and integration with product removal by pervaporation.

    abstract::An integrated solvent (ABE) fermentation and product removal process was investigated. A stable solvent productivity of 3.5 g/L h was achieved by using cells of Clostridium acetobutylicum immobilized onto a packed bed of bonechar, coupled with continuous product removal by pervaporation. Using a concentrated feed solu...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260380510

    authors: Friedl A,Qureshi N,Maddox IS

    更新日期:1991-08-20 00:00:00

  • Optimization of biomass productivity and substrate utility of a hydrogen bacterium, Alcaligenes hydrogenophilus.

    abstract::Optimizations of cell productivity and utility of gaseous substrates were investigated for Alcaligenes hydrogenophilus. Theoretical analyses for the cell productivity and substrate utility were discussed in the light of experimental data. It was proved from the theoretical analyses that the maximum cell productivity w...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260240514

    authors: Miura Y,Okazaki M,Ohi K,Nishimura T,Komemushi S

    更新日期:1982-05-01 00:00:00

  • Metabolic engineering of acid resistance elements to improve acid resistance and propionic acid production of Propionibacterium jensenii.

    abstract::Propionic acid (PA) and its salts are widely used in the food, pharmaceutical, and chemical industries. Microbial production of PA by propionibacteria is a typical product-inhibited process, and acid resistance is crucial in the improvement of PA titers and productivity. We previously identified two key acid resistanc...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.25902

    authors: Guan N,Li J,Shin HD,Du G,Chen J,Liu L

    更新日期:2016-06-01 00:00:00

  • Degradation of ribonucleic acid by immobilized ribonuclease.

    abstract::An immobilized enzyme (pancreatic ribonuclease bound to porous titania) was investigated for the degradation of purified yeast ribonucleic acid as a substrate. The immobilized enzyme is active and stable in the pH range 4--8. Dependence of enzymatic activity on ionic strength, pH, temperature, fluid flow rate, and sub...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260210910

    authors: Dale BE,White DH

    更新日期:1979-09-01 00:00:00

  • Microbial degradation of quinoline: Kinetic studies with Comamonas acidovorans DSM 6426.

    abstract::The microbial degradation of quinoline by Comamonas acidovorans was studied in a laboratory scale stirred tank reactor. In continuous culture experiments using quinoline as a sole source of carbon and nitrogen, it was shown by means of mass balances that quinoline was converted completely to biomass, carbon dioxide, a...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260420506

    authors: Miethling R,Hecht V,Deckwer WD

    更新日期:1993-08-20 00:00:00

  • A mechanistic model of the enzymatic hydrolysis of cellulose.

    abstract::A detailed mechanistic model of enzymatic cellulose hydrolysis has been developed. The behavior of individual cellulase enzymes and parameters describing the cellulose surface properties are included. Results obtained for individual enzymes (T. reesei endoglucanase 2 and cellobiohydrolase I) and systems with both enzy...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22789

    authors: Levine SE,Fox JM,Blanch HW,Clark DS

    更新日期:2010-09-01 00:00:00

  • Effect of electrical charges and fields on injury and viability of airborne bacteria.

    abstract::In this study, the effects of the electric charges and fields on the viability of airborne microorganisms were investigated. The electric charges of different magnitude and polarity were imparted on airborne microbial cells by a means of induction charging. The airborne microorganisms carrying different electric charg...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10290

    authors: Mainelis G,Górny RL,Reponen T,Trunov M,Grinshpun SA,Baron P,Yadav J,Willeke K

    更新日期:2002-07-20 00:00:00

  • Fed-batch culture of Bacillus thuringiensis for thuringiensin production in a tower type bioreactor.

    abstract::Fed-batch culture of Bacillus thuringiensis in a modified airlift reactor has been developed by using adaptive control of glucose concentration in the reactor. The glucose concentration was estimated via a correlation equation between carbon dioxide production rate and glucose consumption rate. The estimated glucose c...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260480307

    authors: Jong JZ,Hsiun DY,Wu WT,Tzeng YM

    更新日期:1995-11-05 00:00:00

  • Production of micronic particles of biocompatible polymer using supercritical carbon dioxide.

    abstract::Three micronization techniques, based on the use of supercritical carbon dioxide, were investigated to produce microspheres of a natural biocompatible polysaccharide. Particles smaller than 20 mum were obtained by means of the rapid expansion of a supercritical solution method (RESS), both with and without cosolvents....

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19970120)53:2<232::AID-BIT

    authors: Benedetti L,Bertucco A,Pallado P

    更新日期:1997-01-20 00:00:00

  • Chemical inhibition of nitrification in activated sludge.

    abstract::Conventional aerobic nitrification was adversely affected by single pulse inputs of six different classes of industrially relevant chemical toxins: an electrophilic solvent (1-chloro-2,4-dinitrobenzene, CDNB), a heavy metal (cadmium), a hydrophobic chemical (1-octanol), an uncoupling agent (2,4-dinitrophenol, DNP), al...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20015

    authors: Kelly RT 2nd,Henriques ID,Love NG

    更新日期:2004-03-20 00:00:00

  • Trehalase immobilization on aminopropyl glass for analytical use.

    abstract::Trehalase is the enzyme which hydrolyzes the disaccharide trehalose into two alpha-D-glucose molecules. In this article, we present the immobilization of trehalase on aminopropyl glass particles. The enzyme was extracted from Escherichia coli Mph2, a strain harboring the pTRE11 plasmid, which contains the trehalase ge...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19970405)54:1<33::AID-BIT4

    authors: Bachinski N,Martins AS,Paschoalin VM,Panek AD,Paiva CL

    更新日期:1997-04-05 00:00:00

  • Optimal production of glutathione by controlling the specific growth rate of yeast in fed-batch culture.

    abstract::The optimal of the specific growth rate was obtained with simple mathematical model in a yeast fed-batch cultures. The model was based on the mass balance around the fed-batch system and the relationship between the specific growth rate, mu, and the specific production rate of glutathione, rho(G). The optimal profile ...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.260380212

    authors: Shimizu H,Araki K,Shioya S,Suga K

    更新日期:1991-06-20 00:00:00

  • Microbiological and geochemical dynamics in simulated-heap leaching of a polymetallic sulfide ore.

    abstract::The evolution of microbial populations involved in simulated-heap leaching of a polymetallic black schist sulfide ore (from the recently-commissioned Talvivaara mine, Finland) was monitored in aerated packed bed column reactors over a period of 40 weeks. The influence of ore particle size (2-6.5 mm and 6.5-12 mm) on c...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.21951

    authors: Wakeman K,Auvinen H,Johnson DB

    更新日期:2008-11-01 00:00:00

  • Novel electrochemical-enzymatic model which quantifies the effect of the solution Eh on the kinetics of ferrous iron oxidation with Acidithiobacillus ferrooxidans.

    abstract::The influence of solution Eh on the rate of ferrous iron oxidation by Acidithiobacillus ferrooxidans is characterized. The experimental approach was based on the use of a two-chamber bioelectrochemical cell, which can determine the ferrous iron oxidation rate at controlled potential. Results enabled the formulation of...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.10371

    authors: Meruane G,Salhe C,Wiertz J,Vargas T

    更新日期:2002-11-05 00:00:00

  • The effect of packing hydrophilization on bacterial attachment and the relationship with the performance of biotrickling filters.

    abstract::Many bioprocesses depend on the effective formation of a biofilm on a solid support. In the present study, three different surface treatments (sandblasting, pure-O(2) plasma, and He-O(2) plasma treatments) were conducted on polypropylene (PP) Pall rings used as a support in biotrickling filters for air pollution contr...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22354

    authors: Prado OJ,Popat SC,Chen G,Walker SL,Lafuente J,Gabriel D,Deshusses MA

    更新日期:2009-08-15 00:00:00

  • High cell density and high monoclonal antibody production through medium design and rational control in a bioreactor.

    abstract::A simple feeding strategy was developed and successfully employed for nutritional control in a 2-L fed-batch culture of hybridoma cells. A previously developed stoichiometric model for animal cell growth was used to design a supplemental medium for feeding. Undialyzed fetal bovine serum and trace metals (Fe(2+), SeO(3...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/(SICI)1097-0290(19960920)51:6<725::AID-BIT

    authors: Xie L,Wang DI

    更新日期:1996-09-20 00:00:00

  • A process for microbial hydrocarbon synthesis: Overproduction of fatty acids in Escherichia coli and catalytic conversion to alkanes.

    abstract::The development of renewable alternatives to diesel and jet fuels is highly desirable for the heavy transportation sector, and would offer benefits over the production and use of short-chain alcohols for personal transportation. Here, we report the development of a metabolically engineered strain of Escherichia coli t...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.22660

    authors: Lennen RM,Braden DJ,West RA,Dumesic JA,Pfleger BF

    更新日期:2010-06-01 00:00:00

  • Growth of Leuconostoc mesenteroides NRRL-B523 in an alkaline medium: suboptimal pH growth inhibition of a lactic acid bacterium.

    abstract::Bacterial profile modification (BPM), a form of tertiary oil recovery, diverts water from the water-flooded high-permeability zone into the oil-bearing low-permeability zone. During field use, exopolymer-producing bacteria plug the high-permeability zone only in the immediate vicinity of the injection point (the near-...

    journal_title:Biotechnology and bioengineering

    pub_type: 杂志文章

    doi:10.1002/bit.20315

    authors: Wolf BF,Fogler HS

    更新日期:2005-01-05 00:00:00