iMechanica - Comments for "Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry"
https://imechanica.org/node/17260
Comments for "Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry"enDear Lihua,
https://imechanica.org/comment/26504#comment-26504
<a id="comment-26504"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/26501#comment-26501">multiple time scales</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Dear Lihua,</p>
<p>Thank you for pointing this out. In electrochemically active biofilms, charge transfer and growth are coupled via the bacteria metabolism. In conduction based extracellular electron transfer, the time scale can be compared to the conductivity coefficient of the biofilm ([1] reports this coefficient at 5 mS cm-1). In diffusion based transfer, the time scale can be compared to the diffusion coefficient of the biofilm ([2] reports the variations in this coefficient depending on biofilm age and condition). Though small amounts of growth may be occurring on the time scale of charge transfer (less than 1 second), measurable growth can be considered to occur over the time scale of hours or days [3]. MFC models must approach large variations in time scales to provide meaningful solutions at realistic computational cost. In [4], the problem is broken into two spatial domains that are solved with two different time steps in order to span the micro- and macro-scale. In [3], the solution algorithm utilizes the fact that the relatively slow growth of the biofilm allows the diffusion, mass transport and conduction equations to be solved as a series of steady state equations. Overall, choosing an approach to address this issue is a crucial component of MFC modeling. Further discussion of alternative approaches to this problem would be an interesting contribution to this journal club.</p>
<p>[1] NS Malvankar et al., Tunable metallic-like conductivity in microbial nanowire networks, Nature Nanotechnology 6 (2011) 573-579.<br />[2] RS Renslow et al., Diffusion in biofilms respiring on electrodes, Energy & Environmental Science 6 (2013) 595-607.<br />[3] AK Marcus et al., Conduction-based modeling of the biofilm anode of a microbial fuel cell, Biotechnology and Bioengineering 98 (2007) 1171-1182.<br />[4] C Picioreanu et al., Model based evaluation of the effect of pH and electroce geometry on microbial fuel cell performance, Bioelectrochemistry 78 (2010) 8-24.</p>
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</ul>Thu, 16 Oct 2014 06:11:45 +0000Christian Lindercomment 26504 at https://imechanica.orgmultiple time scales
https://imechanica.org/comment/26501#comment-26501
<a id="comment-26501"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/26464#comment-26464">Literature on Biofilm Modeling</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Dear Christian, thanks for initiating this interesting discussion. Dear Ravindra, thanks for adding the above papers.</p>
<p>There are different times scales in the problem of MFC, for example growth, swelling, viscosity of biofilms, extracellular electron transfer and mass transport. How large are they? I have seen that growth is 5 orders of magnitude slower than water transportation in the biofilms. I wonder whether people consider the couple between biofilm growth and the charging process, and how they deal with the kinetics with different time scales.</p>
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</ul>Wed, 15 Oct 2014 12:18:47 +0000Lihua Jincomment 26501 at https://imechanica.orgMechanical characterization of biofilms
https://imechanica.org/comment/26481#comment-26481
<a id="comment-26481"></a>
<p><em>In reply to <a href="https://imechanica.org/node/17260">Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Thanks Qiming for the literature on the measurement of biofilm mechanical properties. I am assuming all of the tests you mentioned "sweeping test, creep test, flow test, and indentation test" would be qualify as non-destructive testing; I will have to read through the literature to confirm that. Ideally, it would be great if we could perform a test while the biofilm is growing without affecting it in anyway. <span>- Ravindra</span></p>
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</ul>Tue, 07 Oct 2014 14:51:39 +0000Ravindra Dudducomment 26481 at https://imechanica.orgReply to Ravindra
https://imechanica.org/comment/26478#comment-26478
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<p><em>In reply to <a href="https://imechanica.org/comment/26477#comment-26477">Re: When mechanics meets undesired-biofilms</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p class="MsoNormal">Dear Ravindra,</p>
<p class="MsoNormal">Thank you for your interest in my post.</p>
<p class="MsoNormal">(1) To test the viscoelastic properties of biofilms, people use sweeping test, creep test, flow test and indentation test. Besides Maxwell model, Kelvin model and Zener model may also be used. For more details, I would suggest the following two papers:</p>
<p class="MsoNormal">Shaw, T., et al. "Commonality of elastic relaxation times in biofilms." Physical review letters 93.9 (2004): 098102. </p>
<p class="MsoNormal">Böl, Markus, et al. "Recent advances in mechanical characterization of biofilm and their significance for material modeling." Critical reviews in biotechnology 33.2 (2013): 145-171.</p>
<p class="MsoNormal">In our paper (Advanced Healthcare Materials, DOI:10.1002/adhm.201400035 (2014)), we used frequency sweep test to characterize the viscoelastic property of biofilm. You may refer to the method part for more details.</p>
<p class="MsoNormal">(2) The local mechanical properties of the biofilms can be significantly affected by local compositions, nutrient supports, and others. I do not have concrete answers for you, but I can give you two examples:</p>
<p class="MsoNormal">-Crystalined particles in the biofilm can significantly enhance the elastic modulus of the biofilm. See Advanced Healthcare Materials, DOI:10.1002/adhm.201400035 (2014).</p>
<p class="MsoNormal">-Nutrient and water support can interact with the biofilm to form complex structures, see PNAS 110.3 (2013): 848-852.</p>
<p class="MsoNormal">(3) We may define the cohesive stress on the biofilm-substrate interface as the normal stress or shear stress that is required to debond the biofilm from the substrate. I can imagine measuring this cohesive stress will be extremely challenging.</p>
<p class="MsoNormal">Instead, we just consider adhesion energy density on the biofilm-substrate interface, defined as the work per area required to remove the biofilms from the surface. We have not published the data of measured biofilm-substrate adhesion yet, they will come out soon.</p>
<p class="MsoNormal">Hope my answers have addressed your concerns.</p>
<p class="MsoNormal">With regards,</p>
<p><span>Qiming</span></p>
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</ul>Tue, 07 Oct 2014 04:44:49 +0000Qiming Wangcomment 26478 at https://imechanica.orgRe: When mechanics meets undesired-biofilms
https://imechanica.org/comment/26477#comment-26477
<a id="comment-26477"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/26465#comment-26465">When mechanics meets undesired-biofilms</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Qiming,</p>
<p>One question I have on your post is to do with the continuum viscoelastic model description for the biofilm. Even if we consider a simple Maxwell type model then one needs to know the elastic modulus and viscosity coefficient. Can you please elaborate on how one can estimate such mechanical properties of the biofilm using experimental techniques and any references on this.</p>
<p>Also, other questions I have are: how does the spatial variation of these mechanical properties relate to the heterogeneity of the biofilm and what is the cohesive stress at the biofilm-substrate interface? </p>
<p>Thanks</p>
<p>Ravindra</p>
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</ul>Mon, 06 Oct 2014 20:56:24 +0000Ravindra Dudducomment 26477 at https://imechanica.orgRe: When mechanics meets undesired biofilms
https://imechanica.org/comment/26472#comment-26472
<a id="comment-26472"></a>
<p><em>In reply to <a href="https://imechanica.org/comment/26465#comment-26465">When mechanics meets undesired-biofilms</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Thank you Qiming for raising this important discussion. Biofilm managment via mechanical mechanisms, such as the biofilm detachment due to large surface deformation discussed in the posted papers, is a highly related area of research. Perhaps in the future a more robust computational model for the biofilm and the biofilm/substrate interface would be useful to design surfaces which eradicate biofilms. -Christian</p>
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</ul>Mon, 06 Oct 2014 03:49:12 +0000Christian Lindercomment 26472 at https://imechanica.orgRe: Literature on Biofilm Modeling
https://imechanica.org/comment/26471#comment-26471
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<p><em>In reply to <a href="https://imechanica.org/comment/26464#comment-26464">Literature on Biofilm Modeling</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p>Dear Ravindra,</p>
<p>thank you for adressing the need to consider rate-limiting factors and theoretical maximum current output in MFCs. As indicated by the breadth of the papers you included, MFCs are intriguing because there are many possible and potentially highly coupled rate limiting factors. Computational modeling offers a route by which MFC behavior and coupling can be studied.</p>
<p>Regards,<br />Christian</p>
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</ul>Mon, 06 Oct 2014 03:44:33 +0000Christian Lindercomment 26471 at https://imechanica.orgWhen mechanics meets undesired-biofilms
https://imechanica.org/comment/26465#comment-26465
<a id="comment-26465"></a>
<p><em>In reply to <a href="https://imechanica.org/node/17260">Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p class="MsoNormal">Thank you for posting this excellent entry.</p>
<p class="MsoNormal">Although the biofilms can benefit human beings in microbial fuel cells, they can also cause a number of problems in other situations. For example, biofilms and other foulings attached on the surfaces of maritime machines (e.g., ships, submarine vessels) significantly drag the vessel velocity and thus increase the fuel requirement; biofilms can clog the permeable membrane in water desalination process; biofilms can induce severe contamination in food industries and biomedical devices; biofilms on transplanted organs also can induce chronic infections. Designing environmentally friendly and biocompatible surfaces that can effectively manage biofilms and other biofoulings is an extremely challenging task. State-of-the-art approaches involve either self-polishing surfaces with controlled release of biocides, surface chemistries, or structured coatings. These approaches are generally limited to level of fouling release or may have ecological side effects.</p>
<p class="MsoNormal">Question: when mechanics meets undesired-biofilms, how mechanics palys a significant role in biofilm management? </p>
<p class="MsoNormal">Recent years, we have been working on designing active anti-biofouling coatings by harnessing the dynamic surface deformation of soft materials in response to external stimuli. We consider the biofilm as a continuum viscoelastic film bonded on the elastomer substrate. Once the substrate undergoes sufficiently large deformation, the biofilms are spontaneously detached from the substrate. Here are our two attempts: </p>
<p class="MsoNormal">1. How to use active surface deformation to detach marine biofilms.</p>
<p class="MsoNormal">Phanindhar Shivapooja#, <a href="http://imechanica.org/user/21855">Qiming Wang</a>#, Beatriz Orihuela, Daniel Rittschof, Gabriel P. López, <a href="http://imechanica.org/user/51">Xuanhe Zhao</a>, <a href="http://www.web.mit.edu/zhaox/www/papers/45.pdf">Bioinspired Surfaces with Dynamic Topography for Active Control of Biofouling</a>, Advanced Materials, 25, 1430 (2013) (#: Equal contribution)</p>
<p class="MsoNormal"> </p>
<p class="MsoNormal">2. How to design a urinary catheter to release biomedical biofilms on-demand.</p>
<p class="MsoNormal">Vrad Levering#, <a href="http://imechanica.org/user/21855">Qiming Wang</a>#, Phanindhar Shivapooja, <a href="http://imechanica.org/user/51">Xuanhe Zhao</a>, Gabriel P. López, <a href="http://www.web.mit.edu/zhaox/www/papers/61.pdf">Soft Robotic Concepts in Catheter Design: an On-demand Fouling-release Urinary Catheter</a>, Advanced Healthcare Materials, DOI:10.1002/adhm.201400035 (2014) (#: Equal contribution) </p>
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</ul>Sat, 04 Oct 2014 18:13:00 +0000Qiming Wangcomment 26465 at https://imechanica.orgLiterature on Biofilm Modeling
https://imechanica.org/comment/26464#comment-26464
<a id="comment-26464"></a>
<p><em>In reply to <a href="https://imechanica.org/node/17260">Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p> <span>Hello Christian,</span></p>
<p> <span>Thank you for the excellent discussion emphasizing the role of computational mechanics in realizing a scalable microbial fuel cell (MFC). With the recent advances made in computational mechanics, especially, on the numerical modeling of evolving interfaces [1-3] and Eulerian solid formulations [4,5], it is now possible to revisit the detachment scenarios that greatly affect the performance of the MFC. Further, quorum sensing in biofilms can be incorporated, which is an important mechanism that affects the growth of biofilm colonies and is greatly influenced by the hydrodynamic environment [6-8]. Coming to the MFC, preliminary modeling has shown that competitive growth among bacterial species, anode geometry and the diffusion of soluble products, all affect the MFC’s performance. With all these recent developments, I believe it is now time to address the question of “how do the rate-limiting factors impact the current generated by the microbial fuel cell?” and “what is the theoretical maximum current output from an MFC for a given biomass input?” Below are some journal articles (from the Northwestern Univ. folks).</span></p>
<p> <span><em><span>Numerical modeling of biofilm growth</span></em></span></p>
<p> <span><span>1.</span><span> </span><span>R. Duddu, D. L. Chopp and B. Moran, A two-dimensional continuum model of biofilm growth incorporating fluid flow and shear stress based detachment. Biotechnology and Bioengineering, 103(1): 92-104, </span><strong>2009</strong><span>, doi: 10.1002/bit.22233</span></span></p>
<p> <span>2.<span> </span>R. Duddu, S. Bordas, D. L. Chopp and B. Moran. A combined extended finite element and level set method for biofilm growth. International Journal for Numerical Methods in Engineering, 74(5): 848-870, <strong>2008</strong>, doi: 10.1002/nme.2200</span></p>
<p><span>3.</span><span> </span><span>B. G. Smith, B. L. Vaughan, and D. L. Chopp. The extended finite element method for boundary layer problems in biofilm growth, CAMCoS, 2(1): 35-56, </span><strong>2007</strong><span>.</span></p>
<p> <span><em><span>Eulerian formulations for growth and deformation of hyperelastic solids</span></em></span></p>
<p><span>4.</span><span> </span><span>R. Duddu, L. L. Lavier, T. J. R. Hughes and V. M. Calo, A finite strain Eulerian formulation for compressible and nearly incompressible hyper-elasticity using high-order B-spline finite elements. International Journal for Numerical Methods in Engineering, 89(6):762-785, </span><strong>2012</strong><span>, doi: 10.1002/nme.3262</span></p>
<p> <span>5.<span> </span>L. Foucard, A. Aryal, R. Duddu, F. Vernerey, A coupled Eulerian-Lagrangian extended finite element formulation for simulating large deformations in hyperelastic media with moving free boundaries. Computer Methods in Applied Mechanics and Engineering, in Press, <strong>2014</strong>, doi: 10.1016/j.cma.2014.09.016</span></p>
<p> <span><em><span>Quorum sensing in biofilms</span></em></span></p>
<p> <span>6.<span> </span>B. L. Vaughan, B. G. Smith, D.L. Chopp. The Influence of Fluid Flow on Modeling Quorum Sensing in Bacterial Biofilms, Bull. Math. Biology, 72(5): 1143-1165, <strong>2010</strong></span></p>
<p> <span>7.<span> </span>M. J. Kirisits, J. Margolis, B. L. Purevdorj-Gage, B. Vaughan, D. L. Chopp, P. Stoodley, and M. R. Parsek. The influence of the hydrodynamic environment on quorum sensing in Pseudomonas aeruginosa biofilms, J. Bacteriology, 189(22): 8357-8360, <strong>2007</strong>.</span></p>
<p> <span>8.<span> </span>J. D. Shrout, D. L. Chopp, C. L. Just, M. Hentzer, M. Givskov, and M. R. Parsek. The impact of quorum sensing and swarming motility on Pseudomonas aeruginosa biofilm formation is nutritionally conditional. Molecular Microbiology, 62(5): 1264-1277, <strong>2006.</strong></span></p>
<p> <span><em><span>Microbial fuel cell modeling</span></em></span></p>
<p> <span>9.<span> </span>B. V. Merkey and D. L. Chopp. The Performance of a Microbial Fuel Cell Depends Strongly on Anode Geometry: A Multidimensional Modeling Study, Bull. Math. Biology, 74: 834-857, <strong>2012</strong></span></p>
<p><span>10. <span>B. Merkey, B. E. Rittmann, and D.L. Chopp. Modeling How Soluble Microbial Products (SMP) Support Heterotrophs in Autotroph-Based Biofilms, J. Theoretical Biology, 259: 670-683, </span><strong>2009</strong></span></p>
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</ul>Sat, 04 Oct 2014 17:35:19 +0000Ravindra Dudducomment 26464 at https://imechanica.orgThe Exciting World of Energy Research !
https://imechanica.org/comment/26462#comment-26462
<a id="comment-26462"></a>
<p><em>In reply to <a href="https://imechanica.org/node/17260">Journal Club Theme of October 2014: Microbial fuel cells - When mechanics meets bioelectrochemistry</a></em></p>
<div class="field field-name-comment-body field-type-text-long field-label-hidden"><div class="field-items"><div class="field-item even"><p><span>Dear Prof. Linder, </span></p>
<p><span>Thank you for the interesting post. </span></p>
<p><span>iMechanicians may find my recent papers related to energy interesting :</span></p>
<p><span> ** <a href="http://imechanica.org/node/17127" target="_blank">Enhanced Lithiation in Defective Graphene</a></span></p>
<p><span> ** <a href="http://imechanica.org/node/16905" target="_blank">Atomistic Mechanism of Phase Boundary Evolution during Initial Lithiation of Crysalline Silicon </a></span></p>
<p><span> ** <a href="http://imechanica.org/node/16479" target="_blank">Defect-induced plating of lithium metal within porous graphene networks</a></span></p>
<p><span> ** <a href="http://imechanica.org/node/15942" target="_blank">Defective graphene as promising anode material for Na- and Ca-ion battery</a></span></p>
<p><span class="Apple-style-span">Thank you very much.</span></p>
<p><span>Regards,</span></p>
<p><span>Dibakar</span></p>
<p> </p>
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</ul>Fri, 03 Oct 2014 06:55:11 +0000Dibakar Dattacomment 26462 at https://imechanica.orgError | iMechanica