Some bacteria naturally have the first property. In this case they usually form a biofilm, which is an aggregate of bacteria in the slime they produce. One example of such a bacteria is the wild type Bacillus subtilis. While this bacteria makes a biofilm, our experiments show that this biofilm is not robust enough to withstand being in water for an extended period. In addition for the time that the biofilm is still intact it does not function as an ion exchange membrane.
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Some bacteria naturally have the first property. In this case they usually form a biofilm, which is an aggregate of bacteria in the slime they produce. One example of such a bacteria is the wild type Bacillus subtilis. While this bacteria makes a biofilm, our experiments show that this biofilm is not robust enough to withstand being in water for an extended period. In addition for the time that the biofilm is still intact it does not function as an ion exchange membrane. | Some bacteria naturally have the first property. In this case they usually form a biofilm, which is an aggregate of bacteria in the slime they produce. One example of such a bacteria is the wild type Bacillus subtilis. While this bacteria makes a biofilm, our experiments show that this biofilm is not robust enough to withstand being in water for an extended period. In addition for the time that the biofilm is still intact it does not function as an ion exchange membrane. | ||
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Now, if one wants to add or improve the desirable properties to the biofilm, it is required to understand how the biofilm works. After all if one does not, then it is hard (if not impossible) to make a decent hypothesis to base the experiments in the lab on. What makes understanding the biofilm hard is that the exact composition of the the biofilm is not known, since it depends on the Bacillus Subtilis strain, what genes are expressed, how the bacteria specialize and how heterogeneous the biofilm is. In addition, some genes related to the production of the biofilm are not well understood. While some are known to be responsible for the production of extracellular polymers, the length of the polymers in the biofilm varies a lot. This varying length makes characterization of these polymers hard. | Now, if one wants to add or improve the desirable properties to the biofilm, it is required to understand how the biofilm works. After all if one does not, then it is hard (if not impossible) to make a decent hypothesis to base the experiments in the lab on. What makes understanding the biofilm hard is that the exact composition of the the biofilm is not known, since it depends on the Bacillus Subtilis strain, what genes are expressed, how the bacteria specialize and how heterogeneous the biofilm is. In addition, some genes related to the production of the biofilm are not well understood. While some are known to be responsible for the production of extracellular polymers, the length of the polymers in the biofilm varies a lot. This varying length makes characterization of these polymers hard. | ||
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While studying the literature on Bacillus Subtilis biofilms we found that poly-γ-glutamic acid might help us with both properties. It helps Bacillus stick together, because PGA helps with the underwater growth. This happens probably by increasing the number of sites available for salt bridges. It may also help the aggregation of Bacillus, because PGA forms aggregates even in dilute solutions. Poly-γ-glutamic acid may also form an obstacle for some ions, because is has a high number of fixed charges (as can been seen in its structure as shown in figure<polygammaglumaticacid.png>). With a model of PGA one could gain insight in how it aggregates and how it could improve ion conductivity. Naturally there are multiple ways to approach modeling, usually though one takes a top-down approach or a bottom-up approach. | While studying the literature on Bacillus Subtilis biofilms we found that poly-γ-glutamic acid might help us with both properties. It helps Bacillus stick together, because PGA helps with the underwater growth. This happens probably by increasing the number of sites available for salt bridges. It may also help the aggregation of Bacillus, because PGA forms aggregates even in dilute solutions. Poly-γ-glutamic acid may also form an obstacle for some ions, because is has a high number of fixed charges (as can been seen in its structure as shown in figure<polygammaglumaticacid.png>). With a model of PGA one could gain insight in how it aggregates and how it could improve ion conductivity. Naturally there are multiple ways to approach modeling, usually though one takes a top-down approach or a bottom-up approach. | ||
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When using the top-down approach, the models are usually based on the biomass, individuals(bacteria) or particles. These are useful to study the detachment, mass transfer and species distributions in biofilms, but fail when they are applied in bigger systems like whole reactors. Furthermore, many parameters required for such models are hard to gather experimentally. Since this project is concerned with a complete system like a reverse electrodialysis cell and the electrostatic interactions, which are not included, this type of model would not be a good fit. While there are models for the growth of the biofilm, there are also models about the ion permselectivity of membranes. These models give good results with materials that have known geometries, but are less reliable for materials with pore sizes that are small relative to the Debye length or if the materials in question are heterogeneous. | When using the top-down approach, the models are usually based on the biomass, individuals(bacteria) or particles. These are useful to study the detachment, mass transfer and species distributions in biofilms, but fail when they are applied in bigger systems like whole reactors. Furthermore, many parameters required for such models are hard to gather experimentally. Since this project is concerned with a complete system like a reverse electrodialysis cell and the electrostatic interactions, which are not included, this type of model would not be a good fit. While there are models for the growth of the biofilm, there are also models about the ion permselectivity of membranes. These models give good results with materials that have known geometries, but are less reliable for materials with pore sizes that are small relative to the Debye length or if the materials in question are heterogeneous. | ||
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Our model is based on the the bottom-up approach. Since poly-γ-glutamic acid was identified as a molecule that might have a positive contribution to our modified biofilm, the properties of this polymer were modeled. With molecular dynamics one is able to model the interactions between molecules and atoms. Thus molecular dynamics is able to simulate the interactions between the PGA molecules and to simulate the interaction of PGA with ions. Unfortunately, these simulations take a lot of time and computational power. Luckily it is possible to reduce the time needed by using the MARTINI coarse grained force field due to Marrink et all. While ion exchange membranes and proton exchange membranes have been studied using molecular dynamics before, this has never been done using MARTINI, and certainly not for poly-γ-glutamic acid. | Our model is based on the the bottom-up approach. Since poly-γ-glutamic acid was identified as a molecule that might have a positive contribution to our modified biofilm, the properties of this polymer were modeled. With molecular dynamics one is able to model the interactions between molecules and atoms. Thus molecular dynamics is able to simulate the interactions between the PGA molecules and to simulate the interaction of PGA with ions. Unfortunately, these simulations take a lot of time and computational power. Luckily it is possible to reduce the time needed by using the MARTINI coarse grained force field due to Marrink et all. While ion exchange membranes and proton exchange membranes have been studied using molecular dynamics before, this has never been done using MARTINI, and certainly not for poly-γ-glutamic acid. | ||
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An introduction to molecular dynamics can be found in the supporting material, as well as some additional information on the creation of the protocols in the methods. In methods section protocols are detailed for the parameterize poly-γ-glutamic acid, the aggregation molecules, the membrane formation and the reverse electrodialysis cell simulations. In the results section we will report our findings and discuss them, and we will also mention possible future work. In the appendix an overview is given of the specific tools and scripts we have written to create, modify or analyse topologies and trajectories.</div> | An introduction to molecular dynamics can be found in the supporting material, as well as some additional information on the creation of the protocols in the methods. In methods section protocols are detailed for the parameterize poly-γ-glutamic acid, the aggregation molecules, the membrane formation and the reverse electrodialysis cell simulations. In the results section we will report our findings and discuss them, and we will also mention possible future work. In the appendix an overview is given of the specific tools and scripts we have written to create, modify or analyse topologies and trajectories.</div> | ||
<div class="title">Methods</div> | <div class="title">Methods</div> | ||
Revision as of 02:56, 16 September 2015
Now, if one wants to add or improve the desirable properties to the biofilm, it is required to understand how the biofilm works. After all if one does not, then it is hard (if not impossible) to make a decent hypothesis to base the experiments in the lab on. What makes understanding the biofilm hard is that the exact composition of the the biofilm is not known, since it depends on the Bacillus Subtilis strain, what genes are expressed, how the bacteria specialize and how heterogeneous the biofilm is. In addition, some genes related to the production of the biofilm are not well understood. While some are known to be responsible for the production of extracellular polymers, the length of the polymers in the biofilm varies a lot. This varying length makes characterization of these polymers hard.
While studying the literature on Bacillus Subtilis biofilms we found that poly-γ-glutamic acid might help us with both properties. It helps Bacillus stick together, because PGA helps with the underwater growth. This happens probably by increasing the number of sites available for salt bridges. It may also help the aggregation of Bacillus, because PGA forms aggregates even in dilute solutions. Poly-γ-glutamic acid may also form an obstacle for some ions, because is has a high number of fixed charges (as can been seen in its structure as shown in figure<polygammaglumaticacid.png>). With a model of PGA one could gain insight in how it aggregates and how it could improve ion conductivity. Naturally there are multiple ways to approach modeling, usually though one takes a top-down approach or a bottom-up approach.
When using the top-down approach, the models are usually based on the biomass, individuals(bacteria) or particles. These are useful to study the detachment, mass transfer and species distributions in biofilms, but fail when they are applied in bigger systems like whole reactors. Furthermore, many parameters required for such models are hard to gather experimentally. Since this project is concerned with a complete system like a reverse electrodialysis cell and the electrostatic interactions, which are not included, this type of model would not be a good fit. While there are models for the growth of the biofilm, there are also models about the ion permselectivity of membranes. These models give good results with materials that have known geometries, but are less reliable for materials with pore sizes that are small relative to the Debye length or if the materials in question are heterogeneous.
Our model is based on the the bottom-up approach. Since poly-γ-glutamic acid was identified as a molecule that might have a positive contribution to our modified biofilm, the properties of this polymer were modeled. With molecular dynamics one is able to model the interactions between molecules and atoms. Thus molecular dynamics is able to simulate the interactions between the PGA molecules and to simulate the interaction of PGA with ions. Unfortunately, these simulations take a lot of time and computational power. Luckily it is possible to reduce the time needed by using the MARTINI coarse grained force field due to Marrink et all. While ion exchange membranes and proton exchange membranes have been studied using molecular dynamics before, this has never been done using MARTINI, and certainly not for poly-γ-glutamic acid.
An introduction to molecular dynamics can be found in the supporting material, as well as some additional information on the creation of the protocols in the methods. In methods section protocols are detailed for the parameterize poly-γ-glutamic acid, the aggregation molecules, the membrane formation and the reverse electrodialysis cell simulations. In the results section we will report our findings and discuss them, and we will also mention possible future work. In the appendix an overview is given of the specific tools and scripts we have written to create, modify or analyse topologies and trajectories.
Methods