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| 3. |
- Foloppe, N, et al.
(författare)
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Structure, dynamics and electrostatics of the active site of glutaredoxin 3 from Escherichia coli : Comparison with functionally related proteins
- 2001
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Ingår i: Journal of Molecular Biology. - : Elsevier BV. - 0022-2836 .- 1089-8638. ; 310:2, s. 449-470
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Tidskriftsartikel (refereegranskat)abstract
- The chemistry of active-site cysteine residues is central to the activity of thiol-disulfide oxidoreductases of the thioredoxin superfamily. In these reactions, a nucleophilic thiolate is required, but the associated pK(a), values differ vastly in the superfamily, from less than 4 in DsbA to greater than 7 in Trx. The factors that stabilize this thiolate are, however, not clearly established. The glutaredoxins (Grxs), which are members of this superfamily, contain a Cys-Pro-Tyr-Cys motif in their active site. In reduced Grxs, the pK(a) of the N-terminal active-site nucleophilic cysteine residue is lowered significantly, and the stabilization of the corresponding thiolate is expected to influence the redox potential of these enzymes. Here, we use a combination of long molecular dynamics (MD) simulations, pK(a) calculations, and experimental investigations to derive the structure and dynamics of the reduced active site from Escherichia coli Grx3, and investigate the factors that stabilize the thiolate. Several different MD simulations converged toward a consensus conformation for the active-site cysteine residues (Cys11 and Cys14), after a number of local conformational changes. Key features of the model were tested experimentally by measurement of NMR scalar coupling constants, and determination of pK(a) values of selected residues. The pK(a) values of the Grx3 active-site residues were calculated during the MD simulations, and support the underlying structural model. The structure of Grx3, in combination with the pK(a) calculations, indicate that the pK(a) of the N-terminal active-site cysteine residue in Grx3 is intermediate between that of its counterpart in DsbA and Trx. The pK(a) values in best agreement with experiment are obtained with a low (<4) protein dielectric constant. The calculated pK(a) values fluctuate significantly in response to protein dynamics, which underscores the importance of the details of the underlying structures when calculating pK(a) values. The thiolate of Cys11 is stabilized primarily by direct hydrogen bonding with the amide protons of Tyr13 and Cys14 and the thiol proton of Cys14, rather than by long range interactions from charged groups or from a helix macrodipole. From the comparison of reduced Grx3 with other members of the thioredoxin superfamily, a unifying theme for the structural basis of thiol pK(a) differences in this superfamily begins to emerge.
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- Hadidi, Hooman, et al.
(författare)
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Numerical investigation of capacitive deionization (CDI) with divergent and convergent channels
- 2023
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Ingår i: Journal of Electroanalytical Chemistry. - : Elsevier BV. - 1572-6657. ; 944
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Tidskriftsartikel (refereegranskat)abstract
- This research aims to explore the impact of tilted channel configurations of CDI cells on desalination performance. The results reveal that the titled convergent channels have a faster average salt adsorption rate (ASAR) than the regular straight geometry. For desalination operations that end at a quarter of the equilibrium salt adsorption capacity (SAC), the convergent spacer with a slight slope of 1.5 degrees has a 20 % higher ASAR than the typical straight geometry (0.15 mg/g/min for convergent and 0.12 mg/g/min for straight). This gain increases to about 24, 29.5, and 33%, respectively, for slopes of 3.5, 5.5, and 7 degrees, compared to the straight geometry with the same spacer thickness. By looking at the underlying mechanisms, the spacer geometry is found to shift the location of the initial adsorption. This affects how quickly the device outputs the cleaned water. Interestingly, the geometry angle can also affect the location of the depletion zone, so tilted spacers can also affect the behavior during electrode starvation. Specifically, the convergent geometry has the depletion zone in the middle of the electrode instead of the corner near the outlet, as seen for straight and divergent channels. Together, these findings indicate how to construct tilted spacers to enhance CDI performance.
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- Nilsson, Jonas, et al.
(författare)
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Prostate cancer-derived urine exosomes : a novel approach to biomarkers for prostate cancer.
- 2009
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Ingår i: British journal of cancer. - : Springer Science and Business Media LLC. - 1532-1827 .- 0007-0920. ; 100:10, s. 1603-1607
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Tidskriftsartikel (refereegranskat)abstract
- Herein, we describe a novel approach in the search for prostate cancer biomarkers, which relies on the transcriptome within tumour exosomes. As a proof-of-concept, we show the presence of two known prostate cancer biomarkers, PCA-3 and TMPRSS2:ERG the in exosomes isolated from urine of patients, showing the potential for diagnosis and monitoring cancer patients status.
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| 6. |
- Nordstrand, Johan, et al.
(författare)
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2D Simulations of Water Treatment with Upscaled Capacitive Deionization
- 2022
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Ingår i: Proceedings of the 10th International Workshop on Simulation for Energy, Sustainable Development & Environment (SESDE), 00419th International Multidisciplinary Modeling & Simulation Multiconference. - : Cal-Tek Srl.
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Konferensbidrag (refereegranskat)abstract
- Clean water is a major global challenge. Meanwhile, capacitive deionization (CDI) is an emerging desalination technology that could help produce and reuse water. As the technology develops, the modeling of upscaled systems is becoming increasingly relevant. However, the inherent complexities in the CDI process have historically made such simulations unfeasible. In this work, we leverage the newly published electrolytic-capacitor (ECL) model to efficiently simulate parallel/serial flow modes in CDI stacks. The simulations are based on finite-element methods (FEM) that couple differential equations for describing local charging and ionic transport inside the device. The results show that both parallel and serial connections scale incredibly well with the system size. Still, parallel connections have the advantage of requiring lower pumping energy. Overall, we find that the relationship between adsorption capacity, flowrate, and compartment size is a good indicator of performance. In conclusion, the ELC model is promising for simulating upscaled CDI.
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| 7. |
- Nordstrand, Johan, et al.
(författare)
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A new automated model brings stability to finite‐element simulations of capacitive deionization
- 2022
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Ingår i: Nano Select. - : Wiley. - 2688-4011. ; 3:6, s. 1021-1035
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Tidskriftsartikel (refereegranskat)abstract
- The massive need for freshwater is driving new desalination technologies such as capacitive deionization (CDI), wherein an applied electric field between porous electrodes removes salt ions from water. In this work, we present substantial advances in numerical approaches to 2D finite-element models that make it possible to tractably and accurately simulate the local transport, charge-transfer, and ion-adsorption processes. This is achieved by introducing a new numerical approach that improves the stability of the method (SmD), which further allows precise and effective modeling that was previously too unstable for use in the state-of-the-art 2D models. The results show that the model now accurately and reliably simulates CDI processes while being effectively applicable to a wider range of structural (device level) and operational conditions (like flow). Crucially, this opens up new opportunities that allow us to provide novel insights into the CDI processes, especially relating to ion-starved conditions. Finally, novel algorithms support fully automatic implementation with simultaneous fit to multiple data sets and we openly provide all software code to increase accessibility. Thus, we fundamentally believe that the developed model will provide a solid foundation for 2D spatiotemporal simulations of capacitive deionization and aid the future development of CDI technology.
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| 8. |
- Nordstrand, Johan, et al.
(författare)
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An Easy-to-Use Tool for Modeling the Dynamics of Capacitive Deionization
- 2019
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Ingår i: Journal of Physical Chemistry A. - : American Chemical Society (ACS). - 1089-5639 .- 1520-5215. ; 123:30, s. 6628-6634
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Tidskriftsartikel (refereegranskat)abstract
- Capacitive deionization is an emerging method of desalinating brackish water that has been presented as an alternative to the widely applied technologies such as reverse osmosis. However, for the technology to find more widespread use, it is important not only to improve its efficiency but also to make its modeling more accessible for researchers. In this work, a program has been developed and provided as an open-source with which a user can simulate the performance of a capacitive deionization system by simply entering the basic experimental conditions. The usefulness of this program was demonstrated by predicting how the effluent concentration in a continuous-mode constant-voltage operation varies with time, as well as how it depends on the flow rate, applied voltage, and inlet ion concentration. Finally, the generality of the program has been demonstrated using data from reports in the literature wherein various electrode materials, cell structures, and operational modes were used. Thus, we conclude that the model, termed the dynamic Langmuir model, could be an effective and simple tool for modeling the dynamics of capacitive deionization.
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| 9. |
- Nordstrand, Johan, et al.
(författare)
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An Extended Randles Circuit and a Systematic Model-Development Approach for Capacitive Deionization
- 2021
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Ingår i: Journal of the Electrochemical Society. - : The Electrochemical Society. - 0013-4651 .- 1945-7111. ; 168:1
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Tidskriftsartikel (refereegranskat)abstract
- The global need for freshwater rapidly drives the development of emerging and efficient freshwater-production methods such as capacitive deionization (CDI). To allow the CDI technique to continue to grow, simulations can be important for tractably describing, predicting, and optimizing the desalination processes. Amongst the disparate simulation tools available, the Randles-circuit model is widely used in electrochemical measurements but its simplified structure limits its use for wider CDI operations. Thus, we herein describe a systematic stepwise process for widely developing CDI models, and as a proof-of-concept, transform the core Randles circuit into an extended Randles circuit (ERaC) that is highly relevant for CDI systems. Experimental data from the literature extensively verify that the ERaC model accuracy now describes charge storage, charging rate, ion adsorption, and current leakages for a variety of structural and operational parameters, such as asymmetric electrodes, different ion concentrations, and the applied voltage. In conclusion, this developed stepwise process can systematically and effectively create, enhance, and expand CDI models. Thus, researchers will embrace this method of model development, and benefit from the broad usefulness of the proposed ERaC model for a wide range of CDI operations.
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| 10. |
- Nordstrand, Johan
(författare)
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At the Mountains of Modeling : Multiscale Simulations of Desalination by Capacitive Deionization
- 2022
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- More than 2 billion people are living in water-scarce areas. Meanwhile, there are enormous amounts of water in the salty oceans. Capacitive deionization (CDI) rises to the challenge with electrochemical cells for desalinating the water. As the CDI field expands, modeling becomes an increasingly important part of the development landscape. Multiscale modeling could bring innovations from the material scale to pilot plants. The multiscale work in this thesis has been like climbing a mountain. At the start, we investigate the macroscopic device level. One milestone is the electrolytic-capacitor (ELC) model, which can simulate CDI process dynamics. Whereas previous 2D models were unsteady for a single CDIcell, the ELC model could accurately simulate stacks of over 100 cells at a fraction of the time. It also enables simulations of complex upscaled geometries, such as bipolar electrode stacks, ohmic charging, and asymmetric devices. Going up the mountain, the mesoscopic level reveals the local mechanisms behind the macroscopic behavior. One important stepping stone is the dynamic Langmuir (DL) model, which reveals how isotherm-based modeling can crease stable and tractable simulations. Also, developments in isotherm, double-layer, and circuit modeling make it possible to choose what model structures to lean on depending on the conditions. Near the top of the mountain, the microscopic level shows the fundamental atomic mechanisms behind the mesoscopic material properties. These investigations reveal a ladder mechanism of ion transport in crystals of Prussian blue analogs (PBA), meaning the cations climb frames formed by negative groups in the crystal structure.In the end, we plant a flag by combining the developments from the journey into a complete multiscale model. That model demonstrated that we could predict CDI charging trends from the atomic structure of PBA electrodes. Having the full multiscale model also made it possible to backtrack and determine atomic-level mechanisms by comparing the output of different mechanism cases with macroscopic experiment data. The multiscale mountain is massive and has big potential. A dream is that future research will expand these concepts, in CDI and beyond.
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