| 1. |
- Flyborg, Lena, et al.
(författare)
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A PLS model for predicting rejection of trace organic compounds by nanofiltration using treated wastewater as feed
- 2017
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Ingår i: Separation and Purification Technology. - : Elsevier. - 1383-5866 .- 1873-3794. ; 174, s. 212-221
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Tidskriftsartikel (refereegranskat)abstract
- In this study a Partial Least Squares Projection of Latent Structures (PLS) model has been developed for predicting the rejection of pharmaceutical residuals by nanofiltration (NF) using treated municipal wastewater as feed. The objective was to provide a practical tool for wastewater reuse facilities for estimating the rejection of emerging organic contaminants based on their physiochemical characteristics. The model was developed by identifying the important physiochemical properties of pharmaceutical residuals for rejection by NF. The investigated pharmaceuticals were those present in the effluent from Henriksdal wastewater treatment plant (WWTP), Sweden. The rejection, at volume reduction factors (VRF) ranging from 2 to 20, was examined in a NF pilot plant at two occasions. The important variables for rejection by NF were, in descending order: polarizability, globularity, ratio hydrophobic to polar water accessible surface area and compound charge. Two studies were performed with a time interval of about a year with different wastewater matrices and age of membranes. For different VRFs, but in the same study, the model produced consistent predicted rejections. For the same VRF, but in the different studies, the regression lines were almost parallel, but with a deviation of about 7% for the predicted values. Most of the compounds were within the 95% prediction interval. The model also proved to be able to predict rejection using data from the literature. This confirms that the predictive PLS model can estimate the rejection albeit, with limitations. Generally the proposed predictive rejection model is most likely valid but the model coefficients need to be determined for each individual WWTP or wastewater reuse facility.
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| 2. |
- Grebikova, Lucie, et al.
(författare)
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The persistence length of adsorbed dendronized polymers
- 2016
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Ingår i: Nanoscale. - : Royal Society of Chemistry (RSC). - 2040-3372 .- 2040-3364. ; 8:27, s. 506-13498
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Tidskriftsartikel (refereegranskat)abstract
- The persistence length of cationic dendronized polymers adsorbed onto oppositely charged substrates was studied by atomic force microscopy (AFM) and quantitative image analysis. One can find that a decrease in the ionic strength leads to an increase of the persistence length, but the nature of the substrate and of the generation of the side dendrons influence the persistence length substantially. The strongest effects as the ionic strength is being changed are observed for the fourth generation polymer adsorbed on mica, which is a hydrophilic and highly charged substrate. However, the observed dependence on the ionic strength is much weaker than the one predicted by the Odijk, Skolnik, and Fixman (OSF) theory for semi-flexible chains. Low-generation polymers show a variation with the ionic strength that resembles the one observed for simple and flexible polyelectrolytes in solution. For high-generation polymers, this dependence is weaker. Similar dependencies are found for silica and gold substrates. The observed behavior is probably caused by different extents of screening of the charged groups, which is modified by the polymer generation, and to a lesser extent, the nature of the substrate. For highly ordered pyrolytic graphite (HOPG), which is a hydrophobic and weakly charged substrate, the electrostatic contribution to the persistence length is much smaller. In the latter case, we suspect that specific interactions between the polymer and the substrate also play an important role.
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| 3. |
- Hayashi, Yoshikatsu, et al.
(författare)
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A Monte Carlo study of solutions of oppositely charged polyelectrolytes
- 2002
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 116:15, s. 6836-6845
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Tidskriftsartikel (refereegranskat)abstract
- The formation of complexes appearing in solutions containing oppositely charged polyelectrolytes has been investigated by Monte Carlo simulations using two different models. The polyions are described as flexible chains of 20 connected charged hard spheres immersed in a homogenous dielectric background representing water. The small ions are either explicitly included or their effect described by using a screened Coulomb potential. The simulated solutions contained 10 positively charged polyions with 0, 2, or 5 negatively charged polyions and the respective counterions. Two different linear charge densities were considered, and structure factors, radial distribution functions, and polyion extensions were determined. A redistribution of positively charged polyions involving strong complexes formed between the oppositely charged polyions appeared as the number of negatively charged polyions was increased. The nature of the complexes was found to depend on the linear charge density of the chains. The simplified model involving the screened Coulomb potential gave qualitatively similar results as the model with explicit small ions. Finally, owing to the complex formation, the sampling in configurational space is nontrivial, and the efficiency of different trial moves was examined. (C) 2002 American Institute of Physics.
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| 4. |
- Hayashi, Yoshikatsu, et al.
(författare)
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Complex formation in solutions of oppositely charged polyelectrolytes at different polyion compositions and salt content
- 2003
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:32, s. 8198-8207
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Tidskriftsartikel (refereegranskat)abstract
- The formation of complexes in solutions containing positively charged polyions (polycations) and a variable amount of negatively charged polyions (polyanions) has been investigated by Monte Carlo simulations. The polyions were described as flexible chains of charged hard spheres interacting through a screened Coulomb potential. The systems were analyzed in terms of cluster compositions, structure factors, and radial distribution functions. At 50% charge equivalence or less, complexes involving two polycations nd one polyanion were frequent, while closer to charge equivalence, larger clusters were formed. Small and neutral complexes dominated the solution at charge equivalence in a monodisperse system, while larger clusters again dominated the solution when the polyions were made polydisperse. The cluster composition and solution structure were also examined as functions of added salt by varying the electrostatic screening length. The observed formation of clusters could be rationalized by a few simple rules.
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| 5. |
- Hayashi, Yoshikatsu, et al.
(författare)
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Oppositely charged polyelectrolytes. Complex formation and effects of chain asymmetry
- 2004
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 108:39, s. 15266-15277
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Tidskriftsartikel (refereegranskat)abstract
- The formation of complexes in solutions of oppositely charged polyions has been studied by Monte Carlo simulations. The amount as well as the length, and thus, the absolute charge of one of the polyions have been varied. There is an increasing tendency to form large clusters as the excess of one kind of polyion decreases. When all polyions have the same length, this tendency reaches a maximum near, but off, equivalent amounts of the two types of polyions. When one kind of polyion is made shorter, the propensity to form large clusters decreases and the fluctuations in cluster charge increases. Simple free-energy expressions have been formulated on the basis of a set of simple rules that help rationalize the observations. By calculating cluster distributions in both grand canonical and canonical ensembles, it has been possible to show the extent of finite-size effects in the simulations.
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| 6. |
- Johansson, Charlotta, et al.
(författare)
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The Solution Structures of Mutant Calbindin D9k's, As Determined by NMR, Show That the Calcium-Binding Site Can Adopt Different Folds
- 1993
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 32:33, s. 8429-8438
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Tidskriftsartikel (refereegranskat)abstract
- The complete 1H NMR assignments have been obtained for five mutant proteins of calbindin D9k and the three-dimensional solution structures determined for two of the mutants. The structures have been determined using distance geometry and simulated annealing, with distance constraints from NMR. All mutants have modifications in the first calcium-binding site of calbindin (the N-terminal site designated the pseudo-EF-hand). The 3D structure of the mutant with the most extensive modifications in the pseudo-EF-hand shows that the site has turned inside-out and coordinates calcium as in the normal EF-hand (the C-terminal site). In a pseudo-EF-hand loop the calcium is coordinated by main-chain carbonyls, whereas calcium in the normal EF-hand is coordinated by side-chain carboxylates. The 3D structures and 1H NMR assignments show that in order to accomplish a change in the coordinating ligands of the pseudo-EF-hand the loop must be 12 residues long and have glycine in the sixth position. It does, however, seem possible to have alanine instead of aspartic acid in the first calcium coordinating position. The overall global fold of the proteins has not been affected by the mutations in the calcium-binding site, as compared to the wild-type calbindin D9k [Kördel, J., Skelton, N. J., Akke, M., & Chazin, W. J. (1993) J. Mol. Biol. (in press)]. The structures consist of two helix-calcium-binding loop-helix motifs, the so called EF-hands, and the loops are connected by a short antiparallel β-sheet. All helices are pairwise in an antiparallel orientation.
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| 7. |
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| 8. |
- Jönsson, Bo, et al.
(författare)
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Titrating polyelectrolytes - Variational calculations and Monte Carlo simulations
- 1996
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Ingår i: Journal of Physical Chemistry. - : American Chemical Society (ACS). - 0022-3654 .- 1541-5740. ; 100:1, s. 409-417
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Tidskriftsartikel (refereegranskat)abstract
- Variational methods are used to calculate structural and thermodynamical properties of a titrating polyelectrolyte in a discrete representation. In the variational treatment, the Coulomb potentials are emulated by harmonic repulsive forces between all monomers; the force constants are used as variational parameters. The accuracy of the variational approach is tested against Monte Carlo data. Excellent agreement is obtained for the end-to-end separation and the apparent dissociation constant for the unscreened Coulomb chain. The short-range screened Coulomb potential is more difficult to handle variationally, and its structural features are less well described, although the thermodynamic properties are predicted with the same accuracy as for the unscreened chain. The number of variational parameters is on the order of N2, where N is the number of monomers, and the computational effort scales like N3. In addition, a simplified variational procedure with only two parameters is pursued, based on a rigid-rod approximation of the polymer. It gives surprisingly good accuracy for certain physical properties.
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| 9. |
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| 10. |
- Makita, Naoko, et al.
(författare)
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Conformational change of giant DNA with added salt as revealed by single molecular observation
- 2006
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 39:18, s. 6200-6206
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Tidskriftsartikel (refereegranskat)abstract
- The structural change of individual giant double-stranded T4 DNA (165.6 kilobase pairs) molecules as a function of salt concentration was investigated by single molecular observation with fluorescence microscopy in a wide range of concentration of NaCl, 1 x 10(-6)-3 M. The measured long-axis length was transformed into a persistence length and subjected to a power-law analysis, which showed that the electrostatic contribution to the persistence length is inversely proportional to the square root of the salt concentration; i.e., it has a linear dependence on the screening length. This is interpreted as the behavior of a flexible chain with electrostatic excluded-volume interactions. Although double-stranded DNA is locally stiff, it displays flexibility when the contour length is much longer than the persistence length, as is the case for T4 DNA.
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| 11. |
- Rydén, Jens, et al.
(författare)
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Monte Carlo simulations of oppositely charged macroions in solution
- 2005
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 123:3, s. 1-034909
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Tidskriftsartikel (refereegranskat)abstract
- The structure and phase behavior of oppositely charged macroions in solution have been studied with Monte Carlo simulations using the primitive model where the macroions and small ions are described as charged hard spheres. Size and charge symmetric, size asymmetric, and charge asymmetric macroions at different electrostatic coupling strengths are considered, and the properties of the solutions have been examined using cluster size distribution functions, structure factors, and radial distribution functions. At increasing electrostatic coupling, the macroions form clusters and eventually the system displays a phase instability, in analogy to that of simple electrolyte solutions. The relation to the similar cluster formation and phase instability occurring in solutions containing oppositely charged polymers is also discussed. (c) 2005 American Institute of Physics.
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| 12. |
- Selander-Sunnerhagen, Maria, et al.
(författare)
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How an epidermal growth factor (EGF)-like domain binds calcium. High resolution NMR structure of the calcium form of the NH2-terminal EGF-like domain in coagulation factor X
- 1992
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Ingår i: Journal of Biological Chemistry. - 0021-9258. ; 267:27, s. 19642-19649
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Tidskriftsartikel (refereegranskat)abstract
- Domains homologous to the epidermal growth factor (EGF) are important building blocks for extracellular proteins. Proteins containing these domains have been shown to function in such diverse biological processes as blood coagulation, complement activation, and the developmental determination of embryonic cell fates. Many of these proteins require calcium for their biological function. In the case of coagulation factors IX and X and anticoagulants proteins C and S, calcium has been found to bind to the EGF- like domains. We have now determined the three-dimensional structure of the calcium-bound form of the NH2-terminal EGF-like domain in coagulation factor X by two-dimensional NMR and simulated folding. Ligands to the calcium ion are the two backbone carbonyls in Gly-47 and Gly-64, as well as the side chains in Gln-49, erythro-β-hydroxyaspartic acid (Hya) 63, and possibly Asp- 46. The conserved Asp-48 is not a ligand in our present structures. The remaining ligands are assumed to be solvent molecules or, in the intact protein, ligands from neighboring domains. Other proteins interacting in a calcium-dependent manner may also contribute ligands. A comparison with the calcium-free form shows that calcium binding induces strictly local structural changes in the domain. Residues corresponding to the side chain ligands in factor X are conserved in many other proteins, such as the integral membrane protein TAN-1 of human lymphocytes and its developmentally important homolog, Notch, in Drosophila. Calcium binding to EGF-like domains may be crucial for numerous protein-protein interactions involving EGF-like domains in coagulation factors, plasma proteins, and membrane proteins. Therefore, there is reason to believe that this novel calcium site plays an important role in the biochemistry of extracellular proteins.
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| 13. |
- Thuresson, Axel, et al.
(författare)
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Interaction and Aggregation of Charged Platelets in Electrolyte Solutions: A Coarse-Graining Approach.
- 2014
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 118:26, s. 7405-7413
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Tidskriftsartikel (refereegranskat)abstract
- A coarse-graining approach has been developed to replace the effect of explicit ions with an effective pair potential between charged sites in anisotropic colloidal particles by optimizing a potential of mean force against the results of simulations of two such colloidal particles with all ions in a cell model. More specifically, effective pair potentials were obtained for charged platelets in electrolyte solutions by simulating two rotating parallel platelets with ions at the primitive model level, enclosed in a cylindrical cell. One-component bulk simulations of many platelets interacting via the effective pair potentials are in excellent agreement with the corresponding bulk simulations with all mobile charges present. The bulk simulations were mainly used to study the effects of platelet size, flexibility, and surface charge density on platelet aggregation in an aqueous 2:1 electrolyte, but systems in a 1:1 electrolyte were also investigated.
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| 14. |
- Thuresson, Axel, et al.
(författare)
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Monte carlo simulations of parallel charged platelets as an approach to tactoid formation in clay.
- 2013
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Ingår i: Langmuir. - : American Chemical Society (ACS). - 0743-7463 .- 1520-5827. ; 29:29, s. 9216-9223
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Tidskriftsartikel (refereegranskat)abstract
- The free energy of interaction between parallel charged platelets with divalent counterions has been calculated using Monte Carlo simulations to investigate the electrostatic effects on aggregation. The platelets are primarily intended to represent clay particles. With divalent counterions, the free energy for two platelets or two tactoids (clusters of parallel platelets) shows a minimum at a short separation due to the attraction caused by ion-ion correlations. In a salt-free system, the free energy of interaction has a long-range repulsive tail beyond the minimum. The repulsion increases for tactoids with larger aggregation numbers, whereas the depth of the free-energy minimum is gradually reduced. For large enough aggregation numbers, the repulsion is dominating and the minimum is no longer a global free-energy minimum. This is an effect of the depletion of counterions free in solution (outside tactoids) as counterions and platelets aggregate into tactoids and the resulting redistribution of counterions in the system changes the effective interactions between platelets and tactoids. The difference in tactoid-tactoid interactions as a function of aggregation number can be removed by adding enough salt to mask the depletion. Adding salt also reduces the repulsive tail of the free energy of interaction and enhances the minimum. No dependence on the aggregation number suggests that an isodesmic model with a monotonically decaying distribution of aggregation numbers can be used to describe a clay system. This may help to explain the experimental observations of low average numbers of platelets in tactoids, although factors not included in the simulation model may also play an important role.
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| 15. |
- Ullner, Magnus, et al.
(författare)
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A Debye–Hückel theory for electrostatic interactions in proteins
- 1996
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 105:5, s. 2056-2065
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Tidskriftsartikel (refereegranskat)abstract
- The site–site Ornstein–Zernike equation with a simple mean spherical closure is used to study electrostatic interactions of proteins. Using a Debye–Hückel approximation for the correlation functions of the bulk electrolyte and a simple basis expansion for the protein–salt direct correlation functions, we obtain a very simple variational expression for the electrostatic component of the excess chemical potential of a protein in an electrolyte solution. The predictions of the theory are tested on a model of the protein calbindin D9k. Our calculations for calcium binding affinities and protein acidity constants are found to be in excellent agreement with the results of computer simulations.
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| 16. |
- Ullner, Magnus, et al.
(författare)
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A Monte Carlo study of titrating polyelectrolytes
- 1996
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 104:8, s. 3048-3057
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Tidskriftsartikel (refereegranskat)abstract
- Monte Carlo simulations have been used to study three different models for linear, titrating polyelectrolytes in a salt-free environment: (i) a rigid polymer with rigid bonds (rigid rod); (ii) a flexible polymer with rigid bonds; and (iii) a flexible polymer with flexible bonds. The use of a very efficient pivot algorithm has made it possible to simulate very long chains, with up to several thousand titrating groups. The results have been compared to a mean field approximation for a rigid rod and variational results emanating from a Flory type approach. It is found that the rigid rod mean field model gives a qualitatively correct description for the apparent dissociation constant for all three models. At room temperature, the energy contribution to the apparent dissociation constant often dominates over the entropic term, which partly explains the relative success of this approach. In the case of flexible bonds, both the conformational behavior and the behavior of the apparent dissociation constant are well described by a variational ansatz with a quadratic term, largely thanks to the harmonicity of the bonds themselves. The approach is less successful for rigid bonds, which becomes evident for highly charged chains where a harmonic entropy term is incorrect. This can be remedied by replacing it with an expression valid in the strong coupling regime. Empirical scaling expressions have also been found, primarily for the end-to-end distance.
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| 17. |
- Ullner, Magnus, et al.
(författare)
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A Monte Carlo Study of Titrating Polyelectrolytes in the Presence of Salt
- 1996
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 29:20, s. 6645-6655
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Tidskriftsartikel (refereegranskat)abstract
- Monte Carlo simulations have been performed for two simple models of a titrating polyelectrolyte: (i) a rigid rod and (ii) a freely jointed chain. Both models have fixed bond lengths, and the polyelectrolyte charges interact through a screened Coulomb potential. Chains consisting of 80-1000 monomeric units have been studied at three salt concentrations: 0.001, 0.01, and 0.1 M. Conformational properties and the apparent dissociation constant are reported as functions of chain length, chain ionization, monomer-monomer bond length, and salt concentration. Mean field expressions are compared to the simulation results and are, in general, found to be excellent approximations for the rigid rod, but they are also able to provide semiquantitative descriptions of the apparent dissociation constant for the freely jointed chain. Comparisons with experimental data show that the conformational properties of the flexible model can reproduce features of the titration curves, although the use of a screened Coulomb potential overestimates the response to changes in salt concentration.
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| 18. |
- Ullner, Magnus
(författare)
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Comments on the scaling behavior of flexible polyelectrolytes within the Debye-Huckel approximation
- 2003
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 107:32, s. 8097-8110
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Tidskriftsartikel (refereegranskat)abstract
- Over the years, there has been much debate regarding the conformational behavior of flexible polyelectrolytes with electrostatic interactions described by the D bye-Huckel approximation. In particular, the electrostatic persistence length has been reported to depend both quadratically and linearly on the screening length as well as having no consistent power-law dependence at all. On the basis of simulation results together with a careful analysis of analytical approaches, including Odijk-Skolnick-Fixman (OSF) theory, variational calculations, and renormalization group results, it is possible to present a consistent picture, which contains a better understanding of the true behavior as well as an explanation for the diverse results. The projection length of long chains can be described by power laws in three regimes, and an expression by Odijk is qualitatively correct in two of these regimes. Scaling arguments based on OSF theory and excluded volume considerations give good agreement with the third power law, but the underlying assumptions are not entirely correct. More than one parameter is required to describe the internal chain behavior, which is characterized b short-range flexibility and long-range stiffness. Still, most analytical approaches end up in one of two one-parameter approximations, either an OSF-like perturbation expansion around a rigid-rod state or a Flory-type variational calculation based on an unperturbed chain. The latter describes at best the short-range behavior. A field-theoretic renormalization group treatment, which has suggested that there should be no power law behavior, is not valid in three dimensions. Previous support from simulation results were obtained through an unfortunate mistake.
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| 19. |
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| 20. |
- Ullner, Magnus, et al.
(författare)
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Orientational correlation function and persistence lengths of flexible polyelectrolytes
- 2002
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Ingår i: Macromolecules. - : American Chemical Society (ACS). - 0024-9297 .- 1520-5835. ; 35:4, s. 1437-1445
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Tidskriftsartikel (refereegranskat)abstract
- Orientational correlation functions have been obtained from Monte Carlo simulations of long, freely jointed chains (1000 monomers and more) with screened Coulomb interactions truncated after a certain number of bonds. This makes it possible to study chain-length dependence without "end effects" and to display excluded-volume effects. These correlation functions form the basis for a discussion of the conformational response to electrostatic interactions. In particular, they are related to the concept of electrostatic persistence length and the correlation functions illustrate the differences between different definitions of persistence length. To facilitate future discussions, we have identified four types of definitions and given them separate names: (1.) projection length, which involves: integration of the orientational correlation function; (2) orientational correlation length, which is the decay length of an exponential function; (3) bending coefficient, which is a length representing a bending force constant; and (4) crossover distance, which is the monomer-monomer distance at the boundary between a rodlike and a swollen behavior. Previous conclusions that the projection length obeys a power law at high salt concentrations, while the orientational correlation length does not, are confirmed. Furthermore, a power law is also found in the salt-free limit for the projection length corresponding to an infinite chain with a finite range of interactions. The two power laws make it possible to construct a universal curve that gives an almost quantitative description of the chain behavior.
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| 21. |
- Ullner, Magnus, et al.
(författare)
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Osmotic pressure in polyelectrolyte solutions : cell-model and bulk simulations
- 2018
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-683X .- 1744-6848. ; 14:28, s. 5832-5846
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Tidskriftsartikel (refereegranskat)abstract
- The osmotic pressure of polyelectrolyte solutions as a function of concentration has been calculated by Monte Carlo simulations of a spherical cell model and by molecular dynamics simulations with periodic boundary conditions. The results for the coarse-grained polyelectrolyte model are in good agreement with experimental results for sodium polyacrylate and the cell model is validated by the bulk simulations. The cell model offers an alternative perspective on osmotic pressure and also forms a direct link to even simpler models in the form of the Poisson-Boltzmann approximation applied to cylindrical and spherical geometries. As a result, the non-monotonic behaviour of the osmotic coefficient seen in simulated salt-free solutions is shown not to rely on a transition between a dilute and semi-dilute regime, as is often suggested when the polyion is modelled as a linear flexible chain. The non-monotonic behaviour is better described as the combination of a finite-size effect and a double-layer effect. Parameters that represent the linear nature of the polyion, including an alternative to monomer concentration, make it possible to display a generalised behaviour of equivalent chains, at least at low concentrations. At high concentrations, local interactions become significant and the exact details of the model become important. The effects of added salt are also discussed and one conclusion is that the empirical additivity rule, treating the contributions from the polyelectrolyte and any salt separately, is a reasonable approximation, which justifies the study of salt-free solutions.
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| 22. |
- Ullner, Magnus, et al.
(författare)
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Polyelectrolyte Models in Theory and Simulation
- 2002
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Ingår i: Handbook of Polyelectrolytes and Their Applications : Vol. 3, Applications of polyelectrolytes and theoretical models - Vol. 3, Applications of polyelectrolytes and theoretical models. - 1588830160 ; 3, s. 271-308
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Bokkapitel (övrigt vetenskapligt/konstnärligt)
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| 23. |
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| 24. |
- Ullner, Magnus
(författare)
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Statistical Mechanical Studies of Titrating Polyelectrolytes
- 1996
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Different models and statistical mechanical approximations for titrating polyelectrolytes are studied and the results compared with Monte Carlo simulations and experimental data. Three types of models have been used in the simulations: i) rigid structures and freely jointed chains with ii) rigid bonds and iii) flexible, harmonic bonds. Sampling is facilitated for the latter two by the use of pivot algorithms, which allow simulations of literally thousands of monomers. Electrostatic interactions are treated within the primitive model. There are no interactions between macromolecules; only single chain properties are investigated. The main part of the thesis is devoted to the study of flexible polyelectrolytes, which represent systems like polyacrylic acid and polyglutamic acid. The apparent dissociation constant and the end-to-end separation are calculated for varying degree of dissociation, bond length/bond strength, number of monomers and salt concentration. Simple scaling relations obtained by a Flory type approach are investigated as well as the results of more elaborate variational calculations using a Gaussian Ansatz where all interactions are modelled by harmonic springs. Various rigid models that have appeared in the literature are also examined. The last part of the thesis deals with integral equation theory in the form of RISM-MSA for proteins and other more or less rigid polyelectrolytes. The theory is applied to the calcium binding and titrational behaviour of the protein calbindin D9k.
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| 25. |
- Ullner, Magnus, et al.
(författare)
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The electrostatic persistence length calculated from Monte Carlo, variational and perturbation methods
- 1997
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Ingår i: Journal of Chemical Physics. - 0021-9606. ; 107:4, s. 1279-1287
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Tidskriftsartikel (refereegranskat)abstract
- Monte Carlo simulations and variational calculations using a Gaussian ansatz are applied to a model consisting of a flexible linear polyelectrolyte chain as well as to an intrinsically stiff chain with up to 1000 charged monomers. Addition of salt is treated implicitly through a screened Coulomb potential for the electrostatic interactions. For the flexible model the electrostatic persistence length shows roughly three regimes in its dependence on the Debye-Hückel screening length, κ-1. As long as the salt content is low and κ-1 is longer than the end-to-end distance, the electrostatic persistence length varies only slowly with κ-1. Decreasing the screening length, a controversial region is entered. We find that the electrostatic persistence length scales as √ξp/κ, in agreement with experiment on flexible polyelectrolytes, where ξp is a strength parameter measuring the electrostatic interactions within the polyelectrolyte. For screening lengths much shorter than the bond length, the κ-1 dependence becomes quadratic in the variational calculation. The simulations suffer from numerical problems in this regime, but seem to give a relationship half-way between linear and quadratic. A low temperature expansion only reproduces the first regime and a high temperature expansion, which treats the electrostatic interactions as a perturbation to a Gaussian chain, gives a quadratic dependence on the Debye length. For a sufficiently stiff chain, the persistence length varies quadratically with κ-1 in agreement with earlier theories.
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| 26. |
- Ullner, Magnus, et al.
(författare)
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Three-Dimensional Structure of the Apo Form of the N-Terminal EGF-like Module of Blood Coagulation Factor X As Determined by NMR Spectroscopy and Simulated Folding
- 1992
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Ingår i: Biochemistry. - : American Chemical Society (ACS). - 0006-2960 .- 1520-4995. ; 31:26, s. 5974-5983
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Tidskriftsartikel (refereegranskat)abstract
- The three-dimensional structure of a 42-residue fragment containing the N-terminal EGF-like module of blood coagulation factor X was determined by means of 2D NMR spectroscopy and computer simulation. The spectroscopic data consisted of 370 NOE distances and 27 dihedral angle constraints. These were used to generate peptide conformations by molecular dynamics simulation. The simulations used a novel functional form for the constraint potentials and were performed with two time steps to ensure rapid execution. Apart from preliminary runs to aid assignment of NOEs, 60 runs resulted in 13 accepted structures, which have two antiparallel β sheets, no α helices, and five tight turns. There is no hydrophobic cluster. The root mean square deviation for the backbone of the 13 conformations is 0.65 ± 0.11 Å against their mean conformation. About half of the side chains have well-defined structure. The overall conformation is similar to that of murine EGF.
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