| 1. |
- Botan, Alexandru, et al.
(författare)
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Toward Atomistic Resolution Structure of Phosphatidylcholine Headgroup and Glycerol Backbone at Different Ambient Conditions
- 2015
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 119:49, s. 15075-15088
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Tidskriftsartikel (refereegranskat)abstract
- Phospholipids are essential building blocks of biological membranes. Despite a vast amount of very accurate experimental data, the atomistic resolution structures sampled by the glycerol backbone and choline headgroup in phoshatidylcholine bilayers are not known. Atomistic resolution molecular dynamics simulations have the potential to resolve the structures, and to give an arrestingly intuitive interpretation of the experimental data, but only if the simulations reproduce the data within experimental accuracy. In the present work, we simulated phosphatidylcholine (PC) lipid bilayers with 13 different atomistic models, and compared simulations with NMR. experiments in terms of the highly structurally sensitive C-H bond vector order parameters. Focusing on the glycerol backbone and choline headgroups, we showed that the order parameter comparison can be used to judge the atomistic resolution structural accuracy of the models. Accurate models, in turn, allow molecular dynamics simulations to be used as an interpretation tool that translates these NMR data into a dynamic three-dimensional representation of biomolecules in biologically relevant conditions. In addition to lipid bilayers in fully hydrated conditions, we reviewed previous experimental data for dehydrated bilayers and cholesterol-containing bilayers, and interpreted them with simulations. Although none of the existing models reached experimental accuracy, by critically comparing them we were able to distill relevant chemical information: (1) increase of choline order parameters indicates the P-N vector tilting more parallel to the membrane, and (2) cholesterol induces only minor changes to the PC (glycerol backbone) structure. This work has been done as a fully open collaboration, using nmrlipids.blogspot.fi as a communication platform; all the scientific contributions were made publicly on this blog. During the open research process, the repository holding our simulation trajectories and files (https://zenodo.org/collection/user-nmrlipids) has become the most extensive publicly available collection of molecular dynamics simulation trajectories of lipid bilayers.
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| 2. |
- Kanduc, Matej, et al.
(författare)
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Attraction between neutral dielectrics mediated by multivalent ions in an asymmetric ionic fluid
- 2012
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 137:17
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Tidskriftsartikel (refereegranskat)abstract
- We study the interaction between two neutral plane-parallel dielectric bodies in the presence of a highly asymmetric ionic fluid, containing multivalent as well as monovalent (salt) ions. Image charge interactions, due to dielectric discontinuities at the boundaries, as well as effects from ion confinement in the slit region between the surfaces are taken fully into account, leading to image-generated depletion attraction, ion correlation attraction, and steric-like repulsive interactions. We investigate these effects by employing a combination of Monte Carlo simulation methods, including explicit-ion simulations (where all electrostatic interactions are simulated explicitly) and implicit-ion simulations (where monovalent ions are replaced by an effective screened electrostatic potential between multivalent ions), as well as an approximate analytical theory. The latter incorporates strong ion-image charge correlations, which develop in the presence of high valency ions in the mixture. We show that the implicit-ion simulations and the proposed analytical theory can describe the explicit simulation results on a qualitative level, while excellent quantitative agreement can be obtained for sufficiently large monovalent salt concentrations. The resultant attractive interaction between the neutral surfaces is shown to be significant, as compared with the usual van der Waals interactions between semi-infinite dielectrics, and can thus play an important role at the nano scale. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4763472]
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| 3. |
- Kanduc, Matej, et al.
(författare)
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Dressed counterions: Polyvalent and monovalent ions at charged dielectric interfaces
- 2011
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Ingår i: Physical Review E (Statistical, Nonlinear, and Soft Matter Physics). - 1539-3755. ; 84:1
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Tidskriftsartikel (refereegranskat)abstract
- We investigate the ion distribution and overcharging at charged interfaces with dielectric inhomogeneities in the presence of asymmetric electrolytes containing polyvalent and monovalent ions. We formulate an effective "dressed counterion" approach by integrating out the monovalent salt degrees of freedom and show that it agrees with results of explicit Monte Carlo simulations. We then apply the dressed counterion approach within the framework of the generalized strong-coupling theory, valid for polyvalent ions at low concentrations, which enables an analytical description for salt effects as well as dielectric inhomogeneities in the limit of strong Coulomb interactions. Limitations and applicability of this theory are examined by comparing the results with simulations.
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| 4. |
- Kanduc, Matej, et al.
(författare)
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Dressed counterions: Strong electrostatic coupling in the presence of salt
- 2010
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 132:12
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Tidskriftsartikel (refereegranskat)abstract
- We reformulate the theory of strong electrostatic coupling in order to describe an asymmetric electrolyte solution of monovalent salt ions and polyvalent counterions using field-theoretical techniques and Monte Carlo simulations. The theory is based on an asymmetric treatment of the different components of the electrolyte solution. The weak coupling Debye-Huumlckel approach is used in order to describe the monovalent salt ions while a strong coupling approach is used to tackle the polyvalent counterions. This combined weak-strong coupling approach effectively leads to dressed interactions between polyvalent counterions and thus directly affects the correlation attraction mediated by polyvalent counterions between like-charged objects. The general theory is specifically applied to a system composed of two uniformly charged plane-parallel surfaces in the presence of salt and polyvalent counterions. In the strong coupling limit for polyvalent counterions, the comparison with Monte Carlo simulations shows good agreement for large enough values of the electrostatic coupling parameter. We delineate two limiting laws that in fact encompass all the Monte Carlo data.
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| 5. |
- Kim, Won Kyu, et al.
(författare)
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Tuning the selective permeability of polydisperse polymer networks
- 2020
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Ingår i: Soft Matter. - : Royal Society of Chemistry (RSC). - 1744-6848 .- 1744-683X. ; 16:35, s. 8144-8154
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Tidskriftsartikel (refereegranskat)abstract
- We study the permeability and selectivity ('permselectivity') of model membranes made of polydisperse polymer networks for molecular penetrant transport, using coarse-grained, implicit-solvent computer simulations. In our work, permeability P is determined on the linear-response level using the solution-diffusion model, P = KDin, i.e., by calculating the equilibrium penetrant partition ratio K and penetrant diffusivity Din inside the membrane. We vary two key parameters, namely the network-network interaction, which controls the degree of swelling and collapse of the network, and the network-penetrant interaction, which tunes the selective penetrant uptake and microscopic energy landscape for diffusive transport. We find that the partitioning K covers four orders of magnitude and is a non-monotonic function of the parameters, well interpreted by a second-order virial expansion of the free energy of transferring one penetrant from a reservoir into the membrane. Moreover, we find that the penetrant diffusivity Din in the polydisperse networks, in contrast to highly ordered membrane structures, exhibits relatively simple exponential decays. We propose a semi-empirical scaling law for the penetrant diffusion that describes the simulation data for a wide range of densities and interaction parameters. The resulting permeability P turns out to follow the qualitative behavior (including maximization and minimization) of partitioning. However, partitioning and diffusion are typically anti-correlated, yielding large quantitative cancellations, controlled and fine-tuned by the network density and interactions, as rationalized by our scaling laws. We finally demonstrate that even small changes of network-penetrant interactions, e.g., by half a kBT, modify the permselectivity by almost one order of magnitude.
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| 6. |
- Naji, Ali, et al.
(författare)
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Perspective: Coulomb fluids-Weak coupling, strong coupling, in between and beyond
- 2013
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Ingår i: Journal of Chemical Physics. - : AIP Publishing. - 0021-9606 .- 1089-7690. ; 139:15
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Tidskriftsartikel (refereegranskat)abstract
- We present a personal view on the current state of statistical mechanics of Coulomb fluids with special emphasis on the interactions between macromolecular surfaces, concentrating on the weak and the strong coupling limits. Both are introduced for a (primitive) counterion-only system in the presence of macroscopic, uniformly charged boundaries, where they can be derived systematically. Later we show how this formalism can be generalized to the cases with additional characteristic length scales that introduce new coupling parameters into the problem. These cases most notably include asymmetric ionic mixtures with mono-and multivalent ions that couple differently to charged surfaces, ions with internal charge (multipolar) structure and finite static polarizability, where weak and strong coupling limits can be constructed by analogy with the counterion-only case and lead to important new insights into their properties that cannot be derived by any other means. (C) 2013 AIP Publishing LLC.
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