| 1. |
- B. Brant Carvalho, Paulo H., 1990-, et al.
(författare)
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Neutron scattering study of polyamorphic THF·17(H2O) : toward a generalized picture of amorphous states and structures derived from clathrate hydrates
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry. - 1463-9076 .- 1463-9084. ; 25:21, s. 14981-14991
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Tidskriftsartikel (refereegranskat)abstract
- From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF·17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77-140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, VHDA, upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third form, recovered amorphous (RA). Results from neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF·17H2O solution (∼2.5 M). Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ∼23H2O. The local water structure in HDA is reminiscent of pure HDA-ice featuring 5-coordinated H2O. In VHDA, the hydration structure of HDA is maintained but the local water structure is densified and resembles pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ∼18 H2O molecules and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous.
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| 2. |
- Barros Brant Carvalho, Paulo Henrique, et al.
(författare)
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Neutron scattering study of polyamorphic THF ∙ (H2O)17 – toward a generalized picture of amorphous states and structures derived from clathrate hydrates
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- From crystalline tetrahydrofuran clathrate hydrate, THF-CH (THF ∙ 17H2O, cubic structure II), three distinct polyamorphs can be derived. First, THF-CH undergoes pressure-induced amorphization when pressurized to 1.3 GPa in the temperature range 77–140 K to a form which, in analogy to pure ice, may be called high-density amorphous (HDA). Second, HDA can be converted to a densified form, very-HDA (VHDA), upon heat-cycling at 1.8 GPa to 180 K. Decompression of VHDA to atmospheric pressure below 130 K produces the third, recovered amorphous (RA) form. Results from a compilation of neutron scattering experiments and molecular dynamics simulations provide a generalized picture of the structure of amorphous THF hydrates with respect to crystalline THF-CH and liquid THF ∙ 17H2O solution (~2.5 M). The calculated density of (only in situ observable) HDA and VHDA at 2 GPa and 130 K is 1.287 and 1.328 g/cm3, respectively, whereas that of RA (at 1 atm) is 1.081 g/cm3. Although fully amorphous, HDA is heterogeneous with two length scales for water-water correlations (less dense local water structure) and guest-water correlations (denser THF hydration structure). The hydration structure of THF is influenced by guest-host hydrogen bonding. THF molecules maintain a quasiregular array, reminiscent of the crystalline state, and their hydration structure (out to 5 Å) constitutes ~23 H2O. The local water structure in HDA is reminiscent of pure HDA-ice, featuring 5-coordinated H2O. In VHDA, this structure is maintained but the local water structure is densified to resemble pure VHDA-ice with 6-coordinated H2O. The hydration structure of THF in RA constitutes ~18 H2O and the water structure corresponds to a strictly 4-coordinated network, as in the liquid. Both VHDA and RA can be considered as homogeneous, solid solutions of THF and water. The local water structure of water-rich (1:17) amorphous CHs resembles most that of the corresponding amorphous water ices when compared to guest-rich CHs, e.g., Ar ∙ ~6H2O. The proposed significance of different contributions of water local environments presents a simple view to justify neutron structure factor features.
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| 3. |
- Santosh, Mysore S., et al.
(författare)
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Molecular Dynamics Investigation of Dipeptide - Transition Metal Salts in Aqueous Solutions
- 2010
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Ingår i: Journal of Physical Chemistry B. - : American Chemical Society (ACS). - 1520-6106 .- 1520-5207. ; 114:49, s. 16632-16640
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Tidskriftsartikel (refereegranskat)abstract
- Molecular dynamics (MD) simulations of glycylglycine dipeptide with transition metal ions (Mn2+, Fe2+, Co2+, Ni2+, Cu2+, and Zn2+) in aqueous solutions have been carried out to get an insight into the solvation structure, intermolecular interactions, and salt effects in these systems. The solvation structure and hydrogen bonding were described in terms of radial distribution function (RDF) and spatial distribution function (SDF). The dynamical properties of the solvation structure were also analyzed in terms of diffusion and residence times. The simulation results show the presence of a well-defined first hydration shell around the dipeptide, with water molecules forming hydrogen bonds to the polar groups of the dipeptide. This shell is, however, affected by the strong electric field of divalent metal ions, which at higher ion concentrations lead to the shift in the dipeptide−water RDFs. Higher salt concentrations lead also to increased residence times and slower diffusion rates. In general, smaller ions (Cu2+, Zn2+) demonstrate stronger binding to dipeptide than the larger ones (Fe2+, Mn2+). Simulations do not show any stronger association of peptide molecules indicating their dissolution in water. The above results may be of potential interest to future researchers on these molecular interactions.
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| 4. |
- Sun, Tiedong, et al.
(författare)
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A Bottom-Up Coarse-Grained Model for Nucleosome-Nucleosome Interactions with Explicit Ions
- 2022
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Ingår i: Journal of Chemical Theory and Computation. - : American Chemical Society (ACS). - 1549-9618 .- 1549-9626. ; 18:6, s. 3948-3960
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Tidskriftsartikel (refereegranskat)abstract
- The nucleosome core particle (NCP) is a large complex of 145–147 base pairs of DNA and eight histone proteins and is the basic building block of chromatin that forms the chromosomes. Here, we develop a coarse-grained (CG) model of the NCP derived through a systematic bottom-up approach based on underlying all-atom MD simulations to compute the necessary CG interactions. The model produces excellent agreement with known structural features of the NCP and gives a realistic description of the nucleosome–nucleosome attraction in the presence of multivalent cations (Mg(H2O)62+ or Co(NH3)63+) for systems comprising 20 NCPs. The results of the simulations reveal structural details of the NCP–NCP interactions unavailable from experimental approaches, and this model opens the prospect for the rigorous modeling of chromatin fibers.
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| 5. |
- Grote, Fredrik, 1995-, et al.
(författare)
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Phase equilibrium, dynamics and rheology of phospholipid-ethanol mixtures : a combined molecular dynamics, NMR and viscometry study
- 2023
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Ingår i: Physical Chemistry, Chemical Physics - PCCP. - : Royal Society of Chemistry (RSC). - 1463-9076 .- 1463-9084. ; 25:23, s. 15905-15915
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Tidskriftsartikel (refereegranskat)abstract
- Binary mixtures of ethanol and phospholipids DOPC and DOPE have been investigated in a composition range relevant for topical drug delivery applications. This was done using a combined computer simulation and experimental approach where molecular dynamics simulations of ethanol-lipid mixtures with different compositions were performed. Several key properties including diffusion coefficients, longitudinal relaxation times, and shear viscosity were computed. In addition, diffusion coefficients, viscosities and NMR longitudinal relaxation times were measured experimentally for comparison and in order to validate the results from simulation. Diffusion coefficients and relaxation times obtained from simulations are in good agreement with results from NMR and computed viscosities are in reasonable agreement with viscometry experiments indicating that the simulations provide a realistic description of the ethanol-phospholipid mixtures. Structural changes in the simulated systems were investigated using an analysis based on radial distribution functions. This showed that the structure of ethanol-DOPC mixtures remains essentially unchanged in the investigated concentration range while ethanol-DOPE mixtures undergo structural rearrangements with the tendency for forming small aggregates on the 100 ns time scale consisting of less than 10 lipids. Although our simulations and experiments indicate that no larger aggregates form, they also show that DOPE has stronger aggregation tendency than DOPC. This highlights the importance of the character of the lipid headgroup for lipid aggregation in ethanol and gives new insights into phase equilibrium, dynamics and rheology that could be valuable for the development of advanced topical drug delivery formulations.
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| 6. |
- Ivanov, Mikhail, et al.
(författare)
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Coarse-Grained Modeling Using Neural Networks Trained on Structural Data
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - 1549-9618 .- 1549-9626. ; 19:19, s. 6704-6717
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Tidskriftsartikel (refereegranskat)abstract
- We propose a method of bottom-up coarse-graining, in which interactions within a coarse-grained model are determined by an artificial neural network trained on structural data obtained from multiple atomistic simulations. The method uses ideas of the inverse Monte Carlo approach, relating changes in the neural network weights with changes in average structural properties, such as radial distribution functions. As a proof of concept, we demonstrate the method on a system interacting by a Lennard-Jones potential modeled by a simple linear network and a single-site coarse-grained model of methanol-water solutions. In the latter case, we implement a nonlinear neural network with intermediate layers trained by atomistic simulations carried out at different methanol concentrations. We show that such a network acts as a transferable potential at the coarse-grained resolution for a wide range of methanol concentrations, including those not included in the training set.
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| 7. |
- Ivanov, Mikhail, 1995-, et al.
(författare)
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Development of a bottom-up coarse-grained model for interactions of lipids with TiO2 nanoparticles
- 2024
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Ingår i: Journal of Computational Chemistry. - 0192-8651 .- 1096-987X. ; 45:16, s. 1364-1379
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Tidskriftsartikel (refereegranskat)abstract
- Understanding interactions of inorganic nanoparticles with biomolecules is important in many biotechnology, nanomedicine, and toxicological research, however, the size of typical nanoparticles makes their direct modeling by atomistic simulations unfeasible. Here, we present a bottom-up coarse-graining approach for modeling titanium dioxide (TiO2) nanomaterials in contact with phospholipids that uses the inverse Monte Carlo method to optimize the effective interactions from the structural data obtained in small-scale all-atom simulations of TiO2 surfaces with lipids in aqueous solution. The resulting coarse-grained models are able to accurately reproduce the structural details of lipid adsorption on different titania surfaces without the use of an explicit solvent, enabling significant computational resource savings and favorable scaling. Our coarse-grained simulations show that small spherical TiO2 nanoparticles (?=2 nm) can only be partially wrapped by a lipid bilayer with phosphoethanolamine headgroups, however, the lipid adsorption increases with the radius of the nanoparticle. The current approach can be used to study the effect of the size and shape of TiO2 nanoparticles on their interactions with cell membrane lipids, which can be a determining factor in membrane wrapping as well as the recently discovered phenomenon of nanoquarantining, which involves the formation of layered nanomaterial–lipid structures.
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| 8. |
- Ivanov, Mikhail, 1995-
(författare)
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Development of large-scale molecular and nanomaterial models
- 2024
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Doktorsavhandling (övrigt vetenskapligt/konstnärligt)abstract
- Molecular simulations can access unique atomic-scale information about new materials, pharmaceuticals, and biological environments, making cost-effective predictions and aiding experimental studies. They are particularly useful for describing the mechanisms of nanoscale phenomena and the biological/inorganic interfaces. However, the computational cost of molecular simulations increases with the size of the system as well as with the model complexity, which is related to the accuracy of the simulation. This thesis aims to develop efficient large-scale molecular models that capture important structural details of the atomistic simulations. In particular, we focus on the TiO2-lipid interface, which forms in the living cells, exposed to TiO2 nanomaterials, but is also relevant in the context of biomedical applications. We have studied the interface using atomistic molecular dynamics simulations and found that the characteristics of the lipid adsorption depend on the type of the TiO2 surface, lipid headgroup composition, and the presence of cholesterol. We then derive a coarse-grained molecular model of the TiO2-lipid interface to enable the large-scale simulations of TiO2 nanoparticles interacting with model cell membranes. We show that the strength of the lipid adsorption increases with the size of the nanoparticle and that a small TiO2 nanoparticle can become partially wrapped by a lipid membrane. To improve the transferability of the coarse-grained model, we design and test an artificial neural network that learns the interactions in coarse-grained water-methanol solutions from the structural data obtained in multiple reference simulations at atomistic resolution. We show that in the studied system, the neural network learns the many-body interactions and accurately reproduces the structural properties of the solution at different concentrations.
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| 9. |
- Kokot, Hana, et al.
(författare)
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Prediction of Chronic Inflammation for Inhaled Particles : the Impact of Material Cycling and Quarantining in the Lung Epithelium
- 2020
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Ingår i: Advanced Materials. - : Wiley. - 0935-9648 .- 1521-4095. ; 32:47
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Tidskriftsartikel (refereegranskat)abstract
- On a daily basis, people are exposed to a multitude of health-hazardous airborne particulate matter with notable deposition in the fragile alveolar region of the lungs. Hence, there is a great need for identification and prediction of material-associated diseases, currently hindered due to the lack of in-depth understanding of causal relationships, in particular between acute exposures and chronic symptoms. By applying advanced microscopies and omics to in vitro and in vivo systems, together with in silico molecular modeling, it is determined herein that the long-lasting response to a single exposure can originate from the interplay between the newly discovered nanomaterial quarantining and nanomaterial cycling between different lung cell types. This new insight finally allows prediction of the spectrum of lung inflammation associated with materials of interest using only in vitro measurements and in silico modeling, potentially relating outcomes to material properties for a large number of materials, and thus boosting safe-by-design-based material development. Because of its profound implications for animal-free predictive toxicology, this work paves the way to a more efficient and hazard-free introduction of numerous new advanced materials into our lives.
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| 10. |
- Ménard, Delphine, et al.
(författare)
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Dynamic incorporation of specific lignin residues controls the biomechanics of the plant vasculature and its resilience to environmental changes
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Annan publikation (övrigt vetenskapligt/konstnärligt)abstract
- The accumulation of the cell wall polymer lignin in vascular cells enables long-distance water conduction and structural support in plants. Independently of the plant species, each different vascular cell type accumulates specific lignin amount and composition affecting both aromatic and aliphatic substitutions of its residues. However, the biological role of this conserved and specific lignin chemistry for each cell type remains unclear. Herein, we performed single cell analyses on plant vascular cell morphotypes to investigate the role of specific lignin composition for cellular function. We showed that distinct amounts and compositions of lignin accumulated in the different morphotypes of the sap conducting vascular cells. We discovered that lignin accumulates dynamically, increasing in quantity and changing composition, to fine-tune the cell wall mechanical properties of each conducting cell morphotype. Modification this lignin specificity impaired specifically the cell wall mechanical properties of each morphotype and consequently their capacity to optimally conduct water in normal but also to recover from drought conditions. Altogether, our findings provide the biological role of specific lignin chemistry in sap conducting cells, to dynamically adjust the hydraulic properties of each conducting cell during developmental and environmental constraints.
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