| 1. |
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- 2019
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Tidskriftsartikel (refereegranskat)
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| 2. |
- Berndt, Sonja I., et al.
(författare)
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Genome-wide meta-analysis identifies 11 new loci for anthropometric traits and provides insights into genetic architecture
- 2013
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Ingår i: Nature Genetics. - : Springer Science and Business Media LLC. - 1061-4036 .- 1546-1718. ; 45:5, s. 501-U69
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Tidskriftsartikel (refereegranskat)abstract
- Approaches exploiting trait distribution extremes may be used to identify loci associated with common traits, but it is unknown whether these loci are generalizable to the broader population. In a genome-wide search for loci associated with the upper versus the lower 5th percentiles of body mass index, height and waist-to-hip ratio, as well as clinical classes of obesity, including up to 263,407 individuals of European ancestry, we identified 4 new loci (IGFBP4, H6PD, RSRC1 and PPP2R2A) influencing height detected in the distribution tails and 7 new loci (HNF4G, RPTOR, GNAT2, MRPS33P4, ADCY9, HS6ST3 and ZZZ3) for clinical classes of obesity. Further, we find a large overlap in genetic structure and the distribution of variants between traits based on extremes and the general population and little etiological heterogeneity between obesity subgroups.
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| 3. |
- Hirschmann, Frank, et al.
(författare)
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Effects of flexibility in coarse-grained models for bovine serum albumin and immunoglobulin G
- 2023
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Ingår i: Journal of Chemical Physics. - : American Institute of Physics (AIP). - 0021-9606 .- 1089-7690. ; 158:8
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Tidskriftsartikel (refereegranskat)abstract
- We construct a coarse-grained, structure-based, low-resolution, 6-bead flexible model of bovine serum albumin (BSA, PDB: 4F5S), which is a popular example of a globular protein in biophysical research. The model is obtained via direct Boltzmann inversion using all-atom simulations of a single molecule, and its particular form is selected from a large pool of 6-bead coarse-grained models using two suitable metrics that quantify the agreement in the distribution of collective coordinates between all-atom and coarse-grained Brownian dynamics simulations of solutions in the dilute limit. For immunoglobulin G (IgG), a similar structure-based 12-bead model has been introduced in the literature [Chaudhri et al., J. Phys. Chem. B 116, 8045 (2012)] and is employed here to compare findings for the compact BSA molecule and the more anisotropic IgG molecule. We define several modified coarse-grained models of BSA and IgG, which differ in their internal constraints and thus account for a variation of flexibility. We study denser solutions of the coarse-grained models with purely repulsive molecules (achievable by suitable salt conditions) and address the effect of packing and flexibility on dynamic and static behavior. Translational and rotational self-diffusivity is enhanced for more elastic models. Finally, we discuss a number of effective sphere sizes for the BSA molecule, which can be defined from its static and dynamic properties. Here, it is found that the effective sphere diameters lie between 4.9 and 6.1 nm, corresponding to a relative spread of about ±10% around a mean of 5.5 nm.
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| 4. |
- Sohmen, Benedikt, et al.
(författare)
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The Onset of Molecule-Spanning Dynamics in Heat Shock Protein Hsp90
- 2023
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Ingår i: Advanced Science. - : John Wiley & Sons. - 2198-3844. ; 10:36
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Tidskriftsartikel (refereegranskat)abstract
- Protein dynamics have been investigated on a wide range of time scales. Nano- and picosecond dynamics have been assigned to local fluctuations, while slower dynamics have been attributed to larger conformational changes. However, it is largely unknown how fast (local) fluctuations can lead to slow global (allosteric) changes. Here, fast molecule-spanning dynamics on the 100 to 200 ns time scale in the heat shock protein 90 (Hsp90) are shown. Global real-space movements are assigned to dynamic modes on this time scale, which is possible by a combination of single-molecule fluorescence, quasi-elastic neutron scattering and all-atom molecular dynamics (MD) simulations. The time scale of these dynamic modes depends on the conformational state of the Hsp90 dimer. In addition, the dynamic modes are affected to various degrees by Sba1, a co-chaperone of Hsp90, depending on the location within Hsp90, which is in very good agreement with MD simulations. Altogether, this data is best described by fast molecule-spanning dynamics, which precede larger conformational changes in Hsp90 and might be the molecular basis for allostery. This integrative approach provides comprehensive insights into molecule-spanning dynamics on the nanosecond time scale for a multi-domain protein.
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| 5. |
- Ahlawat, Paramvir, et al.
(författare)
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A combined molecular dynamics and experimental study of two-step process enabling low-temperature formation of phase-pure alpha-FAPbI3
- 2021
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Ingår i: Science Advances. - : American Association for the Advancement of Science (AAAS). - 2375-2548. ; 7:17
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Tidskriftsartikel (refereegranskat)abstract
- It is well established that the lack of understanding the crystallization process in a two-step sequential deposition has a direct impact on efficiency, stability, and reproducibility of perovskite solar cells. Here, we try to understand the solid-solid phase transition occurring during the two-step sequential deposition of methylammonium lead iodide and formamidinium lead iodide. Using metadynamics, x-ray diffraction, and Raman spectroscopy, we reveal the microscopic details of this process. We find that the formation of perovskite proceeds through intermediate structures and report polymorphs found for methylammonium lead iodide and formamidinium lead iodide. From simulations, we discover a possible crystallization pathway for the highly efficient metastable alpha phase of formamidinium lead iodide. Guided by these simulations, we perform experiments that result in the low-temperature crystallization of phase-pure alpha-formamidinium lead iodide.
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| 6. |
- Banerjee, R., et al.
(författare)
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Structure and Morphology of Organic Semiconductor-Nanoparticle Hybrids Prepared by Soft Deposition
- 2015
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Ingår i: The Journal of Physical Chemistry C. - : American Chemical Society (ACS). - 1932-7447 .- 1932-7455. ; 119:9, s. 5225-5237
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Tidskriftsartikel (refereegranskat)abstract
- We present an extensive structural analysis of hybrid architectures prepared by the soft incorporation of gold nanoparticles (AuNPs) within an organic semiconductor matrix of diindenoperylene (DIP). Such soft or noninvasive deposition of nanoparticles within organic semiconducting host matrices not only minimizes the influence of the deposition process on the order and properties of the organic host molecules, but also offers additional control in the process of incorporation. The hybrid structures were characterized by X-ray scattering techniques including grazing incidence small angle X-ray scattering (GISAXS), grazing incidence X-ray diffraction (GIXD), X-ray reflectivity (XRR), and complemented by atomic force microscopy (AFM), photoluminescence (PL) spectroscopy, and transmission electron microscopy (TEM) measurements. We show that different strategies of incorporating the nanoparticles in the host matrix lead to drastically different structure and morphologies. Particularly remarkable is the morphological change observed in the matrix of DIP as well as the AuNPs due to the influence of organic solvents, as evidenced by TEM tomography measurements, which revealed the exact location of the AuNPs within the organic host. It is also demonstrated that AuNPs can be successfully used as tunable templates for the growth of the organic semiconductors with desired island sizes and distances.
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| 7. |
- Barrat, Jean-Louis, et al.
(författare)
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Soft matter roadmap
- 2024
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Ingår i: Journal of Physics. - : Institute of Physics Publishing (IOPP). - 2515-7639. ; 7:1
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Forskningsöversikt (refereegranskat)abstract
- Soft materials are usually defined as materials made of mesoscopic entities, often self-organised, sensitive to thermal fluctuations and to weak perturbations. Archetypal examples are colloids, polymers, amphiphiles, liquid crystals, foams. The importance of soft materials in everyday commodity products, as well as in technological applications, is enormous, and controlling or improving their properties is the focus of many efforts. From a fundamental perspective, the possibility of manipulating soft material properties, by tuning interactions between constituents and by applying external perturbations, gives rise to an almost unlimited variety in physical properties. Together with the relative ease to observe and characterise them, this renders soft matter systems powerful model systems to investigate statistical physics phenomena, many of them relevant as well to hard condensed matter systems. Understanding the emerging properties from mesoscale constituents still poses enormous challenges, which have stimulated a wealth of new experimental approaches, including the synthesis of new systems with, e.g. tailored self-assembling properties, or novel experimental techniques in imaging, scattering or rheology. Theoretical and numerical methods, and coarse-grained models, have become central to predict physical properties of soft materials, while computational approaches that also use machine learning tools are playing a progressively major role in many investigations. This Roadmap intends to give a broad overview of recent and possible future activities in the field of soft materials, with experts covering various developments and challenges in material synthesis and characterisation, instrumental, simulation and theoretical methods as well as general concepts.
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| 8. |
- Beck, Christian, et al.
(författare)
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Following Protein Dynamics in Real Time during Crystallization
- 2019
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Ingår i: Crystal Growth and Design. - : American Chemical Society (ACS). - 1528-7483 .- 1528-7505. ; , s. 7036-7045
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Tidskriftsartikel (refereegranskat)abstract
- The process of protein crystallization from aqueous protein solutions is still insufficiently understood. During macroscopic crystal formation, occurring often on time scales from a few hours to several days, protein dynamics evolves on the molecular level. Here, we present a proof of concept and a framework to observe this evolving diffusive dynamics on the pico- to nanosecond time scale, associated with cluster or precursor formation that ultimately results in emerging crystals. We investigated the model system of the protein β-lactoglobulin in D2O in the presence of ZnCl2, which induces crystallization by electrostatic bridges. First, the structural changes occurring during crystallization were followed by small-angle neutron scattering. Furthermore, we employed neutron backscattering and spin-echo spectroscopy to measure the ensemble-averaged self- and collective diffusion on nanosecond time scales of protein solutions with a kinetic time resolution on the order of 15 min. The experiments provide information on the increasing number fraction of immobilized proteins as well as on the diffusive motion of unbound proteins in an increasingly depleted phase. Simultaneously, information on the internal dynamics of the proteins is obtained.
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| 9. |
- Beck, Christian, et al.
(författare)
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Nanosecond Tracer Diffusion as a Probe of the Solution Structure and Molecular Mobility of Protein Assemblies: The Case of Ovalbumin
- 2018
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Ingår i: The Journal of Physical Chemistry Part B. - : American Chemical Society (ACS). - 1520-5207 .- 1520-6106. ; 122:35, s. 8343-8343
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Tidskriftsartikel (refereegranskat)abstract
- Protein diffusion is not only an important process ensuring biological function but can also be used as a probe to obtain information on structural properties of protein assemblies in liquid solutions. Here, we explore the oligomerization state of ovalbumin at high protein concentrations by means of its short-time self-diffusion. We employ high-resolution incoherent quasielastic neutron scattering to access the self-diffusion on nanosecond timescales, on which interparticle contacts are not altered. Our results indicate that ovalbumin in aqueous (D2O) solutions occurs in increasingly large assemblies of its monomeric subunits with rising protein concentration. It changes from nearly monomeric toward dimeric and ultimately larger than tetrameric complexes. Simultaneously, we access information on the internal molecular mobility of ovalbumin on the nanometer length scale and compare it with results obtained for bovine serum albumin, immunoglobulin, and β-lactoglobulin.
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| 10. |
- Beck, Christian, et al.
(författare)
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Neutron spectroscopy on protein solutions employing backscattering with an increased energy range
- 2019
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Ingår i: Physica B: Condensed Matter. - : Elsevier BV. - 0921-4526. ; 562, s. 31-35
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Tidskriftsartikel (refereegranskat)abstract
- Novel cold neutron backscattering spectrometers contribute substantially to the understanding of the diffusive dynamics of proteins in dense aqueous suspensions. Such suspensions are fundamentally interesting for instance in terms of the so-called macromolecular crowding, protein cluster formation, gelation, and self-assembly. Notably, backscattering spectrometers with the highest flux can simultaneously access the center-of-mass diffusion of the proteins and the superimposed internal molecular diffusive motions. The nearly complete absence of protein-protein collisions on the accessible nanosecond observation time scale even in dense protein suspensions implies that neutron backscattering accesses the so-called short-time limit for the center-of-mass diffusion. This limit is particularly interesting in terms of a theoretical understanding by concepts from colloid physics. Here we briefly review recent progress in studying protein dynamics achieved with the latest generation of backscattering spectrometers. We illustrate this progress by the first data from a protein solution using the backscattering-and-time-of-flight option BATS on IN16B at the ILL and we outline future perspectives.
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