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See detailStructural properties of poly(N-isopropyl acrylamide)-based systems
Philipp, Martine UL; Magerl, D.; Aleksandrova, Ralitsa UL et al

Poster (2011, October 10)

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See detailStructural Relaxations in the Rotator Phase of N-Eicosane
Di Giambattista, Carlo UL

Doctoral thesis (2015)

We present relaxations of the heat capacity of the n-alkane n-eicosane (C20H42) in the metastable rotator phase. These relaxations are not connected to melting but rather to structural changes. A ... [more ▼]

We present relaxations of the heat capacity of the n-alkane n-eicosane (C20H42) in the metastable rotator phase. These relaxations are not connected to melting but rather to structural changes. A comparative study of the relaxation times with calorimetry in the time and frequency domain shows a slowing down of the dynamics on approaching the melting temperature of the rotator phase. Relaxation behaviour is also observed in the lattice structure by investigations with X-ray diffraction. It is shown that the angular position of the two most relevant X-ray lines relaxes on different time scales. One of these two relaxations can be related to the relaxations found in calorimetry. The relaxing behaviour is discussed in the framework of conformational defect formation and compared to known phenomena in literature. [less ▲]

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See detailStructural requirements of the interleukin-6 signal transducer gp130 for its interaction with Janus kinase 1: the receptor is crucial for kinase activation
Haan, Claude UL; Heinrich, P. C.; Behrmann, Iris UL

in Biochemical Journal (2001), 361(Pt 1), 105-11

We analysed the interaction of gp130, the common signal-transducing receptor chain of interleukin (IL)-6 type cytokines, with Jak1, the Janus family kinase which is crucial for signal transduction of this ... [more ▼]

We analysed the interaction of gp130, the common signal-transducing receptor chain of interleukin (IL)-6 type cytokines, with Jak1, the Janus family kinase which is crucial for signal transduction of this group of cytokines. With a truncated chimaeric IL-5Rbeta-gp130 receptor expressed in COS-7 cells, we show that the membrane-proximal 69 amino acids are sufficient to mediate Jak1 binding and activation. Deletion of box2 drastically reduced binding of endogenous, but not of overexpressed, Jak1. Several point mutations in the membrane-proximal region of gp130 (W652A, P671/P672A, F676A, Y683F, where W, A, P, F and Y are tryptophan, alanine, proline, phenylalanine and tyrosine) did not affect Jak1 association. However, stimulation of chimaeric receptors with the mutations P671/P672A and F676A in the interbox1/box2 region resulted in a reduced activation of STAT (signal transducer and activator of transcription) transcription factors. Most importantly, signalling by the receptor with the box1 mutation W652A was totally abrogated. Although this mutation did not affect Jak1 association, stimulation-dependent phosphorylation of Jak1 was prevented. The W652 mutation acts dominantly, since no signalling occured even when only a single cytoplasmic chain of a gp130 dimer contained the mutation. Our data demonstrate that the mere proximity of Jaks in an activated receptor complex is not sufficient to mediate their activation. Rather, it seems that parts of the receptor, including the box1 region, are involved in positioning Jaks correctly so that ligand-induced receptor dimerization and reorientation can lead to their mutual activation and subsequently to downstream signalling events. [less ▲]

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See detailStructural Transition in a Fluid of Spheroids: A Low-Density Vestige of Jamming
Cohen, A. P.; Dorosz, S.; Schofield, A. B. et al

in Physical Review Letters (2016), 116(9),

A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their ... [more ▼]

A thermodynamically equilibrated fluid of hard spheroids is a simple model of liquid matter. In this model, the coupling between the rotational degrees of freedom of the constituent particles and their translations may be switched off by a continuous deformation of a spheroid of aspect ratio t into a sphere (t=1). We demonstrate, by experiments, theory, and computer simulations, that dramatic nonanalytic changes in structure and thermodynamics of the fluids take place, as the coupling between rotations and translations is made to vanish. This nonanalyticity, reminiscent of a second-order liquid-liquid phase transition, is not a trivial consequence of the shape of an individual particle. Rather, free volume considerations relate the observed transition to a similar nonanalyticity at t=1 in structural properties of jammed granular ellipsoids. This observation suggests a deep connection to exist between the physics of jamming and the thermodynamics of simple fluids. © 2016 American Physical Society. [less ▲]

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See detailStructure and energetics of benzene adsorbed on transition-metal surfaces: density-functional theory with van der Waals interactions including collective substrate response
Liu, Wei; Ruiz, Victor G.; Zhang, Guo-Xu et al

in NEW JOURNAL OF PHYSICS (2013), 15

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a ... [more ▼]

The adsorption of benzene on metal surfaces is an important benchmark system for hybrid inorganic/organic interfaces. The reliable determination of the interface geometry and binding energy presents a significant challenge for both theory and experiment. Using the Perdew-Burke-Ernzerhof (PBE), PBE+vdW (van der Waals) and the recently developed PBE+vdW(surf) (density-functional theory with vdW interactions that include the collective electronic response of the substrate) methods, we calculated the structures and energetics for benzene on transition-metal surfaces: Cu, Ag, Au, Pd, Pt, Rh and Ir. Our calculations demonstrate that vdW interactions increase the binding energy by more than 0.70 eV for physisorbed systems (Cu, Ag and Au) and by an even larger amount for strongly bound systems (Pd, Pt, Rh and Ir). The collective response of the substrate electrons captured via the vdW(surf) method plays a significant role for most substrates shortening the equilibrium distance by 0.25 angstrom for Cu and decreasing the binding energy by 0.27 eV for Rh. The reliability of our results is assessed by comparison with calculations using the random-phase approximation including renormalized single excitations and the experimental data from temperature-programmed desorption microcalorimetry measurements and low-energy electron diffraction. [less ▲]

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See detailStructure and formation of synthetic hemozoin: Insights from first-principles calculations
Marom, N.; Tkatchenko, Alexandre UL; Kapishnikov, S. et al

in Crystal Growth and Design (2011), 11(8), 3332-3341

Malaria, an infectious disease once considered eradicated, has reemerged in recent years, primarily due to parasite resistance to commonly used synthetic antimalarial drugs. These drugs act by inhibiting ... [more ▼]

Malaria, an infectious disease once considered eradicated, has reemerged in recent years, primarily due to parasite resistance to commonly used synthetic antimalarial drugs. These drugs act by inhibiting crystallization of the malaria pigment, hemozoin (HZ). Thus, there is a vital need for understanding the process of HZ nucleation. In a companion paper, the pseudopolymorphic behavior of β-hematin, the synthetic form of HZ, has been characterized by X-ray diffraction (XRD) (Straasø, T.; Kapishnikov, S.; Kato, K.; Takata, M.; Als-Nielsen, J.; Leiserowitz, L.Cryst. Growth Des. 2011, 11, DOI: 10.1021/cg200410b). Here, we employ van der Waals (vdW)-corrected density functional theory (DFT) to study the two β-hematin crystal structures and their repeat unit, a heme dimer. We find that vdW interactions play a major role in the binding of the heme dimer and the β-hematin crystal. In addition, accounting for the periodic nature of the system is essential to obtaining the correct geometry of the heme dimer, which is affected by vdW interactions with adjacent dimers in the β-hematin crystal. The different stereoisomers of the heme dimer and their molecular crystals are close in energy, which is consistent with pseudopolymorphism in β-hematin, in agreement with recent XRD experiments. Finally, we use our results to comment on β-hematin crystallization mechanisms. This work demonstrates the viability of vdW-corrected DFT as a tool for gaining valuable insight into pertinent problems involving biological systems. © 2011 American Chemical Society. [less ▲]

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See detailStructure and Stability of Molecular Crystals with Many-Body Dispersion-Inclusive Density Functional Tight Binding
Mortazavi, Majid; Brandenburg, Jan Gerit; Maurer, Reinhard J. et al

in Journal of Physical Chemistry Letters (2018), 9

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic ... [more ▼]

Accurate prediction of structure and stability of molecular crystals is crucial in materials science and requires reliable modeling of long-range dispersion interactions. Semiempirical electronic structure methods are computationally more efficient than their ab initio counterparts, allowing structure sampling with significant speedups. We combine the Tkatchenko−Scheffler van der Waals method (TS) and the many-body dispersion method (MBD) with third-order density functional tight-binding (DFTB3) via a charge population-based method. We find an overall good performance for the X23 benchmark database of molecular crystals, despite an underestimation of crystal volume that can be traced to the DFTB parametrization. We achieve accurate lattice energy predictions with DFT+MBD energetics on top of vdW-inclusive DFTB3 structures, resulting in a speedup of up to 3000 times compared with a full DFT treatment. This suggests that vdW-inclusive DFTB3 can serve as a viable structural prescreening tool in crystal structure prediction. [less ▲]

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See detailLa structure des représentations sociales de la médiation au Luxembourg et en Europe
Houssemand, Claude UL

Scientific Conference (2007, May)

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See detailStructure diagram of binary Lennard-Jones clusters
Mravlak, Marko UL; Kister, Thomas; Kraus, Tobias et al

in Journal of Chemical Physics (2016), 145(024302),

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and ... [more ▼]

We analyze the structure diagram for binary clusters of Lennard-Jones particles by means of a global optimization approach for a large range of cluster sizes, compositions, and interaction energies and present a publicly accessible database of 180 000 minimal energy structures (http://softmattertheory. lu/clusters.html). We identify a variety of structures such as core-shell clusters, Janus clusters, and clusters in which the minority species is located at the vertices of icosahedra. Such clusters can be synthesized from nanoparticles in agglomeration experiments and used as building blocks in colloidal molecules or crystals. We discuss the factors that determine the formation of clusters with specific structures. [less ▲]

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See detailStructure factor of interacting one-dimensional helical systems
Gangadharaiah, Suhas; Schmidt, Thomas UL; Loss, Daniel

in Phys. Rev. B (2014), 89

We calculate the dynamical structure factor $S(q,\omega)$ of a weakly interacting helical edge state in the presence of a magnetic field $B$. The latter opens a gap of width $2B$ in the single-particle ... [more ▼]

We calculate the dynamical structure factor $S(q,\omega)$ of a weakly interacting helical edge state in the presence of a magnetic field $B$. The latter opens a gap of width $2B$ in the single-particle spectrum, which becomes strongly nonlinear near the Dirac point. For chemical potentials $|\mu|>B$, the system then behaves as a nonlinear helical Luttinger liquid, and a mobile-impurity analysis reveals power-law singularities in $S(q,\omega)$ which depend on the interaction strength as well as on the spin texture of the edge states. For $|\mu|<B$, the low-energy excitations are gapped, and we determine $S(q,\omega)$ by using an analogy to exciton physics. [less ▲]

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See detailStructure functions and minimal path sets
Marichal, Jean-Luc UL

in IEEE Transactions on Reliability (2016), 65(2), 763-768

In this short note we give and discuss a general multilinear expression of the structure function of an arbitrary semicoherent system in terms of its minimal path and cut sets. We also examine the link ... [more ▼]

In this short note we give and discuss a general multilinear expression of the structure function of an arbitrary semicoherent system in terms of its minimal path and cut sets. We also examine the link between the number of minimal path and cut sets consisting of one or two components and the concept of structure signature of the system. [less ▲]

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See detailThe structure of academic self-concepts revisited: The nested Marsh/Shavelson model
Brunner, Martin UL; Keller, Ulrich UL; Dierendonck, Christophe UL et al

in Journal of Educational Psychology (2010), 102(4), 964-981

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See detailStructure of Hecke algebras of modular forms modulo $p$
Deo, Shaunak UL

in Algebra & Number Theory (2017), 11(1), 1-38

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See detailThe structure of Poisson cohomology
Ammar, Mourad UL; Kass, Guy; Poncin, Norbert UL

in Universitatis Iagellonicae Acta Mathematica (2009)

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See detailStructure of RdxA--an oxygen-insensitive nitroreductase essential for metronidazole activation in Helicobacter pylori.
Martinez-Julvez, Marta; Rojas, Adriana L.; Olekhnovich, Igor et al

in The FEBS journal (2012), 279(23), 4306-17

The RdxA oxygen-insensitive nitroreductase of the human gastric pathogen Helicobacter pylori is responsible for the susceptibility of this organism to the redox active prodrug metronidazole [2-(2-methyl-5 ... [more ▼]

The RdxA oxygen-insensitive nitroreductase of the human gastric pathogen Helicobacter pylori is responsible for the susceptibility of this organism to the redox active prodrug metronidazole [2-(2-methyl-5-nitro-1H-imidazol-1-yl)ethanol]. Loss-of-function mutations in rdxA are primarily responsible for resistance to this therapeutic. RdxA exhibits potent NADPH oxidase activity under aerobic conditions and metronidazole reductase activity under strictly anaerobic conditions. In the present study, we report the crystal structure of RdxA, which is a homodimer exhibiting domain swapping and containing two molecules of FMN bound at the dimer interface. We have found a gap between the side chain of Tyr47 and the isoalloxazine ring of FMN that appears to be appropriate for substrate binding. The structure does not include residues 97-128, which correspond to a locally unstable part of the NTR from Escherichia coli, and might be involved in cofactor binding. Comparison of H. pylori RdxA with other oxidoreductases of known structure suggests that RdxA may belong to a new subgroup of oxidoreductases in which a cysteine side chain close to the FMN cofactor could be involved in the reductive activity. In this respect, the mutation of C159 to A or S (C159A/S) has resulted in a loss of metronidazole reductase activity but not NADPH oxidase activity. The RdxA structure enables the interpretation of the many loss-of-function mutations described previously, including those affecting C159, a residue whose interaction with FMN is required for the nitroreduction of metronidazole. The present studies provide unique insights into the redox behaviour of the flavin in this key enzyme for metronidazole activation, including a potential use in gene therapy. DATABASE: Structural data have been deposited in the Protein Data Bank under accession number 3QDL. [less ▲]

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See detailThe structure of the Helicobacter pylori ferric uptake regulator Fur reveals three functional metal binding sites.
Dian, Cyril; Vitale, Sylvia; Leonard, Gordon A. et al

in Molecular microbiology (2011), 79(5), 1260-75

Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for ... [more ▼]

Fur, the ferric uptake regulator, is a transcription factor that controls iron metabolism in bacteria. Binding of ferrous iron to Fur triggers a conformational change that activates the protein for binding to specific DNA sequences named Fur boxes. In Helicobacter pylori, HpFur is involved in acid response and is important for gastric colonization in model animals. Here we present the crystal structure of a functionally active HpFur mutant (HpFur2M; C78S-C150S) bound to zinc. Although its fold is similar to that of other Fur and Fur-like proteins, the crystal structure of HpFur reveals a unique structured N-terminal extension and an unusual C-terminal helix. The structure also shows three metal binding sites: S1 the structural ZnS(4) site previously characterized biochemically in HpFur and the two zinc sites identified in other Fur proteins. Site-directed mutagenesis and spectroscopy analyses of purified wild-type HpFur and various mutants show that the two metal binding sites common to other Fur proteins can be also metallated by cobalt. DNA protection and circular dichroism experiments demonstrate that, while these two sites influence the affinity of HpFur for DNA, only one is absolutely required for DNA binding and could be responsible for the conformational changes of Fur upon metal binding while the other is a secondary site. [less ▲]

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See detailStructure of the human APO-1 gene
Behrmann, Iris UL; Walczak, H.; Krammer, P. H.

in European Journal of Immunology (1995), 24(12), 3057-62

APO-1/Fas (CD95) is a type 1 transmembrane protein that belongs to the tumor necrosis factor/nerve growth factor receptor family characterized by cysteine-rich extracellular domains. Cross-linking of APO ... [more ▼]

APO-1/Fas (CD95) is a type 1 transmembrane protein that belongs to the tumor necrosis factor/nerve growth factor receptor family characterized by cysteine-rich extracellular domains. Cross-linking of APO-1 mediates apoptosis in a variety of cells. In the present study we report the isolation and characterization of the human APO-1 gene spanning approximately 25 kb of human chromosome 10. The gene consists of nine exons (25 bp to > 1.44 kb) separated by eight introns (152 bp to approximately 12 kb). The boundaries of exon 2 to 5 encoding the extracellular region do not match the boundaries of the three APO-1 protein subdomains. Exon structure and functional protein domains correspond for exon 6 encoding the transmembrane region and for exon 9 encoding the "death domain". By a polymerase chain reaction-based approach we localized major transcriptional start sites in human spleen cells 77 and 73 nucleotides upstream of the translation initiation codon of the human APO-1 gene. Minor initiation sites were found at positions -128, -111, -91, and -74. The 5' flanking sequence of the human APO-1 gene is GC rich, contains a high number of CpG dinucleotides and lacks a consensus TATA box. Consensus binding sites for the transcription factors Sp1, AP-1, AP-2, GAF, NF-kappa B, and NF-AT were found. The elucidation of the human APO-1 gene structure will facilitate the study of its involvement in various diseases such as in autoimmunity. [less ▲]

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