References of "Remacle, Françoise"
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See detailGlioblastoma cellular architectures are predicted through the characterization of two-cell interactions
Kravchenko-Balasha, Nataly; Wang, Jun; Remacle, Françoise ULg et al

in Proceedings of the National Academy of Sciences (2014), 111

To understand how pairwise cellular interactions influence cellular architectures, we measured the levels of functional proteins associated with EGF receptor (EGFR) signaling in pairs of U87EGFR variant ... [more ▼]

To understand how pairwise cellular interactions influence cellular architectures, we measured the levels of functional proteins associated with EGF receptor (EGFR) signaling in pairs of U87EGFR variant III oncogene receptor cells (U87EGFRvIII) at varying cell separations. Using a thermodynamics-derived approach we analyzed the cell-separation dependence of the signaling stability, and identified that the stable steady state of EGFR signaling exists when two U87EGFRvIII cells are separated by 80–100 μm. This distance range was verified as the characteristic intercellular separation within bulk cell cultures. EGFR protein network signaling coordination for the U87EGFRvIII system was lowest at the stable state and most similar to isolated cell signaling. Measurements of cultures of less tumorigenic U87PTEN cells were then used to correctly predict that stable EGFR signaling occurs for those cells at smaller cell–cell separations. The intimate relationship between functional protein levels and cellular architectures explains the scattered nature of U87EGFRvIII cells relative to U87PTEN cells in glioblastoma multiforme tumors. [less ▲]

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See detailAttoPhotoChemistry. Probing ultrafast electron dynamics by the induced nuclear motion: The prompt and delayed predissociation of N2
Muskatel, B. H.; Remacle, Françoise ULg; Levine, R. D.

in Chemical Physics Letters (2014), 601(0), 45-48

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See detailA full-adder based on reconfigurable DNA-hairpin inputs and DNAzyme computing modules, Edge article
Orbach, Ron; Wang, Fuan; Lioubashevski, Oleg et al

in Chemical Science (2014), 5(9), 3381-3387

In nature, post-transcriptional alternative splicing processes expand the proteome biodiversity, providing means to synthesize various protein isoforms. We describe the input-guided assembly of a DNAzyme ... [more ▼]

In nature, post-transcriptional alternative splicing processes expand the proteome biodiversity, providing means to synthesize various protein isoforms. We describe the input-guided assembly of a DNAzyme-based full-adder computing system, which mimics functions of the natural processes by increasing the diversity of logic elements by the reconfiguration of the inputs. The full-adder comprises the simultaneous operation of three inputs that yield two different output signals, acting as sum and carry bits. The DNAzyme-based full-adder system consists of a library of Mg2+-dependent DNAzyme subunits and their substrates that are modified by two different fluorophore/quencher pairs that encode the sum and carry outputs. The input-guided assembly of DNAzyme subunits, formed by three inputs composed of nucleic acid hairpin structures, leads to computing modules that yield the sum and carry outputs of the full-adder. In the presence of a single input the DNAzyme computing module yields the sum fluorescence output. In the presence of two of the inputs, the reconfiguration of the input structures proceeds, leading to an input-guided computing module that yields the carry fluorescence output. By introducing all the three inputs the sequential inter-input hybridization leads to the reconfiguration of the inputs into polymer wires. These include binding sites for two types of DNAzyme and their substrates leading to the carry and sum fluorescence outputs. The advantages of the simultaneous three-input operation of the full-adder and the possibilities to implement DNAzyme-based computing modules for cascading full-adders are discussed. [less ▲]

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See detailAtomistic account of structural and dynamical changes induced by small binders in the double helix of a short DNA
Fresch, Barbara ULg; Remacle, Françoise ULg

in Physical Chemistry Chemical Physics [=PCCP] (2014), 16

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See detailTuning the Properties of Pd Nanoclusters by Ligand Coatings: Electronic Structure Computations on Phosphine, Thiol, and Mixed PhosphineThiol Ligand Shells
Fresch, Barbara ULg; Remacle, Françoise ULg

in Journal of Physical Chemistry C (2014)

Tuning the properties of Palladium nanoparticles using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis ... [more ▼]

Tuning the properties of Palladium nanoparticles using different protecting ligand shells is an important step toward the application-orientated design of nanoparticles for nano-electronics and catalysis. We present a density functional theoretical characterization of Pd13 and Pd55 metal cores protected by only-thiol, only-phosphine and mixed phosphine-thiol ligand shells. We analyze the ligand contributions to the frontier orbitals and the charge redistribution between the ligand shell and the metal core and show that these properties control the values of the charging energy and the catalytic activity. The charge transfer character of the metal-ligand interaction is influenced by the presence of other ligands in the capping system indicating a cooperative effect in the ligand induced charge redistribution. Because of the interplay between the stabilization of the frontier orbital due to the contribution of the sulfur and the charge donation by the phosphine, the charging energy of the mixed phosphine-thiol protected cluster is larger than that of the only-phosphine and the only-thiol systems. The complementary point of view is adopted for rationalizing the catalytic properties of the clusters by analyzing the effect of the interaction with the metallic core on the properties of the ligand. The impact of solvation on the electronic structure of the ligand capped Pd13 cluster is investigated by including explicitly a layer of water molecules in the model system. [less ▲]

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See detailLigand and solvation effects on the structural and electronic properties of small gold clusters
Dufour, F.; Fresch, Barbara ULg; Durupthy, O. et al

in Journal of Physical Chemistry C: Nanomaterials, Interfaces, and Hard Matter (2014), 118(8), 4362

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See detailPump and probe of ultrafast charge reorganization in small peptides: A computational study through sudden ionizations
Kus, Tomasz ULg; Mignolet, Benoît ULg; Levine, R. D. et al

in Journal of Physical Chemistry A (2013), 117(40), 10513-10525

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See detailHot electron production and diffuse excited states in C70, C82, and Sc3N@C80 characterized by angular-resolved photoelectron spectroscopy
Johansson, J. Olof; Bohl, Elvira; Henderson, Gordon G. et al

in Journal of Chemical Physics (2013), 139

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See detailProbing Rapidly-Ionizing Super-Atom Molecular Orbitals in C60: A Computational and Femtosecond Photoelectron Spectroscopy Study
Mignolet, Benoît ULg; Johansson, Olof; Campbell, Eleanor E. B. et al

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2013)

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See detailImaging Orbitals by Ionization or Electron Attachment: The Role of Dyson Orbitals
Mignolet, Benoît ULg; Kus, Tomasz ULg; Remacle, Françoise ULg

in Joachim, C.; Grill, L. (Eds.) Imaging and Manipulating Molecular Orbitals (2013)

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See detailMolecular decision trees realized by ultrafast electronic spectroscopy
Fresch, Barbara ULg; Hiluf, Dawit; Collini, Elisabetta et al

in Proceedings of the National Academy of Sciences (2013), 110(43), 17183-17188

The outcome of a light–matter interaction depends on both the state of matter and the state of light. It is thus a natural setting for implementing bilinear classical logic. A description of the state of ... [more ▼]

The outcome of a light–matter interaction depends on both the state of matter and the state of light. It is thus a natural setting for implementing bilinear classical logic. A description of the state of a time-varying system requires measuring an (ideally complete) set of time-dependent observables. Typically, this is prohibitive, but in weak-field spectroscopy we can move toward this goal because only a finite number of levels are accessible. Recent progress in nonlinear spectroscopies means that nontrivial measurements can be implemented and thereby give rise to interesting logic schemes where the outputs are functions of the observables. Lie algebra offers a natural tool for generating the outcome of the bilinear light–matter interaction. We show how to synthesize these ideas by explicitly discussing three-photon spectroscopy of a bichromophoric molecule for which there are four accessible states. Switching logic would use the on–off occupancies of these four states as outcomes. Here, we explore the use of all 16 observables that define the time-evolving state of the bichromophoric system. The bilinear laser–system interaction with the three pulses of the setup of a 2D photon echo spectroscopy experiment can be used to generate a rich parallel logic that corresponds to the implementation of a molecular decision tree. Our simulations allow relaxation by weak coupling to the environment, which adds to the complexity of the logic operations. [less ▲]

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See detailFree Energy Rhythms in Saccharomyces cerevisiae: A Dynamic Perspective with Implications for Ribosomal Biogenesis
Gross, A.; Li, Caroline M.; Remacle, Françoise ULg et al

in Biochemistry (2013), 52(9), 1641-1648

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See detailHypoxia induces a phase transition within a kinase signaling network in cancer cells
Wei, Wei; Shia, Qihui; Remacle, Françoise ULg et al

in Proc. Natl. Acad. Sci. USA (2013)

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See detailmiRNA and mRNA cancer signatures determined by analysis of expression levels in large cohorts of patients
Zadran, Sohila; Remacle, Françoise ULg; Levine, R. D.

in Proceedings of the National Academy of Sciences (2013), 110(47), 19160-19165

Toward identifying a cancer-specific gene signature we applied surprisal analysis to the RNAs expression behavior for a large cohort of breast, lung, ovarian, and prostate carcinoma patients. We ... [more ▼]

Toward identifying a cancer-specific gene signature we applied surprisal analysis to the RNAs expression behavior for a large cohort of breast, lung, ovarian, and prostate carcinoma patients. We characterize the cancer phenotypic state as a shared response of a set of mRNA or microRNAs (miRNAs) in cancer patients versus noncancer controls. The resulting signature is robust with respect to individual patient variability and distinguishes with high fidelity between cancer and noncancer patients. The mRNAs and miRNAs that are implicated in the signature are correlated and are known to contribute to the regulation of cancer-signaling pathways. The miRNA and mRNA networks are common to the noncancer and cancer patients, but the disease modulates the strength of the connectivities. Furthermore, we experimentally assessed the cancer-specific signatures as possible therapeutic targets. Specifically we restructured a single dominant connectivity in the cancer-specific gene network in vitro. We find a deflection from the cancer phenotype, significantly reducing cancer cell proliferation and altering cancer cellular physiology. Our approach is grounded in thermodynamics augmented by information theory. The thermodynamic reasoning is demonstrated to ensure that the derived signature is bias-free and shows that the most significant redistribution of free energy occurs in programming a system between the noncancer and cancer states. This paper introduces a platform that can elucidate miRNA and mRNA behavior on a systems level and provides a comprehensive systematic view of both the energetics of the expression levels of RNAs and of their changes during tumorigenicity. [less ▲]

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See detailLocalized electron dynamics in attosecond-pulse-excited molecular systems: Probing the time-dependent electron density by sudden photoionization
Mignolet, Benoît ULg; Levine, Raphael; Remacle, Françoise ULg

in Physical Review. A (2012)

Ultrafast UV excitation can prepare a nonstationary coherent superposition of molecular electronic states. The purely electronic dynamics before the onset of nuclear motion can be probed by a sudden XUV ... [more ▼]

Ultrafast UV excitation can prepare a nonstationary coherent superposition of molecular electronic states. The purely electronic dynamics before the onset of nuclear motion can be probed by a sudden XUV ionization of the electronic wave packet. Dynamical computations at the many-electron level on the LiH and 1-azabicyclo[3.3.3]undecane (C10H19N) molecules showthat molecular frame photoelectron angular distributions reflect the spatial localization and undulations of the electronic coherent superposition accessed by the initial ultrafast UV excitation. The sudden ionization is sensitive to interference effects. [less ▲]

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