References of "Remacle, Françoise"
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See detailMetabolomic analysis of the green microalga Chlamydomonasreinhardtii cultivated under day/night conditions
Willamme, Rémi ULg; Alsafra, Zouheir; Arumugam, Rameshkumar et al

in Journal of Biotechnology (2015)

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See detailCharge Redistribution Effects on the UV-VIS Spectra of Small Ligated Gold Clusters: a Computational Study
Lugo Preciado, Jesus Gustavo ULg; Schwanen, Valérie ULg; Fresch, Barbara ULg et al

in Journal of Physical Chemistry C (2015), 119(20), 10969-10980

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See detailParallel and Multivalued Logic by the Two-Dimensional Photon-Echo Response of a Rhodamine–DNA Complex
Fresch, Barbara ULg; Cipolloni, Marco; Yan, Tian-Min ULg et al

in Journal of Physical Chemistry Letters (2015), 6

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See detailCoherent Electronic Wave Packet Motion in ${\mathrm{C}}_{60}$ Controlled by the Waveform and Polarization of Few-Cycle Laser Fields
Li, H.; Mignolet, Benoît ULg; Wachter, G. et al

in Physical Review Letters (2015), 114(12), 123004

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See detailComputational benchmarking for ultrafast electron dynamics: wavefunction methods vs density functional theory
Oliveira, Micael J. T.; Mignolet, Benoît ULg; Kus, Tomasz et al

in Journal of Chemical Theory and Computation (2015), 11

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See detailTernary DNA computing using 3 x 3 multiplication matrices
Orbach, Ron; Lilienthal, Sivan; Klein, Michael et al

in Chemical Science (2015), 6

Non-Boolean computations implementing operations on multi-valued variables beyond base 2 allow enhanced computational complexity. We introduce DNA as a functional material for ternary computing, and in ... [more ▼]

Non-Boolean computations implementing operations on multi-valued variables beyond base 2 allow enhanced computational complexity. We introduce DNA as a functional material for ternary computing, and in particular demonstrate the use of three-valued oligonucleotide inputs to construct a 3 [times] 3 multiplication table. The system consists of two three-valued inputs of -1; 0; +1 and a fluorophore/quencher functional hairpin acting as computational and reporter module. The interaction of the computational hairpin module with the different values of the inputs yields a 3 [times] 3 multiplication matrix consisting of nine nanostructures that are read out by three distinct fluorescence intensities. By combining three different hairpin computational modules, each modified with a different fluorophore/quencher pair, and using different sets of inputs, the parallel operation of three multiplication tables is demonstrated. [less ▲]

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See detailAn atomistic view of DNA dynamics and its interaction with small binders: insights from Molecular Dynamics and Principal Component Analysis
Fresch, Barbara ULg; Remacle, Françoise ULg

in Joachim, Christian (Ed.) Advances in Atom and Single Molecule Machines (2015)

DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and molecular ... [more ▼]

DNA oligomers are promising building blocks for the development of bottom-up nano-devices and molecular logic machines. To control and exploit their unique capabilities of self-assembling and molecular recognition a deep understanding of their dynamical properties is essential. We theoretically investigate the dynamics of a DNA dodecamer and its complexes with two common ligands, Hoechst33258 and the ethidium cation, by means of classical Molecular Dynamics (MD) simulations and Principal Component Analysis (PCA). We study the structural relation between the flexibility of the double helix and the binding process. The dynamics of a terminal base pair unbinding is also analysed as an example of process that involves multiple energy minima in the underlying free energy landscape. [less ▲]

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See detailCharge Migration in the Bifunctional PENNA Cation Induced and Probed by Ultrafast Ionization: A Dynamical Study.
Mignolet, Benoît ULg; Levine, R. D.; Remacle, Françoise ULg

in Journal of Physics : B Atomic Molecular & Optical Physics (2014), 47

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See detailPrédiction de la réponse moléculaire à des perturbations mesurée sur des cellules uniques
Remacle, Françoise ULg; Levine, R. D.

in Médecine/Science (2014), 30

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See detailComputational Surprisal Analysis Speeds-Up Genomic Characterization of Cancer Processes
Kravchenko-Balasha, N.; Simon, Simcha; Levine, R. D. et al

in Plos One (2014), 9(11), 108549

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See detailDNAzyme-based 2:1 and 4:1 multiplexers and 1:2 demultiplexer
Orbach, Ron; Remacle, Françoise ULg; Levine, R. D. et al

in Chemical Science (2014), 5

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See detailElectronic states and wavefunctions of diatomic donor molecular ions in silicon: multi-valley envelope function theory
Klymenko, Mykhailo ULg; Remacle, Françoise ULg

in Journal of Physics : Condensed Matter (2014), 26(6), 065302

Using the Burt–Foreman envelope function theory and effective mass approximation, we develop a theoretical model for an arbitrary number of interacting donor atoms embedded in silicon which reproduces the ... [more ▼]

Using the Burt–Foreman envelope function theory and effective mass approximation, we develop a theoretical model for an arbitrary number of interacting donor atoms embedded in silicon which reproduces the electronic energy spectrum with high computational efficiency, taking into account the effective mass anisotropy and the valley–orbit coupling. We show that the variation of the relative magnitudes of the electronic coupling between the donor atoms with respect to the valley–orbit coupling as a function of the internuclear distance leads to different kinds of spatial interference patterns of the wavefunction. We also report on the impact of the orientation of the diatomic phosphorus donor molecular ion in the crystal lattice on the ionization energy and on the energy separation between the ground state and the lowest excited state. [less ▲]

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See detailSurprisal Analysis of Glioblastoma Multiform (GBM) MicroRNA Dynamics Unveils Tumor Specific Phenotype
Zadran, Sohila; Remacle, Françoise ULg; Levine, R. D.

in PLoS ONE (2014), 9(9), 10171

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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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