References of "Remacle, Françoise"
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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 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 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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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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