References of "Remacle, Françoise"
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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] (in press)

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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 (in press)

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 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 et al

in 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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See detailUltrafast Predissociation Mechanism of the 1Πu States of 14N2 and Its Isotopomers upon Attosecond Excitation from the Ground State
Muskatel, B. H.; Remacle, Françoise ULg; Levine, R. D.

in The Journal of Physical Chemistry A (2012)

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See detailLogic reversibility and thermodynamic irreversibility demonstrated by DNAzyme-based Toffoli and Fredkin logic gates
Orbach, Ron; Remacle, Françoise ULg; Levine, R. D. et al

in Proceedings of the National Academy of Sciences (2012), 109(52), 21228-21233

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a ... [more ▼]

The Toffoli and Fredkin gates were suggested as a means to exhibit logic reversibility and thereby reduce energy dissipation associated with logic operations in dense computing circuits. We present a construction of the logically reversible Toffoli and Fredkin gates by implementing a library of predesigned Mg2+-dependent DNAzymes and their respective substrates. Although the logical reversibility, for which each set of inputs uniquely correlates to a set of outputs, is demonstrated, the systems manifest thermodynamic irreversibility originating from two quite distinct and nonrelated phenomena. (i) The physical readout of the gates is by fluorescence that depletes the population of the final state of the machine. This irreversible, heat-releasing process is needed for the generation of the output. (ii) The DNAzyme-powered logic gates are made to operate at a finite rate by invoking downhill energy-releasing processes. Even though the three bits of Toffoli’s and Fredkin’s logically reversible gates manifest thermodynamic irreversibility, we suggest that these gates could have important practical implication in future nanomedicine. [less ▲]

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