References of "Levine, R. D"
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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 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 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 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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See detailOn a fundamental structure of gene networks in living cells
Kravchenko-Balasha, Nataly; Levitzki, Alexander; Goldstein, Andrew et al

in Proceedings of the National Academy of Sciences of the United States of America (2012), 109(12), 4702-4707

Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems ... [more ▼]

Computers are organized into hardware and software. Using a theoretical approach to identify patterns in gene expression in a variety of species, organs, and cell types, we found that biological systems similarly are comprised of a relatively unchanging hardware-like gene pattern. Orthogonal patterns of software-like transcripts vary greatly, even among tumors of the same type from different individuals. Two distinguishable classes could be identified within the hardware-like component: those transcripts that are highly expressed and stable and an adaptable subset with lower expression that respond to external stimuli. Importantly, we demonstrate that this structure is conserved across organisms. Deletions of transcripts from the highly stable core are predicted to result in cell mortality. The approach provides a conceptual thermodynamic-like framework for the analysis of gene-expression levels and networks and their variations in diseased cells. [less ▲]

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See detailMaximal entropy multivariate analysis
Remacle, Françoise ULg; Arumugam, Rameshkumar; Levine, R. D.

in Molecular Physics (2012), 110

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See detailStereocontrol of attosecond time-scale electron dynamics in ABCU using ultrafast laser pulses: a computational study
Mignolet, Benoît ULg; Gijsbertsen, A.; Vrakking, M. J. J. et al

in Physical Chemistry Chemical Physics [=PCCP] (2011), 13(18), 8331-8344

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See detailConvergence of Logic of Cellular Regulation in Different Premalignant Cells by an Information Theoretic Approach
Kravchenko-Balasha, N.; Remacle, Françoise ULg; Gross, A. et al

in BMC Systems Biology (2011), 5

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See detailIntegrated logic circuits using single-atom transistors
Mol, J.; Verduijn, J.; Levine, R. D. et al

in Proceedings of the National Academy of Sciences of the United States of America (2011), 108(34), 13969-13972

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See detailOn the strong and selective isotope effect in the UV excitation of N2 with implications toward the nebula and Martian atmosphere
Muskatel, B. H.; Remacle, Françoise ULg; Thiemens, Mark et al

in Proceedings of the National Academy of Sciences of the United States of America (2011), 108(15), 6020-6025

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See detailLogic operations in a doped solid driven by stimulated Raman adiabatic passage
Beil, F.; Halfmann, T.; Remacle, Françoise ULg et al

in Physical Review A (2011), 83

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See detailAttosecond pumping of nonstationary electronic states of LiH: Charge shake-up and electron density distortion
Remacle, Françoise ULg; Levine, R. D.

in Physical Review A : General Physics (2011), 83(1), 013411

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See detailWhose Entropy: A Maximal Entropy Analysis of Phosphorylation Signaling
Remacle, Françoise ULg; Graeber, T.; Levine, R. D.

in Journal of Statistical Physics (2011)

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See detailProtein Signaling Networks from Single Cell Fluctuations and Information Theory Profiling
Shin, Young Shik; Remacle, Françoise ULg; Fan, Rong et al

in Biophysical Journal (2011), 100(10), 2378-2386

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