References of "Remacle, Françoise"
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See detailCoulombic driven multi-conformational aspects of oligorotaxane switches studied by ion mobility mass spectrometry and molecular dynamics
Hanozin, Emeline ULg; Mignolet, Benoît ULg; Morsa, Denis ULg et al

Conference (2017, June)

Introduction Artificial Molecular Machines (AMMs), such as Mechanically Interlocked Molecules (MIMs) and foldamers, have recently raised tremendous interest due to their unique properties. Under the ... [more ▼]

Introduction Artificial Molecular Machines (AMMs), such as Mechanically Interlocked Molecules (MIMs) and foldamers, have recently raised tremendous interest due to their unique properties. Under the influence of an appropriate stimuli (pH, redox potential, light…), such molecules are able to reversibly switch between distinct conformational states. Scientists may capitalize on such exclusive properties to get a better understanding of the biomacromolecular level or to design innovative “smart” materials. At the interface between foldamers and MIMs, oligorotaxanes exhibit a spring-like folded secondary structure with remarkable mechanical and physicochemical properties. In the present study, we use ion mobility coupled with mass spectrometry (IM-MS) to probe the conformational states of differentially charged oligorotaxanes in the gas phase. Method Oligorotaxanes are donor-acceptor polymers composed of a π electron-donating dumbbell over which a discrete number of π electron-accepting tetracationic cyclophanes are threaded. The numerous intra-molecular interactions provide them a highly-stabilized rigid rod-like structure in solution. We use IM-MS as implemented in the Synapt G2 HDMS (Waters, Manchester, UK) to investigate the structure of the ionized oligorotaxanes. Our purposes are to probe (i) the different populations of stable conformers generated according to the charge state z and (ii) the reversibility of an electron-driven or thermal-driven conformational change in the gas phase implemented via an electron transfer or collisional activation process prior to the mobility separation. Our experimental observations are supported by electronic structure optimizations at the PM6 and DFT levels coupled with Born-Oppenheimer Molecular Dynamics simulations. Preliminary data Our results highlight a progressive elongation of the oligorotaxane structure with increasing charge numbers until it reaches a maximum extension state. Matching the experimental data with theoretical simulations, we find that the oligorotaxanes adopt an entropically-favored globular shape at low z. As z increases, coulombic repulsions occurring between the cyclophanes gradually outweigh the stabilizing π-stacking interactions and force the structure to elongate. This process occurs in a multistep fashion, each corresponding to a distinct group of helical-shaped conformers, before it eventually results in a fully stretched structure. On the other hand, our results also highlight that a charge reduction driven by a non-dissociative electron transfer process leads to a refolding of the structure so that it adopts a size similar to its electrospray-generated counterpart when the appropriate number of electrons is added. This observation may be imparted to the gradual decrease of the Coulomb repulsions between the cyclophanes mediated through increasing numbers of transferred electrons. These results suggests that the transition from one conformer to another is reversible so that the electrostatic balance between the cyclophanes may be used to further tune the structural state adopted by this artificial molecular switch. The second stimulus relied on collisional activation whose inelastic component provides a way to build up energy into the accessible vibrational degrees of freedom. The conformational landscapes of such-activated oligorotaxanes ions were found unchanged in term of collision cross section position but the repartition of population was altered with a promotion of the most elongated conformer, provided the absence of selective fragmentation. Altogether, these results highlight the feasibility of handling the elongation state of oligorotaxanes in the gas phase through appropriate inputs and underline its conformational reversibility properties. Novel aspect Stimuli-induced reversible conformational rearrangements of innovative AMMs studied by IM-MS and molecular dynamics in the gas phase. [less ▲]

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See detailThe Role of Super-Atom Molecular Orbitals in Doped Fullerenes in a Femtosecond Intense Laser Field
Xiong, Hui; Mignolet, Benoît ULg; Fang, Li et al

in Scientific Reports (2017), 7

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See detailElectronic states and valley-orbit coupling in linear and planar molecules formed by coupled P donors in silicon
Klymenko, M. V.; Rogge, S.; Remacle, Françoise ULg

in Physical Review. B : Condensed Matter (2017), 95(20), 205301

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See detailImplementation of probabilistic algorithms by multi-chromophoric molecular networks with application to multiple travelling pathways
Fresch, B.; Remacle, Françoise ULg; Levine, R. D.

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2017), 18

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See detailImplementation of multivariable logic functions in parallel by electrical addressing a molecule of three dopants in Silicon
Fresch, B.; Bocquel, J.; Rogge, S. et al

in Chemphyschem : A European Journal of Chemical Physics and Physical Chemistry (2017), 18

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See detailSpatial and temporal control of populations, branching ratios, and electronic coherences in LiH by a single one-cycle infrared pulse
Nikodem, Astrid ULg; Levine, R. D.; Remacle, Françoise ULg

in Physical Review. A : General Physics (2017), 95(5), 053404

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See detailA new electron-ion coincidence 3D momentum-imaging method and its application in probing strong field dynamics of 2-phenylethyl-N, N-dimethylamine
Fan, Lin; Lee, Suk Kyoung; Tu, Yi-Jung et al

in Journal of Chemical Physics (2017), 147

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See detailMultivariate Surprisal Analysis of Gene Expression Levels
Remacle, Françoise ULg; Goldstein, S. Andrew; Levine, D. Raphael

in Entropy (2017), 18(12), 445

We consider here multivariate data which we understand as the problem where each data point i is measured for two or more distinct variables. In a typical situation there are many data points i while the ... [more ▼]

We consider here multivariate data which we understand as the problem where each data point i is measured for two or more distinct variables. In a typical situation there are many data points i while the range of the different variables is more limited. If there is only one variable then the data can be arranged as a rectangular matrix where i is the index of the rows while the values of the variable label the columns. We begin here with this case, but then proceed to the more general case with special emphasis on two variables when the data can be organized as a tensor. An analysis of such multivariate data by a maximal entropy approach is discussed and illustrated for gene expressions in four different cell types of six different patients. The different genes are indexed by i, and there are 24 (4 by 6) entries for each i. We used an unbiased thermodynamic maximal-entropy based approach (surprisal analysis) to analyze the multivariate transcriptional profiles. The measured microarray experimental data is organized as a tensor array where the two minor orthogonal directions are the different patients and the different cell types. The entries are the transcription levels on a logarithmic scale. We identify a disease signature of prostate cancer and determine the degree of variability between individual patients. Surprisal analysis determined a baseline expression level common for all cells and patients. We identify the transcripts in the baseline as the “housekeeping” genes that insure the cell stability. The baseline and two surprisal patterns satisfactorily recover (99.8%) the multivariate data. The two patterns characterize the individuality of the patients and, to a lesser extent, the commonality of the disease. The immune response was identified as the most significant pathway contributing to the cancer disease pattern. Delineating patient variability is a central issue in personalized diagnostics and it remains to be seen if additional data will confirm the power of multivariate analysis to address this key point. The collapsed limits where the data is compacted into two dimensional arrays are contained within the proposed formalism. [less ▲]

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See detailNuclear Motion Driven Ultrafast Photodissociative Charge Transfer of the PENNA Cation: An Experimental and Computational Study
Sun, Shoutian; Mignolet, Benoît ULg; Fan, lin et al

in Journal of Physical Chemistry A (2017), 121(7), 1442

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See detailOptical activity of the super-atom molecular orbital (SAMO) states in Li@C60+ conformers
Mignolet, Benoît ULg; Campbell, Eleanor; Remacle, Françoise ULg

in AIP Conference Proceedings (2017), in press

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See detailA Probabilistic Finite State Logic Machine Realized Experimentally on a Single Dopant Atom
Fresch, Barbara; Bocquel, Juanita; Rogge, Sven et al

in Nano Letters (2017), 17

Exploiting the potential of nanoscale devices for logic processing requires the implementation of computing functionalities departing from the conventional switching paradigm. We report on the design and ... [more ▼]

Exploiting the potential of nanoscale devices for logic processing requires the implementation of computing functionalities departing from the conventional switching paradigm. We report on the design and the experimental realisation of a probabilistic finite state machine in a single phosphorus donor atom placed in a silicon matrix electrically addressed and probed by Scanning Tunneling Spectroscopy (STS). The single atom logic unit simulates the flow of visitors in a maze whose topology is determined by the dynamics of the electronic transport through the states of the dopant. By considering the simplest case of a unique charge state for which three electronic states can be resolved, we demonstrate an efficient solution of the following problem: in a maze of four connected rooms, what is the optimal combination of door opening rates in order to maximize the time that visitors spend in one specific chamber? The implementation takes advantage of the stochastic nature of electron tunneling while the output remains the macroscopic current whose reading can be realized with standard techniques and does not require single electron sensitivity. [less ▲]

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See detailContinuous variables logic via coupled automata using a DNAzyme cascade with feedback
Lilienthal, Sivan; Orbach, Ron; Willner, Itamar et al

in Chemical Science (2017), 8

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To ... [more ▼]

The concentration of molecules can be changed by chemical reactions and thereby offer a continuous readout. Yet computer architecture is cast in textbooks in terms of binary valued, Boolean variables. To enable reactive chemical systems to compute we show how, using the Cox interpretation of probability theory, one can transcribe the equations of chemical kinetics as a sequence of coupled logic gates operating on continuous variables. It is discussed how the distinct chemical identity of a molecule allows us to create a common language for chemical kinetics and Boolean logic. Specifically, the logic AND operation is shown to be equivalent to a bimolecular process. The logic XOR operation represents chemical processes that take place concurrently. The values of the rate constants enter the logic scheme as inputs. By designing a reaction scheme with a feedback we endow the logic gates with a built in memory because their output then depends on the input and also on the present state of the system. Technically such a logic machine is an automaton. We report an experimental realization of three such coupled automata using a DNAzyme multilayer signaling cascade. A simple model verifies analytically that our experimental scheme provides an integrator generating a power series that is third order in time. The model identifies two parameters that govern the kinetics and shows how the initial concentrations of the substrates are the coefficients in the power series. [less ▲]

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See detailTransition from SAMO to Rydberg State Ionization in C60 in Femtosecond Laser Fields
Li, H.; Mignolet, Benoît ULg; Wang, Z. et al

in Journal of Physical Chemistry Letters (2016), 7(22), 4677-4682

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See detailMicrofluidic chip with molecular beacons detects miRNAs in Human CSF to reliably characterize CNS-specific disorders
Zadran, S.; Remacle, Françoise ULg; Levine, R. D.

in RNA & Disease (2016), 3

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See detailProbing in Space and Time the Nuclear Motion Driven by Nonequilibrium Electronic Dynamics in Ultrafast Pumped N2
Ajay, J.; Šmydke, J.; Remacle, Françoise ULg et al

in Journal of Physical Chemistry A (2016), 120(19), 3335-3342

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See detailQuantum Nuclear Dynamics Pumped and Probed by Ultrafast Polarization Controlled Steering of a Coherent Electronic State in LiH
Nikodem, Astrid ULg; Levine, R. D.; Remacle, Françoise ULg

in Journal of Physical Chemistry A (2016), 120(19), 3343-3352

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See detailTechniques for modulating error resilience in emerging multi-value technologies
Sjalander, Magnus; Borgstr, Gustaf; Klymenko, Mykhailo ULg et al

in Proceedings of the ACM International Conference on Computing Frontiers (2016)

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See detailOperation of a quantum dot in the finite-state machine mode: Single-electron dynamic memory
Klymenko, Mykhailo ULg; Klein, M.; Levine, R. D. et al

in Journal of Applied Physics (2016), 120(2), 024503

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See detailControlling coherent quantum nuclear dynamics in LiH by ultra short IR atto pulses
Nikodem, Astrid ULg; Levine, R. D.; Remacle, Françoise ULg et al

in Progress in Ultrafast Laser Science XIII (2016)

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