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Search Results: 1 - 10 of 28852 matches for " Jean-Pierre Aimé "
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DNA Nano Devices as a Biased Random Walk Process: A Case Study of Isothermal Ratchet?  [PDF]
Jean-Pierre Aimé, Juan Elezgaray
Materials Sciences and Applications (MSA) , 2015, DOI: 10.4236/msa.2015.65045
Abstract: Computation and amplification processes based on Networks of Chemical Reactions are at the heart of our understanding of the regulation and error correction of life systems. The recent advances in DNA nanotechnology, with the creation of the modular structures origamis and the development of dynamical networks using the toe hold mediated strand displacement, open fertile areas to construct Hierarchical Cascades of Chemical Reactions with an increasing complexity inspired from systems in biology. DNA strands have the great advantage to design autonomous and homogeneous Networks of Chemical Reactions leaving aside companion chemical reactions as it occurs in biological systems. In the present paper, we use the Fokker Planck equation to extract predictions that address a wider class of systems beyond the case of diluted solutions. We introduce the concept of toehold strength and output strength that leads to an exponential square dependence of the toehold strength divided by the output strength on the escape rate and the probability for the output strand to leave the gate. We highlight the influence of the boundary conditions that may have an important consequence in confined environment when modular structures like origamis are employed.
Cooperativity in the annealing of DNA origamis
Jean-Michel Arbona,Jean-Pierre Aimé,Juan Elezgaray
Quantitative Biology , 2011,
Abstract: DNA based nanostructures built on a long single stranded DNA scaffold, known as DNA origamis, offer the possibility to organize various molecules at the nanometer scale in one pot experiments. The folding of the scaffold is guaranteed by the presence of short, single stranded DNA sequences (staples), that hold together separate regions of the scaffold. In this paper, we modelize the annealing-melting properties of these DNA constructions. The model captures important features such as the hysteresis between melting and annealing, as well as the dependence upon the topology of the scaffold. We show that cooperativity between staples is critical to quantitatively explain the folding process of DNA origamis.
Stability criterions of an oscillating tip-cantilever system in dynamic force microscopy
Laurent Nony,Rodolphe Boisgard,Jean-Pierre Aimé
Physics , 2005, DOI: 10.1007/s100510170009
Abstract: This work is a theoretical investigation of the stability of the non-linear behavior of an oscillating tip-cantilever system used in dynamic force microscopy. Stability criterions are derived that may help to a better understanding of the instabilities that may appear in the dynamic modes, Tapping and NC-AFM, when the tip is close to a surface. A variational principle allows to get the temporal dependance of the equations of motion of the oscillator as a function of the non-linear coupling term. These equations are the basis for the analysis of the stability. One find that the branch associated to frequencies larger than the resonance is always stable whereas the branch associated to frequencies smaller than the resonance exhibits two stable domains and one unstable. This feature allows to re-interpret the instabilities appearing in Tapping mode and may help to understand the reason why the NC-AFM mode is stable.
DNA properties investigated by dynamic force microscopy
Laurent Nony,Rodolphe Boisgard,Jean-Pierre Aimé
Physics , 2005,
Abstract: In this work, we show that by varying the experimental conditions, the driving amplitude, a dynamic force microscope allows DNA properties to be selectively imaged. The substrate on which the DNA is fixed is a silica surface grafted with silanes molecules ended with amine groups. Use of small oscillation amplitudes favors the attractive interaction between the tip and the sample, while use of large amplitudes renders the contribution of the attractive interaction negligible. Particularly, at small amplitudes, the images show that the attractive interaction is strongly enhanced along the DNA. This enhancement is found to be amenable with a model considering a narrow strip of randomly oriented dipoles on each side of the molecule. This work should provide new insights on the DNA interaction and conformational changes with localized charges.
Nonlinear dynamical properties of an oscillating tip-cantilever system in the tapping mode
Laurent Nony,Rodolphe Boisgard,Jean-Pierre Aimé
Physics , 2005, DOI: 10.1063/1.479422
Abstract: The dynamical properties of an oscillating tip-cantilever system are now widely used in the field of scanning force microscopy. The aim of the present work is to get analytical expressions describing the nonlinear dynamical properties of the oscillator in noncontact and intermittent contact situations in the tapping mode. Three situations are investigated: the pure attractive interaction, the pure repulsive interaction, and a mixing of the two. The analytical solutions obtained allow general trends to be extracted: the noncontact and the intermittent contact show a very discriminate variation of the phase. Therefore the measurement of the phase becomes a simple way to identify whether or not the tip touches the surface during the oscillating period. It is also found that the key parameter governing the structure of the dynamical properties is the product of the quality factor by a reduced stiffness. In the attractive regime, the reduced stiffness is the ratio of an attractive effective stiffness and the cantilever one. In the repulsive regime, the reduced stiffness is the ratio between the contact stiffness and the cantilever one. The quality factor plays an important role. For large values of the quality factor; it is predicted that a pure topography can be obtained whatever the value of the contact stiffness. For a smaller quality factor, the oscillator becomes more sensitive to change of the local mechanical properties. As a direct consequence, varying the quality factor, for example with a vacuum chamber, would be a very interesting way to investigate soft materials either to access topographic information or nanomechanical properties.
Growth kinetics of a nanoprotuberance under the action of an oscillating nanotip
Jean-Pierre Aimé,Denis Michel,Rodolphe Boisgard,Laurent Nony
Physics , 2005, DOI: 10.1103/PhysRevB.59.2407
Abstract: The atomic force microscope is a versatile tool that allows many routes to be used for investigating the mechanical properties of soft materials on the nanometer scale. In the present work, experiments were performed on polystyrene polymer films of various molecular weight by approaching a vibrating nanotip towards the surface. The variation of the oscillating amplitude of the cantilever is interpreted as the result of the growth process of a nanoprotuberance. The growth rate is found to be dependent of the magnitude of the oscillating amplitude and of the molecular weight. A model is developed describing in a very simple way the action of the tip and a viscoelastic response of the polymer. The numerical simulation helps in understanding the nonlinear relation between the growth rate and the vibrating amplitude of the microlever and describes qualitatively most of the experimental features. For the softer material, experimental situations are found that allow the experimental results to be amenable with an analytical solution. The analytical solution provides a fruitful comparison with the experimental results showing that some of the nanoprotuberance evolution cannot be explained with the approximation used. The presents results show that there exists a new and fascinating route to better understand the mechanical response at the local scale.
Dissipation induced by attractive interaction in dynamic force microscopy : contribution of adsorbed water layers
Laurent Nony,Touria Bouhacina,Jean-Pierre Aimé
Physics , 2005, DOI: 10.1016/S0039-6028(01)01773-3
Abstract: At room temperature and under ambient conditions, due to the adsorption, a water film is always present on silica surfaces. If the surface is investigated with a scanning probe method in Contact mode, this causes the formation of a meniscus between the tip and the surface. This liquid neck generates additional capillary forces between the nano-tip and the surface. In dynamic mode, due to the action of the oscillating tip on the surface, the mechanical response of the adsorbed water layers can induce additional dissipation that is probed through the phase variations of the oscillator. In the present work, we analyze by dynamic force microscopy the growth of a water film on a silica surface as a function of time. The silica sample is first cleaned and heated at $420^\circ$C, then is exposed to dry conditions. The influence of the water film is checked with the dynamic mode by using intermittent contact and noncontact situations. To describe the experimental observations, additional dissipation is taken into account when the tip approaches the surface. The results of the fits allow the evaluation of the dissipation induced by the attractive interaction between the tip and the silica surface related to the adsorption of water molecules on surface as a function of time. Results are compared to previous tribological studies performed in Contact mode and infra-red spectroscopy measurements on the silica for which the key parameter was the surface temperature instead of time. The two experimental results are in good agreement.
Carbon nanotubes adhesion and nanomechanical behavior from peeling force spectroscopy
Julien Buchoux,Ludovic Bellon,Sophie Marsaudon,Jean-Pierre Aimé
Physics , 2010, DOI: 10.1140/epjb/e2011-20204-1
Abstract: Applications based on Single Walled Carbon Nanotube (SWNT) are good example of the great need to continuously develop metrology methods in the field of nanotechnology. Contact and interface properties are key parameters that determine the efficiency of SWNT functionalized nanomaterials and nanodevices. In this work we have taken advantage of a good control of the SWNT growth processes at an atomic force microscope (AFM) tip apex and the use of a low noise (1E-13 m/rtHz) AFM to investigate the mechanical behavior of a SWNT touching a surface. By simultaneously recording static and dynamic properties of SWNT, we show that the contact corresponds to a peeling geometry, and extract quantities such as adhesion energy per unit length, curvature and bending rigidity of the nanotube. A complete picture of the local shape of the SWNT and its mechanical behavior is provided.
Drying nano particles solution on an oscillating tip at an air liquid interface: what we can learn, what we can do
Bernard Charlotte,Aimé Jean-Pierre,Marsaudon Sophie,Levy Rapha?l
Nanoscale Research Letters , 2007,
Abstract: Evaporation of fluid at micro and nanometer scale may be used to self-assemble nanometre-sized particles in suspension. Evaporating process can be used to gently control flow in micro and nanofluidics, thus providing a potential mean to design a fine pattern onto a surface or to functionalize a nanoprobe tip. In this paper, we present an original experimental approach to explore this open and rather virgin domain. We use an oscillating tip at an air liquid interface with a controlled dipping depth of the tip within the range of the micrometer. Also, very small dipping depths of a few ten nanometers were achieved with multi walls carbon nanotubes glued at the tip apex. The liquid is an aqueous solution of functionalized nanoparticles diluted in water. Evaporation of water is the driving force determining the arrangement of nanoparticles on the tip. The results show various nanoparticles deposition patterns, from which the deposits can be classified in two categories. The type of deposit is shown to be strongly dependent on whether or not the triple line is pinned and of the peptide coating of the gold nanoparticle. In order to assess the classification, companion dynamical studies of nanomeniscus and related dissipation processes involved with thinning effects are presented.
Stability of an oscillating tip in Non-Contact Atomic Force Microscopy: theoretical and numerical investigations
Gérard Couturier,Laurent Nony,Rodolphe Boisgard,Jean-Pierre Aimé
Physics , 2005, DOI: 10.1063/1.1428084
Abstract: This paper is a theoretical and a numerical investigation of the stability of a tip-cantilever system used in Non-Contact Atomic Force Microscopy (NC-AFM) when it oscillates close to a surface. No additional dissipative force is considered. The theoretical approach is based on a variationnal method exploiting a coarse grained operation that gives the temporal dependence of the nonlinear coupled equations of motion in amplitude and phase of the oscillator. Stability criterions for the resonance peak are deduced and predict a stable behavior of the oscillator in the vicinity of the resonance. The numerical approach is based on results obtained with a virtual NC-AFM developped in our group. The effect of the size of the stable domain in phase is investigated. These results are in particularly good agreement with the theoretical predictions. Also they show the influence of the phase shifter in the feedback loop and the way it can affect the damping signal.
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