Dynamical Response of Nanomechanical Oscillators in Immiscible Viscous Fluid for in vitro Biomolecular Recognition

Dynamical response of nanomechanical cantilever structures immersed in a viscous fluid is important to in vitro single-molecule force spectroscopy, biomolecular recognition of disease-specific proteins, and the detection of microscopic dynamics of proteins. Here we study the stochastic response of biofunctionalized nanomechanical cantilevers beam in a viscous fluid. Using the fluctuation-dissipation theorem we derive an exact expression for the spectral density of the displacement and a linear approximation for the resonance frequency shift. We find that in a viscous solution the frequency shift of the nanoscale cantilever is determined by surface stress generated by biomolecular interaction with negligible contributions from mass loading.Comment: 4 pages, 2 figures, RevTex4. See http://nano.bu.edu/ for related paper

Looping and clustering model for the organization of protein-DNA complexes on the bacterial genome

The bacterial genome is organized by a variety of associated proteins inside a structure called the nucleoid. These proteins can form complexes on DNA that play a central role in various biological processes, including chromosome segregation. A prominent example is the large ParB-DNA complex, which forms an essential component of the segregation machinery in many bacteria. ChIP-Seq experiments show that ParB proteins localize around centromere-like parS sites on the DNA to which ParB binds specifically, and spreads from there over large sections of the chromosome. Recent theoretical and experimental studies suggest that DNA-bound ParB proteins can interact with each other to condense into a coherent 3D complex on the DNA. However, the structural organization of this protein-DNA complex remains unclear, and a predictive quantitative theory for the distribution of ParB proteins on DNA is lacking. Here, we propose the looping and clustering model, which employs a statistical physics approach to describe protein-DNA complexes. The looping and clustering model accounts for the extrusion of DNA loops from a cluster of interacting DNA-bound proteins that is organized around a single high-affinity binding site. Conceptually, the structure of the protein-DNA complex is determined by a competition between attractive protein interactions and loop closure entropy of this protein-DNA cluster on the one hand, and the positional entropy for placing loops within the cluster on the other. Indeed, we show that the protein interaction strength determines the 'tightness' of the loopy protein-DNA complex. Thus, our model provides a theoretical framework for quantitatively computing the binding profiles of ParB-like proteins around a cognate (parS) binding site

Supratransmission non linéaire dans les systèmes à plusieurs champs.

International audienceAucu

TRANSFERT ELECTRONIQUE INTER-CHAINE DANS UN MILIEU NON LINEAIRE

PALAISEAU-Polytechnique (914772301) / SudocSudocFranceF

Discrete breathers in nonlinear Schrödinger hypercubic lattices with arbitrary power nonlinearity

International audienceWe study two specific features of onsite breathers in Nonlinear Schrödinger systems on d-dimensional cubic lattices with arbitrary power nonlinearity (i.e., arbitrary nonlinear exponent, n): their wavefunctions and energies close to the anti-continuum limit–small hopping limit–and their excitation thresholds. Exact results are systematically compared to the predictions of the so-called exponential ansatz (EA) and to the solution of the single nonlinear impurity model (SNI), where all nonlinearities of the lattice but the central one, where the breather is located, have been removed. In 1D, the exponential ansatz is more accurate than the SNI solution close to the anti-continuum limit, while the opposite result holds in higher dimensions. The excitation thresholds predicted by the SNI solution are in excellent agreement with the exact results but cannot be obtained analytically except in 1D. An EA approach to the SNI problem provides an approximate analytical solution that is asymptotically exact as n tends to infinity. But the EA result degrades as the dimension, d, increases. This is in contrast to the exact SNI solution which improves as n and/or d increase. Finally, in our investigation of the SNI problem we also prove a conjecture by Bustamante and Molina [C.A. Bustamante, M.I. Molina, Phys. Rev. B 62 (23) (2000) 15287] that the limiting value of the bound state energy is universal when n tends to infinity

Response Spectrum of Coupled Nanomechanical Resonators

International audienceWe develop a simple continuum model to analyze the vibrational modes of a nanomechanical multielement structure. In this model, arrays of submicron cantilevers located symmetrically on both sides of the central clamped-clamped nanobeam are replaced by a continuum. In this approach, the equations of motion of the structure become exactly solvable. Our analytical results capture the main features of the vibrational modes observed both numerically and experimentally and can be applied to a general class of scale-independent elasticaly coupled resonator structures

Modélisation de la ségrégation et du positionnementdu génome bactérien

Compréhension et analyse des systèmes complexes par Agropolis InternationalResumé des activités de l'equipe SCPN sur la modélisation de la ségrégation et du positionnement du génome bactéri

Modélisation de la ségrégation et du positionnementdu génome bactérien

Compréhension et analyse des systèmes complexes par Agropolis InternationalResumé des activités de l'equipe SCPN sur la modélisation de la ségrégation et du positionnement du génome bactéri

Modelling DNA segregation and positioning in the bacterial genome

Compréhension et analyse des systèmes complexes par Agropolis InternationalActivities around modelling DNA segregation and positioning in the bacterial genom

Growth of surface wind-waves in water of finite depth. A theoretical approach

In order to study the growth of wind waves in finite depth we extend Miles' theory to the finite depth domain. A depth-dependent wave growth rate is derived from the dispersion relation of the wind/water interface. A suitable dimensionless finite depth wave age parameter allows us to plot a family of wave growth curves, each family member characterized by the water depth. Two major results are that for small wave age, the wave growth rates are comparable to those of deep water and for large wave age, a finite-depth wave-age-limited growth is reached, with wave growth rates going to zero. The corresponding limiting wave length and limiting phase speed are explicitely calculated in the shallow and in the deep water cases. A qualitative agreement with well-known empirical results is established and shows the robust consistency of the linear theoretical approach