Rigidity of melting DNA

Pal, Tanmoy; Bhattacharjee, Somendra M.

doi:10.1103/physreve.93.052102

Cited by 8 publications

(6 citation statements)

References 62 publications

(85 reference statements)

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“…Under spontaneous thermal fluctuations, DNA base pairs may break to give rise to transient opening of the dsDNA. This local conversion of a few bp of dsDNA into two single stranded DNA (ssDNA) corresponds to the formation of the so-called DNA bubbles, which are ∼25 times more flexible than dsDNA ( 4 , 5 ).…”

Section: Introductionmentioning

confidence: 99%

How does temperature impact the conformation of single DNA molecules below melting temperature?

Brunet

Salomé

Rousseau

et al. 2017

Nucleic Acids Research

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The double stranded DNA molecule undergoes drastic structural changes during biological processes such as transcription during which it opens locally under the action of RNA polymerases. Local spontaneous denaturation could contribute to this mechanism by promoting it. Supporting this idea, different biophysical studies have found an unexpected increase in the flexibility of DNA molecules with various sequences as a function of the temperature, which would be consistent with the formation of a growing number of locally denatured sequences. Here, we take advantage of our capacity to detect subtle changes occurring on DNA by using high throughput tethered particle motion to question the existence of bubbles in double stranded DNA under physiological salt conditions through their conformational impact on DNA molecules ranging from several hundreds to thousands of base pairs. Our results strikingly differ from previously published ones, as we do not detect any unexpected change in DNA flexibility below melting temperature. Instead, we measure a bending modulus that remains stable with temperature as expected for intact double stranded DNA.

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Section: Introductionmentioning

confidence: 99%

How does temperature impact the conformation of single DNA molecules below melting temperature?

Brunet

Salomé

Rousseau

et al. 2017

Nucleic Acids Research

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show abstract

“…We show through experiment and theory that this scenario leads to non-exponential decoherence rates and manifests as sub-diffusive quantum mean energy growth. Besides quantum decoherence, these results are relevant in the general context of transport and diffusion in chaotic quantum systems [26][27][28] and disordered nonlinear lattices [29].The dimensionless Hamiltonian for AOKR, i.e., twolevel atoms in a pulsed standing wave of near-resonant arXiv:1607.05605v2 [quant-ph]…”

mentioning

confidence: 99%

Nonexponential Decoherence and Subdiffusion in Atom-Optics Kicked Rotor

et al. 2017

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Quantum systems lose coherence upon interaction with the environment and tend towards classical states. Quantum coherence is known to exponentially decay in time so that macroscopic quantum superpositions are generally unsustainable. In this work, slower than exponential decay of coherences is experimentally realized in an atom-optics kicked rotor system subjected to nonstationary Lévy noise in the applied kick sequence. The slower coherence decay manifests in the form of quantum subdiffusion that can be controlled through the Lévy exponent. The experimental results are in good agreement with the analytical estimates and numerical simulations for the mean energy growth and momentum profiles of an atom-optics kicked rotor.

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“…In the 3D NS case, the λ m are related to the spectral exponents for the inertial-range, power-law form of the energy spectra [41] ; the analogous relation for the 3D CHNS case is not straightforward because the powerlaw ranges in such spectra depend on several parameters in the CHNS equations (see, e.g., Ref. [25]).…”

Section: B Temporal Evolution Of Dmmentioning

confidence: 99%

“…Here, interfacial regions are characterized by large gradients in φ. The CHNS equations have been used to model many binaryfluid systems that are of great current interest : examples include studies of (a) the Rayleigh-Taylor instability [23,24] ; (b) turbulence-induced suppression of the phase separation of the two components of the binary fluid [19] ; (c) multifractal droplet dynamics in a turbulent, binary-fluid mixture [25] ; (d) the coalescence of droplets [26] ; and (e) lattice-Boltzmann treatments of multi-phase flows [19,27].…”

Section: Introductionmentioning

confidence: 99%

Regularity criterion for solutions of the three-dimensional Cahn-Hilliard-Navier-Stokes equations and associated computations

et al. 2016

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We consider the three-dimensional (3D) Cahn-Hilliard equations coupled to, and driven by, the forced, incompressible 3D Navier-Stokes equations. The combination, known as the Cahn-Hilliard-Navier-Stokes (CHNS) equations, is used in statistical mechanics to model the motion of a binary fluid. The potential development of singularities (blow-up) in the contours of the order parameter ϕ is an open problem. To address this we have proved a theorem that closely mimics the Beale-Kato-Majda theorem for the 3D incompressible Euler equations [J. T. Beale, T. Kato, and A. J. Majda, Commun. Math. Phys. 94, 61 (1984)CMPHAY0010-361610.1007/BF01212349]. By taking an L^{∞} norm of the energy of the full binary system, designated as E_{∞}, we have shown that ∫_{0}^{t}E_{∞}(τ)dτ governs the regularity of solutions of the full 3D system. Our direct numerical simulations (DNSs) of the 3D CHNS equations for (a) a gravity-driven Rayleigh Taylor instability and (b) a constant-energy-injection forcing, with 128^{3} to 512^{3} collocation points and over the duration of our DNSs confirm that E_{∞} remains bounded as far as our computations allow.

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Rigidity of melting DNA

Cited by 8 publications

References 62 publications

How does temperature impact the conformation of single DNA molecules below melting temperature?

How does temperature impact the conformation of single DNA molecules below melting temperature?

Nonexponential Decoherence and Subdiffusion in Atom-Optics Kicked Rotor

Regularity criterion for solutions of the three-dimensional Cahn-Hilliard-Navier-Stokes equations and associated computations

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