Modelling DNA at the mesoscale: a challenge for nonlinear science?

Peyrard, Michel; Cuesta‐López, Santiago; James, Guillaume

doi:10.1088/0951-7715/21/6/t02

Cited by 64 publications

(47 citation statements)

References 27 publications

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“…One could of course introduce base pair dependent parameters in the zipper model, but a fixed set of such parameters does not represent different melting curves well (and the same applies to the nearest-neighbor model) [25]. Other models such as the Peyrard-BishopDauxois model do better in this respect [25,26], but it is not obvious how to couple the elastic energy to them. In the interest of keeping the number of fitting parameters to a minimum, we therefore choose average and in the zipper model.…”

Section: B Modelmentioning

confidence: 99%

Critical Torque for Kink Formation in Double-Stranded DNA

Wang

Tseng

et al. 2011

Phys. Rev. X

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We measure the bending energy of double-stranded DNA in the nonlinear (sharply bent) regime. The measurements are obtained from the melting curves of stressed DNA ring molecules. The nonlinear elastic behavior is captured by a single parameter: the critical torque c at which the molecule develops a kink. In this regime, the elastic energy is linear in the kink angle. This phenomenology is the same as for the previously reported case of nicked DNA. For the sequences examined, we find c ¼ 31 pN Â nm. This critical torque corresponds to a characteristic energy scale ð =2Þ c ¼ 12 kT room relevant for molecular biology processes associated with DNA bending.

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Section: B Modelmentioning

confidence: 99%

Critical Torque for Kink Formation in Double-Stranded DNA

Wang

Tseng

et al. 2011

Phys. Rev. X

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“…A remarkable amount of studies published over the last decades [11,12] has shed some light on the dynamics of DNA and the formation of fluctuational openings, the bubbles, which affect the thermal properties of the double helix including eventually its melting at high temperature. To tackle these issues, two classes of theoretical methods have been developed.…”

Section: Introductionmentioning

confidence: 99%

Thermodynamics of twisted DNA with solvent interaction

Zoli

2011

The Journal of Chemical Physics

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The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base pairs stacked along the molecule backbone. The base pair displacements are described by an ensemble of temperature dependent paths thus incorporating those fluctuational effects which shape the multisteps thermal denaturation. By summing over ∼ 10 7 − 10 8 base pair paths, a large number of double helix configurations is taken into account consistently with the physical requirements of the model potential. The partition function is computed as a function of the twist. It is found that the equilibrium twist angle, peculiar of B-DNA at room temperature, yields the stablest helicoidal geometry against thermal disruption of the base pair hydrogen bonds. This result is corroborated by the computation of thermodynamical properties such as fractions of open base pairs and specific heat.

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“…We can use the Finite difference methods for obtain the ground state wave function and the mean value of the displacement for the Hybrid potential ("hump Morse") 28 when the temperature is low and high. The results of this method is showed in Fig.…”

Section: Thermodynamics: the Mean Value Of The Displacementsmentioning

confidence: 99%

Thermodynamics of DNA with “hump” Morse potential

et al. 2016

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Resumo: A desnaturação térmica do DNA, ou seja, a separação das duas cadeias, é um fenômeno causado pela amplitude das vibrações das bases, portanto, é necessário saber como essa separação é gerada para implementar o modelo alternativo do comportamento de fusão como uma função da sequência de nucleotídeos e terapias para combater o câncer. Propomos usar o modelo de Peyrard-Bishop (PB) de DNA não linear estendido para incluir um potencial enarmônico que represente a interação de empilhamento aromático entre n-e (n-1)-enésimos pares de bases consecutivos para tratar o problema. Nós usamos métodos de diferença finita para determinar o valor médio do deslocamento para o potencial "corcunda de Morse" do modelo Peyrard-Bishop do DNA. Mostramos como o "pseudo-Schrödinger" estendido combinado com método de diferença finita pode ser usado para obter os deslocamentos do valor médio para a desnaturação térmica do DNA com o potencial Morse "da corcunda". Palavras-chave:Método das diferenças finitas, equação pseudo-Schrödinger, "corcunda" do potencial de Morse ___________________________________________________________________________ Abstract: The thermal denaturation of DNA, i.e. the separation of the two strands is a phenomenon caused by the amplitude of the vibrations of the bases, therefore it is necessary to know how such separation is generated in order to implement alternative model of the melting behavior as a function of nucleotide sequence and therapies to combat the cancer. We propose to use the extended nonlinear Peyrard-Bishop(PB) model of DNA to include an anharmonic potential representing the aromatic stacking interaction between n-and (n-1)-th consecutive base pairs to treat the problem. We use Finite-difference methods for determine the mean value of the displacement for the "hump Morse" potential of the Peyrard-Bishop model of DNA. We show how the extended "pseudoSchrödinger" combined with finite difference method can be used to obtain the mean value displacements for the thermal denaturation of DNA with "hump" Morse potential.

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Modelling DNA at the mesoscale: a challenge for nonlinear science?

Cited by 64 publications

References 27 publications

Critical Torque for Kink Formation in Double-Stranded DNA

Critical Torque for Kink Formation in Double-Stranded DNA

Thermodynamics of twisted DNA with solvent interaction

Thermodynamics of DNA with “hump” Morse potential

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