Zobrazeno 1 - 10
of 69
pro vyhledávání: '"Theodorakopoulos, Nikos"'
Autor:
Theodorakopoulos, Nikos
Publikováno v:
Phys. Rev. E 99, 032404, 2019
Overstretching of B-DNA is currently understood as force-induced melting. Depending on the geometry of the stretching experiment, the force threshold for the overstretching transition is around 65 or 110 pN. Although the mechanisms behind force-induc
Externí odkaz:
http://arxiv.org/abs/1902.05780
Autor:
Schindler, Torben, González, Adrián, Boopathi, Ramachandran, Roda, Marta Marty, Romero-Santacreu, Lorena, Wildes, Andrew, Porcar, Lionel, Martel, Anne, Theodorakopoulos, Nikos, Cuesta-López, Santiago, Angelov, Dimitar, Unruh, Tobias, Peyrard, Michel
Publikováno v:
Phys. Rev. E 98, 042417 (2018)
DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$\AA\ is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do n
Externí odkaz:
http://arxiv.org/abs/1809.09335
Publikováno v:
Phys. Rev. Lett. 108, 078104 (2012)
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot model with
Externí odkaz:
http://arxiv.org/abs/1201.6561
Autor:
Wildes, Andrew, Theodorakopoulos, Nikos, Orero, Jessica Valle, Cuesta-Lopez, Santiago, Garden, Jean-Luc, Peyrard, Michel
Publikováno v:
Physical Review E: Statistical, Nonlinear, and Soft Matter Physics (2011)
Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not provide sp
Externí odkaz:
http://arxiv.org/abs/1106.2632
Autor:
Theodorakopoulos, Nikos
Publikováno v:
Journal of Nonlinear Mathematical Physics (JNMP) vol. 18, Supplementary Issue 2(2011) pp. 429-447
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the relevant s
Externí odkaz:
http://arxiv.org/abs/1102.0259
Autor:
Wildes, Andrew, Theodorakopoulos, Nikos, Orero, Jessica Valle, Cuesta-Lopez, Santiago, Garden, Jean-Luc, Peyrard, Michel
Publikováno v:
Physical Review Letters 4, 106 (2011) 048101-1-4
The melting transition of deoxyribonucleic acid (DNA), whereby the strands of the double helix structure completely separate at a certain temperature, has been characterized using neutron scattering. A Bragg peak from B-form fibre DNA has been measur
Externí odkaz:
http://arxiv.org/abs/1101.1797
Autor:
Theodorakopoulos, Nikos
Publikováno v:
Phys. Rev. E 82, 021905 (2010)
The melting behavior of long, heterogeneous DNA chains is examined within the framework of the nonlinear lattice dynamics based Peyrard-Bishop-Dauxois (PBD) model. Data for the pBR322 plasmid and the complete T7 phage have been used to obtain model f
Externí odkaz:
http://arxiv.org/abs/1007.2728
Publikováno v:
J. Stat. Mech. (2009) P04011
We derive an exact formula for the covariance of cartesian distances in two simple polymer models, the freely-jointed chain and a discrete flexible model with nearest-neighbor interaction. We show that even in the interaction-free case correlations e
Externí odkaz:
http://arxiv.org/abs/0903.4816
Autor:
Theodorakopoulos, Nikos
Publikováno v:
Phys. Rev. E 77, 031919 (2008)
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of nonlinear base-sta
Externí odkaz:
http://arxiv.org/abs/0802.2194
Publikováno v:
Eur. Phys. J. E 23, 397-411 (2007)
We report model calculations on DNA single strands which describe the equilibrium dynamics and kinetics of hairpin formation and melting. Modeling is at the level of single bases. Strand rigidity is described in terms of simple polymer models; altern
Externí odkaz:
http://arxiv.org/abs/0706.2458