arXiv subjects

Nikos Theodorakopoulos

Publications and source records attributed to Nikos Theodorakopoulos.

16 recordsLinked to original sources

arXiv2026

DNA melting: intra base-pair dynamics and a vector generalization of the Peyrard-Bishop-Dauxois model

The Peyrard-Bishop-Dauxois (PBD) model of DNA denaturation, although successful in the description of melting profiles, fails to predict melting entropies, unzipping forces and dynamical properties, e.g. hairpin dynamics. The paper presents an atomistic "toy model" of the intra base-pair motion which suggests that the thermodynamics may be better described by a planar vector - rather than a scalar - order parameter. This leads to correct estimates of melting entropy, unzipping force, hairpin opening rates, and the equilibrium constant of open/closed base pair states during imino proton exchange.

physics.bio-ph↗

arXiv2019

Thermodynamics of force-induced B-DNA melting: single-strand discreteness matters

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-induced melting have been correctly described by Rouzina and Bloomfield \cite{RouzinaBloomfield2001a}, neither force threshold has been exactly calculated by theory. In this work, a detailed analysis of the force-extension curve is presented, based on a description of single-stranded DNA in terms of the discrete Kratky-Porod model, consistent with (i) the contour length expected from the crystallographically determined monomer distance, and (ii) a high value of the elastic stretch modulus arising from covalent bonding. The value estimated for the ss-DNA persistence length, $λ= 1.0 $ nm, is at the low end of currently known estimates and reflects the intrinsic stiffness of the partially, or fully stretched state, where electrostatic repulsion effects are expected to be minimal. A detailed analysis of single- and double-stranded DNA free energies provides estimates of the overstretching force thresholds. In the unconstrained geometry, the predicted threshold is 64 pN. In the constrained geometry, after allowing for the entropic penalty of the plectonemic topology of the molten state, the predicted threshold is 111 pN.

physics.bio-ph↗

arXiv2018

Kinky DNA in solution: Small angle scattering study of a nucleosome positioning sequence

DNA is a flexible molecule, but the degree of its flexibility is subject to debate. The commonly-accepted persistence length of $l_p \approx 500\,$Å is inconsistent with recent studies on short-chain DNA that show much greater flexibility but do not probe its origin. We have performed X-ray and neutron small-angle scattering on a short DNA sequence containing a strong nucleosome positioning element, and analyzed the results using a modified Kratky-Porod model to determine possible conformations. Our results support a hypothesis from Crick and Klug in 1975 that some DNA sequences in solution can have sharp kinks, potentially resolving the discrepancy. Our conclusions are supported by measurements on a radiation-damaged sample, where single-strand breaks lead to increased flexibility and by an analysis of data from another sequence, which does not have kinks, but where our method can detect a locally enhanced flexibility due to an $AT$-domain.

physics.bio-ph↗

arXiv2012

Base Pair Openings and Temperature Dependence of DNA Flexibility

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 soft and hard joints, corresponding to open and closed base pairs, and sequence-dependent statistical information about the state of each pair provided by a Peyrard-Bishop-Dauxois (PBD) model calculation with no freely adjustable parameters.

cond-mat.stat-mech↗

arXiv2011

Structural correlations and melting of B-DNA fibres

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 spatial information. We report a measurement using neutron scattering from oriented DNA fibres to determine the size of the regions that stay in the double-helix conformation as the melting temperature is approached from below. A Bragg peak from the B-form of DNA has been observed as a function of temperature and its width and integrated intensity have bean measured. These results, complemented by a differential calorimetry study of the melting of B DNA fibres as well as electrophoresis and optical observation data, are analysed in terms of a one-dimensional mesoscopic model of DNA.

cond-mat.stat-mech↗

arXiv2011

Bubbles, clusters and denaturation in genomic DNA: modeling, parametrization, efficient computation

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 statistical mechanics. Computed melting profiles of long and short heterogeneous sequences are presented, using a recently introduced reparametrization of the PBD model, and critically discussed. The statistics of extended open bubbles and bound clusters is formulated and results are presented for selected examples.

cond-mat.stat-mech↗

arXiv2011

The thermal denaturation of DNA studied with neutron scattering

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 measured as a function of temperature, and its widths and integrated intensities have been interpreted using the Peyrard-Bishop-Dauxois (PBD) model with only one free parameter. The experiment is unique, as it gives spatial correlation along the molecule through the melting transition where other techniques cannot.

cond-mat.stat-mech↗

arXiv2010

Melting of genomic DNA: predictive modeling by nonlinear lattice dynamics

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 fits and determine parameter dependence on salt content. Melting curves predicted for the complete fd phage and the Y1 and Y2 fragments of the $ϕ$X174 phage without any adjustable parameters are in good agreement with experiment. The calculated probabilities for single base-pair opening are consistent with values obtained from imino proton exchange experiments.

physics.bio-ph↗

arXiv2009

On 4-point correlation functions in simple polymer models

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 exist as long as the two distances at least partially share the same segments. For the interacting case, we demonstrate that the naive expectation of increasing correlations with increasing interaction strength only holds in a finite range of values. Some suggestions for future single-molecule experiments are made.

cond-mat.soft↗

arXiv2008

DNA denaturation bubbles at criticality

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-stacking interactions. Small bubbles extending over less than 10 base pairs are associated with much larger free energies of formation per site than larger bubbles. As the critical temperature is approached, the free energy associated with further bubble growth becomes vanishingly small. An analysis of average displacement profiles of bubbles of varying sizes at different temperatures reveals almost identical scaled shapes in the absence of nonlinear stacking; nonlinear stacking leads to distinct scaled shapes of large and small bubbles.

cond-mat.stat-mech↗

arXiv2007

Modeling DNA beacons at the mesoscopic scale

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; alternative calculations performed using the freely rotating chain and the discrete Kratky-Porod models are reported. Stem formation is modeled according to the Peyrard-Bishop-Dauxois Hamiltonian. The kinetics of opening and closing is described in terms of a diffusion-controlled motion in an effective free energy landscape. Melting profiles, dependence of melting temperature on loop length, and kinetic time scales are in semiquantitative agreement with experimental data obtained from fluorescent DNA beacons forming poly(T) loops. Variation in strand rigidity is not sufficient to account for the large activation enthalpy of closing and the strong loop length dependence observed in hairpins forming poly(A) loops. Implications for modeling single strands of DNA or RNA are discussed.

cond-mat.soft↗

arXiv2004

Nonlinear structures and thermodynamic instabilities in a one-dimensional lattice system

The equilibrium states of the discrete Peyrard-Bishop Hamiltonian with one end fixed are computed exactly from the two-dimensional nonlinear Morse map. These exact nonlinear structures are interpreted as domain walls (DW), interpolating between bound and unbound segments of the chain. The free energy of the DWs is calculated to leading order beyond the Gaussian approximation. Thermodynamic instabilities (e.g. DNA unzipping and/or thermal denaturation) can be understood in terms of DW formation.

cond-mat.stat-mech↗

arXiv2003

Thermal denaturation of an helicoidal DNA model

We study the static and dynamical properties of DNA in the vicinity of its melting transition, i.e. the separation of the two strands upon heating. The investigation is based on a simple mechanical model which includes the helicoidal geometry of the molecule and allows an exact numerical evaluation of its thermodynamical properties. Dynamical simulations of long-enough molecular segments allow the study of the structure factors and of the properties of the denaturated regions. Simulations of finite chains display the hallmarks of a first order transition for sufficiently long-ranged stacking forces although a study of the model's ``universality class'' strongly suggests the presence of an ``underlying'' continuous transition.

cond-mat.stat-mech↗

arXiv2003

Thermodynamic instabilities in one dimensional particle lattices: a finite-size scaling approach

One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of particles must be demonstrated on a case-by-case basis by examining the (non-) analyticity properties of the corresponding transfer integral (TI) equation. The present note deals with the generic Peyrard-Bishop model of DNA denaturation. In the absence of exact statements about the spectrum of the singular TI equation, I use Gauss-Hermite quadratures to achieve a single-parameter-controlled approach to rounding effects; this allows me to employ finite-size scaling concepts in order to demonstrate that a phase transition occurs and to derive the critical exponents.

cond-mat.stat-mech↗

arXiv2001

Thermodynamic instabilities in one dimension: correlations, scaling and solitons

Many thermodynamic instabilities in one dimension (e.g. DNA thermal denaturation, wetting of interfaces) can be described in terms of simple models involving harmonic coupling between nearest neighbors and an asymmetric on-site potential with a repulsive core, a stable minimum and a flat top. The paper deals with the case of the Morse on-site potential, which can be treated exactly in the continuum limit. Analytical expressions for correlation functions are derived; they are shown to obey scaling; numerical transfer-integral values obtained for a discrete version of the model exhibit the same critical behavior. Furthermore, it is shown in detail that the onset of the transition can be characterized by an entropic stabilization of an -otherwise unstable-, nonlinear field configuration, a soliton-like domain wall (DW) with macroscopic energy content. The statistical mechanics of the DW provides an exact estimate of the critical temperature for a wide range of the discretization parameter; this suggests that the transition can be accurately viewed as being "driven" by a nonlinear entity.

cond-mat.stat-mech↗

arXiv2000

Order of the phase transition in models of DNA thermal denaturation

We examine the behavior of a model which describes the melting of double-stranded DNA chains. The model, with displacement-dependent stiffness constants and a Morse on-site potential, is analyzed numerically; depending on the stiffness parameter, it is shown to have either (i) a second-order transition with "nu_perpendicular" = - beta = 1, "nu_parallel" = gamma/2 = 2 (characteristic of short range attractive part of the Morse potential) or (ii) a first-order transition with finite melting entropy, discontinuous fraction of bound pairs, divergent correlation lengths, and critical exponents "nu_perpendicular" = - beta = 1/2, "nu_parallel" = gamma/2 = 1.

cond-mat.stat-mech↗