Related papers: Modeling DNA Dynamics by Path Integrals
The flexibility of short DNA chains is investigated via computation of the average correlation function between dimers which defines the persistence length. Path integration techniques have been applied to confine the phase space available…
DNA helicases are molecular motors that use the energy from ATP hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41,…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
In this work we propose a model for DNA double helix within the tight-binding framework that incorporates the helicity of the molecules. We have studied localization properties of three DNAsequences,the periodic poly(dG)-poly(dC) and…
A statistical method is developed to estimate the maximum amplitude of the base pair fluctuations in a three dimensional mesoscopic model for nucleic acids. The base pair thermal vibrations around the helix diameter are viewed as a Brownian…
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
The binding of proteins onto DNA contributes to the shaping and packaging of genome as well as to the expression of specific genetic messages. With a view to understanding the interplay between the presence of proteins and the deformation…
The intrinsic double helix conformation of the DNA strands is known to be the key ingredient of control of the electric current through the DNA by the perpendicular (gate) electric field. We show theoretically that Bloch oscillations in the…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
I present a Hamiltonian model and a computational method suitable to evaluate structural and thermodynamic properties of helical molecules embedded in crowded environments which may confine the space available to the base pair fluctuations.…
While the statistical mechanical description of DNA has a long tradition, renewed interest in DNA melting from a physics perspective is nourished by measurements of the fluctuation dynamics of local denaturation bubbles by single molecule…
In this work we report the study of conformation dependent electronic transport properties of DNA double-helix within tight-binding framework including its helical symmetry. We have studied the changes in localization properties of DNA as…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
The in vivo free energy of looping double-stranded DNA by the lac repressor has a remarkable behavior whose origins are not fully understood. In addition to the intrinsic periodicity of the DNA double helix, the in vivo free energy has an…
The free energy of looping DNA by proteins and protein complexes determines to what extent distal DNA sites can affect each other. We inferred its in vivo value through a combined computational-experimental approach for different lengths of…
A three dimensional mesoscopic model is applied to study the properties of short DNA chains in a confining environment. The cylindrical channel is represented by a hard-wall repulsive potential incorporated in the system Hamiltonian. The…
We present a new dynamical model of DNA. This model has two degrees of freedom per base-pair: one radial variable related to the opening of the hydrogen bonds and an angular one related to the twisting of each base-pair responsible for the…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…