Related papers: Phase Diagram for Unzipping DNA Using a Bond-Force…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
A statistical mechanical description of flexible and semi-flexible polymer chains in a poor solvent is developed in the constant force and constant distance ensembles. We predict the existence of many intermediate states at low temperatures…
While stretching of most polymer chains leads to rather featureless force-extension diagrams, some, notably DNA, exhibit non-trivial behavior with a distinct plateau region. Here we propose a unified theory that connects force-extension…
A phenomenological model for the unbinding transition of multi-component fluid membranes is proposed, where the unbinding transition is described using a theory analogous to Flory-Huggins theory for polymers. The coupling between the…
We study the thermodynamics of an exactly solvable model of a self-interacting partially directed self-avoiding walk (DSAW) in two dimensions, when a force is applied on one end of the chain. The critical force for the unfolding is…
We illuminate the many-body effects underlying the structure, formation, and dissolution of cellular adhesion domains in the presence and absence of forces. We consider mixed Glauber-Kawasaki dynamics of a two-dimensional model of…
Using previous results from boundary conformal field theory and integrability, a phase diagram is derived for the 2 dimensional Ising model at its bulk tri-critical point as a function of boundary magnetic field and boundary spin-coupling…
We examined theory for force-induced unbinding on a two-dimensional free energy surface where the internal dynamics of biomolecules is coupled with the rupture process under constant tension f. We show that only if the transition state…
We develop a theoretical description of the critical zipping dynamics of a self-folding polymer. We use tension propagation theory and the formalism of the generalized Langevin equation applied to a polymer that contains two complementary…
When mixed together, DNA and polyaminoamide (PAMAM) dendrimers form fibers that condense into a compact structure. We use optical tweezers to pull condensed fibers and investigate the decondensation transition by measuring force-extension…
Ferromagnetism in one dimension is a novel observation which has been reported in a recent work (P. Gambardella et.al., Nature {\bf 416}, 301 (2002)), anisotropies are responsibles in that relevant effect. In the present work, another…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded DNA whose ends are subjected to a time dependent periodic force with frequency ($\omega$) and amplitude ($G$). For the static force, i.e., $\omega \to…
We consider self-avoiding lattice polygons, in the hypercubic lattice, as a model of a ring polymer adsorbed at a surface and either being desorbed by the action of a force, or pushed towards the surface. We show that, when there is no…
Einstein-dilaton-$U(2)$ gauge field theory is considered in a spacetime characterised by $\alpha$ and $z$, which are the hyperscaling violation factor and the dynamical critical exponent respectively. We obtain the critical values of…
Using a structure-based coarse-grained model of proteins, we study the mechanism of unfolding of knotted proteins through heating. We find that the dominant mechanisms of unfolding depend on the temperature applied and are generally…
Nucleosomes form the basic unit of compaction within eukaryotic genomes and their locations represent an important, yet poorly understood, mechanism of genetic regulation. Quantifying the strength of interactions within the nucleosome is a…
The stability of a $\beta$-sheeted conformation and its transition into a random coil are studied with a 2D lattice biopolymer model. At low temperature and low external force, the polymer folds back and forth on itself and forms a…
The phase diagram of Zn has been explored up to 140 GPa and 6000 K, by combining optical observations, x-ray diffraction, and ab-initio calculations. In the pressure range covered by this study, Zn is found to retain a hexagonal…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
We generalize the Poland-Scheraga model to consider DNA denaturation in the presence of an external stretching force. We demonstrate the existence of a force-induced DNA denaturation transition and obtain the temperature-force phase…