Related papers: Duplex-single strand denaturing transition in DNA …
A systematic study of electron or hole transfer along DNA dimers, trimers and polymers is presented with a tight-binding approach at the base-pair level, using the relevant on-site energies of the base-pairs and the hopping parameters…
Diblock copolymers by virtue of the chemical dissimilarity between the constituting blocks exhibit microphase separation in the melt state. The phase separated melt can successfully be exploited to control the morphology of the final semi…
We have performed parallel tempering Monte Carlo simulations using a simple continuum heteropolymer model for proteins. All ten heteropolymer sequences which we have studied have shown first-order transitions at low temperature to ordered…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
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…
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
In the short time since the first observation of supersolid states of ultracold dipolar atoms, substantial progress has been made in understanding the zero-temperature phase diagram and low-energy excitations of these systems. Less is…
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…
The glass transition temperature and its connection to statistical properties of confined and free-standing polymer films of varying thickness containing unentangled to highly entangled bead-spring chains are studied by molecular dynamics…
The forming and melting of complementary base pairs in RNA duplexes are conformational transitions required to accomplish a plethora of biological functions. Yet the dynamic steps of these transitions have not been quantitatively…
We discuss possible mechanisms that may impact the order of the transition between denaturated and bound DNA states and lead to changes in the scaling laws that govern conformational properties of DNA strands. To this end, we re-consider…
In a recent paper ["Cluster Model of Decagonal Tilings" (to be published in Phys. Rev. B)], we have introduced a cluster model for decagonal tilings in two dimensions. This model is now extended to three dimensions. Two-dimensional tilings…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
In frameworks of scaling theory of phase transitions and critical phenomena the structure of melt-crystallized polymers is discussed. The model constructed follows drawing polymeric materials and dissipating the energy during the transition…
We show that the temperature of a cavity field can be drastically varied by its interaction with suitably-entangled atom pairs (dimers) traversing the cavity under realistic atomic decoherence. To this end we resort to the hitherto untapped…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
We present a base-pairing model of oligonuleotide duplex formation and show in detail its equivalence to the Nearest-Neighbour dimer methods from fits to free energy of duplex formation data for short DNA-DNA and DNA-RNA hybrids containing…
We study the temperature dependence of static and dynamic responses of Coulomb interacting particles in two-dimensional traps across the thermal crossover from an amorphous solid- to liquid-like behaviors. While static correlations, that…
We investigate the one-dimensional Hubbard model with an additional bond-charge interaction, recently considered in the description of compounds that exhibit strong 1D features above the temperature of ordered phases. The partition function…
Mechanical properties of DNA, in particular their stretch dependent extension and their loop formation characteristics, have been recognized as an effective probe for understanding the possible biochemical role played by them in a living…