Related papers: Helix-coil Transition in Closed Circular DNA
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
{Analytical equations like Richardson-Dushman's or Shockley's provided a general, if simplified conceptual background, which was widely accepted in conventional electronics and made a fundamental contribution to advances in the field. In…
The Poland-Scheraga (PS) model for the helix-coil transition of DNA considers the statistical mechanics of the thermally induced binding of two complementary strands of DNA. In this paper, we show how to modify the PS model when a torque is…
We use super-paramagnetic spherical particles which are arranged in a two-dimensional monolayer at a water/air interface to investigate the crystal to liquid phase transition. According to the KTHNY theory a crystal melts in thermal…
We present a simple unifying model for crystallization and melting temperatures by showing that homogeneous nucleation and phase transformations driven by thickening of pre-existing surface layers are limiting conditions of the more general…
Comparing the obtained experimental data for the proton magnetic relaxation with the microcalorimetric ones it is concluded that in the aqueous solution of collagen + DNA at temperatures below 35oC a stable molecular complex collagen-DNA is…
We explore the coupling between the helix-coil and coil-globule transitions of a helical polymer using Monte Carlo simulations. A very rich state diagram is found. Each state is characterized by a specific configuration of the chain which…
We present a coarse-grained model of DNA-functionalized colloids that is computationally tractable. Importantly, the model parameters are solely based on experimental data. Using this highly simplified model, we can predict the phase…
DNA-coated colloids can crystallize into a multitude of lattices, ranging from face-centered cubic to diamond and thereby contribute to our understanding of crystallization and open avenues to producing structures with useful photonic…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We demonstrate a novel method to ionize molecules or molecular clusters by proton transfer at temperatures below 1 K. The method yields nascent ions and largely eliminates secondary reactions, even for notoriously "delicate" molecules.…
A simple model of a circularly closed dsDNA in a poor solvent is considered as an example of a semi-flexible polymer with self-attraction. To find the ground states, the conformational energy is computed as a sum of the bending and…
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 present understanding of reaction processes involving light unstable nuclei at energies around the Coulomb barrier is reviewed. The effect of coupling to direct reaction channels on elastic scattering and fusion is investigated, with…
In this paper, we show that the coarse grain model for DNA, which has been proposed recently by Knotts, Rathore, Schwartz and de Pablo (J. Chem. Phys. 126, 084901 (2007)), can be adapted to describe the thermal and mechanical denaturation…
Our observations of TMC-1 with the Yebes 40 m radio telescope in the 31.0-50.3 GHz range allowed us to detect a group of unidentified lines, showing a complex line pattern indicative of an open-shell species. {}The observed frequencies of…
We study the coupled rotation-vibration levels of a hydrogen molecule in a confining potential with cylindrical symmetry. We include the coupling between rotations and translations and show how this interaction is essential to obtain the…
A Coupled Natural Circulation Loop (CNCL) consists of two Natural Circulation Loops (NCL) coupled thermally via a common heat exchanger. The transient modelling of such systems that have practical relevance has not been reported in the…
We examine several different simplified approaches for modelling the chemistry of CO in three-dimensional numerical simulations of turbulent molecular clouds. We compare the different models both by looking at the behaviour of integrated…