Related papers: Disorder in DNA-Linked Gold Nanoparticle Assemblie…
In this paper we report direct measurement of large low frequency temperature fluctuations in double stranded (ds) DNA when it undergoes thermal denaturation transition. The fluctuation, which occurs only in the temperature range where the…
In metal nanoparticles (NPs) supracrystals, the metallic core provides some key properties, e.g. magnetization, plasmonic response or conductivity, with the ligand molecules giving rise to others like solubility, assembly or interaction…
Collective response of DNA to THz electric fields is studied in a simple pair bond model. We confirm, with some caveats, a previous observation of destabilising DNA breather modes and explore the parameter-dependence of these modes. It is…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
Peaks in the probabilities of loops or bubbles, helical segments, and unzipping ends in melting DNA are found in this article using a peak finding method that maps the hierarchical structure of certain energy landscapes. The peaks indicate…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
We investigate the influence of a dissipative environment which effectively comprises the effects of counterions and hydration shells, on the transport properties of short \DNA wires. Their electronic structure is captured by a…
For an understanding of DNA elasticity at high mechanical loads (F > 30 pN), its helical nature needs to be taken into account, in the form of coupling between the twist and stretch degrees of freedom. The prevailing model for DNA…
We investigate the impact of pairing correlations on the behavior of unstable asymmetric nuclear matter at low temperature. We focus on the relative role of the pairing interaction, coupling nucleons of the same type (neutrons or protons),…
The melting-like transition in disordered sodium clusters Na_N, with N=92 and 142 is studied by using a first-principles constant-energy molecular dynamics simulation method. Na_142, whose atoms are distributed in two (surface and inner)…
Condensation phenomena in particle systems typically occur as one of two distinct types: either as a spontaneous symmetry breaking in a homogeneous system, in which particle interactions enforce condensation in a randomly located site, or…
In this work, low temperature thermodynamic behaviour in the context of dissipative diamagnetism with anomalous coupling is analyzed. We find that finite dissipation substitutes the zero-coupling result of exponential decay of entropy by a…
The effect of heterogeneous sequence composition on the denaturation of double stranded DNA is investigated. The resulting pair-binding energy variation is found to have a negligible effect on the critical properties of the smooth second…
The thermodynamical properties of heterogeneous DNA sequences are computed by path integral techniques applied to a nonlinear model Hamiltonian. The base pairs relative displacements are interpreted as time dependent paths whose amplitudes…
For short DNA molecules in crowded environments, we evaluate macroscopic parameters such as the average end-to-end distance and the twist conformation by tuning the strength of the site specific confinement driven by the crowders. The…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
The instantaneous normal modes corresponding to base pair vibrations (radial modes) and twist angle fluctuations (angular modes) of a DNA molecule model at ambient temperature are theoretically investigated. Due to thermal disorder, normal…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
We analyze the effects of site-dilution disorder on the thermodynamic properties of the two-dimensional Kondo necklace using finite-temperature stochastic series expansion. Results will be discussed for the dependence on dilution…
Base pair mismatch can relieve mechanical stress in highly strained DNA molecules, but how it affects their kinetic stability is not known. Using single-molecule Fluorescence Resonance Energy Transfer (FRET), we measured the lifetimes of…