Related papers: Anharmonic stacking in supercoiled DNA
The equilibrium statistical properties of DNA denaturation bubbles are examined in detail within the framework of the Peyrard-Bishop-Dauxois model. Bubble formation in homogeneous DNA is found to depend crucially on the presence of…
Self-assembling novel ordered structures with nanoparticles has recently received much attention. Here we use computer simulations to study a two-dimensional model system characterized by a simple isotropic interaction that could be…
We analyze different microscopic RNA models at zero temperature. We discuss both the most simple model, that suffers a large degeneracy of the ground state, and models in which the degeneracy has been remove, in a more or less severe…
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We…
The stability and dynamics of a double-stranded DNA (dsDNA) is affected by the preferential occupancy of small monovalent molecular ions. Small metal and molecular ions such as sodium and alkyl ammonium have crucial biological functions in…
The influence of decoherence and bonding on the linear conductance of single double-stranded DNA molecules is examined by fitting a phenomenological statistical model developed recently (EPJB {\bf 68}, 237 (2009)) to experimental results.…
Mechanical properties of nucleic acids play an important role in many biological processes which often involve physical deformations of these molecules. At sufficiently long length scales (say above $\sim 20-30$ base pairs) the mechanics of…
The nature of stacking faults - whether intrinsic or extrinsic - plays a pivotal role in defect-mediated processes in crystalline materials. Yet, current electron microscopy techniques for their reliable analysis remain limited to either…
A strong-coupling expansion is applied to the anharmonic Holstein model and to the Holstein-Hubbard model through fourth order in the hopping matrix element. Mean-field theory is then employed to determine transition temperatures of the…
We use X-ray scattering and molecular simulations to investigate the structural properties of complexes of multivalent cationic lipids and DNA molecules. At low mole fraction of neutral lipids (NLs), $\Phi_{\rm NL}$, the complexes show…
Thermoelectric properties of Half Heusler alloys are predicted by adopting an ensemble modelling approach, specifically the stacking model integrated using Random Forest and XGBoost scheme. Leveraging a diverse dataset encompassing thermal…
A simplified model for the closed circular DNA (ccDNA) is proposed to describe some specific features of the helix-coil transition in such molecule. The Hamiltonian of ccDNA is related to the one introduced earlier for the linear DNA. The…
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…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Isomorphs are curves in the thermodynamic phase diagram of invariant excess entropy, structure, and dynamics, while pseudoisomorphs are curves of invariant structure and dynamics, but not of the excess entropy. The latter curves have been…
The statistical mechanics of DNA denaturation under fixed linking number is qualitatively different from that of the unconstrained DNA. Quantitatively different melting scenarios are reached from two alternative assumptions, namely, that…
Combining two-color infared pump-probe spectroscopy and anharmonic force field calculations we characterize the anharmonic coupling patterns between fingerprint modes and the hydrogen-bonded symmetric NH$_2$ stretching vibration in…
We present an analysis of the role of global topology on the structural stability of folded proteins in thermal equilibrium with a heat bath. For a large class of single domain proteins, we compute the harmonic spectrum within the Gaussian…
Negatively charged DNA can be compacted by positively charged dendrimers and the degree of compaction is a delicate balance between the strength of the electrostatic interaction and the elasticity of DNA. We report various elastic…
It is shown that curved and flat helical double twisted liquid crystal (DTLC) in blue phase, can be unstable (stable) depending of the sign, negative (positive) of sectional curvature, depending on the pitch of the helix of the nematic…