Related papers: Effect of base-pair sequence on B-DNA thermal cond…
The thermal conductivity of B-form double-stranded DNA (dsDNA) of the Drew-Dickerson sequence d(CGCGAATTCGCG) is computed using classical Molecular Dynamics (MD) simulations. In contrast to previous studies, which focus on a simplified 1D…
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…
BAs was predicted to have an unusually high thermal conductivity at room temperature of 2000$\,$Wm$^{-1}$$\,$K$^{-1}$, comparable to that of diamond. However, the experimentally measured thermal conductivity of BAs single crystals is an…
Dynamics of the polymorphic A<->B transitions in DNA is compared for two polypurine sequences, poly(dA).poly(dT) and poly(dG).poly(dC), long known to exhibit contrasting properties in experiments. In free molecular dynamics simulations…
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal…
Base-pockets (non-complementary base-pairs) in a double-stranded DNA play a crucial role in biological processes. Because of thermal fluctuations, it can lower the stability of DNA, whereas, in case of DNA aptamer, small molecules e.g.…
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…
DNA has a well-defined structural transition -- the denaturation of its double-stranded form into two single strands -- that strongly affects its thermal transport properties. We show that, according to a widely implemented model for DNA…
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…
In this paper, the effect of B and N doping on the phonon induced thermal conductivity of graphene has been investigated. This study is important when one has to evaluate the usefulness of electronic properties of B and N doped graphene. We…
When coupling thermal baths at different temperatures, negative differential thermal conductivity is typically attributed to nonlinear interactions in the connecting medium. In this work, we demonstrate that such an effect can arise purely…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
In this work, we study the thermal energy transport properties of twin graphene, which has been introduced recently as a new two-dimensional carbon nano structure. The thermal conductivity is investigated using non-equilibrium molecular…
Dynamical equations for a polaron and bipolaron in a DNA duplex are obtained on the basis of Holstein-Hubbard Hamiltonian. It is shown that in a PolyA/PolyT duplex especially stable is a bipolaron state in which holes are localized on…
Molecular simulations of polymer rely on accurate force fields to describe the inter-atomic interactions. In this work, we use first-principles density functional theory (DFT) calculations to parameterize a united-atom force field for…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
Single molecule experiments on B-DNA stretching have revealed one or two structural transitions, when increasing the external force. They are characterized by a sudden increase of DNA contour length and a decrease of the bending rigidity.…
We considered a dsDNA polymer in which distribution of bases are random at the base pair level but ordered at a length of 18 base pairs and calculated its force elongation behaviour in the constant extension ensemble. The unzipping force…
We use reverse non-equilibrium molecular dynamics (RNEMD) simulations to determine the thermal conductivity in $\alpha$-RDX in the <100>, <010>, and <001> crystallographic directions. Simulations are carried out with the Smith-Bharadwaj…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…