Related papers: Heat conductivity of DNA double helix
The combination of self-assembly and electronic properties as well as its true nanoscale dimensions make DNA a promising candidate for a building block of single molecule electronics. We argue that the intrinsic double helix conformation of…
Genomes contain rare guanine-rich sequences capable of assembling into four-stranded helical structures, termed G-quadruplexes, with potential roles in gene regulation and chromosome stability. Their mechanical unfolding has only been…
We investigate quantum transport in aligned carbon nanotube (CNT) fibers fabricated via solution spinning, focusing on the roles of structural dimensionality and quantum interference effects. The fibers exhibit metallic behavior at high…
Simulating large-scale protein dynamics using traditional all-atom molecular dynamics (MD) remains computationally prohibitive. We present a unified, universal framework for coarse-grained molecular dynamics (CG-MD) that achieves…
Heat management is crucial in the design of nanoscale devices as the operating temperature determines their efficiency and lifetime. Past experimental and theoretical works exploring nanoscale heat transport in semiconductors addressed…
We report measurements of the heat capacity and cross-plane thermal conductivity of 2D (CxH2x+1NH3)2[MAPbBr3]n-1PbBr4 (MA = methylammonium) lead bromide perovskites (2D LHPs) at room temperature as a function of both the octahedral layer…
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…
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…
We define a DNA as a sequence of $\pm 1$'s and embed it on a path of Cayley tree. Using group representation of the Cayley tree, we give a hierarchy of a countable set of DNAs each of which 'lives' on the same Cayley tree. This hierarchy…
We introduce a model of thermalized conformations in space of RNA -or single stranded DNA- molecules, which includes the possibility of hairpin formation. This model contains the usual secondary structure information, but extends it to the…
The folding of RNA and DNA strands plays crucial roles in biological systems and bionanotechnology. However, studying these processes with high-resolution numerical models is beyond current computational capabilities due to the timescales…
We propose a new strategy to improve the self-assembly properties of DNA-functionalised colloids. The problem that we address is that DNA-functionalised colloids typically crystallize in a narrow temperature window, if at all. The…
Molecular dynamics simulations have been extensively used to predict thermal properties, but simulating different phases with similar precision using a unified force field is often difficult, due to the lack of accurate and transferrable…
To bridge the gap between the sequences and 3-dimensional (3D) structures of RNAs, some computational models have been proposed for predicting RNA 3D structures. However, the existed models seldom consider the conditions departing from the…
To simulate long time and length scale processes involving DNA it is necessary to use a coarse-grained description. Here we provide an overview of different approaches to such coarse graining, focussing on those at the nucleotide level that…
Within a simple elastic theory, we study the elongation versus force characteristics of a supercoiled DNA molecule at thermal equilibrium in the regime of small supercoiling. The partition function is mapped to the path integral…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
Using non-equilibrium molecular dynamics (NEMD) simulation, we study thermal properties of the so-called nanoporous graphene (NPG) sheet which contains a series of nanoporous in an ordered way and was synthesized recently (Science 360…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…