Related papers: Modelling toehold-mediated RNA strand displacement
Tethered particle motion (TPM) --- the motion of a micro- or nanoparticle tethered to a substrate by a macromolecule --- is a system that has proven extremely useful for its ability to reveal physical features of the tether, because the…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
We show that non-steric molecular interactions between RNA polymerase (RNAP) motors that move simultaneously on the same DNA track determine strongly the kinetics of transcription elongation. With a focus on the role of collisions and…
The dielectrophoresis method for trapping and attaching nanoscale double-stranded DNA between nanoelectrodes was developed. The method gives a high yield of trapping single or a few molecules only which enables transport measurements at the…
We develop a simple model to study the effects of an applied force on the melting of a double stranded DNA (dsDNA). Using this model, we could study the stretching, unzipping, rupture and slippage like transition in a dsDNA. We show that in…
We study the properties of moving breathers in a bent DNA-related model with short range interaction, due to the stacking of the base pairs, and long range interaction, due to the finite dipole moment of the bonds within each base pair. We…
The statistical mechanics of heteropolymer structure formation is studied in the context of RNA secondary structures. A designed RNA sequence biased energetically towards a particular native structure (a hairpin) is used to study the…
DNA migration in topologically structured microchannels with periodic cavities is investigated experimentally and with Brownian dynamics simulations of a simple bead-spring model. The results are in very good agreement with one another. In…
The dynamics of molecular motors which occasionally detach from a heterogeneous track like DNA or RNA is considered. Motivated by recent single molecule experiments, we study a simple model for a motor moving along a disordered track using…
The mean-square displacement (MSD) was measured by neutron scattering at various temperatures and pressures for a number of molecular glass-forming liquids. The MSD is invariant along the glass-transition line at the pressure studied, thus…
The kinetic folding of RNA sequences into secondary structures is modeled as a complex adaptive system, the components of which are possible RNA structural rearrangements (SRs) and their associated bases and base pairs. RNA bases and base…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
Translocation through a nanopore is a new experimental technique to probe physical properties of biomolecules. A bulk of theoretical and computational work exists on the dependence of the time to translocate a single unstructured molecule…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
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…
We investigate the translocation of a single stranded DNA (ssDNA) through a pore, which fluctuates between two conformations, by using coupled master equations (ME). The probability density function (PDF) of the first passage times (FPT) of…
The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an…
Recent advances in DNA sequencing and fluorescence imaging have made it possible to monitor the dynamics of ribosomes actively engaged in messenger RNA (mRNA) translation. Here, we model these experiments within the inhomogeneous totally…
The thermophysical properties of supported and free-standing nanomaterials would be different due to the substrate effect. To determine the thermophysical properties of supported 2D nanomaterials, this paper developed a two-step…