A new multiscale coarse-graining (CG) methodology is developed to bridge molecular and hydrodynamic models of a fluid. The hydrodynamic representation considered in this work is based on the equations of fluctuating hydrodynamics (FH). The essence of …
A multiscale computational method is developed to model the nanoscale viscoelasticity of fluids by bridging non-Markovian fluctuating hydrodynamics (FHD) and molecular dynamics (MD) simulations. To capture the elastic responses that emerge at small …
We discuss connections between the nonlinear dynamics of double-stranded DNA, experimental findings, and specific DNA functions. We begin by discussing how thermally induced localized openings (bubbles) of the DNA double strand are important for …
We present single-molecule measurements of the opening rate of DNA hairpins under mechanical tension and compare with the results obtained from a reduced-degrees-of-freedom statistical mechanics model. We extract the apparent position of the …
A study of the micromechanical unzipping of DNA in the framework of the Peyrard-Bishop-Dauxois model is presented. We introduce a Monte Carlo technique that allows accurate determination of the dependence of the unzipping forces on unzipping speed …
Using a well established model, we systematically analyze fundamental limitations on the viability of using mechanical unzipping of DNA as a fast and inexpensive sequencing method. Standard unzipping techniques, where double-stranded DNA is unzipped …
The onset of intermediate states (denaturation bubbles) and their role during the melting transition of DNA are studied using the Peyrard-Bishop- Dauxois model by Monte Carlo simulations with no adjustable parameters. Comparison is made with …
We investigate numerically existence and dynamical properties of intrinsic localization in crystalline silicon through the use of interatomic Tersoff force fields. We find a band of intrinsic localized modes (discrete breathers) each with lifetime of …
We report numerical simulations of the contribution of the transverse hydrogen bond stretching vibrations in the dynamic structure factor of a DNA sequence. We apply a simple nonlinear dynamical model to a finite segment of the bacteriophage T7 core …
We compare numerical calculations and experimental data showing that large, slow thermally-induced openings of double stranded DNA coincide with the location of functionally relevant sites for transcription. Investigating a bacteriophage DNA gene …