Related Experiment Video
Updated: Jan 26, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
Published on: April 4, 2025
Dynamics of DNA Squeezed Inside a Nanochannel via a Sliding Gasket
Aiqun Huang1, Walter Reisner2, Aniket Bhattacharya3
1University of Central Florida, 4000 Central Florida Blvd, Orlando, FL 32816, USA. aiqunhuang@knights.ucf.edu.
Abstract:
We use Brownian dynamics (BD) simulation of a coarse-grained (CG) bead-spring model of DNA to study the nonequilibrim dynamics of a single DNA molecule confined inside a rectangular nanochannel being squeezed with a sliding gasket piston or "nanodozer". From our simulations we extract the nonequilibrim density profile c ( x , t ) of the squeezed molecule along the channel axis (x-coordinate) and then analyze the non-equilibrium profile using a recently introduced phenomenological Nonlinear Partial Differential Equation (NPDE) model. Since the NPDE approach also fits the experimental results well and is numerically efficient to implement, the combined BD + NPDE methods can be a powerful approach to analyze details of the confined molecular dynamics. In particular, the overall excellent agreement between the two complementary sets of data provides a strategy for carrying out large scale simulation on semi-flexible biopolymers in confinement at biologically relevant length scales.
Related Concept Videos
Design Example: Designing Water Slide
Bernoulli's principle determines the water's velocity along the slide....
DNA Helicases
Translesion DNA Polymerases
TLS polymerases are found in all three domains of life - archaea, bacteria, and eukaryotes. Of the different classes of TLS polymerases, members of the Y family are fitted with specialized structures that...
Dynamic Equilibrium
DNA Topoisomerases
Types and Mechanism of action
Topoisomerases are divided into two main types. ...
Recombinant DNA

