Related papers: Statistical physics and mesoscopic modeling to int…
Tethered particle motion is an experimental technique to monitor conformational changes in single molecules of DNA in real time, by observing the position fluctuations of a micrometer-size particle attached to the DNA. This article reviews…
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…
The Tethered Particle Motion (TPM) method has been used to observe and characterize a variety of protein-DNA interactions including DNA looping and transcription. TPM experiments exploit the Brownian motion of a DNA-tethered bead to probe…
The Tethered Particle Motion (TPM) technique informs about conformational changes of DNA molecules, e.g. upon looping or interaction with proteins, by tracking the Brownian motion of a particle probe tethered to a surface by a single DNA…
Tethered particle experiments use light microscopy to measure the position of a micrometer-sized bead tethered to a microscope slide via a ~micrometer length polymer, in order to infer the behavior of the invisible polymer. Currently, this…
In many biochemical processes, proteins bound to DNA at distant sites are brought into close proximity by loops in the underlying DNA. For example, the function of some gene-regulatory proteins depends on such DNA looping interactions. We…
Tethered Particle Motion (TPM) is a single molecule technique, which consists in tracking the motion of a nano-particle (NP) immersed in a fluid and tethered to a glass surface by a DNA molecule. The present work addresses the question of…
Single-particle traces of the diffusive motion of molecules, cells, or animals are by-now routinely measured, similar to stochastic records of stock prices or weather data. Deciphering the stochastic mechanism behind the recorded dynamics…
The statistics of the diffusive motion of particles often serve as an experimental proxy for their interaction with the environment. However, inferring the physical properties from the observed trajectories is challenging. Inspired by a…
Single-molecule stretching experiments are widely utilized within the fields of physics and chemistry to characterize the mechanics of individual bonds or molecules, as well as chemical reactions. Analytic relations describing these…
DNA-interacting proteins have roles multiple processes, many operating as molecular machines which undergo dynamic metastable transitions to bring about their biological function. To fully understand this molecular heterogeneity, DNA and…
We describe a simple numerical simulation, suitable for an undergraduate project (or graduate problem set), of the Brownian motion of a particle in a Hooke-law potential well. Understanding this physical situation is a practical necessity…
Molecular Dynamics (MD) simulations are fundamental computational tools for the study of proteins and their free energy landscapes. However, sampling protein conformational changes through MD simulations is challenging due to the relatively…
We describe a simple automated method to extract and quantify transient heterogeneous dynamical changes from large datasets generated in single molecule/particle tracking experiments. Based on wavelet transform, the method transforms raw…
In the course of evolution, proteins undergo important changes in their amino acid sequences, while their three-dimensional folded structure and their biological function remain remarkably conserved. Thanks to modern sequencing techniques,…
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…
The use of machine learning algorithms is an attractive way to produce very fast detector simulations for scattering reactions that can otherwise be computationally expensive. Here we develop a factorised approach where we deal with each…
Electronic transport properties for single-molecule junctions have been widely measured by several techniques, including mechanically controllable break junctions, electromigration break junctions or by means of scanning tunneling…
A methodology for the statistical mechanical analysis of polymeric chains under tension introduced previously is extended to include torque. The response of individual bonds between monomers or of entire groups of monomers to a combination…
Studying systems where many individual bodies in motion interact with one another is a complex and interesting area. Simple mechanisms that may be determined for biological, chemical, or physical reasons can lead to astonishingly complex…