Related papers: DNA Looping Kinetics Analyzed Using Diffusive Hidd…
The dynamics of particles interacting by key-lock binding of attached biomolecules are studied theoretically. Experimental realizations of such systems include colloids grafted with complementary single-stranded DNA (ssDNA), and particles…
The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible…
We present dynamic light scattering (DLS) measurements of soft polymethyl-methacrylate (PMMA) and polyacrylamide(PA) polymer gels prepared with trapped bodies (latex spheres or maghemite nanoparticles). We show that the anomalous…
The damping effect to the DNA bubble is investigated within the Peyrard-Bishop model. In the continuum limit, the dynamics of the bubble of DNA is described by the damped nonlinear Schrodinger equation and studied by means of variational…
Microrheology, the study of fluids on micron length-scales, promises to reveal insights into cellular biology, including mechanical biomarkers of disease and the interplay between biomechanics and cellular function. Here a…
The short supercoiled circular DNA molecules are shown to be glassy systems and canonical Metropolis Monte Carlo simulations of the systems tend to get stuck in local metastable energy basins. A novel Monte Carlo algorithm is developed to…
Using high-resolution confocal rheometry, we study the shear profiles of well-entangled DNA solutions under large amplitude oscillatory shear (LAOS) in a rectilinear planar shear cell. With increasing Weissenberg number (Wi), we observe…
Sampling from the conditional (or posterior) probability distribution of the latent states of a Hidden Markov Model, given the realization of the observed process, is a non-trivial problem in the context of Markov Chain Monte Carlo. To do…
The dynamics of a loop in DNA molecules at the denaturation transition is studied by scaling arguments and numerical simulations. The autocorrelation function of the state of complementary bases (either closed or open) is calculated. The…
Many fundamental biological processes are regulated by protein-DNA complexes called {\it synaptosomes}, which possess multiple interaction sites. Despite the critical importance of synaptosomes, the mechanisms of their formation remain not…
Mesh-like structures, such as mucus gel or cytoskeleton networks, are ubiquitous in biological systems. These intricate structures are composed of cross-linked, semi-flexible bio-filaments, crucial to numerous biological processes. In many…
Recent work has shown that the resistive force arising from viscous effects within the pore region could explain [Ghosal, S. Phys. Rev. E. vol. 71, 051904 (2006) and Phys. Rev. Lett. vol. 98, 238104 (2007)] observed translocation times in…
Wearable devices including accelerometers are increasingly being used to collect high-frequency human activity data in situ. There is tremendous potential to use such data to inform medical decision making and public health policies.…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
The movement of intracellular cargo transported by molecular motors is commonly marked by switches between directed motion and stationary pauses. The predominant measure for assessing movement is effective diffusivity, which predicts the…
The problem of detecting a sinusoidal signal with randomly varying frequency has a long history. It is one of the core problems in signal processing, arising in many applications including, for example, underwater acoustic frequency line…
Motivated by recent single molecule studies of proteins sliding on a DNA molecule, we explore the targeting dynamics of N particles ("proteins") sliding diffusively along a line ("DNA") in search of their target site (specific target…
Complex DNA topological structures, including polymer loops, are frequently observed in biological processes when protein molecules simultaneously bind to several distant sites on DNA. However, the molecular mechanisms of formation of these…
We carry out uniaxial continuous and step stretching of various crosslinked polymer networks to demonstrate how characteristics of rupture (from continuous stretching) and delayed rupture (from step stretching) can be used to probe the…
The mechanical properties of DNA play a critical role in many biological functions. For example, DNA packing in viruses involves confining the viral genome in a volume (the viral capsid) with dimensions that are comparable to the DNA…