Related papers: Probing DNA conformational changes with high tempo…
The dynamics of the DNA denaturation is studied using the Peyrard-Bishop-Dauxois model. The denaturation rate of double stranded polymers decreases exponentially as function of length below the denaturation temperature. Above Tc, the rate…
Interest in studying the interaction of small molecules with DNA is caused by the need to develop new, highly effective, and low-toxic drugs for cancer treatment. The strong and highly specific binding of thionine with DNA makes it a…
Dynamics of individual DNA undergoing constant field gel electrophoresis (CFGE) is studied by a Brownian dynamics (BD) simulation method which we have developed. The method simulates electrophoresis of DNA in a 3 dimensional (3D) space by a…
To characterize the thermodynamical equilibrium of DNA chains interacting with a solution of non-specific binding proteins, a Flory-Huggins free energy model was implemented. We explored the dependence on DNA and protein concentrations of…
We study the first passage time for a polymer, that we call the narrow encounter time (NETP), to reach a small target located on the surface of a microdomain. The polymer is modeled as a Freely Joint Chain (beads connected by springs with a…
Long DNA molecules can be mapped by cutting them with restriction enzymes inside a narrow channel. Once cut, the individual fragments thus produced move away from each other due to diffusion and entropic effects. We investigate how long it…
Cells deploy robust mechanisms to repair DNA damage, safeguarding genomic stability and cellular health, but the physical principles underlying these processes remain incompletely understood. Experiments show \emph{in vitro} that upon a DNA…
Motivated by subdiffusive motion of bio-molecules observed in living cells we study the stochastic properties of a non-Brownian particle whose motion is governed by either fractional Brownian motion or the fractional Langevin equation and…
We characterize the equilibrium thermodynamics of a thick polymer confined in a spherical region of space. This is used to gain insight into the DNA packaging process. The experimental reference system for the present study is the recent…
Diffusion and flow matching models have achieved remarkable success in text-to-image generation. However, these models typically rely on the predetermined denoising schedules for all prompts. The multi-step reverse diffusion process can be…
The exact analytical expressions for the time-dependent cross-correlations of the translational and rotational Brownian displacements of a particle with arbitrary shape were derived by us in [J. Chem. Phys. 142, 214902 (2015) and 144,…
By combining analytical theory and Molecular Dynamics simulations we study the relaxation dynamics of DNA circular plasmids that initially undergo a local twist perturbation. We identify three distinctive time scales; (I) a rapid relaxation…
Based on analytical and numerical calculations we study the dynamics of an overdamped colloidal particle moving in two dimensions under time-delayed, non-linear feedback control. Specifically, the particle is subject to a force derived from…
Helical molecules change their twist number under the effect of a mechanical load. We study the twist-stretch relation for a set of short DNA molecules modeled by a mesoscopic Hamiltonian. Finite temperature path integral techniques are…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
We apply Thermostatted Ring Polymer Molecular Dynamics (TRPMD), a recently-proposed approximate quantum dynamics method, to the computation of thermal reaction rates. Its short-time Transition-State Theory (TST) limit is identical to…
Electromagnetic scattering and absorption by material particles is a fundamental physical problem with a broad range of applications, going from laboratory experiments, biology and material sciences, all the way up to environmental studies…
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…
In a typical single molecule experiment, dynamics of an unfolded proteins is studied by determining the reconfiguration time using long-range Forster resonance energy transfer where the reconfiguration time is the characteristic decay time…
We deduced the torque applied on a single stretched and twisted DNA by integrating with respect to force the change in the molecule's extension as it is coiled. While consistent with previous direct measurements of the torque at high forces…