Related papers: DNA unzipping via stopped birth and death processe…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
DNA hairpin molecules with periodic base sequences can be expected to exhibit a regular coarse-grained free energy landscape (FEL) as function of the number of open base pairs and applied mechanical force. Using a commonly employed model,…
A solid-state nanopore can electrophoretically capture a DNA molecule and pull it through in a folded configuration. The resulting ionic current signal indicates where along its length the DNA was captured. A statistical study using an 8 nm…
Active (catalysed) and passive (intrinsic) nucleosome repositioning is known to be a crucial event during the transcriptional activation of certain eucaryotic genes. Here we consider theoretically the intrinsic mechanism and study in detail…
Denoising Diffusion Probabilistic Models (DDPMs) are a very popular class of deep generative model that have been successfully applied to a diverse range of problems including image and video generation, protein and material synthesis,…
Cells use genetic switches to shift between alternate gene expression states, e.g., to adapt to new environments or to follow a developmental pathway. Here, we study the dynamics of switching in a generic-feedback on/off switch. Unlike…
Experiments indicate that unbinding rates of proteins from DNA can depend on the concentration of proteins in nearby solution. Here we present a theory of multi-step replacement of DNA-bound proteins by solution-phase proteins. For four…
It was first suggested by Englander et al to model the nonlinear dynamics of DNA relevant to the transcription process in terms of a chain of coupled pendulums. In a related paper [q-bio.BM/0604014] we argued for the advantages of an…
Recently, some authors have shown that a DNA molecule produces electromagnetic signals and communicates with other DNA molecules or other molecules. In fact, a DNA acts like a receiver or transmitter of radio waves. In this paper, we…
Using Monte Carlo simulations, we study the hysteresis in unzipping of a double stranded block copolymer DNA with $-A_n B_n-$ repeat units. Here $A$ and $B$ represent two different types of base pairs having two- and three-bonds,…
Dynamic Causal Modeling (DCM) is a Bayesian framework for inferring on hidden (latent) neuronal states, based on measurements of brain activity. Since its introduction in 2003 for functional magnetic resonance imaging data, DCM has been…
We unzip DNA molecules using optical tweezers and determine the sizes of the cooperatively unzipping and zipping regions separating consecutive metastable intermediates along the unzipping pathway. Sizes are found to be distributed…
We study a diagnostic strategy which is based on the anticipation of the diagnostic process by simulation of the dynamical process starting from the initial findings. We show that such a strategy could result in more accurate diagnoses…
Stochastic dynamics govern many important processes in cellular biology, and an underlying theoretical approach describing these dynamics is desirable to address a wealth of questions in biology and medicine. Mathematical tools exist for…
DNA looping is important in DNA condensation and regulation. One method for forming a DNA loop, thought to be used by the condensing agent protamine, is bind-and-bend. In bind-and-bend, molecules bind all along the DNA, each creating a bend…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
Simple mechanical models of DNA play an important role in studying the dynamics of its open states. The main requirement when developing a DNA model is the correct selection of its effective potentials and parameters based on experimental…
The Peyrard-Bishop DNA model describes the molecular interactions with simple potentials which allow efficient calculations of melting temperatures. However, it is based on a Hamiltonian that does not consider the helical twist or any other…
{\it Transcription} is the process whereby RNA molecules are polymerized by molecular machines, called RNA polymerase (RNAP), using the corresponding DNA as the template. Recent {\it in-vivo} experiments with single cells have established…
We propose a stochastic model for evolution. Births and deaths of species occur with constant probabilities. Each new species is associated with a fitness sampled from the uniform distribution on [0,1]. Every time there is a death event…