相关论文: DNA loop statistics and torsional modulus
1) We introduce random discrete Morse theory as a computational scheme to measure the complicatedness of a triangulation. The idea is to try to quantify the frequence of discrete Morse matchings with a certain number of critical cells. Our…
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…
We introduce a novel construction of a contour deformation within the framework of Loop-Tree Duality for the numerical computation of loop integrals featuring threshold singularities in momentum space. The functional form of our contour…
Effect of bending anisotropy on a planar DNA loop, using energy minimization and neglecting entropic effects, is studied. We show that the anisotropy results in polygonal shape of the loop and increasing the anisotropy makes the edges…
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…
A key goal of systems biology is the predictive mathematical description of gene regulatory circuits. Different approaches are used such as deterministic and stochastic models, models that describe cell growth and division explicitly or…
The linking and writhing numbers are key quantities when characterizing the structure of a piece of supercoiled DNA. Defined as double integrals over the shape of the double-helix, these numbers are not always straightforward to compute,…
Recent experimental data indicate that the elastic wormlike rod model of DNA that works well on long length scales may break down on shorter scales relevant to biology. According to Noy and Golestanian (Phys. Rev. Lett. 109, 228101, 2012)…
A quantum spin model representing tautomeric mutation is proposed for any DNA molecule. Based on this model, the quantum mechanical calculations for mutational rate and complementarity restoring repair rate in the replication processes are…
Tandem-duplication-random-loss (TDRL) is an important genome rearrangement operation studied in evolutionary biology. This paper investigates some of the formal properties of TDRL operations on the symmetric group (the space of permutations…
We present a self-contained theory for the mechanical response of DNA in single molecule experiments. Our model is based on a 1D continuum description of the DNA molecule and accounts both for its elasticity and for DNA-DNA electrostatic…
The two strands of a DNA molecule with a repetitive sequence can pair into many different basepairing patterns. For perfectly periodic sequences, early bulk experiments of Poerschke indicate the existence of a sliding process, permitting…
We derive the single molecule equation of state (force-extension relation) for DNA molecules bearing sliding loops and deflection defects. Analytical results are obtained in the large force limit by employing an analogy with instantons in…
This paper focuses on the probability that a portion of DNA closes on itself through thermal fluctuations. We investigate the dependence of this probability upon the size r of a protein bridge and/or the presence of a kink at half DNA…
Determining gene regulatory network (GRN) structure is a central problem in biology, with a variety of inference methods available for different types of data. For a widely prevalent and challenging use case, namely single-cell gene…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
We propose a new approach to the problem of neural network expressivity, which seeks to characterize how structural properties of a neural network family affect the functions it is able to compute. Our approach is based on an interrelated…
Ordinary differential equations (ODEs) are foundational in modeling intricate dynamics across a gamut of scientific disciplines. Yet, a possibility to represent a single phenomenon through multiple ODE models, driven by different…
We present micro-rheological measurments of the drag force on colloids pulled through a solution of lambda-DNA (used here as a monodisperse model polymer) with an optical tweezer. The experiments show a violation of the Stokes-Einstein…
We study the electric properties of single-stranded DNA molecules with hairpin-like shapes in the presence of a magnetic flux. It is shown that the current amplitude can be modulated by the applied field. The details of the electric…