Related papers: A composite model for DNA torsion dynamics
We present an elastic model of B-form DNA as a stack of thin, rigid plates or base pairs that are not permitted to deform. The symmetry of DNA and the constraint of plate rigidity limit the number of bulk elastic constants contributing to a…
Computer simulations are indispensable for analyzing complex systems, yet high-fidelity models often incur prohibitive computational costs. Multi-fidelity frameworks address this challenge by combining inexpensive low-fidelity simulations…
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…
As a first step in the search of an analytical study of mechanical denaturation of DNA in terms of the sequence, we study stable, stationary solutions in the discrete, finite and homogeneous Peyrard-Bishop DNA model. We find and classify…
We use a coarse-grained molecular model to study the self-assembly process of complexes of cationic and neutral lipids with DNA molecules ("lipoplexes") - a promising nonviral carrier of DNA for gene therapy. We identify the resulting…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
While the behavior of double stranded DNA at mesoscopic scales is fairly well understood, less is known about its relation to the rich mechanical properties in the base-pair scale, which is crucial, for instance, to understand DNA-protein…
Nanopore based sequencing has demonstrated significant potential for the development of fast, accurate, and cost-efficient fingerprinting techniques for next generation molecular detection and sequencing. We propose a specific multi-layered…
We study the effects of the sequence on the propagation of nonlinear excitations in simple models of DNA in which we incorporate actual DNA sequences obtained from human genome data. We show that kink propagation requires forces over a…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
Novel mathematical models of three different repressilator topologies are introduced. As designable transcription factors have been shown to bind to DNA non-cooperatively, we have chosen models containing non-cooperative elements. The…
We propose a new statistical mechanics model for the melting transition of DNA. Base pairing and stacking are treated as separate degrees of freedom, and the interplay between pairing and stacking is described by a set of local rules which…
Magnetic tweezers are used to study the mechanical response under torsion of single nucleosome arrays reconstituted on tandem repeats of 5S positioning sequences. Regular arrays are extremely resilient and can reversibly accommodate a large…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
DNA supercoiling is central to many fundamental processes of living organisms. Its average level along the chromosome and over time reflects the dynamic equilibrium of opposite activities of topoisomerases, which are required to relax…
Gene transcription is a highly stochastic and dynamic process. As a result, the mRNA copy number of a given gene is heterogeneous both between cells and across time. We present a framework to model gene transcription in populations of cells…
In the course of various biological processes, specific DNA-binding proteins must find a particular target sequence/protein or a damaged site on the DNA efficiently. DNA-binding proteins perform this task based on diffusion. Yet,…
Replication and transcription are two important processes in living systems. To execute such processes, various proteins work far away from equilibrium in a staggered way. Motivated by this, aspects of hysteresis during unzipping of DNA…
Nucleic acids physical properties have been investigated by theoretical methods based both on fully atomistic representations and on coarse grained models, e.g. the worm-like-chain, taken from polymer physics. In this article, I present an…
Topology affects physical and biological properties of DNA and impacts fundamental cellular processes, such as gene expression, genome replication, chromosome structure and segregation. In all organisms DNA topology is carefully modulated…