Related papers: Sequence-dependent thermodynamics of a coarse-grai…
We define a DNA as a sequence of $1, 2$'s and embed it on a path of Cayley tree in such a way that each vertex of the Cayley tree belongs only to one of DNA and each DNA has its own countably many set of neighboring DNAs. The Hamiltonian of…
In this work we employ various methods of analysis (unfolding simulations and comparative analysis of structures and sequences of proteomes of thermophilic organisms) to show that organisms can follow two major strategies of thermophilic…
A model of self-avoiding walk with suitable constraints on self-attraction is developed to describe the conformational behaviour of a single stranded short DNA molecule that form hairpin structure. Using exact enumeration method we…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
The influence of tension on DNA looping has been studied both experimentally and theoretically in the past. However, different theoretical models have yielded different predictions, leaving uncertainty about their validity. We briefly…
We report experimental observations on the effect of disorder on the phase behavior of DNA-linked nanoparticle assemblies. Variation in DNA linker lengths results in different melting temperatures of the DNA-linked nanoparticle assemblies.…
Quantifying interactions in DNA microarrays is of central importance for a better understanding of their functioning. Hybridization thermodynamics for nucleic acid strands in aqueous solution can be described by the so-called…
The force induced unzipping transition of a double stranded DNA is considered from a purely thermodynamic point of view. This analysis provides us with a set of relations that can be used to test microscopic theories and experiments. The…
The accurate knowledge of the elastic properties of single-stranded DNA (ssDNA) is key to characterize the thermodynamics of molecular reactions that are studied by force spectroscopy methods where DNA is mechanically unfolded. Examples…
A versatile approach to modeling the conformations and energetics of DNA loops is presented. The model is based on the classical theory of elasticity, modified to describe the intrinsic twist and curvature of DNA, the DNA bending…
The incredible thermo-mechanical properties of biological materials arise from the microscopic scale due to a complex hierarchical mechanism, regulated by microinstabilities at the molecular level. The description of such complex structures…
In human cells, estrogenic signals induce cyclical association and dissociation of specific proteins with the DNA in order to activate transcription of estrogen-responsive genes. These oscillations can be modeled by assuming a large number…
DNA code design aims to generate a set of DNA sequences (codewords) with minimum likelihood of undesired hybridizations among sequences and their reverse-complement (RC) pairs (cross-hybridization). Inspired by the distinct hybridization…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
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…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
Thermal conductivity of isolated single molecule DNA fragments is of importance for nanotechnology, but has not yet been measured experimentally. Theoretical estimates based on simplified (1D) models predict anomalously high thermal…
We introduce and numerically study a model designed to mimic the bulk behavior of a system composed of single-stranded DNA dendrimers. Complementarity of the base sequences of different strands results in the formation of strong cooperative…
A unified model is constructed to study the recently observed DNA entropic elasticity, cooperative extensibility, and supercoiling property. With the introduction of a new structural parameter (the folding angle $\phi$), bending…