相关论文: Towards more realistic dynamical models for DNA se…
The central dogma of molecular biology is the principal framework for understanding how nucleic acid information is propagated and used by living systems to create complex biomolecules. Here, by integrating the structural and dynamic…
A general model for the early recognition and colocalization of homologous DNA sequences is proposed. We show, on a thermodynamic ground, how the distance between two homologous DNA sequences is spontaneously regulated by the concentration…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
DNA and RNA are generally regarded as central molecules in molecular biology. Recent advancements in the field of DNA/RNA nanotechnology successfully used DNA/RNA as programmable molecules to construct molecular machines and nanostructures…
The paper uses mesoscopic, non-linear lattice dynamics based (Peyrard-Bishop-Dauxois, PBD) modeling to describe thermal properties of DNA below and near the denaturation temperature. Computationally efficient notation is introduced for the…
Unbinding of a double-stranded DNA reduces to an unscreened long range interaction and maps on various problems. Heterogeneity renormalizes interaction. Renormalization is temperature dependent. At an unbinding transition it approaches…
We view the folding of RNA-sequences as a map that assigns a pattern of base pairings to each sequence, known as secondary structure. These preimages can be constructed as random graphs (i.e. the neutral networks associated to the structure…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
By resorting to a model inspired to the standard Davydov and Holstein-Fr\"ohlich models, in the present paper we study the motion of an electron along a chain of heavy particles modelling a sequence of nucleotides proper to a DNA fragment.…
The local opening of DNA is an intriguing phenomenon from a statistical physics point of view, but is also essential for its biological function. For instance, the transcription and replication of our genetic code can not take place without…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
We apply a recently-developed coarse-grained model of DNA, designed to capture the basic physics of nanotechnological DNA systems, to the study of a `burnt-bridges' DNA motor consisting of a single-stranded cargo that steps processively…
We study the coupled dynamics of primary and secondary structure formation (i.e. slow genetic sequence selection and fast folding) in the context of a solvable microscopic model that includes both short-range steric forces and and…
In this paper we model several simple biochemical operations on RNA molecules that modify their secondary structure by means of a suitable variation of Gro\ss e-Rhode's Algebra Transformation Systems.
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
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 demonstrate how the stochastic global optimization scheme of Simulated Annealing can be used to evaluate optimum parameters in the problem of DNA breathing dynamics. The breathing dynamics is followed in accordance with the stochastic…
An 1d model with time-dependent random hopping is proposed to describe charge transport in DNA. It admits to investigate both diffusion of electrons and their tunneling between different sites in DNA. The tunneling appears to be strongly…
The phase transition of $(PolyA/PolyT)_{100}$ duplex into the denaturated state is studied in the Peyrard-Bishop-Dauxois model by the method of direct molecular-dynamical modeling. The temperature dependencies of the total energy and heat…