相关论文: Stacking Interactions in Denaturation of DNA Fragm…
We present a thermodynamically robust coarse-grained model to simulate folding of RNA in monovalent salt solutions. The model includes stacking, hydrogen bond and electrostatic interactions as fundamental components in describing the…
In this paper we have investigated, through computer simulations, dislocation nucleation and dislocation dynamics in a heterostructure system with the lattice-mismatch interface, i.e. a system with internal strain. In particular, we have…
We explore in detail the structural, mechanical and thermodynamic properties of a coarse-grained model of DNA similar to that introduced in Thomas E. Ouldridge, Ard A. Louis, Jonathan P.K. Doye, Phys. Rev. Lett. 104 178101 (2010). Effective…
One-dimensional thermodynamic instabilities are phase transitions not prohibited by Landau's argument, because the energy of the domain wall (DW) which separates the two phases is infinite. Whether they actually occur in a given system of…
DNA is now firmly established as a versatile and robust platform for achieving synthetic nanostructures. While the folding of single molecules into complex structures is routinely achieved through engineering basepair sequences, much less…
We investigate the denaturation dynamics of nucleic acids through extensive molecular dynamics simulations of a coarse-grained RNA hairpin model. In apparent contradiction with Arrhenius' law, our findings reveal that the denaturation time…
Test experiments of hybridization in DNA microarrays show systematic deviations from the equilibrium isotherms. We argue that these deviations are due to the presence of a partially hybridized long-lived state, which we include in a kinetic…
The linking number (topological entanglement) and the writhe (geometrical entanglement) of a model of circular double stranded DNA undergoing a thermal denaturation transition are investigated by Monte Carlo simulations. By allowing the…
Using numerical and analytical methods implemented for different models we conduct a systematic study of thermodynamic properties of pairing correlation in mesoscopic nuclear systems. Various quantities are calculated and analyzed using the…
We use a simplified model which is based on the same physics as inherent in most statistical models for nuclear multifragmentation. The simplified model allows exact calculations for thermodynamic properties of systems of large number of…
We investigate a binary Lennard-Jones mixture with molecular dynamics simulations. We consider first a system cooled linearly in time with the cooling rate gamma. By varying gamma over almost four decades we study the influence of the…
The situation of the decay of the metastable phase on the several types of heterogeneous centers is described analytically. The total number of heterogeneous centers is supposed to be equal for different types. This description decomposes…
We demonstrate spectroscopy and thermometry of individual motional modes in a mesoscopic 2D ion array using entanglement-induced decoherence as a method of transduction. Our system is a $\sim$400 $\mu$m-diameter planar crystal of several…
We investigate the voltage-driven transport of hybridized DNA through membrane channels. As membrane channels are typically too narrow to accommodate hybridized DNA, the dehybridization of the DNA is the critical rate limiting step in the…
The agreement between the fragments' internal and kinetic temperatures with the breakup temperature is investigated using a Statistical Multifragmentation Model which makes no a priori as- sumption on the relationship between them. We thus…
Temperature-induced phase transition in BaTiO3 has been explored using the machine learning analysis of domain morphologies visualized via variable-temperature scanning transmission electron microscopy (STEM) imaging data. This approach is…
We develop further a statistical model coupling denaturation and chain conformations in DNA (Palmeri J, Manghi M and Destainville N 2007 Phys. Rev. Lett. 99 088103). Our Discrete Helical Wormlike Chain model takes explicitly into account…
We examine the crystallization dynamics of nanoparticles reversibly tethered by DNA hybridization. We show that the crystallization happens readily only in a narrow temperature "slot," and always proceeds via a two-step process, mediated by…
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 oligomers with properly designed sequences self-assemble into well defined constructs. Here, we exploit this methodology to produce bulk quantities of tetravalent DNA nanostars (each one composed by 196 nucleotides) and to explore the…