Related papers: A thermodynamic switch for chromosome colocalizati…
Recent works on localized charge transport along DNA, based on a three--dimensional, tight--binding model (Eur. Phys. J. B 30:211, 2002; Phys. D 180:256, 2003), suggest that charge transport is mediated by the coupling of the radial and…
We suggest that the thermodynamic stability parameters (nearest neighbor stacking and hydrogen bonding free energies) of double-stranded DNA molecules can be inferred reliably from time series of the size fluctuations (breathing) of local…
Diffusional dynamics of the donor-acceptor distance in electron-transfer reactions are responsible for the appearance of a new time scale of diffusion over the distance of falloff of electronic tunneling. The distance dynamics compete with…
Bose condensed light can form new phases [1] in a dye filled cavity due to the presence of the orientational disorder created by dye molecules which are essentially frozen on the time scale of the photonic thermalization (few ps). At longer…
The proper design of DNA sequences allows for the formation of well defined supramolecular units with controlled interactions via a consecution of self-assembling processes. Here, we benefit from the controlled DNA self-assembly to…
Bacterial genomes are partitioned into kilobases long domains that are topologically independent from each other, meaning that change of DNA superhelicity in one domain does not propagate to neighbours. This is made possible by proteins…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…
We discuss the phenomenon of spontaneous self-compactification in a model colloidal system, proposed in a recent work on DNA-mediated self-assembly. We focus on the effect of thermal fluctuations on the stability of membrane-like…
We study chemical oscillators in the presence of phase separation. By imposing timescale separation between slow reactions and fast diffusion, we define a dynamics at phase equilibrium for the relevant degrees of freedom. We demonstrate…
Here we investigate how the positions of a condensed phase can be controlled by using concentration gradients of a regulator that influences phase separation. We consider a mean field model of a ternary mixture where a concentration…
We show that a liquid mixture in the thermodynamically stable homogeneous phase can undergo a phase-separation transition when rotated at sufficiently high frequency $\omega$. This phase-transition is different from the usual case where two…
A toggle switch consists of two genes that mutually repress each other. This regulatory motif is active during cell differentiation and is thought to act as a memory device, being able to choose and maintain cell fate decisions. In this…
Differences in activities in colloidal particles are sufficient to drive phase separation between active and passive (or less active) particles, even if they have only excluded volume interactions. In this paper, we study the phase…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of a pi-stacking interaction $b$ smearing a charge between different base pairs and…
We study the propagation of very large amplitude localized excitations in a model of DNA that takes explicitly into account the helicoidal structure. These excitations represent the ``transcription bubble'', where the hydrogen bonds between…
Dynamics of topological solitons describing open states in the DNA double helix are studied in the frameworks of the model which takes into account asymmetry of the helix. It is shown that three types of topological solitons can occur in…
Spontaneous synchronisation is a collective phenomenon that can occur in both dynamical classical and quantum systems. Here, we analyse the spontaneous synchronisation dynamics of vibrations assisting energy transfer in a bio-inspired…
We use a statistical mechanical model to study nonthermal denaturation of DNA in the presence of protein-mediated loops. We find that looping proteins which randomly link DNA bases located at a distance along the chain could cause a…
We present a nonlinear dynamical model for DNA thermal denaturation, which is based on the finite stacking enthalpies used in thermodynamical nearest-neighbour calculations. Within this model, the finiteness of stacking enthalpies is shown…
Homologous recombination facilitates the exchange of genetic material between homologous DNA molecules. This crucial process requires detecting a specific homologous DNA sequence within a huge variety of heterologous sequences. The…