Related papers: Bubble relaxation dynamics in homopolymer DNA sequ…
We consider a general discrete model for heterogeneous semiflexible polymer chains. Both the thermal noise and the inhomogeneous character of the chain (the disorder) are modeled in terms of random rotations. We focus on the quenched…
The formation of gas bubbles in a liquid occurs in various engineering processes, such as during foam generation or agitation and mixing in bubbly flows. A challenge in describing the initial formation of a gas bubble is due to the singular…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
We investigate the dynamics of atomic and molecular bosons weakly coupled via Feshbach detuning in the presence of Gaussian white noise. The time-evolution of the population imbalance between the two species, as well as the coherence of the…
Activity-mediated unjamming of a confluent glassy system is crucial for several biological processes, such as embryogenesis and cancer metastasis. During these processes, the cells progressively change their junction properties,…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
The attenuation of phonon modes of the DNA is due to the exchange of water molecules adsorbed by a molecule of DNA and the bulk solvent. Using Maxwell's mechanism of relaxation and a simple lattice model of the DNA, we show that the…
Flexibility of short DNA helices is important for the biological functions such as nucleosome formation and DNA-protein recognition. Recent experiments suggest that short DNAs of tens of base pairs (bps) may have apparently higher…
We report experimental results on the dynamics of large bubbles in a Hele-Shaw cell subject to various inclination angles with respect to gravity. Low Reynolds number cases are studied by injecting bubbles in an stagnant water/UCON mixture…
This paper presents a numerical study of the dynamics of DNA double helix breakage under the influence of external forces using the Peyrard-Bishop-Dauxois (PBD) model. The PBD model represents DNA as a chain of nonlinearly coupled…
The normal modes and relaxation rates of weak colloidal gels are investigated in computations employing different models of the hydrodynamic interactions between colloids. The eigenspectrum is computed for freely draining,…
Single molecule studies, at constant force, of the separation of double-stranded DNA into two separated single strands may provide information relevant to the dynamics of DNA replication. At constant applied force, theory predicts that the…
The Glauber dynamics of the Hopfield model at low storage level is considered. We analytically derive the spectrum of relaxation times for large system sizes. The longest time scales are gathered in families, each family being in one to one…
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…
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 rotational evolution of stars is still an open question of stellar physics because of the numerous phenomena that can contribute to the distribution of angular momentum. This paper aims at determining the time scale over which a…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
We discuss the relaxation kinetics of a one-dimensional dimer adsorption model as recently proposed for the binding of biological dimers like kinesin on microtubules. The non-equilibrium dynamics shows several regimes: irreversible…
Short blunt-ended DNA duplexes comprising 6 to 20 base pairs self-assemble into polydisperse semi-flexible chains due to hydrophobic stacking interactions between terminal base pairs. Above a critical concentration, which depends on…