Related papers: Fluctuation Pressure Assisted Ejection of DNA From…
Intermittent fluctuations in the boundary of magnetically confined plasmas are investigated by numerical turbulence simulations of a reduced fluid model describing the evolution of the plasma density and electric drift vorticity in the…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
The thermalization of quark-gluon plasma created in heavy-ion collisions is crucial for understanding its behavior as a relativistic fluid and the thermodynamic properties of the Quantum Chromodynamics (QCD). This study investigates the…
We investigate the statistical mechanics of a torsionally constrained polymer. The polymer is modeled as a fluctuating rod with bend stiffness A kT and twist stiffness C kT. In such a model, thermal bend fluctuations couple geometrically to…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
Various charge migration mechanisms in the DNA are studied within the framework of the Peyrard-Bishop-Holstein model which has been widely used to address charge dynamics in this macromolecule. To analyze these mechanisms we consider…
Most spherical viruses exhibit icosahedral symmetry, yet the growth of viral shells remains poorly understood due to the short lifetimes and broad size distribution of assembly intermediates. Classical nucleation theory has been widely…
Small magnetic fluctuations ($B_1/B_0 \sim 10^{-4}$) are intrinsically present in a magnetic confinement plasma due to turbulent currents. While the perpendicular transport of particles and heat is typically dominated by fluctuations of the…
The interplay between bending of the molecule axis and appearance of disruptions in circular DNA molecules, with $\sim 100$ base pairs, is addressed. Three minicircles with different radii and almost equal content of AT and GC pairs are…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
The effect of molecule size (excluded volume) and the range of interaction on the surface tension, phase diagram and nucleation properties of a model globular protein is investigated using a combinations of Monte Carlo simulations and…
The formation of bubbles in nucleic acids (NAs) are fundamental in many biological processes such as DNA replication, recombination, telomeres formation, nucleotide excision repair, as well as RNA transcription and splicing. These precesses…
We review recent computer simulation studies of undulating lipid bilayers. Theoretical interpretations of such fluctuating membranes are most commonly based on generalized Helfrich-type elastic models, with additional contributions of local…
The thermodynamic properties of DNA circular molecules are investigated by a new path integral computational method which treats in the real space the fundamental forces stabilizing the molecule. The base pair and stacking contributions to…
The influence of the temperature and its fluctuations on the ion saturation current and the floating potential, which are typical quantities measured by Langmuir probes in the turbulent edge region of fusion plasmas, is analysed by global…
Fluctuation-induced forces are investigated for ideal and imperfect Bose gases confined to $d$-dimensional films of size $\infty^{d-1}\times D$ under periodic (P), antiperiodic (A), Dirichlet-Dirichlet (DD), Neumann-Neumann (NN), and Robin…
Nanochannels provide means for detailed experiments on the effect of confinement on biomacromolecules, such as DNA. We here introduce a model for the complete unfolding of DNA from the circular to linear configuration. Two main ingredients…
We experimentally study density fluctuations and energy spectra of bulk \textit{E. coli} suspensions of different concentrations. Our results verify the predicted scaling law of giant number fluctuations in three-dimensional (3D) wet active…
We study the fluctuation dynamics of localized denaturation bubbles in heteropolymer DNA with a master equation and complementary stochastic simulation based on novel DNA stability data. A significant dependence of opening probability and…
Understanding the nature of compressible fluctuations in a broad range of turbulent plasmas, from the intracluster medium to the solar wind, has been an active field of research in the past decades. Theoretical frameworks for weakly…