@article{BeshnovaCherstvyVainshteinetal.2014,
  author    = {Beshnova, Daria A. and Cherstvy, Andrey G. and Vainshtein, Yevhen and Teif, Vladimir B.},
  title     = {Regulation of the nucleosome repeat length in vivo by the DNA sequence, protein concentrations and long-range interactions},
  series = {PLoS Computational Biology : a new community journal},
  volume    = {10},
  journal   = {PLoS Computational Biology : a new community journal},
  number    = {7},
  publisher = {PLoS},
  address   = {San Fransisco},
  issn      = {1553-734X},
  doi       = {10.1371/journal.pcbi.1003698},
  pages     = {14},
  year      = {2014},
  abstract  = {The nucleosome repeat length (NRL) is an integral chromatin property important for its biological functions. Recent experiments revealed several conflicting trends of the NRL dependence on the concentrations of histones and other architectural chromatin proteins, both in vitro and in vivo, but a systematic theoretical description of NRL as a function of DNA sequence and epigenetic determinants is currently lacking. To address this problem, we have performed an integrative biophysical and bioinformatics analysis in species ranging from yeast to frog to mouse where NRL was studied as a function of various parameters. We show that in simple eukaryotes such as yeast, a lower limit for the NRL value exists, determined by internucleosome interactions and remodeler action. For higher eukaryotes, also the upper limit exists since NRL is an increasing but saturating function of the linker histone concentration. Counterintuitively, smaller H1 variants or non-histone architectural proteins can initiate larger effects on the NRL due to entropic reasons. Furthermore, we demonstrate that different regimes of the NRL dependence on histone concentrations exist depending on whether DNA sequence-specific effects dominate over boundary effects or vice versa. We consider several classes of genomic regions with apparently different regimes of the NRL variation. As one extreme, our analysis reveals that the period of oscillations of the nucleosome density around bound RNA polymerase coincides with the period of oscillations of positioning sites of the corresponding DNA sequence. At another extreme, we show that although mouse major satellite repeats intrinsically encode well-defined nucleosome preferences, they have no unique nucleosome arrangement and can undergo a switch between two distinct types of nucleosome positioning.},
  language  = {en}
}
@article{Cherstvy2014,
  author    = {Cherstvy, Andrey G.},
  title     = {Electrostatics and charge regulation in polyelectrolyte multi layered assembly},
  series = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  volume    = {118},
  journal   = {The journal of physical chemistry : B, Condensed matter, materials, surfaces, interfaces \& biophysical chemistry},
  number    = {17},
  publisher = {American Chemical Society},
  address   = {Washington},
  issn      = {1520-6106},
  doi       = {10.1021/jp502460v},
  pages     = {4552 -- 4560},
  year      = {2014},
  abstract  = {We examine the implications of electrostatic interactions on formation of polyelectrolyte multilayers, in application to field-effect based biosensors for label-free detection of charged macromolecules. We present a quantitative model to describe the experimental potentiometric observations and discuss its possibilities and limitations for detection of polyelectrolyte adsorption. We examine the influence of the ionic strength and pH on the sensor response upon polyelectrolyte layer-by-layer formation. The magnitude of potential oscillations on the sensor-electrolyte interface predicted upon repetitive adsorption charge-alternating polymers agrees satisfactorily with experimental results. The model accounts for different screening by mobile ions in electrolyte and inside tightly interdigitated multilayered structure. In particular, we show that sensors' potential oscillations are larger and more persistent at lower salt conditions, while they decay faster with the number of layers at higher salt conditions, in agreement with experiments. The effects of polyelectrolyte layer thickness, substrate potential, and charge regulation on the sensor surface triggered by layer-by-layer deposition are also analyzed.},
  language  = {en}
}
@article{CherstvyChechkinMetzler2014,
  author    = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity},
  series = {Soft matter},
  volume    = {2014},
  journal   = {Soft matter},
  number    = {10},
  publisher = {Royal Society of Chemistry},
  issn      = {2046-2069},
  doi       = {10.1039/c3sm52846d},
  pages     = {1591 -- 1601},
  year      = {2014},
  abstract  = {We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.},
  language  = {en}
}
@article{CherstvyChechkinMetzler2014,
  author    = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Ageing and confinement in non-ergodic heterogeneous diffusion processes},
  series = {Journal of physics : A, Mathematical and theoretical},
  volume    = {47},
  journal   = {Journal of physics : A, Mathematical and theoretical},
  number    = {48},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1751-8113},
  doi       = {10.1088/1751-8113/47/48/485002},
  pages     = {18},
  year      = {2014},
  abstract  = {We study the effects of ageing-the time delay between initiation of the physical process at t = 0 and start of observation at some time t(a) > 0-and spatial confinement on the properties of heterogeneous diffusion processes (HDPs) with deterministic power-law space-dependent diffusivities, D(x) = D-0 vertical bar x vertical bar(alpha). From analysis of the ensemble and time averaged mean squared displacements and the ergodicity breaking parameter quantifying the inherent degree of irreproducibility of individual realizations of the HDP we obtain striking similarities to ageing subdiffusive continuous time random walks with scale-free waiting time distributions. We also explore how both processes can be distinguished. For confined HDPs we study the long-time saturation of the ensemble and time averaged particle displacements as well as the magnitude of the inherent scatter of time averaged displacements and contrast the outcomes to the results known for other anomalous diffusion processes under confinement.},
  language  = {en}
}
@article{CherstvyChechkinMetzler2014,
  author    = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf},
  title     = {Particle invasion, survival, and non-ergodicity in 2D diffusion processes with space-dependent diffusivity},
  series = {Soft matter},
  volume    = {10},
  journal   = {Soft matter},
  number    = {10},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1744-683X},
  doi       = {10.1039/c3sm52846d},
  pages     = {1591 -- 1601},
  year      = {2014},
  abstract  = {We study the thermal Markovian diffusion of tracer particles in a 2D medium with spatially varying diffusivity D(r), mimicking recently measured, heterogeneous maps of the apparent diffusion coefficient in biological cells. For this heterogeneous diffusion process (HDP) we analyse the mean squared displacement (MSD) of the tracer particles, the time averaged MSD, the spatial probability density function, and the first passage time dynamics from the cell boundary to the nucleus. Moreover we examine the non-ergodic properties of this process which are important for the correct physical interpretation of time averages of observables obtained from single particle tracking experiments. From extensive computer simulations of the 2D stochastic Langevin equation we present an in-depth study of this HDP. In particular, we find that the MSDs along the radial and azimuthal directions in a circular domain obey anomalous and Brownian scaling, respectively. We demonstrate that the time averaged MSD stays linear as a function of the lag time and the system thus reveals a weak ergodicity breaking. Our results will enable one to rationalise the diffusive motion of larger tracer particles such as viruses or submicron beads in biological cells.},
  language  = {en}
}
@article{CherstvyMetzler2014,
  author    = {Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Nonergodicity, fluctuations, and criticality in heterogeneous diffusion processes},
  series = {Physical review : E, Statistical, nonlinear and soft matter physics},
  volume    = {90},
  journal   = {Physical review : E, Statistical, nonlinear and soft matter physics},
  number    = {1},
  publisher = {American Physical Society},
  address   = {College Park},
  issn      = {1539-3755},
  doi       = {10.1103/PhysRevE.90.012134},
  pages     = {11},
  year      = {2014},
  abstract  = {We study the stochastic behavior of heterogeneous diffusion processes with the power-law dependence D(x) similar to vertical bar x vertical bar(alpha) of the generalized diffusion coefficient encompassing sub- and superdiffusive anomalous diffusion. Based on statistical measures such as the amplitude scatter of the time-averaged mean-squared displacement of individual realizations, the ergodicity breaking and non-Gaussianity parameters, as well as the probability density function P(x, t), we analyze the weakly nonergodic character of the heterogeneous diffusion process and, particularly, the degree of irreproducibility of individual realizations. As we show, the fluctuations between individual realizations increase with growing modulus vertical bar alpha vertical bar of the scaling exponent. The fluctuations appear to diverge when the critical value alpha = 2 is approached, while for even larger alpha the fluctuations decrease, again. At criticality, the power-law behavior of the mean-squared displacement changes to an exponentially fast growth, and the fluctuations of the time-averaged mean-squared displacement do not converge for increasing number of realizations. From a systematic comparison we observe some striking similarities of the heterogeneous diffusion process with the familiar subdiffusive continuous time random walk process with power-law waiting time distribution and diverging characteristic waiting time.},
  language  = {en}
}
@article{CherstvyPetrov2014,
  author    = {Cherstvy, Andrey G. and Petrov, Eugene P.},
  title     = {Modeling DNA condensation on freestanding cationic lipid membranes},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {16},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {5},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c3cp53433b},
  pages     = {2020 -- 2037},
  year      = {2014},
  abstract  = {Motivated by recent experimental observations of a rapid spontaneous DNA coil-globule transition on freestanding cationic lipid bilayers, we propose simple theoretical models for DNA condensation on cationic lipid membranes. First, for a single DNA rod, we examine the conditions of full wrapping of a cylindrical DNA-like semi-flexible polyelectrolyte by an oppositely charged membrane. Then, for two parallel DNA rods, we self-consistently analyze the shape and the extent of the membrane enveloping them, focusing on membrane elastic deformations and the membrane-DNA embracing angle, which enables us to compute the membrane-mediated DNA-DNA interactions. We examine the effects of the membrane composition and its charge density, which are the experimentally tunable parameters. We show that membrane-driven rod-rod attraction is more pronounced for higher charge densities and for smaller surface tensions of the membrane. Thus, we demonstrate that for a long DNA chain adhered to a cationic lipid membrane, such membrane-induced DNA-DNA attraction can trigger compaction of DNA.},
  language  = {en}
}
@article{CherstvyTeif2014,
  author    = {Cherstvy, Andrey G. and Teif, Vladimir B.},
  title     = {Electrostatic effect of H1-histone protein binding on nucleosome repeat length},
  series = {Physical biology : a journal for the fundamental understanding of biological systems},
  volume    = {11},
  journal   = {Physical biology : a journal for the fundamental understanding of biological systems},
  number    = {4},
  publisher = {IOP Publ. Ltd.},
  address   = {Bristol},
  issn      = {1478-3967},
  doi       = {10.1088/1478-3975/11/4/044001},
  pages     = {6},
  year      = {2014},
  abstract  = {Within a simple biophysical model we describe the effect of electrostatic binding of H1 histone proteins on the nucleosome repeat length in chromatin. The length of wrapped DNA optimizes its binding energy to the histone core and the elastic energy penalty of DNA wrapping. The magnitude of the effect predicted from our model is in agreement with the systematic experimental data on the linear variation of nucleosome repeat lengths with H1/nucleosome ratio (Woodcock C L et al 2006 Chromos. Res. 14 17-25). We compare our model to the data for different cell types and organisms, with a widely varying ratio of bound H1 histones per nucleosome. We underline the importance of this non-specific histone-DNA charge-balance mechanism in regulating the positioning of nucleosomes and the degree of compaction of chromatin fibers in eukaryotic cells.},
  language  = {en}
}
@article{deCarvalhoMetzlerCherstvy2014,
  author    = {de Carvalho, Sidney J. and Metzler, Ralf and Cherstvy, Andrey G.},
  title     = {Critical adsorption of polyelectrolytes onto charged Janus nanospheres},
  series = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  volume    = {16},
  journal   = {Physical chemistry, chemical physics : a journal of European Chemical Societies},
  number    = {29},
  publisher = {Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  doi       = {10.1039/c4cp02207f},
  pages     = {15539 -- 15550},
  year      = {2014},
  abstract  = {Based on extensive Monte Carlo simulations and analytical considerations we study the electrostatically driven adsorption of flexible polyelectrolyte chains onto charged Janus nanospheres. These net-neutral colloids are composed of two equally but oppositely charged hemispheres. The critical binding conditions for polyelectrolyte chains are analysed as function of the radius of the Janus particle and its surface charge density, as well as the salt concentration in the ambient solution. Specifically for the adsorption of finite-length polyelectrolyte chains onto Janus nanoparticles, we demonstrate that the critical adsorption conditions drastically differ when the size of the Janus particle or the screening length of the electrolyte are varied. We compare the scaling laws obtained for the adsorption-desorption threshold to the known results for uniformly charged spherical particles, observing significant disparities. We also contrast the changes to the polyelectrolyte chain conformations close to the surface of the Janus nanoparticles as compared to those for simple spherical particles. Finally, we discuss experimentally relevant physicochemical systems for which our simulations results may become important. In particular, we observe similar trends with polyelectrolyte complexation with oppositely but heterogeneously charged proteins.},
  language  = {en}
}
@article{GhoshCherstvyMetzler2014,
  author    = {Ghosh, Surya K. and Cherstvy, Andrey G. and Metzler, Ralf},
  title     = {Non-universal tracer diffusion in crowded media of non-inert obstacles},
  series = {Physical Chemistry Chemical Physics},
  volume    = {3},
  journal   = {Physical Chemistry Chemical Physics},
  number    = {17},
  editor    = {Metzler, Ralf},
  publisher = {The Royal Society of Chemistry},
  address   = {Cambridge},
  issn      = {1463-9076},
  pages     = {1847 -- 1858},
  year      = {2014},
  abstract  = {We study the diffusion of a tracer particle, which moves in continuum space between a lattice of excluded volume, immobile non-inert obstacles. In particular, we analyse how the strength of the tracer-obstacle interactions and the volume occupancy of the crowders alter the diffusive motion of the tracer. From the details of partitioning of the tracer diffusion modes between trapping states when bound to obstacles and bulk diffusion, we examine the degree of localisation of the tracer in the lattice of crowders. We study the properties of the tracer diffusion in terms of the ensemble and time averaged mean squared displacements, the trapping time distributions, the amplitude variation of the time averaged mean squared displacements, and the non-Gaussianity parameter of the diffusing tracer. We conclude that tracer-obstacle adsorption and binding triggers a transient anomalous diffusion. From a very narrow spread of recorded individual time averaged trajectories we exclude continuous type random walk processes as the underlying physical model of the tracer diffusion in our system. For moderate tracer-crowder attraction the motion is found to be fully ergodic, while at stronger attraction strength a transient disparity between ensemble and time averaged mean squared displacements occurs. We also put our results into perspective with findings from experimental single-particle tracking and simulations of the diffusion of tagged tracers in dense crowded suspensions. Our results have implications for the diffusion, transport, and spreading of chemical components in highly crowded environments inside living cells and other structured liquids.},
  language  = {en}
}