@misc{WinklerCherstvy2014, author = {Winkler, Roland G. and Cherstvy, Andrey G.}, title = {Strong and weak polyelectrolyte adsorption onto oppositely charged curved surfaces}, series = {Advances in polymer science}, volume = {255}, journal = {Advances in polymer science}, editor = {Muller, M.}, publisher = {Springer}, address = {Berlin}, isbn = {978-3-642-40734-5; 978-3-642-40733-8}, issn = {0065-3195}, doi = {10.1007/12_2012_183}, pages = {1 -- 56}, year = {2014}, abstract = {Polyelectrolytes are macromolecules composed of charged monomers and exhibit unique properties due to the interplay of their flexibility and electrostatic interactions. In solution, they are attracted to oppositely charged surfaces and interfaces and exhibit a transition to an adsorbed state when certain conditions are met concerning the charge densities of the polymer and surface and the properties of the solution. In this review, we discuss two limiting cases for adsorption of flexible polyelectrolytes on curved surfaces: weak and strong adsorption. In the first case, adsorption is strongly influenced by the entropic degrees of freedom of a flexible polyelectrolyte. By contrast, in the strong adsorption limit, electrostatic interactions dominate, which leads to particular adsorption patterns, specifically on spherical surfaces. We discuss the corresponding theoretical approaches, applying a mean-field description for the polymer and the polymer-surface interaction. For weak adsorption, we discuss the critical adsorption behavior by exactly solvable models for planar and spherical geometries and a generic approximation scheme, which is additionally applied to cylindrical surfaces. For strong adsorption, we investigate various polyelectrolyte patterns on cylinders and spheres and evaluate their stability. The results are discussed in the light of experimental results, mostly of DNA adsorption experiments.}, language = {en} } @article{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Sensing viruses by mechanical tension of DNA in responsive hydrogels}, series = {Physical review : X, Expanding access}, volume = {4}, journal = {Physical review : X, Expanding access}, number = {2}, publisher = {American Physical Society}, address = {College Park}, issn = {2160-3308}, doi = {10.1103/PhysRevX.4.021002}, pages = {13}, year = {2014}, abstract = {The rapid worldwide spread of severe viral infections, often involving novel mutations of viruses, poses major challenges to our health-care systems. This means that tools that can efficiently and specifically diagnose viruses are much needed. To be relevant for broad applications in local health-care centers, such tools should be relatively cheap and easy to use. In this paper, we discuss the biophysical potential for the macroscopic detection of viruses based on the induction of a mechanical stress in a bundle of prestretched DNA molecules upon binding of viruses to the DNA. We show that the affinity of the DNA to the charged virus surface induces a local melting of the double helix into two single-stranded DNA. This process effects a mechanical stress along the DNA chains leading to an overall contraction of the DNA. Our results suggest that when such DNA bundles are incorporated in a supporting matrix such as a responsive hydrogel, the presence of viruses may indeed lead to a significant, macroscopic mechanical deformation of the matrix. We discuss the biophysical basis for this effect and characterize the physical properties of the associated DNA melting transition. In particular, we reveal several scaling relations between the relevant physical parameters of the system. We promote this DNA-based assay as a possible tool for efficient and specific virus screening.}, language = {en} } @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{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 = {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{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} } @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{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects}, series = {New journal of physics : the open-access journal for physics}, volume = {16}, journal = {New journal of physics : the open-access journal for physics}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/16/5/053047}, pages = {19}, year = {2014}, abstract = {During the life cycle of bacterial cells the non-mixing of the two ring-shaped daughter genomes is an important prerequisite for the cell division process. Mimicking the environments inside highly crowded biological cells, we study the dynamics and statistical behavior of two flexible ring polymers in the presence of cylindrical confinement and crowding molecules. From extensive computer simulations we determine the degree of ring-ring overlap and the number of inter-monomer contacts for varying volume fractions phi of crowders. We also examine the entropic demixing of polymer rings in the presence of mobile crowders and determine the characteristic times of the internal polymer dynamics. Effects of the ring length on ring-ring overlap are also analyzed. In particular, on systematic variation of the fraction of crowding molecules, a (1 - phi)-scaling is found for the ring-ring overlap length along the cylinder axis, and a non-monotonic dependence of the 3D ring-ring contact number with a maximum at phi approximate to 0.2 is obtained. Our results demonstrate that polymer rings are demixed and separated by particular entropy-favourable partitioning of crowders along the axis of the cylindrical simulation box. These findings help to rationalize the implications of macromolecular crowding for circular DNA molecules in confined spaces inside bacteria as well as in localized cellular compartments inside eukaryotic cells.}, language = {en} } @article{ShinCherstvyMetzler2014, author = {Shin, Jaeoh and Cherstvy, Andrey G. and Metzler, Ralf}, title = {Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size}, series = {Soft Matter}, journal = {Soft Matter}, editor = {Metzler, Ralf}, publisher = {The Royal Society of Chemistry}, address = {Cambridge}, issn = {1744-683X}, pages = {472 -- 488}, year = {2014}, abstract = {The looping of polymers such as DNA is a fundamental process in the molecular biology of living cells, whose interior is characterised by a high degree of molecular crowding. We here investigate in detail the looping dynamics of flexible polymer chains in the presence of different degrees of crowding. From the analysis of the looping-unlooping rates and the looping probabilities of the chain ends we show that the presence of small crowders typically slows down the chain dynamics but larger crowders may in fact facilitate the looping. We rationalise these non-trivial and often counterintuitive effects of the crowder size on the looping kinetics in terms of an effective solution viscosity and standard excluded volume. It is shown that for small crowders the effect of an increased viscosity dominates, while for big crowders we argue that confinement effects (caging) prevail. The tradeoff between both trends can thus result in the impediment or facilitation of polymer looping, depending on the crowder size. We also examine how the crowding volume fraction, chain length, and the attraction strength of the contact groups of the polymer chain affect the looping kinetics and hairpin formation dynamics. Our results are relevant for DNA looping in the absence and presence of protein mediation, DNA hairpin formation, RNA folding, and the folding of polypeptide chains under biologically relevant high-crowding conditions.}, language = {en} }