@article{CherstvyMetzler2013, author = {Cherstvy, Andrey G. and Metzler, Ralf}, title = {Population splitting, trapping, and non-ergodicity in heterogeneous diffusion processes}, series = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, volume = {15}, journal = {Physical chemistry, chemical physics : a journal of European Chemical Societies}, number = {46}, publisher = {Royal Society of Chemistry}, address = {Cambridge}, issn = {1463-9076}, doi = {10.1039/c3cp53056f}, pages = {20220 -- 20235}, year = {2013}, abstract = {We consider diffusion processes with a spatially varying diffusivity giving rise to anomalous diffusion. Such heterogeneous diffusion processes are analysed for the cases of exponential, power-law, and logarithmic dependencies of the diffusion coefficient on the particle position. Combining analytical approaches with stochastic simulations, we show that the functional form of the space-dependent diffusion coefficient and the initial conditions of the diffusing particles are vital for their statistical and ergodic properties. In all three cases a weak ergodicity breaking between the time and ensemble averaged mean squared displacements is observed. We also demonstrate a population splitting of the time averaged traces into fast and slow diffusers for the case of exponential variation of the diffusivity as well as a particle trapping in the case of the logarithmic diffusivity. Our analysis is complemented by the quantitative study of the space coverage, the diffusive spreading of the probability density, as well as the survival probability.}, language = {en} } @article{CherstvyTeif2013, author = {Cherstvy, Andrey G. and Teif, V. B.}, title = {Structure-driven homology pairing of chromatin fibers the role of electrostatics and protein-induced bridging}, series = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences}, volume = {39}, journal = {Journal of biological physics : emphasizing physical principles in biological research ; an international journal for the formulation and application of mathematical models in the biological sciences}, number = {3}, publisher = {Springer}, address = {Dordrecht}, issn = {0092-0606}, doi = {10.1007/s10867-012-9294-4}, pages = {363 -- 385}, year = {2013}, abstract = {Chromatin domains formed in vivo are characterized by different types of 3D organization of interconnected nucleosomes and architectural proteins. Here, we quantitatively test a hypothesis that the similarities in the structure of chromatin fibers (which we call "structural homology") can affect their mutual electrostatic and protein-mediated bridging interactions. For example, highly repetitive DNA sequences in heterochromatic regions can position nucleosomes so that preferred inter-nucleosomal distances are preserved on the surfaces of neighboring fibers. On the contrary, the segments of chromatin fiber formed on unrelated DNA sequences have different geometrical parameters and lack structural complementarity pivotal for stable association and cohesion. Furthermore, specific functional elements such as insulator regions, transcription start and termination sites, and replication origins are characterized by strong nucleosome ordering that might induce structure-driven iterations of chromatin fibers. We propose that shape-specific protein-bridging interactions facilitate long-range pairing of chromatin fragments, while for closely-juxtaposed fibers electrostatic forces can in addition yield fine-tuned structure-specific recognition and pairing. These pairing effects can account for some features observed for mitotic and inter-phase chromatins.}, language = {en} } @article{PoghossianWeilCherstvyetal.2013, author = {Poghossian, A. and Weil, M. and Cherstvy, Andrey G. and Sch{\"o}ning, M. J.}, title = {Electrical monitoring of polyelectrolyte multilayer formation by means of capacitive field-effect devices}, series = {Analytical \& bioanalytical chemistry}, volume = {405}, journal = {Analytical \& bioanalytical chemistry}, number = {20}, publisher = {Springer}, address = {Heidelberg}, issn = {1618-2642}, doi = {10.1007/s00216-013-6951-9}, pages = {6425 -- 6436}, year = {2013}, abstract = {The semiconductor field-effect platform represents a powerful tool for detecting the adsorption and binding of charged macromolecules with direct electrical readout. In this work, a capacitive electrolyte-insulator-semiconductor (EIS) field-effect sensor consisting of an Al-p-Si-SiO2 structure has been applied for real-time in situ electrical monitoring of the layer-by-layer formation of polyelectrolyte (PE) multilayers (PEM). The PEMs were deposited directly onto the SiO2 surface without any precursor layer or drying procedures. Anionic poly(sodium 4-styrene sulfonate) and cationic weak polyelectrolyte poly(allylamine hydrochloride) have been chosen as a model system. The effect of the ionic strength of the solution, polyelectrolyte concentration, number and polarity of the PE layers on the characteristics of the PEM-modified EIS sensors have been studied by means of capacitance-voltage and constant-capacitance methods. In addition, the thickness, surface morphology, roughness and wettabilityof the PE mono- and multilayers have been characterised by ellipsometry, atomic force microscopy and water contact-angle methods, respectively. To explain potential oscillations on the gate surface and signal behaviour of the capacitive field-effect EIS sensor modified with a PEM, a simplified electrostatic model that takes into account the reduced electrostatic screening of PE charges by mobile ions within the PEM has been proposed and discussed.}, language = {en} } @article{CherstvyChechkinMetzler2013, author = {Cherstvy, Andrey G. and Chechkin, Aleksei V. and Metzler, Ralf}, title = {Anomalous diffusion and ergodicity breaking in heterogeneous diffusion processes}, series = {New journal of physics : the open-access journal for physics}, volume = {15}, journal = {New journal of physics : the open-access journal for physics}, number = {15}, publisher = {IOP Publ. Ltd.}, address = {Bristol}, issn = {1367-2630}, doi = {10.1088/1367-2630/15/8/083039}, pages = {13}, year = {2013}, abstract = {We demonstrate the non-ergodicity of a simple Markovian stochastic process with space-dependent diffusion coefficient D(x). For power-law forms D(x) similar or equal to vertical bar x vertical bar(alpha), this process yields anomalous diffusion of the form < x(2)(t)> similar or equal to t(2/(2-alpha)). Interestingly, in both the sub- and superdiffusive regimes we observe weak ergodicity breaking: the scaling of the time-averaged mean-squared displacement <(delta(2)(Delta))over bar> remains linear in the lag time Delta and thus differs from the corresponding ensemble average < x(2)(t)>. We analyse the non-ergodic behaviour of this process in terms of the time-averaged mean- squared displacement (delta(2)) over bar and its random features, i.e. the statistical distribution of (delta(2)) over bar and the ergodicity breaking parameters. The heterogeneous diffusion model represents an alternative approach to non- ergodic, anomalous diffusion that might be particularly relevant for diffusion in heterogeneous media.}, language = {en} } @article{Cherstvy2013, author = {Cherstvy, Andrey G.}, title = {Detection of DNA hybridization by field-effect DNA-based biosensors - mechanisms of signal generation and open questions}, series = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, volume = {46}, journal = {Biosensors and bioelectronics : the principal international journal devoted to research, design development and application of biosensors and bioelectronics}, number = {2}, publisher = {Elsevier}, address = {Oxford}, issn = {0956-5663}, doi = {10.1016/j.bios.2013.02.026}, pages = {162 -- 170}, year = {2013}, abstract = {We model theoretically the electrostatic effects taking place upon DNA hybridization in dense DNA arrays immobilized on a layer of Au nano-particles deposited on the surface of a field-effect-based DNA capacitive biosensor. We consider the influence of separation of a charged analyte from the sensor surface and the salinity of electrolyte solution, in the framework of both linear and nonlinear Poisson-Boltzmann theories. The latter predicts a substantially weaker sensor signals due to electrostatic saturation effects that is the main conclusion of this paper. We analyze how different physical parameters of dense DNA brushes affect the magnitude of hybridization signals. The list includes the fraction of DNA charge neutralization, the length and spatial conformations of adsorbed DNA molecules, as well as the discreteness of DNA charges. We also examine the effect of Donnan ionic equilibrium in DNA lattices on the sensor response. The validity of theoretical models is contrasted against recent experimental observations on detection of DNA hybridization via its intrinsic electric charge. The sensitivity of such biochemical sensing devices, their detection limit, and DNA hybridization efficiency are briefly discussed in the end.}, language = {en} }