Helmut Schiessel - Academia.edu (original) (raw)

Papers by Helmut Schiessel

Physical Review E Statistical Nonlinear and Soft Matter Physics, Aug 1, 2004

We use Monte Carlo simulations to study attractive and excluded volume interactions between nucle... more We use Monte Carlo simulations to study attractive and excluded volume interactions between nucleosome core particles in 30-nm chromatin fibers. The nucleosomes are treated as disklike objects having an excluded volume and short-range attraction modeled by a variant of the Gay-Berne potential. The nucleosomes are connected via bendable and twistable linker DNA in the crossed linker fashion. We investigate the influence of the nucleosomal excluded volume on the stiffness of the fiber. For parameter values that correspond to chicken erythrocyte chromatin, we find that the persistence length is governed to a large extent by that excluded volume whereas the soft linker backbone elasticity plays only a minor role. We further find that internucleosomal attraction can induce the formation of hairpin configurations. Tension-induced opening of such configurations into straight fibers manifests itself in a quasiplateau in the force-extension curve that resembles results from recent micromanipulation experiments. Such hairpins may play a role in the formation of higher-order structures in chromosomes like chromonema fibers.

Reversible coordinated condensation of long eukaryotic DNA strands into a highly compacted packag... more Reversible coordinated condensation of long eukaryotic DNA strands into a highly compacted package (chromatin), and the controlled swelling of chromatin, are essential requirements for the successful expression and replication of DNA. In this talk we discuss the two lowest levels in the hierarchy of "DNA folding": (1) The complexation of DNA with oppositely charged proteins, the histone octomers. (2) The folding of the resulting bead-on-string configuration into the 30nm fiber. Another feature that we address is the diffusion of histone octomers along the DNA. This nucleosome mobilty is a result of a process in which parts of the DNA move around the histone octomer in the form of loops; we give an estimation of the resulting mobility.

Physical Review E 88 2013, Aug 1, 2013

We use the wormlike chain model to study supercoiling of DNA under tension and torque. The model ... more We use the wormlike chain model to study supercoiling of DNA under tension and torque. The model reproduces experimental data for a broad range of forces, salt concentrations, and contour lengths. We find a plane of first-order phase transitions ending in a smeared-out line of critical points, the multiplectoneme phase, which is characterized by a fast twist-mediated diffusion of plectonemes and a torque that rises after plectoneme formation with increasing linking number. The discovery of this phase at the same time resolves the discrepancies between existing models and experiment.

The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuati... more The buckling of biopolymers is a frequently studied phenomenon The influence of thermal fluctuations on the buckling transition is, however, often ignored and not completely understood. A quantitative theory of the buckling of a wormlike chain based on a semiclassical approximation of the partition function is presented. The contribution of thermal fluctuations to the force-extension relation that allows one to go beyond the classical Euler buckling is derived in the linear and nonlinear regimes as well. It is shown that the thermal fluctuations in the nonlinear buckling regime increase the end-to-end distance of the semiflexible rod if it is confined to two dimensions as opposed to the three-dimensional case. The transition to a buckled state softens at finite temperature. We derive the scaling behavior of the transition shift with increasing ratio of contour length versus persistence length.

Biophysical Journal, Jun 3, 2009

Three-quarters of eukaryotic DNA are wrapped around protein cylinders forming so-called nucleosom... more Three-quarters of eukaryotic DNA are wrapped around protein cylinders forming so-called nucleosomes that block the access to the genetic information. Nucleosomes need therefore to be repositioned, either passively (by thermal fluctuations) or actively (by molecular motors). Here we introduce a theoretical model that allows us to study the interplay between a motor protein that moves along DNA (e.g., an RNA polymerase) and a nucleosome that it encounters on its way. We aim at describing the displacement mechanisms of the nucleosome and the motor protein on a microscopic level to understand better the intricate interplay between the active step of the motor and the nucleosome-repositioning step. Different motor types (Brownian ratchet versus power-stroke mechanism) that perform very similarly under a constant load are shown to have very different nucleosome repositioning capacities.

In addition to being the gateway for all access to the eukaryotic genome, chromatin has in recent... more In addition to being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. Though much is known about the biochemistry of this code, little is understood regarding the different fiber structures through which the regulation is mediated. Over the last three decades many fiber models have been suggested, but none are able to predict even the basic characteristics of the fiber. In this work, we characterize the set of all possible dense fibers, which includes, but is not limited to, all previously suggested structures. To guide future experimental efforts, we show which fiber characteristics depend on the underlying structure and, crucially, which do not. Addressing the predictive power of these models, we suggest a simple geometric criterion based on the nucleosome shape alone. This enables us to predict the observed characteristics of the condensed chromatin fiber, and how these change with varying nucleosome repeat length. Our approach sheds light on how the in vivo observed heterogeneity in linker lengths can be accommodated within the 30 nm fiber, and suggest an important role for nucleosome surface interactions in the regulation of chromatin structure and function.

Physical Review E, 1997

We consider polyampholytes ͑PAs͒, which are polymers carrying positive and negative charges. The ... more We consider polyampholytes ͑PAs͒, which are polymers carrying positive and negative charges. The PAs are submitted to electric fields and collide with single obstacles. Field separation of PAs depends drastically on u , the time to unhook. Our analysis shows u to be very sensitive to the charge distribution of the chains: Unhooking is diffusional for regular, multiblock PAs, with u depending on the length of the blocks; for random charge distributions u increases exponentially with the PAs' length and unhooking is subdiffusive.

$Research paper thumbnail of Constitutive behavior modeling and fractional derivatives$

Progress in Colloid & Polymer Science, 1994

In this work we focus on hierarchical relaxation in complex systems.

Physical Review E, 1998

In this paper we study the conformational properties of polyampholytes ͑PAs; polymers with positi... more In this paper we study the conformational properties of polyampholytes ͑PAs; polymers with positively and negatively charged monomers͒ by molecular-dynamics ͑MD͒ simulations and by scaling arguments. As is well known, in the absence of external electrical fields PAs with a small total charge Q tot collapse into spherical globules, whereas PAs whose Q tot exceeds a critical value Q c are expanded; our MD simulations confirm this fact. For Q tot ϭ0 we study the influence of external electric fields on single PAs. We find that the PA globule is unstable above a critical field strength E c1 ; for EϾE c1 the PA becomes highly stretched. Lowering the external field again, one observes hysteresis; the PA collapses back into a globule only for EϽE c2 where E c2 ϽE c1 . In the weak coupling limit ͑when the intrachain electrostatic interactions can be neglected͒ the PA attains in an external field a trumpetlike shape, whose end-to-end distance obeys Pincus scaling.

Journal of Physics Condensed Matter

This special issue is devoted to the physics of chromatin, the complex of DNA and proteins that f... more This special issue is devoted to the physics of chromatin, the complex of DNA and proteins that fills the nuclei of eukaryotic cells (eukaryotes include animals, plants and fungi). The structure of chromatin is hierarchical with length scales ranging from the subnanometer height of a base pair via the 10 nm sized nucleosomes (DNA wrapped protein cylinders) up to the micrometer sized nuclear compartment (that typically stores meters of DNA molecules). As a consequence, to learn about the structure and function of chromatin one needs to employ a vast range of experimental and theoretical methods. One only has to realize that 11 years ago it was still acceptable to write a review [1] with the same title as this special issue that dealt mainly with elastic beams ('DNA') and balls ('nucleosomes') to understand what tremendous progress, experimentally and theoretically, has taken place in the meantime. The contributions to this special issue reflect this.

Macromolecules, 2014

We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and u... more We study the rotational dynamics of a flexible polymer initially wrapped around a rigid rod and unwinding from it. This dynamics is of interest in several problems in biology and constitutes a fundamental instance of polymer relaxation from a state of minimal entropy. We investigate the dynamics of several quantities such as the total and local winding angles and metric quantities. The results of simulations performed in two and three dimensions, with and without self-avoidance, are explained by a theory based on scaling arguments and on a balance between frictional and entropic forces. The early stage of the dynamics is particularly rich, being characterized by three coexisting phases.

Biophysical Journal, 2015

Journal of Physics: Condensed Matter, 2015

HFSP Journal, 2008

Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin ... more Gene activation in eukaryotes involves the concerted action of histone tail modifiers, chromatin remodelers, and transcription factors, whose precise coordination is currently unknown. We demonstrate that the experimentally observed interactions of the molecules are in accord with a kinetic proofreading scheme. Our finding could provide a basis for the development of quantitative models for gene regulation in eukaryotes based on the combinatorical interactions of chromatin modifiers.

Physical Review E, 2003

The classical problem of two uniformly charged infinite planes in electrochemical equilibrium wit... more The classical problem of two uniformly charged infinite planes in electrochemical equilibrium with an infinite monovalent salt reservoir is solved exactly at the mean-field nonlinear Poisson-Boltzmann (PB) level, including an explicit expression of the associated nonlinear electrostatic contribution to the semi-grand-canonical potential. A linearization of the nonlinear functional is presented that leads to Debye-Hückel-like equations agreeing asymptotically with the nonlinear PB results in the weak-coupling (high-temperature) and counterionic ideal-gas limits. This linearization scheme yields artifacts in the lowtemperature, large-separation or high-surface charge limits. In particular, the osmotic-pressure difference between the interplane region and the salt reservoir becomes negative in the above limits, in disagreement with the exact (at mean-field level) nonlinear PB solution. By using explicitly gauge-invariant forms of the electrostatic potential we show that these artifacts -although thermodynamically consistent with quadratic expansions of the nonlinear functional -can be traced back to the non-fulfillment of the underlying assumptions of the linearization. Explicit comparison between the analytical expressions of the exact nonlinear solution and the corresponding linearized equations allows us to show that the linearized results are asymptotically exact in the weak-coupling and counterionic ideal-gas limits, but always fail otherwise, predicting negative osmotic-pressure differences. By taking appropriate limits of the full nonlinear PB solution, we provide asymptotic expressions for the semi-grand-canonical potential and the osmotic-pressure difference that involve only elementary functions, which cover the complementary region where the linearized theory breaks down.

PHYSICAL REVIEW E, 2006

We study a possible electrostatic mechanism underlying the compaction of DNA inside the nuclei of... more We study a possible electrostatic mechanism underlying the compaction of DNA inside the nuclei of eucaryotes: the tail-bridging effect between nucleosomes, the fundamental DNA packaging units of the chromatin complex. As a simple model of the nucleosome we introduce the eight-tail colloid, a charged sphere with eight oppositely charged, flexible, grafted chains that represent the terminal histone tails. We show that our complexes attract each other via the formation of chain bridges and contrast this to the effect of attraction via charge patches. We demonstrate that the attraction between eight-tail colloids can be tuned by changing the fraction of charged monomers on the tails. This suggests a physical mechanism of chromatin compaction where the degree of DNA condensation is controlled via biochemical means, namely the acetylation and deacetylation of lysines in the histone tails.

Physical Review E, 2002

We study long-range morphological changes in atomic monolayers on solid substrates induced by dif... more We study long-range morphological changes in atomic monolayers on solid substrates induced by different types of defects; e.g., by monoatomic steps in the surface, or by the tip of an atomic force microscope ͑AFM͒, placed at some distance above the substrate. Representing the monolayer in terms of a suitably extended Frenkel-Kontorova-type model, we calculate the defect-induced density profiles for several possible geometries. In case of an AFM tip, we also determine the extra force exerted on the tip due to the tip-induced dehomogenization of the monolayer.