PoL – Physics of Life | Publications

Publications

H. Schiessel
Computer simulations of chromatin phase separation
submitted

M. Zuiddam, B. Shakiba and H. Schiessel
Multiplexing mechanical and translation cues on genes
submitted

T. Nishio, T. Masaoka, Y. Yoshikawa, K. Sadakane, T. Kenmotsu, H. Schiessel and K. Yoshikawa
Markedly different effects of monovalent cations on the efficiency of gene expression
Advanced Biology, in press

H. Schiessel
Spatial and temporal organization of chromatin at small and large scales
Annu. Rev. Condens. Matter Phys., in press

T. Yamamoto and H. Schiessel
Loop extrusion driven volume phase transition of entangled chromosomes
Biophys. J. 121, 2742–2750 (2022)

J.-U. Sommer, H. Merlitz and H. Schiessel
Polymer-assisted condensation: a mechanism for heterochromatin formation and epigenetic memory
Macromolecules 55, 4841–4851 (2022)  [bioRxiv]

B. Scalvini, H. Schiessel, A. Golovnev and A. Mashaghi
Circuit topology analysis of cellular genome reveals signature motifs, conformational heterogeneity and scaling
iScience 25, 103866 (2022) [pdf (3.6 MB)]

H. Schiessel
Biophysics for beginners: a journey through the cell nucleus
Jenny Stanford Publishing (2022), 513 pages

T. Yamamoto, T. Sakaue and H. Schiessel
Slow chromatin dynamics enhances promoter accessibility to transcriptional condensates
Nucl. Acids Res. 49, 5017–5027 (2021) [pdf (4.2 MB)]

H. Schiessel
New and Notable: A polymer model of the whole genome
Biophys. J. 119, 1699–1700 (2020) [pdf (197 kB)]

M. Heidari, H. Schiessel and A. Mashaghi
Circuit topology analysis of polymer folding reactions
ACS Central Science 6, 839–847 (2020) [pdf (3.1 MB)]

K. van Deelen, H. Schiessel and L. de Bruin
Ensembles of breathing nucleosomes: a computational study
Biophys. J. 118, 2297–2308 (2020) [pdf (944 kB)]

H. Schiessel and R. Blossey
Pioneer transcription factors in chromatin remodeling: the kinetic proofreading view
Phys. Rev. E (Rapid Communication) 99, 040401(R) (2020) [pdf (266 kB)]

J. Neipel, G. Brandani and H. Schiessel
Translational nucleosome positioning: a computational study
Phys. Rev. E 15, 022405–1-16 (2020) [pdf (3.4 MB)]

T. Yamamoto and H. Schiessel
Dilution of contact frequency between superenhancers by loop extrusion at interfacess
Soft Matter 15, 7635–7643 (2019) [pdf (2.1 MB)]

T. Yamamoto, T. Sakaue and H. Schiessel
Loop extrusion drives very different dynamics for Rouse chains in bulk solutions and at interfaces
Europhys. Lett. 127, 38002–1-6 (2019) [pdf (323 kB)]

R. Blossey and H. Schiessel
Histone mark recognition controls nucleosome translocation via a kinetic proofreading mechanism: confronting theory and high-throughput experiments
Phys. Rev. E (Rapid Communication) 99, 060401(R) (2019) [pdf (235 kB)]

A. V. Onufriev and H. Schiessel
The nucleosome: from structure to function through physics
Curr. Opin. Struct. Biol. 56, 119–130 (2019) [pdf (1.5 MB)]

H. Schiessel
Nucleosomes as treadmills
Journal Club for Condensed Matter Physics, March 03 (2019) [pdf (151 kB)]

M. Zuiddam and H. Schiessel
Shortest paths through synonymous genomes
Phys. Rev. E 99, 012422–1-9 (2019) [pdf (1.2 MB)]

R. Blossey and H. Schiessel
Chromatin remodelers as active Brownian dimers
J. Phys. A: Math Theor. 52, 085601 (2019) [pdf (734 kB)]

H. Schiessel
New and Notable: Telling left from right in breathing nucleosomes
Biophys. J. 115, 749–750 (2018) [pdf (205 kB)]

R. Blossey and H. Schiessel
Biophysical perspective: the latest twists in chromatin remodeling
Biophys. J. 114, 2255–2261 (2018) [pdf (840 kB)]

H. Schiessel
DNA and chromatin
Lecture Notes of the 49th IFF Spring School 'Physics of Life' (Forschungszentrum Juelich, 2018) B5, 1–15 (2018) [pdf (7.1 MB)]

S. Sazer and H. Schiessel
The biology and polymer physics underlying large scale chromosome organizations
Traffic 19, 87–104 (2018) [pdf (5.3 MB)]

M. Zuiddam, R. Everaers and H. Schiessel
Physics behind the mechanical nucleosome positioning code
Phys. Rev. E 96, 052412–1-15 (2017) [pdf (1.7 MB)]

J. Culkin, L. de Bruin, M. Tompitak, R. Phillips and H. Schiessel
The role of DNA sequence in nucleosome breathing
Eur. Phys. J. E 40, 106–1-12 (2017) [pdf (1.1 MB)]

J. A. J. Wondergem, H. Schiessel and M. Tompitak
Performing SELEX experiments in silico
J. Chem. Phys. 147, 174101–1-11 (2017) [pdf (2.0 MB)]

T. Yamamoto and H. Schiessel
Osmotic mechanism of loop extrusion process
Phys. Rev. E (Rapid Communications) 96, 030402(R)-1–4 (2017) [pdf (184 kB); supplementary material: pdf (119 kB)]

T. Yamamoto and H. Schiessel
Transcription stabilizes nucleus-like layer structure in chromatin brush
Soft Matter 13, 5307–5316 (2017) [pdf (2.3 MB)]

H. Schiessel
How cells overcome their topological troubles
Journal Club for Condensed Matter Physics, June 03 (2017) [pdf (119 kB)]

T. Yamamoto and H. Schiessel
Chromatin gels are auxetic due to cooperative nucleosome assembly and disassembly dynamics
Europhys. Lett. 118, 28003–1-7 (2017) [pdf (279 kB)]

M. Tompitak, and H. Schiessel
Mechanische informatie in DNA- moleculen schrijven en lezen
Nederlands Tijdschrift voor Natuurkunde 83, 164–167 (2017)

M. Tompitak, L. de Bruin, B. Eslami-Mossallam and H. Schiessel
Designing nucleosomal force sensors
Phys. Rev. E 95, 052402–1-6 (2017) [pdf (498 kB)]

M. Tompitak, G. Barkema and H. Schiessel
Benchmarking and refining probability-based models for nucleosome-DNA interaction
BMC Bioinformatics 18, 157–1-7 (2017) [pdf (561 kB)]

M. Tompitak, C. Vaillant and H. Schiessel
Genomes of multicellular organisms have evolved to attract nucleosomes to promoter regions
Biophys. J. 112, 505–511 (2017) [pdf (1.1 MB); supplementary material: pdf (1.0 MB)]

M. Tompitak, H. Schiessel and G. T. Barkema
Force responses of strongly intrinsically curved DNA helices deviate from Worm-Like Chain predictions
Europhys. Lett. 116, 68005–1-6 (2016) [pdf (881 kB)]

B. Eslami-Mossallam, R. D. Schram, M. Tompitak, J. van Noort and H. Schiessel
Multiplexing genetic and nucleosome positioning codes: a computational approach
PLoS ONE 11, e0156905 (2016) [pdf (1.8 MB); supplementary material: pdf (4.5 MB)]

L. de Bruin, M. Tompitak, B. Eslami-Mossallam and H. Schiessel
Why do nucleosomes unwrap asymmetrically?
J. Phys. Chem. B 120, 5855–5863 (2016) [pdf (1.9 MB)]

B. Eslami-Mossallam, H. Schiessel and J. van Noort
Nucleosome dynamics: sequence matters
Adv. Colloid Interface Sci. 232, 101–113 (2016) [pdf (1.3 MB)]

T. Yamamoto and H. Schiessel
Transcription driven phase separation in chromatin brush
Langmuir 32, 3036–3044 (2016) [pdf (741 kB); supplementary material: pdf (299 kB)]

R. D. Schram, H. Klinker, P. B. Becker and H. Schiessel
Computational study of remodelling in a nucleosomal array
Eur. Phys. J. E 38, 85–1-8 (2015) [pdf (918 kB)]

R. Everaers and H. Schiessel (Guest Editors)
Preface: The physics of chromatin
J. Phys.: Condens. Matter 27, 060301–1-2 (2015) [pdf (48 kB)]

L. Lenz, M. Hoenderdos, P. Prinsen and H. Schiessel
The influence of DNA shape fluctuations on FRET efficiency measurements in nucleosomes
special issue "Physics of chromatin", J. Phys.: Condens. Matter 27, 064104–1-7 (2015) [pdf (1.2 MB)]

A. Fathizadeh, H. Schiessel and M. R. Ejtehadi
Molecular dynamics simulation of supercoiled DNA rings
Macromolecules 48, 164–172 (2015) [pdf (2.5 MB)]

J.-C. Walter, M. Baiesi, E. Carlon and H. Schiessel
Unwinding dynamics of a helically wrapped polymer
Macromolecules 47, 4840–4846 (2014) [pdf (1.9 MB)]

R. D. Schram and H. Schiessel
Exact enumeration of Hamiltonian walks on the 4 x 4 x 4 cube and applications to protein folding
J. Phys. A: Math Theor. 46, 485001–1-14 (2013) [pdf (362 kB)]

M. Emanuel, G. Lanzani and H. Schiessel
Multi-plectoneme phase of double-stranded DNA under torsion
Phys. Rev. E 88, 022706–1-20 (2013) [pdf (2.6 MB)]

R. D. Schram, G. T. Barkema and H. Schiessel
On the stability of fractal globules
J. Chem. Phys. 138, 224901–1-11 (2013) [pdf (2.6 MB)]

A. Fathizadeh, A. B. Besya, M. R. Ejtehadi and H. Schiessel
Rigid body molecular dynamics of DNA inside a nucleosome
Eur. Phys. J. E 36, 21–1-10 (2013) [pdf (844 kB)], see also EPJE Highlight.

B. van Opheusden, F. Redig and H. Schiessel
A Markov model for the dynamics of the nucleosome
J. Phys. A: Math Theor. 46, 095005–1-15 (2013) [pdf (406 kB)]

R. P. C. Driessen, H. Meng, G. Suresh, R. Shahapure, G. Lanzani, U. D. Priyakumar, M. F. White, H. Schiessel, J. van Noort and R. T. Dame
Crenarchaeal chromatin proteins Cren7 and Sul7 compact DNA by inducing rigid bends
Nucl. Acids Res. 41, 196–205 (2013) [pdf (4.3 MB)]

G. Lanzani and H. Schiessel
Nucleosome response to tension and torque
Europhys. Lett. 100, 48001–1-5 (2012) [pdf (602 kb)]

A.-M. Florescu, H. Schiessel and R. Blossey
Kinetic control of nucleosome displacement by ISWI/ACF chromatin remodelers
Phys. Rev. Lett. 109, 118103–1-5 (2012) [pdf (365 kB)]

H. Schiessel, M. D. Correa-Rodriguez, S. Rudiuk, D. Baigl and K. Yoshikawa
Theory of DNA-cationic micelle complexation
Soft Matter 8, 9406–9411 (2012) [pdf (295 kB)]

L. Mollazadeh-Beidokhti, F. Mohammad-Rafiee and H. Schiessel
Nucleosome dynamics between tension-induced states
Biophys. J. 96, 2235–2240 (2012) [pdf (226 kB)]

G. Lanzani and H. Schiessel
Out of register: how DNA determines the chromatin fiber geometry
Europhys. Lett. 97, 38002–1-6 (2012) [pdf (1.9 Mb)]

R. T. Dame, M. Tark-Dame and H. Schiessel
A physical approach to segregation and folding of the Caulibactor crescentus genome. Microcommentary
Mol. Microbiol. 86, 1311–1315 (2011) [pdf (82 kB)]

R. Blossey and H. Schiessel
The dynamics of the nucleosome: thermal effects, external forces, and ATP
FEBS journal 278, 3619–3632 (2011) [pdf (340 kB)]

R. Blossey and H. Schiessel
Kinetic proofreading in chromatin remodeling: the case of ISWI/ACF
Biophys. J. 101, L30-L32 (2011) [pdf (105 kB)]

H. Schiessel
Verwickelter Zellkern
Physik Journal 10, 31–36 (2011) [pdf (1.4 MB)]

P. Prinsen and H. Schiessel
Nucleosome stability and accessibility of its DNA to proteins
Biochimie 92, 1722–1728 (2010) [pdf (316 kB)]

M. Emanuel, N. Hamedani Radja, A. Henriksson and H. Schiessel
The physics behind the large-scale organisation of DNA in eukaryotes
Phys. Biol. 6, 025008–1-11 (2009) [pdf (315 kB)]

L. Mollazadeh-Beidokhti, F. Mohammad-Rafiee and H. Schiessel
Active nucleosome displacement: a theoretical approach
Biophys. J. 96, 777–784 (2009) [pdf (991 kB)]

L. Mollazadeh-Beidokhti, J. Deseigne, D. Lacoste, F. Mohammad-Rafiee and H. Schiessel
Stochastic model for nucleosome sliding in the presence of ligands
Phys. Rev. E,79, 031922–1-11 (2009) [pdf (268kB)]

M. Depken and H. Schiessel
Nucleosome shape dictates chromatin-fiber structure
Biophys. J. 96, 777–784 (2009) [pdf (504 kB)]

R. Blossey and H. Schiessel
Kinetic proofreading of gene activation by chromatin remodelling
HFSP Journal 2, 167–170 (2008) [pdf (185kB)]

I. M. Kulic and H. Schiessel
Opening and closing DNA: theories on the nucleosome
in: "Interaction of DNA with Surfactants and Polymers", R. Dias and B. Lindman (Eds.) (Wiley-Blackwell, 2008) p. 173–208 [pdf (565kB)]

R. M. Thaokar, H. Schiessel and I. M. Kulic
Hydrodynamics of a rotating torus
Eur. Phys. J. B 60, 325–336 (2007) [pdf (330kB)]

M. Emanuel, H. Mohrbach, M. Sayar, H. Schiessel and I. M. Kulic
Buckling of stiff polymers: influence of thermal fluctuations
Phys. Rev. E 75, 061907–1-13 (2007) [pdf (556kB)]

I. M. Kulic, H. Mohrbach, R. Thaokar and H. Schiessel
Equation of state of looped DNA
Phys. Rev. E 75, 011913–1-23 (2007) [pdf (534kB)]

I. M. Kulic, R. Thaokar and H. Schiessel
From sliding nucleosomes to twirling DNA motors
J. Comp. and Theor. Nanoscience 3, 912–921 (2006) [pdf (719 kB)]

F. Muehlbacher, H. Schiessel and C. Holm
Tail-induced attraction between nucleosome core particles
Phys. Rev. E 74, 031919–1-11 (2006) [pdf (1044kB)]

J. Langowski and H. Schiessel
Chromatin Simulations
in: "Computational studies of RNA and DNA", J. Sponer and F. Lankas (Eds.) (Springer, Berlin, 2006) p. 605–634 [pdf (5.1 MB)]

M. N. Tamashiro and H. Schiessel
Rayleigh instability of charged aggregates: role of dimensionality, added salt and dielectric contrast
Phys. Rev. E 74, 021412–1-10 (2006) [pdf (316kB)]

H. Schiessel
Comment on "Chromatin fiber functional organization: Some plausible models
Eur. Phys. J. E 19, 291–292 (2006) [pdf (61kB)]

H. Schiessel
The nucleosome: a transparent, slippery, sticky and yet stable DNA-protein complex
Eur. Phys. J. E 19, 251–262 (2006) [pdf (248kB)]

F. Muehlbacher, C. Holm and H. Schiessel
Controlled DNA compaction within chromatin: the tail-bridging effect
Europhys. Lett. 73, 135 (2006) [pdf (196 kB)]

N. Bagatella-Flores, H. Schiessel and W. M. Gelbart
Statics and dynamics of polymer-wrapped colloid complexes
J. Phys. Chem. B 109, 21305–21312 (2005) [pdf (148 kB)]

I. M. Kulic, R. Thaokar and H. Schiessel
A DNA ring acting as a thermal ratchet
J. Phys.: Cond. Mat. 17, S3965-S3978 (2005) [pdf (720 kB)]

I. M. Kulic, R. Thaokar and H. Schiessel
Twirling DNA rings - swimming nanomotors ready for a kickstart
Europhys. Lett. 72, 527–533 (2005) [pdf (213 kB)]

I. M. Kulic, H. Mohrbach, V. Lobaskin, R. Thaokar and H. Schiessel
Apparent persistence length renormalization of bent DNA
Phys. Rev. E 72, 041905–1-5 (2005) [pdf (246 kB)]

F. Mohammad-Rafiee, I. M. Kulic and H. Schiessel
Theory of nucleosome corkscrew sliding in the presence of synthetic DNA ligands
J. Mol. Biol. 344, 47–58 (2004) [pdf (293 kB)]

B. Mergell, R. Everaers and H. Schiessel
Nucleosome interactions in chromatin: fiber stiffening and hairpin formation
Phys. Rev. E 70, 011915–1-9 (2004) [pdf (812 kB)]

J. Langowski and H. Schiessel
Theory and computer modeling of the 30nm chromatin fiber
New Comprehensive Biochemistry 39, 397–420 (2004) [pdf (1.7 MB)]

I. Kulic and H. Schiessel
DNA spools under tension
Phys. Rev. Lett. 92, 228101 (2004) [pdf (224 kB)]

M. N. Tamashiro and H. Schiessel
Where the linearized Poisson-Boltzmann cell model fails: the planar case as a prototype study
Phys. Rev. E 68, 066106–1-14 (2003) [pdf (246 kB)]

I. M. Kulic and H. Schiessel
Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects
Phys. Rev. Lett. 91, 148103 (2003) [pdf (345 kB)]

M. N. Tamashiro and H. Schiessel
Where the linearized Poisson-Boltzmann cell model fails: spurious phase separation in charged colloidal suspensions
J. Chem. Phys. 119, 1855–1865 (2003) [pdf (295 kB); supplementary material: pdf (259 kB)]

H. Schiessel
Topical Review: The physics of chromatin
J. Phys.: Condens. Matter 15, R699-R774 (2003) [pdf (961 kB)]

H. Schiessel
Charged rosettes at high and low ionic strengths
Macromolecules 36, 3424–3431 (2003) [pdf (92 kB)]

I. M. Kulic and H. Schiessel
Nucleosome repositioning via loop formation
Biophys. J. 84, 3197–3211 (2003) [pdf (428 kB)]

H. Schiessel, G. Oshanin, A. M. Cazabat and M. Moreau
Defect-induced perturbations of atomic monolayers on solid surfaces
Phys. Rev. E 66, 056130 (2002) [pdf (369 kB)]

H. Schiessel
How short-ranged electrostatics controls the chromatin structure on much larger scales
Europhys. Lett. 58, 140–146 (2002) [pdf (132 kB)]

H. Schiessel, R. Bruinsma and W. M. Gelbart
Electostatic complexation of spheres and chains under elastic stress
J. Chem. Phys. 115, 7245–7252 (2001) [pdf (114 kB)]

H. Schiessel and H. Aranda-Espinoza
Electrostatically induced undulations of lamellar DNA-lipid complexes
Eur. Phys. J. E 5, 499–506 (2001) [pdf (246 kB)]

H. Schiessel, W. M. Gelbart and R. Bruinsma
DNA folding: structural and mechanical properties of the two-angle model for chromatin
Biophys. J. 80, 1940–1956 (2001) [pdf (208 kB)]

H. Schiessel, J. Widom, R. F. Bruinsma and W. M. Gelbart
Polymer reptation and nucleosome repositioning
Phys. Rev. Lett. 86, 4414–4417 (2001) [pdf (84 kB); Erratum: pdf (27 kB)]

H. Schiessel, J. Rudnick, R. Bruinsma and W. M. Gelbart
Organized condensation of worm-like chains
Europhys. Lett. 51, 237–243 (2000) [pdf (208 kB)]

M. N. Tamashiro and H. Schiessel
Stepwise unwinding of polyelectrolytes under stretching
Macromolecules 33, 5263–5272 (2000) [pdf (192 kB)]

H. Schiessel, Chr. Friedrich and A. Blumen
Application to problems in polymer physics and rheology
in: "Applications of fractional calculus in physics". R. Hilfer (Ed.) (World Scientific, Singapore, 2000) p. 331–376 [pdf (8.2 Mb kB)]

H. Schiessel
Counterion condensation on flexible polyelectrolytes: dependence on ionic strength and chain concentration
Macromolecules 32, 5673–5680 (1999) [pdf (171 kB)]

Chr. Friedrich, H. Schiessel and A. Blumen
Constitutive behavior modelling and fractional derivatives
in: "Advances in the flow and rheology of non-Newtonian fluids - Part A", D. A. Siginer, R. P. Chabra, and D. DeKee (Eds.) (Elsevier, Amsterdam, 1999) p. 429–466 [pdf (233 kB)]

H. Schiessel and P. Pincus
Counterion-condensation-induced collapse of highly charged polyelectrolytes
Macromolecules 31, 7953–7959 (1998) [pdf (92 kB)]

H. Schiessel
Bending of charged flexible membranes due to the presence of macroions
Eur. Phys. J. B 6, 373–380 (1998) [pdf (332 kB)]

H. Schiessel
Unfold dynamics of generalized Gaussian structures
Phys. Rev. E 57, 5775–5781 (1998) [pdf (169 kB)]

T. Soddemann, H. Schiessel and A. Blumen
Molecular dynamics simulations of polyampholytes: instabilities due to excess charges and external fields
Phys. Rev. E 57, 2081–2090 (1998) [pdf (378 kB)]

H. Schiessel, I. M. Sokolov and A. Blumen
Dynamics of a polyampholyte hooked around an obstacle
Phys. Rev. E 56, R2390-R2393 (1997) [pdf (95 kB)]

D. Loomans, H. Schiessel and A. Blumen
Biased reptation of polyampholytes: trapping and enhancement effects
J. Chem. Phys. 107, 2636–2642 (1997) [pdf (132 kB)]

H. Schiessel and A. Blumen
Theory of dilute polyampholyte solutions in external electrical fields
Macrom. Theory Simul. 6, 103–143 (1997) [pdf (2 MB)]

H. Schiessel and A. Blumen
Instabilities of polyampholytes in external electrical fields
J. Chem. Phys. 105, 4250–4256 (1996) [pdf (129 kB)]

H. Schiessel and A. Blumen
Conformations of freely jointed polyampholytes in external electrical fields
J. Chem. Phys. 104, 6036–6040 (1996) [pdf (99 kB)]

H. Schiessel, G. Oshanin and A. Blumen
Dynamics and conformational properties of polyampholytes in external electrical fields: influence of charge distribution
Macrom. Theory Simul. 5, 45–66 (1996) [pdf (930 kB)]

H. Schiessel, R. Metzler, T. F. Nonnenmacher and A. Blumen
Generalized viscoelastic models: their fractional equation with solutions
J. Phys. A: Math. Gen. 28, 6567–6584 (1995) [pdf (651 kB)]

H. Schiessel and A. Blumen
Fractal aspects in polymer science
Fractals 3, 483–490 (1995) [pdf (1.2 Mb kB)] [also published in: "Fractal geometry and analysis - The Mandelbrot Festschrift, Curacao 1995", C. J. G. Evertsz, H.-G. Peitgen, and R. F. Voss (Eds.) (World Scientific, Singapore, 1996) p. 79–86]

H. Schiessel, G. Oshanin and A. Blumen
Dynamics and conformational properties of polyampholytes in external electrical fields
J. Chem. Phys. 103, 5070–5074 (1995) [pdf (114 kB)]

H. Schiessel and A. Blumen
Mesoscopic pictures of the sol-gel transition: ladder models and fractal networks
Macromolecules 28, 4013–4019 (1995) [pdf (812 kB)]

H. Schiessel, P. Alemany and A. Blumen
Dynamics in disordered systems
Progr. Colloid Polym. Sci. 96, 15–21 (1994) [pdf (877 kB)]

H. Schiessel and A. Blumen
Hierarchical analogues to fractional relaxation equations
J. Phys. A: Math. Gen. 15, 5057–5069 (1993) [pdf (424 kB)]