Search Menu
DOE PAGES title logo U.S. Department of Energy
Office of Scientific and Technical Information
Search Scholarly Publications

Title: 1CPN: A coarse-grained multi-scale model of chromatin

Abstract

A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recentlymore » developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. In conclusion, the 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.« less

Authors:
ORCiD logo [1]; ORCiD logo [1];  [1]; ORCiD logo [2]
+ Show Author Affiliations
  1. Univ. of Chicago, Chicago, IL (United States)
  2. Univ. of Chicago, Chicago, IL (United States); Argonne National Lab. (ANL), Argonne, IL (United States)
Publication Date:
Research Org.:
Argonne National Laboratory (ANL), Argonne, IL (United States)
Sponsoring Org.:
National Science Foundation (NSF); Chilean Comision Nacional de Investigacion Cientifica y Tecnologica (CONICYT); Fondo Nacional de Desarrollo Científico y Tecnologico (FONDECYT); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Materials Sciences & Engineering Division - Midwest Integrated Center for Computational Materials (MICCoM); USDOE
OSTI Identifier:
1557992
Alternate Identifier(s):
OSTI ID: 1524467
Grant/Contract Number:  
AC02-06CH11357
Resource Type:
Accepted Manuscript
Journal Name:
Journal of Chemical Physics
Additional Journal Information:
Journal Volume: 150; Journal Issue: 21; Journal ID: ISSN 0021-9606
Publisher:
American Institute of Physics (AIP)
Country of Publication:
United States
Language:
English
Subject:
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CHEMISTRY

Citation Formats

Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, and de Pablo, Juan J. 1CPN: A coarse-grained multi-scale model of chromatin. United States: N. p., 2019. Web. doi:10.1063/1.5092976.
Copy to clipboard
Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, & de Pablo, Juan J. 1CPN: A coarse-grained multi-scale model of chromatin. United States. https://doi.org/10.1063/1.5092976
Copy to clipboard
Lequieu, Joshua, Córdoba, Andrés, Moller, Joshua, and de Pablo, Juan J. Tue . "1CPN: A coarse-grained multi-scale model of chromatin". United States. https://doi.org/10.1063/1.5092976. https://www.osti.gov/servlets/purl/1557992.
Copy to clipboard
@article{osti_1557992,
title = {1CPN: A coarse-grained multi-scale model of chromatin},
author = {Lequieu, Joshua and Córdoba, Andrés and Moller, Joshua and de Pablo, Juan J.},
abstractNote = {A central question in epigenetics is how histone modifications influence the 3D structure of eukaryotic genomes and, ultimately, how this 3D structure is manifested in gene expression. The wide range of length scales that influence the 3D genome structure presents important challenges; epigenetic modifications to histones occur on scales of angstroms, yet the resulting effects of these modifications on genome structure can span micrometers. There is a scarcity of computational tools capable of providing a mechanistic picture of how molecular information from individual histones is propagated up to large regions of the genome. In this work, a new molecular model of chromatin is presented that provides such a picture. This new model, referred to as 1CPN, is structured around a rigorous multiscale approach, whereby free energies from an established and extensively validated model of the nucleosome are mapped onto a reduced coarse-grained topology. As such, 1CPN incorporates detailed physics from the nucleosome, such as histone modifications and DNA sequence, while maintaining the computational efficiency that is required to permit kilobase-scale simulations of genomic DNA. The 1CPN model reproduces the free energies and dynamics of both single nucleosomes and short chromatin fibers, and it is shown to be compatible with recently developed models of the linker histone. It is applied here to examine the effects of the linker DNA on the free energies of chromatin assembly and to demonstrate that these free energies are strongly dependent on the linker DNA length, pitch, and even DNA sequence. In conclusion, the 1CPN model is implemented in the LAMMPS simulation package and is distributed freely for public use.},
doi = {10.1063/1.5092976},
journal = {Journal of Chemical Physics},
number = 21,
volume = 150,
place = {United States},
year = {Tue Jun 04 00:00:00 EDT 2019},
month = {Tue Jun 04 00:00:00 EDT 2019}
}
Copy to clipboard
Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record
https://doi.org/10.1063/1.5092976
Copyright Statement
Other availability
Search WorldCat Search WorldCat to find libraries that may hold this journal
Citation Metrics:
Cited by: 18 works
Citation information provided by
Web of Science
Save / Share:
Export Metadata
Save to My Library
You must Sign In or Create an Account in order to save documents to your library.

Works referenced in this record:

Mapping and analysis of chromatin state dynamics in nine human cell types
journal, March 2011

  • Ernst, Jason; Kheradpour, Pouya; Mikkelsen, Tarjei S.
  • Nature, Vol. 473, Issue 7345
  • DOI: 10.1038/nature09906

Dynamics of Nucleosome Invasion by DNA Binding Proteins
journal, August 2011

  • Tims, Hannah S.; Gurunathan, Kaushik; Levitus, Marcia
  • Journal of Molecular Biology, Vol. 411, Issue 2
  • DOI: 10.1016/j.jmb.2011.05.044

Effect of force on mononucleosomal dynamics
journal, October 2006

  • Mihardja, S.; Spakowitz, A. J.; Zhang, Y.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 43
  • DOI: 10.1073/pnas.0607526103

Nucleosome Geometry and Internucleosomal Interactions Control the Chromatin Fiber Conformation
journal, October 2008

Cryo-EM Study of the Chromatin Fiber Reveals a Double Helix Twisted by Tetranucleosomal Units
journal, April 2014

The Effect of Internucleosomal Interaction on Folding of the Chromatin Fiber
journal, October 2008

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing
journal, February 2012

  • Davtyan, Aram; Schafer, Nicholas P.; Zheng, Weihua
  • The Journal of Physical Chemistry B, Vol. 116, Issue 29
  • DOI: 10.1021/jp212541y

Rotational and translational diffusion of short rodlike molecules in solution: Oligonucleotides
journal, February 1991

  • Eimer, Wolfgang; Pecora, R.
  • The Journal of Chemical Physics, Vol. 94, Issue 3
  • DOI: 10.1063/1.459904

Multidimensional free-energy calculations using the weighted histogram analysis method
journal, November 1995

  • Kumar, Shankar; Rosenberg, John M.; Bouzida, Djamal
  • Journal of Computational Chemistry, Vol. 16, Issue 11
  • DOI: 10.1002/jcc.540161104

Superresolution intrinsic fluorescence imaging of chromatin utilizing native, unmodified nucleic acids for contrast
journal, August 2016

  • Dong, Biqin; Almassalha, Luay M.; Stypula-Cyrus, Yolanda
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 35
  • DOI: 10.1073/pnas.1602202113

Mapping Nucleosome Resolution Chromosome Folding in Yeast by Micro-C
journal, July 2015

Nucleosome sliding mechanisms: new twists in a looped history
journal, September 2013

  • Mueller-Planitz, Felix; Klinker, Henrike; Becker, Peter B.
  • Nature Structural & Molecular Biology, Vol. 20, Issue 9
  • DOI: 10.1038/nsmb.2648

An experimentally-informed coarse-grained 3-site-per-nucleotide model of DNA: Structure, thermodynamics, and dynamics of hybridization
journal, October 2013

  • Hinckley, Daniel M.; Freeman, Gordon S.; Whitmer, Jonathan K.
  • The Journal of Chemical Physics, Vol. 139, Issue 14
  • DOI: 10.1063/1.4822042

Frustration, specific sequence dependence, and nonlinearity in large-amplitude fluctuations of allosteric proteins
journal, February 2011

  • Li, Wenfei; Wolynes, Peter G.; Takada, Shoji
  • Proceedings of the National Academy of Sciences, Vol. 108, Issue 9
  • DOI: 10.1073/pnas.1018983108

Dependence of the torsional rigidity of DNA on base composition
journal, March 1990

  • Fujimoto, Bryant S.; Schurr, J. Michael
  • Nature, Vol. 344, Issue 6262
  • DOI: 10.1038/344175a0

Exploring the Free Energy Landscape of Nucleosomes
journal, June 2016

  • Zhang, Bin; Zheng, Weihua; Papoian, Garegin A.
  • Journal of the American Chemical Society, Vol. 138, Issue 26
  • DOI: 10.1021/jacs.6b02893

Single-molecule super-resolution imaging of chromosomes and in situ haplotype visualization using Oligopaint FISH probes
journal, May 2015

  • Beliveau, Brian J.; Boettiger, Alistair N.; Avendaño, Maier S.
  • Nature Communications, Vol. 6, Issue 1
  • DOI: 10.1038/ncomms8147

Nucleosome structural studies
journal, February 2011

Chromatin fibers are left-handed double helices with diameter and mass per unit length that depend on linker length
journal, January 1986

Chromatin structure-dependent conformations of the H1 CTD
journal, June 2016

DNA Methylation Effects on Tetra-Nucleosome Compaction and Aggregation
journal, October 2014

  • Jimenez-Useche, Isabel; Nurse, Nathan P.; Tian, Yuqing
  • Biophysical Journal, Vol. 107, Issue 7
  • DOI: 10.1016/j.bpj.2014.05.055

Activation of proto-oncogenes by disruption of chromosome neighborhoods
journal, March 2016

Rapid spontaneous accessibility of nucleosomal DNA
journal, December 2004

  • Li, Gu; Levitus, Marcia; Bustamante, Carlos
  • Nature Structural & Molecular Biology, Vol. 12, Issue 1
  • DOI: 10.1038/nsmb869

Crystal structure of the nucleosome core particle at 2.8 Å resolution
journal, September 1997

  • Luger, Karolin; Mäder, Armin W.; Richmond, Robin K.
  • Nature, Vol. 389, Issue 6648
  • DOI: 10.1038/38444

Variable chromatin structure revealed by in situ spatially correlated DNA cleavage mapping
journal, December 2016

  • Risca, Viviana I.; Denny, Sarah K.; Straight, Aaron F.
  • Nature, Vol. 541, Issue 7636
  • DOI: 10.1038/nature20781

The Free Energy Landscape of Internucleosome Interactions and Its Relation to Chromatin Fiber Structure
journal, January 2019

Kinetics of DNA supercoiling studied by Brownian dynamics simulation
journal, March 1994

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster
journal, December 2010

  • Kharchenko, Peter V.; Alekseyenko, Artyom A.; Schwartz, Yuri B.
  • Nature, Vol. 471, Issue 7339
  • DOI: 10.1038/nature09725

A Method for the In Vitro Reconstitution of a Defined “30nm” Chromatin Fibre Containing Stoichiometric Amounts of the Linker Histone
journal, February 2005

  • Huynh, Van A. T.; Robinson, Philip J. J.; Rhodes, Daniela
  • Journal of Molecular Biology, Vol. 345, Issue 5
  • DOI: 10.1016/j.jmb.2004.10.075

Linker DNA bending induced by the core histones of chromatin
journal, August 1991

A relationship between the helical twist of DNA and the ordered positioning of nucleosomes in all eukaryotic cells.
journal, February 1992

Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome
journal, October 2009

Chromatin structure: does the 30-nm fibre exist in vivo?
journal, June 2010

  • Maeshima, Kazuhiro; Hihara, Saera; Eltsov, Mikhail
  • Current Opinion in Cell Biology, Vol. 22, Issue 3
  • DOI: 10.1016/j.ceb.2010.03.001

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data
journal, May 2013

  • Dekker, Job; Marti-Renom, Marc A.; Mirny, Leonid A.
  • Nature Reviews Genetics, Vol. 14, Issue 6
  • DOI: 10.1038/nrg3454

Determinants of nucleosome positioning
journal, March 2013

  • Struhl, Kevin; Segal, Eran
  • Nature Structural & Molecular Biology, Vol. 20, Issue 3
  • DOI: 10.1038/nsmb.2506

Crystal structure of globular domain of histone H5 and its implications for nucleosome binding
journal, March 1993

  • Ramakrishnan, V.; Finch, J. T.; Graziano, V.
  • Nature, Vol. 362, Issue 6417
  • DOI: 10.1038/362219a0

Characterization of Nucleosome Unwrapping within Chromatin Fibers Using Magnetic Tweezers
journal, July 2014

Ionic effects on the elasticity of single DNA molecules
journal, June 1997

  • Baumann, C. G.; Smith, S. B.; Bloomfield, V. A.
  • Proceedings of the National Academy of Sciences, Vol. 94, Issue 12
  • DOI: 10.1073/pnas.94.12.6185

Regulation of nucleosome dynamics by histone modifications
journal, March 2013

  • Zentner, Gabriel E.; Henikoff, Steven
  • Nature Structural & Molecular Biology, Vol. 20, Issue 3
  • DOI: 10.1038/nsmb.2470

Statistical mechanics of helical wormlike chains. I. Differential equations and moments
journal, June 1976

  • Yamakawa, Hiromi; Fujii, Motoharu
  • The Journal of Chemical Physics, Vol. 64, Issue 12
  • DOI: 10.1063/1.432197

Influence of histone H1 on chromatin structure
journal, September 1977

The Effect of Linker Histone's Nucleosome Binding Affinity on Chromatin Unfolding Mechanisms
journal, October 2011

H1 histones: current perspectives and challenges
journal, August 2013

  • Harshman, S. W.; Young, N. L.; Parthun, M. R.
  • Nucleic Acids Research, Vol. 41, Issue 21
  • DOI: 10.1093/nar/gkt700

Nucleosome Arrays Reveal the Two-Start Organization of the Chromatin Fiber
journal, November 2004

Histone acetylation dependent energy landscapes in tri-nucleosome revealed by residue-resolved molecular simulations
journal, October 2016

  • Chang, Le; Takada, Shoji
  • Scientific Reports, Vol. 6, Issue 1
  • DOI: 10.1038/srep34441

A chromatin folding model that incorporates linker variability generates fibers resembling the native structures.
journal, October 1993

  • Woodcock, C. L.; Grigoryev, S. A.; Horowitz, R. A.
  • Proceedings of the National Academy of Sciences, Vol. 90, Issue 19
  • DOI: 10.1073/pnas.90.19.9021

Hierarchical looping of zigzag nucleosome chains in metaphase chromosomes
journal, January 2016

  • Grigoryev, Sergei A.; Bascom, Gavin; Buckwalter, Jenna M.
  • Proceedings of the National Academy of Sciences, Vol. 113, Issue 5
  • DOI: 10.1073/pnas.1518280113

Computer Simulation of the 30-Nanometer Chromatin Fiber
journal, June 2002

Direct detection of linker DNA bending in defined-length oligomers of chromatin.
journal, October 1990

  • Yao, J.; Lowary, P. T.; Widom, J.
  • Proceedings of the National Academy of Sciences, Vol. 87, Issue 19
  • DOI: 10.1073/pnas.87.19.7603

Structure of the ‘30nm’ chromatin fibre: A key role for the linker histone
journal, June 2006

  • Robinson, Philip JJ; Rhodes, Daniela
  • Current Opinion in Structural Biology, Vol. 16, Issue 3
  • DOI: 10.1016/j.sbi.2006.05.007

Sequence dependence of DNA bending rigidity
journal, August 2010

  • Geggier, S.; Vologodskii, A.
  • Proceedings of the National Academy of Sciences, Vol. 107, Issue 35
  • DOI: 10.1073/pnas.1004809107

Unraveling the 3D genome: genomics tools for multiscale exploration
journal, July 2015

A coarse grain model for DNA
journal, February 2007

  • Knotts, Thomas A.; Rathore, Nitin; Schwartz, David C.
  • The Journal of Chemical Physics, Vol. 126, Issue 8
  • DOI: 10.1063/1.2431804

A dynamic light scattering study of four DNA restriction fragments
journal, March 1990

Tension-Dependent Free Energies of Nucleosome Unwrapping
journal, August 2016

Role of histone tails in chromatin folding revealed by a mesoscopic oligonucleosome model
journal, October 2006

  • Arya, G.; Schlick, T.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 44
  • DOI: 10.1073/pnas.0604817103

Evidence for heteromorphic chromatin fibers from analysis of nucleosome interactions
journal, July 2009

  • Grigoryev, S. A.; Arya, G.; Correll, S.
  • Proceedings of the National Academy of Sciences, Vol. 106, Issue 32
  • DOI: 10.1073/pnas.0903280106

X-ray structure of a tetranucleosome and its implications for the chromatin fibre
journal, July 2005

  • Schalch, Thomas; Duda, Sylwia; Sargent, David F.
  • Nature, Vol. 436, Issue 7047
  • DOI: 10.1038/nature03686

Solvent Mediated Interactions in the Structure of the Nucleosome Core Particle at 1.9Å Resolution
journal, June 2002

Cancer Genetics and Epigenetics: Two Sides of the Same Coin?
journal, July 2012

Higher-Order Structures of Chromatin: The Elusive 30 nm Fiber
journal, February 2007

Dynamic condensation of linker histone C-terminal domain regulates chromatin structure
journal, June 2014

  • Luque, Antoni; Collepardo-Guevara, Rosana; Grigoryev, Sergei
  • Nucleic Acids Research, Vol. 42, Issue 12
  • DOI: 10.1093/nar/gku491

Single-molecule force spectroscopy reveals a highly compliant helical folding for the 30-nm chromatin fiber
journal, April 2009

  • Kruithof, Maarten; Chien, Fan-Tso; Routh, Andrew
  • Nature Structural & Molecular Biology, Vol. 16, Issue 5
  • DOI: 10.1038/nsmb.1590

Specific Contributions of Histone Tails and their Acetylation to the Mechanical Stability of Nucleosomes
journal, February 2005

  • Brower-Toland, Brent; Wacker, David A.; Fulbright, Robert M.
  • Journal of Molecular Biology, Vol. 346, Issue 1
  • DOI: 10.1016/j.jmb.2004.11.056

Living without 30nm chromatin fibers
journal, January 2011

  • Fussner, Eden; Ching, Reagan W.; Bazett-Jones, David P.
  • Trends in Biochemical Sciences, Vol. 36, Issue 1
  • DOI: 10.1016/j.tibs.2010.09.002

Single-Nucleosome Mapping of Histone Modifications in S. cerevisiae
journal, August 2005

Mechanical Response of DNA–Nanoparticle Crystals to Controlled Deformation
journal, August 2016

The structure of histone H1 and its location in chromatin
journal, December 1980

  • Allan, J.; Hartman, P. G.; Crane-Robinson, C.
  • Nature, Vol. 288, Issue 5792
  • DOI: 10.1038/288675a0

Nucleosomes in Solution Exist as a Mixture of Twist-defect States
journal, January 2005

  • Edayathumangalam, Rajeswari S.; Weyermann, Philipp; Dervan, Peter B.
  • Journal of Molecular Biology, Vol. 345, Issue 1
  • DOI: 10.1016/j.jmb.2004.10.012

Fast Parallel Algorithms for Short-Range Molecular Dynamics
journal, March 1995

Uncovering the forces between nucleosomes using DNA origami
journal, November 2016

  • Funke, Jonas J.; Ketterer, Philip; Lieleg, Corinna
  • Science Advances, Vol. 2, Issue 11
  • DOI: 10.1126/sciadv.1600974

Flexible Histone Tails in a New Mesoscopic Oligonucleosome Model
journal, July 2006

Spatial organization of chromatin domains and compartments in single chromosomes
journal, July 2016

Rotational Brownian motion in an external potential: The Langevin equation approach
journal, July 1996

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1
journal, May 2017

Role of linker histone in chromatin structure and function: H1 stoichiometry and nucleosome repeat length
journal, February 2006

  • Woodcock, Christopher L.; Skoultchi, Arthur I.; Fan, Yuhong
  • Chromosome Research, Vol. 14, Issue 1
  • DOI: 10.1007/s10577-005-1024-3

Metadynamics: a method to simulate rare events and reconstruct the free energy in biophysics, chemistry and material science
journal, November 2008

Liquid-like behavior of chromatin
journal, April 2016

  • Maeshima, Kazuhiro; Ide, Satoru; Hibino, Kayo
  • Current Opinion in Genetics & Development, Vol. 37
  • DOI: 10.1016/j.gde.2015.11.006

Super-resolution imaging reveals distinct chromatin folding for different epigenetic states
journal, January 2016

  • Boettiger, Alistair N.; Bintu, Bogdan; Moffitt, Jeffrey R.
  • Nature, Vol. 529, Issue 7586
  • DOI: 10.1038/nature16496

Exploring the Conformational Space of Chromatin Fibers and Their Stability by Numerical Dynamic Phase Diagrams
journal, March 2010

Measuring the translational diffusion coefficients of small DNA molecules by capillary electrophoresis
journal, January 2001

Topological domains in mammalian genomes identified by analysis of chromatin interactions
journal, April 2012

  • Dixon, Jesse R.; Selvaraj, Siddarth; Yue, Feng
  • Nature, Vol. 485, Issue 7398
  • DOI: 10.1038/nature11082

Coarse-grained modeling of DNA curvature
journal, October 2014

  • Freeman, Gordon S.; Hinckley, Daniel M.; Lequieu, Joshua P.
  • The Journal of Chemical Physics, Vol. 141, Issue 16
  • DOI: 10.1063/1.4897649

A Molecular View of the Dynamics of dsDNA Packing Inside Viral Capsids in the Presence of Ions
journal, April 2017

  • Córdoba, Andrés; Hinckley, Daniel M.; Lequieu, Joshua
  • Biophysical Journal, Vol. 112, Issue 7
  • DOI: 10.1016/j.bpj.2017.02.015

Blocking Transcription Through a Nucleosome with Synthetic DNA Ligands
journal, August 2002

  • Gottesfeld, Joel M.; Belitsky, Jason M.; Melander, Christian
  • Journal of Molecular Biology, Vol. 321, Issue 2
  • DOI: 10.1016/s0022-2836(02)00598-3

In silico evidence for sequence-dependent nucleosome sliding
journal, October 2017

  • Lequieu, Joshua; Schwartz, David C.; de Pablo, Juan J.
  • Proceedings of the National Academy of Sciences, Vol. 114, Issue 44
  • DOI: 10.1073/pnas.1705685114

Chromatin remodeling by DNA bending, not twisting
journal, January 2005

  • Lorch, Y.; Davis, B.; Kornberg, R. D.
  • Proceedings of the National Academy of Sciences, Vol. 102, Issue 5
  • DOI: 10.1073/pnas.0409413102

Mesoscale Modeling Reveals Hierarchical Looping of Chromatin Fibers Near Gene Regulatory Elements
journal, May 2016

  • Bascom, Gavin D.; Sanbonmatsu, Karissa Y.; Schlick, Tamar
  • The Journal of Physical Chemistry B, Vol. 120, Issue 33
  • DOI: 10.1021/acs.jpcb.6b03197

EM measurements define the dimensions of the "30-nm" chromatin fiber: Evidence for a compact, interdigitated structure
journal, April 2006

  • Robinson, P. J. J.; Fairall, L.; Huynh, V. A. T.
  • Proceedings of the National Academy of Sciences, Vol. 103, Issue 17
  • DOI: 10.1073/pnas.0601212103

Pulling a single chromatin fiber reveals the forces that maintain its higher-order structure
journal, January 2000

  • Cui, Y.; Bustamante, C.
  • Proceedings of the National Academy of Sciences, Vol. 97, Issue 1
  • DOI: 10.1073/pnas.97.1.127

Magnetic torque tweezers: measuring torsional stiffness in DNA and RecA-DNA filaments
journal, October 2010

  • Lipfert, Jan; Kerssemakers, Jacob W. J.; Jager, Tessa
  • Nature Methods, Vol. 7, Issue 12
  • DOI: 10.1038/nmeth.1520

Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects
journal, October 2003

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria
journal, September 2011

Umbrella sampling: Umbrella sampling
journal, May 2011

  • Kästner, Johannes
  • Wiley Interdisciplinary Reviews: Computational Molecular Science, Vol. 1, Issue 6
  • DOI: 10.1002/wcms.66

Nucleosome repeat length and linker histone stoichiometry determine chromatin fiber structure
journal, June 2008

  • Routh, Andrew; Sandin, Sara; Rhodes, Daniela
  • Proceedings of the National Academy of Sciences, Vol. 105, Issue 26
  • DOI: 10.1073/pnas.0802336105

Dynamics of low molecular weight DNA fragments in dilute and semidilute solutions
journal, November 1991

A Mesoscale Model of DNA and Its Renaturation
journal, March 2009

Homogeneous reconstituted oligonucleosomes, evidence for salt-dependent folding in the absence of histone H1
journal, November 1989

  • Hansen, Jeffrey C.; Ausio, Juan; Stanik, Valerie H.
  • Biochemistry, Vol. 28, Issue 23
  • DOI: 10.1021/bi00449a026

Computer-simulation studies of diskotic liquid crystals
journal, February 1998

Changes in chromatin folding in solution
journal, July 1980

Solenoidal model for superstructure in chromatin.
journal, June 1976

  • Finch, J. T.; Klug, A.
  • Proceedings of the National Academy of Sciences, Vol. 73, Issue 6
  • DOI: 10.1073/pnas.73.6.1897

A Tale of Tails: How Histone Tails Mediate Chromatin Compaction in Different Salt and Linker Histone Environments †
journal, April 2009

  • Arya, Gaurav; Schlick, Tamar
  • The Journal of Physical Chemistry A, Vol. 113, Issue 16
  • DOI: 10.1021/jp810375d

Force spectroscopy of chromatin fibers: Extracting energetics and structural information from Monte Carlo simulations
journal, February 2011

  • Kepper, Nick; Ettig, Ramona; Stehr, Rene
  • Biopolymers, Vol. 95, Issue 7
  • DOI: 10.1002/bip.21598

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
journal, December 2014

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
journal, April 2014

  • Brackley, C. A.; Morozov, A. N.; Marenduzzo, D.
  • The Journal of Chemical Physics, Vol. 140, Issue 13
  • DOI: 10.1063/1.4870088

The fractal globule as a model of chromatin architecture in the cell
journal, January 2011

Rotational brownian motion in an external potential: the langevin equation approach
journal, July 1996

Structure and Dynamics of a 197 bp Nucleosome in Complex with Linker Histone H1
journal, June 2017

Dynamic condensation of linker histone C-terminal domain regulates chromatin structure.
journalarticle, January 2014

  • Luque, Antoni; Collepardo-Guevara, Rosana; Grigoryev, Sergei
  • Oxford University Press (OUP)
  • DOI: 10.17863/cam.66338

Chromosome Organization by a Nucleoid-Associated Protein in Live Bacteria
journal, January 2012

A 3D Map of the Human Genome at Kilobase Resolution Reveals Principles of Chromatin Looping
journal, July 2015

Spatial Organization of Chromatin Domains and Compartments in Single Chromosomes
journal, February 2017

Models for twistable elastic polymers in Brownian dynamics, and their implementation for LAMMPS
text, January 2014

Coarse-grained Modeling of DNA Curvature
text, January 2014

Tension-dependent Free Energies of Nucleosome Unwrapping
text, January 2016

    Sort by:
    [ × clear filter / sort ]

    Works referencing / citing this record:

    Polymer physics across scales: Modeling the multiscale behavior of functional soft materials and biological systems
    journal, December 2019

    • Spakowitz, Andrew J.
    • The Journal of Chemical Physics, Vol. 151, Issue 23
    • DOI: 10.1063/1.5126852
      Sort by:
      [ × clear filter / sort ]

      Similar Records in DOE PAGES and OSTI.GOV collections: