Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size

Macromolecular Crowding as a Regulator of Gene Transcription

(2014) Hiroaki Matsuda et al.   BIOPHYSICAL JOURNAL

Unveiling the hidden structure of complex stochastic biochemical networks

(2014) Angelo Valleriani et al.   JOURNAL OF CHEMICAL PHYSICS

Mixing and segregation of ring polymers: spatial confinement and molecular crowding effects

(2014) Jaeoh Shin et al.   NEW JOURNAL OF PHYSICS

Crowding effects on the temperature and pressure dependent structure, stability and folding kinetics of Staphylococcal Nuclease

(2014) M. Erlkamp et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Anomalous diffusion models and their properties: non-stationarity, non-ergodicity, and ageing at the centenary of single particle tracking

(2014) Ralf Metzler et al.   PHYSICAL CHEMISTRY CHEMICAL PHYSICS

Anomalous Dynamics of DNA Hairpin Folding

(2014) R. Frederickx et al.   PHYSICAL REVIEW LETTERS

Molecular-crowding effects on single-molecule RNA folding/unfolding thermodynamics and kinetics

(2014) N. F. Dupuis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Ultraslow relaxation of confined DNA

(2014) Y. R. Chemla et al.   SCIENCE

Unusual size-dependence of effective interactions between collapsed polymers in crowded environments

(2014) Inrok Oh et al.   Soft Matter

Stabilizing colloidal crystals by leveraging void distributions

(2014) Nathan A. Mahynski et al.   Nature Communications

Effects of Molecular Crowding on the Structures, Interactions, and Functions of Nucleic Acids

(2013) Shu-ichi Nakano et al.   CHEMICAL REVIEWS

Structure-driven homology pairing of chromatin fibers: the role of electrostatics and protein-induced bridging

(2013) A. G. Cherstvy et al.   JOURNAL OF BIOLOGICAL PHYSICS

Reactive conformations and non-Markovian cyclization kinetics of a Rouse polymer

(2013) T. Guérin et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamics of polymer translocation through a nanopore induced by different sizes of crowding agents

(2013) Yuhao Chen et al.   JOURNAL OF CHEMICAL PHYSICS

Dual effect of crowders on fibrillation kinetics of polypeptide chains revealed by lattice models

(2013) Nguyen Truong Co et al.   JOURNAL OF CHEMICAL PHYSICS

Mechanisms and topology determination of complex chemical and biological network systems from first-passage theoretical approach

(2013) Xin Li et al.   JOURNAL OF CHEMICAL PHYSICS

Dynamic simulation of concentrated macromolecular solutions with screened long-range hydrodynamic interactions: Algorithm and limitations

(2013) Tadashi Ando et al.   JOURNAL OF CHEMICAL PHYSICS

Molecular crowding shapes gene expression in synthetic cellular nanosystems

(2013) Cheemeng Tan et al.   Nature Nanotechnology

Kinetics of conformational fluctuations in DNA hairpin-loops in crowded fluids

(2013) Olivia Stiehl et al.   NEW JOURNAL OF PHYSICS

Modelling of crowded polymers elucidate effects of double-strand breaks in topological domains of bacterial chromosomes

(2013) Julien Dorier et al.   NUCLEIC ACIDS RESEARCH

Quantitative influence of macromolecular crowding on gene regulation kinetics

(2013) M. Tabaka et al.   NUCLEIC ACIDS RESEARCH

Strong bending of the DNA double helix

(2013) A. Vologodskii et al.   NUCLEIC ACIDS RESEARCH

Structure of phase-separated athermal colloid-polymer systems in the protein limit

(2013) Nathan A. Mahynski et al.   PHYSICAL REVIEW E

Quantitation of the DNA tethering effect in long-range DNA looping in vivo and in vitro using the Lac and   repressors

(2013) D. G. Priest et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Anomalous transport in the crowded world of biological cells

(2013) Felix Höfling et al.   REPORTS ON PROGRESS IN PHYSICS

High-Resolution Mapping of the Spatial Organization of a Bacterial Chromosome

(2013) T. B. K. Le et al.   SCIENCE

Transcription-Factor-Mediated DNA Looping Probed by High-Resolution, Single-Molecule Imaging in Live E. coli Cells

(2013) Zach Hensel et al.   PLOS BIOLOGY

Anomalous and normal diffusion of proteins and lipids in crowded lipid membranes

(2012) Matti Javanainen et al.   FARADAY DISCUSSIONS

Effects of static and temporally fluctuating tensions on semiflexible polymer looping

(2012) Jaeoh Shin et al.   JOURNAL OF CHEMICAL PHYSICS

Confinement and viscoelastic effects on chain closure dynamics

(2012) Pinaki Bhattacharyya et al.   JOURNAL OF CHEMICAL PHYSICS

Influence of the Shape of Crowding Particles on the Structural Transitions in a Polymer

(2012) Alexander Kudlay et al.   JOURNAL OF PHYSICAL CHEMISTRY B

Hard Quasispherical Particle Models for the Viscosity of Solutions of Protein Mixtures

(2012) Allen P. Minton   JOURNAL OF PHYSICAL CHEMISTRY B

Non-Markovian polymer reaction kinetics

(2012) T. Guérin et al.   Nature Chemistry

RNA catalysis through compartmentalization

(2012) Christopher A. Strulson et al.   Nature Chemistry

Dynamics of end-to-end loop formation for an isolated chain in viscoelastic fluid

(2012) Rajarshi Chakrabarti   PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS

Anomalous Diffusion of Phospholipids and Cholesterols in a Lipid Bilayer and its Origins

(2012) Jae-Hyung Jeon et al.   PHYSICAL REVIEW LETTERS

Transition Path Times for Nucleic Acid Folding Determined from Energy-Landscape Analysis of Single-Molecule Trajectories

(2012) Krishna Neupane et al.   PHYSICAL REVIEW LETTERS

Strange kinetics of single molecules in living cells

(2012) Eli Barkai et al.   PHYSICS TODAY

Temperature dependence of protein folding kinetics in living cells

(2012) M. Guo et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Hydrodynamic screening near planar boundaries: Effects on semiflexible polymer dynamics

(2011) Yann von Hansen et al.   JOURNAL OF CHEMICAL PHYSICS

Failure of one-dimensional Smoluchowski diffusion models to describe the duration of conformational rearrangements in floppy, diffusive molecular systems: A case study of polymer cyclization

(2011) Ryan R. Cheng et al.   JOURNAL OF CHEMICAL PHYSICS

DNA Cyclization: Suppression or Enhancement by Electrostatic Repulsions?

(2011) A. G. Cherstvy   JOURNAL OF PHYSICAL CHEMISTRY B

Crowding Promotes the Switch from Hairpin to Pseudoknot Conformation in Human Telomerase RNA

(2011) Natalia A. Denesyuk et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

Crowding-Induced Structural Alterations of Random-Loop Chromosome Model

(2011) Jun Soo Kim et al.   PHYSICAL REVIEW LETTERS

Polymers with spatial or topological constraints: Theoretical and computational results

(2011) Cristian Micheletti et al.   PHYSICS REPORTS-REVIEW SECTION OF PHYSICS LETTERS

Ergodic and nonergodic processes coexist in the plasma membrane as observed by single-molecule tracking

(2011) A. V. Weigel et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Confinement driven spatial organization of semiflexible ring polymers: Implications for biopolymer packaging

(2011) Miriam Fritsche et al.   Soft Matter

Capturing the essence of folding and functions of biomolecules using coarse-grained models

(2011) Changbong Hyeon et al.   Nature Communications

Chromosome Territories

(2010) T. Cremer et al.   Cold Spring Harbor Perspectives in Biology

Diffusion, Crowding & Protein Stability in a Dynamic Molecular Model of the Bacterial Cytoplasm

(2010) Sean R. McGuffee et al.   PLoS Computational Biology

Fundamental Aspects of Protein−Protein Association Kinetics

(2009) G. Schreiber et al.   CHEMICAL REVIEWS

Effect of Macromolecular Crowding on Protein Folding Dynamics at the Secondary Structure Level

(2009) Smita Mukherjee et al.   JOURNAL OF MOLECULAR BIOLOGY

Effects of macromolecular crowding and DNA looping on gene regulation kinetics

(2009) Gene-Wei Li et al.   Nature Physics

Viscoelasticity in Homogeneous Protein Solutions

(2009) Weichun Pan et al.   PHYSICAL REVIEW LETTERS

Elucidating the Origin of Anomalous Diffusion in Crowded Fluids

(2009) Jedrzej Szymanski et al.   PHYSICAL REVIEW LETTERS

Colloidal glasses and gels: The interplay of bonding and caging

(2009) E. Zaccarelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Facilitated diffusion with DNA coiling

(2009) M. A. Lomholt et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA looping provides stability and robustness to the bacteriophage   switch

(2009) M. J. Morelli et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Experimental determination of upper bound for transition path times in protein folding from single-molecule photon-by-photon trajectories

(2009) H. S. Chung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Macromolecular Crowding and Confinement: Biochemical, Biophysical, and Potential Physiological Consequences

(2008) Huan-Xiang Zhou et al.   Annual Review of Biophysics

Macromolecular Crowding and Size Effects on Probe Microviscosity

(2008) Aron B. Goins et al.   BIOPHYSICAL JOURNAL

A Unified Poland-Scheraga Model of Oligo- and Polynucleotide DNA Melting: Salt Effects and Predictive Power

(2008) Daniel Jost et al.   BIOPHYSICAL JOURNAL

Kinetics of Loop Formation in Polymer Chains†

(2008) Ngo Minh Toan et al.   JOURNAL OF PHYSICAL CHEMISTRY B

How DNA coiling enhances target localization by proteins

(2008) B. van den Broek et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Protein folding in confined and crowded environments

(2007) Huan-Xiang Zhou   ARCHIVES OF BIOCHEMISTRY AND BIOPHYSICS