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Perez Ocampo L, Weiss LB, Jardat M, Likos CN, Dahirel V. Electroosmotic Flow Induced Lift Forces on Polymer Chains in Nanochannels. ACS POLYMERS AU 2022; 2:245-256. [PMID: 35971422 PMCID: PMC9372999 DOI: 10.1021/acspolymersau.1c00058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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A major objective
of research in nanofluidics is to achieve better
selectivity in manipulating the fluxes of nano-objects and in particular
of biopolymers. Numerical simulations allow one to better understand
the physical mechanisms at play in such situations. We performed hybrid
mesoscale simulations to investigate the properties of polymers under
flows in slit pores at the nanoscale. We use multiparticle collision
dynamics, an algorithm that includes hydrodynamics and thermal fluctuations,
to investigate the properties of fully flexible and stiff polymers
under several types of flow, showing that Poiseuille flows and electroosmotic
flows can lead to quantitatively and qualitatively different behaviors
of the chain. In particular, a counterintuitive phenomenon occurs
in the presence of an electroosmotic flow: When the monomers are attracted
by the solid surfaces through van der Waals forces, shear-induced
forces lead to a stronger repulsion of the polymers from these surfaces.
Such focusing of the chain in the middle of the channel increases
its flowing velocity, a phenomenon that may be exploited to separate
different types of polymers.
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Affiliation(s)
- Lisbeth Perez Ocampo
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
| | - Lisa B. Weiss
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Marie Jardat
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
| | - Christos N. Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, A-1090 Vienna, Austria
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physico-chimie des électrolytes et nano-systèmes interfaciaux, PHENIX, F-75005 Paris, France
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Asta AJ, Palaia I, Trizac E, Levesque M, Rotenberg B. Lattice Boltzmann electrokinetics simulation of nanocapacitors. J Chem Phys 2019; 151:114104. [DOI: 10.1063/1.5119341] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Adelchi J. Asta
- Sorbonne Universités, CNRS, Physico-Chimie des électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
| | - Ivan Palaia
- LPTMS, UMR 8626, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Emmanuel Trizac
- LPTMS, UMR 8626, CNRS, Univ. Paris-Sud, Université Paris-Saclay, 91405 Orsay, France
| | - Maximilien Levesque
- PASTEUR, Département de Chimie, École Normale Supérieure, PSL University, Sorbonne Université, CNRS, 75005 Paris, France
| | - Benjamin Rotenberg
- Sorbonne Universités, CNRS, Physico-Chimie des électrolytes et Nanosystèmes Interfaciaux, F-75005 Paris, France
- Réseau sur le Stockage Electrochimique de l’Energie (RS2E), FR CNRS 3459, Amiens, France
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Socol M, Wang R, Jost D, Carrivain P, Vaillant C, Le Cam E, Dahirel V, Normand C, Bystricky K, Victor JM, Gadal O, Bancaud A. Rouse model with transient intramolecular contacts on a timescale of seconds recapitulates folding and fluctuation of yeast chromosomes. Nucleic Acids Res 2019; 47:6195-6207. [PMID: 31114898 PMCID: PMC6614813 DOI: 10.1093/nar/gkz374] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Revised: 04/25/2019] [Accepted: 05/09/2019] [Indexed: 01/08/2023] Open
Abstract
DNA folding and dynamics along with major nuclear functions are determined by chromosome structural properties, which remain, thus far, elusive in vivo. Here, we combine polymer modeling and single particle tracking experiments to determine the physico-chemical parameters of chromatin in vitro and in living yeast. We find that the motion of reconstituted chromatin fibers can be recapitulated by the Rouse model using mechanical parameters of nucleosome arrays deduced from structural simulations. Conversely, we report that the Rouse model shows some inconsistencies to analyze the motion and structural properties inferred from yeast chromosomes determined with chromosome conformation capture techniques (specifically, Hi-C). We hence introduce the Rouse model with Transient Internal Contacts (RouseTIC), in which random association and dissociation occurs along the chromosome contour. The parametrization of this model by fitting motion and Hi-C data allows us to measure the kinetic parameters of the contact formation reaction. Chromosome contacts appear to be transient; associated to a lifetime of seconds and characterized by an attractive energy of -0.3 to -0.5 kBT. We suggest attributing this energy to the occurrence of histone tail-DNA contacts and notice that its amplitude sets chromosomes in 'theta' conditions, in which they are poised for compartmentalization and phase separation.
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Affiliation(s)
- Marius Socol
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
- IRIM, CNRS, University of Montpellier, France
| | - Renjie Wang
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
- Material Science & Engineering School, Henan University of Technology, 450001 Zhengzhou, P.R. China
| | - Daniel Jost
- Univ. Grenoble Alpes, CNRS, CHU Grenoble Alpes, Grenoble INP, TIMC-IMAG, F-38000 Grenoble, France
| | - Pascal Carrivain
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Cédric Vaillant
- Laboratoire de Physique, Ecole Normale Supérieure de Lyon, CNRS UMR 5672, Lyon 69007, France
| | - Eric Le Cam
- Genome Maintenance and Molecular Microscopy UMR8126, CNRS, Université Paris-Sud, Université Paris-Saclay, Gustave Roussy, F-94805 Villejuif Cedex France
| | - Vincent Dahirel
- Sorbonne Université, CNRS, Physicochimie des Electrolytes et Nanosystèmes interfaciaux, laboratoire PHENIX, F-75005 Paris, France
| | - Christophe Normand
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Kerstin Bystricky
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Jean-Marc Victor
- Sorbonne Université, CNRS, Laboratoire de Physique Théorique de la Matière Condensée, LPTMC, F-75005 Paris, France
| | - Olivier Gadal
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Aurélien Bancaud
- LAAS-CNRS, Université de Toulouse, CNRS, F-31400 Toulouse, France
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Asta A, Levesque M, Rotenberg B. Moment propagation method for the dynamics of charged adsorbing/desorbing species at solid-liquid interfaces. Mol Phys 2018. [DOI: 10.1080/00268976.2018.1461944] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Adelchi Asta
- Sorbonne Université, CNRS, Physicochimie des électrolytes et nanosystèmes interfaciaux, UMR PHENIX , Paris, France
| | - Maximilien Levesque
- PASTEUR, Département de chimie, École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris, France
| | - Benjamin Rotenberg
- Sorbonne Université, CNRS, Physicochimie des électrolytes et nanosystèmes interfaciaux, UMR PHENIX , Paris, France
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