1
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Paul A, Chakrabarti J. Dynamics of an aqueous suspension of short hyaluronic acid chains near a DPPC bilayer. Phys Chem Chem Phys 2024. [PMID: 39021115 DOI: 10.1039/d4cp01088d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
The synergy between hyaluronic acid (HA) and lipid molecules plays a crucial role in synovial fluids, cell coatings, etc. Diseased cells in cancer and arthritis show changes in HA concentration and chain size, impacting the viscoelastic and mechanical properties of the cells. Although the solution behavior of HA is known in experiments, a molecular-level understanding of the role of HA in the dynamics at the interface of HA-water and the cellular boundary is lacking. Here, we perform atomistic molecular dynamics simulation of short HA chains in an explicit water solvent in the presence of a DPPC bilayer, relevant in pathological cases. We identify a stable interface between HA-water and the bilayer where the water molecules are in contact with the bilayer and the HA chains are located away without any direct contact. Both translation and rotation of the interfacial waters in contact with the lipid bilayer and translation of the HA chains exhibit subdiffusive behavior. The diffusive behavior sets in slightly away from the bilayer, where the diffusion coefficients of water and HA decrease monotonically with increase in HA concentration. On the contrary, the dependence on HA chain size is only marginal due to enhanced chain flexibility as their size increases.
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Affiliation(s)
- Anirban Paul
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
| | - Jaydeb Chakrabarti
- Department of Physics of Complex Systems, S. N. Bose National Centre for Basic Sciences, Block JD, Sector - III, Salt Lake, Kolkata 700106, India.
- Department of Chemical and Biological Sciences and the Technical Research Centre, S. N. Bose National Centre for Basic Sciences, Block-JD, Sector-III, Salt Lake, Kolkata 700106, India.
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2
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Lamura A. Excluded volume effects on tangentially driven active ring polymers. Phys Rev E 2024; 109:054611. [PMID: 38907431 DOI: 10.1103/physreve.109.054611] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 05/08/2024] [Indexed: 06/24/2024]
Abstract
The conformational and dynamical properties of active ring polymers are studied by numerical simulations. The two-dimensionally confined polymer is modeled as a closed bead-spring chain, driven by tangential forces, put in contact with a heat bath described by the Brownian multiparticle collision dynamics. Both phantom polymers and chains comprising excluded volume interactions are considered for different bending rigidities. The size and shape are found to be dependent on persistence length, driving force, and bead mutual exclusion. The lack of excluded volume interactions is responsible for a shrinkage of active rings when increasing driving force in the flexible limit, while the presence induces a moderate swelling of chains. The internal dynamics of flexible phantom active rings shows activity-enhanced diffusive behavior at large activity values while, in the case of self-avoiding active chains, it is characterized by active ballistic motion not depending on stiffness. The long-time dynamics of active rings is marked by rotational motion whose period scales as the inverse of the applied tangential force, irrespective of persistence length and beads' self-exclusion.
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Affiliation(s)
- A Lamura
- Istituto Applicazioni Calcolo, Consiglio Nazionale delle Ricerche (CNR), Via Amendola 122/D, 70126 Bari, Italy
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3
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Sorichetti V, Lenz M. Transverse Fluctuations Control the Assembly of Semiflexible Filaments. PHYSICAL REVIEW LETTERS 2023; 131:228401. [PMID: 38101392 DOI: 10.1103/physrevlett.131.228401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 10/24/2023] [Indexed: 12/17/2023]
Abstract
The kinetics of the assembly of semiflexible filaments through end-to-end annealing is key to the structure of the cytoskeleton, but is not understood. We analyze this problem through scaling theory and simulations, and uncover a regime where filaments' ends find each other through bending fluctuations without the need for the whole filament to diffuse. This results in a very substantial speedup of assembly in physiological regimes, and could help with understanding the dynamics of actin and intermediate filaments in biological processes such as wound healing and cell division.
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Affiliation(s)
- Valerio Sorichetti
- Institute of Science and Technology Austria, 3400 Klosterneuburg, Austria
- Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), CNRS, Université Paris-Saclay, F-91405 Orsay, France
| | - Martin Lenz
- Laboratoire de Physique Théorique et Modèles Statistiques (LPTMS), CNRS, Université Paris-Saclay, F-91405 Orsay, France
- PMMH, CNRS, ESPCI Paris, PSL University, Sorbonne Université, Université de Paris, F-75005 Paris, France
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4
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Mai X, Hao P, Liu D, Ding M. Conformation of a Comb-like Chain in Solution: Effect of Backbone Rigidity. ACS OMEGA 2023; 8:11177-11183. [PMID: 37008139 PMCID: PMC10061535 DOI: 10.1021/acsomega.2c08018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 03/09/2023] [Indexed: 06/19/2023]
Abstract
We study the effect of backbone rigidity on the conformation of comb-like chains in dilute solution by using Brownian dynamics simulations. Our results demonstrate that the backbone rigidity can control the effect of side chains on the conformation of comb-like chains; that is, the relative strength of the excluded-volume interactions from backbone monomer-graft and graft-graft to backbone monomer-monomer gradually weakens with the increase of backbone rigidity. Only when the rigidity of the backbone tends to be flexible and the grafting density is high is the effect of excluded volume of graft-graft on the conformation of comb-like chains significant enough, and other cases can be ignored. Our results show that the radius of gyration of comb-like chains and the persistence length of the backbone are exponentially related to the stretching factor, where the power exponent exhibits an increase with the increase of the strength of bending energy. These finds provide new insights for characterizing the structure properties of comb-like chains.
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Affiliation(s)
- Xinghong Mai
- Xinjiang
Laboratory of Phase Transitions and Microstructures in Condensed Matter
Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, P.R. China
| | - Peng Hao
- Xinjiang
Laboratory of Phase Transitions and Microstructures in Condensed Matter
Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, P.R. China
| | - Danfeng Liu
- Xinjiang
Laboratory of Phase Transitions and Microstructures in Condensed Matter
Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, P.R. China
| | - Mingming Ding
- Xinjiang
Laboratory of Phase Transitions and Microstructures in Condensed Matter
Physics, College of Physical Science and Technology, Yili Normal University, Yining 835000, P.R. China
- School
of Chemical Engineering and Light Industry, Guangdong University of Technology, Guangzhou 510006, P.R. China
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5
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Devarajan DS, Rekhi S, Nikoubashman A, Kim YC, Howard MP, Mittal J. Effect of Charge Distribution on the Dynamics of Polyampholytic Disordered Proteins. Macromolecules 2022; 55:8987-8997. [PMID: 38250712 PMCID: PMC10798675 DOI: 10.1021/acs.macromol.2c01390] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The stability and physiological function of many biomolecular coacervates depend on the structure and dynamics of intrinsically disordered proteins (IDPs) that typically contain a significant fraction of charged residues. Although the effect of relative arrangement of charged residues on IDP conformation is a well-studied problem, the associated changes in dynamics are far less understood. In this work, we systematically interrogate the effects of charge distribution on the chain-level and segmental dynamics of polyampholytic IDPs in dilute solutions. We study a coarse-grained model polyampholyte consisting of an equal fraction of two oppositely charged residues (glutamic acid and lysine) that undergoes a transition from an ideal chain-like conformation for uniformly charge-patterned sequences to a semi-compact conformation for highly charge-segregated sequences. Changes in the chain-level dynamics with increasing charge segregation correlate with changes in conformation. The chain-level and segmental dynamics conform to simple homopolymer models for uniformly charge-patterned sequences but deviate with increasing charge segregation, both in the presence and absence of hydrodynamic interactions. We discuss the significance of these findings, obtained for a model polyampholyte, in the context of a charge-rich intrinsically disordered region of the naturally occurring protein LAF-1. Our findings have important implications for understanding the effects of charge patterning on the dynamics of polyampholytic IDPs in dilute conditions using polymer scaling theories.
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Affiliation(s)
| | - Shiv Rekhi
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Young C. Kim
- Center for Materials Physics and Technology, Naval Research Laboratory, Washington, DC 20375, United States
| | - Michael P. Howard
- Department of Chemical Engineering, Auburn University, Auburn, AL 36849, United States
| | - Jeetain Mittal
- Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, United States
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6
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Milchev A, Binder K. Surface enrichment and interdiffusion in blends of semiflexible polymers of different stiffness. SOFT MATTER 2022; 18:3781-3792. [PMID: 35514321 DOI: 10.1039/d2sm00036a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
A model for a mixture of two kinds of semiflexible polymers (A and B) with the same chain length (NA = NB = 32), but different persistence lengths, confined between parallel planar repulsive walls in a common good solvent is studied by molecular dynamics simulations. In the isotropic phase at low polymer concentrations, both polymers are repelled by the walls, and the system is anisotropic near the walls over a range controlled by the polymer linear dimensions. Close to the concentrations where in the bulk nematic order sets in, precursors of thick nematic layers at the walls are observed, strongly enriched by a stiffer component, which hence is depleted in the center of the slit pore. At larger concentrations, where in the bulk a uniformly mixed nematic phase occurs, the enrichment of B-chains at the walls is rather minor, extending over the scale of the transverse correlation length of concentration fluctuations, which is of the order of a few monomeric diameters only for the present model. In this ordered phase, both self-diffusion and interdiffusion of chains (in the direction perpendicular to the director) are found to be significantly slowed down in comparison to dilute solutions. Since equilibration times scale with the square of the slit thickness, incomplete equilibration is predicted when polymeric coatings on substrate containing polymers differing in stiffness are produced.
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Affiliation(s)
- Andrey Milchev
- Institute for Physical Chemistry, Bulgarian Academia of Sciences, 1113, Sofia, Bulgaria.
| | - Kurt Binder
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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7
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Chen Y, Yan R, Zhao N. Passive and active tracer dynamics in polymer solutions with isotropic-to-nematic phase transition. Phys Chem Chem Phys 2022; 24:7415-7429. [PMID: 35266498 DOI: 10.1039/d2cp00323f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Macromolecular crowding plays a crucial role in determining the dynamics in a living cell. We adopt Langevin dynamics simulations to investigate the anomalous diffusion dynamics of passive and active particles in a solution of polymer chains with tunable stiffness. The solution's anisotropic feature is modulated by changing both the polymer stiffness and volume fraction, where isotropic-to-nematic phase transition is involved. Our results demonstrate the significant impact of polymer flexibility on the dynamics of both passive and active probes. The distinct diffusion mechanism for an active particle is clarified by the interplay between polymer stiffness, crowdedness and activity. Polymer stiffness leads to a global inhibition effect on passive particle diffusion. The diffusion coefficient exhibits an intriguing non-monotonic variation at increasing polymer stiffness, which is due to the fact that the alignment of polymer chains is beneficial for diffusion along the nematic direction but unfavorable for that in the direction perpendicular to it. In sharp contrast, polymer stiffness plays a dominant role in facilitating active particle diffusion. Self-propulsion of the particle can utilize stiffness-induced elastic interactions more efficiently, which promotes its mobility in both directions. Meanwhile, an active particle might have a stronger ability to take advantage of the polymer alignment, contributing substantially enhanced diffusivity. In addition, the diffusion coefficient of an active particle is subject to a tendency of degeneration against varying volume fraction. This counter-intuitive behavior is due to the contrasting factors that increasing crowdedness induces a lower particle speed but a longer persistent motion time.
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Affiliation(s)
- Ying Chen
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Ran Yan
- College of Chemistry, Sichuan University, Chengdu 610064, China.
| | - Nanrong Zhao
- College of Chemistry, Sichuan University, Chengdu 610064, China.
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8
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Silmore KS, Strano MS, Swan JW. Buckling, crumpling, and tumbling of semiflexible sheets in simple shear flow. SOFT MATTER 2021; 17:4707-4718. [PMID: 33978658 DOI: 10.1039/d0sm02184a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
As 2D materials such as graphene, transition metal dichalcogenides, and 2D polymers become more prevalent, solution processing and colloidal-state properties are being exploited to create advanced and functional materials. However, our understanding of the fundamental behavior of 2D sheets and membranes in fluid flow is still lacking. In this work, we perform numerical simulations of athermal semiflexible sheets with hydrodynamic interactions in shear flow. For sheets initially oriented near the flow-vorticity plane, we find buckling instabilities of different mode numbers that vary with bending stiffness and can be understood with a quasi-static model of elasticity. For different initial orientations, chaotic tumbling trajectories are observed. Notably, we find that sheets fold or crumple before tumbling but do not stretch again upon applying greater shear.
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Affiliation(s)
- Kevin S Silmore
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - Michael S Strano
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
| | - James W Swan
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
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9
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Duarte LKR, Teixeira AVNC, Rizzi LG. Microrheology of semiflexible filament solutions based on relaxation simulations. SOFT MATTER 2021; 17:2920-2930. [PMID: 33587085 DOI: 10.1039/d0sm01976c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
We present an efficient computational methodology to obtain the viscoelastic response of dilute solutions of semiflexible filaments. By considering an approach based on the fluctuation-dissipation theorem, we were able to evaluate the dynamical properties of probe particles immersed in solutions of semiflexible filaments from relaxation simulations with a relatively low computational cost and higher precision in comparison to those based on stochastic dynamics. We used a microrheological approach to obtain the complex shear modulus and the complex viscosity of the solution through its compliance which was obtained directly from the dynamical properties of a probe particle attached to an effective medium described by a mesoscopic model, i.e., an effective filament model (EFM). The relaxation simulations were applied to assess the effects of the bending energy on the viscoelasticity of the semiflexible filament solutions, and our methodology was validated by comparing the numerical results to the experimental data on DNA and collagen solutions.
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Affiliation(s)
- L K R Duarte
- Departamento de Física, Universidade Federal do Viçosa, CEP 36570-000, Viçosa, MG, Brazil. and Instituto Federal de Educação, Ciência e Tecnologia de Minas Gerais, CEP 35588-000, Arcos, MG, Brazil
| | - A V N C Teixeira
- Departamento de Física, Universidade Federal do Viçosa, CEP 36570-000, Viçosa, MG, Brazil.
| | - L G Rizzi
- Departamento de Física, Universidade Federal do Viçosa, CEP 36570-000, Viçosa, MG, Brazil.
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10
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Nikoubashman A. Ordering, phase behavior, and correlations of semiflexible polymers in confinement. J Chem Phys 2021; 154:090901. [DOI: 10.1063/5.0038052] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
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11
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Howard MP, Sherman ZM, Sreenivasan AN, Valenzuela SA, Anslyn EV, Milliron DJ, Truskett TM. Effects of linker flexibility on phase behavior and structure of linked colloidal gels. J Chem Phys 2021; 154:074901. [DOI: 10.1063/5.0038672] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Affiliation(s)
- Michael P. Howard
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Zachary M. Sherman
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Adithya N Sreenivasan
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | | | - Eric V. Anslyn
- Department of Chemistry, University of Texas at Austin, Austin, Texas 78712, USA
| | - Delia J. Milliron
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
| | - Thomas M. Truskett
- McKetta Department of Chemical Engineering, University of Texas at Austin, Austin, Texas 78712, USA
- Department of Physics, University of Texas at Austin, Austin, Texas 78712, USA
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12
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Chen S, Olson E, Jiang S, Yong X. Nanoparticle assembly modulated by polymer chain conformation in composite materials. NANOSCALE 2020; 12:14560-14572. [PMID: 32613987 DOI: 10.1039/d0nr01740j] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/11/2023]
Abstract
Mixing nanoparticles into a strategically selected polymer matrix yields nanocomposites with well-controlled microstructures and unique properties and functions. The modulation of nanoparticle assembly by polymer chain conformation can play a dominant role in determining nanocomposite structures, yet such a physical mechanism remains largely unexplored. We hypothesize that highly ordered microdomains of rigid linear polymers provide a template for nanoparticle assembly into open fractal structures. We conducted mesoscopic computer simulations and physical experiments to elucidate how polymer chain conformation regulates the dynamic evolution of nanoparticle structures during the drying processing of polymer nanocomposite films. The evaporation of polymer-nanoparticle mixtures with varying chain stiffnesses was simulated using dissipative particle dynamics. The formation of distinguished nanoparticle assemblies as a result of matrix selection was further corroborated by probing nanoparticle aggregation in different polymer nanocomposite coatings. The results show that polymer conformation not only influences the dispersion states of individual particles (dispersed vs. aggregated), but also modulates the morphologies of large-scale assembly (globular vs. fractal). The emergence of nematically ordered polymer clusters when the chain rigidity is increased creates local solvent-rich "voids" that promote anisotropic particle aggregates, which then percolate into open fractal structures upon solvent evaporation. The nanoparticle dynamics also exhibits an intriguing non-monotonic behavior attributed to the transitions between the coupling and decoupling with polymer dynamics. The nanoparticle assembly morphologies obtained in simulations match well with the electron microscopy images taken in physical experiments.
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Affiliation(s)
- Shensheng Chen
- Department of Mechanical Engineering, Binghamton University, Binghamton, New York 13902, USA.
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13
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Relaxation Time Spectrum and Dynamics of Stretched Polymer Chain in Dilute θ Solution: Implicit Solvent Model versus Explicit Solvent Model. MACROMOL THEOR SIMUL 2020. [DOI: 10.1002/mats.201900064] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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14
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Milchev A, Binder K. How does stiffness of polymer chains affect their adsorption transition? J Chem Phys 2020; 152:064901. [DOI: 10.1063/1.5139940] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023] Open
Affiliation(s)
- A. Milchev
- Institute of Physical Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
| | - K. Binder
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudinger Weg 9, D-55099 Mainz, Germany
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15
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Moreno-Guerra JA, Romero-Sánchez IC, Martinez-Borquez A, Tassieri M, Stiakakis E, Laurati M. Model-Free Rheo-AFM Probes the Viscoelasticity of Tunable DNA Soft Colloids. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2019; 15:e1904136. [PMID: 31460707 DOI: 10.1002/smll.201904136] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Indexed: 05/23/2023]
Abstract
Atomic force microscopy rheological measurements (Rheo-AFM) of the linear viscoelastic properties of single, charged colloids having a star-like architecture with a hard core and an extended, deformable double-stranded DNA (dsDNA) corona dispersed in aqueous saline solutions are reported. This is achieved by analyzing indentation and relaxation experiments performed on individual colloidal particles by means of a novel model-free Fourier transform method that allows a direct evaluation of the frequency-dependent linear viscoelastic moduli of the system under investigation. The method provides results that are consistent with those obtained via a conventional fitting procedure of the force-relaxation curves based on a modified Maxwell model. The outcomes show a pronounced softening of the dsDNA colloids, which is described by an exponential decay of both the Young's and the storage modulus as a function of the salt concentration within the dispersing medium. The strong softening is related to a critical reduction of the size of the dsDNA corona, down to ≈70% of its size in a salt-free solution. This can be correlated to significant topological changes of the dense star-like polyelectrolyte forming the corona, which are induced by variations in the density profile of the counterions. Similarly, a significant reduction of the stiffness is obtained by increasing the length of the dsDNA chains, which we attribute to a reduction of the DNA density in the outer region of the corona.
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Affiliation(s)
- José A Moreno-Guerra
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, 37150, León, Mexico
| | - Ivany C Romero-Sánchez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, 37150, León, Mexico
| | - Alejandro Martinez-Borquez
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, 37150, León, Mexico
| | - Manlio Tassieri
- Division of Biomedical Engineering, School of Engineering, University of Glasgow, Glasgow, G12 8LT, UK
| | - Emmanuel Stiakakis
- Forschungszentrum Jülich, Institute of Complex Systems 3, Leo-Brandt-Strasse, 52425, Jülich, Germany
| | - Marco Laurati
- División de Ciencias e Ingenierías, Universidad de Guanajuato, Lomas del Bosque 103, 37150, León, Mexico
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16
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Howard MP, Nikoubashman A, Palmer JC. Modeling hydrodynamic interactions in soft materials with multiparticle collision dynamics. Curr Opin Chem Eng 2019. [DOI: 10.1016/j.coche.2019.02.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Chen R, Poling-Skutvik R, Howard MP, Nikoubashman A, Egorov SA, Conrad JC, Palmer JC. Influence of polymer flexibility on nanoparticle dynamics in semidilute solutions. SOFT MATTER 2019; 15:1260-1268. [PMID: 30444237 DOI: 10.1039/c8sm01834k] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The hierarchical structure and dynamics of polymer solutions control the transport of nanoparticles (NPs) through them. Here, we perform multi-particle collision dynamics simulations of solutions of semiflexible polymer chains with tunable persistence length lp to investigate the effect of chain stiffness on NP transport. The NPs exhibit two distinct dynamical regimes - subdiffusion on short time scales and diffusion on long time scales. The long-time NP diffusivities are compared with predictions from the Stokes-Einstein relation (SER), mode-coupling theory (MCT), and a recent polymer coupling theory (PCT). Increasing deviations from the SER as the polymer chains become more rigid (i.e. as lp increases) indicate that the NP motions become decoupled from the bulk viscosity of the polymer solution. Likewise, polymer stiffness leads to deviations from PCT, which was developed for fully flexible chains. Independent of lp, however, the long-time diffusion behavior is well-described by MCT, particularly at high polymer concentration. We also observed that the short-time subdiffusive dynamics are strongly dependent on polymer flexibility. As lp is increased, the NP dynamics become more subdiffusive and decouple from the dynamics of the polymer chain center-of-mass. We posit that these effects are due to differences in the segmental mobility of the semiflexible chains.
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Affiliation(s)
- Renjie Chen
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX 77204, USA.
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18
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Speyer K, Pastorino C. Pressure responsive gating in nanochannels coated by semiflexible polymer brushes. SOFT MATTER 2019; 15:937-946. [PMID: 30644495 DOI: 10.1039/c8sm02388c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
We study by coarse-grained molecular-dynamics simulations the liquid flow in a slit channel with the inner walls coated by semiflexible polymer brushes. The distance between walls is close enough such that polymers grafted to opposing walls interact among each other and form bundles across the channel in poor solvent conditions. The solvent is simulated explicitly, including particles that fill the interior of the channel. The system is studied in equilibrium and under flow, by applying a constant body force on each particle of the system. A non-linear relation between external force and flow rate is observed, for a particular set of parameters. This non-linear response is linked to a morphological change of the polymer brushes. For large enough forces, the bundle structures formed across the channel break as the chains lean in the direction of the flow, and clear the middle of the channel. This morphological alteration of the polymer configurations translates in a sudden increase in the flow rate, acting as a pressure-responsive gate. The relation between flow and external force is investigated for various parameters, such as grafting density, quality of the solvent and polymer bending rigidity. We observe a non-monotonic dependence of the flow as a function of the polymer rigidity, and find an optimum value for the persistence length. We also find that the force threshold at which the morphological changes happen in the polymer brush, depends linearly on the grafting density. These findings can lead to new flow control techniques in micro and nano-fluidic devices.
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Affiliation(s)
- K Speyer
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA, Av. Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina.
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19
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Peng Y, Zhang H, Huang XW, Huang JH, Luo MB. Monte Carlo simulation on the dynamics of a semi-flexible polymer in the presence of nanoparticles. Phys Chem Chem Phys 2018; 20:26333-26343. [PMID: 30303200 DOI: 10.1039/c8cp05136d] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The dynamics of a semi-flexible polymer chain in the presence of periodically distributed nanoparticles is simulated by using off-lattice Monte Carlo simulations. For repulsive or weak attractive nanoparticles, the dynamics are slowed down monotonically by increasing the chain stiffness kθ or decreasing the inter-particle distance d. For strong attractive nanoparticles, however, the dynamics show nonmonotonic behaviors with kθ and d. An interesting result is that a stiff polymer may move faster than a flexible one. The underlying mechanism is that the nanoparticle's attraction is weakened by the chain stiffness. The nonmonotonic behavior of the polymer's dynamics with kθ is explained by the competition between the weakening effect of the chain stiffness on the nanoparticle's attraction and the intrinsic effect of chain stiffness which reduces the dynamics of the polymer. In addition, the nonmonotonic behavior of the polymer's dynamics with d is explained by the competition between the nanoparticle-exchange motion of the polymer dominated at small d and the desorption-and-adsorption motion at large d. The excluded volume effect of the nanoparticles plays a more important role for stiffer polymers as the attraction of the nanoparticles is weakened by the chain stiffness.
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Affiliation(s)
- Yi Peng
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Huan Zhang
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Xiao-Wei Huang
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Jian-Hua Huang
- Department of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China.
| | - Meng-Bo Luo
- Department of Physics, Zhejiang University, Hangzhou 310027, China
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Khadilkar MR, Nikoubashman A. Self-assembly of semiflexible polymers confined to thin spherical shells. SOFT MATTER 2018; 14:6903-6911. [PMID: 30091775 DOI: 10.1039/c8sm01170b] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Confinement effects are critical for stiff macromolecules in biological cells, vesicles, and other systems in soft matter. For these molecules, the competition between the packing entropy and the enthalpic cost of bending is further shaped by strong confinement effects. Through coarse-grained molecular dynamics simulations, we explore the self-assembly of semiflexible polymers confined in thin spherical shells for various chain lengths, chain stiffnesses, and shell thicknesses. Here, we focus on the case where the contour and persistence length of the polymers are comparable to the radius of the confining cavity. The range of ordered structures is analyzed using several order parameters to elucidate the nature of orientational ordering in different parameter regimes. Previous simulations have revealed the emergence of bipolar and quadrupolar topological defects on the surface when the entire cavity was filled with a concentrated polymer solution [Phys. Rev. Lett., 2017, 118, 217803]. In contrast, spherical shell confinement restricts the appearance of a bipolar order. Instead, only the extent of the quadrupolar order changes with chain stiffness, as evidenced by the relative motion of topological defects. In the case of monolayers, we observe a nematic to smectic transition accompanied by a change in the nematic grain-size distribution as the contour length was decreased.
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Affiliation(s)
- Mihir R Khadilkar
- Johannes Gutenberg University Mainz, Staudinger Weg 7, Mainz 55128, Germany.
| | - Arash Nikoubashman
- Johannes Gutenberg University Mainz, Staudinger Weg 7, Mainz 55128, Germany.
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21
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Wu J, Cheng C, Liu G, Zhang P, Chen T. The folding pathways and thermodynamics of semiflexible polymers. J Chem Phys 2018; 148:184901. [PMID: 29764123 DOI: 10.1063/1.5018114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Inspired by the protein folding and DNA packing, we have systematically studied the thermodynamic and kinetic behaviors of single semiflexible homopolymers by Langevin dynamics simulations. In line with experiments, a rich variety of folding products, such as rod-like bundles, hairpins, toroids, and a mixture of them, are observed in the complete diagram of states. Moreover, knotted structures with a significant population are found in a certain range of bending stiffness in thermal equilibrium. As the solvent quality becomes poorer, the population of the intermediate occurring in the folding process increases, which leads to a severe chevron rollover for the folding arm. However, the population of the intermediates in the unfolding process is very low, insufficient to induce unfolding arm rollover. The total types of folding pathways from the coil state to the toroidal state for a semiflexible polymer chain remain unchanged by varying the solvent quality or temperature, whereas the kinetic partitioning into different folding events can be tuned significantly. In the process of knotting, three types of mechanisms, namely, plugging, slipknotting, and sliding, are discovered. Along the folding evolution, a semiflexible homopolymer chain can knot at any stage of folding upon leaving the extended coil state, and the probability to find a knot increases with chain compactness. In addition, we find rich types of knotted topologies during the folding of a semiflexible homopolymer chain. This study should be helpful in gaining insight into the general principles of biopolymer folding.
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Affiliation(s)
- Jing Wu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Chenqian Cheng
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Gaoyuan Liu
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Ping Zhang
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
| | - Tao Chen
- Key Laboratory of Synthetic and Natural Functional Molecular Chemistry of the Ministry of Education, College of Chemistry and Materials Science, Northwest University, Xi'an 710127, People's Republic of China
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Chen R, Poling-Skutvik R, Nikoubashman A, Howard MP, Conrad JC, Palmer JC. Coupling of Nanoparticle Dynamics to Polymer Center-of-Mass Motion in Semidilute Polymer Solutions. Macromolecules 2018. [DOI: 10.1021/acs.macromol.7b02441] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Renjie Chen
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Ryan Poling-Skutvik
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Michael P. Howard
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
| | - Jacinta C. Conrad
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
| | - Jeremy C. Palmer
- Department of Chemical and Biomolecular Engineering, University of Houston, Houston, Texas 77204, United States
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Speyer K, Pastorino C. Droplet Transport in a Nanochannel Coated by Hydrophobic Semiflexible Polymer Brushes: The Effect of Chain Stiffness. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2017; 33:10753-10763. [PMID: 28892398 DOI: 10.1021/acs.langmuir.7b02640] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We study the influence of chain stiffness on droplet flow in a nanochannel, coated with semiflexible hydrophobic polymers by means of nonequilibrium molecular dynamics simulations. The studied system is then a moving droplet in the slit channel, coexisting with its vapor and subjected to periodic boundary conditions in the flow direction. The polymer chains, grafted by the terminal bead to the confining walls, are described by a coarse-grained model that accounts for chain connectivity, excluded volume interactions and local chain stiffness. The rheological, frictional and dynamical properties of the brush are explored over a wide range of persistence lengths. We find a rich behavior of polymer conformations and concomitant changes in the friction properties over the wide range of studied polymer stiffnesses. A rapid decrease in the droplet velocity was observed as the rigidity of the chains is increased for polymers whose persistence length is smaller than their contour length. We find a strong relation between the internal dynamics of the brush and the droplet transport properties, which could be used to tailor flow properties by surface functionalization. The monomers of the brush layer, under the droplet, present a collective "treadmill belt" like dynamics which can only be present due the existence of grafted chains. We describe its changes in spatial extension upon variations of polymer stiffness, with bidimensional velocity and density profiles. The deformation of the polymer brushes due to the presence of the droplet is analyzed in detail. Lastly, the droplet-gas interaction is studied by varying the liquid to gas ratio, observing a 16% speed increase for droplets that flow close to each other, compared to a train of droplets that present a large gap between consecutive droplets.
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Affiliation(s)
- K Speyer
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA , Av.Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina
- CONICET , Godoy Cruz 2290 (C1425FQB) Buenos Aires, Argentina
| | - C Pastorino
- Departamento de Física de la Materia Condensada, Centro Atómico Constituyentes, CNEA , Av.Gral. Paz 1499, 1650 Pcia. de Buenos Aires, Argentina
- CONICET , Godoy Cruz 2290 (C1425FQB) Buenos Aires, Argentina
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Nikoubashman A, Howard MP. Equilibrium Dynamics and Shear Rheology of Semiflexible Polymers in Solution. Macromolecules 2017. [DOI: 10.1021/acs.macromol.7b01876] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Arash Nikoubashman
- Institute of Physics, Johannes Gutenberg University Mainz, Staudingerweg 7, 55128 Mainz, Germany
| | - Michael P. Howard
- Department of Chemical and Biological Engineering, Princeton University, Princeton, New Jersey 08544, United States
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