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Chandrasekaran A, Giniger E, Papoian GA. Nucleation causes an actin network to fragment into multiple high-density domains. Biophys J 2022; 121:3200-3212. [PMID: 35927959 PMCID: PMC9463697 DOI: 10.1016/j.bpj.2022.07.035] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/20/2021] [Accepted: 07/28/2022] [Indexed: 11/02/2022] Open
Abstract
Actin networks rely on nucleation mechanisms to generate new filaments because spontaneous nucleation is kinetically disfavored. Branching nucleation of actin filaments by actin-related protein (Arp2/3), in particular, is critical for actin self-organization. In this study, we use the simulation platform for active matter MEDYAN to generate 2000 s long stochastic trajectories of actin networks, under varying Arp2/3 concentrations, in reaction volumes of biologically meaningful size (>20 μm3). We find that the dynamics of Arp2/3 increase the abundance of short filaments and increases network treadmilling rate. By analyzing the density fields of F-actin, we find that at low Arp2/3 concentrations, F-actin is organized into a single connected and contractile domain, while at elevated Arp2/3 levels (10 nM and above), such high-density actin domains fragment into smaller domains spanning a wide range of volumes. These fragmented domains are extremely dynamic, continuously merging and splitting, owing to the high treadmilling rate of the underlying actin network. Treating the domain dynamics as a drift-diffusion process, we find that the fragmented state is stochastically favored, and the network state slowly drifts toward the fragmented state with considerable diffusion (variability) in the number of domains. We suggest that tuning the Arp2/3 concentration enables cells to transition from a globally coherent cytoskeleton, whose response involves the entire cytoplasmic network, to a fragmented cytoskeleton, where domains can respond independently to locally varying signals.
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Affiliation(s)
- Aravind Chandrasekaran
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland; National Institutes of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Edward Giniger
- National Institutes of Neurological Diseases and Stroke, National Institutes of Health, Bethesda, Maryland
| | - Garegin A Papoian
- Department of Chemistry and Biochemistry, University of Maryland, College Park, Maryland; Institute for Physical Science and Technology, University of Maryland, College Park, Maryland.
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Paul S, Majumder S, Das SK, Janke W. Effects of alignment activity on the collapse kinetics of a flexible polymer. SOFT MATTER 2022; 18:1978-1990. [PMID: 35023525 DOI: 10.1039/d1sm01055g] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
The dynamics of various biological filaments can be understood within the framework of active polymer models. Here we consider a bead-spring model for a flexible polymer chain in which the active interaction among the beads is introduced via an alignment rule adapted from the Vicsek model. Following quenching from the high-temperature coil phase to a low-temperature state point, we study the coarsening kinetics via molecular dynamics (MD) simulations using the Langevin thermostat. For the passive polymer case the low-temperature equilibrium state is a compact globule. The results from our MD simulations reveal that though the globular state is also the typical final state in the active case, the nonequilibrium pathways to arrive at such a state differ from the picture for the passive case due to the alignment interaction among the beads. We notice that deviations from the intermediate "pearl-necklace"-like arrangement, which is observed in the passive case, and the formation of more elongated dumbbell-like structures increase with increasing activity. Furthermore, it appears that while a small active force on the beads certainly makes the coarsening process much faster, there exists a nonmonotonic dependence of the collapse time on the strength of active interaction. We quantify these observations by comparing the scaling laws for the collapse time and growth of pearls with the passive case.
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Affiliation(s)
- Subhajit Paul
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Suman Majumder
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
| | - Subir K Das
- Theoretical Sciences Unit and School of Advanced Materials, Jawaharlal Nehru Centre for Advanced Scientific Research, Jakkur P.O., Bangalore-560064, India.
| | - Wolfhard Janke
- Institut für Theoretische Physik, Universität Leipzig, IPF 231101, 04081 Leipzig, Germany.
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Neppalli SN, Collins TW, Gholamvand Z, Cummins C, Morris MA, Mokarian-Tabari P. Defining Swelling Kinetics in Block Copolymer Thin Films: The Critical Role of Temperature and Vapour Pressure Ramp. Polymers (Basel) 2021; 13:4238. [PMID: 34883741 PMCID: PMC8659708 DOI: 10.3390/polym13234238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/26/2021] [Accepted: 11/30/2021] [Indexed: 11/25/2022] Open
Abstract
We studied the kinetics of swelling in high-χ lamellar-forming poly(styrene)-block- poly(lactic acid) (PS-b-PLA) block copolymer (BCP) by varying the heating rate and monitoring the solvent vapour pressure and the substrate temperature in situ during solvo-thermal vapour annealing (STVA) in an oven, and analysing the resulting morphology. Our results demonstrate that there is not only a solvent vapour pressure threshold (120 kPa), but also that the rate of reaching this pressure threshold has a significant effect on the microphase separation and the resulting morphologies. To study the heating rate effect, identical films were annealed in a tetrahydrofuran (THF) vapour environment under three different ramp regimes, low (rT<1 °C/min), medium (2
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Affiliation(s)
- Sudhakara Naidu Neppalli
- School of Chemistry, The University of Dublin, Trinity College Dublin, D02 PN40 Dublin, Ireland; (S.N.N.); (Z.G.); (M.A.M.)
- Advance Material and BioEngineering Research (AMBER) Centre and CRANN, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Timothy W. Collins
- Department of Chemistry, University College Cork, Tyndall National Institute, T12 K8AF Cork, Ireland;
| | - Zahra Gholamvand
- School of Chemistry, The University of Dublin, Trinity College Dublin, D02 PN40 Dublin, Ireland; (S.N.N.); (Z.G.); (M.A.M.)
- Advance Material and BioEngineering Research (AMBER) Centre and CRANN, Trinity College Dublin, D02 PN40 Dublin, Ireland
| | - Cian Cummins
- Centre de Recherche Paul Pascal (CRPP), The French National Centre for Scientific Research (CNRS), University of Bordeaux, UMR 5031, 115 Avenue Schweitzer, 33600 Pessac, France;
- Laboratoire de Chimie des Polymeres Organiques (LCPO), University of Bordeaux, CNRS, Bordeaux INP, 16 Avenue Pey-Berland, CEDEX, 33607 Pessac, France
| | - Michael A. Morris
- School of Chemistry, The University of Dublin, Trinity College Dublin, D02 PN40 Dublin, Ireland; (S.N.N.); (Z.G.); (M.A.M.)
- Department of Chemistry, University College Cork, Tyndall National Institute, T12 K8AF Cork, Ireland;
| | - Parvaneh Mokarian-Tabari
- School of Chemistry, The University of Dublin, Trinity College Dublin, D02 PN40 Dublin, Ireland; (S.N.N.); (Z.G.); (M.A.M.)
- Advance Material and BioEngineering Research (AMBER) Centre and CRANN, Trinity College Dublin, D02 PN40 Dublin, Ireland
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Ghosh S, Vemparala S. Kinetics of charged polymer collapse in poor solvents. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 34:045101. [PMID: 34352747 DOI: 10.1088/1361-648x/ac1aef] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 08/05/2021] [Indexed: 06/13/2023]
Abstract
Extensive molecular dynamics simulations, using simple charged polymer models, have been employed to probe the collapse kinetics of a single flexible polyelectrolyte (PE) chain under implicit poor solvent conditions. We investigate the role of the charged nature of PE chain (A), valency of counterions (Z) on the kinetics of such PE collapse. Our study shows that the collapse kinetics of charged polymers are significantly different from those of the neutral polymer and that the finite-size scaling behavior of PE collapse times does not follow the Rouse scaling as observed in the case of neutral polymers. The critical exponent for charged PE chains is found to be less than that of neutral polymers and also exhibits dependence on counterion valency. The coarsening of clusters along the PE chain suggests a multi-stage collapse and exhibits opposite behavior of exponents compared to neutral polymers: faster in the early stages and slower in the later stages of collapse.
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Affiliation(s)
- Susmita Ghosh
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
| | - Satyavani Vemparala
- The Institute of Mathematical Sciences, C.I.T. Campus, Taramani, Chennai 600113, India
- Homi Bhabha National Institute, Training School Complex, Anushakti Nagar, Mumbai 400094, India
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