Article
Multidisciplinary Sciences
Jan Smrek, Jonathan Garamella, Rae Robertson-Anderson, Davide Michieletto
Summary: The study reveals that larger supercoiling in dense supercoiled DNA increases the size of entangled plasmids and enhances DNA mobility. These findings suggest a way to tune DNA mobility via supercoiling, enabling topological control over the (micro)rheology of DNA-based complex fluids.
Article
Mathematics, Applied
Michal Lepek, Agata Fronczak, Piotr Fronczak
Summary: This paper investigates the evolution of cluster size distribution for a system of coagulating particles under a linear-chain kernel. A combinatorial framework and modified solution for the linear-chain kernel were used to obtain the exact expression of the cluster size distribution and its standard deviation. The theoretical predictions were accurate across different stages of aggregation process and for a wide range of alpha values.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Mechanics
Oluseye Adeyemi, Shiping Zhu, Li Xi
Summary: The study explored the dynamics of bidisperse polymer melts and found that adding short chains can significantly accelerate the dynamics of long chains by lessening their extent of entanglement. The introduction of long chains hinders the motion of short chains, but does not qualitatively alter their dynamics, as unentangled short chains still follow classical Rouse dynamics even in a matrix containing entangled chains.
Article
Polymer Science
Takahiro Murashima, Katsumi Hagita, Toshihiro Kawakatsu
Summary: Coarse-grained molecular dynamics simulations were used to analyze blends of multicyclic and linear polymers under biaxial elongational flow. The blends exhibited an overshoot behavior in the normal stress difference, with multicyclic/linear blends showing a steeper overshoot compared to monocyclic/linear blends. The origin of the overshoot was found to be a topological transition mechanism in the multicyclic chains, which resulted in a drastic change in the stress of the rings.
Article
Polymer Science
Jiaxin Wu, Fuchen Guo, Ke Li, Linxi Zhang
Summary: This study investigates the sliding dynamics of ring chains along axial chains using molecular dynamics simulations, revealing a new sub-diffusion behavior. The sliding velocity of the ring chains is influenced by the bending energy and distance of the axial chains, and a maximum diffusion coefficient is observed. The symmetry of the axial chains also affects the sliding velocity of the ring chains.
Article
Physics, Applied
Ji-Xuan Hou
Summary: In this paper, a coarse-graining method is presented to obtain the primitive chain from a polymer chain configuration in the entangled polymer melt by eliminating high-frequency Rouse modes. Theoretical demonstration shows that the tube step length is twice the tube diameter using this coarse-graining procedure. Additionally, a simple method to visualize the tube by adding high-frequency modes to the primitive chain is also provided.
MODERN PHYSICS LETTERS B
(2023)
Article
Polymer Science
Konstantin I. Morozov, Alexander M. Leshansky
Summary: This paper presents theoretical modeling of transport through crowded heterogeneous viscous environments and derives analytical expressions for the frictional resistance of particles in polymer solutions. The study shows that for particles with adhering polymers, the frictional resistance is Stokesian, while for particles with nonadsorbing polymers, the frictional resistance is strongly non-Stokesian, depending on the network mesh size and the depletion layer thickness. The theoretical predictions are in good agreement with experimental results.
Article
Polymer Science
Xiao-yue Han, Xiao-lin Zhou, Xiang-hong Wang, Lin-li He
Summary: Using coarse-grained molecular dynamics simulations, this study investigates the conformation and dynamic behavior of ring polymer chains in ring/linear blends confined into cylinders. The spatial distribution of rings in the constrained binary polymer blends is examined by varying particle number density, polymer chain bending energy, and length. An ordered tubular structure composed of several quasi-parallel rings is observed. The diffusion behavior of rings is found to change from inhibition to promotion with increasing linear chain bending energy. This study provides insights into the special conformation and dynamic behavior of ring polymer chains in constrained systems.
MACROMOLECULAR CHEMISTRY AND PHYSICS
(2023)
Article
Mechanics
Enny Tran, Andrew Clarke
Summary: It is generally understood that the entanglement effects of viscoelastic polymer solutions are weakened under strong flow. However, recent research has found that high molecular weight HPAM solutions, which are entangled at use concentrations, exhibit a characteristic relaxation time when transitioning to elastic turbulence in porous flow. In this study, we directly measure the apparent characteristic relaxation time under shear using controlled-stress parallel-superposition background shear, and our results align with previous calculations using Rolie-poly and Rolie-double-poly models.
JOURNAL OF NON-NEWTONIAN FLUID MECHANICS
(2023)
Article
Mechanics
Yuya Doi, Atsushi Takano, Yoshiaki Takahashi, Yushu Matsushita
Summary: The terminal relaxation behavior of entangled linear polystyrene blended with ring and dumbbell-shaped polymers was investigated. The results showed that linear chains could penetrate into the rings, but the rings did not act as entanglement cross-linkers. The terminal relaxation of the dumbbell-shaped polymer was slower and broader compared to linear polystyrene.
Article
Polymer Science
Linlin Chu, Yan Zhao, Robert Graf, Xiao-Liang Wang, Ye-Feng Yao
Summary: This study investigated the influence of short-chain polymers on the entangled polymer network and found that they can significantly alter the network formed by long-chain polymers. The number of chain ends and the size of the short-chain polymer were also found to have clear effects on the network.
Article
Polymer Science
Fuchen Guo, Jiaxin Wu, Zhiyong Yang, Ke Li, Linxi Zhang
Summary: This study investigates the effects of chain rigidity on the penetration of knotted rings threaded by linear chains in mixtures of linear and ring chains. The results show that there is a non-monotonic dependence of the chain-penetration on chain rigidity, and the semiflexible knotted rings have the maximum chain-penetration ability. This anomalous result is due to the competing effects of chain swelling and the formation of ordered clusters for rings.
Article
Polymer Science
Riccardo Chiarcos, Diego Antonioli, Valentina Gianotti, Michele Laus, Gianmarco Munao, Giuseppe Milano, Antonio De Nicola, Michele Perego
Summary: In this study, two copolymers were thermally grafted from melt to a silicon wafer, and it was observed that the lower molecular weight component of the blend preferentially grafted to the polymeric brush layer. The enrichment of short chains in the brush layer was found to be independent of time. Molecular dynamics simulations supported this observation, providing insights for further investigation and control of brush layer characteristics.
Article
Physics, Multidisciplinary
M. Zamponi, M. Kruteva, M. Monkenbusch, L. Willner, A. Wischnewski, I Hoffmann, D. Richter
Summary: By using neutron spin echo spectroscopy, we found that the center of mass motion of short tracer chains within a highly entangled polymer matrix exhibits subdiffusion at short times and then transitions to Fickian diffusion. This transition is attributed to important interchain couplings that lead to cooperative chain motion within the entanglement volume.
PHYSICAL REVIEW LETTERS
(2021)
Article
Mechanics
Manfred H. Wagner, Esmaeil Narimissa, Qian Huang
Summary: The study extends the criterion for brittle fracture of entangled polymer liquids by considering the effects of finite chain extensibility and polymer concentration. Experimental data and models support the finding that crack initiation originates from the rupture of C-C bonds, leading to the fracture of polymer chains and crack propagation.
JOURNAL OF RHEOLOGY
(2021)
Article
Chemistry, Physical
Angelo Rosa, Ralf Everaers
EUROPEAN PHYSICAL JOURNAL E
(2019)
Article
Polymer Science
Jan Smrek, Kurt Kremer, Angelo Rosa
Review
Biochemistry & Molecular Biology
Alessandra Merlotti, Angelo Rosa, Daniel Remondini
BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS
(2020)
Article
Chemistry, Physical
Irene Adroher-Benitez, Angelo Rosa
JOURNAL OF CHEMICAL PHYSICS
(2020)
Article
Polymer Science
Angelo Rosa, Jan Smrek, Matthew S. Turner, Davide Michieletto
Article
Chemistry, Physical
Ralf Everaers, Nils B. Becker, Angelo Rosa
Summary: The study proposes a formalism for deriving mechanical properties of flexible chain molecules, revealing force-elongation and elongation-force relations by analyzing the radial distribution function, providing insights into factors influencing asymptotic behavior and finite chain length corrections. The results show that the proposed method offers high-quality analytical and numerical corrections, suitable for studying the wormlike chain end-to-end distance.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Polymer Science
Mattia Alberto Ubertini, Jan Smrek, Angelo Rosa
Summary: Current theories describe unknotted and non-concatenated ring polymers in melt conditions as tree-like double-folded objects, but simulations show that pairs of rings can also thread each other. We use Monte Carlo simulations to reconcile this dichotomy and find that rings are double-folded on larger scales and localized threading occurs on smaller scales. Existing theories have disagreements on the tree structure and often neglect the impact of threading constraints and progressive constraint release on ring relaxation.
Article
Chemistry, Physical
Domen Vaupotic, Angelo Rosa, Luca Tubiana, Anze Bozic
Summary: Formation of base pairs between nucleotides in an RNA sequence leads to a complex and highly branched RNA structure. Using the theory of branching polymers, we investigate the scaling properties of RNA secondary structures and find that they exhibit annealed random branching and scale similarly to self-avoiding trees. The obtained scaling exponents are robust to variations in nucleotide composition, tree topology, and folding energy parameters. Additionally, we demonstrate a method to obtain both scaling exponents from distributions of topological quantities of fixed-length RNA molecules.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Article
Polymer Science
Mattia Alberto Ubertini, Angelo Rosa
Summary: The macroscopic rheological properties of highly entangled polymer systems are mainly determined by topological constraints when the single-chain contour length, N, exceeds the characteristic scale Ne. This study investigates the occurrence of knots and links in lattice melts of randomly knotted and randomly concatenated ring polymers with different bending stiffness values. By analyzing minimal conformations using suitable topological invariants, the topological properties at the intrachain level (knots) and the links between distinct chains are characterized. Furthermore, the ratio N/Ne, representing the number of entanglements per chain, can be effectively reconstructed using only two-chain links.
Article
Physics, Fluids & Plasmas
Mattia Alberto Ubertini, Angelo Rosa
Summary: The study utilizes a dynamic Monte Carlo algorithm to simulate the behavior of polymer chains on an fcc lattice, explicitly considering the possibility of overcoming topological constraints by controlling the mechanism of strand crossing. The results indicate that higher strand crossing rates lead to faster polymer dynamics, while slower rates result in a slower melting process.
Article
Chemistry, Physical
Andrea Papale, Jan Smrek, Angelo Rosa
Summary: The study compares the motion of dispersed nanoprobes in entangled active-passive polymer mixtures with different architectures of linear vs. unconcatenated and unknotted circular polymers. It reveals that smaller nanoprobes move faster in solutions with increased activity and energy input, whereas larger nanoprobes exhibit a surprising deceleration in active-passive ring solutions compared to purely passive conditions. This effect is attributed to non-equilibrium, topology-dependent association of nanoprobes in the ring mixture, resembling phase separation in scalar active-passive mixtures. Potential connection to microrheology of chromatin in cell nuclei is considered.
Article
Biochemistry & Molecular Biology
Angelo Rosa, Marco Di Stefano, Cristian Micheletti
FRONTIERS IN MOLECULAR BIOSCIENCES
(2019)
Article
Biochemistry & Molecular Biology
Andrea Papale, Angelo Rosa
Article
Chemistry, Physical
Raoul D. Schram, Angelo Rosa, Ralf Everaers
