Article
Polymer Science
Anna Braghetto, Sumanta Kundu, Marco Baiesi, Enzo Orlandini
Summary: This study uses long-short-term memory neural networks (LSTM NNs) to simulate configurations of flexible knotted rings confined inside a spherical cavity and successfully distinguish different knot types. The results show that even for flexible, strongly confined, and highly geometrically entangled rings, LSTM NNs perform well in knot recognition. Coarse-graining on configurations of longer rings than those used for training improves the performance of LSTMs in knot identification.
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
Polymer Science
Tom Herschberg, Jan-Michael Y. Carrillo, Bobby G. Sumpter, Eleni Panagiotou, Rajeev Kumar
Summary: The study found that the topology of polymer chains significantly influences the order-disorder transition of AB diblock copolymer melts, with linear and ring chains remaining stretched while knot chains experience stretching and tightening in disordered melts.
Article
Chemistry, Physical
Michael J. Servis, Biswajit Sadhu, L. Soderholm, Aurora E. Clark
Summary: This study investigates the impact of dipole-dipole interactions and molecular structure on the morphology of amphiphile assemblies. The research demonstrates that appropriate conformational sampling significantly influences the self-assembly of malonamide-based amphiphiles. Quantitative analysis reveals that dipole alignment and alkyl tail sterics play crucial roles in determining the structure of aggregates, with dipole alignment promoting linear patterns of intermolecular interactions within aggregates.
JOURNAL OF MOLECULAR LIQUIDS
(2022)
Article
Polymer Science
Pietro Chiarantoni, Cristian Micheletti
Summary: We use Langevin dynamics simulations to study the behavior of linear catenanes under confinement in cylindrical channels. We analyze the statics and dynamics of model poly[n]catenanes consisting of n = 100 rings and m = 40 beads in channels of different diameters. By comparing the catenane behavior to an equivalent chain of beads, we show that linear catenanes exhibit different confinement regimes and unique overstretching response under strong confinement. The relaxation dynamics of catenanes also differ from conventional polymers, with slower modes observed at strong confinement. A systematic analysis of the size, shape, and orientation of the concatenated rings and their mechanical bonds provides insights into the underlying mechanisms driving the catenane's response to confinement.
Article
Chemistry, Applied
Guang-Li Wang, Jun Wang, Luyi Zhou, Mi Zhou, Xiaoxiong Wang, Shan-He Zhou, Lu Lu, Manoj Trivedi, Abhinav Kumar
Summary: In this study, four new Zn(II)/Cd(II) coordination polymers were synthesized and showed efficient photocatalytic performances in selectively degrading methylene blue among other dyes under UV irradiation. The photocatalytic properties of these materials were investigated using LC-MS studies, band gap calculations, and Hirshfeld surface analysis.
Article
Biochemistry & Molecular Biology
Linnea Isaksson, Emil Gustavsson, Cecilia Persson, Ulrika Brath, Lidija Vrhovac, Goran Karlsson, Vladislav Orekhov, Sebastian Westenhoff
Summary: Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria, with changes in their structure playing a critical role in the phototransformation process.
Article
Polymer Science
Yuya Doi, Atsushi Takano, Yoshiaki Takahashi, Yushu Matsushita
Summary: The study found that dumbbell polymers form a unique network structure with distinctive entanglement characteristics in the system. Dumbbell PS samples with longer central chains exhibit slower terminal relaxation and retain entanglement features in high-concentration DOP solutions.
Article
Chemistry, Multidisciplinary
Yuna Bae, Min Young Ha, Ki-Taek Bang, Sanghee Yang, Sung Yun Kang, Joodeok Kim, Jongbaek Sung, Sungsu Kang, Dohun Kang, Won Bo Lee, Tae-Lim Choi, Jungwon Park
Summary: This paper utilizes liquid-phase transmission electron microscopy to track the real-time dynamics of single-chain polymers, revealing the conformational characteristics of these polymers and their dependence on intrachain interactions and environmental factors.
ADVANCED MATERIALS
(2022)
Article
Chemistry, Multidisciplinary
Yihan Nie, Chengkai Li, Haifei Zhan, Liangzhi Kou, Yuantong Gu
Summary: This study investigates the effects of chain scission and water erosion on the mechanical properties of degraded PCL through molecular dynamics simulation, revealing the influence of nonaffine squared displacements on mechanical performance. In both chain scission and water erosion models, the modulus of PCL is affected by short polymer chains and graphene network, demonstrating the importance of diffusion control in tuning the mechanical properties of degradable implants.
Article
Chemistry, Multidisciplinary
Yao Wu, Zi-Hao Jiang, Jin-Yu Lei, Ping Shang, Xuan-Feng Jiang
Summary: Aurophilicity interaction is crucial for the self-assembly of polynuclear clusters with tunable photoluminescence properties. A multi-component synergistic self-assembly strategy was proposed for the controlled synthesis of a hexadeca-nuclei gold(I) supramolecular cluster. The cluster exhibited intense emission properties and reversible mechanochromic luminescence behavior.
CRYSTAL GROWTH & DESIGN
(2023)
Article
Chemistry, Inorganic & Nuclear
V. N. Serezhkin, M. S. Grigoriev, E. F. Rogaleva, S. A. Novikov, L. B. Serezhkina
Summary: Two new uranium compounds were synthesized and studied, revealing different coordination number preferences in their crystal structures depending on the oxalate:U(VI) ratio.
SOLID STATE SCIENCES
(2021)
Article
Polymer Science
Adam Linscott, Rene Zhu, Lauren Hong, Madison Castellanos, Svetlana Morozova
Summary: The effects of grafting density on the extensional flow properties of polymer solutions were studied. At low grafting densities, the added side chains counteract the losses in extensibility to the backbone, leading to an increase in relaxation time. At higher grafting densities, the extension of the backbone reduces the relaxation time. By characterizing the effects of graft density architecture on extensional flows, the breakup dynamics of elastic solutions can be finely tuned and controlled.
JOURNAL OF POLYMER SCIENCE
(2023)
Article
Chemistry, Medicinal
Veselina Marinova, Laurence Dodd, Song-Jun Lee, Geoffrey P. F. Wood, Ivan Marziano, Matteo Salvalaglio
Summary: The study presents a systematic approach for identifying statistically relevant conformational macrostates of organic molecules and investigates the equilibrium conformational ensemble of Sildenafil in different environments through unsupervised clustering. It demonstrates that only a few conformational states of Sildenafil are significantly populated across all environments, with the most abundant conformers in solution being closest to those in the crystal phase.
JOURNAL OF CHEMICAL INFORMATION AND MODELING
(2021)
Article
Polymer Science
Tatchaphon Leelaprachakul, Atsushi Kubo, Yoshitaka Umeno
Summary: We conducted coarse-grained molecular dynamics simulations to investigate the impact of topological constraints and spatial distribution on the mechanical performance of a specific range of molecular weights in polycarbonate. The results show that structures with a larger radius of gyration or more entanglements exhibit higher maximum stress, attributed to a well-developed entanglement network. We provide constitutive relationships between the mechanical properties and initial molecular structure parameters.
Review
Physics, Condensed Matter
Enzo Orlandini, Cristian Micheletti
Summary: This article reviews the latest advances in the study of linking in soft matter systems and organizes the topic from various perspectives, including the concepts and manifestations of entanglement, models of mutual entanglements in polymer mixtures, and the observation of entanglements in liquid crystals and non-filamentous systems.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2022)
Article
Physics, Multidisciplinary
Sankaran Nampoothiri, Enzo Orlandini, Flavio Seno, Fulvio Baldovin
Summary: We investigate the anomalous behavior of the Brownian non-Gaussian diffusion of a polymer center of mass (CM) and its microscopic cause, the polymerization/depolymerization phenomenon, when the polymer interacts with a monomer chemostat. We establish a connection to queuing theory in the mean-field limit and discover that the kurtosis of the polymer CM diverges similarly to a response function at the critical point of the system, which is applicable to various polymer dynamics models. This study provides exact solutions for both equilibrium and nonequilibrium behaviors, serving as a reference for stochastic modeling and experimental setups.
NEW JOURNAL OF PHYSICS
(2022)
Article
Physics, Multidisciplinary
L. N. Carenza, G. Gonnella, D. Marenduzzo, G. Negro, E. Orlandini
Summary: This study investigates the phase behavior of quasi-two-dimensional cholesteric liquid crystal shells and discovers novel topological phases that differ from those observed on flat geometries. For spherical shells, finite quasicrystals and amorphous structures are identified, which are made up of mixtures of polygonal tessellations of half-skynnions. For toroidal shells, variations in local curvature lead to the stabilization of heterogeneous phases where cholesteric patterns coexist with hexagonal lattices of half-skyrmions. These findings provide important insights for experimental self-assembling of cholesteric shells.
PHYSICAL REVIEW LETTERS
(2022)
Article
Polymer Science
Giulia Amici, Michele Caraglio, Enzo Orlandini, Cristian Micheletti
Summary: In this study, catenated ring polymers confined inside channels and slits were investigated using Langevin dynamics simulations. It was found that catenation constraints generate a drag that couples the contour motion of the interlocked regions. The strength of this coupling decreases as the interlocking becomes tighter and shorter due to confinement, with the results having implications for linked biomolecules in experimental or biological confining conditions.
Article
Chemistry, Physical
Valerio Sorichetti, Andrea Ninarello, Jose Ruiz-Franco, Virginie Hugouvieux, Emanuela Zaccarelli, Cristian Micheletti, Walter Kob, Lorenzo Rovigatti
Summary: We used simulations to self-assemble polymer networks with a mixture of bivalent and tri- or tetravalent patchy particles, resulting in an exponential strand length distribution similar to experimental cross-linked systems. The fractal structure of the network depends on the assembly number density, but systems with the same mean valence and assembly density have the same structural properties. We also examined the dynamics of long strands using the tube model and found a relation between the localization lengths and shear modulus.
JOURNAL OF CHEMICAL PHYSICS
(2023)
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
Physics, Multidisciplinary
Antonio Suma, Vincenzo Carnevale, Cristian Micheletti
Summary: Using theory and simulations, the authors studied DNA unzipping via nanopore translocation and found three dynamical regimes depending on the applied force. They showed that the normal regime can be modeled as a one-dimensional stochastic process and used the theory of stochastic processes to recover the free-energy landscape. This approach can be applied to other single-molecule systems with periodic potentials to obtain detailed free-energy landscapes from out-of-equilibrium trajectories.
PHYSICAL REVIEW LETTERS
(2023)
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
Polymer Science
Anna Braghetto, Sumanta Kundu, Marco Baiesi, Enzo Orlandini
Summary: This study uses long-short-term memory neural networks (LSTM NNs) to simulate configurations of flexible knotted rings confined inside a spherical cavity and successfully distinguish different knot types. The results show that even for flexible, strongly confined, and highly geometrically entangled rings, LSTM NNs perform well in knot recognition. Coarse-graining on configurations of longer rings than those used for training improves the performance of LSTMs in knot identification.
Article
Polymer Science
Pietro Chiarantoni, Cristian Micheletti
Summary: We use Langevin dynamics simulations to study the behavior of linear catenanes under confinement in cylindrical channels. We analyze the statics and dynamics of model poly[n]catenanes consisting of n = 100 rings and m = 40 beads in channels of different diameters. By comparing the catenane behavior to an equivalent chain of beads, we show that linear catenanes exhibit different confinement regimes and unique overstretching response under strong confinement. The relaxation dynamics of catenanes also differ from conventional polymers, with slower modes observed at strong confinement. A systematic analysis of the size, shape, and orientation of the concatenated rings and their mechanical bonds provides insights into the underlying mechanisms driving the catenane's response to confinement.
Article
Physics, Multidisciplinary
Pinyao He, Allard J. Katan, Luca Tubiana, Cees Dekker, Davide Michieletto
Summary: Researchers have used AFM and molecular dynamics simulations to study the topology of kDNA network, revealing variations in density and valence of the minicircles, and the role of DNA hubs. The study also estimated the 2D Young modulus of the network and provided insights into a unique topological material at the single-molecule level.
Article
Chemistry, Physical
Anna Braghetto, Enzo Orlandini, Marco Baiesi
Summary: Explainable and interpretable unsupervised machine learning helps to understand the underlying structure of data. An ensemble analysis of machine learning models is introduced to consolidate their interpretation. The application of this method reveals unexpected properties of amino acids and protein secondary structure.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2023)
Article
Chemistry, Physical
G. Negro, L. N. Carenza, G. Gonnella, D. Marenduzzo, E. Orlandini
Summary: We investigate the phase behavior of cholesteric liquid crystal shells with different geometries. Comparing cases of tangential anchoring and no anchoring, we focus on the former case where there is competition between the intrinsic tendency of the cholesteric to twist and the anchoring free energy that suppresses it. We then characterize the topological phases near the isotropic-cholesteric transition, which consist of quasi-crystalline or amorphous tessellations of the shell surface by half-skyrmions.