Article
Polymer Science
Yani Zhao, Jan Rothoerl, Pol Besenius, Peter Virnau, Kostas Ch. Daoulas
Summary: We investigate the effect of helicity in isolated polymers on the topological chirality of their knots with computer simulations. The corrugation of the helix is adjusted via the radius R of a spherical, hard excluded volume around each WLC segment. Statistical analysis of conformations forming the simplest chiral knots demonstrates that knots formed by helices with a given sense prefer one handedness over the other.
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
Optics
Ling-Jun Kong, Jingfeng Zhang, Furong Zhang, Xiangdong Zhang
Summary: After more than 70 years of development, holography has become an essential tool in modern optics with various applications. Introducing optical topological structures into holography, the concept of optical topological holography is demonstrated to solve stability and antijamming problems. This new technology is not only developed theoretically but also experimentally proven. Furthermore, a new topological holographic coding is established to achieve high capacity and robust properties.
LASER & PHOTONICS REVIEWS
(2023)
Article
Physics, Multidisciplinary
X. M. Yang, L. Jin, Z. Song
Summary: The use of knot theory in understanding topological phases in a quantum spin system is explored in this paper. By analyzing exactly solvable models with long-range interactions, and mapping Majorana modes of the quantum spin system into different knots and links, the topological properties of ground states of the spin system are visualized and characterized using crossing and linking numbers to capture the geometric topologies of knots and links.
CHINESE PHYSICS LETTERS
(2021)
Article
Chemistry, Physical
Xin Zhou, Junsheng Yang, Jie Yang, Panchao Yin
Summary: Topological interaction plays a dominant role in the viscoelasticity of subnanoscale polyhedral oligomeric silsesquioxane assemblies, offering broad tunability. By tailoring molecular topologies, their viscoelasticity can be widely adjusted. The assembly also exhibits unique hierarchical relaxation dynamics, which inspire the design of impact resistant materials.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
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
Physics, Multidisciplinary
Dmitry Melnikov
Summary: This article discusses the basic problem of signal transmission in quantum mechanics through the lens of topological theories. By utilizing the analogy between knot diagrams and quantum amplitudes, the transmission coefficients of topological quantum devices can be defined and calculated. The desired transmission or filtering properties can be achieved by varying the topology of the device or an external parameter, which controls the topological phase.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2021)
Article
Multidisciplinary Sciences
Ling-Jun Kong, Weixuan Zhang, Peng Li, Xuyue Guo, Jingfeng Zhang, Furong Zhang, Jianlin Zhao, Xiangdong Zhang
Summary: The authors develop a topological all-optical coding scheme using nested vortex knots and links, which exhibits good stability and high capacity. By designing and fabricating metasurface holograms, light fields sustaining different kinds of nested vortex links are generated, and the feasibility of the high-capacity coding scheme is verified.
NATURE COMMUNICATIONS
(2022)
Article
Polymer Science
Yu-Ting Guo, Changxia Shi, Tian-Yi Du, Xiang-Yue Cheng, Fu-Sheng Du, Zi-Chen Li
Summary: The design and synthesis of closed-loop recyclable polymers using ring-opening polymerization (ROP) is a promising solution to address plastic pollution and economic loss. The resulting poly(ester-amide)s (PEAs) exhibit tunable mechanical properties, good thermal stability, and excellent recyclability.
Article
Mechanics
Weiyu Shen, Jie Yao, Fazle Hussain, Yue Yang
Summary: This study investigates the topological transition and helicity conversion of vortex torus knots and links using numerical simulations. Three topological transitional routes are found, including merging, reconnection, and transition to turbulence. The transition depends on both the initial topology and geometry of the knots/links. Different transition mechanisms are observed for small, large, and moderate torus aspect ratios.
JOURNAL OF FLUID MECHANICS
(2022)
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
Chemistry, Physical
Runfang Mao, Kevin D. Dorfman
Summary: We used Langevin dynamics simulations to study the knot diffusion mechanisms and time scales governing the untying of trefoil knots in DNA molecules confined in nanochannels. Knot untying follows a process of expanding and fluctuating before annihilation. The average knot size increases with chain length, and knot diffusion in nanochannel-confined DNA molecules is subdiffusive. The identified scaling exponent and knot conformations suggest a combination of self-reptation and knot region breathing.
JOURNAL OF CHEMICAL PHYSICS
(2023)
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
Chemistry, Physical
Zixue Ma, Kevin D. Dorfman
Summary: Experimental data on DNA knots confined in nanochannels show that separated knots are more stable than intertwined knots, contrary to interactions observed in stretched polymers.
JOURNAL OF CHEMICAL PHYSICS
(2021)
Article
Optics
Jinzhan Zhong, Sheng Liu, Xuyue Guo, Peng Li, Bingyan Wei, Lei Han, Shuxia Qi, Jianlin Zhao
Summary: This study established the mapping between torus knots/links and the integer topological charge of optical vortex, and observed the transformation process of three-dimensional topological structure by changing the topological charge. Two different reconnection mechanisms associated with odd or even index of torus topology were revealed. These findings may offer new insights for the study of singular optics and evolution in other physical fields.
Article
Biochemistry & Molecular Biology
Davide Michieletto, Yair A. G. Fosado, Elias Melas, Marco Baiesi, Luca Tubiana, Enzo Orlandini
Summary: This study explores how type 2 Topoisomerase (TopoII) proteins enhance the relaxation of DNA molecules by speeding up the topological search and optimizing the sampling of the topological space. The findings suggest that the time scale of topological relaxation is independent of the substrate length. These results are significant for understanding the role of DNA topological simplification in vitro and in vivo.
NUCLEIC ACIDS RESEARCH
(2022)
Article
Physics, Multidisciplinary
Boris Marcone, Sankaran Nampoothiri, Enzo Orlandini, Flavio Seno, Fulvio Baldovin
Summary: Three-dimensional Monte Carlo simulations provide a strong confirmation to the recent theoretical prediction regarding the Brownian non-Gaussian diffusion of critical self-avoiding walks. Despite the linear growth of the polymer center of mass's mean square displacement over time (Brownian behavior), the initial probability density function is strongly non-Gaussian and only transitions to Gaussianity at larger time scales. Full agreement between theory and simulations is achieved without the need for fitting parameters, and discussions on simulation techniques capable of studying anomalous diffusion under complex conditions are provided.
JOURNAL OF PHYSICS A-MATHEMATICAL AND THEORETICAL
(2022)
Article
Physics, Multidisciplinary
Austin Hopkins, Michael Chiang, Benjamin Loewe, Davide Marenduzzo, M. Cristina Marchetti
Summary: The rheology of biological tissue is important in various processes, and this study uses a multiphase field model to simulate the microrheology within a tissue monolayer. The results show that the tissue undergoes a transition between solid and fluid states when perturbed, and the onset of motion varies with deformability.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Andrea Bonato, Davide Marenduzzo, Davide Michieletto, Enzo Orlandini
Summary: This research investigates the cutting and reconnection operations of semiflexible polymer rings in a confined environment. The study reveals a topological gelation transition in DNA recombination systems, where increasing stiffness or concentration of the rings triggers the transition. The findings have implications for understanding the biophysics and topology of genomes undergoing DNA reconnection, as well as for designing polymeric complex fluids with desired topologies.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Shun Imamura, Kohei Sawaki, John J. Molina, Matthew S. Turner, Ryoichi Yamamoto
Summary: This study uses numerical simulations to investigate the influence of hydrodynamic interactions on the collective behavior of wet active matter systems. Quincke rollers, which are artificial microswimmers, are used as the model system. The study reveals that far-field hydrodynamic effects drive ordered collective motion, while near-field hydrodynamic effects drive disordered collective behavior. The simulations are able to capture the role of hydrodynamic effects between rollers without resorting to previous approximations.
ADVANCED THEORY AND SIMULATIONS
(2023)
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
Mechanics
A. Tiribocchi, M. Durve, M. Lauricella, A. Montessori, D. Marenduzzo, S. Succi
Summary: Active droplets are artificial microswimmers that exhibit self-propelled motion. The authors study the effect of activity on a droplet containing a contractile polar fluid confined within microfluidic channels of various sizes. They find a range of shapes and dynamic regimes, regulated by contractile stress, droplet elasticity, and microchannel width.
Article
Multidisciplinary Sciences
A. Tiribocchi, M. Durve, M. Lauricella, A. Montessori, D. Marenduzzo, S. Succi
Summary: This study numerically investigates the behavior of active fluid droplets in microchannels with adhesive properties. The results demonstrate that non-uniform adhesion forces play a crucial role in the droplets' crossing of narrow constrictions, while a balance between speed and elasticity is sufficient for transitions through larger gaps.
NATURE COMMUNICATIONS
(2023)
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
Biochemistry & Molecular Biology
Giada Forte, Adam Buckle, Shelagh Boyle, Davide Marenduzzo, Nick Gilbert, Chris A. A. Brackley
Summary: The authors combine computer modeling based on polymer physics with experimental validation to study the dynamic 3D structure of specific loci. Their results show that chromatin dynamics are fast enough to sample all possible locus conformations within minutes, generating wide dynamic variability within single cells. This study provides important insights into the dynamic 3D structure of gene loci in living cells.
NATURE STRUCTURAL & MOLECULAR BIOLOGY
(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.
Article
Chemistry, Physical
Austin Hopkins, Benjamin Loewe, Michael Chiang, Davide Marenduzzo, M. Cristina Marchetti
Summary: By using a multi-phase field model, this study explores the effect of cell stiffness on motility induced phase separation (MIPS) and finds that increased deformability enhances phase separation and leads to increased disorder in dense regions.
Article
Chemistry, Physical
Austin Hopkins, Benjamin Loewe, Michael Chiang, Davide Marenduzzo, M. Cristina Marchetti
Summary: Using a multi-phase field model, this study explores the influence of cell stiffness on motility induced phase separation (MIPS). The findings indicate that deformable cells exhibit more effective phase separation compared to rigid cells, which can be attributed to the increased duration of collisions. Additionally, the dense regions become more disordered as deformability increases. These results offer insight into the applicability of MIPS in biological systems and shed light on the self-organization of cells in such systems.
Article
Cell Biology
Giada Forte, Lora Boteva, Filippo Conforto, Nick Gilbert, Peter R. Cook, Davide Marenduzzo
Summary: Forte et al. conducted simulations to demonstrate the importance of bridging condensins in condensing chromosomes into mitotic cylinders. These findings highlight the significance of the bridging and looping activities of condensins, and propose a mechanistic model for chromatin structure at chromosome fragile sites.
JOURNAL OF CELL BIOLOGY
(2023)