Article
Physics, Fluids & Plasmas
Nayana Venkatareddy, Shiang-Tai Lin, Prabal K. Maiti
Summary: Phase separation in a mixture of hot and cold three-dimensional dumbbells interacting with Lennard-Jones potential was investigated. The asymmetry of dumbbells and the ratio of hot and cold dumbbells were found to affect the phase separation. The high kinetic pressure of hot dumbbells led to the formation of dense clusters of cold dumbbells and solidlike ordering.
Article
Chemistry, Physical
Lorenzo Caprini, Rahul Kumar Gupta, Hartmut Loewen
Summary: This study investigates the effect of rotational inertia on the collective phenomena of underdamped active systems. It shows that the increase of rotational inertia favors non-equilibrium phase coexistence and counteracts its suppression due to translational inertia. The correlation length of spatial velocity correlations in dense clusters is also found to increase with rotational inertia. The enhancement of rotational persistence due to rotational inertia is strongly linked to the occurrence of collective phenomena, such as motility induced phase separation and spatial velocity correlations.
PHYSICAL CHEMISTRY CHEMICAL PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Mauricio Rojas-Vega, Pablo de Castro, Rodrigo Soto
Summary: We studied the active surface wetting phenomenon by using a minimal model of bacteria, considering the diversity of motility in living matter. The presence of a wall was taken into account in a mixture of fast and slow self-propelled Brownian particles. The evolution of the wetting layer thickness showed an overshoot before reaching stationarity, and its composition changed in two stages, reaching equilibrium after a slow elimination of excess particles. Nonmonotonic evolutions were observed due to delayed avalanches towards the dilute phase, combined with the emergence of a transient particle front.
Article
Materials Science, Ceramics
Peiping Zhang, Xue Sun, Jiankang Guo, Yan Wang, Wei Zhang, Weikun Ning, Wenqing Li, Cundi Wei, Xuefa Shi, Shiding Miao
Summary: Raw deep-sea clays collected from the Indian Ocean, containing high levels of iron and manganese, can act as Fenton catalysts and self-propelled micromotors. These clays have been observed to automatically move and generate oxygen bubbles in H2O2 solution, enhancing catalytic performance. Additionally, the removal of Rhodamine B is greatly influenced by the acidity or alkalinity of the solution and the self-propulsion of motors present in the clays.
JOURNAL OF THE AMERICAN CERAMIC SOCIETY
(2022)
Article
Chemistry, Physical
Haiqin Wang, Tiezheng Qian, Xinpeng Xu
Summary: Onsager's variational principle is a powerful tool for formulating thermodynamically consistent models and finding approximate solutions, especially in the study of soft matter dynamics. By extending OVP to active matter dynamics, analyzing the directional motion of active units, and formulating diffuse-interface models, it provides a general approach to better understand the emergent behaviors of individual animal cells and cell aggregates or tissues.
Article
Multidisciplinary Sciences
Jens Grauer, Falko Schmidt, Jesus Pineda, Benjamin Midtvedt, Hartmut Loewen, Giovanni Volpe, Benno Liebchen
Summary: Active matter can spontaneously form complex patterns and assemblies via a one-way energy flow from the environment into the system. The authors demonstrate that a two-way coupling, where active particles act back on the environment, can give rise to novel superstructures, named as active droploids.
NATURE COMMUNICATIONS
(2021)
Review
Physics, Applied
Suraj Shankar, Anton Souslov, Mark J. Bowick, M. Cristina Marchetti, Vincenzo Vitelli
Summary: This review focuses on topological defects and topologically protected edge modes in active matter, highlighting their distinctive properties in non-equilibrium systems. The review also emphasizes the significance of topological excitations in non-equilibrium settings.
NATURE REVIEWS PHYSICS
(2022)
Article
Physics, Multidisciplinary
Noah Ziethen, Jan Kirschbaum, David Zwicker
Summary: Driven chemical reactions can control the macroscopic properties of droplets, like their size, which is critical for structuring the interior of biological cells. Numerical simulations and an equilibrium surrogate model show that reactions suppress droplet nucleation by increasing the energy barrier. The model also allows the construction of a phase diagram, providing accurate predictions of how driven reactions delay nucleation, which is relevant for understanding droplets in biological cells and chemical engineering.
PHYSICAL REVIEW LETTERS
(2023)
Article
Physics, Fluids & Plasmas
C. Reichhardt, C. J. O. Reichhardt
Summary: The study reveals the significant influence of driving direction on different activity and clogging states of run-and-tumble active matter disks driven over a periodic obstacle array. Diluting obstacles can enhance mobility under low activity conditions, but mobility is more robust against obstacle dilution under high activity conditions.
Article
Physics, Fluids & Plasmas
Joshua Eglinton, Mike Smith, Michael R. Swift
Summary: This paper describes simulations of active Brownian particles to investigate the influence of particle shape on dynamics and clustering. The study shows that composite particles can exhibit collective motion and modify the effective Peclet number. It also demonstrates how particle geometry can explain the phase behavior of multiple particles.
Article
Chemistry, Multidisciplinary
Zhihua Lin, Changyong Gao, Daolin Wang, Qiang He
Summary: This study presents a bubble-propelled Janus gallium/zinc (Ga/Zn) micromotor with good biocompatibility and biodegradability, which can actively target bacteria for treatment. The micromotors exhibit self-propulsion in simulated gastroenteric acid and enhanced antibacterial efficiency against H. pylori compared to passive Ga microparticles. The Ga/Zn micromotors combine self-propulsion, biocompatibility, biodegradability, and Ga-based antibacterial properties, showing promise for active treatment of bacterial infections.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Physics, Multidisciplinary
Benjamin Loewe, Tyler N. Shendruk
Summary: This research proposes a method of suspending colloidal particles with Janus anchoring conditions in active liquid crystal/colloidal composites. Once immersed into the active nematic medium, these colloidal particles exhibit self-propulsion. This work demonstrates the potential of using engineered colloids in active liquid crystals to extract activity for driving functionality.
NEW JOURNAL OF PHYSICS
(2022)
Review
Physics, Multidisciplinary
Igor S. Aranson
Summary: Bacteria, as one of the oldest and most abundant species on Earth, play a significant role in various ecological cycles and can cause infectious diseases. Bacterial suspensions, as examples of active matter, exhibit complex collective behavior. This study provides a critical assessment of the progress in bacterial active matter from a physics perspective, covering experimental results and theoretical approaches.
REPORTS ON PROGRESS IN PHYSICS
(2022)
Article
Physics, Fluids & Plasmas
Kunal Bhattacharya, Abhijit Chakraborty
Summary: In this study, we investigate a system of self-propelled particles where the alignment state of each particle can switch between fast aligning and slow nonaligning states based on the alignment of neighboring particles. We find that the introduction of a threshold for the local order parameter results in the emergence of a mixed phase and clusters of nonaligning particles, unlike the ordered phases observed in clean self-propelled particle systems. Additionally, the system shows different behaviors in terms of the clustering of nonaligning particles at low and high global densities, with the latter exhibiting a continuous percolation transition and the former showing a logarithmic growth of the largest cluster size with the total number of particles. Moreover, the speed differences between aligning and nonaligning particles play an important role in their segregation.
Review
Physics, Applied
J. O'Byrne, Y. Kafri, J. Tailleur, F. van Wijland
Summary: This Review discusses the non-equilibrium features in active matter, including the violation of time-reversal symmetry and departure from Boltzmann statistics, as well as the time-reversible description of active systems and the non-equilibrium nature of microscopic energy sources. Methods from equilibrium statistical mechanics can guide the design of new active materials.
NATURE REVIEWS PHYSICS
(2022)
Article
Chemistry, Multidisciplinary
Yang Xin, Petteri Piskunen, Antonio Suma, Changyong Li, Heini Ijas, Sofia Ojasalo, Iris Seitz, Mauri A. Kostiainen, Guido Grundmeier, Veikko Linko, Adrian Keller
Summary: The internal design of DNA nanostructures plays a crucial role in determining their behavior in different environments. Crossover design can optimize the performance and stability of these structures, particularly in biomedical applications.
Article
Chemistry, Physical
G. Negro, C. B. Caporusso, P. Digregorio, G. Gonnella, A. Lamura, A. Suma
Summary: In this study, we numerically investigate the role of hydrodynamics in the liquid-hexatic transition of active colloids under intermediate activity. We find that increasing the particle's mass enhances ordering, while self-propulsion has the opposite effect. Active hydrodynamic particles undergo the transition at higher packing fractions compared to active Brownian particles, indicating that hydrodynamics tend to disorder the system. At higher densities near the hexatic-liquid transition, organized motion with coherent particle clusters is observed in active hydrodynamic particles.
EUROPEAN PHYSICAL JOURNAL E
(2022)
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
Polymer Science
Antonio Lamura
Summary: The dynamical response of a tethered semiflexible polymer with self-attractive interactions under an external force field was numerically investigated by varying stiffness and self-interaction strength. Different parameters led to various transitions and morphological changes in the polymer chain. The study showed that the external force had significant effects on the conformation and deformation of the polymer chain.
Article
Physics, Mathematical
F. Fadda, A. Lamura, A. Tiribocchi
Summary: In this study, numerical simulations were used to investigate the dynamics of quasi-two dimensional cholesteric liquid crystal droplets under the influence of a time-dependent electric field rotating at a constant angular velocity. The addition of a surfactant at the droplet interface prevented droplet coalescence. The results showed that the liquid crystal rotation caused concurrent orbital motion of the droplets around each other, and the topological defects exhibited chaotic-like motion in cholesterics with a high pitch.
COMMUNICATIONS IN COMPUTATIONAL PHYSICS
(2023)
Article
Biochemistry & Molecular Biology
Pierluigi Scalia, Carmen Merali, Carlos Barrero, Antonio Suma, Vincenzo Carnevale, Salim Merali, Stephen J. Williams
Summary: EphB4 angiogenic kinase expression in Mesothelioma cells is regulated by autocrine IGF-II activation of Insulin Receptor A, and its rapid degradation upon IGF-II signal deprivation involves a novel ubiquitin E3 ligase complex, including DTX3c, UBA1, UBE2N, and Cdc48/p97. The ATPase/unfoldase activity of Cdc48/p97 is necessary for EphB4 recruitment. The 3D modeling analysis of the DTX3c Nt domain suggests isoform-specific biological functions. This study sheds light on the molecular machinery involved in autocrine IGF-II regulation of oncogenic EphB4 kinase expression.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Chemistry, Physical
Mohsen Farshad, Mark J. DelloStritto, Antonio Sum, Vincenzo Carneval
Summary: In this study, we analyzed a methanol/hexane mixture to investigate the phase diagram and structural changes associated with demixing. We found that the topological properties of the H-bond network abruptly change as the system crosses the demixing line, which can be detected using spectral clustering. We further validated the effectiveness of spectral clustering analysis in detecting demixing transitions in a Lennard-Jones system without H-bonds.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Physics, Multidisciplinary
Massimiliano Semeraro, Giuseppe Negro, Antonio Suma, Giuseppe Gonnella, Davide Marenduzzo
Summary: We used a diffusing transcription factors model for numerical simulation of chromatin topology conformations and transcriptional processes of human chromatin. Simulations showed that transcriptional activity can be regulated by either the chain structural properties or external factors, such as the number of transcription factors. Furthermore, comparisons with experimental data demonstrated that the model provides reliable and statistically significant predictions for transcription across different cell-lines.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2023)
Article
Physics, Multidisciplinary
Massimiliano Semeraro, Giuseppe Gonnella, Antonio Suma, Marco Zamparo
Summary: This paper investigates the active work fluctuations of an active Ornstein-Uhlenbeck particle in the presence of a confining harmonic potential. The results show that the harmonic confinement can induce singularities in the active work rate function, particularly at large active and harmonic force constants.
PHYSICAL REVIEW LETTERS
(2023)
Article
Physics, Multidisciplinary
Claudio B. Caporusso, Leticia F. Cugliandolo, Pasquale Digregorio, Giuseppe Gonnella, Demian Levis, Antonio Suma
Summary: In this paper, we study the dynamics of clusters formed by active Brownian disks generated through motility-induced phase separation. By using a novel algorithm, we identify an aggregation mechanism that goes beyond Ostwald ripening and find a dynamic exponent describing cluster growth. These clusters, driven by self-propelled motion, form large fractal structures containing diverse hexatic orders, as well as smaller, orientationally uniform structures. A comparative study with a passive system highlights the significant differences brought by activity.
PHYSICAL REVIEW LETTERS
(2023)
Article
Chemistry, Multidisciplinary
Anushree Dutta, Kosti Tapio, Antonio Suma, Amr Mostafa, Yuya Kanehira, Vincenzo Carnevale, Giovanni Bussi, Ilko Bald
Summary: This study detects and investigates the molecular states of single hemin using SM-SERS, demonstrating a conceptual advancement towards successful monitoring of single molecular chemical interaction using DNA aptamers.
Article
Mathematics
Antonio Lamura
Summary: This study investigates the dynamics and rheology of a vesicle confined in a channel under shear flow at finite temperature. A two-dimensional numerical model is used to analyze the effect of temperature on vesicle motion and system viscosity. It is found that the suspension viscosity is influenced by the viscosity contrast and different temperature-dependent mechanisms.
Meeting Abstract
Medicine, General & Internal
A. Lamura
EUROPEAN JOURNAL OF CLINICAL INVESTIGATION
(2022)
Article
Physics, Fluids & Plasmas
Quentin Novinger, Antonio Suma, Daniel Sigg, Giuseppe Gonnella, Vincenzo Carnevale
Summary: The study characterizes the equilibrium properties and relaxation dynamics of a two-dimensional lattice system, finding that the system's equilibrium properties can be accurately described by a two-dimensional Ising model, and the relaxation dynamics can be understood by calculating the cluster size as a function of time.
