Article
Physics, Fluids & Plasmas
Remi Goerlich, Luis Barbosa Pires, Giovanni Manfredi, Paul-Antoine Hervieux, Cyriaque Genet
Summary: This study proposes the use of a correlated noise bath to drive an optically trapped Brownian particle that mimics active biological matter. By controlling different parameters with unprecedented accuracy, the researchers are able to reach strongly correlated regimes that are not easily accessible in real active matter. They found that by adjusting the correlation time of the noise as a control parameter, transitions between two nonequilibrium steady states can be triggered without expending work but with a calorific cost. The measured heat production is directly proportional to the spectral entropy of the correlated noise, similar to Landauer's principle.
Article
Physics, Fluids & Plasmas
Jeremy Vachier, J. S. Wettlaufer
Summary: Self-propelled particles undergo thermal regelation phenomenon in a host solid, which has significant influence on the redistribution of bioparticles. By studying the thermal regelation phenomenon in a stochastic framework, predictions can be made for related phenomena in biological and geophysical problems. In the context of ice core dating, the activity enhances particle dynamics during thermal regelation and requires a quantitative treatment for accurate dating.
Article
Physics, Fluids & Plasmas
C. P. Sanjay, Ashwin Joy
Summary: This paper investigates the effective temperature of interacting particles in active matter systems. The authors propose an exact expression of the effective temperature for particles in a dense bacterial suspension and observe that it is linearly related to particle diffusivity, with the slope defining particle mobility.
Article
Physics, Fluids & Plasmas
Zeinab Sadjadi, M. Reza Shaebani
Summary: The study developed a theoretical framework to describe the decay of directional correlations in a class of stochastic active processes, including persistence and switching probabilities between different motion states. It analytically derived the characteristic times of orientation autocorrelation and showed the impact of non-exponential sojourn-time distributions under history-dependent transitions.
Review
Physics, Condensed Matter
Subhadip Ghosh, Ambika Somasundar, Ayusman Sen
Summary: Enzymes play a crucial role in supporting life by performing essential tasks through energy released from chemical reactions. Studies have shown that enzyme motion at low Reynolds numbers remains at the epicenter of life. Understanding the mechanisms of enzyme motion is important for designing biomimetic systems and molecular machines.
ANNUAL REVIEW OF CONDENSED MATTER PHYSICS, VOL 12, 2021
(2021)
Review
Neurosciences
Alexey Semyanov, Alexei Verkhratsky
Summary: A new concept of 'active milieu' is defined in this study, which integrates all components of nervous tissue into a dynamic information processing system, with a focus on the role of astrocytic processes. These processes are involved in reciprocal interactions with neuronal compartments and communicate with other elements of the nervous tissue within this framework.
TRENDS IN NEUROSCIENCES
(2021)
Article
Chemistry, Physical
Kuntal Patel, Holger Stark
Summary: In recent years, the combination of nonlinear microfluidics and lab-on-a-chip devices has provided new opportunities for chemical and biomedical applications. This article presents a study on the integration of active matter into a microfluidic setting, where active particles generate flows and destabilize the fluid interface, leading to droplet formation. The study utilizes lattice-Boltzmann simulations, phase field dynamics, and advection-diffusion equations to analyze the behavior of the system. The results demonstrate the potential for controlling droplet formation using switchable activity.
Review
Physics, Applied
Oskar Hallatschek, Sujit S. Datta, Knut Drescher, Joern Dunkel, Jens Elgeti, Bartek Waclaw, Ned S. Wingreen
Summary: The fascinating patterns of collective motion created by autonomously driven particles have fueled active-matter research for over two decades. In this Perspective, researchers argue that the unique features emerging in systems with proliferation represent a distinct form of activity, and propose proliferation as another direction of active-matter physics. They believe that by extending the conceptual framework developed for conventional active matter to proliferating active matter, researchers can have a profound impact on quantitative biology and reveal fascinating emergent physics.
NATURE REVIEWS PHYSICS
(2023)
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)
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
Neurosciences
Xianjun Li, Mengxuan Li, Miaomiao Wang, Fan Wu, Heng Liu, Qinli Sun, Yuli Zhang, Congcong Liu, Chao Jin, Jian Yang
Summary: The study investigated white matter maturation in neonates using diffusion kurtosis imaging (DKI) with multiparametric analysis, revealing additional changing patterns and stronger negative correlations compared to traditional diffusion tensor (DT) metrics. Results suggest that DKI benefits the understanding of white matter maturation processes and degrees in neonates.
HUMAN BRAIN MAPPING
(2022)
Article
Clinical Neurology
Zhi-gang Min, Hai-rong Shan, Long Xu, Dai-hai Yuan, Xue-xia Sheng, Wen-chao Xie, Ming Zhang, Chen Niu, Tahir Mehmood Shakir, Zhi-hong Cao
Summary: Research suggests that distinct pathological processes can be identified between frontal periventricular WMH and other regions, indicating potential severe demyelination effects within the frontal periventricular WMH.
News Item
Physics, Multidisciplinary
Patrick Pietzonka
Summary: The macroscopic properties of active matter can be attributed to the non-equilibrium character and handedness of interactions between individual particles.
Article
Mathematics
Yingxu Tian, Haoyan Zhang
Summary: This work investigates the existence of a unique solution to the perturbed skew diffusion process. The solution is constructed through iteration, dividing the time interval into manageable parts where the perturbed skew diffusion process is split into two tractable portions: one for the perturbed diffusion process and the other for the skew diffusion process. By focusing on the process in each time interval, and considering the continuity of the process at the boundary of each interval determined by a sequence of stopping times, the main result of this paper is obtained along with a time change for the perturbed skew process.
Article
Physics, Fluids & Plasmas
Alexander Petroff, Alejandra Rosselli-Calderon, Ben Roque, Pradeep Kumar
Summary: We investigated the motion of multicellular magnetotactic bacteria near a hard surface and found that they form an active gas when directed towards a flat surface. Increasing the magnetic field past a critical value causes the active gas to condense into a two-dimensional active fluid. Contact with the surface enhances rotational diffusion and velocity fluctuations follow a Laplace distribution. The fluid undergoes a percolation transition at a critical magnetic field and exhibits dynamic voids in supercritical conditions, limiting the relaxation of density fluctuations.
PHYSICAL REVIEW FLUIDS
(2022)
Article
Chemistry, Physical
Matteo Becchi, Pietro Chiarantoni, Antonio Suma, Cristian Micheletti
Summary: In this study, MD simulations were used to investigate the pore translocation properties of a pseudoknotted viral RNA. The xrRNA from the Zika virus exhibited delayed onset of translocation when driven by static forces, with activation times differing significantly at the two ends. The findings also showed that periodic forces amplify differences in activation times and translocation duration, providing insights into the hindrance of specific RNA elements during translocation.
JOURNAL OF PHYSICAL CHEMISTRY B
(2021)
Article
Chemistry, Multidisciplinary
Kosti Tapio, Amr Mostafa, Yuya Kanehira, Antonio Suma, Anushree Dutta, Ilko Bald
Summary: DNA origami technology enables precise assembly of chemical entities at the nanoscale, creating sophisticated functional materials. By assembling Au or Ag nanoparticle dimers, a versatile DNA origami nanofork antenna (DONA) has been developed, achieving signal enhancements in surface-enhanced Raman scattering (SERS) up to 10(11). Using the DNA origami structure, single-molecule SERS measurements of three dyes, cytochrome c, and horseradish peroxidase proteins have been successfully demonstrated.
Article
Multidisciplinary Sciences
Jinglei Xiao, Vasyl Bondarenko, Yali Wang, Antonio Suma, Marta Wells, Qiang Chen, Tommy Tillman, Yan Luo, Buwei Yu, William P. Dailey, Roderic Eckenhoff, Pei Tang, Vincenzo Carnevale, Michael L. Klein, Yan Xu
Summary: This study identifies residue T140 in the S4-S5 linker of bacterial sodium channels as critical for channel activation and drug effects on inactivation. The drug propofol binds to a pocket between the S4-S5 linker and S6 helix in a conformation-dependent manner, promoting and stabilizing inactivated states. The results provide direct evidence of distinct interactions between the S4-S5 linker and S6 helix in activated and inactivated states, pointing towards a potential direction for conformation-dependent drug development.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Mechanics
Massimiliano Semeraro, Antonio Suma, Isabella Petrelli, Francesco Cagnetta, Giuseppe Gonnella
Summary: The study investigates the large deviations of the power injected by an active force into an active Ornstein-Uhlenbeck particle, both in free and confined potential cases. Analytical and numerical computations reveal the rate function behavior in different dimensions and potential scenarios. The validity of a fluctuation relation for the active work distribution is also examined, showing different slopes for different potentials and activity levels.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2021)
Article
Multidisciplinary Sciences
Willow Coyote-Maestas, David Nedrud, Antonio Suma, Yungui He, Kenneth A. Matreyek, Douglas M. Fowler, Vincenzo Carnevale, Chad L. Myers, Daniel Schmidt
Summary: The research conducted a large-scale, high-throughput biochemical assay to determine the compatibility of over 300,000 domain recombination variants of the inward rectifier K+ channel Kir2.1. They found that genomic and biophysical mechanisms acted together to favor gain of large, structured domains at protein termini during ion channel evolution.
NATURE COMMUNICATIONS
(2021)
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
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
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.
Article
Mathematics, Interdisciplinary Applications
Bo Li, Tian Huang
Summary: This paper proposes an approximate optimal strategy based on a piecewise parameterization and optimization (PPAO) method for solving optimization problems in stochastic control systems. The method obtains a piecewise parameter control by solving first-order differential equations, which simplifies the control form and ensures a small model error.
CHAOS SOLITONS & FRACTALS
(2024)
Article
Mathematics, Interdisciplinary Applications
Guram Mikaberidze, Sayantan Nag Chowdhury, Alan Hastings, Raissa M. D'Souza
Summary: This study explores the collective behavior of interacting entities, focusing on the co-evolution of diverse mobile agents in a heterogeneous environment network. Increasing agent density, introducing heterogeneity, and designing the network structure intelligently can promote agent cohesion.
CHAOS SOLITONS & FRACTALS
(2024)
Article
Mathematics, Interdisciplinary Applications
Gengxiang Wang, Yang Liu, Caishan Liu
Summary: This investigation studies the impact behavior of a contact body in a fluidic environment. A dissipated coefficient is introduced to describe the energy dissipation caused by hydrodynamic forces. A new fluid damping factor is derived to depict the coupling between liquid and solid, as well as the coupling between solid and solid. A new coefficient of restitution (CoR) is proposed to determine the actual physical impact. A new contact force model with a fluid damping factor tailored for immersed collision events is proposed.
CHAOS SOLITONS & FRACTALS
(2024)
