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.
Editorial Material
Multidisciplinary Sciences
Sam Cameron, Tannie Liverpool
Summary: This theory suggests that active agents can cooperate even in the presence of disorder. This finding is important for the design of robots and the study of cell migration mechanisms.
Review
Multidisciplinary Sciences
Giorgio Volpe, Clemens Bechinger, Frank Cichos, Ramin Golestanian, Hartmut Lowen, Matthias Sperl, Giovanni Volpe
Summary: Active matter research is an important field that combines non-equilibrium thermodynamics with applications in biology, robotics, and nano-medicine. Gravity-driven phenomena on Earth can limit the study of soft active matter systems, but these limitations can be overcome in space to unify our understanding of active matter systems and provide guidance for space exploration and colonization.
Article
Physics, Fluids & Plasmas
Remi Goerlich, Luis Barbosa Pires, Giovanni Manfredi, Paul-Antoine Hervieux, Cyriaque Genet
Summary: The limitations of the results in the paper have been acknowledged and discussed in the original publication. The observed relationship between released heat and spectral entropy is not universal but limited to one-parameter Lorentzian spectra. However, it provides a convincing explanation for thermodynamics in nonequilibrium steady states and offers new tools for analyzing nontrivial baths.
Article
Physics, Fluids & Plasmas
Nikita P. Kryuchkov, Artur D. Nasyrov, Konstantin D. Gursky, Stanislav O. Yurchenko
Summary: The effects of inertia and motility-induced phase separation (MIPS) in active matter have gained attention, but are still poorly understood. Through molecular dynamic simulations, we investigated MIPS behavior in Langevin dynamics across a wide range of particle activity and damping rate values. Our results show that the MIPS stability region consists of multiple domains separated by abrupt changes in susceptibility of mean kinetic energy. These domain boundaries are reflected in the system's kinetic energy fluctuations and properties of gas, liquid, and solid phases. The observed cascade of domains is most stable at intermediate damping rates, but disappears in the limit of Brownian motion or along with phase separation at lower damping values.
Article
History & Philosophy Of Science
Collin Rice
Summary: Both ecologists and statistical physicists use highly idealized models to study active matter and self-organizing critical phenomena. In this paper, the author shows how universality classes can justify the use of minimal models to explain the critical behaviors of various systems, despite differences in causes and mechanisms. The author argues that identifying common causes or mechanisms is insufficient in explaining these cases, and instead, the use of minimal models is justified by their membership in the same universality class as real systems with different causes and mechanisms.
Editorial Material
Multidisciplinary Sciences
Jason Detwiler
Summary: This article discusses the use of a cubic metre of tellurium held at cryogenic temperatures over many years to search for matter created in a rare nuclear process. The achievement paves the way for stabilizing other complex systems at low temperatures.
Article
Astronomy & Astrophysics
Ilidio Lopes
Summary: Our study investigates the complex interaction between active neutrinos and the ultralight bosonic dark matter halo surrounding the Sun, and reveals that novel models do not surpass the performance of the conventional neutrino flavour oscillation model based on available solar neutrino flux data. Next-generation solar neutrino detectors have the potential to provide evidence for the existence or absence of the ultralight-dark matter halo.
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
Physics, Multidisciplinary
Matteo Paoluzzi, Demian Levis, Ignacio Pagonabarraga
Summary: This study investigates the transition between glassy and fluid states in dense active materials, revealing that the mechanisms leading to fluidization in active systems do not have an equilibrium counterpart.
COMMUNICATIONS PHYSICS
(2022)
Article
Astronomy & Astrophysics
Claudio Andrea Manzari, Stefano Profumo
Summary: The discrepancies between data on rare b-hadron decays and the corresponding Standard Model predictions could be a hint for new physics. This study suggests that leptoquarks, particularly the scalar leptoquark S3, could explain these anomalies and also serve as a portal to a fermionic dark sector consisting of two additional vectorlike fermions, one of which could be a candidate for cosmological dark matter. The study explores different scenarios and discusses the implications for direct and indirect dark matter searches, finding that high-energy gamma-ray telescopes such as HESS and the Cherenkov Telescope Array could provide powerful constraints on these models.
Article
Multidisciplinary Sciences
Yair A. G. Fosado, Davide Michieletto, Chris A. Brackley, Davide Marenduzzo
Summary: The study investigates the effect of transcription on DNA supercoiling kinetics, revealing the formation of writhe structures at a distance from the transcribing RNA polymerase. Additionally, it shows that positive supercoils generated by RNAP can destabilize nucleosomes long before the transcriptional machinery reaches the histone octamer. The research also analyzes the relaxation dynamics of supercoiled DNA, highlighting the significantly different timescales of twist diffusion and writhe relaxation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Editorial Material
Multidisciplinary Sciences
Alberto Crepaldi
Summary: When black phosphorus, a semiconductor material, is exposed to intense laser light, it was observed that the behavior of its electrons changed. This discovery paves the way for time-dependent engineering of exotic electronic phases in solids.
Article
Multidisciplinary Sciences
Andrew Lucas
Summary: This study investigates a competitive market with demand-side network effects using agent-based models inspired by statistical physics. The findings show that with weak network effects, the market exhibits conventional perfect competition, but as network effects increase, a phase transition occurs leading to a robust nonequilibrium phase. In this nonequilibrium phase, spontaneous price fluctuations, persistent seller profits, and broad distributions of firm market shares are observed, which are not accounted for in the standard theory of competitive markets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Astronomy & Astrophysics
Chenxiao Zeng, Christopher M. Hirata
Summary: The epoch of reionization signifies the end of Cosmic Dawn and the beginning of large-scale structure formation in the universe, with gas temperature evolution being a key factor in current models. By studying nonequilibrium effects, a new model of the ionization front temperature evolution is proposed to show deviations from equilibrium, especially for faster ionization fronts, resulting in lower post-front temperatures.
ASTROPHYSICAL JOURNAL
(2021)
Article
Physics, Multidisciplinary
Viktor Skultety, Cesare Nardini, Joakim Stenhammar, Davide Marenduzzo, Alexander Morozov
Review
Genetics & Heredity
Michael Chiang, Chris A. Brackley, Davide Marenduzzo, Nick Gilbert
Summary: Fitting-free mechanistic models based on polymer simulations predict chromatin folding in 3D by focussing on the underlying biophysical mechanisms. This class of models has been increasingly used in conjunction with experiments to study the spatial organisation of eukaryotic chromosomes. Feedback from experiments to models leads to successive model refinement and has previously led to the discovery of new principles for genome organisation.
TRENDS IN GENETICS
(2022)
Article
Multidisciplinary Sciences
C. A. Brackley, N. Gilbert, D. Michieletto, A. Papantonis, M. C. F. Pereira, P. R. Cook, D. Marenduzzo
Summary: The study suggests that gene regulatory networks are relatively simple, but influenced by spatial correlations from 3D genome organization, leading to stochastic and bursty transcription, forming complex small-world regulatory networks.
NATURE COMMUNICATIONS
(2021)
Article
Multidisciplinary Sciences
C. A. Brackley, A. Lips, A. Morozov, W. C. K. Poon, D. Marenduzzo
Summary: Research using simulations has uncovered the mechanism behind the inactivation of viruses as they approach an air-water interface, showing that the electrostatic repulsive free energy is a key factor. Understanding this interaction between viruses and surfaces could help in designing effective strategies for surface disinfection.
NATURE COMMUNICATIONS
(2021)
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
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
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)
Article
Chemistry, Physical
Ivan Maryshev, Alexander Morozov, Andrew B. Goryachev, Davide Marenduzzo
Article
Chemistry, Physical
Wilson C. K. Poon, Aidan T. Brown, Susana O. L. Direito, Daniel J. M. Hodgson, Lucas Le Nagard, Alex Lips, Cait E. MacPhee, Davide Marenduzzo, John R. Royer, Andreia F. Silva, Job H. J. Thijssen, Simon Titmuss
Article
Physics, Multidisciplinary
Xiaoyu Shi, Jian Zhang, Xia Jiang, Juan Chen, Wei Hao, Bo Wang
Summary: This study presents a novel framework using offline reinforcement learning to improve energy consumption in road transportation. By leveraging real-world human driving trajectories, the proposed method achieves significant improvements in energy consumption. The offline learning approach demonstrates generalizability across different scenarios.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Junhyuk Woo, Soon Ho Kim, Hyeongmo Kim, Kyungreem Han
Summary: Reservoir computing (RC) is a new machine-learning framework that uses an abstract neural network model to process information from complex dynamical systems. This study investigates the neuronal and network dynamics of liquid state machines (LSMs) using numerical simulations and classification tasks. The findings suggest that the computational performance of LSMs is closely related to the dynamic range, with a larger dynamic range resulting in higher performance.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Yuwei Yang, Zhuoxuan Li, Jun Chen, Zhiyuan Liu, Jinde Cao
Summary: This paper proposes an extreme learning machine (ELM) algorithm based on residual correction and Tent chaos sequence (TRELM-DROP) for accurate prediction of traffic flow. The algorithm reduces the impact of randomness in traffic flow through the Tent chaos strategy and residual correction method, and avoids weight optimization using the iterative method. A DROP strategy is introduced to improve the algorithm's ability to predict traffic flow under varying conditions.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Chengwei Dong, Min Yang, Lian Jia, Zirun Li
Summary: This work presents a novel three-dimensional system with multiple types of coexisting attractors, and investigates its dynamics using various methods. The mechanism of chaos emergence is explored, and the periodic orbits in the system are studied using the variational method. A symbolic coding method is successfully established to classify the short cycles. The flexibility and validity of the system are demonstrated through analogous circuit implementation. Various chaos-based applications are also presented to show the system's feasibility.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Viorel Badescu
Summary: This article discusses the maximum work extraction from confined particles energy, considering both reversible and irreversible processes. The results vary for different types of particles and conditions. The concept of exergy cannot be defined for particles that undergo spontaneous creation and annihilation. It is also noted that the Carnot efficiency is not applicable to the conversion of confined thermal radiation into work.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
P. M. Centres, D. J. Perez-Morelo, R. Guzman, L. Reinaudi, M. C. Gimenez
Summary: In this study, a phenomenological investigation of epidemic spread was conducted using a model of agent diffusion over a square region based on the SIR model. Two possible contagion mechanisms were considered, and it was observed that the number of secondary infections produced by an individual during its infectious period depended on various factors.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Zuan Jin, Minghui Ma, Shidong Liang, Hongguang Yao
Summary: This study proposes a differential variable speed limit (DVSL) control strategy considering lane assignment, which sets dynamic speed limits for each lane to attract vehicle lane-changing behaviors before the bottleneck and reduce the impact of traffic capacity drop. Experimental results show that the proposed DVSL control strategy can alleviate traffic congestion and improve efficiency.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Matthew Dicks, Andrew Paskaramoorthy, Tim Gebbie
Summary: In this study, we investigate the learning dynamics of a single reinforcement learning optimal execution trading agent when it interacts with an event-driven agent-based financial market model. The results show that the agents with smaller state spaces converge faster and are able to intuitively learn to trade using spread and volume states. The introduction of the learning agent has a robust impact on the moments of the model, except for the Hurst exponent, which decreases, and it can increase the micro-price volatility as trading volumes increase.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Zhouzhou Yao, Xianyu Wu, Yang Yang, Ning Li
Summary: This paper developed a cooperative lane-changing decision system based on digital technology and indirect reciprocity. By introducing image scoring and a Q-learning based reinforcement learning algorithm, drivers can continuously evaluate gains and adjust their strategies. The study shows that this decision system can improve driver cooperation and traffic efficiency, achieving over 50% cooperation probability under any connected vehicles penetration and traffic density, and reaching 100% cooperation probability under high penetration and medium to high traffic density.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Josephine Nanyondo, Henry Kasumba
Summary: This paper presents a multi-class Aw-Rascle (AR) model with area occupancy expressed in terms of vehicle class proportions. The qualitative properties of the proposed equilibrium velocity and the stability conditions of the model are established. The numerical results show the effect of proportional densities on the flow of vehicle classes, indicating the realism of the proposed model.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Oliver Smirnov
Summary: This study proposes a new method for simultaneously estimating the parameters of the 2D Ising model. The method solves a constrained optimization problem, where the objective function is a pseudo-log-likelihood and the constraint is the Hamiltonian of the external field. Monte Carlo simulations were conducted using models of different shapes and sizes to evaluate the performance of the method with and without the Hamiltonian constraint. The results demonstrate that the proposed estimation method yields lower variance across all model shapes and sizes compared to a simple pseudo-maximum likelihood.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Przemyslaw Chelminiak
Summary: The study investigates the first-passage properties of a non-linear diffusion equation with diffusivity dependent on the concentration/probability density through a power-law relationship. The survival probability and first-passage time distribution are determined based on the power-law exponent, and both exact and approximate expressions are derived, along with their asymptotic representations. The results pertain to diffusing particles that are either freely or harmonically trapped. The mean first-passage time is finite for the harmonically trapped particle, while it is divergent for the freely diffusing particle.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Hidemaro Suwa
Summary: The choice of transition kernel is crucial for the performance of the Markov chain Monte Carlo method. A one-parameter rejection control transition kernel is proposed, and it is shown that the rejection process plays a significant role in determining the sampling efficiency.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
Article
Physics, Multidisciplinary
Xudong Wang, Yao Chen
Summary: This article investigates the joint influence of expanding medium and constant force on particle diffusion. By starting from the Langevin picture and introducing the effect of external force in two different ways, two models with different force terms are obtained. Detailed analysis and derivation yield the Fokker-Planck equations and moments for the two models. The sustained force behaves as a decoupled force, while the intermittent force changes the diffusion behavior with specific effects depending on the expanding rate of the medium.
PHYSICA A-STATISTICAL MECHANICS AND ITS APPLICATIONS
(2024)
