Article
Multidisciplinary Sciences
Abdallah Daddi-Moussa-Ider, Ramin Golestanian, Andrej Vilfan
Summary: The energy dissipation and entropy production of self-propelled microswimmers differ significantly from passive particles. Researchers have derived a general theorem to determine the lower limit of dissipation and applied it to optimize the shapes of microswimmers.
NATURE COMMUNICATIONS
(2023)
Article
Physics, Multidisciplinary
Zeeshan Asghar
Summary: The article discusses the motion of five different undulating swimming sheets under the influence of an electric field and dynamical interactions. These sheets, which can resemble the surface of spermatozoa, are studied in the context of a two-dimensional channel representing the human cervix. The flow of viscus mucus is modeled using Navier-Stokes equations, and the electroosmotic term is simulated using the Poisson-Boltzmann equation. The numerical results of cell speed, flow rate, and power delivered are obtained and plotted using MATLAB R2022b.
EUROPEAN PHYSICAL JOURNAL PLUS
(2023)
Article
Engineering, Multidisciplinary
Megan Morrison, J. Nathan Kutz
Summary: This study develops a mathematical framework for controlling nonlinear, networked dynamical systems, using dimensionality reduction, bifurcation theory, and model discovery tools to find low-dimensional subspaces for feed-forward control. By leveraging the fact that high-dimensional networked systems have many fixed points, control signals can be computed to move the system between any pair of fixed points. The approach involves fitting a nonlinear dynamical system to a low-rank subspace with the SINDy algorithm, then using bifurcation theory to identify constant control signals for achieving desired outcomes.
IEEE TRANSACTIONS ON NETWORK SCIENCE AND ENGINEERING
(2021)
Article
Multidisciplinary Sciences
Jasmine A. Nirody, Lisset A. Duran, Deborah Johnston, Daniel J. Cohen
Summary: The study found that tardigrades exhibit key features of walking similar to insects and show flexibility in interleg coordination under different environmental conditions. This suggests functional similarities in walking coordination between tardigrades and arthropods, possibly due to a common locomotor control circuit or independent convergence onto an optimal control strategy.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Review
Ecology
John H. Costello, Sean P. Colin, John O. Dabiri, Brad J. Gemmell, Kelsey N. Lucas, Kelly R. Sutherland
Summary: The study of jellyfish provides insight into important components of animal propulsion, demonstrating that swimming occurs through careful orchestration of fluid interactions and with broader educational significance. Due to their structural simplicity, comparative energetic efficiency, and ease of use in laboratory experimentation, jellyfish are favorable test subjects for exploration of animal propulsion.
ANNUAL REVIEW OF MARINE SCIENCE, VOL 13, 2021
(2021)
Article
Physics, Multidisciplinary
Zeeshan Asghar, Nasir Ali, Khurram Javid, Muhammad Waqas, Waqar Azeem Khan
Summary: This study investigates the motion characteristics of soft nano-robots in a fluid environment and their regulatory effects on the reproductive system. Key parameters such as the speed of active swimmers in the fluid and the work done by microorganisms are obtained, and numerical simulation and analytical solutions are used to study the dynamic equilibrium conditions.
EUROPEAN PHYSICAL JOURNAL PLUS
(2021)
Article
Biochemistry & Molecular Biology
Erick Rafael Dias Rates, Charles Duarte Almeida, Elaine de Paula Fiod Costa, Roberta Jansen de Mello Farias, Ralph Santos-Oliveira, Luciana Magalhaes Rebelo Alencar
Summary: This study used atomic force microscopy (AFM) to evaluate four layers of the cornea and analyze their adhesion, stiffness, and roughness. The findings revealed microvilli in the epithelial and endothelial layers, pores in the basement membrane, and collagen fibers in the stroma. These data contribute to a better understanding of the ultrastructures of the human cornea layers and provide new information about their biophysical properties.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Chemistry, Physical
Quentin Brosseau, Florencio Balboa Usabiaga, Enkeleida Lushi, Yang Wu, Leif Ristroph, Michael D. Ward, Michael J. Shelley, Jun Zhang
Summary: This study demonstrates that tail-heavy swimmers have a preference for upward orientation and ascending along inclined planes when propelled by autophoretic bimetallic nanorods in hydrogen peroxide fuel. The interaction with solid boundaries greatly facilitates this gravitaxis, allowing even extremely heavy microswimmers to climb nearly vertical surfaces. The theory and simulations suggest that the alignment of the rods is reinforced by a fore-aft drag asymmetry induced by hydrodynamic interactions with the wall.
Article
Mathematics, Applied
A. Amiri-Hezaveh, M. Ostoja-Starzewski
Summary: A new solver based on alternative field equations is developed to obtain the solution of nonlinear dynamical systems in this paper. The method is higher order accurate and conserves constants of motion.
APPLIED MATHEMATICS LETTERS
(2022)
Article
Engineering, Mechanical
R. Fuentes, R. Nayek, P. Gardner, N. Dervilis, T. Rogers, K. Worden, E. J. Cross
Summary: This paper presents a new Bayesian approach to equation discovery in nonlinear structural dynamics, combining structure detection and parameter estimation. By using a sparsity-inducing prior and an over-complete dictionary, the method successfully identifies and validates equations for nonlinear dynamic systems. Unlike other sparse learners, this approach utilizes hierarchical Bayesian priors and hyperpriors to achieve accurate results.
MECHANICAL SYSTEMS AND SIGNAL PROCESSING
(2021)
Article
Engineering, Mechanical
Joar Axas, Mattia Cenedese, George Haller
Summary: In this study, we propose a fast method for nonlinear data-driven model reduction of dynamical systems onto their slowest nonresonant spectral submanifolds (SSMs). We reformulate the tasks as explicit problems under simplifying assumptions and provide a novel method for timelag selection. Experimental results demonstrate that our alternative approach yields accurate and sparse models for essentially nonlinear dynamics on both numerical and experimental datasets.
NONLINEAR DYNAMICS
(2023)
Editorial Material
Automation & Control Systems
Michael W. Fisher, Ian A. Hiskens
Summary: The text discusses a lemma regarding the intersection of manifolds of hyperbolic closed orbits and the dimensions of their unstable manifolds. However, the author provides a counterexample where the dimensions of the manifolds are equal.
IEEE TRANSACTIONS ON AUTOMATIC CONTROL
(2021)
Article
Automation & Control Systems
Wassim M. Haddad, Manuel Lanchares
Summary: This paper develops stochastic dissipativity theory for discrete-time nonlinear dynamical systems and presents conditions for stochastic dissipativity and losslessness in terms of the system functions. The results are then extended to feedback interconnection stability in probability for discrete-time stochastic systems.
INTERNATIONAL JOURNAL OF ROBUST AND NONLINEAR CONTROL
(2022)
Article
Automation & Control Systems
Yahya Sattar, Samet Oymak
Summary: This study investigates the problem of learning a nonlinear dynamical system by using gradient-based algorithms with samples obtained from a single finite trajectory. The researchers demonstrate that if the system is run by a stabilizing input policy, temporally-dependent samples can be approximated by i.i.d. samples using a mixing-time argument. They also provide new guarantees for the uniform convergence of the gradient of the empirical loss induced by these i.i.d. samples.
JOURNAL OF MACHINE LEARNING RESEARCH
(2022)
Article
Mathematics, Applied
Priscila F. S. Guedes, Eduardo M. A. M. Mendes, Erivelton Nepomuceno
Summary: This paper introduces a computationally efficient discretization scheme for nonlinear dynamical systems. By neglecting high-order terms in the Runge-Kutta method, computational efficiency is improved without sacrificing accuracy and system characteristics. Experimental results demonstrate the effectiveness and reliability of the proposed scheme for embedded and large-scale applications.
APPLIED MATHEMATICS AND COMPUTATION
(2022)
Article
Biochemistry & Molecular Biology
Claudia Trejo-Soto, Guillermo R. Lazaro, Ignacio Pagonabarraga, Aurora Hernandez-Machado
Summary: This article provides insights into the general features of red blood cell membranes and their impact on blood flow and rheology. It covers the basic description of membranes and focuses on the characteristics and modeling of red blood cell membranes. It also reviews recent studies on the effect of the elastic properties of red blood cell membranes on blood flow and hemorheology, as well as specific hemorheological pathologies associated with the mechanical properties of red blood cells and their influence on microcirculation. The article concludes by discussing the potential of microfluidic applications for diagnosing and treating these diseases, thereby highlighting the importance of studying red blood cell membranes and their role in blood flow.
Article
Multidisciplinary Sciences
Javier Diaz, Marco Pinna, Andrei Zvelindovsky, Ignacio Pagonabarraga
Summary: This study uses 2D and 3D mesoscopic simulations to explore the phase behavior of block copolymer/nanoparticle systems, finding that the anisotropic ordered nanoparticles can enhance the lamellar phase of block copolymers and induce a phase transition. Anisotropic nanoparticles within circular-forming block copolymers lead to a competition between nematic colloidal ordering and hexagonally ordered mesophases.
ADVANCED THEORY AND SIMULATIONS
(2022)
Article
Mechanics
Elfego Ruiz-Gutierrez, Steven Armstrong, Simon Leveque, Celestin Michel, Ignacio Pagonabarraga, Gary G. Wells, Aurora Hernandez-Machado, Rodrigo Ledesma-Aguilar
Summary: In this study, we investigate the duration of the cross-over between the initial linear growth and the diffusive-like growth in spontaneous capillary imbibition. We find that local-resistance sources, such as inertial resistance and friction caused by the advancing meniscus, always limit the motion of the imbibing front. Our results show that this cross-over is much longer than previously thought, even longer than the time it takes for the liquid to fill the porous medium. This slowly slowing-down dynamics is likely to cause similar long cross-over phenomena in processes governed by wetting.
JOURNAL OF FLUID MECHANICS
(2022)
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
Chemistry, Physical
Shan Chen, Zhenjiang Guo, Hongguang Zhang, Ignacio Pagonabarraga, Xianren Zhang
Summary: In this study, molecular dynamics simulations are used to reveal the characteristics and changes induced by plug flow at the nanoscale. The flow behavior of the liquid shows different friction intensity and liquid/solid interaction compared to macroscopic situations.
EUROPEAN PHYSICAL JOURNAL E
(2022)
Article
Chemistry, Physical
Lucas S. Palacios, Andrea Scagliarini, Ignacio Pagonabarraga
Summary: We introduce a novel mesoscopic computational model based on a multiphase-multicomponent lattice Boltzmann method for the simulation of self-phoretic particles in the presence of liquid-liquid interfaces. Our model features fully resolved solvent hydrodynamics and can handle important aspects of the multiphysics of the problem.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Sergi G. Leyva, Ralph L. Stoop, Ignacio Pagonabarraga, Pietro Tierno
Summary: In this study, we demonstrate the significant impact of the dispersing medium on the collective dynamics of interacting Brownian particles in a ratchet transport system. The long-range hydrodynamic interactions (His) result in a speed-up effect, leading to a higher translational speed and the formation and growth of clusters perpendicular to the driving direction. This research sheds light on the role of the dispersing medium in the dynamics of driven colloidal matter and the morphology of clusters.
Article
Chemistry, Physical
Marco De Corato, Ignacio Pagonabarraga
Summary: This paper investigates the self-propulsion mechanism of chemically active colloids and their coupling relationship with chemical reactions and momentum transport. By studying Onsager reciprocal relations, it is found that if a chemical reaction drives the motion of the colloid, an external force generates a reaction rate. The validity of reciprocal relations is verified through numerical simulations, and the key role of solute advection in maintaining the symmetry of the Onsager matrix is highlighted. Furthermore, it is discovered that Onsager reciprocal relations break down under nonequilibrium steady states, which has implications for the thermal fluctuations of active colloids used in experiments.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Chemistry, Physical
Elena Sese-Sansa, Demian Levis, Ignacio Pagonabarraga
Summary: This article discusses a dynamical field theory for self-propelled particles subjected to generic torques and forces. By coarse-graining their microscopic dynamics, the study investigates the instabilities of macroscopic and finite structures, and the influence of intrinsic torques on phase separation and non-equilibrium patterns.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Physics, Multidisciplinary
C. Rorai, F. Toschi, I. Pagonabarraga
Summary: In active nematic liquid crystals, activity can drive chaotic flows known as active turbulence. Experimental and theoretical studies have characterized active turbulence as a low Reynolds number phenomenon. In two dimensions, it has been shown that active forcing alone can trigger hydrodynamic turbulence, resulting in the coexistence of active and inertial turbulence.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Simone Pompei, Marco Cosentino Lagomarsino
Summary: The early development of aneuploidy from chromosome missegregation has contrasting effects - it causes cellular stress and decreased fitness, but also provides a quick solution to external stress. However, a comprehensive mathematical evolutionary modeling framework is lacking to capture these trends. This study introduces a fitness model that successfully captures the emergence of extra chromosomes in a laboratory evolution setup and explores the fitness landscape, supporting the existence of a per-gene cost of extra chromosomes. The substitution dynamics of the model explain the relative abundance of duplicated chromosomes observed in yeast population genomics data, providing testable predictions.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Biology
Viola Introini, Gururaj Rao Kidiyoor, Giancarlo Porcella, Pietro Cicuta, Marco Cosentino Lagomarsino
Summary: The nucleus plays a central role in key cellular processes, and recent research suggests an association between nuclear mechanics and cell-cycle progression. By monitoring nuclear shape fluctuations, this study reveals an increasing inward deformation in late G2 and early prophase, which correlates with chromatin condensation and possibly links it with nuclear-envelope breakdown during mitosis. These findings provide insights into the mechanical connection between chromosome condensation and nuclear envelope dynamics.
COMMUNICATIONS BIOLOGY
(2023)
Article
Chemistry, Physical
Joan Codina, Helena Massana-Cid, Pietro Tierno, Ignacio Pagonabarraga
Summary: Investigated the directed motion in clusters composed of passive and catalytically active particles and explained the reversal in transport direction using a theoretical model. Further built complex architectures capable of rapid assembly and disassembly under light control.
Article
Chemistry, Physical
Elena Sese-Sansa, Guo-Jun Liao, Demian Levis, Ignacio Pagonabarraga, Sabine H. L. Klapp
Summary: We present a hydrodynamic theory for systems of dipolar active Brownian particles and verify the theory's predictions of motility-induced phase separation (MIPS) with Brownian dynamics simulations. The simulations show that dipolar interactions hinder MIPS, and the analysis of angle-dependent correlation functions reveals the microscopic mechanisms behind the destabilization of the homogeneous phase.
Review
Polymer Science
Javier Diaz, Marco Pinna, Andrei V. Zvelindovsky, Ignacio Pagonabarraga
Summary: Block copolymer melts are excellent for positioning colloidal nanoparticles at the nanoscale and have wide applications in lithography. They can self-assemble into ordered structures where nanoparticles segregate based on polymer-particle interactions, size, and shape. The combination of the time-dependent Ginzburg-Landau model and Brownian dynamics provides an efficient mesoscopic model for studying block copolymer nanocomposites. This review focuses on recent developments and applications of this model.
