Article
Multidisciplinary Sciences
Chaojie Mo, Dmitry A. A. Fedosov
Summary: This study uses two-dimensional simulations in viscoelastic fluids to investigate the interaction of microswimmers. It is found that stiff sheets form stronger clusters than soft sheets. A doublet of soft sheets swims faster than a single swimmer, while a pair of stiff sheets does not show speed enhancement. Clustering of two identical swimmers is stable, but differences in beating amplitudes and frequencies can destroy the stability of the doublet. The stability of two distinct swimmers clustering is most stable at Deborah numbers of De = tau omega approximate to 1, in agreement with experimental observations. Therefore, cluster stability is a key factor in determining the cluster size of flagellated swimmers.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2023)
Article
Engineering, Marine
Zhijie Zhao, Qichen Shi
Summary: In this study, a muscle-contraction model is used to explore the collective swimming of two self-propelled fish-like swimmers. A PID control algorithm is integrated into the numerical simulation model to mimic the conscious swimming control exhibited by live fish. The effects of phase difference and initial spacing on the collective behavior of the fish are investigated, and the results show that the fish can achieve the same swimming speed and observe similar flow patterns by adjusting these parameters.
Article
Physics, Multidisciplinary
Ahmed Abouhussein, Yulia T. Peet
Summary: Optimal fish array hydrodynamics in accelerating phalanx schools are studied using a combination of high-fidelity Computational Fluid Dynamics (CFD) simulations and a gradient-free surrogate-based optimization algorithm. The study investigates critical parameters relevant to a phalanx fish school, including midline kinematics, separation distance, and phase synchronization, for efficient propulsion during accelerating fish motion. The results suggest that the optimal midline kinematics in accelerating phalanx schools resemble those of accelerating solitary swimmers. Additionally, the study shows that the optimal separation distance for thunniform biologically-inspired swimmers in a phalanx school is around 2L (where L is the swimmer's total length) and separation distance has a stronger effect on propulsion efficiency compared to phase synchronization, ceteris paribus.
Article
Chemistry, Physical
Lorenzo Turetta, Marco Lattuada
Summary: The aggregation kinetics of sedimenting colloidal particles under fully destabilized conditions has been investigated using different methods. It has been observed that long-range hydrodynamic interactions are crucial in capturing the fast aggregation rates induced by increasing cluster mass, while simulations without long-range hydrodynamic interactions are unable to predict this rapid kinetics. Additionally, a gel point can be formed at high particle volume fractions and a decrease in anisotropy of resulting clusters is observed as the Peclet number increases.
Article
Engineering, Marine
Chang Wei, Qiao Hu, Tangjia Zhang, Yangbin Zeng
Summary: This study investigates the effects of pure passive hydrodynamic interactions on schooling swimming using a numerical model and finds that individuals cannot maintain a stable formation solely relying on these interactions. The study also discusses the different effects induced by hydrodynamic interactions in detail.
Article
Engineering, Civil
Patrick Arnaud Wandji Zoumb, Xiaozhen Li, Ming Wang
Summary: This study utilizes a machine learning-based method to evaluate the response of train-bridge interactions induced by earthquakes and establishes a back-propagation neural network (BPNN) surrogate model. The results show that the proposed method is robust and accurate, which can be helpful for the design of railway bridges in coastal areas.
JOURNAL OF BRIDGE ENGINEERING
(2022)
Article
Mechanics
Andres Cordoba, Jay D. Schieber
Summary: In this study, the dynamics and stability of a swarm of microswimmers are examined using a thermodynamically compliant microswimmer model. The research findings show that microswimmers in the swarm can swim much faster than when alone in an infinite sea, and the crystalline arrangement of the swarm plays a crucial role in the hydrodynamic interaction between swimmers. Moreover, the study reveals that hydrodynamic torques have a stabilizing effect on swarms of pullers but destabilize swarms of pushers. By considering fuel consumption and high order hydrodynamic interactions, the full dynamics of the swarm's stability are investigated.
Article
Engineering, Ocean
Chenxi Qin, Lunliang Duan, Duoyin Wang, Bingchuan Duan, Meiling Fan, Haicui Wang
Summary: This study simulates the wave-cofferdam-seabed interaction process using a numerical model and investigates the wave-induced oscillatory seabed response around a dumbbell-shaped cofferdam. The effects of submerged depth, wave incidence angle, and wave height on the oscillatory pore pressure response are studied. The numerical results show that the wave height has a significant impact on the seabed response, while the wave incidence angle has a minor effect.
APPLIED OCEAN RESEARCH
(2023)
Article
Mechanics
Carlos Quental, Francisca Simoes, Mariana Sequeira, Jorge Ambrosio, Joao Paulo Vilas-Boas, Motomu Nakashima
Summary: This study discusses the limitations of external forces acquisition in musculoskeletal modeling and analysis of swimmers and proposes a methodology for inverse dynamic analysis that integrates motion-capture data, hydrodynamic force estimation by Swumsuit, and computation of internal forces. The proposed methodology is demonstrated by analyzing a full-body biomechanical model for a front-crawl swimming stroke, and the results are consistent with existing literature, showing the feasibility of the proposed method.
MULTIBODY SYSTEM DYNAMICS
(2023)
Article
Chemistry, Physical
Turetta Lorenzo, Lattuada Marco
Summary: This work employs Brownian dynamics simulations to investigate the aggregation kinetics of electrostatically-stabilized colloidal suspensions exposed to simple shear. The results show that an increase in shear rate leads to an increase in aggregation rate and the formation of large aggregates. The simulations further indicate that at the highest shear rate, the aggregation dynamics is entirely controlled by shear.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2022)
Article
Water Resources
Mostafa Farrag, Fabio Brill, Nguyen Viet Dung, Nivedita Sairam, Kai Schroeter, Heidi Kreibich, Bruno Merz, Karin M. de Bruijn, Sergiy Vorogushyn
Summary: Hydrodynamic interactions and floodplain storage have significant impacts on flood risk and risk assessments. Accurate risk assessments require a systematic approach and careful consideration of floodplain storage and hydrodynamic interactions.
HYDROLOGICAL SCIENCES JOURNAL
(2022)
Article
Mechanics
Linlin Kang, Weicheng Cui, Xi-Yun Lu, Haibo Huang
Summary: This study proposes a vorticity-based force expression to investigate the collective behaviors of two-dimensional tandem flapping plates. The research reveals that the wake vortices of the leader indirectly influence the hydrodynamic force on the rear plate by inducing an additional oncoming flow. The trajectory of the rear plate affects the generation of vorticity, with suppressed vorticity generation and weakened thrust effect when passing through vortex cores, and enhanced vorticity generation and thrust effect when slaloming between the vortices. The findings also highlight the ability of wake vortices to trap the rear plate into orderly configurations.
Article
Chemistry, Multidisciplinary
Ruchao Gao, S. Mohsen Beladi-Mousavi, Gerardo Salinas, Patrick Garrigue, Lin Zhang, Alexander Kuhn
Summary: Graphene monolayers can be postmodified with high precision by highly site-selective functionalization with platinum (Pt) clusters, resulting in catalytically active two-dimensional nanomaterials. The type and speed of motion of these materials can be controlled by controlling the deposition time and location of the Pt clusters.
Article
Mechanics
Pijush Patra, Donald L. Koch, Anubhab Roy
Summary: In this article, we study the collision behavior of particles in a gaseous medium, considering the effects of van der Waals attraction and non-continuum hydrodynamics in a simple shear flow. We find the influence of continuum lubrication forces and attractive interactions, as well as the significance of non-continuum interactions, and calculate the collision efficiency.
JOURNAL OF FLUID MECHANICS
(2022)
Article
Engineering, Civil
Xiaodong Ming, Qiuhua Liang, Richard Dawson, Xilin Xia, Jingming Hou
Summary: This study focuses on addressing the challenges in compound flood risk assessment and proposes an integrated assessment framework to quantify compound flood risk by analyzing hazard, vulnerability, and exposure. The framework is applied to the Greater London and Thames estuary to demonstrate its capability in analyzing hazard interactions and dependencies, and generating fully quantitative risk assessment results.
JOURNAL OF HYDROLOGY
(2022)
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