Article
Physics, Multidisciplinary
Hongbo Zhao, Andrej Kosmrlj, Sujit S. Datta
Summary: Research shows that there is a strong competition between collective chemotaxis and motility-induced phase separation (MIPS). Collective chemotaxis can suppress or inhibit phase separation, and it can also generate new dynamic instabilities. These findings contribute to the understanding and clarification of the rich physics underlying active matter systems, ranging from cells to robots.
PHYSICAL REVIEW LETTERS
(2023)
Article
Biology
Tapomoy Bhattacharjee, Daniel B. Amchin, Ricard Alert, Jenna Anne Ott, Sujit Sankar Datta, Irene Giardina
Summary: Collective migration, a fascinating behavior in active matter, has functional implications for biological systems. This study investigates how bacterial populations persist in migration despite perturbations. The researchers discover that the bacteria autonomously smooth out large-scale perturbations by adjusting their ability to sense and respond to the local nutrient gradient, enabling them to continue migrating together.
Article
Mechanics
Lloyd Fung
Summary: In a dilute suspension, analytical solutions have been found for the steady distributions of sinking spheroids or motile gyrotactic micro-organisms under arbitrary continuous vertical shear flow. The nonlinear two-way coupling between their distribution and the vertical flow leads to a bifurcation of the uniform base state into a structure resembling streamers or plumes. This bifurcation depends on a single parameter proportional to the average number of particles on a horizontal cross-section. In a three-dimensional axisymmetric system, the plume structure undergoes a blow-up when the parameter exceeds a threshold. We discuss the analogy of this singularity to the chemotactic collapse of a Keller-Segel model and its significance.
JOURNAL OF FLUID MECHANICS
(2023)
Article
Physics, Multidisciplinary
Ricard Alert, Alejandro Martinez-Calvo, Sujit S. Datta
Summary: This article theoretically demonstrates the limitations in stability of chemotactic fronts to morphological perturbations caused by the ability of individual cells to sense and respond to chemical gradients. The competition between cells at bulging parts of a front, where they are exposed to a smaller gradient but respond more strongly to it, determines whether the front is stable or not. The study suggests that the sensory machinery of cells might have evolved to avoid these limitations and ensure stable front propagation, and this principle may also apply to other types of directed migration.
PHYSICAL REVIEW LETTERS
(2022)
Article
Multidisciplinary Sciences
Bradley D. Frank, Saveh Djalali, Agata W. Baryzewska, Paolo Giusto, Peter H. Seeberger, Lukas Zeininger
Summary: Researchers have achieved chemotactic motion of emulsion droplets, which can be controllably altered by modifying the droplets' geometry and composition. This finding has implications for the design of smart and adaptive microbots.
NATURE COMMUNICATIONS
(2022)
Article
Chemistry, Physical
Tsuyoshi Yamaguchi
Summary: Molecular dynamics simulation was used to study sound dispersion on the molecular scale in molecular liquids. The relationship between the longitudinal modulus and frequency was analyzed and compared with the frequency-dependent longitudinal modulus evaluated by the Kubo-Green theory. The findings showed that the sound dispersion in both monoatomic and polyatomic liquids can be explained by considering the viscoelasticity in the q = 0 limit.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Biotechnology & Applied Microbiology
Josep Ferre-Torres, Adria Noguera-Monteagudo, Adrian Lopez-Canosa, J. Roberto Romero-Arias, Rafael Barrio, Oscar Castano, Aurora Hernandez-Machado
Summary: In this study, a simulation model is presented to replicate a microfluidic assay where endothelial cells sprout into a biomimetic extracellular matrix influenced by chemotactic factors. The model incorporates the effects of the extracellular matrix and chemotactic factors into a unified term using a single parameter, primarily focusing on modelling sprouting dynamics and morphology. The model is validated through comparison with experimental results derived from the microfluidic setup, highlighting the intricate relationship between the extracellular matrix structure and angiogenic sprouting.
FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY
(2023)
Article
Chemistry, Physical
Rangsiman Ketkaew, Fabrizio Creazzo, Sandra Luber
Summary: Researchers have developed a non-instructor-led deep autoencoder neural network (DAENN) for discovering general-purpose collective variables (CVs). By training the model with unbiased trajectories that contain only reactant conformers, the network can learn molecular representations. Additionally, the introduction of topology variables and a loss-like penalty function allows for an expansion of the configurational space, improving the efficiency of CVs discovery.
JOURNAL OF PHYSICAL CHEMISTRY LETTERS
(2022)
Article
Biochemical Research Methods
Szymon Wisniewski, Paulina Dragan, Anna Makal, Dorota Latek
Summary: This article discusses the activation of the complement system and the role of C5a and C5aR1 in host response to infection. It also explores the differences in signaling pathways between C5aR1 and C5aR2, and explains the impact of the inverted helix H8 on C5aR1 activation through molecular dynamics analysis.
PLOS COMPUTATIONAL BIOLOGY
(2022)
Article
Multidisciplinary Sciences
Thamara Liz Gabuardi, Hyun Gyu Lee, Kyoung J. Lee
Summary: Cell migration in a confluent population is determined by cell-to-cell interactions and cell-intrinsic properties, while the presence of anisotropies in biological tissues can also affect cell motility. This study investigates the impact of spatially localized cellular senescence on the motility of active cells using in vitro cultures. The researchers find that the adhesion between normal cells and senescent cells is weaker than that between normal cells, and the 'arclength' traveled by normal cells along the boundary of senescent cells is significantly longer than their persistence length in a densely packed homogeneous population. The study suggests that the expansion of senescent cell's membrane may decrease the density of cell adhesion molecules.
SCIENTIFIC REPORTS
(2022)
Article
Multidisciplinary Sciences
Paula C. Soto, Valeri H. Terry, Mary K. Lewinski, Savitha Deshmukh, Nadejda Beliakova-Bethell, Celsa A. Spina
Summary: This study investigates the relationship between T cell activation and proliferation and the establishment of HIV latency. The findings suggest that cells infected during the height of cell proliferation retain the least amount of latent infection, while cells that did not divide or exhibited limited division after virus exposure and stimulation contained greater amounts of latent HIV. Co-culture experiments demonstrate that latent infection can be established directly in non-dividing cells through cell-to-cell transmission.
Article
Multidisciplinary Sciences
Margherita De Marzio, Ayse Kilic, Enrico Maiorino, Jennifer Mitchel, Chimwemwe Mwase, Michael J. O'Sullivan, Maureen McGill, Robert Chase, Jeffrey J. Fredberg, Jin-Ah Park, Kimberly Glass, Scott T. Weiss
Summary: By conducting compression experiments on bronchial epithelial cells, the genome-wide analysis of UJT revealed different activation stages of intracellular and extracellular molecular networks induced by compression. Furthermore, the study found common genomic patterns associated with ECM remodeling in nonasthmatic and asthmatic bronchial epithelial cells.
Article
Multidisciplinary Sciences
Song Liu, Suraj Shankar, M. Cristina Marchetti, Yilin Wu
Summary: Active matter is composed of units that generate mechanical work by consuming energy, such as living systems and biopolymers. The goal is to understand and control the self-organization in space and time. Most active systems exhibit spatial order or temporal synchronization, while simultaneous control of spatial and temporal organization requires complex interactions.
Article
Multidisciplinary Sciences
Debraj Ghose, Katherine Jacobs, Samuel Ramirez, Timothy Elston, Daniel Lew
Summary: This study investigated how small eukaryotic cells interpret chemical gradients, focusing on Saccharomyces cerevisiae cells. Experimental and computational modeling revealed that the movement of polarity sites is biased by local pheromone gradients, leading to effective gradient tracking. This mechanism may be relevant for cells navigating complex chemical landscapes to find targets.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Md. Istiaq Obaidi Tanvir, Go Itoh, Hiroyuki Adachi, Shigehiko Yumura
Summary: The study observed wound repair in dividing cells for the first time and found dynamic changes of myosin II during cell membrane repair. It was discovered that myosin II is not essential for cell wound repair, and a novel mechanism for its delocalization from the cortex through phosphorylation was proposed. Additionally, the disappearance of several furrow-localizing proteins upon wounding was observed, indicating potential mechanisms for myosin dynamics during wound repair.
Article
Biochemistry & Molecular Biology
Gerard C. L. Wong, Jyot D. Antani, Pushkar P. Lele, Jing Chen, Beiyan Nan, Marco J. Kuhn, Alexandre Persat, Jean-Louis Bru, Nina Molin Hoyland-Kroghsbo, Albert Siryaporn, Jacinta C. Conrad, Francesco Carrara, Yutaka Yawata, Roman Stocker, Yves Brun, Gregory B. Whitfield, Calvin K. Lee, Jaime de Anda, William C. Schmidt, Ramin Golestanian, George A. O'Toole, Kyle A. Floyd, Fitnat H. Yildiz, Shuai Yang, Fan Jin, Masanori Toyofuku, Leo Eberl, Nobuhiko Nomura, Lori A. Zacharoff, Mohamed Y. El-Naggar, Sibel Ebru Yalcin, Nikhil S. Malvankar, Mauricio D. Rojas-Andrade, Allon Hochbaum, Jing Yan, Howard A. Stone, Ned S. Wingreen, Bonnie L. Bassler, Yilin Wu, Haoran Xu, Knut Drescher, Jorn Dunkel
Summary: Bacterial biofilms are communities of bacteria that are essential to microbial physiology, with a complex relationship between single-cell behavior and collective community behavior. Biofilm microbiology, a relatively young field, has attracted physicists who use physics to study fundamental concepts in bacterial biofilms. The combination of physics and biology in this field exemplifies a new synthesis, rather than just a division of labor.
Article
Physics, Multidisciplinary
Babak Nasouri, Andrej Vilfan, Ramin Golestanian
Summary: The research derives a theorem for the lower bound on energy dissipation rate by microswimmers and proposes a new definition of energetic efficiency for microswimmers. Experimental results validate the theory.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Multidisciplinary
Fanlong Meng, Daiki Matsunaga, Benoit Mahault, Ramin Golestanian
Summary: The study reveals that the collective behavior of magnetic microswimmers in a microfluidic channel can be analogized to Bose-Einstein condensation, achieved through a non-equilibrium phase transition, with the potential to generate exotic classical nonequilibrium phases of matter similar to those observed in quantum systems.
PHYSICAL REVIEW LETTERS
(2021)
Article
Physics, Multidisciplinary
Saeed Mahdisoltani, Ramin Golestanian
Summary: This study shows that electrolytes driven by an external electric field exhibit scale invariance despite Debye screening. Long-range correlations result in a Casimir-like fluctuation-induced force between neutral boundaries that can be controlled by the electric field, behaving differently from other fluctuation-induced forces.
PHYSICAL REVIEW LETTERS
(2021)
Article
Chemistry, Physical
Vincent Ouazan-Reboul, Jaime Agudo-Canalejo, Ramin Golestanian
Summary: Biomolecular condensates in cells are often rich in catalytically active enzymes, particularly in large enzymatic complexes called metabolons. The self-organization of these enzymes may be explained by a combination of catalytic activity and chemotactic responses to gradients of substrates, leading to non-reciprocal interactions with exotic features. The study of phase separation in mixtures of catalytically active particles reveals a Michaelis-Menten-like dependence and transient oscillations, highlighting non-equilibrium organizing principles important for biological liquid-liquid phase separation.
EUROPEAN PHYSICAL JOURNAL E
(2021)
Article
Mechanics
Abdallah Daddi-Moussa-Ider, Babak Nasouri, Andrej Vilfan, Ramin Golestanian
Summary: The study reveals that the optimal propulsion strategy of microswimmers depends on their shape profile, which could be puller, pusher or neutral. Among all the modes of the shape function, only the third mode determines the swimming type of the optimal swimmer at leading order.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Multidisciplinary Sciences
Fanlong Meng, Rachel R. Bennett, Nariya Uchida, Ramin Golestanian
Summary: In this study, a theoretical framework connecting the dynamics of an individual cilium to the collective dynamics of a ciliary carpet via coarse graining is presented. The criteria controlling the selection of frequency and wave vector of stable metachronal waves of the cilia are uncovered and examined. Agent-based numerical simulations of arrays of cilia with hydrodynamic interactions show quantitative agreement with the predictions of the analytical framework.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Biology
David Hickey, Andrej Vilfan, Ramin Golestanian
Summary: The protruding geometry of cilia could be one of the reasons why so many receptors are located on cilia, as shown by comparing the capture rates. The study also highlights the advantage of combining motility with chemical reception.
Article
Physics, Multidisciplinary
Jaime Agudo-Canalejo, Tunrayo Adeleke-Larodo, Pierre Illien, Ramin Golestanian
Summary: This study explores the stochastic dynamics of two enzymes that are mechanically coupled to each other, demonstrating that this coupling can greatly enhance their catalytic rate. The findings suggest that enzymes, despite being on a molecular scale, can cooperate and improve performance in metabolic clusters.
PHYSICAL REVIEW LETTERS
(2021)
Article
Multidisciplinary Sciences
Laura Collesano, Isabella Guido, Ramin Golestanian, Andrej Vilfan
Summary: This study focuses on a system that consists of a pair of microtubules clamped at one end, and investigates the static shapes and active dynamics of this system. The results show that the system transitions from a planar shape to a non-planar shape and then back to planar shape as the length ratio between the two filaments increases. The predicted shapes of the microtubule pairs agree with experimental observations. The dynamical system of this two-filament system can have stable fixed points or limit cycle oscillations, which resemble ciliary motility.
JOURNAL OF THE ROYAL SOCIETY INTERFACE
(2022)
Article
Multidisciplinary Sciences
Andrea Testa, Mirco Dindo, Aleksander A. Rebane, Babak Nasouri, Robert W. Style, Ramin Golestanian, Eric R. Dufresne, Paola Laurino
Summary: Living cells can harvest environmental energy to drive chemical processes. Here the authors design a minimal artificial system that achieves steady states at similar metabolic densities to microorganisms.
NATURE COMMUNICATIONS
(2021)
Article
Physics, Multidisciplinary
Lorenzo Piro, Evelyn Tang, Ramin Golestanian
Summary: This study builds an analytical formalism for overdamped microswimmers on curved manifolds and arbitrary flows, revealing that the solution corresponds to the geodesics of a Randers metric. Swimmer performance following this Randers policy consistently outperforms a more direct policy, with relative gains growing significantly when specific structures related to either the geometry or the flow are exploited. Analysis of isochrone shape unveils features such as self-intersections, cusps, and abrupt nonlinear effects. This work establishes a connection between microswimmer physics and geodesics in generalizations of general relativity.
PHYSICAL REVIEW RESEARCH
(2021)
Article
Medicine, General & Internal
Philip Bittihn, Lukas Hupe, Jonas Isensee, Ramin Golestanian
Summary: The effectiveness of regional containment strategies during COVID-19 pandemic is influenced by key parameters such as leakiness and regional structure. Lower proportion of cross-regional contacts and subdivision of regions can lead to more efficient epidemic control without impacting local socioeconomic freedom.
Meeting Abstract
Biophysics
Evelyn M. Tang, Jaime Agudo-Canalejo, Ramin Golestanian
BIOPHYSICAL JOURNAL
(2021)
Article
Physics, Multidisciplinary
Saeed Mahdisoltani, Riccardo Ben Ali Zinati, Charlie Duclut, Andrea Gambassi, Ramin Golestanian
Summary: The study presents an unconventional mechanism for interactions within biological systems, proposing that self-organization is driven by the interaction of polarity particles via chemical signals. The research utilizes an exact stochastic formulation and dynamical renormalization group analysis to reveal the emergent Galilean symmetry and dynamical scaling exponents at the critical point. These findings indicate superdiffusive density fluctuations and non-Poissonian number fluctuations that can determine the large-scale behavior of cell colonies and tissues.
PHYSICAL REVIEW RESEARCH
(2021)
