Article
Chemistry, Physical
Avraham Moriel, Ariel Livne, Eran Bouchbinder
Summary: The ability of living cells to sense and respond to the physical properties of their microenvironment is crucial for their structure, function, and fate. This study focuses on the cellular sensitivity and response to periodic driving forces and explores the intra-cellular nematic order. The findings provide insights into the quantitative analysis of cell mechanosensitivity.
Article
Physics, Fluids & Plasmas
Pappu Acharya, Debankur Das, Surajit Sengupta, Kabir Ramola
Summary: In this study, we obtained exact results for the fluctuations in energy caused by microscopic disorder in near-crystalline athermal systems and predicted the distribution of interaction energy between two defects in a disordered background. The results showed that the interaction energy displayed a disorder-averaged power-law behavior with sixfold symmetry of the underlying reference crystal at large distances between the defects. Additionally, the fluctuations in the interaction energy encoded the athermal correlations introduced by the disordered background.
Article
Physics, Multidisciplinary
Finn Lasse Buessen, Sopheak Sorn, Ivar Martin, Arun Paramekanti
Summary: The interplay between nematicity and superconductivity in quantum materials was investigated by simulating a 2D array of nematogens coupled to Josephson junction wires, revealing that superconductivity can promote nematic ordering. The study discussed the implications of these findings in 2D electron gases and doped topological insulators.
Article
Materials Science, Multidisciplinary
Hui-Ke Jin, Andrea Pizzi, Johannes Knolle
Summary: Many-body systems subject to high-frequency drive can display intriguing thermalization behavior. This study uncovers the rich nonequilibrium phase diagram of a frustrated two-dimensional Ising magnet driven by competing short-range ferromagnetic and long-range dipolar interactions. The study discusses the implications for experiments on ferromagnetic thin films and other driving-induced phenomena in frustrated magnets.
Article
Physics, Fluids & Plasmas
Michely P. Rosseto, Jonathan Selinger
Summary: Recent theoretical research has developed a framework to understand director deformations and modulated phases in nematic liquid crystals. Four fundamental director deformation modes are considered, including a fourth mode related to saddle-splay. The research shows that this mode can induce spontaneous cholesteric or splay nematic phases.
Article
Chemistry, Physical
Antoni Kocot, Malgorzata Czarnecka, Yuki Arakawa, Katarzyna Merkel
Summary: Dielectric spectroscopy has been used to study the molecular orientation dynamics of symmetrical and asymmetrical liquid crystal dimers with cyanobiphenyl mesogenic groups in the twist-bend nematic phase. The results were analyzed within the framework of the molecular theory of dielectric permittivity for nematogens. The precessional rotation of the cyanobiphenyl groups and the end-over-end rotation of the cyanobiphenyl dipole around the short molecular axis were identified as the two molecular processes involved in the reorientation of the monomeric unit.
JOURNAL OF PHYSICAL CHEMISTRY B
(2023)
Article
Multidisciplinary Sciences
Bijaya Basnet, Mojtaba Rajabi, Hao Wang, Priyanka Kumari, Kamal Thapa, Sanjoy Paul, Maxim O. Lavrentovich, Oleg D. Lavrentovich
Summary: This study demonstrates the role of surface polarity in the formation of polar monodomains and domain walls in ferroelectric nematic liquid crystals, and its contribution to the total surface anchoring strength.
NATURE COMMUNICATIONS
(2022)
Article
Physics, Multidisciplinary
Tian-Wei Mao, Qi Liu, Xin-Wei Li, Jia-Hao Cao, Feng Chen, Wen-Xin Xu, Meng Khoon Tey, Yi-Xiao Huang, Li You
Summary: A record enhancement in nonlinear interferometry has been achieved by using spin-nematic squeezed states of atomic Bose-Einstein condensates, which can have potential applications in atomic magnetometers, atomic clocks, and fundamental tests of Lorentz symmetry violations.
Article
Mathematics, Applied
Francisco Guillen-Gonzalez, Maria Angeles Rodriguez-Bellido, Giordano Tierra
Summary: In this study, a new model was proposed to represent the interaction between flows and vesicle membranes with liquid crystalline phases. A new numerical scheme was introduced to approximate the model, demonstrating good performance and showcasing the dynamics of such vesicle membranes through several numerical results.
PHYSICA D-NONLINEAR PHENOMENA
(2021)
Article
Physics, Condensed Matter
Minaspi Bantawa, Wayan A. Fontaine-Seiler, Peter D. Olmsted, Emanuela Del Gado
Summary: By varying the model parameters of particulate gels, different gel morphologies can be obtained, and the local elastic structures identified to estimate their contribution to the gel elasticity.
JOURNAL OF PHYSICS-CONDENSED MATTER
(2021)
Article
Computer Science, Artificial Intelligence
Lei Zhao, Shumao Pang, Yangfan Chen, Xiongfeng Zhu, Ziyue Jiang, Zhihai Su, Hai Lu, Yujia Zhou, Qianjin Feng
Summary: SpineRegNet is a novel affine-elastic registration framework that achieves spine image registration through a Multiple Affine Matrices Estimation (MAME) Module, an Affine-Elastic Fusion (AEF) Module, and a Local Rigidity Constraint (LRC) Module. Experimental results show that the proposed approach has impressive performance in spine image registration.
MEDICAL IMAGE ANALYSIS
(2023)
Article
Multidisciplinary Sciences
Fereshteh L. Memarian, Joseph D. Lopes, Fabian Jan Schwarzendahl, Madhuvanthi Guruprasad Athani, Niranjan Sarpangala, Ajay Gopinathan, Daniel A. Beller, Kinjal Dasbiswas, Linda S. Hirst
Summary: The study demonstrates the formation of dynamic lanes and long-range active nematic alignment by directly coupling kinesin motors to a lipid bilayer during microtubule gliding. The lipid membrane promotes filament-filament alignment and enhances globally aligned active nematic state formation.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Cell Biology
Ai Kia Yip, Songjing Zhang, Lor Huai Chong, Elsie Cheruba, Jessie Yong Xing Woon, Theng Xuan Chua, Corinna Jie Hui Goh, Haibo Yang, Chor Yong Tay, Cheng-Gee Koh, Keng-Hwee Chiam
Summary: The study found that zyxin is a crucial protein involved in cellular rigidity sensing and durotaxis regulation. Knocking down zyxin impairs cell's ability to sense and respond to changes in extracellular matrix rigidity, resulting in migration speed independent of substrate rigidity.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2021)
Article
Multidisciplinary Sciences
Luka Mesarec, Wojciech Gozdz, Veronika Kralj-Iglic, Samo Kralj, Ales Iglic
Summary: The impact of the intrinsic curvature of in-plane orientationally ordered curved flexible nematic molecules attached to closed 3D flexible shells was studied numerically. A Helfrich-Landau-de Gennes-type mesoscopic approach was adopted where the flexible shell's curvature field and in-plane nematic field are coupled and concomitantly determined in the process of free energy minimisation. We demonstrate that this coupling has the potential to generate a rich diversity of qualitatively new shapes of closed 3D nematic shells and the corresponding specific in-plane orientational ordering textures, which strongly depend on the shell's volume-to-surface area ratio, so far not predicted in mesoscopic-type numerical studies of 3D shapes of closed flexible nematic shells.
SCIENTIFIC REPORTS
(2023)
Article
Physics, Multidisciplinary
Luca Gallo, Riccardo Muolo, Lucia Valentina Gambuzza, Vito Latora, Mattia Frasca, Timoteo Carletti
Summary: The authors introduce the concept of M-directed hypergraphs and study the synchronization of systems with directed higher-order interactions. They find that directed higher-order interactions can destroy synchronization, but also stabilize otherwise unstable synchronized states.
COMMUNICATIONS PHYSICS
(2022)
Review
Biology
A. Gong, S. Rode, U. B. Kauppl, G. Gompper, J. Elgeti, B. M. Friedrich, L. Alvarez
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2020)
Article
Polymer Science
Omar Adame-Arana, Samuel A. Safran
Summary: In this study, we analytically predicted the concentration profile of a long polymer chain in a poor solvent, confined between two walls, where some monomers can form strong bonds with the walls. We observed nonmonotonic variations in concentration profiles due to boundary conditions that lead to a decrease in monomer concentration at the walls. This has implications for understanding chromatin organization in the nucleus of living cells.
Article
Biochemical Research Methods
Steffen Lange, Benjamin M. Friedrich
Summary: Marine invertebrate sperm need to find egg cells in the ocean through turbulent mixing and cellular chemotaxis. External flows elongate concentration filaments of signaling molecules, along which sperm cells 'surf' towards the eggs. The theory of chemotactic navigation in external flow provides insights into how cells navigate in complex environments under turbulent conditions.
PLOS COMPUTATIONAL BIOLOGY
(2021)
Article
Biology
Gaurav Bajpai, Daria Amiad Pavlov, Dana Lorber, Talila Volk, Samuel Safran
Summary: Intact-organism imaging of Drosophila larvae reveals and quantifies chromatin-aqueous phase separation, with different chromatin distributions controlled by nuclear volume changes and chromatin-lamina interaction. Theoretical models show that the competition between chromatin self-attraction and its binding to the lamina determines the distribution mode. Simulations with few physical variables can identify generic mechanisms underlying observed phase separations.
Article
Chemistry, Physical
A. Gong, S. Rode, G. Gompper, U. B. Kaupp, J. Elgeti, B. M. Friedrich, L. Alvarez
Summary: This study employed refined holographic imaging methods to record high-quality three-dimensional flagellar bending waves, revealing how different flagellar beat patterns result in distinct swimming paths. Human sperm flagella exhibit specific torsion waves during 3D swimming, believed to be intrinsic properties of axonemes and impacting the dynamics of swimming paths. The research provides insights into axoneme dynamics, 3D flagellar beat, and resulting swimming behavior.
EUROPEAN PHYSICAL JOURNAL E
(2021)
Article
Multidisciplinary Sciences
Dan Deviri, Samuel A. Safran
Summary: Homeostasis is a fundamental characteristic of living systems, which is maintained by biochemically distinct organelles and liquid-liquid phase separation (LLPS) in cells. The coexisting concentrations in LLPS are related to expression noise, and changes in molecular interactions can increase the efficiency of concentration buffering in a given system, suggesting an evolutionary optimization of concentration buffering for maintaining LLPS homeostasis.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Chemistry, Multidisciplinary
Justus A. Kromer, Andrea Auconi, Benjamin M. Friedrich
Summary: The study examines minimal search strategies of self-propelled particles in three-dimensional space towards hidden targets, where particles can sense the proximity of targets but cannot deduce directional cues. The research finds that two search strategies significantly increase target encounter rates, with the optimal inner search time scaling as a power law with target density, reflecting a trade-off between exploration and exploitation.
Article
Multidisciplinary Sciences
Daria Amiad-Pavlov, Dana Lorber, Gaurav Bajpai, Adriana Reuveny, Francesco Roncato, Ronen Alon, Samuel Safran, Talila Volk
Summary: The research revealed that the three-dimensional organization of chromatin plays a crucial role in transcriptional control, with active and repressed chromatin separating from the nuclear interior to form a peripheral layer underneath the nuclear lamina. This peripheral chromatin organization, sensitive to lamina composition, was observed in various Drosophila tissues as well as in live human cells, indicating an evolutionarily conserved mode of mesoscale chromatin organization.
Article
Physics, Multidisciplinary
Anton Solovev, Benjamin M. Friedrich
Summary: This study investigates the phenomenon of metachronal synchronization in cilia systems through a multi-scale model and experimental data, and predicts different wave modes. The study finds that global order does not exist in infinite systems, but synchronization transitions do exist in finite systems and are related to frequency disorder.
NEW JOURNAL OF PHYSICS
(2022)
Article
Physics, Multidisciplinary
Andrea Auconi, Maja Novak, Benjamin M. Friedrich
Summary: Bayesian chemotaxis is an information-based target search problem inspired by biological chemotaxis. In this study, we extend a previous point-like agent model to a circle-shaped agent model. We identify gradient sensing and a Laplacian correction to concentration sensing as the dominant factors affecting the expected entropy variation. Numerical results show that gradient sensing is the most relevant factor in breaking the symmetry of likelihood distributions generated by concentration sensing.
Article
Multidisciplinary Sciences
Dan Deviri, Samuel A. Safran
Summary: The volume of the cell nucleus is not solely determined by the size of the genome and chromatin compaction, but also by the osmotic pressure of localized proteins and RNA molecules. A physical model based on this localized protein pressure predicts a constant ratio between cell and nuclear volumes, which is robust to various manipulations.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Physics, Multidisciplinary
Saroj Kumar Nandi, Daniel Osterle, Meta Heidenreich, Emmanuel D. Levy, Samuel A. Safran
Summary: Biomolecular self-assembly can spatially segregate proteins with a limited number of binding sites into condensates that coexist with a dilute phase. By comparing experimental phase diagrams to model predictions, we find that the extent of phase separation exponentially increases with binding site affinity and valency. Valency alone determines the symmetry of the phase diagram.
PHYSICAL REVIEW LETTERS
(2022)
Article
Biophysics
Ram M. Adar, Amit Singh Vishen, Jean-Francois Joanny, Pierre Sens, Samuel A. Safran
Summary: The volume of adhered cells decreases during spreading due to a modulation of ion transport rates. Swollen cells are more susceptible to volume loss when tension increases. This explains the discrepancies between recent experiments on adhered cells, where both the magnitude of volume change and its dynamics varied substantially. The roles of cell swelling and surface tension in cellular volume regulation and their microscopic origins are discussed.
BIOPHYSICAL JOURNAL
(2023)
Article
Biochemical Research Methods
Gaurav Bajpai, Samuel Safran
Summary: Chromosomes in animal cells are arranged in distinct territories within the nucleus, but recent experiments have shown that these territories overlap, indicating partial mixing during interphase. Knocking down of condensin II proteins during interphase increases chromosome mixing, demonstrating control of the mixing process. This study uses a polymer simulation to quantify the dynamics of chromosome mixing and introduces a chromosome mixing index to quantify the mixing of distinct chromosomes in the nucleus.
PLOS COMPUTATIONAL BIOLOGY
(2023)
Article
Cell Biology
Daria Amiad Pavlov, C. P. Unnikannan, Dana Lorber, Gaurav Bajpai, Tsviya Olender, Elizabeth Stoops, Adriana Reuveny, Samuel Safran, Talila Volk
Summary: The LINC complex is essential for minimizing chromatin repression in muscle tissue by controlling the binding of Polycomb repressors and RNA-Pol II to muscle genes. It also regulates the repressive modifications and activation of chromatin in muscle fibers. Computer simulation indicates that the dissociation of chromatin from the nuclear envelope leads to the growth of repressive H3K27 tri-methylated clusters. These findings suggest that the LINC complex plays a crucial role in directing robust transcription in muscle fibers.
