Article
Mechanics
S. Candelaresi, G. Hornig, B. Podger, D. Pontin
Summary: The study focuses on the relaxation of a topologically nontrivial vortex braid with zero net helicity in a barotropic fluid. It investigates how the topology of the vorticity field affects dynamics, particularly the asymptotic behavior during vortex reconnection at high Reynolds numbers. The relaxation of the vortex braid leads to a simplification of topology into large-scale regions of opposite swirl, influenced by a cascade of vortex reconnection events and the existence of positive and negative kinetic helicity regions setting a lower bound for kinetic energy.
Article
Multidisciplinary Sciences
Suvrajit Saha, Amit Das, Chandrima Patra, Anupama Ambika Anilkumar, Parijat Sil, Satyajit Mayor, Andmadan Rao
Summary: The spatiotemporal organization of proteins and lipids on the cell surface plays a crucial role in cellular functions. This study investigates the molecular interactions that drive the formation of nanoclusters of GPI-APs and transmembrane proteins, and proposes a theoretical model to explain the organization of membrane domains in living cells.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Multidisciplinary Sciences
Dominic J. Skinner, Hannah Jeckel, Adam C. Martin, Knut Drescher, Jorn Dunkel
Summary: Complex disordered matter plays a central role in various disciplines. Comparing structural features across different systems is challenging due to their differences. By using statistical properties of Delaunay tessellations, a mathematical framework is introduced to measure topological distances between 3D point clouds. The metric reveals subtle structural differences and recovers temporal ordering in embryonic development.
Article
Physics, Fluids & Plasmas
Roozbeh Saghatchi, Mehmet Yildiz, Amin Doostmohammadi
Summary: We investigate the impact of fluid inertia on collective pattern formation in active nematics using numerical simulations. Our findings show that inertial effects result in gradual melting of nematic order and an increase in topological defect density before a discontinuous transition to a vortex-condensate state. We also observe that flow field around topological defects is substantially affected by inertial effects. Additionally, we find a dependence of the kinetic energy spectrum on inertial effects, recovering Kolmogorov scaling within the vortex-condensate phase.
Article
Chemistry, Physical
D. J. G. Pearce, K. Kruse
Summary: The study reveals that topological defects in liquid crystals can be partially relieved through the creation and annihilation of defect pairs, and the interactions between defects involve four distinct elements: attraction, repulsion, co-rotation, and co-translation. The interplay of these effects can result in intricate defect trajectories, which can be controlled by setting relevant timescales.
Article
Mechanics
R. Corsini, A. Fregni, M. Spinolo, E. Stalio
Summary: Turbulence in the lee of an open-cell metal foam layer was investigated through direct numerical simulation, revealing significant pressure and turbulent transports of turbulent kinetic energy in the region close to the foam. The study also found that the turbulence characteristics deviated from Saffman turbulence, with weakly intermittent small-scale fluctuations.
JOURNAL OF FLUID MECHANICS
(2021)
Article
Chemistry, Multidisciplinary
Liangbo Hu, Ying Li, Xinhui Lin, Yucheng Huo, Hongyue Zhang, Huaimin Wang
Summary: By designing, synthesizing, and assembling an enzymatic programmable peptide system, we induced molecular assemblies formation spatiotemporally in living cancer cells, resulting in mainly necroptosis of glioblastoma cells. The stability and glycosylation of molecules play a crucial role in determining the bioactivity, as evidenced by detailed mechanistic studies showing site-specific formation of assemblies capable of activating the downstream cell death pathway.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Cell Biology
Jingcheng Wang, Sungwon Han, Jin Ye
Summary: Ceramide regulates the topology of TM4SF20 by delaying the retrotranslocation of glycosylated N-linked glycans, causing protein accumulation. The results suggest that retrotranslocation plays a crucial role in the topological regulation of transmembrane proteins.
Article
Chemistry, Multidisciplinary
Liangbo Hu, Ying Li, Xinhui Lin, Yucheng Huo, Hongyue Zhang, Huaimin Wang
Summary: The research article reports a structure-based programming approach of supramolecular assemblies in living cells for selective cancer cell inhibition by Wang et al.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2021)
Article
Chemistry, Physical
Enrica Soprano, Martina Migliavacca, Miriam Lopez-Ferreiro, Beatriz Pelaz, Ester Polo, Pablo del Pino
Summary: A surface-engineered cell-derived nanocarrier was developed for efficient cytosolic delivery of encapsulated biologically active molecules inside living cells. The nanocarriers, composed of biomimetic shell formed from cell membrane extracts, were loaded with various molecules. The fusogenic behavior of the nanocarriers, imparted by the intercalated exogenous lipids, allows for efficient delivery into the cytosolic milieu where cargo regains function.
JOURNAL OF COLLOID AND INTERFACE SCIENCE
(2023)
Article
Engineering, Chemical
Xiangjun Liao, Shuren Chou, Chuanyu Gu, Xiaocheng Zhang, Minghao Shi, Xiaofei You, Yuan Liao, Abdul Ghani Razaqpur
Summary: Membrane scaling is a common issue in continuous membrane distillation. The use of omniphobic corrugated membranes can effectively alleviate membrane scaling. Different modes of operation and membrane designs have different effects on scale formation. Parallel flow and corrugation patterns contribute to better scaling resistance.
JOURNAL OF MEMBRANE SCIENCE
(2023)
Article
Physics, Multidisciplinary
Nuris Figueroa-Morales, Mikhail M. Genkin, Andrey Sokolov, Igor S. Aranson
Summary: In this study, the authors demonstrate the control of topological defects in a living liquid crystal by introducing microscopic obstacles. They find that negative defects can be immobilized while positive defects remain motile. This immobilization is attributed to the attraction between opposite defects.
COMMUNICATIONS PHYSICS
(2022)
Review
Biochemistry & Molecular Biology
Leia Colin, Raquel Martin-Arevalillo, Simone Bovio, Amelie Bauer, Teva Vernoux, Marie-Cecile Caillaud, Benoit Landrein, Yvon Jaillais
Summary: Biological imaging is an interdisciplinary field crucial in cell biology research, involving techniques, probe development, and image analysis. Recent advances in live imaging of plant cells include studies on cell structure, hormones, mechanical properties, etc. driving the field forward.
Article
Chemistry, Multidisciplinary
Yousef Bagheri, Ahsan Ausaf Ali, Puspam Keshri, James Chambers, Anne Gershenson, Mingxu You
Summary: A new DNA-based probe called DNA Zipper was introduced in this study, which enables imaging of membrane order and transient interactions in living cells. These programmable DNA probes, by fine-tuning DNA hybridization, can precisely extend the duration of membrane lipid interactions and have been applied to study the correlation between membrane order and T-cell receptor signaling activation.
ANGEWANDTE CHEMIE-INTERNATIONAL EDITION
(2022)
Article
Engineering, Chemical
Minsik Kim, Kwanho Kim, Kwangsuk You
Summary: The turbulence eddy dissipation and shear stress in the flotation cell are influenced by bubble breakup. The flotation rate constant is correlated with the bubble surface area flux, which depends on the bubble size and dispersion characteristics. Numerical analysis was conducted to study the turbulence characteristics and shear stress in the flotation cell based on the stator-rotor clearance. It was found that a narrow clearance between the rotor and stator promotes high turbulence eddy dissipation and shear stress.
MINERALS ENGINEERING
(2023)
Article
Physics, Multidisciplinary
Mark J. Bowick, Nikta Fakhri, M. Cristina Marchetti, Sriram Ramaswamy
Summary: This article outlines current and emerging directions in active matter research, aiming to provide a pedagogical introduction for newcomers to the field and a road map of open challenges and future directions for established researchers.
Article
Physics, Multidisciplinary
Alexander Mietke, Jorn Dunkel
Summary: Researchers studied dihedral (k-atic) liquid crystals (DLCs) by generalizing the half-integer defects in nematic liquid crystals. They developed a unified hydrodynamic description model and investigated its behavior through particle simulations. They also predicted a novel spontaneous chiral symmetry-breaking transition in antialigning DLCs.
Article
Multidisciplinary Sciences
Honesty Kim, Dominic J. Skinner, David S. Glass, Alexander E. Hamby, Bradey A. R. Stuart, Joern Dunkel, Ingmar H. Riedel-Kruse
Summary: Multicellular systems form interfaces between different cell collectives and serve versatile functions. Synthetic biology aims to engineer multicellular systems for practical applications and as a methodology to understand natural systems. However, our ability to engineer multicellular interface patterns is limited.
Article
Multidisciplinary Sciences
Tzer Han Tan, Alexander Mietke, Junang Li, Yuchao Chen, Hugh Higinbotham, Peter J. Foster, Shreyas Gokhale, Jorn Dunkel, Nikta Fakhri
Summary: Researchers have discovered that swimming starfish embryos can spontaneously assemble into chiral crystals that persist for hours. The formation, dynamics, and dissolution of these living crystals are controlled by the hydrodynamic properties and natural development of the embryos. The living chiral crystals exhibit self-sustained chiral oscillations and unconventional deformation response behaviors, providing direct experimental evidence for the role of non-reciprocal interactions between multicellular organisms in non-equilibrium phases of chiral active matter.
Article
Multidisciplinary Sciences
Ziga Kos, Joern Dunkel
Summary: In this study, the concept of nematic bits (nbits) is introduced in liquid crystals, and it is demonstrated through theory and simulations how single-bit operations can be implemented using electric fields and how universal classical logic gates and generalized logical functions can be realized using nematoelastic interactions.
Article
Nanoscience & Nanotechnology
Alexandru Bacanu, James F. Pelletier, Yoon Jung, Nikta Fakhri
Summary: In living systems, molecular interactions form multiscale structures that mediate processes in a close relationship between structure and function. However, their dynamics remain poorly characterized due to a lack of methods to quantify non-equilibrium activity. By measuring time-reversal asymmetry encoded in conformational dynamics of carbon nanotubes, we characterize the multiscale dynamics of non-equilibrium activity and relate it to physical parameters. Our analysis provides a general tool to characterize non-equilibrium activity in high-dimensional spaces.
NATURE NANOTECHNOLOGY
(2023)
Article
Physics, Multidisciplinary
Alexander E. Cohen, Alasdair D. Hastewell, Sreeparna Pradhan, Steven W. Flavell, Joern Dunkel
Summary: Mode-based linear models inferred from experimental live-imaging data can accurately describe undulatory locomotion in various living systems. The shape dynamics are governed by Schrodinger equations in mode space, and efficient classification and differentiation of locomotion behaviors can be achieved using Grassmann distances and Berry phases. This approach can be generalized to other physical or living systems with mode representation subject to geometric shape constraints.
PHYSICAL REVIEW LETTERS
(2023)
Article
Multidisciplinary Sciences
Rohit Supekar, Boya Song, Alasdair Hastewell, Gary P. T. Choi, Alexander Mietke, Jorn Dunkel
Summary: Recent advances in imaging and simulation techniques have allowed for precise characterization of collective dynamics in active matter systems. A framework using spectral basis representations and sparse regression algorithms has been developed to discover hydrodynamic equations from microscopic simulation and experimental data. This framework has shown promise in reproducing self-organized collective dynamics and measuring hydrodynamic parameters directly from video data.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Multidisciplinary Sciences
Vishal P. Patil, Harry Tuazon, Emily Kaufman, Tuhin Chakrabortty, David Qin, Jorn Dunkel, M. Saad Bhamla
Summary: Tangled active filaments are common in nature and understanding their collective topological transformations is important. By studying California blackworms, researchers developed a mechanistic model that explains their tangle formation and ultrafast untangling. These findings can provide guidance for designing topologically tunable active materials.
Article
Mechanics
Freddy A. Cisneros, Nikta Fakhri, Jordan M. Horowitz
Summary: We propose and investigate a method for identifying timescales of dissipation in nonequilibrium steady states modeled as discrete-state Markov jump processes. The method is based on how the irreversibility, measured by the statistical breaking of time-reversal symmetry, varies under temporal coarse-graining. We observe a sigmoidal-like shape of the irreversibility as a function of the coarse-graining time, which allows us to develop a method for estimating the dissipative time scale from time-series data.
JOURNAL OF STATISTICAL MECHANICS-THEORY AND EXPERIMENT
(2023)
Article
Multidisciplinary Sciences
Dominic J. Skinner, Hannah Jeckel, Adam C. Martin, Knut Drescher, Jorn Dunkel
Summary: Complex disordered matter plays a central role in various disciplines. Comparing structural features across different systems is challenging due to their differences. By using statistical properties of Delaunay tessellations, a mathematical framework is introduced to measure topological distances between 3D point clouds. The metric reveals subtle structural differences and recovers temporal ordering in embryonic development.
Article
Computer Science, Interdisciplinary Applications
Pearson W. Miller, Daniel Fortunato, Cyrill Muratov, Leslie Greengard, Stanislav Shvartsman
Summary: This study investigates how altering the symmetry of a model impacts the dynamics of cell polarization. Through numerical and analytical techniques, non-trivial solutions for symmetry breaking are discovered.
NATURE COMPUTATIONAL SCIENCE
(2022)
Article
Physics, Fluids & Plasmas
Shreyas Gokhale, Junang Li, Alexandre Solon, Jeff Gore, Nikta Fakhri
Summary: A dynamic clustering phase is observed in mixtures of colloids and motile bacteria, where colloidal clustering is a result of the balance between bond breaking caused by persistent active motion and bond stabilization caused by torques that align active particle velocity tangentially to the passive particle surface.