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#dynamics

4 Beiträge3 Beteiligte0 Beiträge heute
Charo del Genio

New paper!

If you want to assess the stability of the synchronization of a system of identical oscillators, you can use the Master Stability Function. However, what do you do in a real-world case, when the elements of the system are not exactly identical? We show how to extend the formalism and use it also when there are many-body interactions, such as in a simplicial complex.

journals.aps.org/prresearch/ab

#mathematics#physics#science
Rxiv mechanobio

📰 "Cost Functions in Economic Complexity"
arxiv.org/abs/2507.04054 #Physics.Soc-Ph #Dynamics #Matrix

arXiv logo
arXiv.orgCost Functions in Economic ComplexityEconomic complexity algorithms, including the Economic Complexity Index (ECI) and Non-Homogeneous Economic Fitness and Complexity (NHEFC), have proven effective at capturing the intricate dynamics of economic systems. Here, we present a fundamental reinterpretation of these algorithms by reformulating them as optimization problems that minimize specific cost functions. We show that ECI computation is equivalent to finding eigenvectors of the network's transition matrix by minimizing the quadratic form associated with the network's Laplacian. For NHEFC, we derive a novel cost function that exploits the algorithm's intrinsic logarithmic structure and clarifies the role of its regularization parameter. Additionally, we establish the uniqueness of the NHEFC solution, providing theoretical foundations for its application. This optimization-based reformulation bridges economic complexity and established frameworks in spectral theory, network science, and optimization. The theoretical insights translate into practical computational advantages: we introduce a conservative, gradient-based update rule that substantially accelerates algorithmic convergence. Beyond advancing our theoretical understanding of economic complexity indicators, this work opens new pathways for algorithmic improvements and extends applicability to general network structures beyond traditional bipartite economic networks.
Rxiv mechanobio

📰 "From Filamentation to Stratification: Instability Dynamics in Scissors-Shaped Relativistic Beam-Plasma System"
arxiv.org/abs/2507.04336 #Physics.Plasm-Ph #Dynamics #Cell

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arXiv.orgFrom Filamentation to Stratification: Instability Dynamics in Scissors-Shaped Relativistic Beam-Plasma SystemCounter-streaming systems are a canonical model for beam-plasma instabilities, such as the filamentation instability, which is critical in high energy density physics. However, scenarios involving intersecting fast electron beams break the cylindrical symmetry inherent to such systems. Here, we introduce the scissors-shaped configuration, a fundamental multi-velocity-component system that captures this broken symmetry. Through theoretical analysis and particle-in-cell simulations, we reveal a dramatic shift in the instability dynamics: the system undergoes a stratification mode instead of filamentation. This mode is rapidly quenched by magnetic reconnection, leading to a quasi-stable state with magnetic energy two orders of magnitude lower than in the counter-streaming case. This discovery establishes a new principle of passive instability control via geometric configuration, offering a new perspective on beam-plasma interactions in astrophysics and inertial confinement fusion. The underlying physics is verifiable in upcoming multi-laser experiments.
Charo del Genio

All those who couldn't join us in Natal for the International School and Workshop in Complex Networks Beyond Pairwise Interactions can still access all the lectures and talks, courtesy of the International Institute of Physics! 😎

- Fundamental definitions and properties
- Dynamical processes
- Synchronisation
- Control
- Belief propagation
- Community detection

and more!

Please boost to reach the largest possible audience.

youtube.com/playlist?list=PLqT

YouTubeComplex Networks beyond Pairwise Interactions: From Theory to ApplicationsVon iiptv
#mathematics#physics#structure
Rxiv mechanobio

📰 "Functional classification of metabolic networks"
arxiv.org/abs/2503.14437 #Physics.Bio-Ph #Q-Bio.Mn #Dynamics #Matrix

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arXiv.orgFunctional classification of metabolic networksChemical reaction networks underpin biological and physical phenomena across scales, from microbial interactions to planetary atmosphere dynamics. Bacterial communities exhibit complex competitive interactions for resources, human organs and tissues demonstrate specialized biochemical functions, and planetary atmospheres are capable of displaying diverse organic and inorganic chemical processes. Despite their complexities, comparing these networks methodically remains a challenge due to the vast underlying degrees of freedom. In biological systems, comparative genomics has been pivotal in tracing evolutionary trajectories and classifying organisms via DNA sequences. However, purely genomic classifications often fail to capture functional roles within ecological systems. Metabolic changes driven by nutrient availability highlight the need for classification schemes that integrate metabolic information. Here we introduce and apply a computational framework for a classification scheme of organisms that compares matrix representations of chemical reaction networks using the Grassmann distance, corresponding to measuring distances between the fundamental subspaces of stoichiometric matrices. Applying this framework to human gut microbiome data confirms that metabolic distances are distinct from phylogenetic distances, underscoring the limitations of genetic information in metabolic classification. Importantly, our analysis of metabolic distances reveals functional groups of organisms enriched or depleted in specific metabolic processes and shows robustness to metabolically silent genetic perturbations. The generalizability of metabolic Grassmann distances is illustrated by application to chemical reaction networks in human tissue and planetary atmospheres, highlighting its potential for advancing functional comparisons across diverse chemical reaction systems.
Rxiv mechanobio

📰 "Gliding microtubules exhibit tunable collective rotation driven by chiral active forces"
arxiv.org/abs/2507.00245 #Physics.Bio-Ph #Cond-Mat.Soft #Cytoskeletal #Dynamics

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arXiv.orgGliding microtubules exhibit tunable collective rotation driven by chiral active forcesHow chirality propagates across scales remains an open question in many biological and synthetic systems. An especially clear manifestation of this propagation is found in in vitro gliding assays of cytoskeletal filaments on surfaces, driven by molecular motors. These assays have become model systems of active matter dynamics, as they spontaneously organize into diverse dynamical states, including collective motions with chiral rotation. However, the microscopic mechanisms underlying these chiral collective dynamics have remained unclear. Here, we investigate rotating active nematic order in microtubule gliding assay experiments under two stabilization conditions, each on two types of substrates. We propose that chirality in active forces exerted by motors on microtubules represents a viable mechanism for this large-scale chirality. Using Brownian dynamics simulations of self-propelled, semiflexible filaments with chiral activity, we demonstrate that coherently rotating active nematic order emerges by this mechanism even in the absence of curvature, i.e. shape chirality, of the constituent filaments. Moreover, we predict that the angular speed and handedness of the collective rotation can be tuned by modulating filament stiffness. Our findings identify a new set of sufficient microscopic ingredients for predictable propagation of chiral handedness from the molecular to the material scale in living and active matter.
Hacker News

Hilbert's sixth problem: derivation of fluid equations via Boltzmann's theory

arxiv.org/abs/2503.01800

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arXiv.orgHilbert's sixth problem: derivation of fluid equations via Boltzmann's kinetic theoryIn this paper, we rigorously derive the fundamental PDEs of fluid mechanics, such as the compressible Euler and incompressible Navier-Stokes-Fourier equations, starting from the hard sphere particle systems undergoing elastic collisions. This resolves Hilbert's sixth problem, as it pertains to the program of deriving the fluid equations from Newton's laws by way of Boltzmann's kinetic theory. The proof relies on the derivation of Boltzmann's equation on 2D and 3D tori, which is an extension of our previous work (arXiv:2408.07818).
#HackerNews#sixth#problem
Pustam | पुस्तम | পুস্তম🇳🇵

Imagine being a brilliant physicist/mathematician and still avoiding the most important problems because your career depends on publishing frequent papers, not solving the biggest mysteries in the world.

That's why you can't do things like this in academia.

english.elpais.com/science-tec

#NavierStokes#GoogleDeepMind#DeepMind
Rxiv mechanobio

📰 "Patterning surface textured plates with a viscoplastic fluid"
arxiv.org/abs/2506.23746 #Physics.Flu-Dyn #Dynamics #Cell

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arXiv.orgPatterning surface textured plates with a viscoplastic fluidThe deposition of a viscoplastic fluid onto a substrate can be achieved by simply moving apart two plates initially separated by a fluid filled gap, where the footprint shape depends on the initiation of a fingering instability. Here, we present another approach for the controlled deposition of a viscoplastic fluid by designing the macroscopic structures of the solid substrate. Through experiments in a lifted Hele-Shaw cell, we explore how slot, square, pyramid, and triangle-shaped patterns affect the dynamics of liquid deposition. These substrate structures directly control the final shape of the viscoplastic fluid footprint. It turns out that these substrate patterns have little influence on the normal adhesive force acting on the plates.
Rxiv mechanobio

📰 "Stern-Gerlach deflection of cryogenically cold polyatomic molecules in superfluid nanodroplets"
arxiv.org/abs/2506.20785 #Cond-Mat.Quant-Gas #Cond-Mat.Mes-Hall #Physics.Atm-Clus #Physics.Chem-Ph #Dynamics #Matrix

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arXiv.orgStern-Gerlach deflection of cryogenically cold polyatomic molecules in superfluid nanodropletsBeam deflection is capable of providing valuable information about the magnetic moments of molecules and clusters as well as the relaxation dynamics of their spins. However, observations have been hampered by magnetic couplings to excited vibrational and rotational states of polyatomic systems, which are challenging to control, characterize, and systematize. In this work, we carried out deflection measurements on superfluid helium nanodroplets doped with high-spin FeCl2 and CoCl2 molecules and their complexes. This enabled quantitative determination of the magnetic moments of molecules and clusters at extremely low, and fully defined, temperature of all of their degrees of freedom. The spin magnetic moments become thermalized and oriented along the applied field. Dimers and trimers are found to be antiferromagnetically ordered. The issue of rates and mechanisms of molecular spin relaxation within the cryogenic helium matrix is highlighted.
Rxiv mechanobio

📰 "A Comprehensive Evaluation of the Bernoulli-Trial Collisions Families in Treating Rarefied Micro Flows and Hypersonic Flows"
arxiv.org/abs/2506.17256 #Physics.Comp-Ph #Physics.Flu-Dyn #Dynamics #Cell

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arXiv.orgA Comprehensive Evaluation of the Bernoulli-Trial Collisions Families in Treating Rarefied Micro Flows and Hypersonic FlowsThe collision process is essential to the Direct Simulation Monte Carlo (DSMC) method, as it incorporates the fundamental principles of the Boltzmann and Kac stochastic equations. A series of collision algorithms, known as the Bernoulli-trials (BT) family schemes, have been proposed based on the Kac stochastic equation. The impetus of this paper is to present a comprehensive evaluation of different BT-based collision partner selection schemes, including the simplified Bernoulli-trials (SBT), generalized Bernoulli-trials (GBT), symmetrized and simplified Bernoulli-trials (SSBT), and newly proposed symmetrized and generalized Bernoulli-trials (SGBT), in treating some standard rarefied gas dynamics problems. In these algorithms, the first particle is chosen in a specific order from the list of particles in the cell. For the SBT and GBT, the second particle is chosen from the remaining particles in the list placed after the first particle; however, for SSBT and SGBT, the second particle is chosen from all particles in the list. This means that the SBT and GBT select pairs from the upper triangle of the collision probability matrix, while symmetrized algorithms such as SSBT and SGBT utilize the entire matrix. The results show that the BT-based collision algorithms, compared to the standard "No Time Counter (NTC)" and "Nearest Neighbor (NN)", successfully maintain the collision frequency as the number of particles per cell decreases. Simulation of the Bobylev-Krook-Wu (BKW) exact solution of the Boltzmann equation indicates that, like the GBT, the SGBT algorithm produces the same results as the theory for the average of the 4th moment of the velocity distribution function (VDF).
Rxiv mechanobio

📰 "Observation of laser plasma accelerated electrons with transverse momentum spread below the thermal level"
arxiv.org/abs/2506.18047 #Physics.Plasm-Ph #Dynamics #Cell

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arXiv.orgObservation of laser plasma accelerated electrons with transverse momentum spread below the thermal levelAchieving high-quality electron beams from laser-plasma accelerators critically relies on density tailoring to control electron dynamics during injection, acceleration, and extraction. We report on the experimental observation of electron beam acceleration and 3D shaping, in transverse momentum and longitudinal phase space, controlled by plasma density tailoring in a gas cell. It leads to relativistic electron beams with a transverse momentum spread of 0.2 mec, below the thermal level imprinted by the process of ionization injection in a laser-driven wakefield accelerator. These beams have a charge of 40 pC at an energy of 190 MeV with 1.9% energy spread and an rms divergence of 0.54 mrad, resulting in single-peak spectra with a brightness of up to 8 pC/MeV/mrad. Using numerical simulations, we show that the decrease in transverse momentum spread starts in the downramp and continues in a 10 mm long plasma tail at the exit of the gas cell, where it is accompanied by energy dechirping.
Rxiv mechanobio

📰 "Plasmon Polaritons in Disordered Nanoparticle Assemblies"
arxiv.org/abs/2506.18138 #Cond-Mat.Mtrl-Sci #Cond-Mat.Mes-Hall #Cond-Mat.Dis-Nn #Physics.Optics #Dynamics #Matrix

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arXiv.orgPlasmon Polaritons in Disordered Nanoparticle AssembliesMultilayer assemblies of metal nanoparticles can act as photonic structures, where collective plasmon resonances hybridize with cavity modes to create plasmon-polariton states. For sufficiently strong coupling, plasmon polaritons qualitatively alter the optical properties of light-matter systems, with applications ranging from sensing to solar energy. However, results from experimental studies have raised questions about the role of nanoparticle structural disorder in plasmon-polariton formation and light-matter coupling in plasmonic assemblies. Understanding how disorder affects optical properties has practical implications since methods for assembling low-defect nanoparticle superlattices are slow and scale poorly. Modeling realistic disorder requires large system sizes, which is challenging using conventional electromagnetic simulations. We employ Brownian dynamics simulations to construct large-scale nanoparticle multilayers with controlled structural order. We investigate their optical response using a superposition T-matrix method with 2-D periodic boundary conditions. We find that while structural disorder broadens the polaritonic stop band and the near-field hot-spot distribution, the polariton dispersion and coupling strength remain unaltered. To understand effects of nanoparticle composition, we consider assemblies with model particles mimicking gold or tin-doped indium oxide (ITO) nanocrystals. Losses due to higher damping in ITO nanocrystals prevent their assemblies from achieving the deep strong coupling of gold nanoparticle multilayers, although the former still exhibit ultrastrong coupling. We demonstrate that while computationally efficient mutual polarization method calculations employing the quasistatic approximation modestly overestimate the strength of the collective plasmon, they reproduce the polariton dispersion relations determined by electrodynamic simulations.
Rxiv mechanobio

📰 "The role of dendritic spines in water exchange measurements with diffusion MRI: Time-Dependent Single Diffusion Encoding MRI"
arxiv.org/abs/2506.18229 #Physics.Med-Ph #Physics.Bio-Ph #Extracellular #Dynamics

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arXiv.orgThe role of dendritic spines in water exchange measurements with diffusion MRI: Time-Dependent Single Diffusion Encoding MRITime-dependent diffusion MRI (dMRI) with single diffusion encoding (SDE) probes water dynamics in biological tissues, but signal interpretation depends on microstructure. While prior work focused on restricted/hindered diffusion and membrane permeation, diffusion-mediated exchange between dendritic shafts and spines in gray matter (GM) remains understudied. We hypothesize that impermeable spiny dendrites produce time-dependent SDE signals mimicking permeative exchange and investigate how spine density biases exchange time estimates. Using Monte Carlo simulations and narrow escape theory, we quantify spine-shaft exchange times (3-26 ms), matching cortical permeative exchange estimates. A modified two-compartment Karger model characterizes time-dependent SDE signals but yields biased exchange estimates, reflecting spine volume fraction rather than morphology. Unaccounted diffusion-mediated exchange introduces up to 80% bias in NEXI/SMEX model estimates. We propose an extended three-compartment Karger model incorporating both diffusion-mediated (spine-shaft) and permeative (intra-extracellular) exchange. However, this model cannot uniquely separate membrane permeability from spine volume effects. Our findings emphasize that dendritic spines should be considered in SDE-based exchange studies and caution against attributing exchange solely to permeability. Advanced methods are needed to disentangle these mechanisms in GM.
Rxiv mechanobio

📰 "Simulating ultrarelativistic beam-plasma instabilities with a quasistatic particle-in-cell code"
arxiv.org/abs/2506.18567 #Physics.Plasm-Ph #Dynamics #Cell

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arXiv.orgSimulating ultrarelativistic beam-plasma instabilities with a quasistatic particle-in-cell codeQuasistatic particle-in-cell (PIC) codes are increasingly employed to study laser or plasma wakefield accelerators. By decoupling the slow dynamics of the driver (a laser or ultrarelativistic particle beam) from the fast plasma response, these codes can reduce the computational time by several orders of magnitude compared to conventional PIC codes. In this work, we demonstrate that quasistatic PIC codes can also be utilized to investigate relativistic beam-plasma instabilities, with a focus on the oblique two-stream instability (OTSI). For this purpose, we have developed a 2D quasistatic PIC code, QuaSSis, based on a new numerical scheme that can handle transversely periodic boundary conditions, a capability absent in previous quasistatic codes. The accuracy of QuaSSis is benchmarked first against standard PIC simulations performed with the CALDER code, and then against an analytical spatiotemporal model of the OTSI. Physically, this instability grows exponentially from initial fluctuations in the particle charge or current densities. Since the numerical noise inherent to PIC simulations can mimic these fluctuations to some extent, its control is crucial to seed the beam-plasma instability at the desired amplitude. Common methods for tuning this noise involve modifying the resolution or adding filters, but these can be computationally costly when aiming at very low noise levels. Here, we show that this noise can be finely controlled by properly initializing the positions and weights of the macroparticles.
Rxiv mechanobio

📰 "Static Three-Dimensional Structures Determine Fast Dynamics Between Distal Loci Pairs in Interphase Chromosomes"
arxiv.org/abs/2501.10004 #Physics.Bio-Ph #Dynamics #Q-Bio.Gn #Q-Bio.Bm #Cell

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arXiv.orgStatic Three-Dimensional Structures Determine Fast Dynamics Between Distal Loci Pairs in Interphase ChromosomesLive-cell imaging experiments have shown that the distal dynamics between enhancers and promoters are unexpectedly rapid and incompatible with standard polymer models. The discordance between the compact static chromatin organization and dynamics is a conundrum that violates the expected structure-function relationship. We developed a theory to predict chromatin dynamics by accurately determining three-dimensional (3D) structures from static Hi-C contact maps or fixed-cell imaging data. Using the calculated 3D coordinates, the theory accurately forecasts experimentally observed two-point chromatin dynamics. It predicts rapid enhancer-promoter interactions and uncovers a scaling relationship between two-point relaxation time and genomic separation, closely matching recent measurements. The theory predicts that cohesin depletion accelerates single-locus diffusion while significantly slowing relaxation dynamics within topologically associating domains (TADs). Our results demonstrate that chromatin dynamics can be reliably inferred from static structural data, reinforcing the notion that 3D chromatin structure governs dynamic behavior. This general framework offers powerful tools for exploring chromatin dynamics across diverse biological contexts.
Rxiv mechanobio

📰 "Contactless Precision Steering of Particles in a Fluid inside a Cube with Rotating Walls"
arxiv.org/abs/2506.15958 #Physics.Flu-Dyn #Dynamics #Cs.Ro #Cs.Lg #Cell

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arXiv.orgContactless Precision Steering of Particles in a Fluid inside a Cube with Rotating WallsContactless manipulation of small objects is essential for biomedical and chemical applications, such as cell analysis, assisted fertilisation, and precision chemistry. Established methods, including optical, acoustic, and magnetic tweezers, are now complemented by flow control techniques that use flow-induced motion to enable precise and versatile manipulation. However, trapping multiple particles in fluid remains a challenge. This study introduces a novel control algorithm capable of steering multiple particles in flow. The system uses rotating disks to generate flow fields that transport particles to precise locations. Disk rotations are governed by a feedback control policy based on the Optimising a Discrete Loss (ODIL) framework, which combines fluid dynamics equations with path objectives into a single loss function. Our experiments, conducted in both simulations and with the physical device, demonstrate the capability of the approach to transport two beads simultaneously to predefined locations, advancing robust contactless particle manipulation for biomedical applications.
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