An official website of the United States government
Abstract Filamentous bundles are ubiquitous in Nature, achieving highly adaptive functions and structural integrity from assembly of diverse mesoscale supramolecular elements. Engineering routes to synthetic, topologically integrated analogs demands precisely coordinated control of multiple filaments’ shapes and positions, a major challenge when performed without complex machinery or labor-intensive processing. Here, we demonstrate a photocreasing design that encodes local curvature and twist into mesoscale polymer filaments, enabling their programmed transformation into target 3-dimensional geometries. Importantly, patterned photocreasing of filament arrays drives autonomous spinning to form linked filament bundles that are highly entangled and structurally robust. In individual filaments, photocreases unlock paths to arbitrary, 3-dimensional curves in space. Collectively, photocrease-mediated bundling establishes a transformative paradigm enabling smart, self-assembled mesostructures that mimic performance-differentiating structures in Nature (e.g., tendon and muscle fiber) and the macro-engineered world (e.g., rope).
more »
« less
Spaghetti Tracer: A Framework for Tracing Semiregular Filamentous Densities in 3D Tomograms
Within cells, cytoskeletal filaments are often arranged into loosely aligned bundles. These fibrous bundles are dense enough to exhibit a certain regularity and mean direction, however, their packing is not sufficient to impose a symmetry between—or specific shape on—individual filaments. This intermediate regularity is computationally difficult to handle because individual filaments have a certain directional freedom, however, the filament densities are not well segmented from each other (especially in the presence of noise, such as in cryo-electron tomography). In this paper, we develop a dynamic programming-based framework, Spaghetti Tracer, to characterizing the structural arrangement of filaments in the challenging 3D maps of subcellular components. Assuming that the tomogram can be rotated such that the filaments are oriented in a mean direction, the proposed framework first identifies local seed points for candidate filament segments, which are then grown from the seeds using a dynamic programming algorithm. We validate various algorithmic variations of our framework on simulated tomograms that closely mimic the noise and appearance of experimental maps. As we know the ground truth in the simulated tomograms, the statistical analysis consisting of precision, recall, and F1 scores allows us to optimize the performance of this new approach. We find that a bipyramidal accumulation scheme for path density is superior to straight-line accumulation. In addition, the multiplication of forward and backward path densities provides for an efficient filter that lifts the filament density above the noise level. Resulting from our tests is a robust method that can be expected to perform well (F1 scores 0.86–0.95) under experimental noise conditions.
more »
« less
- Award ID(s):
- 2136095
- PAR ID:
- 10393685
- Date Published:
- Journal Name:
- Biomolecules
- Volume:
- 12
- Issue:
- 8
- ISSN:
- 2218-273X
- Page Range / eLocation ID:
- 1022
- Format(s):
- Medium: X
- Sponsoring Org:
- National Science Foundation
More Like this
-
-
Nonzero sum games typically have multiple Nash equilibriums (or no equilibrium), and unlike the zero-sum case, they may have different values at different equilibriums. Instead of focusing on the existence of individual equilibriums, we study the set of values over all equilibriums, which we call the set value of the game. The set value is unique by nature and always exists (with possible value [Formula: see text]). Similar to the standard value function in control literature, it enjoys many nice properties, such as regularity, stability, and more importantly, the dynamic programming principle. There are two main features in order to obtain the dynamic programming principle: (i) we must use closed-loop controls (instead of open-loop controls); and (ii) we must allow for path dependent controls, even if the problem is in a state-dependent (Markovian) setting. We shall consider both discrete and continuous time models with finite time horizon. For the latter, we will also provide a duality approach through certain standard PDE (or path-dependent PDE), which is quite efficient for numerically computing the set value of the game.more » « less
-
Merks, Roeland M.H. (Ed.)Cross-linked actin networks are the primary component of the cell cytoskeleton and have been the subject of numerous experimental and modeling studies. While these studies have demonstrated that the networks are viscoelastic materials, evolving from elastic solids on short timescales to viscous fluids on long ones, questions remain about the duration of each asymptotic regime, the role of the surrounding fluid, and the behavior of the networks on intermediate timescales. Here we perform detailed simulations of passively cross-linked non-Brownian actin networks to quantify the principal timescales involved in the elastoviscous behavior, study the role of nonlocal hydrodynamic interactions, and parameterize continuum models from discrete stochastic simulations. To do this, we extend our recent computational framework for semiflexible filament suspensions, which is based on nonlocal slender body theory, to actin networks with dynamic cross linkers and finite filament lifetime. We introduce a model where the cross linkers are elastic springs with sticky ends stochastically binding to and unbinding from the elastic filaments, which randomly turn over at a characteristic rate. We show that, depending on the parameters, the network evolves to a steady state morphology that is either an isotropic actin mesh or a mesh with embedded actin bundles. For different degrees of bundling, we numerically apply small-amplitude oscillatory shear deformation to extract three timescales from networks of hundreds of filaments and cross linkers. We analyze the dependence of these timescales, which range from the order of hundredths of a second to the actin turnover time of several seconds, on the dynamic nature of the links, solvent viscosity, and filament bending stiffness. We show that the network is mostly elastic on the short time scale, with the elasticity coming mainly from the cross links, and viscous on the long time scale, with the effective viscosity originating primarily from stretching and breaking of the cross links. We show that the influence of nonlocal hydrodynamic interactions depends on the network morphology: for homogeneous meshworks, nonlocal hydrodynamics gives only a small correction to the viscous behavior, but for bundled networks it both hinders the formation of bundles and significantly lowers the resistance to shear once bundles are formed. We use our results to construct three-timescale generalized Maxwell models of the networks.more » « less
-
Abstract We investigate the eruptive process of two filaments, which is associated with an M-class flare that occurred in 2011 August 4. The filaments are partly overlapped, one in the active region and the other just beside it, and erupt together as a halo coronal mass ejection. For this study, we used the Atmospheric Imaging Assembly and the Heliospheric Magnetic Imager on board the Solar Dynamics Observatory, the Nobeyama Radioheliograph 17 GHz, and the RHESSI Hard X-ray satellite. We found three distinct phases in the microwave flux profile and in the rising pattern of the filaments during the event. In the first phase, there was weak nonthermal emission at 17 GHz and hard X-rays. Those nonthermal sources appeared on one edge of the western filament (F2) in the active region. The F2 began to be bright and rose upward rapidly, while the eastern filament (F1), which was extended to the quiet region, started to brighten from the peak time of the 17 GHz flux. In the second phase, the nonthermal emission weakened and the F2 rose up slowly, while the F1 began to rise up. In the third phase, two filaments erupted together. Since the F1 was stable for a long time in the quiet region, breaking the equilibrium state of the F1 would be decisive for the successful eruption of two filaments and it seems clear that the evolution of the F2 provoked the unstable F1. We suggest that tether-cutting reconnection between two overlapped filaments triggers the eruption of the two filaments as a tangled identity.more » « less
-
ABSTRACT The interstellar medium is threaded by a hierarchy of filaments from large scales (∼100 pc) to small scales (∼0.1 pc). The masses and lengths of these nested structures may reveal important constraints for cloud formation and evolution, but it is difficult to investigate from an evolutionary perspective using single observations. In this work, we extract simulated molecular clouds from the ‘Cloud Factory’ galactic-scale ISM suite in combination with 3D Monte Carlo radiative transfer code polaris to investigate how filamentary structure evolves over time. We produce synthetic dust continuum observations in three regions with a series of snapshots and use the filfinder algorithm to identify filaments in the dust derived column density maps. When the synthetic filaments mass and length are plotted on an mass–length (M–L) plot, we see a scaling relation of L ∝ M0.45 similar to that seen in observations, and find that the filaments are thermally supercritical. Projection effects systematically affect the masses and lengths measured for the filaments, and are particularly severe in crowded regions. In the filament M–L diagram we identify three main evolutionary mechanisms: accretion, segmentation, and dispersal. In particular we find that the filaments typically evolve from smaller to larger masses in the observational M–L plane, indicating the dominant role of accretion in filament evolution. Moreover, we find a potential correlation between line mass and filament growth rate. Once filaments are actively star forming they then segment into smaller sections, or are dispersed by internal or external forces.more » « less
- Free Publicly Accessible Full Text
-
Accepted Manuscript1.0
- Journal Article:
- https://doi.org/10.3390/biom12081022
