skip to main content
US FlagAn official website of the United States government
dot gov icon
Official websites use .gov
A .gov website belongs to an official government organization in the United States.
https lock icon
Secure .gov websites use HTTPS
A lock ( lock ) or https:// means you've safely connected to the .gov website. Share sensitive information only on official, secure websites.

Explore Research Products in the PAR
It may take a few hours for recently added research products to appear in PAR search results.


This content will become publicly available on July 26, 2026

Title: Stressful Tree Modeling: Breaking Branches with Strands
We propose a novel approach for the computational modeling of lignified tissues, such as those found in tree branches and timber. We leverage a stateof the-art strand-based representation for tree form, which we extend to describe biophysical processes at short and long time scales. Simulations at short time scales enable us to model different breaking patterns due to branch bending, twisting, and breaking. On long timescales, our method enables the simulation of realistic branch shapes under the influence of plausible biophysical processes, such as the development of compression and tension wood. We specifically focus on computationally fast simulations of woody material, enabling the interactive exploration of branches and wood breaking. By leveraging Cosserat rod physics, our method enables the generation of a wide variety of breaking patterns. We showcase the capabilities of our method by performing and visualizing numerous experiments.  more » « less
Award ID(s):
2412928
PAR ID:
10620548
Author(s) / Creator(s):
; ; ; ; ;
Publisher / Repository:
ACM
Date Published:
ISBN:
9798400715402
Page Range / eLocation ID:
1 to 11
Format(s):
Medium: X
Location:
Vancouver BC Canada
Sponsoring Org:
National Science Foundation
More Like this
  1. ; (, Journal of The Royal Society Interface)
    x (Ed.)
    Natural biological branching processes can form tree-like structures at all scales and, moreover, can perform various functions to achieve specific goals; these include receiving stimuli, performing two-way communication along their branches, and dynamically reforming (extending or retracting branches). They underlie many biological systems with considerable diversity, frequency, and geometric complexity; these include networks of neurons, organ tissue, mycorrhizal fungal networks, plant growth, foraging networks, etc. This paper presents a biomimetic DNA tile assembly model (Y-STAM) to implement dynamic branching processes. The Y-STAM is a relatively compact mathematical model providing a design space where complex, biomimetic branch-like growth and behaviour can emerge from the appropriate parametrization of the model. We also introduce a class of augmented models (Y-STAM+) that provide time- and space-dependent modulations of tile glue strengths, which enable further diverse behaviours that are not possible in the Y-STAM; these additional behaviours include refinement of network assemblies, obstacle avoidance, and programmable growth patterns. We perform and discuss extensive simulations of the Y-STAM and the Y-STAM+. We envision that these models could be applied at the mesoscale and the molecular scale to dynamically assemble branching DNA nanostructures and offer insights into complex biological self-assembly processes. 
    more » « less
  2. ; ; ; (, IEEE International Conference on Robotics and Automation)
    This paper proposes an optimization-based task and motion planning framework, named “Logic Network Flow”, to integrate signal temporal logic (STL) specifications into efficient mixed-binary linear programmings. In this framework, temporal predicates are encoded as polyhedron constraints on each edge of the network flow, instead of as constraints between the nodes as in the traditional Logic Tree formulation. Synthesized with Dynamic Network Flows, Logic Network Flows render a tighter convex relaxation compared to Logic Trees derived from these STL specifications. Our formulation is evaluated on several multi-robot motion planning case studies. Empirical results demonstrate that our formulation outperforms Logic Tree formulation in terms of computation time for several planning problems. As the problem size scales up, our method still discovers better lower and upper bounds by exploring fewer number of nodes during the branch-andbound process, although this comes at the cost of increased computational load for each node when exploring branches. 
    more » « less
  3. ; (, Bioinformatics)
    Abstract MotivationPhylogenomics faces a dilemma: on the one hand, most accurate species and gene tree estimation methods are those that co-estimate them; on the other hand, these co-estimation methods do not scale to moderately large numbers of species. The summary-based methods, which first infer gene trees independently and then combine them, are much more scalable but are prone to gene tree estimation error, which is inevitable when inferring trees from limited-length data. Gene tree estimation error is not just random noise and can create biases such as long-branch attraction. ResultsWe introduce a scalable likelihood-based approach to co-estimation under the multi-species coalescent model. The method, called quartet co-estimation (QuCo), takes as input independently inferred distributions over gene trees and computes the most likely species tree topology and internal branch length for each quartet, marginalizing over gene tree topologies and ignoring branch lengths by making several simplifying assumptions. It then updates the gene tree posterior probabilities based on the species tree. The focus on gene tree topologies and the heuristic division to quartets enables fast likelihood calculations. We benchmark our method with extensive simulations for quartet trees in zones known to produce biased species trees and further with larger trees. We also run QuCo on a biological dataset of bees. Our results show better accuracy than the summary-based approach ASTRAL run on estimated gene trees. Availability and implementationQuCo is available on https://github.com/maryamrabiee/quco. Supplementary informationSupplementary data are available at Bioinformatics online. 
    more » « less
  4. ; ; (, New Phytologist)
    Summary Wood formation is the Rosetta stone of tree physiology: a traceable, integrated record of physiological and morphological status. It also produces a large and persistent annual sink for terrestrial carbon, motivating predictive understanding. Xylogenesis studies have greatly expanded our knowledge of the intra‐annual controls on wood formation, while dendroecology has quantified the environmental drivers of multi‐annual variability. But these fields operate on different timescales, making it challenging to predict how short (e.g. turgor) and long timescale processes (e.g. disturbance) interactively influence wood formation. Toward this challenge, wood growth responses to natural climate events provide useful but incomplete explanations of tree growth variability. By contrast, direct manipulations of the tree vascular system have yielded unexpected insights, particularly outside of model species like boreal conifers, but they remain underutilized. To improve prediction of global wood formation, we argue for a new generation of experimental manipulations of wood growth across seasons, species, and ecosystems. Such manipulations should expand inference to diverse forests and capture inter‐ and intra‐specific differences in wood growth. We summarize the endogenous and exogenous factors influencing wood formation to guide future experimental design and hypotheses. We highlight key opportunities for manipulative studies integrating measurements from xylogenesis, dendroanatomy, dendroecology, and ecophysiology. 
    more » « less
  5. ; ; ; ; ; ; (, AIP Advances)
    The effects of various branches geometry and dimensions such as length, thickness, and width for H-, U-, O-, YH- and YU-shaped alnico structures on coercivity (Hci) using micromagnetic simulation for coherent rotation and curling modes are investigated. The simulation results suggest that the H-shaped structure needs long and short branch length for the coherent rotation and curling, respectively, regardless of branch thickness and width to realize high Hci. Short branch length with thin thickness and short width are recommended for both rotations for the U- and O-shaped structures. Lastly, both Y-shaped structures need branch with long length, thin thickness, and mid-long width for the coherent rotation, but short width for the YH-shaped and mid-long width for the YU-shaped regardless of length and thickness for curling are desired. Furthermore, among the five studied structures, H- or YH-shaped structure for coherent rotation and O-shaped structure for curling are highly recommended for fabrication to realize a high Hci. 
    more » « less
  • Citation Formats
  • MLA
  • APA
  • Chicago
  • BibTeX
  • Save / Share this Record
  • Send to Email