skip to main content

Search for: All records

Creators/Authors contains: "Patino-Ramirez, Fernando"

Note: When clicking on a Digital Object Identifier (DOI) number, you will be taken to an external site maintained by the publisher. Some full text articles may not yet be available without a charge during the embargo (administrative interval).
What is a DOI Number?

Some links on this page may take you to non-federal websites. Their policies may differ from this site.

  1. Abstract

    Estimating soil properties from the mechanical reaction to a displacement is a common strategy, used not only in in situ soil characterization (e.g., pressuremeter and dilatometer tests) but also by biological organisms (e.g., roots, earthworms, razor clams), which sense stresses to explore the subsurface. Still, the absence of analytical solutions to predict the stress and deformation fields around cavities subject to geostatic stress, has prevented the development of characterization methods that resemble the strategies adopted by nature. We use the finite element method (FEM) to model the displacement-controlled expansion of cavities under a wide range of stress conditions and soil properties. The radial stress distribution at the cavity wall during expansion is extracted. Then, methods are proposed to prepare, transform and use such stress distributions to back-calculate the far field stresses and the mechanical parameters of the material around the cavity (Mohr-Coulomb friction angle$$\phi $$ϕ, Young’s modulusE). Results show that: (i) The initial stress distribution around the cavity can be fitted to a sum of cosines to estimate the far field stresses; (ii) By encoding the stress distribution as intensity images, in addition to certain scalar parameters, convolutional neural networks can consistently and accurately back-calculate the friction angle andmore »Young’s modulus of the soil.

    « less
  2. Abstract

    The acellular slime moldPhysarum polycephalumprovides an excellent model to study network formation, as its network is remodelled constantly in response to mass gain/loss and environmental conditions. How slime molds networks are built and fuse to allow for efficient exploration and adaptation to environmental conditions is still not fully understood. Here, we characterize the network organization of slime molds exploring homogeneous neutral, nutritive and adverse environments. We developed a fully automated image analysis method to extract the network topology and followed the slime molds before and after fusion. Our results show that: (1) slime molds build sparse networks with thin veins in a neutral environment and more compact networks with thicker veins in a nutritive or adverse environment; (2) slime molds construct long, efficient and resilient networks in neutral and adverse environments, whereas in nutritive environments, they build shorter and more centralized networks; and (3) slime molds fuse rapidly and establish multiple connections with their clone-mates in a neutral environment, whereas they display a late fusion with fewer connections in an adverse environment. Our study demonstrates that slime mold networks evolve continuously via pruning and reinforcement, adapting to different environmental conditions.

  3. Abstract State-of-the-Art models of Root System Architecture (RSA) do not allow simulating root growth around rigid obstacles. Yet, the presence of obstacles can be highly disruptive to the root system. We grew wheat seedlings in sealed petri dishes without obstacle and in custom 3D-printed rhizoboxes containing obstacles. Time-lapse photography was used to reconstruct the wheat root morphology network. We used the reconstructed wheat root network without obstacle to calibrate an RSA model implemented in the R-SWMS software. The root network with obstacles allowed calibrating the parameters of a new function that models the influence of rigid obstacles on wheat root growth. Experimental results show that the presence of a rigid obstacle does not affect the growth rate of the wheat root axes, but that it does influence the root trajectory after the main axis has passed the obstacle. The growth recovery time, i.e. the time for the main root axis to recover its geotropism-driven growth, is proportional to the time during which the main axis grows along the obstacle. Qualitative and quantitative comparisons between experimental and numerical results show that the proposed model successfully simulates wheat RSA growth around obstacles. Our results suggest that wheat roots follow patterns that couldmore »inspire the design of adaptive engineering flow networks.« less
  4. Abstract

    Cells, including unicellulars, are highly sensitive to external constraints from their environment. Amoeboid cells change their cell shape during locomotion and in response to external stimuli. Physarum polycephalum is a large multinucleated amoeboid cell that extends and develops pseudopods. In this paper, changes in cell behavior and shape were measured during the exploration of homogenous and non-homogenous environments that presented neutral, and nutritive and/or adverse substances. In the first place, we developed a fully automated image analysis method to measure quantitatively changes in both migration and shape. Then we measured various metrics that describe the area covered, the exploration dynamics, the migration rate and the slime mold shape. Our results show that: (1) Not only the nature, but also the spatial distribution of chemical substances affect the exploration behavior of slime molds; (2) Nutritive and adverse substances both slow down the exploration and prevent the formation of pseudopods; and (3) Slime mold placed in an adverse environment preferentially occupies previously explored areas rather than unexplored areas using mucus secretion as a buffer. Our results also show that slime molds migrate at a rate governed by the substrate up until they get within a critical distance to chemical substances.