Biology subjects

Ptashnyk, M.

Publications and source records attributed to Ptashnyk, M..

7 recordsLinked to original sources

bioRxiv2025

Modelling the influence of rhizodeposits on root water uptake

The chemical compounds produced by plant roots, referred to generally as rhizodeposits, affect several soil hydraulic properties. For example, the surface tension of soil water, and the contact angle between menisci and the pore surface. What remains less clear is how these effects manifest when considering soil water infiltration and retention, and the consequent impact on the availability of water for uptake by plant roots. By modifying the Richards equation, a novel model for soil water transport was developed which incorporates the influences of rhizodeposits. The finite-element method was used for simulations of model equations and calibration against experimental data was achieved through Bayesian optimisation. Numerical simulations from the calibrated model were used to investigate the effects of rhizodeposits on root water uptake under various precipitation regimes. It was found that the impact of rhizodeposits on the availability of water to the roots can be either positive or negative depending on precipitation regime and root system maturity. This, therefore, suggests that rhizodeposit characteristics require careful consideration when developing crops for improved water use efficiency and stress-resilience.

systems biology↗

bioRxiv2025

Root exudation facilitate water infiltration and rewetting of dry soil

The way plant roots facilitate water infiltration in soil may be just as important as the efficiency with which the root system in turn extracts it from the soil. Here we studied the mechanisms through which the root system facilitates water infiltration through a dry soil layer. Dye tracing experiments were conducted in model soil microcosms to characterise how root growth and exudation affects the permeability of dry layers of the model soil. Results showed that dissolved root exudates may be the primary facilitator of water infiltration, which may be linked to water surface tension. We conclude that in dry soil, root architecture and root exudation may combine to facilitate the infiltration of water and decrease the water lost by evaporation. These findings could enhance our understanding of the traits that provide drought resistance in crops.

plant biology↗

bioRxiv2023

Non-local model of chemotaxis based on peer attraction

Movement is critical for bacterial species inhabiting soils because nutrient availability is limited and heterogeneously distributed both in space and time. Recent live microscopy experiments show that bacteria form flocks when navigating through porous medium, and complex cell-cell interactions may be required to maintain such flocks. Here we propose a non-local model to study how peer attraction can affect flocking patterns in a porous medium. We establish the existence and uniqueness of the solution of the problem, propose a numerical scheme for simulations of the non-local convection-diffusion equation, and investigate the numerical convergence of the scheme. Numerical simulations showed that the strength of peer attraction is critical to control the size, shape, and nature of movement of the flocks in a porous network. MSC Classification35F31, 92Cxx, 92-10

cell biology↗

bioRxiv2022

Can root systems redistribute soil water to mitigate the effects of drought?

Plants adapt both morphologically and physiologically in response to drought. This work considers another potential mechanism of plant drought resistance. Namely, the capacity of root systems to modify the hydraulic properties of surrounding soil, and extend the post-precipitation lifetime of water in the rooted zone. In studies of plant drought resistance, the effect of root-oriented preferential soil water transport is seldom considered, despite experimental evidence that it occurs. We developed a model for water transport through soil that incorporates preferential flow induced by a root system. Bayesian optimisation was employed to calibrate the model against experimental data, and the finite element method was used to obtain model simulations for the influence of different root architectures on post-precipitation water lifetime. When increasing preferential flow strength, simulations indicated a trade-off between evaporation and deep percolation losses. It was also observed that the soil surrounding root systems with a reduced gravitropic response, retained the most water following precipitation. This work provides new insight into the role of root system traits in plant drought resistance, and identifies potential crop phenotypes for improved water use efficiency.

systems biology↗

bioRxiv2022

Cell-based model shows complex rearrangement of tissue mechanical properties are needed for roots to grow in hard soil

When exposed to increased mechanical resistance from the soil, plant roots display non-linear growth responses that can not be solely explained by mechanical principles. Here, we aim to investigate how changes in tissue mechanical properties are biologically regulated in response to soil strength. A particle-based model was developed to solve root-soil mechanical interactions at the cellular scale, and a detailed numerical study explored factors that affect root responses to soil resistance. Results showed that growth through increasing soil strength is maintained through the softening of cell walls at the tip, a response likely linked to soil cavity expansion. The model also predicts the shortening and decreased anisotropy of the zone of cell elongation, which may improve the mechanical stability of the root against axial forces. The study demonstrates the potential of advanced modeling tools to help identify traits that confer plant resistance to abiotic stress.

developmental biology↗

bioRxiv2021

Model predicts the impact of root system architecture on soil water infiltration.

There is strong experimental evidence that root systems substantially change the saturated hydraulic conductivity of soil. However, the mechanisms by which roots affect soil hydraulic properties remain largely unknown. In this work, we made the hypothesis that preferential soil moisture transport occurs along the axes of roots, and that this is what changes a soils saturated hydraulic conductivity. We modified Richards equation to incorporate the preferential flow of soil moisture along the axes of roots. Using the finite element method and Bayesian optimisation, we developed a pipeline to calibrate our model with respect to a given root system. When applied to simulated root systems, the pipeline successfully predicted the pore-water pressure profiles corresponding to saturated hydraulic conductivity values, observed by Leung et al. (2018), for soils vegetated with willow and grass. Prediction accuracy improved for root systems with more realistic architectures, therefore suggesting that changes in saturated hydraulic conductivity are a result of roots enabling preferential soil moisture transport along their axes. The model proposed in this work improves our ability to predict moisture transport through vegetated soil and could help optimise irrigation, forecast flood events and plan landslide prevention strategies.

systems biology↗

bioRxiv2019

A spatio-temporal mathematical model for the dynamics of paclitaxel in cell monolayers.

The authors have withdrawn their manuscript due to the discovery of fundamental issues with the implementation of the ODE/PDE model, whose output was shown in Figure 5 of the original version of this paper, rendering the results and conclusion unreliable. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding author.

cancer biology↗