Aquaporins (AQPs) are a family of transmembrane channels that are found from archaea, eubacteria, and fungi kingdoms to plants and animals. These proteins play a major role in water and small solutes transport across biological cell membranes and maintain the osmotic balance of living cells. In this sense, many works in recent years have been devoted to understanding their behavior, including in plants, where 5 major groups of AQPs have been identified, whose physiological function details still have open questions waiting for an answer. In this direction, we observed in the literature very few Molecular Modeling studies focusing on plant AQPs. It creates a gap in the proper depiction of AQPs since Molecular Simulations allow us to get information that is usually inaccessible by experiments. Likewise, many efforts have been made to create artificial nanochannels with improved properties. It has the potential to help humanity (and plants) to face water stress -- a current problem that will be worsened by Climate Change. In this short review, we will revisit and discuss important computational studies about plant aquaporins and artificial transmembrane channels. With this, we aim to
Plant classification is vital for ecological conservation and agricultural productivity, enhancing our understanding of plant growth dynamics and aiding species preservation. The advent of deep learning (DL) techniques has revolutionized this field by enabling autonomous feature extraction, significantly reducing the dependence on manual expertise. However, conventional DL models often rely solely on single data sources, failing to capture the full biological diversity of plant species comprehensively. Recent research has turned to multimodal learning to overcome this limitation by integrating multiple data types, which enriches the representation of plant characteristics. This shift introduces the challenge of determining the optimal point for modality fusion. In this paper, we introduce a pioneering multimodal DL-based approach for plant classification with automatic modality fusion. Utilizing the multimodal fusion architecture search, our method integrates images from multiple plant organs -- flowers, leaves, fruits, and stems -- into a cohesive model. To address the lack of multimodal datasets, we contributed Multimodal-PlantCLEF, a restructured version of the PlantCLEF2015 dat
This paper presents the Sesame Plant Segmentation Dataset, an open source annotated image dataset designed to support the development of artificial intelligence models for agricultural applications, with a specific focus on sesame plants. The dataset comprises 206 training images, 43 validation images, and 43 test images in YOLO compatible segmentation format, capturing sesame plants at early growth stages under varying environmental conditions. Data were collected using a high resolution mobile camera from farms in Jirdede, Daura Local Government Area, Katsina State, Nigeria, and annotated using the Segment Anything Model version 2 with farmer supervision. Unlike conventional bounding box datasets, this dataset employs pixel level segmentation to enable more precise detection and analysis of sesame plants in real world farm settings. Model evaluation using the Ultralytics YOLOv8 framework demonstrated strong performance for both detection and segmentation tasks. For bounding box detection, the model achieved a recall of 79 percent, precision of 79 percent, mean average precision at IoU 0.50 of 84 percent, and mean average precision from 0.50 to 0.95 of 58 percent. For segmentation
AI-assisted molecular property prediction has become a promising technique in early-stage drug discovery and materials design in recent years. However, due to high-cost and complex wet-lab experiments, real-world molecules usually experience the issue of scarce annotations, leading to limited labeled data for effective supervised AI model learning. In light of this, few-shot molecular property prediction (FSMPP) has emerged as an expressive paradigm that enables learning from only a few labeled examples. Despite rapidly growing attention, existing FSMPP studies remain fragmented, without a coherent framework to capture methodological advances and domain-specific challenges. In this work, we present the first comprehensive and systematic survey of few-shot molecular property prediction. We begin by analyzing the few-shot phenomenon in molecular datasets and highlighting two core challenges: (1) cross-property generalization under distribution shifts, where each task corresponding to each property, may follow a different data distribution or even be inherently weakly related to others from a biochemical perspective, requiring the model to transfer knowledge across heterogeneous predi
Rapid environmental change and advances in data-driven analysis highlight the need not only to use computational tools, but also to foster understanding of the natural world and inspire creativity. Photosynthesis, the process that fuels nearly all life on Earth, provides a compelling context for such learning, particularly in understanding how plants alter their photosynthetic strategies in response to environmental changes. However, existing tools for studying photosynthesis are often inaccessible or limited to demonstrating its presence, rather than capturing its temporal dynamics. We present PhytoBits, a frugal in situ gas-exchange sensing toolkit for distinguishing and teaching photosynthetic strategies. PhytoBits combines leaf enclosure with accessible materials, an off-the-shelf CO2 sensor, and a low-cost microcontroller, to support multi-day monitoring of plant gas-exchange in educational and research contexts. We validated PhytoBits against research-grade gas-exchange systems, confirming that it identifies C3 and CAM (Crassulacean Acid Metabolism) photosynthetic pathways. In addition to obligate CAM, PhytoBits also resolves facultative CAM and developmental CAM dynamics in
In plant-pollinator communities many pollinators are potential generalists and their preferences for certain plants can change quickly in response to changes in plant and pollinator densities. These changes in preferences affect coexistence within pollinator guilds as well as within plant guilds. Using a mathematical model, we study how adaptations of pollinator preferences influence population dynamics of a two-plant-two-pollinator community interaction module. Adaptation leads to coexistence between generalist and specialist pollinators, and produces complex plant population dynamics, involving alternative stable states and discrete transitions in the plant community. Pollinator adaptation also leads to plant-plant apparent facilitation that is mediated by changes in pollinator preferences. We show that adaptive pollinator behavior reduces niche overlap and leads to coexistence by specialization on different plants. Thus, this article documents how adaptive pollinator preferences for plants change the structure and coexistence of plant-pollinator communities.
Reliable and automated 3D plant shoot segmentation is a core prerequisite for the extraction of plant phenotypic traits at the organ level. Combining deep learning and point clouds can provide effective ways to address the challenge. However, fully supervised deep learning methods require datasets to be point-wise annotated, which is extremely expensive and time-consuming. In our work, we proposed a novel weakly supervised framework, Eff-3DPSeg, for 3D plant shoot segmentation. First, high-resolution point clouds of soybean were reconstructed using a low-cost photogrammetry system, and the Meshlab-based Plant Annotator was developed for plant point cloud annotation. Second, a weakly-supervised deep learning method was proposed for plant organ segmentation. The method contained: (1) Pretraining a self-supervised network using Viewpoint Bottleneck loss to learn meaningful intrinsic structure representation from the raw point clouds; (2) Fine-tuning the pre-trained model with about only 0.5% points being annotated to implement plant organ segmentation. After, three phenotypic traits (stem diameter, leaf width, and leaf length) were extracted. To test the generality of the proposed met
We introduce MOSCITO (MOlecular Dynamics Subspace Clustering with Temporal Observance), a subspace clustering for molecular dynamics data. MOSCITO groups those timesteps of a molecular dynamics trajectory together into clusters in which the molecule has similar conformations. In contrast to state-of-the-art methods, MOSCITO takes advantage of sequential relationships found in time series data. Unlike existing work, MOSCITO does not need a two-step procedure with tedious post-processing, but directly models essential properties of the data. Interpreting clusters as Markov states allows us to evaluate the clustering performance based on the resulting Markov state models. In experiments on 60 trajectories and 4 different proteins, we show that the performance of MOSCITO achieves state-of-the-art performance in a novel single-step method. Moreover, by modeling temporal aspects, MOSCITO obtains better segmentation of trajectories, especially for small numbers of clusters.
We evaluate different Neural Radiance Fields (NeRFs) techniques for the 3D reconstruction of plants in varied environments, from indoor settings to outdoor fields. Traditional methods usually fail to capture the complex geometric details of plants, which is crucial for phenotyping and breeding studies. We evaluate the reconstruction fidelity of NeRFs in three scenarios with increasing complexity and compare the results with the point cloud obtained using LiDAR as ground truth. In the most realistic field scenario, the NeRF models achieve a 74.6% F1 score after 30 minutes of training on the GPU, highlighting the efficacy of NeRFs for 3D reconstruction in challenging environments. Additionally, we propose an early stopping technique for NeRF training that almost halves the training time while achieving only a reduction of 7.4% in the average F1 score. This optimization process significantly enhances the speed and efficiency of 3D reconstruction using NeRFs. Our findings demonstrate the potential of NeRFs in detailed and realistic 3D plant reconstruction and suggest practical approaches for enhancing the speed and efficiency of NeRFs in the 3D reconstruction process.
In this paper we show how inter-cellular molecular communication may change the overall levels of photosynthesis in plants. Individual plant cells respond to external stimuli, such as illumination levels, to regulate their photosynthetic output. Here, we present a mathematical model which shows that by sharing information internally using molecular communication, plants may increase overall photosynthate production. Numerical results show that higher mutual information between cells corresponds to an increase in overall photosynthesis by as much as 25 per cent. This suggests that molecular communication plays a vital role in maximising the photosynthesis in plants and therefore suggests new routes to influence plant development in agriculture and elsewhere.
Compared with classical process-based models, the functional-structural plant models provide more efficient tools to explore the impact of changes in plant structures on plant functioning. In this paper we investigated the effects of branches on the sourcesink interaction for the cotton plant (Gossypium hirsutum L.) based on a two-treatment experiment conducted on cotton grown in the field: the singlestem plants and the plants with only two vegetative branches. It was observed that the branched cotton had more organs for the whole plant but the organs on the trunk were smaller than those on the single-stem cotton. The phytomer production of the branches was four or five growth cycles delayed compared with the main stem. The organs on the trunk had similar dynamics of expansion for both treatments. Effects of branches were evaluated by using the functionalstructural model GREENLAB. It allowed estimating the coefficients of sink strength to differentiate the biomass acquisition abilities of organs between different physiological ages. We found that the presence of the two vegetative branches increased the ground projection area of plant leaves and had led to slight changes on the dir
Precision agriculture leverages data and machine learning so that farmers can monitor their crops and target interventions precisely. This enables the precision application of herbicide only to weeds, or the precision application of fertilizer only to undernourished crops, rather than to the entire field. The approach promises to maximize yields while minimizing resource use and harm to the surrounding environment. To this end, we propose a hierarchical panoptic segmentation method that simultaneously determines leaf count (as an identifier of plant growth)and locates weeds within an image. In particular, our approach aims to improve the segmentation of smaller instances like the leaves and weeds by incorporating focal loss and boundary loss. Not only does this result in competitive performance, achieving a PQ+ of 81.89 on the standard training set, but we also demonstrate we can improve leaf-counting accuracy with our method. The code is available at https://github.com/madeleinedarbyshire/HierarchicalMask2Former.
The function of the organism hinges on the performance of its information-processing networks, which convey information via molecular recognition. Many paths within these networks utilize molecular codebooks, such as the genetic code, to translate information written in one class of molecules into another molecular "language" . The present paper examines the emergence and evolution of molecular codes in terms of rate-distortion theory and reviews recent results of this approach. We discuss how the biological problem of maximizing the fitness of an organism by optimizing its molecular coding machinery is equivalent to the communication engineering problem of designing an optimal information channel. The fitness of a molecular code takes into account the interplay between the quality of the channel and the cost of resources which the organism needs to invest in its construction and maintenance. We analyze the dynamics of a population of organisms that compete according to the fitness of their codes. The model suggests a generic mechanism for the emergence of molecular codes as a phase transition in an information channel. This mechanism is put into biological context and demonstrated
Planning an optimal route in a complex environment requires efficient reasoning about the surrounding scene. While human drivers prioritize important objects and ignore details not relevant to the decision, learning-based planners typically extract features from dense, high-dimensional grid representations containing all vehicle and road context information. In this paper, we propose PlanT, a novel approach for planning in the context of self-driving that uses a standard transformer architecture. PlanT is based on imitation learning with a compact object-level input representation. On the Longest6 benchmark for CARLA, PlanT outperforms all prior methods (matching the driving score of the expert) while being 5.3x faster than equivalent pixel-based planning baselines during inference. Combining PlanT with an off-the-shelf perception module provides a sensor-based driving system that is more than 10 points better in terms of driving score than the existing state of the art. Furthermore, we propose an evaluation protocol to quantify the ability of planners to identify relevant objects, providing insights regarding their decision-making. Our results indicate that PlanT can focus on the
Numerical plant models can predict the outcome of plant traits modifications resulting from genetic variations, on plant performance, by simulating physiological processes and their interaction with the environment. Optimization methods complement those models to design ideotypes, i.e. ideal values of a set of plant traits resulting in optimal adaptation for given combinations of environment and management, mainly through the maximization of a performance criteria (e.g. yield, light interception). As use of simulation models gains momentum in plant breeding, numerical experiments must be carefully engineered to provide accurate and attainable results, rooting them in biological reality. Here, we propose a multi-objective optimization formulation that includes a metric of performance, returned by the numerical model, and a metric of feasibility, accounting for correlations between traits based on field observations. We applied this approach to two contrasting models: a process-based crop model of sunflower and a functional-structural plant model of apple trees. In both cases, the method successfully characterized key plant traits and identified a continuum of optimal solutions, rang
Supervised learning is often used to count objects in images, but for counting small, densely located objects, the required image annotations are burdensome to collect. Counting plant organs for image-based plant phenotyping falls within this category. Object counting in plant images is further challenged by having plant image datasets with significant domain shift due to different experimental conditions, e.g. applying an annotated dataset of indoor plant images for use on outdoor images, or on a different plant species. In this paper, we propose a domain-adversarial learning approach for domain adaptation of density map estimation for the purposes of object counting. The approach does not assume perfectly aligned distributions between the source and target datasets, which makes it more broadly applicable within general object counting and plant organ counting tasks. Evaluation on two diverse object counting tasks (wheat spikelets, leaves) demonstrates consistent performance on the target datasets across different classes of domain shift: from indoor-to-outdoor images and from species-to-species adaptation.
Existing molecular communication systems, both theoretical and experimental, are characterized by low information rates. In this paper, inspired by time-of-flight mass spectrometry (TOFMS), we consider the design of a molecular communication system in which the channel is a vacuum and demonstrate that this method has the potential to increase achievable information rates by many orders of magnitude. We use modelling results from TOFMS to obtain arrival time distributions for accelerated ions and use them to analyze several species of ions, including hydrogen, nitrogen, argon, and benzene. We show that the achievable information rates can be increased using a velocity (Wien) filter, which reduces uncertainty in the velocity of the ions. Using a simplified communication model, we show that data rates well above 1 Gbit/s/molecule are achievable.
Segmentation of structural parts of 3D models of plants is an important step for plant phenotyping, especially for monitoring architectural and morphological traits. Current state-of-the art approaches rely on hand-crafted 3D local features for modeling geometric variations in plant structures. While recent advancements in deep learning on point clouds have the potential of extracting relevant local and global characteristics, the scarcity of labeled 3D plant data impedes the exploration of this potential. We adapted six recent point-based deep learning architectures (PointNet, PointNet++, DGCNN, PointCNN, ShellNet, RIConv) for segmentation of structural parts of rosebush models. We generated 3D synthetic rosebush models to provide adequate amount of labeled data for modification and pre-training of these architectures. To evaluate their performance on real rosebush plants, we used the ROSE-X data set of fully annotated point cloud models. We provided experiments with and without the incorporation of synthetic data to demonstrate the potential of point-based deep learning techniques even with limited labeled data of real plants. The experimental results show that PointNet++ produce
Molecular recognition, which is essential in processing information in biological systems, takes place in a crowded noisy biochemical environment and requires the recognition of a specific target within a background of various similar competing molecules. We consider molecular recognition as a transmission of information via a noisy channel and use this analogy to gain insights on the optimal, or fittest, molecular recognizer. We focus on the optimal structural properties of the molecules such as flexibility and conformation. We show that conformational changes upon binding, which often occur during molecular recognition, may optimize the detection performance of the recognizer. We thus suggest a generic design principle termed 'conformational proofreading' in which deformation enhances detection. We evaluate the optimal flexibility of the molecular recognizer, which is analogous to the stochasticity in a decision unit. In some scenarios, a flexible recognizer, i.e., a stochastic decision unit, performs better than a rigid, deterministic one. As a biological example, we discuss conformational changes during homologous recombination, the process of genetic exchange between two DNA s
Plant or soil water status are required in many scientific fields to understand plant responses to drought. Because the transcriptomic response to abiotic conditions, such as water deficit, reflects plant water status, genomic tools could be used to develop a new type of molecular biomarker. Using the sunflower (Helianthus annuus L.) as a model species to study the transcriptomic response to water deficit both in greenhouse and field conditions, we specifically identified three genes that showed an expression pattern highly correlated to plant water status as estimated by the pre-dawn leaf water potential, fraction of transpirable soil water, soil water content or fraction of total soil water in controlled conditions. We developed a generalized linear model to estimate these classical water status indicators from the expression levels of the three selected genes under controlled conditions. This estimation was independent of the four tested genotypes and the stage (pre- or post-flowering) of the plant. We further validated this gene expression biomarker under field conditions for four genotypes in three different trials, over a large range of water status, and we were able to corre