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Reactive settling denotes the process of sedimentation of small solid particles dispersed in a viscous fluid with simultaneous reactions between the components that constitute the solid and liquid phases. This process is of particular…

Numerical Analysis · Mathematics 2021-05-25 Raimund Bürger , Julio Careaga , Stefan Diehl

To understand the system-wide organization of metabolism, different lines of study have devised different categorizations of metabolites. The relationship and difference between categories can provide new insights for a more detailed…

Molecular Networks · Quantitative Biology 2009-07-24 Jing Zhao , Petter Holme

Assembly theory predicts that a distinguishing signature of life is its ability to produce complex molecules in abundance, opening new possibilities for life detection. Experimental validation of this approach has so far relied on abiotic…

Biological Physics · Physics 2025-09-08 Alexandre Champagne-Ruel , Christopher P. Kempes , Cole Mathis

Phylogenetic networks are becoming of increasing interest to evolutionary biologists due to their ability to capture complex non-treelike evolutionary processes. From a combinatorial point of view, such networks are certain types of rooted…

Combinatorics · Mathematics 2019-10-21 Katharina T. Huber , Guillaume E. Scholz

Water flow in plant tissues takes place in two different physical domains separated by semipermeable membranes: cell insides and cell walls. The assembly of all cell insides and cell walls are termed symplast and apoplast, respectively.…

Analysis of PDEs · Mathematics 2013-05-28 Andrés Chavarría-Krauser , Mariya Ptashnyk

To fulfill their killing functions, cytotoxic T lymphocytes (CTLs) need to migrate to search for their target cells in complex biological microenvironments, a key component of which is extracellular matrix (ECM). The mechanisms underlying…

Biological Physics · Physics 2020-12-30 Z. Sadjadi , R. Zhao , M. Hoth , B. Qu , H. Rieger

Metabolites, small molecules that are involved in cellular reactions, provide a direct functional signature of cellular state. Untargeted metabolomics experiments usually relies on tandem mass spectrometry to identify the thousands of…

Quantitative Methods · Quantitative Biology 2015-01-29 Kai Dührkop , Sebastian Böcker

In this paper we will consider a mathematical model that describes, the tritrophic interaction between plants, herbivores and their natural enemies, where volatiles organic compounds (VOCs) released by plants play an important role. We show…

Dynamical Systems · Mathematics 2020-11-20 Arturo J. Nic May , Eric J. Avila Vales

Myxococcus xanthus cells self-organize into aligned groups, clusters, at various stages of their lifecycle. Formation of these clusters is crucial for the complex dynamic multi-cellular behavior of these bacteria. However, the mechanism…

Biological Physics · Physics 2016-02-17 Rajesh Balagam , Oleg A. Igoshin

Seagrass meadows contribute to the conservation of marine ecosystems, reduction in global warming impacts and pathogen controls. However, the decline in seagrass habitats due to environmental loads has become an urgent global issue. One way…

Engineered living materials (ELMs) are the most relevant contemporary revolution in materials science and engineering. These ELMs aim to outperform current examples of "smart", active or multifunctional materials, enabling countless…

Biological Physics · Physics 2021-10-19 Andrés Díaz Lantada , Jan G. Korvink , Monsur Islam

We analyze plankton-nutrient food chain models composed of phytoplankton, herbivorous zooplankton and a limiting nutrient. These models have played a key role in understanding the dynamics of plankton in the oceanic layer. Given the strong…

Probability · Mathematics 2024-07-10 Alexandru Hening , Nguyen Trong Hieu , Dang Hai Nguyen , Nhu Ngoc Nguyen

Several classification methods assume that the underlying distributions follow tree-structured graphical models. Indeed, trees capture statistical dependencies between pairs of variables, which may be crucial to attain low classification…

Machine Learning · Statistics 2021-05-31 Yaniv Tenzer , Amit Moscovich , Mary Frances Dorn , Boaz Nadler , Clifford Spiegelman

Complex biological systems are very robust to genetic and environmental changes at all levels of organization. Many biological functions of Escherichia coli metabolism can be sustained against single-gene or even multiple-gene mutations by…

Molecular Networks · Quantitative Biology 2007-08-30 Pan-Jun Kim , Dong-Yup Lee , Tae Yong Kim , Kwang Ho Lee , Hawoong Jeong , Sang Yup Lee , Sunwon Park

Living tissue is able to withstand large stresses in everyday life, yet it also actively adapts to dynamic loads. This remarkable mechanical behaviour emerges from the interplay between living cells and their non-living extracellular…

Biological Physics · Physics 2022-02-02 Iain Muntz , Michele Fenu , Gerjo J. V. M. van Osch , Gijsje H. Koenderink

Plant reflectance spectra - the profile of light reflected by leaves across different wavelengths - supply the spectral signature for a species at a spatial location to enable estimation of functional and taxonomic diversity for plants. We…

Applications · Statistics 2021-03-26 Philip A. White , Henry Frye , Michael F. Christensen , Alan E. Gelfand , John A. Silander

Many methods have been developed for finding the commonalities between different organisms to study their phylogeny. The structure of metabolic networks also reveal valuable insights into metabolic capacity of species as well as into the…

Molecular Networks · Quantitative Biology 2016-04-08 Krishanu Deyasi , Anirban Banerjee , Bony Deb

We investigate the propagation of random fluctuations through biochemical networks in which the concentrations of species are large enough so that the unperturbed problem is well-described by ordinary differential equation. We characterize…

Probability · Mathematics 2007-05-23 David Anderson , Jonathan Mattingly , H. Frederik Nijhout , Michael Reed

Motility is an essential factor for an organism's survival and diversification. With the advent of novel single-cell technologies, analytical frameworks and theoretical methods, we can begin to probe the complex lives of microscopic motile…

Soil-transmitted helminth (STH) infections, one of the most prevalent neglected tropical diseases, pose a significant threat to public health in tropical and subtropical areas. These parasites infect humans and animals through direct…

Populations and Evolution · Quantitative Biology 2025-04-07 Rafiatu Imoro , Maica Krizna Gavina , Vachel Gay Paller , Jomar Rabajante , Mark Jayson Cortez , Editha Jose