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Biofilm growth changes many physical properties of porous media such as porosity, permeability and mass transport parameters. The growth depends on various environmental conditions, and in particular, on flow rates. Modeling the evolution…
Biomaterial systems have allowed for the in vitro production of complex, emergent tissue behaviors that were not possible with conventional 2D culture systems allowing for analysis of the normal development as well as disease processes. We…
Electrochemical communication is a mechanism that enables intercellular interaction among bacteria within communities. Bacteria achieves synchronization and coordinates collective actions at the population level through the utilization of…
Non-equilibrium thermodynamics has long been an area of substantial interest to ecologists because most fundamental biological processes, such as protein synthesis and respiration, are inherently energy-consuming. Microbial communities are…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Background: Many mathematical models have now been employed across every area of systems biology. These models increasingly involve large numbers of unknown parameters, have complex structure which can result in substantial evaluation time…
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…
With the astonishing rate that the genomic and metagenomic sequence data sets are accumulating, there are many reasons to constrain the data analyses. One approach to such constrained analyses is to focus on select subsets of gene families…
Bacteria can form a great variety of spatially heterogeneous cell density patterns, ranging from simple concentric rings to dynamical spiral waves appearing in growing colonies. These pattern formation phenomena are important as they…
We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken…
In systems of active programmable matter, individual modules require a constant supply of energy to participate in the system's collective behavior. These systems are often powered by an external energy source accessible by at least one…
Biofilms are microbial collectives that occupy a diverse array of surfaces. The function and evolution of biofilms are strongly influenced by the spatial arrangement of different strains and species within them, but how spatiotemporal…
In this paper, we present an approach for modeling bio-tissues that incorporates the variability in properties as part of their characteristics. This is achieved by considering the parameters of the model of a biomaterial to themselves be…
Generative artificial intelligence models learn probability distributions from data and produce novel samples that capture the salient properties of their training sets. Proteins are particularly attractive for such approaches given their…
A crop can be represented as a biotechnical system in which components are either chosen (cultivar, management) or given (soil, climate) and whose combination generates highly variable stress patterns and yield responses. Here, we used…
Plant breeding programs use data obtained from multi-environment selection experiments to produce improved varieties with the ultimate aim of maintaining high levels of genetic gain. Selection accuracy can be improved with the use of…
Bacterial growth and division generally occur by the process known as binary fission, in which the cells grow polarly until they divide into two daughter cells. Although this process is affected by factors that introduce stochastic…
Bioprinting is an enabling biofabrication technique to create heterogeneous tissue constructs according to patient-specific geometries and compositions. Optimization of bioinks as per requirements for specific tissue applications is a…
In natural environments, solid surfaces present both opportunities and challenges for bacteria. On one hand, they serve as platforms for biofilm formation, crucial for bacterial colonization and resilience in harsh conditions. On the other…
We propose a modeling approach to study how mature biofilms spread and colonize new surfaces by predicting the formation and growth of satellite colonies generated by dispersing biofilms. This model provides the basis for better…