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Biofilms exposed to flow experience shear stress, which leads to a competitive interaction between the growth and development of a biofilm and shearing. In this study, Pseudonomas fluorescene biofilm was grown in a microfluidic channel and…
Reaction-diffusion systems have been proposed as a model for pattern formation and morphogenesis. The Fickian diffusion typically employed in these constructions model the Brownian motion of particles. The biological and chemical elements…
The fundamental processes of biological development are governed by multiple signaling molecules that create non-uniform concentration profiles known as morphogen gradients. It is widely believed that the establishment of morphogen…
The family of TGFb ligands is large and its members are involved in many different signaling processes. These signaling processes strongly differ in type with TGFb ligands eliciting both sustained or transient responses. Members of the TGFb…
We solve a simple model that supports a dynamic phase transition and show conditions for the existence of the transition. Using methods of large deviation theory we analytically compute the probability distribution for activity and entropy…
The mechanisms by which adaptive phenotypes spread within an evolving population after their emergence are understood fairly well. Much less is known about the factors that influence the evolutionary accessibility of such phenotypes, a…
To improve the global optimization ability of traditional GEP algorithm, a Multicellular gene expression programming algorithm based on fuzzy control (Multicellular GEP Algorithm Based On Fuzzy Control, MGEP-FC) is proposed. The MGEP-FC…
The properties of the spectral evolution during the prompt emission phase of gamma-ray bursts (GRBs), which are closely related to the radiation mechanism (synchrotron or photosphere), are still a subject of debate. Two spectral evolution…
It is well known that, under suitable conditions, microRNAs are able to fine tune the relative concentration of their targets to any desired value. We show that this function is particularly effective when one of the targets is a…
Hysteresis and bet-hedging (random choice of phenotypes) are two different observations typically linked with multiplicity of phenotypes in biological systems. Hysteresis can be viewed as form of the system's persistent memory of past…
Background: The availability of high throughput methods for measurement of mRNA concentrations makes the reliability of conclusions drawn from the data and global quality control of samples and hybridization important issues. We address…
Longitudinal studies with binary or ordinal responses are widely encountered in various disciplines, where the primary focus is on the temporal evolution of the probability of each response category. Traditional approaches build from the…
Network analysis provides a powerful framework for the interpretation of genome-wide data. While static network approaches have proved fruitful, there is increasing interest in the insights gained from the analysis of cellular networks…
GTPases are molecular switches that regulate a wide range of cellular processes, such as organelle biogenesis, position, shape, and signal transduction. These enzymes operate by toggling between an active ("ON") guanosine triphosphate…
The unwelcome evolution of malignancy during cancer progression emerges through a selection process in a complex heterogeneous population structure. In the present work, we investigate evolutionary dynamics in a phenotypically heterogeneous…
Numerous experimental studies have demonstrated that the microenvironment is a key regulator influencing the proliferative and migrative potentials of species. Spatial and temporal disturbances lead to adverse and hazardous…
Gene expression in cells is stochastic, yet differentiation is robust. We propose a mechanism in which frustrated genes with weakly stable intermediate expression undergo noise-driven switching between basins of attraction, followed by…
Understanding the patterns and causes of phenotypic divergence is a central goal in evolutionary biology. Much work has shown that mRNA abundance is highly variable between closely related species. However, the extent and mechanisms of…
Embryonic development is driven by spatial patterns of gene expression that determine the fate of each cell in the embryo. While gene expression is often highly erratic, embryonic development is usually exceedingly precise. In particular,…
We present a theoretical framework to analyze the dynamics of gene expression with stochastic bursts. Beginning with an individual-based model which fully accounts for the messenger RNA (mRNA) and protein populations, we propose a novel…