Related papers: Controlled protein synthesis and spatial organisat…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
Systems biology and whole-cell modelling are demanding increasingly comprehensive mathematical models of cellular biochemistry. These models require the development of simplified models of specific processes which capture essential…
The performances of lubricated systems widely used in natural, biological, and artificial settings are traditionally dictated by their load bearing capacities. Here we unveil that, by exploiting a unique coupling between interfacial…
Effect of molecular crowding and confinement experienced by protein in the cell during unfolding has been studied by modeling a linear polymer chain on a percolation cluster. It is known that internal structure of the cell changes in time,…
This paper gives an overview of the use of control systems engineering in synthetic biology, motivated by applications such as cell therapy and cell fate reprogramming for regenerative medicine. A ubiquitous problem in these and other…
Life relies on a sophisticated metabolic molecular machinery that turns over high-energy molecules to evolve complex macromolecules and assemblies. At the molecular origin of life, such machinery was absent, implying the need for simple yet…
We present and discuss a framework for computer-aided multiscale analysis, which enables models at a "fine" (microscopic/stochastic) level of description to perform modeling tasks at a "coarse" (macroscopic, systems) level. These…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
Reaction-diffusion systems offer a powerful framework for understanding self-organized patterns in biological systems, yet controlling these patterns remains a significant challenge. As a consequence, we present a rigorous framework of…
The Dynamic Template model of biological cell membranes and the cytoplasm as spatially organised fluid layers is extended to plant cells, and is shown to offer a feasible shear driven mechanism for the co-alignment of internal and external…
Multi-sample microarray experiments have become a standard experimental method for studying biological systems. A frequent goal in such studies is to unravel the regulatory relationships between genes. During the last few years, regression…
Protein synthesis is an important determinant of microbial growth and response that demands a high amount of metabolic and biosynthetic resources. Despite these costs, microbial species from different taxa and habitats massively synthesize…
Biomedical and biochemical processes in paper-based microfluidic devices often deal with mixing of two analytes to perform important functions. Uniform mixing of analytes in paper matrix is a challenging proposition, often necessitating…
Flux analysis is a class of constraint-based approaches to the study of biochemical reaction networks: they are based on determining the reaction flux configurations compatible with given stoichiometric and thermodynamic constraints. One of…
A distinguishing feature of a multicellular living system is that it operates at various scales, from the intracellular to organismal. Very little is known at present on how tissue level properties are related to cell and subcellular…
Multicellular collective migration is a ubiquitous strategy of cells to translocate spatially in diverse tissue environments to accomplish a wide variety of biological phenomena, viz. embryonic development, wound healing, and tumor…
Randomness is an unavoidable feature of the intracellular environment due to chemical reactants being present in low copy number. That phenomenon, predicted by Delbr\"uck long ago \cite{delbruck40}, has been detected in both prokaryotic…
Under dehydration conditions, amphipathic Late Embryogenesis Abundant (LEA) proteins fold spontaneously from a random conformation into alpha-helical structures and this transition is promoted by the presence of membranes. To gain insight…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
We introduce an infinite particle system dynamics, which includes stochastic chemical kinetics models, the classical Kac model and free space movement. We study energy redistribution between two energy types (kinetic and chemical) in…