Related papers: The Effect of Macromolecular Crowding, Ionic Stren…
In systems biomedicine, an experimenter encounters different potential sources of variation in data such as individual samples, multiple experimental conditions, and multi-variable network-level responses. In multiparametric cytometry,…
Understanding cellular response to mechanical forces is immensely important for a plethora of biological processes. Focal adhesions are multi-molecular protein assemblies that connect the cell to the extracellular matrix and play a pivotal…
Movement of cell clusters along extracellular matrices (ECM) during tissue development, wound healing, and early stage of cancer invasion involve various inter-connected migration modes such as: (1) cell movement within clusters, (2)…
Protein-ligand binding is the process by which a small molecule (drug or inhibitor) attaches to a target protein. Binding affinity, which characterizes the strength of biomolecular interactions, is essential for tackling diverse challenges…
Proteins fold to a specific functional conformation with a densely packed hydrophobic core that controls their stability. We develop a geometric, yet all-atom model for proteins that explains the universal core packing fraction of…
In the recent paper (2011) Faas and co-workers claimed that calmodulin could directly detect Ca2+ signals by acting as extremely fast calcium buffer. However the results and their interpretation raise serious doubts about this conclusion.
Many animal cells change their shape depending on the stiffness of the substrate on which they are cultured: they assume small, rounded shapes in soft ECMs, they elongate within stiffer ECMs, and flatten out on hard substrates. Cells tend…
Understanding the role that structure plays in the dynamical arrest observed in glassy systems remains an open challenge. Over the last decade, machine learning (ML) strategies have emerged as an important tool for probing this…
Cellular manufacturing (CM) is an approach that includes both flexibility of job shops and high production rate of flow lines. Although CM provides many benefits in reducing throughput times, setup times, work-in-process inventories but the…
Recent observations demonstrate that densely packed tissues exhibit features of glassy dynamics, such as caging behavior and dynamical heterogeneities, although it has remained unclear how single-cell properties control this behavior. Here…
This paper proposes a Clustered Unit Commitment (CUC) formulation to accurately model flexibility requirements such as ramping, reserve, and startup/shutdown constraints. The CUC is commonly applied in large and long-term planning models to…
In many cellular signaling pathways, key components form clusters at the cell membrane. Although much work has focused on the mechanisms behind such cluster formation, the implications for downstream signaling remain poorly understood.…
We discuss the implementation of a multiscale biophysico-chemical model able to cope with the main mechanisms underlying cumulative exocytosis in cells. The model is based on a diffusion equation in the presence of external forces that…
Mathematical models of a cellular action potential in cardiac modelling have become increasingly complex, particularly in gating kinetics which control the opening and closing of individual ion channel currents. As cardiac models advance…
Crowded environments modify the diffusion of macromolecules, generally slowing their movement and inducing transient anomalous subdiffusion. The presence of obstacles also modifies the kinetics and equilibrium behavior of tracers. While…
The folding of the cholesterol trapping apolipoprotein A1 in aqueous solution at increasing ionic strength is studied using atomically detailed molecular dynamics simulations. We calculate various structural properties to characterize the…
In embryogenesis, epithelial cells, acting as individual entities or as coordinated aggregates in a tissue, exhibit strong coupling between chemical signalling and mechanical responses to internally or externally applied stresses.…
Chromatin is a complex of DNA, RNA and proteins whose primary function is to package genomic DNA into the tight confines of a cell nucleus. A fundamental repeating unit of chromatin is the nucleosome, an octamer of histone proteins around…
A computer-aided detection (CADe) system for microcalcification cluster identification in mammograms has been developed in the framework of the EU-founded MammoGrid project. The CADe software is mainly based on wavelet transforms and…
Current mathematical frameworks for predicting the flux state and macromolecular composition of the cell do not rely on thermodynamic constraints to determine the spontaneous direction of reactions. These predictions may be biologically…