Related papers: Allovalency revisited: an analysis of multisite ph…
Many dynamical systems arising in biology and other areas exhibit multistationarity (two or more positive steady states with the same conserved quantities). Although deciding multistationarity for a polynomial dynamical system is an…
Multisite phosphorylation plays an important role in regulating switchlike protein activity and has been used widely in mathematical models. With the development of new experimental techniques and more molecular data, molecular…
The adhesion of cells is mediated by receptors and ligands anchored in apposing membranes. A central question is how to characterize the binding affinity of these membrane-anchored molecules. For soluble molecules, the binding affinity is…
Apoptosis is a highly regulated cell death mechanism involved in many physiological processes. A key component of extrinsically activated apoptosis is the death receptor Fas, which, on binding to its cognate ligand FasL, oligomerize to form…
Cells often have tens of thousands of receptors, even though only a few activated receptors can trigger full cellular responses. Reasons for the overabundance of receptors remain unclear. We suggest that, in certain conditions, the large…
Interaction with divalent cations is of paramount importance for RNA structural stability and function. We here report a detailed molecular dynamics study of all the possible binding sites for Mg$^{2+}$ on a RNA duplex, including both…
The methylation of DNA regulates gene expression. On cell division the methylation state of the DNA is typically inherited from parent to daughter cells. While the chemical bond between the methyl group and the DNA is very strong, changes…
Hill function is one of the widely used gene transcription regulation models. Its attribute of fitting may result in a lack of an underlying physical picture, yet the fitting parameters can provide information about biochemical reactions,…
Accurate prediction of binding free energies is critical to streamlining the drug development and protein design process. With the advent of GPU acceleration, absolute alchemical methods, which simulate the removal of ligand electrostatics…
Protein adsorption at the solid-liquid interface is an important phenomenon that often can be observed as a first step in biological processes. Despite its inherent importance, still relatively little is known about the underlying…
The theory of receptor-ligand binding equilibria has long been well-established in biochemistry, and was primarily constructed to describe dilute aqueous solutions. Accordingly, few computational approaches have been developed for making…
The multisite phosphorylation-dephosphorylation cycle is a motif repeatedly used in cell signaling. This motif itself can generate a variety of dynamic behaviors like bistability and ultrasensitivity without direct positive feedbacks. In…
Molecular Relational Learning (MRL) is widely applied in natural sciences to predict relationships between molecular pairs by extracting structural features. The representational similarity between substructure pairs determines the…
Cell polarization is a critical process that separates molecular species into two distinct regions in prokaryotic and eukaryotic cells, guiding biological processes such as cell division and cell differentiation. Although several underlying…
We present a model, in which some nodes (called interconnecting nodes) in two networks merge and play the roles in both the networks. The model analytic and simulation discussions show a monotonically increasing dependence of…
In this paper we obtain the first general multi-component solution to thermodynamic perturbation theory for the case that molecules can participate in cyclic double bonds. In contrast to previous authors, we do not restrict double bonding…
Molecular docking, a key technique in structure-based drug design, plays pivotal roles in protein-ligand interaction modeling, hit identification and optimization, in which accurate prediction of protein-ligand binding mode is essential.…
The activities and interactions of proteins that govern the cellular response to a signal generate a multitude of protein phosphorylation states and heterogeneous protein complexes. Here, using a computational model that accounts for 307…
We develop a model-based boosting approach for multivariate distributional regression within the framework of generalized additive models for location, scale, and shape. Our approach enables the simultaneous modeling of all distribution…
This work addresses whether a reaction network, taken with mass-action kinetics, is multistationary, that is, admits more than one positive steady state in some stoichiometric compatibility class. We build on previous work on the effect…