Related papers: Dynamical hysteresis in multisite protein modifica…
Protein functions in cells may be activated or modified by the attachment of several kinds of chemical groups. While protein phosphorylation, i.e. the attachment of a phosphoryl (PO$_3^-$) group, is the most studied form of protein…
Post-transductional modifications tune the functions of proteins and regulate the collective dynamics of biochemical networks that determine how cells respond to environmental signals. For example, protein phosphorylation and nitrosylation…
Multisite protein phosphorylation plays a pivotal role in regulating cellular signaling and decision-making processes. In this study, we focus on the mathematical underpinnings and informational aspects of sequential, distributive…
Hysteresis is a phenomenon that is observed in a great variety of physical systems, which leads to a nonlinear and multivalued behavior, making their modeling and control difficult. Even though the analysis and mathematical properties of…
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…
When an interacting many-body system, such as a magnet, is driven in time by an external perturbation, such as a magnetic field,the system cannot respond instantaneously due to relaxational delay. The response of such a system under a…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…
We study the dynamics of intracellular calcium oscillations in the presence of proteins that bind calcium on multiple sites and that are generally believed to act as passive calcium buffers in cells. We find that multisite calcium-binding…
Human joint dynamic stiffness plays an important role in the stability of performance augmentation exoskeletons. In this paper, we consider a new frequency domain model of the human joint dynamics which features a complex value stiffness.…
Various biological sensory systems exhibit a response to a relative change of the stimulus, often referred to as fold-change detection. In the last few years fold-change detecting mechanisms, based on transcriptional networks, have been…
The decay of the hysteresis loop area of the system, which is obeying a site diluted kinetic Ising model, is considered by the disorder parameter using the effective field theory analysis. The exhibition focuses on the understanding of…
Understanding the link between structure and function in proteins is fundamental in molecular biology and proteomics. A central question in this context is whether allostery - where the binding of a molecule at one site affects the activity…
Under normal operations, memristive devices undergo variability in time and space and have internal dynamics. Interplay of memory and stochastic signal processing in memristive devices makes them candidates for performing bio-inspired tasks…
We study the ultrasensitivity of multisite binding processes where ligand molecules can bind to several binding sites, considering more particularly recent models involving complex chemical reactions in phosphorylation systems such as…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
Protein translation is a multistep process which can be represented as a cascade of biochemical reactions (initiation, ribosome assembly, elongation, etc.), the rate of which can be regulated by small non-coding microRNAs through multiple…
A mathematical model for a two-gene regulatory network is derived and several of their properties analyzed. Due to the presence of mixed continuous/discrete dynamics and hysteresis, we employ a hybrid systems model to capture the dynamics…
Mutation is a critical mechanism by which evolution explores the functional landscape of proteins. Despite our ability to experimentally inflict mutations at will, it remains difficult to link sequence-level perturbations to systems-level…
Allostery refers to the puzzling phenomenon of long-range communication between distant sites in proteins. Despite its importance in biomolecular regulation and signal transduction, the underlying dynamical process is not well understood.…
Multisite phosphorylation networks are encountered in many intracellular processes like signal transduction, cell-cycle control or nuclear signal integration. In this contribution networks describing the phosphorylation and…