Subcellular Processes
The metazoan genome is replicated in precise cell lineage specific temporal order. However, the mechanism controlling this orchestrated process is poorly understood as no molecular mechanisms have been identified that actively regulate the…
For many viruses assembly and budding occur simultaneously during virion formation. Understanding the mechanisms underlying this process could promote biomedical efforts to block viral propagation and enable use of capsids in nanomaterials…
The mechanisms controlling the transport of proteins across the Golgi stack of mammalian and plant cells is the subject of intense debate, with two models, cisternal progression and inter-cisternal exchange, emerging as major contenders. A…
During M phase, Endosulfine (Endos) family proteins are phosphorylated by Greatwall kinase (Gwl), and the resultant pEndos inhibits the phosphatase PP2A-B55, which would otherwise prematurely reverse many CDK-driven phosphorylations. We…
Cadherin adhesion receptors are fundamental determinants of tissue organization in health and disease. Increasingly, we have come to appreciate that classical cadherins exert their biological actions through active cooperation with the…
The physiology of voltage gated ion channels is complex and insights into their gating mechanism is incomplete. Their function is best represented by Markov models with relatively large number of distinct states that are connected by…
In the past one hundred years, deterministic rate equations have been successfully used to infer enzyme-catalysed reaction mechanisms and to estimate rate constants from reaction kinetics experiments conducted in vitro. In recent years,…
Many models have been developed to study the role of branching actin networks in motility. One important component of those models is the distribution of filament orientations relative to the cell membrane. Two mean-field models previously…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
Messenger RNA encodes a sequence of amino acids by using codons. For most amino acids there are multiple synonymous codons that can encode the amino acid. The translation speed can vary from one codon to another, thus there is room for…
We present a generic analytical scheme for the quantification of fluctuations due to bifunctionality-induced signal transduction within the members of bacterial two-component system. The proposed model takes into account post-translational…
Transcription factor (TF) molecules translocate by facilitated diffusion (a combination of 3D diffusion around and 1D random walk on the DNA). Despite the attention this mechanism received in the last 40 years, only a few studies…
Multimodal oncological strategies which combine chemotherapy or radiotherapy with hyperthermia have a potential of improving the efficacy of the non-surgical methods of cancer treatment. Hyperthermia engages the heat-shock response…
Background: A fundamental problem in cancer research is identifying the cell type that is capable of sustaining neoplastic growth and its origin from normal tissue cells. Recent investigations of a variety of tumor types have shown that…
Multiple Sclerosis (MS) is a disorder that usually appears in adults in their thirties. It has a prevalence that ranges between 2 and 150 per 100 000. Epidemiological studies of MS have provided hints on possible causes for the disease…
In this work we examine how volume exclusion caused by regions of high chromatin density might influence the time required for proteins to find specific DNA binding sites. The spatial variation of chromatin density within mouse olfactory…
Metabolic substrates, such as oxygen and glucose, are rapidly delivered to the cell through filtration across microvessels walls. Modelling this important process is complicated by the coupling between flow and transport equations, which…
In numerous systems in biophysics and related fields, scientists measure (with very smart methods) individual molecules (e.g. biopolymers (proteins, DNA, RNA, etc), nano - crystals, ion channels), aiming at finding a model from the data.…
We formulate a dynamical model for microtubules interacting with a catastrophe-inducing boundary. In this model microtubules are either waiting to be nucleated, actively growing or shrinking, or stalled at the boundary. We first determine…
The spatiotemporal oscillations of the Min proteins in the bacterium Escherichia coli play an important role in cell division. A number of different models have been proposed to explain the dynamics from the underlying biochemistry. Here,…