Subcellular Processes
A mechanism of extraction of tubular membranes from a lipid vesicle is presented. A concentration gradient of anchoring amphiphilic polymers generates tubes from bud-like vesicle protrusions. We explain this mechanism in the framework of…
The collective behavior of molecular motor proteins have been investigated in the literature using models to describe the long-time dynamics of a unidimensional continuum motor distribution. Here, we consider the phenomena related to the…
As the past decade barely dawned, a fundamentally novel view of cancer relating to signal transduction through intracellular hormones/growth factors and their subunits began to unfold. Further along, it gained additional substance with the…
A practical introduction to stochastic modelling of reaction-diffusion processes is presented. No prior knowledge of stochastic simulations is assumed. The methods are explained using illustrative examples. The article starts with the…
Until presently, most approaches for understanding physiological or pathological phenomena have been based on the assumption that these processes start from individual cells, a concept introduced primarily by Virchow in the 19th century.…
In this paper we use a simple toy model to explore the function of the gene Osteosarcoma-9. We are in particular interested in understanding the role of this gene as a potent anti-apoptotic factor. The theoretical description is constrained…
An endogenous molecular-cellular network for both normal and abnormal functions is assumed to exist. This endogenous network forms a nonlinear stochastic dynamical system, with many stable attractors in its functional landscape. Normal or…
During the eukaryotic cell cycle, chromatin undergoes several conformational changes, which are believed to play key roles in gene expression regulation during interphase, and in genome replication and division during mitosis. In this…
Using a theoretical model for spontaneous partial DNA unwrapping from histones, we study the transient exposure of protein-binding DNA sites within nucleosomes. We focus on the functional dependence of the rates for site exposure and…
In the present study, we show that ascorbic acid dose-dependently inhibited interleukin-1beta (IL-1beta)-mediated PGE2 synthesis in the human neuronal cell line, SK-N-SH. Furthermore, in combination with aspirin, ascorbic acid augmented the…
The multiple worlds of genetically manipulated laboratory organisms such as transgenic mice or worms with certain gene mutations are somewhat reminiscent of parallel worlds in quantum mechanics. So are various models of aging tested in such…
Fifteen years ago, a structural analysis of the hormone insulin and the retinoblastoma tumor suppressor protein (RB) revealed that they may physically interact with one another. Subsequently, an RB peptide corresponding to the proposed RB…
In 1968, Sorin Comorosan first reported a phenomenon wherein irradiation of the substrate of an enzyme reaction, in the crystalline state, for a specific number of seconds could lead to an enhanced aqueous solution reaction rate for the…
Initial reaction rate data for lactic dehydrogenase / pyruvate, lactic dehydrogenase / lactate and malic dehydrogenase / malate enzyme reactions were analyzed to obtain activation free energy changes of -329, -195 and -221 cal/mole,…
We discuss various models of ion transport through cell membrane channels. Recent experimental data shows that sizes of ion channels are compared to those of ions and that only few ions may be simultaneously in any single channel.…
We present a model for diffusion in a molecularly crowded environment. The model consists of random barriers in percolation network. Random walks in the presence of slowly moving barriers show normal diffusion for long times, but anomalous…
I point out the similarity between the microtubule experiment reported by Priel et al [Biophys. J. 90, 4639 (2006)] and the ZnO nanowire experiment of Wang et al [Nanolett. 6, 2768 (2006)]. It is quite possible that MTs are similar to a…
The question of how to validate and interpret correctly the waiting time probability density functions (WT-PDFs) from single molecule data is addressed. It is shown by simulation that when a stretched exponential WT-PDF, with a stretched…
Mechanosensation is a key part of the sensory repertoire of a vast array of different cells and organisms. The molecular dissection of the origins of mechanosensation is rapidly advancing as a result of both structural and functional…
All living cells transport molecules and ions across membranes, often against concentration gradients. This active transport requires continual energy expenditure and is clearly a nonequilibrium process for which standard equilibrium…