In the cell division cycle of budding yeast, START refers to a set tightly linked events that prepare for and DNA replication, FINISH denotes interrelated by which exits from mitosis divides into mother daughter cells. On basis recent progress made molecular biologists in characterizing genes proteins control FINISH, we crafted new mathematical model progression yeast. Our exploits natural separation time scales network construct system differential-algebraic equations protein synthesis...

Abstract Different cancer cell lines can have varying responses to the same perturbations or stressful conditions. Cancer cells that DNA damage checkpoint-related mutations are often more sensitive gene including altered Plk1 and p53 activities than without these mutations. The induce a cycle arrest in former cancer, whereas they only delay progression latter cancer. To study crosstalk between Plk1, p53, G2/M checkpoint leading differential regulations, we developed computational model by...

We theoretically study the cooperative behavior of cytoskeletal filaments in motility assays which immobilized motor proteins bind to substrate surfaces and actively pull them along these surfaces. Because mutual exclusion filaments, coupled dynamics heads, tails leads a nonequilibrium phase transition generalizes isotropic-nematic corresponding equilibrium system, hard-rod fluid. Langevin simulations show that activity enhances tendency for nematic ordering. develop quantitative theory...

Microtubule (MT)-based transport of organelles driven by the opposing MT motors kinesins and dynein is tightly regulated in cells, but underlying molecular mechanisms remain largely unknown. Here we tested regulation ubiquitous protein MAP4 using Xenopus melanophores as an experimental system. In these pigment granules (melanosomes) move along MTs to cell center (aggregation) or periphery (dispersion) means cytoplasmic kinesin-2, respectively. We found that aggregation signals induced...

Networks have become ubiquitous in systems biology. Visualization is a crucial component their analysis. However, collaborations within research teams network biology are hampered by software that either specific to computational algorithm, create visualizations not biologically meaningful, or limited features for sharing networks and visualizations. We present GraphSpace, web-based platform fosters team science allowing collaborating groups easily store, interact with, layout share...

Abstract Bidirectional transport of membrane organelles along microtubules ( MTs ) is driven by plus‐end directed kinesins and minus‐end dynein bound to the same cargo. Activities opposing MT motors produce bidirectional movement cytoplasmic particles tracks. Directionality ‐based might be controlled a protein complex that determines which motor type active at any given moment time, or determined outcome tug‐of‐war between dragging cargo in opposite directions. However, evidence support each...

Abstract The cell division cycle is regulated by a complex network of interacting genes and proteins. control system has been modeled in many ways, from qualitative Boolean switching-networks to quantitative differential equations highly detailed stochastic simulations. Here we develop continuous-time model using seven variables represent the activities major regulators budding yeast plus one continuous variable representing growth. are updated asynchronously logical rules based on known...

Optical tweezers are now a widespread tool based on three-dimensional trapping by tightly focused single laser beam. This configuration only works with large numerical aperture and short-working-distance (SWD) objectives, restricting optical manipulation to the high magnification end of microscope nosepiece. Certain applications demand long-working distances (LWDs) at moderate magnification, imposing more complex two-beam configuration. In this article, we describe complete setup that...

We study the active dynamics of single and interacting cytoskeletal filaments in motility assays, which immobilized motor proteins bind to a surface actively pull them along this surface. present model couples overdamped filaments, heads, elasticity stalks can be used for Langevin simulations. Single perform persistent random walk, we characterize by several simulation results. For with repulsive interaction motor-driven leads non-equilibrium phase transition generalizes isotropic-nematic...

Bundling of rapidly polymerizing actin filaments underlies the dynamics filopodial protrusions that play an important role in cell migration and cell-cell interaction. Recently, formation bundles has been reconstituted vitro, two scenarios bundle initiation, involving binding filament tips and, alternatively, linking tip one to side other, have discussed. A first theoretical analysis is presented indicating mechanisms can be distinguished experimentally. While both them result...

We consider the motion of semiflexible polymers in double-well potentials. calculate shape, energy, and effective diffusion constant kink excitations, particular their dependence on bending rigidity polymer. For symmetric potentials, is purely diffusive whereas becomes directed presence a driving force determine average velocity polymer based dynamics. The Kramers escape over potential barriers proceeds by nucleation kink-antikink pairs, relaxation to straight configuration annihilation...

Efficient and accurate numerical techniques are used to examine similarities of effective diffusion in a void between random overlapping obstacles: essential invariance coefficients (Deff) with respect obstacle shapes applicability two-parameter power law over nearly entire range excluded volume fractions (ϕ), except for small vicinity percolation threshold. It is shown that while neither the properties exact, deviations from them remarkably small. This allows quick estimation thresholds...

Cytoplasmic microtubules (MTs) continuously grow and shorten at their free plus ends, a behavior that allows them to capture membrane organelles destined for MT minus end–directed transport. In Xenopus melanophores, the of pigment granules (melanosomes) involves +TIP CLIP-170, which is enriched growing ends. Here we used melanophores test whether signals stimulate end transport also enhance CLIP-170–dependent binding melanosomes tips. We found these significantly (>twofold) increased...

Semiexible polymers and lamen ts play an important role in biological chemical physics. Single are characterized by a certain bending rigidity which governs their persistence length buckling instabilities. Attractive mutual interactions of bundles or the attractive interaction with adhesive substrate lead to equilibrium phase transitions, such as bundling adsorption. Finally, on level active systems consisting many interacting ts, we discuss cooperative ordering eects non-equilibrium...

Adaptive modulation of the global cellular growth state unicellular organisms is crucial for their survival in fluctuating nutrient environments. Because these must be able to respond reliably ever varying and unpredictable nutritional conditions, signaling networks have a certain inbuilt robustness. In eukaryotes, such as budding yeast Saccharomyces cerevisiae, distinct signals are relayed by specific plasma membrane receptors signal transduction pathways that interconnected complex...

The brain’s ability to create a unified conscious representation of an object by integrating information from multiple perception pathways is called perceptual binding. Binding crucial for normal cognitive function. Some binding errors and disorders have been linked certain neurological conditions, brain lesions, conditions that give rise illusory conjunctions. However, the mechanism remains elusive. Here, we present computational model using two sets coupled oscillatory processes...

Abstract Over the last 30 years, computational biologists have developed increasingly realistic mathematical models of regulatory networks controlling division eukaryotic cells. These capture data resulting from two complementary experimental approaches: low-throughput experiments aimed at extensively characterizing functions small numbers genes, and large-scale genetic interaction screens that provide a systems-level perspective on cell process. The former is insufficient to...

Random fluctuations in neuronal processes may contribute to variability perception and increase the information capacity of networks. Various sources random have been characterized nervous system on different levels. However, context neural correlates consciousness, robustness mechanisms conscious against inherent noise dynamical systems is poorly understood. In this paper, a stochastic model developed study implications that mimic consciousness. We computed power spectral densities entropy...