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At least 127 records · Page 7Linked to original sources
arXiv2010

Heterogeneous anomalous diffusion of virus in cytoplasm of a living cell

The infection pathway of virus in cytoplasm of a living cell is studied from the viewpoint of diffusion theory. The cytoplasm plays a role of a medium for stochastic motion of the virus contained in the endosome as well as the free virus. It is experimentally known that the exponent of anomalous diffusion fluctuates in localized areas of the cytoplasm. Here, generalizing fractional kinetic theory, such fluctuations are described in terms of the exponent locally distributed over the cytoplasm, and a theoretical proposition is presented for its statistical form. The proposed fluctuations may be examined in an experiment of heterogeneous diffusion in the infection pathway.

physics.bio-ph↗
arXiv2010

Computational Modelling of Nonlinear Calcium Waves

The calcium transport in biological systems is modelled as a reaction-diffusion process. Nonlinear calcium waves are then simulated using a stochastic cellular automaton whose rules are derived from the corresponding coupled partial differential equations. Numerical simulations show self-organized criticality in the complex calcium waves and patterns. Both the stochastic cellular automaton approach and the equation-based simulations can predict the characteristics of calcium waves and complex pattern formation. The implication of locality of calcium distribution with positional information in biological systems is also discussed.

nlin.PS↗
arXiv2010

The Aldous-Shields model revisited (with application to cellular ageing)

In Aldous and Shields (1988), a model for a rooted, growing random binary tree was presented. For some c>0, an external vertex splits at rate c^(-i) (and becomes internal) if its distance from the root (depth) is i. For c>1, we reanalyse the tree profile, i.e. the numbers of external vertices in depth i=1,2,.... Our main result are concrete formulas for the expectation and covariance-structure of the profile. In addition, we present the application of the model to cellular ageing. Here, we assume that nodes in depth h+1 are senescent, i.e. do not split. We obtain a limit result for the proportion of non-senescent vertices for large h.

math.PR↗
arXiv2010

Spatial and Temporal Correlates of Vesicular Release at Hippocampal Synapses

We develop a spatially explicit biophysical model of the hippocampal CA3-CA1 presynaptic bouton to study local calcium dynamics leading to vesicle fusion. A kinetic model with two calcium sensors is formulated specifically for the CA3-CA1 synapse. The model includes a sensor for fast synchronous release that lasts a few tens of milliseconds and a sensor for slow asynchronous release that lasts a few hundred milliseconds. We show that a variety of extant data on CA3-CA1 synapse can be accounted for consistently only when a refractory period of the order of few milliseconds between releases is introduced. Including a second sensor for asynchronous release that has a slow unbinding site and therefore an embedded long memory, is shown to play a role in short-term plasticity by facilitating release. For synchronous release mediated by Synaptotagmin II a third time scale is revealed in addition to the fast and slow release. This third time scale corresponds to "stimulus-correlated super-fast" neurotransmitter release. Our detailed spatial simulation indicates that all three-time scales of neurotransmitter release are an emergent property of the calcium sensor and independent of synaptic ultrastructure. Furthermore, it allows us to identify features of synaptic transmission that are universal and those that are modulated by structure.

q-bio.NC↗
arXiv2010

Polymorphic Dynamics of Microtubules

Starting from the hypothesis that the tubulin dimer is a conformationally bistable molecule - fluctuating between a curved and a straight configuration at room temperature - we develop a model for polymorphic dynamics of the microtubule lattice. We show that tubulin bistability consistently explains unusual dynamic fluctuations, the apparent length-stiffness relation of grafted microtubules and the curved-helical appearance of microtubules in general. Analyzing experimental data we conclude that taxol stabilized microtubules exist in highly cooperative yet strongly fluctuating helical states. When clamped by the end the microtubule undergoes an unusual zero energy motion - in its effect reminiscent of a limited rotational hinge.

q-bio.BM↗
arXiv2010

Microtubule Dynamics and Oscillating State for Mitotic Spindle

We present a physical mechanism that can cause the mitotic spindle to oscillate. The driving force for this mechanism emerges from the polymerization of astral microtubules interacting with the cell cortex. We show that Brownian ratchet model for growing microtubules reaching the cell cortex, mediate an effective mass to the spindle body and therefore force it to oscillate. We compare the predictions of this mechanism with the previous mechanisms which were based on the effects of motor proteins. Finally we combine the effects of microtubules polymerization and motor proteins, and present the detailed phase diagram for possible oscillating states.

physics.bio-ph↗
arXiv2010

Demixing of compact polymers chains in three dimensions

We present a Monte Carlo algorithm that provides efficient and unbiased sampling of polymer melts consisting of two chains of equal length that jointly visit all the sites of a cubic lattice with rod geometry L x L x rL and non-periodic (hard wall) boundary conditions. Using this algorithm for chains of length up to 40 000 monomers and aspect ratios 1 <= r <= 10, we show that in the limit of a large lattice the two chains phase separate. This demixing phenomenon is present already for r=1, and becomes more pronounced, albeit not perfect, as r is increased.

cond-mat.stat-mech↗
arXiv2010

Phase Transition Induced Fission in Lipid Vesicles

In this work we demonstrate how the first order phase transition in giant unilamellar vesicles (GUVs) can function as a trigger for membrane fission. When driven through their gel-fluid phase transition GUVs exhibit budding or pearl formation. These buds remain connected to the mother vesicle presumably by a small neck. Cooling these vesicles from the fluid phase (T>Tm) through the phase transition into the gel state (T<Tm), leads to complete rupture and fission of the neck, while the mother vesicle remains intact. Pearling tubes which formed upon heating break-up and decay into multiple individual vesicles which then diffuse freely. Finally we demonstrate that mimicking the intracellular bulk viscosity by increasing the bulk viscosity to 40cP does not affect the overall fission process, but leads to a significant decrease in size of the released vesicles.

physics.bio-ph↗
arXiv2010

Computational modelling of the collective stochastic motion of Kinesin nano motors

We have developed a two dimensional stochastic molecular dynamics model for the description of intra cellular collective motion of bio motors, in particular Kinesins, on a microtubular track. The model is capable or reproducing the hand-over-hand mechanism of the directed motion along the microtubule. The model gives the average directed velocity and the current of Kinesins along the microtubule. It is shown that beyond a certain density of Kinesins, the average velocity and current undergo notable decrease which is due to formation of traffic jams in the system.

cond-mat.soft↗
arXiv2011

Optimal orientation in branched cytoskeletal networks

Actin cytoskeletal protrusions in crawling cells, or lamellipodia, exhibit various morphological properties such as two characteristic peaks in the distribution of filament orientation with respect to the leading edge. To understand these properties, using the dendritic nucleation model as a basis for cytoskeletal restructuring, a kinetic-population model with orientational-dependent branching (birth) and capping (death) is constructed and analyzed. Optimizing for growth yields a relation between the branch angle and filament orientation that explains the two characteristic peaks. The model also exhibits a subdominant population that allows for more accurate modeling of recent measurements of filamentous actin density along the leading edge of lamellipodia in keratocytes. Finally, we explore the relationship between orientational and spatial organization of filamentous actin in lamellipodia and address recent observations of a prevalence of overlapping filaments to branched filaments---a finding that is claimed to be in contradiction with the dendritic nucleation model.

q-bio.SC↗
arXiv2010

The Effects of Stator Compliance, Backs Steps, Temperature, and Clockwise Rotation on the Torque-Speed Curve of Bacterial Flagellar Motor

Rotation of a single bacterial flagellar motor is powered by multiple stators tethered to the cell wall. In a "power-stroke" model the observed independence of the speed at low load on the number of stators is explained by a torque-dependent stepping mechanism independent of the strength of the stator tethering spring. On the other hand, in models that depend solely on the stator spring to explain the observed behavior, exceedingly small stator spring constants are required. To study the dynamics of the motor driven by external forces (such as those exerted by an optical tweezer), back-stepping is introduced when stators are driven far out of equilibrium. Our model with back-stepping reproduces the observed absence of a barrier to backward rotation, as well the behaviors in the high-speed negative-torque regime. Recently measured temperature dependence of the motor speed near zero load (Yuan & Berg 2010 Biophys J) is explained quantitatively by the thermally activated stepping rates in our model. Finally, we suggest that the general mechanical properties of all molecular motors (linear and rotary), characterized by their force(torque)-speed curve, can be determined by their power-stroke potentials and the dependence of the stepping rates on the mechanical state of the motor (force or speed). The torque-speed curve for the clockwise rotating flagellar motor has been observed for the first time recently (Yuan et al. 2010 PNAS). Its quasi-linear behavior is quantitatively reproduced by our model. In particular, we show that concave and convex shapes of the torque-speed curve can be achieved by changing the interaction potential from linear to quadratic form. We also show that reversing the stepping rate dependence on force (torque) can lead to non-monotonicity in the speed-load dependency.

q-bio.SC↗
arXiv2010

Modeling the effects of cymene on the distribution of germination and growth of Beauveria bassiana

Essential oils have antifungal and antipathogenic effects and therefore are targets in plant pathology research for their potential uses as natural substitutes for inorganic plant pesticides. Beauveria bassiana, an entomopathogenic fungus, can endophytically colonize a vast number of plant species and trigger induced systemic resistance against plant pathogens. Spore germination is the most vulnerable in the fungal life cycle and is therefore a good candidate for monitoring the effect of essential oils on the growth of B. bassiana. Percentage germination of fungal spores and length of germination tubes were recorded from experiments. A mathematical model that was able to capture the effects of cymene, an essential oil produced by Monarda, on the germination and growth was developed. This is the first report of a model for the impact of essential oils on B. bassiana spore germination.

q-bio.QM↗
arXiv2010

Linear noise approximation of noise-induced oscillation in NF-κB signaling network

NF-κB, one of key regulators of inflammation, apoptosis, and differentiation, was found to have noisy oscillatory shuttling between the nucleus and the cytoplasm in single cells when cells are stimulated by cytokine TNFα. We present the analytical analysis which uncovers the underlying physical mechanisms of this spectacular noise-induced transition in biological networks. Starting with the master equation describing both signaling and transcription events in NF-κB signaling network, we derived the macroscopic and the Fokker-Planck equations by using van Kampen's sysem size expansion. Using the noise-induced oscillatory signatures present in the power spectrum, we constructed the two-dimensional phase diagram where the noise-induced oscillation emerges in the dynamically stable parameter space.

q-bio.MN↗
arXiv2010

RSC remodeling of oligo-nucleosomes: an atomic force microscopy study

RSC is an essential chromatin remodeling factor that is required for the control of several processes including transcription, repair and replication. The ability of RSC to relocate centrally positioned mononucleosomes at the end of nucleosomal DNA is firmly established, but the data on RSC action on oligo-nucleosomal templates remains still scarce. By using Atomic Force Microscopy (AFM) imaging, we have quantitatively studied the RSC- induced mobilization of positioned di- and trinucleosomes as well as the directionality of mobilization on mononucleosomal template labeled at one end with streptavidin. AFM imaging showed only a limited set of distinct configurational states for the remodeling products. No stepwise or preferred directionality of the nucleosome motion was observed. Analysis of the corresponding reaction pathways allows deciphering the mechanistic features of RSC-induced nucleosome relocation. The final outcome of RSC remodeling of oligosome templates is the packing of the nucleosomes at the edge of the template, providing large stretches of DNA depleted of nucleosomes. This feature of RSC may be used by the cell to overcome the barrier imposed by the presence of nucleosomes.

physics.bio-ph↗
arXiv2010

Estimation of the number of biophotons involved in the visual perception of a single-object image: Biophoton intensity can be considerably higher inside cells than outside

Recently, we have proposed a redox molecular hypothesis about the natural biophysical substrate of visual perception and imagery (Bókkon, 2009. BioSystems; Bókkon and D'Angiulli, 2009. Bioscience Hypotheses). Namely, the retina transforms external photon signals into electrical signals that are carried to the V1 (striate cortex). Then, V1 retinotopic electrical signals (spike-related electrical signals along classical axonal-dendritic pathways) can be converted into regulated ultraweak bioluminescent photons (biophotons) through redox processes within retinotopic visual neurons that make it possible to create intrinsic biophysical pictures during visual perception and imagery. However, the consensus opinion is to consider biophotons as by-products of cellular metabolism. This paper argues that biophotons are not by-products, other than originating from regulated cellular radical/redox processes. It also shows that the biophoton intensity can be considerably higher inside cells than outside. Our simple calculations, within a level of accuracy, suggest that the real biophoton intensity in retinotopic neurons may be sufficient for creating intrinsic biophysical picture representation of a single-object image during visual perception.

q-bio.NC↗
arXiv2010

A Stochastic Markov Model for Coordinated Molecular Motors

Many cell functions are accomplished thanks to intracellular transport mechanisms of macromolecules along filaments. Molecular motors such as dynein or kinesin are proteins playing a primary role in these processes. The behavior of such proteins is quite well understood when there is only one of them moving a cargo particle. Indeed, numerous in vitro experiments have been performed to derive accurate models for a single molecular motor. However, in vivo macromolecules are often carried by multiple motors. The main focus of this paper is to provide an analysis of the behavior of more molecular motors interacting together in order to improve the understanding of their actual physiological behavior. Previous studies provide analyses based on results obtained from Monte Carlo simulations. Different from these studies, we derive an equipollent probabilistic model to describe the dynamics of multiple proteins coupled together and provide an exact theoretical analysis. We are capable of obtaining the probability density function of the motor protein configurations, thus enabling a deeper understanding of their behavior.

nlin.CD↗
arXiv2012

The mechanics of a microscopic mixer: microtubules and cytoplasmic streaming in Drosophila oocytes

Large scale motion of cytoplasm called cytoplasmic streaming occurs in some large eukaryotic cells to stir the cell's constituents. In Drosophila oocytes, microtubules have been observed to undergo undulating motion, curving to form travelling waves during cytoplasmic streaming. Here we show that this wave-like motion can be understood physically as due to the hydrodynamic drag of streaming impellers attached to kinesin motors moving toward the plus-ends of microtubules whose minus ends are anchored to the cell cortex. The tangential forces applied to such microtubules by kinesin give rise to bending and leads to chiral symmetry breaking causing the microtubules to propagate long travelling waves. The waves are reminiscent of those seen in flagellar motion but of a much longer time scale and by a different physical mechanism. We show how kinesin movement can produce a bulk flow of cytoplasm surrounding a microtubule with the range of flow greatly enhanced by the effect of hydrodynamic coupling between impellers. That is, a relatively small number of motors can move a large amount of fluid. The chaotic nature of the fluid motion of cytoplasm caused by kinesin movement along constantly changing microtubule trajectories is important as it greatly enhances the efficiency of mixing. Existing data on in vitro microtubule gliding assays also show this chiral instability in two dimensions and an analysis of this gives quantitative estimates for the forces exerted by motors and the drag coefficient.

q-bio.SC↗