Biomedical subjects

A B Kolomeisky

Publications and source records attributed to A B Kolomeisky.

4 recordsLinked to original sources

PubMed2003

Localization of shocks in driven diffusive systems without particle number conservation.

We study the formation of localized shocks in one-dimensional driven diffusive systems with spatially homogeneous creation and annihilation of particles (Langmuir kinetics). We show how to obtain hydrodynamic equations that describe the density profile in systems with uncorrelated steady state as well as in those exhibiting correlations. As a special example of the latter case, the Katz-Lebowitz-Spohn model is considered. The existence of a localized double density shock is demonstrated in one-dimensional driven diffusive systems. This corresponds to phase separation into regimes of three distinct densities, separated by localized domain walls. Our analytical approach is supported by Monte Carlo simulations.

Journal Article↗

PubMed2001

Simple mechanochemistry describes the dynamics of kinesin molecules.

Recently, Block and coworkers [Visscher, K., Schnitzer, M. J., & Block, S. M. (1999) Nature (London) 400, 184--189 and Schnitzer, M. J., Visscher, K. & Block, S. M. (2000) Nat. Cell Biol. 2, 718--723] have reported extensive observations of individual kinesin molecules moving along microtubules in vitro under controlled loads, F = 1 to 8 pN, with [ATP] = 1 microM to 2 mM. Their measurements of velocity, V, randomness, r, stalling force, and mean run length, L, reveal a need for improved theoretical understanding. We show, presenting explicit formulae that provide a quantitative basis for comparing distinct molecular motors, that their data are satisfactorily described by simple, discrete-state, sequential stochastic models. The simplest (N = 2)-state model with fixed load-distribution factors and kinetic rate constants concordant with stopped-flow experiments, accounts for the global (V, F, L, [ATP]) interdependence and, further, matches relative acceleration observed under assisting loads. The randomness, r(F,[ATP]), is accounted for by a waiting-time distribution, psi(1)(+)(t), [for the transition(s) following ATP binding] with a width parameter nu identical with (2)/<(Delta t)(2)> approximately 2.5, indicative of a dispersive stroke of mechanicity approximately 0.6 or of a few ( greater than or similar to nu - 1) further, kinetically coupled states: indeed, N = 4 (but not N = 3) models do well. The analysis reveals: (i) a substep of d(0) = 1.8--2.1 nm on ATP binding (consistent with structurally based suggestions); (ii) comparable load dependence for ATP binding and unbinding; (iii) a strong load dependence for reverse hydrolysis and subsequent reverse rates; and (iv) a large ( greater than or similar to 50-fold) increase in detachment rate, with a marked load dependence, following ATP binding.

Animals↗

PubMed2001

Force-velocity relation for growing microtubules.

Forces generated by microtubule polymerization and depolymerization are important for the biological functioning of cells. The mean growth velocity, V, under an opposing force, F, has been measured by; Science 278:856-860) for single microtubules growing in vitro, but their analysis of the data suggested that V decreased more rapidly with F than equilibrium (or "thermodynamic") theory predicted and entailed negative values for the dissociation rate and undefined (or unreasonable) values for the stall force, at which V vanishes. By contrast, considering the mean work done against the external load and allowing for load-distribution factors for the "on" and "off" rates, we find good agreement with a simple theory that yields a plausible stalling force. Although specific numerical results are sensitive to choice of fitting criteria, about 80% of the variation with load is carried by the "off" (or dissociation) rate, but, since that is small (in accordance with independent observations), the dominant force dependence comes from the "on" rate, which is associated with a displacement length, d(1), significantly longer than d(0) approximately 1/13(8.2 nm), the mean length increase per added tubulin dimer. Measuring the dispersion in length of the growing microtubules could provide a check. The theory implies that the stationary stall state (at V = 0) is not one of simple associative thermal equilibrium, as previously supposed; rather, it appears to be dissipative and kinetically controlled.

Biophysical Phenomena↗

PubMed1999

The force exerted by a molecular motor.

The stochastic driving force exerted by a single molecular motor (e. g., a kinesin, or myosin) moving on a periodic molecular track (microtubule, actin filament, etc.) is discussed from a general viewpoint open to experimental test. An elementary "barometric" relation for the driving force is introduced that (i) applies to a range of kinetic and stochastic models, (ii) is consistent with more elaborate expressions entailing explicit representations of externally applied loads, and (iii) sufficiently close to thermal equlibrium, satisfies an Einstein-type relation in terms of the velocity and diffusion coefficient of the (load-free) motor. Even in the simplest two-state models, the velocity-vs.-load plots exhibit a variety of contrasting shapes (including nonmonotonic behavior). Previously suggested bounds on the driving force are shown to be inapplicable in general by analyzing discrete jump models with waiting time distributions.

Animals↗