Searcharxiv⌕ Search

arXiv subjects

Mark S. Alber

Publications and source records attributed to Mark S. Alber.

7 recordsLinked to original sources
arXiv2015

Foam-like compression behavior of fibrin networks

The rheological properties of fibrin networks have been of long-standing interest. As such there is a wealth of studies of their shear and tensile responses, but their compressive behavior remains unexplored. Here, by characterization of the network structure with synchronous measurement of the fibrin storage and loss moduli at increasing degrees of compression, we show that the compressive behavior of fibrin networks is similar to that of cellular solids. A non-linear stress-strain response of fibrin consists of three regimes: 1) an initial linear regime, in which most fibers are straight, 2) a plateau regime, in which more and more fibers buckle and collapse, and 3) a markedly non-linear regime, in which network densification occurs {by bending of buckled fibers} and inter-fiber contacts. Importantly, the spatially non-uniform network deformation included formation of a moving "compression front" along the axis of strain, which segregated the fibrin network into compartments with different fiber densities and structure. The Young's modulus of the linear phase depends quadratically on the fibrin volume fraction while that in the densified phase depends cubically on it. The viscoelastic plateau regime corresponds to a mixture of these two phases in which the fractions of the two phases change during compression. We model this regime using a continuum theory of phase transitions and analytically predict the storage and loss moduli which are in good agreement with the experimental data. Our work shows that fibrin networks are a member of a broad class of natural cellular materials which includes cancellous bone, wood and cork.

cond-mat.soft↗
arXiv2013

Microtubule dynamic instability: the role of cracks between protofilaments

Microtubules (MTs) are cytoplasmic protein polymers that are essential for fundamental cellular processes including the maintenance of cell shape, organelle transport and formation of the mitotic spindle. Microtubule dynamic instability is critical for these processes, but it remains poorly understood, in part because the relationship between the structure of the MT tip and the growth/depolymerization transitions is enigmatic. What are the functionally significant aspects of a tip structure that is capable of promoting MT growth, and how do changes in these characteristics cause the transition to depolymerization (catastrophe)? Here we use computational models to investigate the connection between cracks (laterally unbonded regions) between protofilaments and dynamic instability. Our work indicates that it is not the depth of the cracks per se that governs MT dynamic instability. Instead it is whether the cracks terminate in GTP-rich or GDP-rich areas of the MT that governs whether a particular MT tip structure is likely to grow, shrink, or transition: the identity of the crack-terminating subunit pairs has a profound influence on the moment-by-moment behavior of the MT.

q-bio.BM↗
arXiv2006

Analysis of a microscopic stochastic model of microtubule dynamic instability

A novel theoretical model of dynamic instability of a system of linear (1D) microtubules (MTs) in a bounded domain is introduced for studying the role of a cell edge in vivo and analyzing the effect of competition for a limited amount of tubulin. The model differs from earlier models in that the evolution of MTs is based on the rates of single unit (e.g., a heterodimer per protofilament) transformations, in contrast to postulating effective rates/frequencies of larger-scale changes, extracted, e.g., from the length history plots of MTs. Spontaneous GTP hydrolysis with finite rate after polymerization is assumed, and theoretical estimates of an effective catastrophe frequency as well as other parameters characterizing MT length distributions and cap size are derived. We implement a simple cap model which does not include vectorial hydrolysis. We demonstrate that our theoretical predictions, such as steady state concentration of free tubulin, and parameters of MT length distributions, are in agreement with the numerical simulations. The present model establishes a quantitative link between microscopic parameters governing the dynamics of MTs and macroscopic characteristics of MTs in a closed system. Lastly, we use a computational Monte Carlo model to provide an explanation for non-exponential MT length distributions observed in experiments. In particular, we show that appearance of such non-exponential distributions in the experiments can occur because the true steady state has not been reached, and/or due to the presence of a cell edge.

q-bio.SC↗
arXiv2004

Lattice gas cellular automata model for rippling and aggregation in myxobacteria

A lattice-gas cellular automaton (LGCA) model is used to simulate rippling and aggregation in myxobacteria. An efficient way of representing cells of different cell size, shape and orientation is presented that may be easily extended to model later stages of fruiting body formation. This LGCA model is designed to investigate whether a refractory period, a minimum response time, a maximum oscillation period and non-linear dependence of reversals of cells on C-factor are necessary assumptions for rippling. It is shown that a refractory period of 2-3 minutes, a minimum response time of up to 1 minute and no maximum oscillation period best reproduce rippling in the experiments of {\it Myxoccoccus xanthus}. Non-linear dependence of reversals on C-factor is critical at high cell density. Quantitative simulations demonstrate that the increase in wavelength of ripples when a culture is diluted with non-signaling cells can be explained entirely by the decreased density of C-signaling cells. This result further supports the hypothesis that levels of C-signaling quantitatively depend on and modulate cell density. Analysis of the interpenetrating high density waves shows the presence of a phase shift analogous to the phase shift of interpenetrating solitons. Finally, a model for swarming, aggregation and early fruiting body formation is presented.

q-bio.QM↗
arXiv2001

The Complex Geometry of Weak Piecewise Smooth Solutions of Integrable Nonlinear PDE's of Shallow Water and Dym Type

An extension of the algebraic-geometric method for nonlinear integrable PDE's is shown to lead to new piecewise smooth weak solutions of a class of $N$-component systems of nonlinear evolution equations. This class includes, among others, equations from the Dym and shallow water equation hierarchies. The main goal of the paper is to give explicit theta-functional solutions of these nonlinear PDE's, which are associated to nonlinear subvarieties of hyperelliptic Jacobians. The main results of the present paper are twofold. First, we exhibit some of the special features of integrable PDE's that admit piecewise smooth weak solutions, which make them different from equations whose solutions are globally meromorphic, such as the KdV equation. Second, we blend the techniques of algebraic geometry and weak solutions of PDE's to gain further insight into, and explicit formulas for, piecewise-smooth finite-gap solutions.

nlin.CD↗
arXiv2000

On Soliton-type Solutions of Equations Associated with N-component Systems

The algebraic geometric approach to $N$-component systems of nonlinear integrable PDE's is used to obtain and analyze explicit solutions of the coupled KdV and Dym equations. Detailed analysis of soliton fission, kink to anti-kink transitions and multi-peaked soliton solutions is carried out. Transformations are used to connect these solutions to several other equations that model physical phenomena in fluid dynamics and nonlinear optics.

nlin.PS↗