Morphogenesis of the Fission Yeast Cell through Cell Wall Expansion.

The shape of walled cells such as fungi, bacteria, and plants are determined by the cell wall. Models for cell morphogenesis postulate that the effects of turgor pressure and mechanical properties of the cell wall can explain the shapes of these diverse cell types. However, in general, these models await validation through quantitative experiments.

The local forces acting on the mechanotransduction channel in hair cell stereocilia.

In hair cells, mechanotransduction channels are located in the membrane of stereocilia tips, where the base of the tip link is attached. The tip-link force determines the system of other forces in the immediate channel environment, which change the channel open probability. This system of forces includes components that are out of plane and in plane relative to the membrane; the magnitude and direction of these components depend on the channel environment and arrangement.

Manipulating cell shape by placing cells into micro-fabricated chambers.

Cell shape is an important cellular parameter that influences the spatial organization and function of cells. However, it has often been challenging to study the effects of cell shape because of difficulties in experimentally controlling cell shape in a defined way. We describe here a method of physically manipulating sea urchin cells into specified shapes by inserting them into micro-fabricated chambers of different shapes.

Localization of cytokinesis factors to the future cell division site by microtubule-dependent transport.

The mechanism by which spindle microtubules (MTs) determine the site of cell division in animal cells is still highly controversial. Putative cytokinesis "signals" have been proposed to be positioned by spindle MTs at equatorial cortical regions to increase cortical contractility and/or at polar regions to decrease contractility [Rappaport, 1986; von Dassow, 2009]. Given the relative paucity of MTs at the future division site, it has not been clear how MTs localize cytokinesis factors there.

Stereocilia membrane deformation: implications for the gating spring and mechanotransduction channel.

In hair cells, although mechanotransduction channels have been localized to tips of shorter stereocilia of the mechanically sensitive hair bundle, little is known about how force is transmitted to the channel. Here, we use a biophysical model of the membrane-channel complex to analyze the nature of the gating spring compliance and channel arrangement. We use a triangulated surface model and Monte Carlo simulation to compute the deformation of the membrane under the action of tip link force.

Reflectivity and topography of cells grown on glass-coverslips measured with phase-shifted laser feedback interference microscopy.

In spite of the advantages associated with the molecular specificity of fluorescence imaging, there is still a significant need to augment these approaches with label-free imaging. Therefore, we have implemented a form of interference microscopy based upon phase-shifted, laser-feedback interferometry and developed an algorithm that can be used to separate the contribution of the elastically scattered light by sub-cellular structures from the reflection at the coverslip-buffer interface. The method offers an opportunity to probe protein aggregation, index of refraction variations and structure.

Membrane deformation at integrin adhesions.

In order to measure the nucleation of nouveau adhesions on the ventral surface of a cell, we have combined phase shifting laser feedback interferometry with a high numerical aperture inverted fluorescence microscope. We use fluorescence to image molecules at the adhesion site and stage scanning interference microscopy in order to measure the distance between the ventral surface of a cell and the substratum with several nanometer precision. Our analytic and Monte Carlo simulations of integrin mediated adhesions predict several features of these nouveau adhesions.

Nucleation and growth of integrin adhesions.

We present a model that provides a mechanistic understanding of the processes that govern the formation of the earliest integrin adhesions ex novo from an approximately planar plasma membrane. Using an analytic analysis of the free energy of a dynamically deformable membrane containing freely diffusing receptors molecules and long repeller molecules that inhibit integrins from binding with ligands on the extracellular matrix, we predict that a coalescence of polymerizing actin filaments can deform the membrane toward the extracellular matrix and facilitate integrin binding. Monte Carlo simulations of this system show that thermally induced membrane fluctuations can either zip-up and increase the radius of a nucleated adhesion or unzip and shrink an adhesion, but the fluctuations cannot bend the ventral membrane to nucleate an adhesion.

Chapter 23: Stochastic modeling methods in cell biology.

Stochastic methods have been a staple for understanding complex systems in chemistry and physics. In the biological context, they are useful for understanding phenomena ranging from molecular-level fluctuations to cellular movement. We review the basic formalism behind stochastic methods and outline how they can be implemented for quantifying gene expression, movement of molecular motors, and the dynamics of cytoplasmic components.

Shape transitions in lipid membranes and protein mediated vesicle fusion and fission.

In the cell, the plasma membrane is often densely decorated by transmembrane proteins. The morphology and dynamics of the membrane are strongly influenced by the presence of proteins. In this paper, we use a coarse-grained model to explore the composite membrane-protein system and develop a simulation methodology based on thermodynamic integration to examine free energy changes during membrane shape transitions.

Mechanics and dynamics of actin-driven thin membrane protrusions.

Motile cells explore their surrounding milieu by extending thin dynamic protrusions, or filopodia. The growth of filopodia is driven by actin filament bundles that polymerize underneath the cell membrane. We compute the mechanical and dynamical features of the protrusion growth process by explicitly incorporating the flexible plasma membrane.

Morphology of the lamellipodium and organization of actin filaments at the leading edge of crawling cells.

Lamellipodium extension, incorporating actin filament dynamics and the cell membrane, is simulated in three dimensions. The actin filament network topology and the role of actin-associated proteins such as Arp2/3 are examined. We find that the orientational pattern of the filaments is in accord with the experimental data only if the spatial orientation of the Arp2/3 complex is restricted during each branching event.

Equilibrium free energy estimates based on nonequilibrium work relations and extended dynamics.

Jarzynski's relation and the fluctuation theorem have established important connections between nonequilibrium statistical mechanics and equilibrium thermodynamics. In particular, an exact relationship between the equilibrium free energy and the nonequilibrium work is useful for computer simulations. In this paper, we exploit the fact that the free energy is a state function, independent of the pathway taken to change the equilibrium ensemble.

An application of error reduction and harmonic inversion schemes to the semiclassical calculation of molecular vibrational energy levels.

A singular value decomposition based harmonic inversion signal processing scheme is applied to the semiclassical initial value representation (IVR) calculation of molecular vibrational states. Relative to usual IVR procedure of Fourier analysis of a signal made from the Monte Carlo evaluation of the phase space integral in which many trajectories are needed, the new procedure obtains acceptable results with many fewer trajectories. Calculations are carried out for vibrational energy levels of H2O to illustrate the overall procedure.

Classical, semiclassical, and quantum investigations of the four-sphere scattering system.

A genuinely three-dimensional system, viz. the hyperbolic four-sphere scattering system, is investigated with classical, semiclassical, and quantum mechanical methods at various center-to-center separations of the spheres. The efficiency and scaling properties of the computations are discussed by comparisons to the two-dimensional three-disk system.