Tatiana Kuriabova

Linear aggregation and liquid-crystalline order: comparison of Monte Carlo simulation and analytic theory

Many soft-matter and biophysical systems are composed of monomers that reversibly assemble into rod-like aggregates. The aggregates can then order into liquid-crystal phases if the density is high enough, and liquid-crystal ordering promotes increased growth of aggregates. Systems that display coupled aggregation and liquid-crystal ordering include wormlike micelles, chromonic liquid crystals, DNA and RNA, and protein polymers and fibrils. Coarse-grained molecular models that capture key features of coupled aggregation and liquid-crystal ordering common to many different systems are lacking; in particular, the roles of monomer aspect ratio and aggregate flexibility in controlling the phase behavior are not well understood. Here we study a minimal system of sticky cylinders using Monte Carlo simulations and analytic theory. Cylindrical monomers interact primarily by hard-core interactions but can stack and bind end to end. We present results for several different cylinder aspect ratios and a range of end-to-end binding energies. The phase diagrams are qualitatively similar to those of chromonic liquid crystals, with an isotropic-nematic-columnar triple point. The location of the triple point is sensitive to the monomer aspect ratio. We find that the aggregate persistence length varies with temperature in a way that is controlled by the interaction potential; this suggests that the form of the interaction potential affects the phase behavior of the system. Our analytic theory shows improvement compared to previous theory in quantitatively predicting the I–N transition for relatively stiff aggregates, but requires a better treatment of aggregate flexibility.

Nanorheology of viscoelastic shells : Applications to viral capsids

We study the microrheology of nanoparticle shells [A. D. Dinsmore, Science 298, 1006 (2002)] and viral capsids [I. L. Ivanovska, Proc. Natl. Acad. Sci. U.S.A. 101, 7600 (2004)] by computing the mechanical response function and thermal fluctuation spectrum of a viscoelastic spherical shell that is permeable to the surrounding solvent. We determine analytically the damped dynamics of bend and compression modes of the shell coupled to the solvent both inside and outside the sphere in the zero Reynolds number limit. We identify fundamental length and time scales in the system, and compute the thermal correlation function of displacements of antipodal points on the sphere and the mechanical response to pinching forces applied at these points. We describe how such a frequency-dependent antipodal correlation and/or response function, which should be measurable in new AFM-based microrheology experiments, can probe the viscoelasticity of these synthetic and biological shells constructed of nanoparticles.

Mutual diffusion of inclusions in freely suspended smectic liquid crystal films.

We study experimentally and theoretically the hydrodynamic interaction of pairs of circular inclusions in two-dimensional, fluid smectic membranes suspended in air. By analyzing their Brownian motion, we find that the radial mutual mobilities of identical inclusions are independent of their size but that the angular coupling becomes strongly size dependent when their radius exceeds a characteristic hydrodynamic length. These observations are described well for arbitrary inclusion separations by a model that generalizes the Levine-MacKintosh theory of point-force response functions and uses a boundary-element approach to calculate the mobility matrix for inclusions of finite extent.

Effect of external stress on the thermal melting of DNA

We discuss the effects of external stress on the thermal denaturation of homogeneous DNA. Pulling double-stranded DNA at each end exerts a profound effect on the thermal denaturation, or melting, of a long segment of this molecule. We discuss the effects on this transition of a stretching force applied to opposite ends of the DNA, including full consideration of the consequences of excluded volume, the analysis of which is greatly simplified in this case. We find that in three dimensions the heat capacity acquires a logarithmic dependence on reduced temperature.

Active microrheology of smectic membranes

Thin fluid membranes embedded in a bulk fluid of different viscosity are of fundamental interest as experimental realizations of quasi-two-dimensional fluids and as models of biological membranes. We have probed the hydrodynamics of thin fluid membranes by active microrheology using small tracer particles to observe the highly anisotropic flow fields generated around a rigid oscillating post inserted into a freely suspended smectic liquid crystal film that is surrounded by air. In general, at distances more than a few Saffman lengths from the meniscus around the post, the measured velocities are larger than the flow computed by modeling a moving disklike inclusion of finite extent by superposing Levine-MacKintosh response functions for pointlike inclusions in a viscous membrane. The observed discrepancy is attributed to additional coupling of the film with the air below the film that is displaced directly by the shaft of the moving post.

Accommodating Drift in Hidden Markov Analysis of Single-Molecule Data

Single-molecule techniques are increasingly used to measure state transitions in biomolecules. These data are typically a noisy time series with discrete transitions that reflect underlying distinct states; examples include the opening and closing of DNA hairpins, and the folding and unfolding of proteins. Hidden Markov models (HMMs) have been successfully used to infer transitions between the underlying states from noisy data. However, HMMs are typically applied to ratiometric data (e.g., FRET studies of RNA folding) and do not perform well on data that include drift. Yet, drift is common in real-space records from optical traps and atomic force microscopes. We developed a HMM that accommodates experimental drift using low-order Fourier modes. We use simulated traces to demonstrate the improved performance of our method and illustrate its use on measurements of single TATA-box binding proteins bending and unbending DNA.