Mikko Haataja

Modeling Elasticity in Crystal Growth

A new model of crystal growth is presented that describes the phenomena on atomic length and diffusive time scales. The former incorporates elastic and plastic deformation in a natural manner, and the latter enables access to time scales much larger than conventional atomic methods. The model is shown to be consistent with the predictions of Read and Shockley for grain boundary energy, and Matthews and Blakeslee for misfit dislocations in epitaxial growth.

Ionic surfactant aggregates in saline solutions: Sodium dodecyl sulfate (SDS) in the presence of excess sodium chloride (NaCl) or calcium chloride (CaCl2)

The properties of sodium dodecyl sulfate (SDS) aggregates in saline solutions of excess sodium chloride (NaCl) or calcium chloride (CaCl(2)) ions were studied through extensive molecular dynamics simulations with explicit solvent. We find that the ionic strength of the solution affects not only the aggregate size of the resulting anionic micelles but also their structure. Specifically, the presence of CaCl(2) induces more compact and densely packed micelles with a significant reduction in gauche defects in the SDS hydrocarbon chains in comparison with NaCl. Furthermore, we observe significantly more stable salt bridges between the charged SDS head groups mediated by Ca(2+) than Na(+). The presence of these salt bridges helps stabilize the more densely packed micelles.

Formation and Regulation of Lipid Microdomains in Cell Membranes: Theory, Modeling, and Speculation

Compositional lipid microdomains (“lipid rafts”) in plasma membranes are believed to be important components of many cellular processes. The biophysical mechanisms by which cells regulate the size, lifetime, and spatial localization of these domains are rather poorly understood at the moment. Over the years, experimental studies of raft formation have inspired several phenomenological theories and speculations incorporating a wide variety of thermodynamic assumptions regarding lipid–lipid and lipid–protein interactions, and the potential role of active cellular processes on membrane structure. Here we critically review and discuss these theories, models, and speculations, and present our view on future directions.

RNA transcription modulates phase transition-driven nuclear body assembly

Significance Living cells contain various membraneless organelles whose size and assembly appear to be governed by equilibrium thermodynamic phase separation. However, the dynamics of this process are poorly understood. Here, we quantify the assembly dynamics of liquid-phase nuclear bodies and find that they can be explained by classical models of phase separation and coarsening. In addition, active nonequilibrium processes, particularly rRNA transcription, can locally modulate thermodynamic parameters to stabilize nucleoli. Our findings demonstrate that the classical phase separation mechanisms long associated with nonliving condensed matter can mediate organelle assembly in living cells, whereas chemical activity may serve to regulate these processes in response to developmental or environmental conditions. Nuclear bodies are RNA and protein-rich, membraneless organelles that play important roles in gene regulation. The largest and most well-known nuclear body is the nucleolus, an organelle whose primary function in ribosome biogenesis makes it key for cell growth and size homeostasis. The nucleolus and other nuclear bodies behave like liquid-phase droplets and appear to condense from the nucleoplasm by concentration-dependent phase separation. However, nucleoli actively consume chemical energy, and it is unclear how such nonequilibrium activity might impact classical liquid–liquid phase separation. Here, we combine in vivo and in vitro experiments with theory and simulation to characterize the assembly and disassembly dynamics of nucleoli in early Caenorhabditis elegans embryos. In addition to classical nucleoli that assemble at the transcriptionally active nucleolar organizing regions, we observe dozens of “extranucleolar droplets” (ENDs) that condense in the nucleoplasm in a transcription-independent manner. We show that growth of nucleoli and ENDs is consistent with a first-order phase transition in which late-stage coarsening dynamics are mediated by Brownian coalescence and, to a lesser degree, Ostwald ripening. By manipulating C. elegans cell size, we change nucleolar component concentration and confirm several key model predictions. Our results show that rRNA transcription and other nonequilibrium biological activity can modulate the effective thermodynamic parameters governing nucleolar and END assembly, but do not appear to fundamentally alter the passive phase separation mechanism.

Tunable helical ribbons

The helix angle, chirality, and radius of helical ribbons are predicted with a comprehensive, three-dimensional analysis that incorporates elasticity, differential geometry, and variational principles. In many biological and engineered systems, ribbon helicity is commonplace and may be driven by surface stress, residual strain, and geometric or elastic mismatch between layers of a laminated composite. Unless coincident with the principle geometric axes of the ribbon, these anisotropies will lead to spontaneous, three-dimensional helical deformations. Analytical, closed-form ribbon shape predictions are validated with table-top experiments. More generally, our approach can be applied to develop materials and systems with tunable helical geometries.

Nonlinear geometric effects in mechanical bistable morphing structures.

Bistable structures associated with nonlinear deformation behavior, exemplified by the Venus flytrap and slap bracelet, can switch between different functional shapes upon actuation. Despite numerous efforts in modeling such large deformation behavior of shells, the roles of mechanical and nonlinear geometric effects on bistability remain elusive. We demonstrate, through both theoretical analysis and tabletop experiments, that two dimensionless parameters control bistability. Our work classifies the conditions for bistability, and extends the large deformation theory of plates and shells.

Electrostatic Screening and Charge Correlation Effects in Micellization of Ionic Surfactants

We have used atomistic simulations to study the role of electrostatic screening and charge correlation effects in self-assembly processes of ionic surfactants into micelles. Specifically, we employed grand canonical Monte Carlo simulations to investigate the critical micelle concentration (cmc), aggregation number, and micellar shape in the presence of explicit sodium chloride (NaCl). The two systems investigated are cationic dodecyltrimethylammonium chloride (DTAC) and anionic sodium dodecyl sulfate (SDS) surfactants. Our explicit-salt results, obtained from a previously developed potential model with no further adjustment of its parameters, are in good agreement with experimental data for structural and thermodynamic micellar properties. We illustrate the importance of ion correlation effects by comparing these results with a Yukawa-type surfactant model that incorporates electrostatic screening implicitly. While the effect of salt on the cmc is well-reproduced even with the implicit Yukawa model, the aggregate size predictions deviate significantly from experimental observations at low salt concentrations. We attribute this discrepancy to the neglect of ion correlations in the implicit-salt model. At higher salt concentrations, we find reasonable agreement of the Yukawa model with experimental data. The crossover from low to high salt concentrations is reached when the electrostatic screening length becomes comparable to the headgroup size.

Hydrodynamic effects on spinodal decomposition kinetics in planar lipid bilayer membranes

The formation and dynamics of spatially extended compositional domains in multicomponent lipid membranes lie at the heart of many important biological and biophysical phenomena. While the thermodynamic basis for domain formation has been explored extensively in the past, domain growth in the presence of hydrodynamic interactions both within the (effectively) two-dimensional membrane and in the three-dimensional solvent in which the membrane is immersed has received little attention. In this work, we explore the role of hydrodynamic effects on spinodal decomposition kinetics via continuum simulations of a convective Cahn-Hilliard equation for membrane composition coupled to the Stokes equation. Our approach explicitly includes hydrodynamics both within the planar membrane and in the three-dimensional solvent in the viscously dominated flow regime. Numerical simulations reveal that dynamical scaling breaks down for critical lipid mixtures due to distinct coarsening mechanisms for elongated versus more isotropic compositional lipid domains. The breakdown in scaling should be readily observable in experiments on model membrane systems.

Simulations of micellization of sodium hexyl sulfate

Micellization of the ionic surfactant sodium hexyl sulfate has been studied using atomistic explicit-solvent molecular dynamics simulations with and without excess NaCl or CaCl(2). Simulations were performed at surfactant loadings near the critical micellization concentration. Equilibrium micelle size distributions and estimates of the critical micellization concentration obtained from the simulations are in agreement with experimental data. In comparison to the sodium dodecyl sulfate surfactant, the shorter alkyl chain of sodium hexyl sulfate results in increased disorder of the micellar core and water exposure of the hydrocarbon tail groups. However, water and ions do not penetrate into the micellar core even for these weakly micellizing surfactants. Excess NaCl is observed to have a minor influence on the micelle structure but excess CaCl(2) induces drastic changes both in the structure and the dynamics of the micellar system. Furthermore, in the absence of excess salt, sodium hexyl sulfate forms predominantly spherical, disorganized aggregates but an increase in ionic strength drives an increase in aggregate size and leads to prolate aggregates.

Micelle fission through surface instability and formation of an interdigitating stalk

We report on the first detailed atomic-scale studies of micelle fission in micellar systems consisting of anionic sodium dodecyl sulfate with explicit solvent. We demonstrate a new micelle fission pathway for ionic surfactants and show how micelle fission can be induced by varying the ionic concentration. We argue that this fission pathway proceeds through an initial Rayleigh instability driven by Coulombic interactions and show how the intermediate stages proceed through the formation of a highly interdigitated stalk. This pathway may facilitate easier compartmentalization and functionalization of micelles.