Biscale Chaos in Propagating Fronts

The propagating chemical fronts found in cubic autocatalytic reaction-diffusion processes are studied. Simulations of the reaction-diffusion equation near to and far from the onset of the front instability are performed and the structure and dynamics of chemical fronts are studied. Qualitatively different front dynamics are observed in these two regimes. Close to onset the front dynamics can be characterized by a single length scale and described by the Kuramoto-Sivashinsky equation. Far from onset the front dynamics exhibits two characteristic lengths and cannot be modeled by this amplitude equation. An amplitude equation is proposed for this biscale chaos. The reduction of the cubic autocatalysis reaction-diffusion equation to the Kuramoto-Sivashinsky equation is explicitly carried out. The critical diffusion ratio delta, where the planar front loses its stability to transverse perturbations, is determined and found to be delta=2.300.Comment: Typeset using RevTeX, fig.1 and fig.4 are not available, mpeg simulations are at http://www.chem.utoronto.ca/staff/REK/Videos/front/front.htm

Statistical mechanics of hydrodynamic lattice gases

grantor: University of TorontoIn this thesis we present a model for fluid dynamics computations. The model combines a stochastic propagation scheme with special collision rules. We consider a class of collision rules with local mass, momentum and energy conservation laws. We derive the Boltzmann equation for the model and show that the Boltzmann H-theorem holds. By carrying out a Chapman-Enskog analysis we deduce that the macroscopic evolution of the system is governed by the Navier-Stokes equations. In the linear response approximation we derive Green-Kubo formulae for the discrete system and show that the Onsager reciprocal relations are valid for the model without microscopic reversibility. We derive expressions for the transport coefficients in terms of autocorrelation functions. Numerical experiments performed on the model support the theoretical analysis and demonstrate that the model provides a stable simulation method for turbulent hydrodynamic flows.Ph.D

Where Do the Ions Reside in a Highly Charged Droplet?

Droplets in atmospheric and electrosprayed aerosols carry more often than less, a multitude of ions. We address the question of the location of a collection of ions in charged aqueous droplets with linear dimensions in the nanometerrange using atomistic molecular dynamics and analytical theory. All the details of the computations have been described in the manuscript.<br /

Mechanism and Energy Landscape of Domain Swapping in the B1 Domain of Protein G

Three-dimensional domain swapping has emerged as a ubiquitous process for homo-oligomer formation in many unrelated proteins, but the molecular mechanism of this process is still poorly understood. Here we present a mechanism for the swapping reaction in the B1 domain of the immunoglobulin G binding protein from group G of Streptococcus (GB1). This is a particularly attractive system for investigating the swapping process, as the swapped dimer formed by the quadruple mutant (L5V/F30V/Y33F/A34F) of GB1 was recently shown to exist in equilibrium with a monomer-like conformation over time scales of minutes. According to our mechanism, swapping in GB1 starts from the C-terminus of the polypeptide chain and progresses by exchanging an increasing portion of the chains until a stable conformational state is reached. This exchange process does not involve unfolding. Rather, the conformational changes of individual monomers and their association are tightly coupled to minimize solvent exposure and maximize the total number of native contacts at all times, thereby closely approximating the minimum energy path of the reaction. Using detailed atomic descriptions, we compute the complete free-energy profiles of the exchange reaction for the GB1 quadruple mutant that forms swapped dimers and for the wild-type protein, which is monomeric. In both GB1 forms, intermediates sample a surprisingly wide range of nearly isoenergetic association modes and hinge conformations, indicating that the exchange reaction is a non-specific process akin to encounter complex formation where the amino acid sequence plays a marginal role. The main role of the mutations in the swapping process is to destabilize the GB1 monomer state, while stabilizing the swapped dimer conformation, with non-native intersubunit interactions, fostered by mutant side chains, contributing significantly to this stabilization. Our findings are rationalized in terms of a generic swapping mechanism that involves the association of activated molecular species, and it is argued that a similar mechanism may apply to swapping in other protein systems. © 2008.SCOPUS: ar.jinfo:eu-repo/semantics/publishe

Advances in Modeling the Stability of Noncovalent Complexes in Charged Droplets with Applications in Electrospray Ionization-MS Experiments

Electrospray ionization mass spectrometry is used extensively to measure the equilibrium constant of noncovalent complexes. In this Perspective, we attempt to present an accessible introduction to computational methodologies that can be applied to determine the stability of weak noncovalent complexes in their journey from bulk solution into the gaseous state. We demonstrate the usage of the methods on two typical examples of noncovalent complexes drawn from a broad class of nucleic acids and transient protein complexes found in aqueous droplets. We conclude that this new emerging direction in the use of simulations can lead to estimates of equilibrium constant corrections due to complex dissociation in the carrier droplet and finding of agents that may stabilize the protein interfaces

Supplementary Material from Interplay of self-association and conformational flexibility in regulating protein function

3 supporting Figures, 1 supporting Table; Figure and Table caption