Microscopic Theory of Protein Folding Rates.I: Fine Structure of the Free Energy Profile and Folding Routes from a Variational Approach

A microscopic theory of the free energy barriers and folding routes for minimally frustrated proteins is presented, greatly expanding on the presentation of the variational approach outlined previously [J. J. Portman, S. Takada, P. G. Wolynes, Phys. Rev. Lett. {\bf 81}, 5237 (1998)]. We choose the $\lambda$-repressor protein as an illustrative example and focus on how the polymer chain statistics influence free energy profiles and partially ordered ensembles of structures. In particular, we investigate the role of chain stiffness on the free energy profile and folding routes. We evaluate the applicability of simpler approximations in which the conformations of the protein molecule along the folding route are restricted to have residues that are either entirely folded or unfolded in contiguous stretches. We find that the folding routes obtained from only one contiguous folded region corresponds to a chain with a much greater persistence length than appropriate for natural protein chains, while the folding route obtained from two contiguous folded regions is able to capture the relatively folded regions calculated within the variational approach. The free energy profiles obtained from the contiguous sequence approximations have larger barriers than the more microscopic variational theory which is understood as a consequence of partial ordering.Comment: 16 pages, 11 figure

Spatial networks with wireless applications

Many networks have nodes located in physical space, with links more common between closely spaced pairs of nodes. For example, the nodes could be wireless devices and links communication channels in a wireless mesh network. We describe recent work involving such networks, considering effects due to the geometry (convex,non-convex, and fractal), node distribution, distance-dependent link probability, mobility, directivity and interference.Comment: Review article- an amended version with a new title from the origina

Stable Frank-Kasper phases of self-assembled, soft matter spheres

Single molecular species can self-assemble into Frank Kasper (FK) phases, finite approximants of dodecagonal quasicrystals, defying intuitive notions that thermodynamic ground states are maximally symmetric. FK phases are speculated to emerge as the minimal-distortional packings of space-filling spherical domains, but a precise quantitation of this distortion and how it affects assembly thermodynamics remains ambiguous. We use two complementary approaches to demonstrate that the principles driving FK lattice formation in diblock copolymers emerge directly from the strong-stretching theory of spherical domains, in which minimal inter-block area competes with minimal stretching of space-filling chains. The relative stability of FK lattices is studied first using a diblock foam model with unconstrained particle volumes and shapes, which correctly predicts not only the equilibrium {\sigma} lattice, but also the unequal volumes of the equilibrium domains. We then provide a molecular interpretation for these results via self-consistent field theory, illuminating how molecular stiffness regulates the coupling between intra-domain chain configurations and the asymmetry of local packing. These findings shed new light on the role of volume exchange on the formation of distinct FK phases in copolymers, and suggest a paradigm for formation of FK phases in soft matter systems in which unequal domain volumes are selected by the thermodynamic competition between distinct measures of shape asymmetry.Comment: 40 pages, 22 figure

Cross-Recurrence Quantification Analysis of Categorical and Continuous Time Series: an R package

This paper describes the R package crqa to perform cross-recurrence quantification analysis of two time series of either a categorical or continuous nature. Streams of behavioral information, from eye movements to linguistic elements, unfold over time. When two people interact, such as in conversation, they often adapt to each other, leading these behavioral levels to exhibit recurrent states. In dialogue, for example, interlocutors adapt to each other by exchanging interactive cues: smiles, nods, gestures, choice of words, and so on. In order for us to capture closely the goings-on of dynamic interaction, and uncover the extent of coupling between two individuals, we need to quantify how much recurrence is taking place at these levels. Methods available in crqa would allow researchers in cognitive science to pose such questions as how much are two people recurrent at some level of analysis, what is the characteristic lag time for one person to maximally match another, or whether one person is leading another. First, we set the theoretical ground to understand the difference between 'correlation' and 'co-visitation' when comparing two time series, using an aggregative or cross-recurrence approach. Then, we describe more formally the principles of cross-recurrence, and show with the current package how to carry out analyses applying them. We end the paper by comparing computational efficiency, and results' consistency, of crqa R package, with the benchmark MATLAB toolbox crptoolbox. We show perfect comparability between the two libraries on both levels

Topological Signals of Singularities in Ricci Flow

We implement methods from computational homology to obtain a topological signal of singularity formation in a selection of geometries evolved numerically by Ricci flow. Our approach, based on persistent homology, produces precise, quantitative measures describing the behavior of an entire collection of data across a discrete sample of times. We analyze the topological signals of geometric criticality obtained numerically from the application of persistent homology to models manifesting singularities under Ricci flow. The results we obtain for these numerical models suggest that the topological signals distinguish global singularity formation (collapse to a round point) from local singularity formation (neckpinch). Finally, we discuss the interpretation and implication of these results and future applications.Comment: 24 pages, 14 figure

Flow field computations for blunt bodies in planetary environments /equilibrium/ Final report

Radiative and convective heat transfer about two blunt bodies traveling at hypersonic speeds at zero angle of attack in assumed Mars atmosphere of nitrogen and carbon dioxid

Statics and Dynamics of Strongly Charged Soft Matter

Soft matter materials, such as polymers, membranes, proteins, are often electrically charged. This makes them water soluble, which is of great importance in technological application and a prerequisite for biological function. We discuss a few static and dynamic systems that are dominated by charge effects. One class comprises complexation between oppositely charged objects, for example the adsorption of charged ions or charged polymers (such as DNA) on oppositely charged substrates of different geometry. The second class comprises effective interactions between similarly charged objects. Here the main theme is to understand the experimental finding that similarly and highly charged bodies attract each other in the presence of multi-valent counterions. This is demonstrated using field-theoretic arguments as well as Monte-Carlo simulations for the case of two homogeneously charged bodies. Realistic surfaces, on the other hand, are corrugated and also exhibit modulated charge distributions, which is important for static properties such as the counterion-density distribution, but has even more pronounced consequences for dynamic properties such as the counterion mobility. More pronounced dynamic effects are obtained with highly condensed charged systems in strong electric fields. Likewise, an electrostatically collapsed highly charged polymer is unfolded and oriented in strong electric fields. At the end of this review, we give a very brief account of the behavior of water at planar surfaces and demonstrate using ab-initio methods that specific interactions between oppositely charged groups cause ion-specific effects that have recently moved into the focus of interest.Comment: 61 pages, 31 figures, Physics Reports (2005)-in press (high quality figures available from authors

A New Mechanism of Model Membrane Fusion Determined from Monte Carlo Simulation

We have carried out extensive Monte Carlo simulations of the fusion of tense apposed bilayers formed by amphiphilic molecules within the framework of a coarse grained lattice model. The fusion pathway differs from the usual stalk mechanism. Stalks do form between the apposed bilayers, but rather than expand radially to form an axial-symmetric hemifusion diaphragm of the trans leaves of both bilayers, they promote in their vicinity the nucleation of small holes in the bilayers. Two subsequent paths are observed: (i) The stalk encircles a hole in one bilayer creating a diaphragm comprised of both leaves of the other intact bilayer, and which ruptures to complete the fusion pore. (ii) Before the stalk can encircle a hole in one bilayer, a second hole forms in the other bilayer, and the stalk aligns and encircles them both to complete the fusion pore. Both pathways give rise to mixing between the cis and trans leaves of the bilayer and allow for transient leakage.Comment: revised version, accepted to Biophys. J. (11 figures