Thermodynamic Prediction of Protein Neutrality

We present a simple theory that uses thermodynamic parameters to predict the probability that a protein retains the wildtype structure after one or more random amino acid substitutions. Our theory predicts that for large numbers of substitutions the probability that a protein retains its structure will decline exponentially with the number of substitutions, with the severity of this decline determined by properties of the structure. Our theory also predicts that a protein can gain extra robustness to the first few substitutions by increasing its thermodynamic stability. We validate our theory with simulations on lattice protein models and by showing that it quantitatively predicts previously published experimental measurements on subtilisin and our own measurements on variants of TEM1 beta-lactamase. Our work unifies observations about the clustering of functional proteins in sequence space, and provides a basis for interpreting the response of proteins to substitutions in protein engineering applications

MLD Relations of Pisot Substitution Tilings

We consider 1-dimensional, unimodular Pisot substitution tilings with three intervals, and discuss conditions under which pairs of such tilings are locally isomorhphic (LI), or mutually locally derivable (MDL). For this purpose, we regard the substitutions as homomorphisms of the underlying free group with three generators. Then, if two substitutions are conjugated by an inner automorphism of the free group, the two tilings are LI, and a conjugating outer automorphism between two substitutions can often be used to prove that the two tilings are MLD. We present several examples illustrating the different phenomena that can occur in this context. In particular, we show how two substitution tilings can be MLD even if their substitution matrices are not equal, but only conjugate in $GL(n,\mathbb{Z})$. We also illustrate how the (in our case fractal) windows of MLD tilings can be reconstructed from each other, and discuss how the conjugating group automorphism affects the substitution generating the window boundaries.Comment: Presented at Aperiodic'09 (Liverpool

Incoherent non-Fermi liquid scattering in a Kondo lattice

One of the most notorious non-Fermi liquid properties of both archetypal heavy-fermion systems [1-4] and the high-Tc copper oxide superconductors [5] is an electrical resistivity that evolves linearly with temperature, T. In the heavy-fermion superconductor CeCoIn5 [5], this linear behaviour was one of the first indications of the presence of a zero-temperature instability, or quantum critical point. Here, we report the observation of a unique control parameter of T-linear scattering in CeCoIn5, found through systematic chemical substitutions of both magnetic and non-magnetic rare-earth, R, ions into the Ce sub-lattice. We find that the evolution of inelastic scattering in Ce1-xRxCoIn5 is strongly dependent on the f-electron configuration of the R ion, whereas two other key properties -- Cooper-pair breaking and Kondo-lattice coherence -- are not. Thus, T-linear resistivity in CeCoIn5 is intimately related to the nature of incoherent scattering centers in the Kondo lattice, which provides insight into the anomalous scattering rate synonymous with quantum criticality [7].Comment: 4 pages, 3 figures (published version

Predicting the Volumes of Crystals

New crystal structures are frequently derived by performing ionic substitutions on known crystal structures. These derived structures are then used in further experimental analysis, or as the initial guess for structural optimization in electronic structure calculations, both of which usually require a reasonable guess of the lattice parameters. In this work, we propose two lattice prediction schemes to improve the initial guess of a candidate crystal structure. The first scheme relies on a one-to-one mapping of species in the candidate crystal structure to a known crystal structure, while the second scheme relies on data-mined minimum atom pair distances to predict the crystal volume of the candidate crystal structure and does not require a reference structure. We demonstrate that the two schemes can effectively predict the volumes within mean absolute errors (MAE) as low as 3.8% and 8.2%. We also discuss the various factors that may impact the performance of the schemes. Implementations for both schemes are available in the open-source pymatgen software.Comment: 8 figures, 2 table

Controlled Fuzzy Parallel Rewriting

We study a Lindenmayer-like parallel rewriting system to model the growth of filaments (arrays of cells) in which developmental errors may occur. In essence this model is the fuzzy analogue of the derivation-controlled iteration grammar. Under minor assumptions on the family of control languages and on the family of fuzzy languages in the underlying iteration grammar, we show (i) regular control does not provide additional generating power to the model, (ii) the number of fuzzy substitutions in the underlying iteration grammar can be reduced to two, and (iii) the resulting family of fuzzy languages possesses strong closure properties, viz. it is a full hyper-AFFL, i.e., a hyper-algebraically closed full Abstract Family of Fuzzy Languages