Building effective models from sparse but precise data

A common approach in computational science is to use a set of of highly precise but expensive calculations to parameterize a model that allows less precise, but more rapid calculations on larger scale systems. Least-squares fitting on a model that underfits the data is generally used for this purpose. For arbitrarily precise data free from statistic noise, e.g. ab initio calculations, we argue that it is more appropriate to begin with a ensemble of models that overfit the data. Within a Bayesian framework, a most likely model can be defined that incorporates physical knowledge, provides error estimates for systems not included in the fit, and reproduces the original data exactly. We apply this approach to obtain a cluster expansion model for the Ca[Zr,Ti]O3 solid solution.Comment: 10 pages, 3 figures, submitted to Physical Review Letter

Interatomic potentials for mixed oxide (MOX) nuclear fuels

We extend our recently developed interatomic potentials for UO_{2} to the mixed oxide fuel system (U,Pu,Np)O_{2}. We do so by fitting against an extensive database of ab initio results as well as to experimental measurements. The applicability of these interactions to a variety of mixed environments beyond the fitting domain is also assessed. The employed formalism makes these potentials applicable across all interatomic distances without the need for any ambiguous splining to the well-established short-range Ziegler-Biersack-Littmark universal pair potential. We therefore expect these to be reliable potentials for carrying out damage simulations (and Molecular Dynamics simulations in general) in nuclear fuels of varying compositions for all relevant atomic collision energies

Design and fabrication of chemically robust three-dimensional microfluidic valves

A current problem in microfluidics is that poly(dimethylsiloxane) (PDMS), used to fabricate many microfluidic devices, is not compatible with most organic solvents. Fluorinated compounds are more chemically robust than PDMS but, historically, it has been nearly impossible to construct valves out of them by multilayer soft lithography (MSL) due to the difficulty of bonding layers made of non-stick fluoropolymers necessary to create traditional microfluidic valves. With our new three-dimensional (3D) valve design we can fabricate microfluidic devices from fluorinated compounds in a single monolithic layer that is resistant to most organic solvents with minimal swelling. This paper describes the design and development of 3D microfluidic valves by molding of a perfluoropolyether, termed Sifel, onto printed wax molds. The fabrication of Sifel-based microfluidic devices using this technique has great potential in chemical synthesis and analysis

Self-limited oxide formation in Ni(111) oxidation

The oxidation of the Ni(111) surface is studied experimentally with low energy electron microscopy and theoretically by calculating the electron reflectivity for realistic models of the NiO/Ni(111) surface with an ab-initio scattering theory. Oxygen exposure at 300 K under ultrahigh-vacuum conditions leads to the formation of a continuous NiO(111)-like film consisting of nanosized domains. At 750 K, we observe the formation of a nano-heterogeneous film composed primarily of NiO(111)-like surface oxide nuclei, which exhibit virtually the same energy-dependent reflectivity as in the case of 300 K and which are separated by oxygen-free Ni(111) terraces. The scattering theory explains the observed normal incidence reflectivity R(E) of both the clean and the oxidized Ni(111) surface. At low energies R(E) of the oxidized surface is determined by a forbidden gap in the k_parallel=0 projected energy spectrum of the bulk NiO crystal. However, for both low and high temperature oxidation a rapid decrease of the reflectivity in approaching zero kinetic energy is experimentally observed. This feature is shown to characterize the thickness of the oxide layer, suggesting an average oxide thickness of two NiO layers.Comment: 10 pages (in journal format), 9 figure

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca\u3csup\u3e2+\u3c/sup\u3e-calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 A resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using lowcontour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal

Atomic resolution experimental phase information reveals extensive disorder and bound 2-methyl-2,4-pentanediol in Ca\u3csup\u3e2+\u3c/sup\u3e-calmodulin

Calmodulin (CaM) is the primary calcium signaling protein in eukaryotes and has been extensively studied using various biophysical techniques. Prior crystal structures have noted the presence of ambiguous electron density in both hydrophobic binding pockets of Ca2+-CaM, but no assignment of these features has been made. In addition, Ca2+-CaM samples many conformational substates in the crystal and accurately modeling the full range of this functionally important disorder is challenging. In order to characterize these features in a minimally biased manner, a 1.0 A resolution single-wavelength anomalous diffraction data set was measured for selenomethionine-substituted Ca2+-CaM. Density-modified electron-density maps enabled the accurate assignment of Ca2+-CaM main-chain and side-chain disorder. These experimental maps also substantiate complex disorder models that were automatically built using lowcontour features of model-phased electron density. Furthermore, experimental electron-density maps reveal that 2-methyl-2,4-pentanediol (MPD) is present in the C-terminal domain, mediates a lattice contact between N-terminal domains and may occupy the N-terminal binding pocket. The majority of the crystal structures of target-free Ca2+-CaM have been derived from crystals grown using MPD as a precipitant, and thus MPD is likely to be bound in functionally critical regions of Ca2+-CaM in most of these structures. The adventitious binding of MPD helps to explain differences between the Ca2+-CaM crystal and solution structures and is likely to favor more open conformations of the EF-hands in the crystal

Moderating the neutralist–selectionist debate: exactly which propositions are we debating, and which arguments are valid?

Half a century after its foundation, the neutral theory of molecular evolution continues to attract controversy. The debate has been hampered by the coexistence of different interpretations of the core proposition of the neutral theory, the ‘neutral mutation–random drift’ hypothesis. In this review, we trace the origins of these ambiguities and suggest potential solutions. We highlight the difference between the original, the revised and the nearly neutral hypothesis, and re-emphasise that none of them equates to the null hypothesis of strict neutrality. We distinguish the neutral hypothesis of protein evolution, the main focus of the ongoing debate, from the neutral hypotheses of genomic and functional DNA evolution, which for many species are generally accepted. We advocate a further distinction between a narrow and an extended neutral hypothesis (of which the latter posits that random non-conservative amino acid substitutions can cause non-ecological phenotypic divergence), and we discuss the implications for evolutionary biology beyond the domain of molecular evolution. We furthermore point out that the debate has widened from its initial focus on point mutations, and also concerns the fitness effects of large-scale mutations, which can alter the dosage of genes and regulatory sequences. We evaluate the validity of neutralist and selectionist arguments and find that the tested predictions, apart from being sensitive to violation of underlying assumptions, are often derived from the null hypothesis of strict neutrality, or equally consistent with the opposing selectionist hypothesis, except when assuming molecular panselectionism. Our review aims to facilitate a constructive neutralist–selectionist debate, and thereby to contribute to answering a key question of evolutionary biology: what proportions of amino acid and nucleotide substitutions and polymorphisms are adaptive?

First-principles study of ternary fcc solution phases from special quasirandom structures

In the present work, ternary Special Quasirandom Structures (SQSs) for a fcc solid solution phase are generated at different compositions, $x_A=x_B=x_C=\tfrac{1}{3}$ and $x_A=\tfrac{1}{2}$, $x_B=x_C=\tfrac{1}{4}$, whose correlation functions are satisfactorily close to those of a random fcc solution. The generated SQSs are used to calculate the mixing enthalpy of the fcc phase in the Ca-Sr-Yb system. It is observed that first-principles calculations of all the binary and ternary SQSs in the Ca-Sr-Yb system exhibit very small local relaxation. It is concluded that the fcc ternary SQSs can provide valuable information about the mixing behavior of the fcc ternary solid solution phase. The SQSs presented in this work can be widely used to study the behavior of ternary fcc solid solutions.Comment: 20 pages, 7 figure

Thermodynamic properties of binary HCP solution phases from special quasirandom structures

Three different special quasirandom structures (SQS) of the substitutional hcp $A_{1-x}B_x$ binary random solutions ($x=0.25$, 0.5, and 0.75) are presented. These structures are able to mimic the most important pair and multi-site correlation functions corresponding to perfectly random hcp solutions at those compositions. Due to the relatively small size of the generated structures, they can be used to calculate the properties of random hcp alloys via first-principles methods. The structures are relaxed in order to find their lowest energy configurations at each composition. In some cases, it was found that full relaxation resulted in complete loss of their parental symmetry as hcp so geometry optimizations in which no local relaxations are allowed were also performed. In general, the first-principles results for the seven binary systems (Cd-Mg, Mg-Zr, Al-Mg, Mo-Ru, Hf-Ti, Hf-Zr, and Ti-Zr) show good agreement with both formation enthalpy and lattice parameters measurements from experiments. It is concluded that the SQS's presented in this work can be widely used to study the behavior of random hcp solutions.Comment: 15 pages, 8 figure