PubMed Health⌕ Search

Biomedical subjects

Gerbrand Ceder

Publications and source records attributed to Gerbrand Ceder.

11 recordsLinked to original sources
PubMed2006

Configurational electronic entropy and the phase diagram of mixed-valence oxides: the case of LixFePO4.

We demonstrate that configurational electronic entropy, previously neglected, in ab initio thermodynamics of materials can qualitatively modify the finite-temperature phase stability of mixed-valence oxides. While transformations from low-T ordered or immiscible states are almost always driven by configurational disorder (i.e., random occupation of lattice sites by multiple species), in FePO4-LiFePO4 the formation of a solid solution is almost entirely driven by electronic rather than ionic configurational entropy. We argue that such an electronic entropic mechanism may be relevant to most other mixed-valence systems.

Journal Article↗
PubMed2006

Predicting crystal structure by merging data mining with quantum mechanics.

Modern methods of quantum mechanics have proved to be effective tools to understand and even predict materials properties. An essential element of the materials design process, relevant to both new materials and the optimization of existing ones, is knowing which crystal structures will form in an alloy system. Crystal structure can only be predicted effectively with quantum mechanics if an algorithm to direct the search through the large space of possible structures is found. We present a new approach to the prediction of structure that rigorously mines correlations embodied within experimental data and uses them to direct quantum mechanical techniques efficiently towards the stable crystal structure of materials.

Journal Article↗
PubMed2006

Ultra-fast evaluation of protein energies directly from sequence.

The structure, function, stability, and many other properties of a protein in a fixed environment are fully specified by its sequence, but in a manner that is difficult to discern. We present a general approach for rapidly mapping sequences directly to their energies on a pre-specified rigid backbone, an important sub-problem in computational protein design and in some methods for protein structure prediction. The cluster expansion (CE) method that we employ can, in principle, be extended to model any computable or measurable protein property directly as a function of sequence. Here we show how CE can be applied to the problem of computational protein design, and use it to derive excellent approximations of physical potentials. The approach provides several attractive advantages. First, following a one-time derivation of a CE expansion, the amount of time necessary to evaluate the energy of a sequence adopting a specified backbone conformation is reduced by a factor of 10(7) compared to standard full-atom methods for the same task. Second, the agreement between two full-atom methods that we tested and their CE sequence-based expressions is very high (root mean square deviation 1.1-4.7 kcal/mol, R2 = 0.7-1.0). Third, the functional form of the CE energy expression is such that individual terms of the expansion have clear physical interpretations. We derived expressions for the energies of three classic protein design targets-a coiled coil, a zinc finger, and a WW domain-as functions of sequence, and examined the most significant terms. Single-residue and residue-pair interactions are sufficient to accurately capture the energetics of the dimeric coiled coil, whereas higher-order contributions are important for the two more globular folds. For the task of designing novel zinc-finger sequences, a CE-derived energy function provides significantly better solutions than a standard design protocol, in comparable computation time. Given these advantages, CE is likely to find many uses in computational structural modeling.

Algorithms↗
PubMed2006

Electrodes with high power and high capacity for rechargeable lithium batteries.

New applications such as hybrid electric vehicles and power backup require rechargeable batteries that combine high energy density with high charge and discharge rate capability. Using ab initio computational modeling, we identified useful strategies to design higher rate battery electrodes and tested them on lithium nickel manganese oxide [Li(Ni(0.5)Mn(0.5))O2], a safe, inexpensive material that has been thought to have poor intrinsic rate capability. By modifying its crystal structure, we obtained unexpectedly high rate-capability, considerably better than lithium cobalt oxide (LiCoO2), the current battery electrode material of choice.

Journal Article↗
PubMed2005

First experimental evidence of potassium ordering in layered k4co7o14.

The layered P2-K4Co7O14 oxide has been prepared and characterized by means of X-ray diffraction, electrical conductivity, thermopower, and magnetic measurements. The crystal structure of K4Co7O14 (P6(3)/m space group, Z=2, a=7.5171(1) A, and c=12.371(1) A) consists of a stacking of slabs of edge-shared CoO6 octahedra with K+ ions occupying ordered positions in the interslab space, leading to a a0 radical7xa0 radical7 supercell. Potential energy calculations at 0 K are in good agreement with the ordered distribution of potassium ions in the (ab) plane. This oxide is metallic, and the magnetic susceptibility is of Pauli-type, which contrasts with the Curie-Weiss behavior of the homologous NaxCoO2 (x approximately 0.6) oxide with close alkali content. The thermopower at room temperature is about one-third that of polycrystalline Na0.6CoO2.

Journal Article↗
PubMed2005

A density functional theory study of hydrogen adsorption in MOF-5.

Ab initio molecular dynamics in the generalized gradient approximation to density functional theory and ground-state relaxations are used to study the interaction between molecular hydrogen and the metal-organic framework with formula unit Zn4O(O2C-C6H4-CO2)3. Five symmetrically unique adsorption sites are identified, and calculations indicate that the sites with the strongest interaction with hydrogen are located near the Zn4O clusters. Twenty total adsorption sites are found around each Zn4O cluster, but after 16 of these are populated, the interaction energy at the remaining four sites falls off significantly. The adsorption of hydrogen on the pore walls creates an attractive potential well for hydrogen in the center of the pore. The effect of the framework on the physical structure and electronic structure of the organic linker is calculated, suggesting ways by which the interaction between the framework and hydrogen could be modified.

Journal Article↗
PubMed2005

Coarse-graining protein energetics in sequence variables.

We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties such as energy can be unambiguously expanded in the amino-acid sequence space. The CE coarse grains over nonsequence degrees of freedom (e.g., side-chain conformations) and thereby simplifies the problem of designing proteins, or predicting the compatibility of a sequence with a given structure, by many orders of magnitude. The CE is physically transparent, and can be evaluated through linear regression on the energies of training sequences. We show, as example, that good prediction accuracy is obtained with up to pairwise interactions for a coiled-coil backbone, and that triplet interactions are important in the energetics of a more globular zinc-finger backbone.

Algorithms↗
PubMed2005

Electronic-enthalpy functional for finite systems under pressure.

We introduce the notion of electronic enthalpy for first-principles structural and dynamical calculations of finite systems under pressure. An external pressure field is allowed to act directly on the electronic structure of the system studied via the ground-state minimization of the functional E+PV(q), where V(q) is the quantum volume enclosed by a charge isosurface. The Hellmann-Feynman theorem applies, and assures that the ionic equations of motion follow an isoenthalpic dynamics. No pressurizing medium is explicitly required, while coatings of environmental ions or ligands can be introduced if chemically relevant. We apply this novel approach to the study of group-IV nanoparticles during a shock wave, highlighting the significant differences in the plastic or elastic response of the diamond cage under load, and their potential use as novel nanostructured impact-absorbing materials.

Journal Article↗
PubMed2003

Predicting crystal structures with data mining of quantum calculations.

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. It is typically addressed with highly accurate quantum mechanical computations on a small set of candidate structures, or with empirical rules that have been extracted from a large amount of experimental information, but have limited predictive power. In this Letter, we transfer the concept of heuristic rule extraction to a large library of ab initio calculated information, and we demonstrate that this can be developed into a tool for crystal structure prediction.

Journal Article↗
PubMed2002

Dynamics of an inhomogeneously coarse grained multiscale system.

To study material phenomena simultaneously at various length scales, descriptions in which matter can be coarse grained to arbitrary levels are necessary. Attempts to do this in the static regime (i.e., zero temperature) have already been developed. We present an approach that leads to a dynamics for such coarse grained models. This allows us to obtain temperature-dependent and transport properties. Renormalization group theory is used to create new local potential models between nodes, within the approximation of local thermodynamical equilibrium. Assuming that these potentials give an average description of node dynamics, we calculate thermal and mechanical properties. If this method can be sufficiently generalized it may form the basis of a multiscale molecular dynamics method with time and spatial coarse graining.

Journal Article↗