arXiv subjects

Gerbrand Ceder

Publications and source records attributed to Gerbrand Ceder.

99 records · Page 6Linked to original sources

arXiv2005

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.

physics.bio-ph↗

arXiv2005

The Li intercalation potential of LiMPO4 and LiMSiO4 olivines with M = Fe, Mn, Co, Ni

The Li intercalation potential of LiMPO4 and LiMSiO4 compounds with M = Fe, Mn, Co, and Ni is computed with the GGA+U method. It is found that this approach is considerably more accurate than standard LDA or GGA methods. The calculated potentials for LiFePO4, LiMnPO4 and LiCoOPO4 agree to within 0.1 V with experimental results. The LiNiPO4 potential is predicted to be above 5 V. The potentials of the silicate materials are all found to be rather high, but LiFeSiO4 and LiCoSiO4 have negligible volume change upon Li extraction.

cond-mat.mtrl-sci↗

arXiv2005

The electronic structure and band gap of LiFePO4 and LiMnPO4

Materials with the olivine LixMPO4 structure form an important new class of materials for rechargeable Li batteries. There is significant interest in their electronic properties because of the importance of electronic conductivity in batteries for high rate applications. The density of states of LixMPO4 (x = 0, 1 and M = Fe, Mn) has been determined with the ab initio GGA+U method, appropriate for these correlated electron systems. Computed results are compared with the optical gap of LiFePO4, as measured using UV-Vis-NIR diffuse reflectance spectroscopy. The results obtained from experiment (3.8-4.0 eV) and GGA+U computations (3.7 eV) are in very good agreement. However, standard GGA, without the same level of treatment of electron correlation, is shown to make large errors in predicting the electronic structure. It is argued that olivines are likely to be polaronic conductors with extrinsically determined carrier levels and that their electronic conductivity is therefore not simply related to the band gap.

cond-mat.mtrl-sci↗

arXiv2005

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 inthe plastic or elastic response of the diamond cage under load, and their potential use as novel nanostructured impact-absorbing materials.

cond-mat.mtrl-sci↗

arXiv2005

Accuracy of ab initio methods in predicting the crystal structures of metals: review of 80 binary alloys

Predicting and characterizing the crystal structure of materials is a key problem in materials research and development. We report the results of ab initio LDA/GGA computations for the following systems: AgAu, AgCd, AgMg, AgMo*, AgNa, AgNb*, AgPd, AgRh*, AgRu*, AgTc*, AgTi, AgY, AgZr, AlSc, AuCd, AuMo*, AuNb, AuPd, AuPt*, AuRh*, AuRu*, AuSc, AuTc*, AuTi, AuY, AuZr, CdMo*, CdNb*, CdPd, CdPt, CdRh, CdRu*, CdTc*, CdTi, CdY, CdZr, CrMg*, MoNb, MoPd, MoPt, MoRh, MoRu, MoTc*, MoTi, MoY*, MoZr, NbPd, NbPt, NbRh, NbRu, NbTc, NbY*, NbZr*, PdPt, PdRh*, PdRu*, PdTc, PdTi, PdY, PdZr, PtRh, PtRu, PtY, PtTc, PtTi, PtZr, RhRu, RhTc, RhTi, RhY, RhZr, RuTi, RuTc, RuY, RuZr, TcTi, TcY, TcZr, TiZr*, YZr* (*= systems in which the ab initio method predicts that no compounds are stable). A detailed comparison to experimental data confirms the high accuracy with which ab initio methods can predict ground states. Keywords: Binary Alloys, Ab initio, Intermetallics, Transition Metals, StructureAluminum, Cadmium, Gold, Magnesium, Molybdenum, Niobium, Palladium, Platinum, Rhodium, Ruthenium, Scandium, Silver, Sodium, Titanium, Technetium, Yttrium, Zirconium.

cond-mat.mtrl-sci↗

arXiv2003

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 demonstrate that this can be developed into a tool for crystal structure prediction.

cond-mat.mtrl-sci↗

arXiv2003

Using bond-length dependent transferable force constants to predict vibrational entropies in Au-Cu, Au-Pd, and Cu-Pd alloys

A model is tested to rapidly evaluate the vibrational properties of alloys with site disorder. It is shown that length-dependent transferable force constants exist, and can be used to accurately predict the vibrational entropy of substitutionally ordered and disordered structures in Au-Cu, Au-Pd, and Cu-Pd. For each relevant force constant, a length- dependent function is determined and fitted to force constants obtained from first-principles pseudopotential calculations. We show that these transferable force constants can accurately predict vibrational entropies of L1$_{2}$-ordered and disordered phases in Cu$_{3}$Au, Au$_{3}$Pd, Pd$_{3}$Au, Cu$_{3}$Pd, and Pd$_{3}$Au. In addition, we calculate the vibrational entropy difference between L1$_{2}$-ordered and disordered phases of Au$_{3}$Cu and Cu$_{3}$Pt.

cond-mat.stat-mech↗

arXiv2002

S=1/2 chains and spin-Peierls transition in TiOCl

We study TiOCl as an example of an S=1/2 layered Mott insulator. From our analysis of new susceptibility data, combined with LDA and LDA+U band structure calculations, we conclude that orbital ordering produces quasi-one-dimensional spin chains and that TiOCl is a new example of Heisenberg-chains which undergo a spin-Peierls transition. The energy scale is an order of magnitude larger than that of previously known examples. The effects of non-magnetic Sc impurities are explained using a model of broken finite chains.

cond-mat.str-el↗

arXiv2002

Dynamic of a non homogeneously coarse grained system

To study materials 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. In this letter, 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 potentials model between nodes, within the approximation of local thermodynamical equilibrium. Assuming that these potentials give an averaged description of node dynamics, we calculate thermal and mechanical properties. If this method can be sufficiently generalized it may form the basis of a Molecular Dynamics method with time and spatial coarse-graining.

cond-mat.mtrl-sci↗