Interstitial Fe-Cr alloys: Tuning of magnetism by nanoscale structural control and by implantation of nonmagnetic atoms

Using the density functional theory, we perform a full atomic relaxation of the bulk ferrite with 12.5%-concentration of monoatomic interstitial Cr periodically located at the edges of the bcc Fe$_\alpha$ cell. We show that structural relaxation in such artificially engineered alloys leads to significant atomic displacements and results in the formation of novel highly stable configurations with parallel chains of octahedrically arranged Fe. The enhanced magnetic polarization in the low-symmetry metallic state of this type of alloys can be externally controlled by additional inclusion of nonmagnetic impurities like nitrogen. We discuss possible applications of generated interstitial alloys in spintronic devices and propose to consider them as a basis of novel durable types of stainless steels.Comment: 8 pages, 10 figure

Polymeric forms of carbon in dense lithium carbide

The immense interest in carbon nanomaterials continues to stimulate intense research activities aimed to realize carbon nanowires, since linear chains of carbon atoms are expected to display novel and technologically relevant optical, electrical and mechanical properties. Although various allotropes of carbon (e.g., diamond, nanotubes, graphene, etc.) are among the best known materials, it remains challenging to stabilize carbon in the one-dimensional form because of the difficulty to suitably saturate the dangling bonds of carbon. Here, we show through first-principles calculations that ordered polymeric carbon chains can be stabilized in solid Li$_2$C$_2$ under moderate pressure. This pressure-induced phase (above 5 GPa) consists of parallel arrays of twofold zigzag carbon chains embedded in lithium cages, which display a metallic character due to the formation of partially occupied carbon lone-pair states in \emph{sp}$^2$-like hybrids. It is found that this phase remains the most favorable one in a wide range of pressure. At extreme pressure (larger the 215 GPa) a structural and electronic phase transition towards an insulating single-bonded threefold-coordinated carbon network is predicted.Comment: 10 pages, 6 figure

Deterministic Consistency: A Programming Model for Shared Memory Parallelism

The difficulty of developing reliable parallel software is generating interest in deterministic environments, where a given program and input can yield only one possible result. Languages or type systems can enforce determinism in new code, and runtime systems can impose synthetic schedules on legacy parallel code. To parallelize existing serial code, however, we would like a programming model that is naturally deterministic without language restrictions or artificial scheduling. We propose "deterministic consistency", a parallel programming model as easy to understand as the "parallel assignment" construct in sequential languages such as Perl and JavaScript, where concurrent threads always read their inputs before writing shared outputs. DC supports common data- and task-parallel synchronization abstractions such as fork/join and barriers, as well as non-hierarchical structures such as producer/consumer pipelines and futures. A preliminary prototype suggests that software-only implementations of DC can run applications written for popular parallel environments such as OpenMP with low (<10%) overhead for some applications.Comment: 7 pages, 3 figure

Using Density Functional Theory to Model Realistic TiO2 Nanoparticles, Their Photoactivation and Interaction with Water

Computational modeling of titanium dioxide nanoparticles of realistic size is extremely relevant for the direct comparison with experiments but it is also a rather demanding task. We have recently worked on a multistep/scale procedure to obtain global optimized minimum structures for chemically stable spherical titania nanoparticles of increasing size, with diameter from 1.5 nm (~300 atoms) to 4.4 nm (~4000 atoms). We use first self-consistent-charge density functional tight-binding (SCC-DFTB) methodology to perform thermal annealing simulations to obtain globally optimized structures and then hybrid density functional theory (DFT) to refine them and to achieve high accuracy in the description of structural and electronic properties. This allows also to assess SCC-DFTB performance in comparison with DFT(B3LYP) results. As a further step, we investigate photoexcitation and photoemission processes involving electron/hole pair formation, separation, trapping and recombination in the nanosphere of medium size by hybrid DFT. Finally, we show how a recently defined new set of parameters for SCC-DFTB allows for a proper description of titania/water multilayers interface, which paves the way for modeling large realistic nanoparticles in aqueous environment

New CHARMM force field parameters for dehydrated amino acid residues, the key to lantibiotic molecular dynamics simulations

Lantibiotics are an important class of naturally occurring antimicrobial peptides containing unusual dehydrated amino acid residues. In order to enable molecular dynamics simulations of lantibiotics, we have developed empirical force field parameters for dehydroalanine and dehydrobutyrine, which are compatible with the CHARMM all-atom force field. The parameters reproduce the geometries and energy barriers from MP2/6-31G*//MP2/cc-pVTZ quantum chemistry calculations. Experimental, predicted and calculated NMR chemical shifts for the amino protons and alpha-, beta- and carbonyl carbon atoms of the dehydrated residues are consistent with a significant charge redistribution. The new parameters are used to perform the first molecular dynamics simulations of nisin, a widely used but poorly understood lantibiotic, in an aqueous environment and in a phospholipid bilayer. The simulations show surface association of the peptide with membranes in agreement with solid state NMR data and formation of beta-turns in agreement with solution NMR

Nanoscale domains in ionic liquids: A statistical mechanics definition for molecular dynamics studies

One of the many open questions concerning Ionic Liquids (ILs) is the existence of nanoscale supramolecular domains which characterize the bulk. The hypothesis of their existence does not meet a general consensus since their definition seems to be based on ad hoc arbitrary criteria rather than on general and solid first principles of physics. In this work, we propose a suitable definition of supramolecular domains based on first principles of statistical mechanics. Such principles can be realized through the application of a recently developed computational tool which employs adaptive molecular resolution. The method can identify the smallest region of a liquid for which the atomistic details are strictly required, while the exterior plays the role of a generic structureless thermodynamic reservoir. We consider four different imidazolium-based ILs and show that indeed one can quantitatively represent the liquid as a collection of atomistically self-contained nanodroplets embedded in a generic thermodynamic bath. Such nanodroplets express a characteristic length scale for heterogeneity in ILs.Comment: 9 page

A computational method for the systematic screening of reaction barriers in enzymes:searching for Bacillus circulans xylanase mutants with greater activity towards a synthetic substrate

We present a semi-empirical (PM6-based) computational method for systematically estimating the effect of all possible single mutants, within a certain radius of the active site, on the barrier height of an enzymatic reaction. The intent of this method is not a quantitative prediction of the barrier heights, but rather to identify promising mutants for further computational or experimental study. The method is applied to identify promising single and double mutants of Bacillus circulans xylanase (BCX) with increased hydrolytic activity for the artificial substrate ortho-nitrophenyl β-xylobioside (ONPX2). The estimated reaction barrier for wild-type (WT) BCX is 18.5 kcal/mol, which is in good agreement with the experimental activation free energy value of 17.0 kcal/mol extracted from the observed kcat using transition state theory (Joshi et al., 2001). The PM6 reaction profiles for eight single point mutations are recomputed using FMO-MP2/PCM/6-31G(d) single points. PM6 predicts an increase in barrier height for all eight mutants while FMO predicts an increase for six of the eight mutants. Both methods predict that the largest change in barrier occurs for N35F, where PM6 and FMO predict a 9.0 and 15.8 kcal/mol increase, respectively. We thus conclude that PM6 is sufficiently accurate to identify promising mutants for further study. We prepared a set of all theoretically possible (342) single mutants in which every amino acid of the active site (except for the catalytically active residues E78 and E172) was mutated to every other amino acid. Based on results from the single mutants we construct a set of 111 double mutants consisting of all possible pairs of single mutants with the lowest barrier for a particular position and compute their reaction profile. None of the mutants have, to our knowledge, been prepared experimentally and therefore present experimentally testable predictions

Molecular Mechanism of the Piezoelectric Response in the β-Phase PVDF Crystals Interpreted by Periodic Boundary Conditions DFT Calculations

A theoretical approach based on Periodic Boundary Conditions (PBC) and a Linear Combination of Atomic Orbitals (LCAO) in the framework of the density functional theory (DFT) is used to investigate the molecular mechanism that rules the piezoelectric behavior of poly(vinylidene fluoride) (PVDF) polymer in the crystalline beta-phase. We present several computational tests highlighting the peculiar electrostatic potential energy landscape the polymer chains feel when they change their orientation by a rigid rotation in the lattice cell. We demonstrate that a rotation of the permanent dipole through chain rotation has a rather low energy cost and leads to a lattice relaxation. This justifies the macroscopic strain observed when the material is subjected to an electric field. Moreover, we investigate the effect on the molecular geometry of the expansion of the lattice parameters in the (a, b) plane, proving that the rotation of the dipole can take place spontaneously under mechanical deformation. By band deconvolution of the IR and Raman spectra of a PVDF film with a high content of beta-phase, we provide the experimental phonon wavenumbers and relative band intensities, which we compare against the predictions from DFT calculations. This analysis shows the reliability of the LCAO approach, as implemented in the CRYSTAL software, for calculating the vibrational spectra. Finally, we investigate how the IR/Raman spectra evolve as a function of inter-chain distance, moving towards the isolated chain limit and to the limit of a single crystal slab. The results show the relevance of the inter-molecular interactions on the vibrational dynamics and on the electro-optical features ruling the intensity pattern of the vibrational spectra