Metric tensor as the dynamical variable for variable cell-shape molecular dynamics

We propose a new variable cell-shape molecular dynamics algorithm where the dynamical variables associated with the cell are the six independent dot products between the vectors defining the cell instead of the nine cartesian components of those vectors. Our choice of the metric tensor as the dynamical variable automatically eliminates the cell orientation from the dynamics. Furthermore, choosing for the cell kinetic energy a simple scalar that is quadratic in the time derivatives of the metric tensor, makes the dynamics invariant with respect to the choice of the simulation cell edges. Choosing the densitary character of that scalar allows us to have a dynamics that obeys the virial theorem. We derive the equations of motion for the two conditions of constant external pressure and constant thermodynamic tension. We also show that using the metric as variable is convenient for structural optimization under those two conditions. We use simulations for Ar with Lennard-Jones parameters and for Si with forces and stresses calculated from first-principles of density functional theory to illustrate the applications of the method.Comment: 10 pages + 6 figures, Latex, to be published in Physical Review

Boundary Conditions on Internal Three-Body Wave Functions

For a three-body system, a quantum wave function $\Psi^\ell_m$ with definite $\ell$ and $m$ quantum numbers may be expressed in terms of an internal wave function $\chi^\ell_k$ which is a function of three internal coordinates. This article provides necessary and sufficient constraints on $\chi^\ell_k$ to ensure that the external wave function $\Psi^\ell_m$ is analytic. These constraints effectively amount to boundary conditions on $\chi^\ell_k$ and its derivatives at the boundary of the internal space. Such conditions find similarities in the (planar) two-body problem where the wave function (to lowest order) has the form $r^{|m|}$ at the origin. We expect the boundary conditions to prove useful for constructing singularity free three-body basis sets for the case of nonvanishing angular momentum.Comment: 41 pages, submitted to Phys. Rev.

Scarring Effects on Tunneling in Chaotic Double-Well Potentials

The connection between scarring and tunneling in chaotic double-well potentials is studied in detail through the distribution of level splittings. The mean level splitting is found to have oscillations as a function of energy, as expected if scarring plays a role in determining the size of the splittings, and the spacing between peaks is observed to be periodic of period {$2\pi\hbar$} in action. Moreover, the size of the oscillations is directly correlated with the strength of scarring. These results are interpreted within the theoretical framework of Creagh and Whelan. The semiclassical limit and finite-{$\hbar$} effects are discussed, and connections are made with reaction rates and resonance widths in metastable wells.Comment: 22 pages, including 11 figure

A Novel Peptide-Based SILAC Method to Identify the Posttranslational Modifications Provides Evidence for Unconventional Ubiquitination in the ER-Associated Degradation Pathway

The endoplasmic reticulum-associated degradation (ERAD) pathway is responsible for disposing misfolded proteins from the endoplasmic reticulum by inducing their ubiquitination and degradation. Ubiquitination is conventionally observed on lysine residues and has been demonstrated on cysteine residues and protein N-termini. Ubiquitination is fundamental to the ERAD process; however, a mutant T-cell receptor α (TCRα) lacking lysine residues is targeted for the degradation by the ERAD pathway. We have shown that ubiquitination of lysine-less TCRα occurs on internal, non-lysine residues and that the same E3 ligase conjugates ubiquitin to TCRα in the presence or absence of lysine residues. Mass-spectrometry indicates that WT-TCRα is ubiquitinated on multiple lysine residues. Recent publications have provided indirect evidence that serine and threonine residues may be modified by ubiquitin. Using a novel peptide-based stable isotope labeling in cell culture (SILAC) approach, we show that specific lysine-less TCRα peptides become modified. In this study, we demonstrate that it is possible to detect both ester and thioester based ubiquitination events, although the exact linkage on lysine-less TCRα remains elusive. These findings demonstrate that SILAC can be used as a tool to identify modified peptides, even those with novel modifications that may not be detected using conventional proteomic work flows or informatics algorithms

Solution Structure of the Iron−Sulfur Cluster Cochaperone HscB and Its Binding Surface for the Iron−Sulfur Assembly Scaffold Protein IscU†‡

ABSTRACT: The interaction between IscU and HscB is critical for successful assembly of iron-sulfur clusters. NMR experiments were performed on HscB to investigate which of its residues might be part of the IscU binding surface. Residual dipolar couplings ( 1 DHN and 1 DCRHR) indicated that the crystal structure of HscB [Cupp-Vickery, J. R., and Vickery, L. E. (2000) Crystal structure of Hsc20, a J-type cochaperone from Escherichia coli, J. Mol. Biol. 304, 835-845] faithfully represents its solution state. NMR relaxation rates ( 15 N R1, R2) and 1 H- 15 N heteronuclear NOE values indicated that HscB is rigid along its entire backbone except for three short regions which exhibit flexibility on a fast time scale. Changes in the NMR spectrum of HscB upon addition of IscU mapped to the J-domain/C-domain interface, the interdomain linker, and the C-domain. Sequence conservation is low in the interface and in the linker, and NMR changes observed for these residues likely result from indirect effects of IscU binding. NMR changes observed in the conserved patch of residues in the C-domain (L92, M93, L96, E97, E100, E104, and F153) were suggestive of a direct interaction with IscU. To test this, we replaced several of these residues with alanine and assayed for the ability of HscB to interact with IscU and to stimulate HscA ATPase activity. HscB(L92A,M93A,F153A) and HscB(E97A,E100A,E104A) both showed decreased binding affinity for IscU; the (L92A,M93A,F153A) substitution also strongly perturbed the allosteric interactio

Linac Coherent Light Source Undulator RF BPM System

The Linac Coherent Light Source (LCLS) will be the world's first x-ray free-electron laser (FEL) when it becomes operational in 2009. The LCLS is currently in the construction phase. The beam position monitor (BPM) system planned for the LCLS undulator will incorporate a high-resolution X-band cavity BPM system described in this paper. The BPM system will provide high-resolution measurements of the electron beam trajectory on a pulse-to-pulse basis and over many shots. The X-band cavity BPM size, simple fabrication, and high resolution make it an ideal choice for LCLS beam position detection. We will discuss the system specifications, design, and prototype test results

Mechanically Induced Amorphization of Diaqua-bis(Omeprazolate)-Magnesium Dihydrate

The influence of milling diaqua-bis(omeprazolate)-magnesium dihydrate (DABOMD), an active pharmaceutical ingredient (API), was investigated. DABOMD was processed in a planetary ball mill at different milling times, from 1 to 300 min. The milling process resulted in a prominent comminution (size reduction) and amorphization of the API. DABOMD amorphization was identified with various characterization techniques including thermogravimetric analysis, differential scanning calorimetry, powder X-ray diffraction, and attenuated total reflection-Fourier transform infrared spectroscopy. The solid–solid crystalline to amorphous phase transformation is driven by compression, shear stresses, and heat generated in the planetary ball mill. This leads to distortion and breakage of hydrogen bonds, release of water molecules from the crystalline lattice of DABOMD and the accumulation of defects, and eventually a collapse of the crystalline order. Model fitting of the kinetics of comminution and the amorphization of DABOMD revealed a series of events: a rapid comminution at the start of milling driven by crystal cleavage of DABOMD, followed by partial amorphization, which is driven by rapid water diffusion, and subsequently, a slow steady comminution and amorphization

Luminescence tuning of MOFs via ligand to metal and metal to metal energy transfer by co-doping of 2∞[Gd2Cl6(bipy)3]*2bipy with europium and terbium

The series of anhydrous lanthanide chlorides LnCl3, Ln=Pr–Tb, and 4,4'-bipyridine (bipy) constitute isotypic MOFs of the formula 2∞[Ln2Cl6(bipy)3]*2bipy. The europium and terbium containing compounds both exhibit luminescence of the referring trivalent lanthanide ions, giving a red luminescence for Eu3+ and a green luminescence for Tb3+ triggered by an efficient antenna effect of the 4,4'-bipyridine linkers. Mixing of different lanthanides in one MOF structure was undertaken to investigate the potential of this MOF system for colour tuning of the luminescence. Based on the gadolinium containing compound, co-doping with different amounts of europium and terbium proves successful and yields solid solutions of the formula 2∞[Gd2-x-yEuxTbyCl6(bipy)3]*2bipy (1–8), 0≤x, y≤0.5. The series of MOFs exhibits the opportunity of tuning the emission colour in-between green and red. Depending on the atomic ratio Gd:Eu:Tb, the yellow region was covered for the first time for an oxygen/carboxylate-free MOF system. In addition to a ligand to metal energy transfer (LMET) from the lowest ligand-centered triplet state of 4,4'-bipyridine, a metal to metal energy transfer (MMET) between 4f-levels from Tb3+ to Eu3+ is as well vital for the emission colour. However, no involvement of Gd3+ in energy transfers is observed rendering it a suitable host lattice ion and connectivity centre for diluting the other two rare earth ions in the solid state. The materials retain their luminescence during activation of the MOFs for microporosity

Design and Performance of the LCLS Cavity BPM System

In this paper we present the design of the beam position monitor (BPM) system for the LCLS undulator, which features a high-resolution X-band cavity BPM. Each BPM has a TM{sub 010} monopole reference cavity and a TM{sub 110} dipole cavity designed to operate at a center frequency of 11.384 GHz. The signal processing electronics features a low noise single-stage three-channel heterodyne receiver that has selectable gain and a phase locking local oscillator. We will discuss the system specifications, design, and prototype test results

A mitochondrial half-size ABC transporter is involved in cadmium tolerance in Chlamydomonas reinhardtii

Five cadmium-sensitive insertional mutants, all affected at the CDS1 ('cadmium-sensitive 1') locus, have been previously isolated in the unicellular green alga Chlamydomonas reinhardtii. We here describe the cloning of the Cds1 gene (8314 bp with 26 introns) and the corresponding cDNA. The Cds1 gene, strongly induced by cadmium, encodes a putative protein (CrCds1) of 1062 amino acid residues that belongs to the ATM/HMT subfamily of half-size ABC transporters. This subfamily includes both vacuolar HMT-type proteins transporting phytochelatin-cadmium complexes from the cytoplasm to the vacuole and mitochondrial ATM-type proteins involved in the maturation of cytosolic Fe/S proteins. Unlike the Delta sphmt1 cadmium-sensitive mutant of Schizosaccharomyces pombe that lacks a vacuolar HMT-type transporter, the cds1 mutant accumulates a high amount of phytochelatin-cadmium complexes. By epitope tagging, the CrCds1 protein was localized in the mitochondria. Even though mitochondria of cds1 do not accumulate important amounts of 'free' iron, the mutant cells are hypersensitive to high iron concentrations. Our data show for the first time that a mitochondrial ATM-like transporter plays a major role in tolerance to cadmium.Peer reviewe