A new electron diffraction approach for structure refinement applied to Ca3Mn2O7.

The digital large-angle convergent-beam electron diffraction (D-LACBED) technique is applied to Ca3Mn2O7 for a range of temperatures. Bloch-wave simulations are used to examine the effects that changes in different parameters have on the intensity in D-LACBED patterns, and atomic coordinates, thermal atomic displacement parameters and apparent occupancy are refined to achieve a good fit between simulation and experiment. The sensitivity of the technique to subtle changes in structure is demonstrated. Refined structures are in good agreement with previous determinations of Ca3Mn2O7 and show the decay of anti-phase oxygen octahedral tilts perpendicular to the c axis of the A21am unit cell with increasing temperature, as well as the robustness of oxygen octahedral tilts about the c axis up to ∼400°C. The technique samples only the zero-order Laue zone and is therefore insensitive to atom displacements along the electron-beam direction. For this reason it is not possible to distinguish between in-phase and anti-phase oxygen octahedral tilting about the c axis using the [110] data collected in this study.

Robust nodal structure of Landau level wave functions revealed by Fourier transform scanning tunneling spectroscopy.

Scanning tunneling spectroscopy is used to study the real-space local density of states of a two-dimensional electron system in a magnetic field, in particular within higher Landau levels. By Fourier transforming the local density of states, we find a set of n radial minima at fixed momenta for the nth Landau levels. The momenta of the minima depend only on the inverse magnetic length. By comparison with analytical theory and numerical simulations, we attribute the minima to the nodes of the quantum cyclotron orbits, which decouple in a Fourier representation from the random guiding center motion due to disorder. Adequate Fourier filtering reveals the nodal structure in real space in some areas of the sample with relatively smooth potential disorder.

Localization-delocalization transition for disordered cubic harmonic lattices.

We study numerically the disorder-induced localization-delocalization phase transitions that occur for mass and spring constant disorder in a three-dimensional cubic lattice with harmonic couplings. We show that, while the phase diagrams exhibit regions of stable and unstable waves, the universality of the transitions is the same for mass and spring constant disorder throughout all the phase boundaries. The combined value for the critical exponent of the localization lengths of ν = 1.550(-0.017)(+0.020) confirms the agreement with the universality class of the standard electronic Anderson model of localization. We further support our investigation with studies of the density of states, the participation numbers and wave function statistics.

Inhibition of HIV-1 protease: the rigidity perspective.

MOTIVATION: HIV-1 protease is a key drug target due to its role in the life cycle of the HIV-1 virus. Rigidity analysis using the software First is a computationally inexpensive method for inferring functional information from protein crystal structures. We evaluate the rigidity of 206 high-resolution (2 Å or better) X-ray crystal structures of HIV-1 protease and compare the effects of different inhibitors binding to the enzyme. RESULTS: Inhibitor binding has little effect on the overall rigidity of the protein homodimer, including the rigidity of the active site. The principal effect of inhibitor binding on rigidity is to constrain the flexibility of the ß-hairpin flaps, which move to allow access to the active site of the enzyme. We show that commercially available antiviral drugs which target HIV-1 protease can be divided into two classes, those which significantly affect flap rigidity and those which do not. The non-peptidic inhibitor tipranavir is distinctive in its consistently strong effect on flap rigidity. CONTACT: jack.heal@warwick.ac.uk; r.roemer@warwick.ac.uk SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Rapid simulation of protein motion: merging flexibility, rigidity and normal mode analyses.

Protein function frequently involves conformational changes with large amplitude on timescales which are difficult and computationally expensive to access using molecular dynamics. In this paper, we report on the combination of three computationally inexpensive simulation methods--normal mode analysis using the elastic network model, rigidity analysis using the pebble game algorithm, and geometric simulation of protein motion--to explore conformational change along normal mode eigenvectors. Using a combination of ElNemo and First/Froda software, large-amplitude motions in proteins with hundreds or thousands of residues can be rapidly explored within minutes using desktop computing resources. We apply the method to a representative set of six proteins covering a range of sizes and structural characteristics and show that the method identifies specific types of motion in each case and determines their amplitude limits.

Comparative analysis of rigidity across protein families.

We present a comparative study in which 'pebble game' rigidity analysis is applied to multiple protein crystal structures, for each of six different protein families. We find that the main-chain rigidity of a protein structure at a given hydrogen bond energy cutoff is quite sensitive to small structural variations, and conclude that the hydrogen bond constraints in rigidity analysis should be chosen so as to form and test specific hypotheses about the rigidity of a particular protein. Our comparative approach highlights two different characteristic patterns ('sudden' or 'gradual') for protein rigidity loss as constraints are removed, in line with recent results on the rigidity transitions of glassy networks.

Quantum Hall transition in real space: from localized to extended states.

Using scanning tunneling spectroscopy in an ultrahigh vacuum at low temperature (T=0.3 K) and high magnetic fields (B

Direct comparison between potential landscape and local density of states in a disordered two-dimensional electron system.

The local density of states (LDOS) of the adsorbate-induced two-dimensional electron system (2DES) on n-InAs(110) is studied by scanning tunneling spectroscopy. In contrast to a similar 3DES, the 2DES LDOS exhibits 20 times stronger corrugations and rather irregular structures. Both results are interpreted as consequences of weak localization. Fourier transforms of the LDOS reveal that the k values of the unperturbed 2DES still dominate the 2DES, but additional lower k values contribute. To clarify the origin of the LDOS patterns, we measure the potential landscape of the 2DES area. We use it to calculate the expected LDOS and find reasonable agreement between calculation and experiment.