Interactions between immunoglobulin-like and catalytic modules in Clostridium thermocellum cellulosomal cellobiohydrolase CbhA

Cellobiohydrolase CbhA from Clostridium thermocellum cellulosome is a multi-modular protein composed starting from the N-terminus of a carbohydrate-binding module (CBM) of family 4, an immunoglobulin(Ig)-like module, a catalytic module of family 9 glycoside hydrolases (GH9), X1(1) and X1(2) modules, a CBM of family 3 and a dockerin module. Deletion of the Ig-like module from the Ig-GH9 construct results in complete inactivation of the GH9 module. The crystal structure of the Ig-GH9 module pair reveals the existence of an extensive module interface composed of over 40 amino acid residues of both modules and maintained through a large number of hydrophilic and hydrophobic interactions. To investigate the importance of these interactions between the two modules, we compared the secondary and tertiary structures and thermostabilities of the individual Ig-like and GH9 modules and the Ig-GH9 module pair using both circular dichroism (CD) spectroscopy and differential scanning calorimetry (DSC). Thr230, Asp262 and Asp264 of the Ig-like module are located in the module interface of the Ig-GH9 module pair and are suggested to be important in 'communication' between the modules. These residues were mutated to alanyl residues. The structure, stability and catalytic properties of the native Ig-GH9 and its D264A and T230A/D262A mutants were compared. The results indicate that despite being able to fold relatively independently, the Ig-like and GH9 modules interact and these interactions affect the final fold and stability of each module. Mutations of one or two amino acid residues lead to destabilization and change of the mechanism of thermal unfolding of the polypeptides. The enzymatic properties of native Ig-GH9, D264A and T230A/D262A mutants are similar. The results indicate that inactivation of the GH9 module occurs as a result of multiple structural disturbances finally affecting the topology of the catalytic center.     

Optical–microphysical properties of smoke haze from Siberian forest fires in summer 2012

A comprehensive experiment on the study of dynamics of optical and microphysical characteristics of submicron aerosols in the near-ground air layer was carried out in June–August of 2012 under conditions of extremely strong smoke haze originating from vast forest fires in Siberia. Variations of the spectral angular scattering coefficients and the degree of linear polarization in the visible wavelength range are studied, as well as the mass concentrations of dry fractions of aerosol and black carbon, relative content of black carbon (BC fraction), single scattering albedo, particle size distribution function, complex refractive index of the particulate matter, and parameter of condensation activity of aerosol. Peculiarities of differences between optical and microphysical characteristics of near-ground aerosol in smoke haze and under smokeless conditions are revealed. This study is important for validation of results of remote sensing of the composition of smoke haze and background atmosphere obtained from satellite data and sun photometric measurements at the Aerosol Robotic Network (AERONET).     

ShapeSynth: Parameterizing model collections for coupled shape exploration and synthesis

Recent advances in modeling tools enable non‐expert users to synthesize novel shapes by assembling parts extracted from model databases. A major challenge for these tools is to provide users with relevant parts, which is especially difficult for large repositories with significant geometric variations. In this paper we analyze unorganized collections of 3D models to facilitate explorative shape synthesis by providing high‐level feedback of possible synthesizable shapes. By jointly analyzing arrangements and shapes of parts across models, we hierarchically embed the models into low‐dimensional spaces. The user can then use the parameterization to explore the existing models by clicking in different areas or by selecting groups to zoom on specific shape clusters. More importantly, any point in the embedded space can be lifted to an arrangement of parts to provide an abstracted view of possible shape variations. The abstraction can further be realized by appropriately deforming parts from neighboring models to produce synthesized geometry. Our experiments show that users can rapidly generate plausible and diverse shapes using our system, which also performs favorably with respect to previous modeling tools.     

A new set distance and its application to shape registration

We propose a new distance measure, called Complement weighted sum of minimal distances, between finite sets in ${\mathbb Z }^n$ and evaluate its usefulness for shape registration and matching. In this set distance the contribution of each point of each set is weighted according to its distance to the complement of the set. In this way, outliers and noise contribute less to the new similarity measure. We evaluate the performance of the new set distance for registration of shapes in binary images and compare it to a number of often used set distances found in the literature. The most extensive evaluation uses a set of synthetic 2D images. We also show three examples of real problems: registering a set of 2D images extracted from synchrotron radiation micro-computed tomography (SR $\upmu $ CT) volumes depicting bone implants; the difficult multi-modal registration task of finding the exact location of a 2D slice of a bone implant, as imaged by a light microscope, within a 3D SR $\upmu $ CT volume of the same implant; and finally recognition of handwritten characters. The evaluation shows that our new set distance performs well for all tasks and outperforms the other observed distance measures in most cases. It is therefore useful in many image registration and shape comparison tasks.     

Quantum correlations at negative absolute temperatures

We study behavior of quantum discord, a kind of quantum correlation, in systems of dipole–dipole interacting spins in an external magnetic field in the whole temperature range ( \(-\infty ). It was shown that negative temperatures, which are introduced to describe inversions in the population in a finite level system, provide more favorable conditions for emergence of quantum correlations including entanglement. We show that at negative temperature, the correlations become more intense and discord exists between remote spins being in separated states.     

Raman Spectroscopy of Nanocrystalline Ceria and Zirconia Thin Films

The results of Raman-scattering studies of nanocrystalline CeO₂ and ZrO₂:16% Y (YSZ) thin films are presented. The relationship between the lattice disorder and the form of the Raman spectra is discussed and correlated with the microstructure. It is shown that the Raman line shape results from phonon confinement and spatial correlation effects and yields information about the material nonstoichiometry level.     

Thermoplastic extrusion—the mechanism of the formation of extrudate structure and properties

Systems processed by thermoplastic extrusion can be regarded as heterophase polymer melts of incompatible water-plasticized biopolymers. In the process of thermoplastic extrusion, proteins and polysaccharides are melted at high pressure and temperature below the temperature region of their thermal decomposition. Dispersed particles of these systems can be deformed in flow. The mixed-melt anisotropic structure, formed in flow, is fixed by rapid conversion of the melt jet that lets the extruder die from a viscous state to a rubber-like state and then to a glassy state caused by cooling and drying. Incompatibility of proteins and polysaccharides in their water-plasticized melt mixtures impacts on structure formation and texturization during thermoplastic extrusion. Presented at the 20th ISF World Congress and 83rd AOCS Annual Meeting and Expo, May 10–14, 1992, Toronto, Ontario, Canada.     

Self-diffusion of low-generation PAMAM dendrimers with hydroxyl surface groups in solutions: a general regularity

An experimental study of the self-diffusion and nuclear magnetic relaxation of poly(amidoamine) dendrimers with hydroxyl surface groups (PAMAM-OH) dissolved in methanol over a wide range of concentration (?) is reported. It is shown that experimental concentration dependences of PAMAM-OH self-diffusion coefficients (D) can be reduced to the so-called generalized ? dependence. Over macromolecular concentration range studied, the generalized concentration dependence of PAMAM-OH D coincides with analogous curve obtained for poly(allylcarbosilane) dendrimers of high generations. This result confirms the existence of common regularities of the dendritic macromolecule self-diffusion, and their independence of the individual physicochemical and structural properties of dendrimer, solvent, and features of their interactions in the given systems. The concentration dependence of the PAMAM-OH diffusion also exhibits a clear signature of an inflexible molecule.     

Structures and electronic properties of surface/edges of nanodiamond and nanographite

The structure, electronic and magnetic properties of nanodiamond and nanographite/nanographene are investigated. Detonation nanodiamond particles that are covered with amorphous graphitic composites are hydrothermally treated to remove the graphitic surface composites and to terminate the surface carbon atoms with hydrogen. The number of localized spins of dangling bonds and the hydrogen concentration increase upon the increase in the hydrothermal treatment time up to 40 h. Above 40 h, both drop discontinuously, a surface structural reconstruction was suggested. The creation of dangling bonds and an incomplete hydrogenation of the surface carbon atoms destabilize the surface, resulting in the structural reconstruction. Nanodiamond particles are thermally converted to nanographite/nanographene. A single nanographene sheet is successfully prepared by heat-treating nanodiamond particles. The edge of graphene sheet with its edge carbon atoms being hydrogen-terminated is investigated by UHV-STM/STS. Zigzag edges are found to have non-bonding π-state of edge origin, in good agreement with theoretical prediction.