Impact of glycosylation on stability, structure and unfolding of soybean agglutinin (SBA): an insight from thermal perturbation molecular dynamics simulations

Glycosylation has been recognized as one of the most prevalent and complex post-translational modifications of proteins involving numerous enzymes and substrates. Its effect on the protein conformational transitions is not clearly understood yet. In this study, we have examined the effect of glycosylation on protein stability using molecular dynamics simulation of legume lectin soybean agglutinin (SBA). Its glycosylated moiety consists of high mannose type N-linked glycan (Man(9)GlcNAc(2)). To unveil the structural perturbations during thermal unfolding of these two forms, we have studied and compared them to the experimental results. From the perspective of dynamics, our simulations revealed that the nonglycosylated monomeric form is less stable than corresponding glycosylated form at normal and elevated temperatures. Moreover, at elevated temperature thermal destabilization is more prominent in solvent exposed loops, turns and ends of distinct beta sheets. SBA maintains it folded structure due to some important saltbridges, hydrogen bonds and hydrophobic interactions within the protein. The reducing terminal GlcNAc residues interact with the protein residues VAL161, PRO182 and SER225 via hydrophobic and via hydrogen bonding with ASN 9 and ASN 75. Our simulations also revealed that single glycosylation (ASN75) has no significant effect on corresponding cis peptide angle orientation. This atomistic description might have important implications for understanding the functionality and stability of Soybean agglutinin.

Thermal conductivity of beta-FeSi2/Si endogenous composites formed by the eutectoid decomposition of alpha-Fe2Si5

Thermoelectric properties of semiconducting beta-FeSi2 containing a homogeneous distribution of Si secondary phase have been studied. The synthesis was carried out using arc melting followed by the densification by uniaxial hot pressing. Endogenous beta-FeSi2/Si composites were produced by the eutectoid decomposition of high-temperature alpha-Fe2Si5 phase. The aging heat treatments have been carried out at various temperatures below the equilibrium eutectoid temperature for various durations in order to tune the size of the eutectoid product. Thermal properties of the samples were studied in the temperature range of 100-350 A degrees C. The microstructural investigations support the fact that the finest microstructure generated through the eutectoid decomposition of the alpha-Fe2Si5 metastable phase is responsible of the phonon scattering. The results suggest an opportunity to produce bulk iron silicide alloys with reduced thermal conductivity in order to enhance its thermoelectric performance.

Role of the Molar Volume on Estimated Diffusion Coefficients

The role of the molar volume on the estimated diffusion parameters has been speculated for decades. The Matano-Boltzmann method was the first to be developed for the estimation of the variation of the interdiffusion coefficients with composition. However, this could be used only when the molar volume varies ideally or remains constant. Although there are no such systems, this method is still being used to consider the ideal variation. More efficient methods were developed by Sauer-Freise, Den Broeder, and Wagner to tackle this problem. However, there is a lack of research indicating the most efficient method. We have shown that Wagner's method is the most suitable one when the molar volume deviates from the ideal value. Similarly, there are two methods for the estimation of the ratio of intrinsic diffusion coefficients at the Kirkendall marker plane proposed by Heumann and van Loo. The Heumann method, like the Matano-Boltzmann method, is suitable to use only when the molar volume varies more or less ideally or remains constant. In most of the real systems, where molar volume deviates from the ideality, it is safe to use the van Loo method. We have shown that the Heumann method introduces large errors even for a very small deviation of the molar volume from the ideal value. On the other hand, the van Loo method is relatively less sensitive to it. Overall, the estimation of the intrinsic diffusion coefficient is more sensitive than the interdiffusion coefficient.

Design of symmetric TIM barrel proteins from first principles

Background: Computational protein design is a rapidly maturing field within structural biology, with the goal of designing proteins with custom structures and functions. Such proteins could find widespread medical and industrial applications. Here, we have adapted algorithms from the Rosetta software suite to design much larger proteins, based on ideal geometric and topological criteria. Furthermore, we have developed techniques to incorporate symmetry into designed structures. For our first design attempt, we targeted the (alpha/beta)(8) TIM barrel scaffold. We gained novel insights into TIM barrel folding mechanisms from studying natural TIM barrel structures, and from analyzing previous TIM barrel design attempts. Methods: Computational protein design and analysis was performed using the Rosetta software suite and custom scripts. Genes encoding all designed proteins were synthesized and cloned on the pET20-b vector. Standard circular dichroism and gel chromatographic experiments were performed to determine protein biophysical characteristics. 1D NMR and 2D HSQC experiments were performed to determine protein structural characteristics. Results: Extensive protein design simulations coupled with ab initio modeling yielded several all-atom models of ideal, 4-fold symmetric TIM barrels. Four such models were experimentally characterized. The best designed structure (Symmetrin-1) contained a polar, histidine-rich pore, forming an extensive hydrogen bonding network. Symmetrin-1 was easily expressed and readily soluble. It showed circular dichroism spectra characteristic of well-folded alpha/beta proteins. Temperature melting experiments revealed cooperative and reversible unfolding, with a T-m of 44 degrees C and a Gibbs free energy of unfolding (Delta G degrees) of 8.0 kJ/mol. Urea denaturing experiments confirmed these observations, revealing a C-m of 1.6 M and a Delta G degrees of 8.3 kJ/mol. Symmetrin-1 adopted a monomeric conformation, with an apparent molecular weight of 32.12 kDa, and displayed well resolved 1D-NMR spectra. However, the HSQC spectrum revealed somewhat molten characteristics. Conclusions: Despite the detection of molten characteristics, the creation of a soluble, cooperatively folding protein represents an advancement over previous attempts at TIM barrel design. Strategies to further improve Symmetrin-1 are elaborated. Our techniques may be used to create other large, internally symmetric proteins.

Synthesis, photoluminescence and Judd-Ofelt parameters of LiNa3P2O7:Eu3+ orthorhombic microstructures

We report, for the first time, the photoluminescence properties of Eu3+-doped LiNa3P2O7 phosphor, synthesized by a facile solid-state reaction method in air atmosphere. The crystal structure and phase purity of the phosphors were analyzed by X-ray diffraction analysis. Orthorhombic structural morphology was identified by scanning electron microscopy. The phosphate groups in the phosphor were confirmed by Fourier transform infrared analysis. Bandgap of the phosphor was calculated from the diffuse reflectance spectra data using Kubelka-Munk function. Under 395-nm UV excitation, the phosphors show signs of emitting red color due to the D-5(0) -> F-7(2) transition. In accordance with Judd-Ofelt theory, spectroscopic parameters such as oscillator intensity parameter Omega(t) (t = 2), spontaneous emission probabilities, fluorescence branching ratios and radiative lifetimes were calculated and analyzed for the first time in this system.

Router Attack toward NoC-enabled MPSoC and Monitoring Countermeasures against such Threat

The growing number of applications and processing units in modern Multiprocessor Systems-on-Chips (MPSoCs) come along with reduced time to market. Different IP cores can come from different vendors, and their trust levels are also different, but typically they use Network-on-Chip (NoC) as their communication infrastructure. An MPSoC can have multiple Trusted Execution Environments (TEEs). Apart from performance, power, and area research in the field of MPSoC, robust and secure system design is also gaining importance in the research community. To build a secure system, the designer must know beforehand all kinds of attack possibilities for the respective system (MPSoC). In this paper we survey the possible attack scenarios on present-day MPSoCs and investigate a new attack scenario, i.e., router attack targeted toward NoC architecture. We show the validity of this attack by analyzing different present-day NoC architectures and show that they are all vulnerable to this type of attack. By launching a router attack, an attacker can control the whole chip very easily, which makes it a very serious issue. Both routing tables and routing logic-based routers are vulnerable to such attacks. In this paper, we address attacks on routing tables. We propose different monitoring-based countermeasures against routing table-based router attack in an MPSoC having multiple TEEs. Synthesis results show that proposed countermeasures, viz. Runtime-monitor, Restart-monitor, Intermediate manager, and Auditor, occupy areas that are 26.6, 22, 0.2, and 12.2 % of a routing table-based router area. Apart from these, we propose Ejection address checker and Local monitoring module inside a router that cause 3.4 and 10.6 % increase of a router area, respectively. Simulation results are also given, which shows effectiveness of proposed monitoring-based countermeasures.

Investigation of schemes for incorporating generator Q limits in the fast decoupled load flow method

Fast Decoupled Load Flow (FDLF) is a very popular and widely used power flow analysis method because of its simplicity and efficiency. Even though the basic FDLF algorithm is well investigated, the same is not true in the case of additional schemes/modifications required to obtain adjusted load flow solutions using the FDLF method. Handling generator Q limits is one such important feature needed in any practical load flow method. This paper presents a comprehensive investigation of two classes of schemes intended to handle this aspect i.e. the bus type switching scheme and the sensitivity scheme. We propose two new sensitivity based schemes and assess their performance in comparison with the existing schemes. In addition, a new scheme to avoid the possibility of anomalous solutions encountered while using the conventional schemes is also proposed and evaluated. Results from extensive simulation studies are provided to highlight the strengths and weaknesses of these existing and proposed schemes, especially from the point of view of reliability.

Estimation of mechanical properties of single wall carbon nanotubes using molecular mechanics approach

Molecular mechanics based finite element analysis is adopted in the current work to evaluate the mechanical properties of Zigzag, Armchair and Chiral Single wall Carbon Nanotubes (SWCNT) of different diameters and chiralities. Three different types of atomic bonds, that is Carbon Carbon covalent bond and two types of Carbon Carbon van der Waals bonds are considered in the carbon nanotube system. The stiffness values of these bonds are calculated using the molecular potentials, namely Morse potential function and Lennard-Jones interaction potential function respectively and these stiffness's are assigned to spring elements in the finite element model of the CNT. The geometry of CNT is built using a macro that is developed for the finite element analysis software. The finite element model of the CNT is constructed, appropriate boundary conditions are applied and the behavior of mechanical properties of CNT is studied.

Effect of Size Reduction on Magnetic Ordering in Sm1-x Ca (x) MnO3 (x=0.35, 0.65 and 0.92) Manganites: Magnetic and EMR Studies

We have employed the highly sensitive electron magnetic resonance technique complimented by magnetization measurements to study the impact of size reduction on the magnetic ordering in nanosized Sm1-x Ca (x) MnO3 (x = 0.35, 0.65 and 0.92). In the bulk form, x = 0.35 sample shows a charge ordering transition at 235 K followed by a mixed magnetic phase, the sample with x = 0.65 exhibits charge order below 275 K and shows an antiferromagnetic insulator phase below 135 K while that with x = 0.92 has a ferromagnetic-cluster glass ground state. Thus, a comparative study of magnetic ground states of bulk and nanoparticles (diameter similar to 25 nm) enables us to investigate size-induced effects on different types of magnetic ordering. It is seen that in the bulk samples the temperature dependences of the EPR parameters are quite different from each other. This difference diminishes for the nanosamples where all the three samples show qualitatively similar behavior. The magnetization measurements corroborate this conclusion.

Electron Magnetic Resonance Studies of Nanosized Nd0.65Ca0.35 Mn1-xCrxO3 (x=0, 0.06, 0.1) Manganite

We report a systematic investigation of the temperature dependence of electron magnetic resonance (EMR) line width, intensity and resonance field for similar to 25 nm Nd0.65Ca0.35MnO3 (NCMO1), Nd0.65Ca0.35Mn0.94Cr0.06O3 (NCMO2) and Nd0.65Ca0.35Mn0.9Cr0.1O3 (NCMO3) nanoparticles prepared by sol-gel method. The EMR line widths for the three nano-samples differ significantly from one another below a temperature T (min) where the line width has a minimum. T (min) was found to be 130, 100 and 120 K for NCMO1, NCMO2 and NCMO3, respectively. Well above T (min) the line width values for the three samples are close to one another. The sharp upturn of EMR line width below T (min) is attributed to the formation of short range, ferromagnetically ordered clusters. Temperature dependence of EMR intensity shows a residual CO transition in NCMO1 and NCMO2 and a complete disappearance of it in NCMO3. The intensity undergoes significant increase below 120, 80 and 100 K for NCMO1, NCMO2 and NCMO3, respectively, indicating the onset of ferromagnetic transitions. The occurrence of ferromagnetic transition is further confirmed by magnetization hysteresis measurements. The decrease in T (C) in NCMO2 and NCMO3 compared to NCMO1 nanoparticles is understood to be due to the destruction of the double-exchange interaction by chromium doping. The resonance field decreases below the ferromagnetic onset temperatures for all the samples as expected. The combined effects of the reduction in size and of chromium doping in Mn site are discussed.

Single Spin Asymmetry in Charmonium Production

We present estimates of single spin asymmetry (SSA) in the electroproduction of taking into account the transverse momentum dependent (TMD) evolution of the gluon Sivers function and using Color Evaporation Model of charmonium production. We estimate SSA for JLab, HERMES, COMPASS and eRHIC energies using recent parameters for the quark Sivers functions which are fitted using an evolution kernel in which the perturbative part is resummed up to next-to-leading logarithms accuracy. We find that these SSAs are much smaller as compared to our first estimates obtained using DGLAP evolution but are comparable to our estimates obtained using TMD evolution where we had used approximate analytical solution of the TMD evolution equation for the purpose.

Enhancement in Strain Hardening on Boron Addition in As-Cast Ti-6Al-4V Alloy

It has been previously reported that the addition of boron to Ti-6Al-4V results in significant refinement of the as-cast microstructure and enhancement in the strain hardening. However, the mechanism for the latter effect has not been adequately studied. The aim of this study was to understand the reasons for the enhancement in room temperature strain hardening on addition of boron to as cast Ti-6Al-4V alloy. A study was conducted on slip transmission using SEM, TEM, optical profilometry and four point probe resistivity measurements on un-deformed and deformed samples of Ti-6Al-4V-xB with five levels of boron. Optical profilometry was used to quantify the magnitude of offsets on slip traces which in turn provided information about the extent of planar or multiple slip. Studies on deformed samples reveal that while lath boundaries appear to easily permit dislocation slip transmission, colony boundaries are potent barriers to slip. From TEM studies it was also observed that while alloys containing lower boron underwent planar slip, deformation was more homogeneous in higher boron alloys due to multiple slip resulting from large number of colony boundaries. Multiple slip is also proposed to be the prime cause of the enhanced strain hardening.

Generation of Temperature Dependent Transversely Isotropic Properties for Zigzag and Armchair Single-Walled Carbon Nanotubes

Finite element analysis has been carried out to obtain temperature dependent transversely isotropic properties of the single-walled carbon nanotubes (SWCNTs). Finite element models of SWCNTs are generated by specifying the C-C bond rigidities. The five independent transversely isotropic properties for different chiralities are evaluated using the stress fields of thick-walled cylinders and the elastic deformations of SWCNTs subjected to pure extension, internal pressure and pure torsion loads. Empirical relations are provided for the five independent elastic constants useful to armchair and zigzag SWCNTs.

Conductivity studies on microwave synthesized glasses

Conductivity measurements have been made on x V O-2(5) - (100-x) 0.5 Na2O + 0.5 B2O3] (where 10 a parts per thousand currency sign x a parts per thousand currency sign 50) glasses prepared by using microwave method. DC conductivity (sigma) measurements exhibit temperature-and compositional-dependent trends. It has been found that conductivity in these glasses changes from the predominantly `ionic' to predominantly `electronic' depending upon the chemical composition. The dc conductivity passes through a deep minimum, which is attributed to network disruption. Also, this nonlinear variation in sigma (dc) and activation energy can be interpreted using ion-polaron correlation effect. Electron paramagnetic resonance (EPR) and impedance spectroscopic techniques have been used to elucidate the nature of conduction mechanism. The EPR spectra reveals, in least modified (25 Na2O mol%) glasses, conduction is due to the transfer of electrons via aliovalent vanadium sites, while in highly modified (45 Na2O mol%) glasses Na+ ion transport dominates the electrical conduction. For highly modified glasses, frequency-dependent conductivity has been analysed using electrical modulus formalism and the observations have been discussed.