A DFT study of the mechanism of Ni superoxide dismutase (NiSOD): role of the active site cysteine-6 residue in the oxidative half-reaction

In the present DFT study, the catalytic mechanism of H2O2 formation in the oxidative half-reaction of NiSOD, E-Ni(II) + O2- + 2H+ --> E-Ni(III) + H2O2, has been investigated. The main objective of this study is to investigate the source of two protons required in this half-reaction. The proposed mechanism consists of two steps: superoxide coordination and H2O2 formation. The effect of protonation of Cys6 and the proton donating roles of side chains (S) and backbones (B) of His1, Asp3, Cys6, and Tyr9 residues in these two steps have been studied in detail. For protonated Cys6, superoxide binding generates a Ni(III)-O2H species in a process that is exothermic by 17.4 kcal/mol (in protein environment using the continuum model). From the Ni(III)-O2H species, H2O2 formation occurs through a proton donation by His1 via Tyr9, which relative to the resting position of the enzyme is exothermic by 4.9 kcal/mol. In this pathway, a proton donating role of His1 residue is proposed. However, for unprotonated Cys6, a Ni(II)-O2- species is generated in a process that is exothermic by 11.3 kcal/mol. From the Ni(II)-O2- species, the only feasible pathway for H2O2 formation is through donation of protons by the Tyr9(S)-Asp3(S) pair. The results discussed in this study elucidate the role of the active site residues in the catalytic cycle and provide intricate details of the complex functioning of this enzyme.     

Protonation states of the catalytic dyad of β-secretase (BACE1) in the presence of chemically diverse inhibitors: a molecular docking study

In this molecular docking study, the protonation states of the catalytic Asp dyad of the beta-secretase (BACE1) enzyme in the presence of eight chemically diverse inhibitors have been predicted. BACE1 catalyzes the rate-determining step in the generation of Alzheimer amyloid beta peptides and is widely considered as a promising therapeutic target. All the inhibitors were redocked into their corresponding X-ray structures using a combination of eight different protonation states of the Asp dyad for each inhibitor. Five inhibitors were primarily found to favor two different monoprotonated states, and the remaining three favor a dideprotonated state. In addition, five of them exhibited secondary preference for a diprotonated state. These results show that the knowledge of a single protonation state of the Asp dyad is not sufficient to search for the novel inhibitors of BACE1 and the most plausible state for each inhibitor must be determined prior to conducting in-silico screening.     

Surfactant-Assisted Acid Pretreatment of Sugarcane Tops for Bioethanol Production

Sugarcane tops is one of the largest biomass resources in India and in tropical countries such as Brazil in terms of surplus availability. Conversion of this feedstock to ethanol requires pretreatment to make it more accessible for the enzymes used in saccharification. Though several pretreatment regimens have been developed for addressing biomass recalcitrance, very few seem to be promising as an industrial process. A novel hybrid method involving use of mild acid and surfactant was developed which could effectively remove lignin and improve the sugar yield from sugar cane tops. Operational parameters that affect the pretreatment efficiency (measured as yield of sugars) were studied and optimized. Changes in structural properties of the biomass were studied in relation to the pretreatment process using scanning electron microscopy (SEM), X-ray diffraction (XRD), and Fourier Transform Infrared (FTIR) analysis, and the changes in chemical composition was also monitored. The biomass pretreated with the optimized novel method could yield 0.798?g of reducing sugars per gram of pretreated biomass upon enzymatic hydrolysis.     

Self-organized transition to coherent activity in disordered media

Synchronized oscillations are of critical functional importance in many biological systems. We show that such oscillations can arise without centralized coordination in a disordered system of electrically coupled excitable and passive cells. Increasing the coupling strength results in waves that lead to coherent periodic activity, exhibiting cluster, local and global synchronization under different conditions. Our results may explain the self-organized transition in a pregnant uterus from transient, localized activity initially to system-wide coherent excitations just before delivery.     

Thermoelectrically pumped light-emitting diodes operating above unity efficiency

A heated semiconductor light-emitting diode at low forward bias voltage V相似文献   

Adsorption of Cu2+ from aqueous solution onto iron oxide coated eggshell powder: Evaluation of equilibrium,isotherms, kinetics,and regeneration capacity

This study explored the adsorption behavior of Cu²⁺ onto iron oxide coated eggshell powder (IOESP) from aqueous solution. The effect of various operational parameters such as pH, contact time, initial adsorbate concentration, surfactant, and temperature on adsorption of Cu²⁺ ions was investigated using batch adsorption experiments. The optimum pH for Cu²⁺ adsorption was found to be 6.0. Kinetics of adsorption was found to follow the pseudo-second-order rate equation. The suitability of Langmuir and Freundlich adsorption models to the equilibrium data was investigated. The adsorption was well described by the Freundlich isotherm model indicating the presence of heterogeneous sites for Cu²⁺ adsorption. The adsorption of Cu²⁺ was increased in the presence of anionic surfactant (SDS) while cationic surfactant (CTAB) shows no significant change in adsorption capacity. Thermodynamic parameters showed that the adsorption of Cu²⁺ onto IOESP was feasible, spontaneous, and exothermic. Regeneration studies were performed using HCl, HCOOH, EDTA, and NaOH as eluting agent for Cu²⁺ desorption from saturated IOESP and the maximum regeneration was observed with HCl.     

Optical bandgap and electrical conductivity studies on near stoichiometric LiNbO3 crystals prepared by VTE process

Vapour transport equilibrium (VTE) technique was used to prepare near stoichiometric LiNbO₃ (NSLN) crystals. Simultaneous occurrence of reduction has been observed during the Li-enrichment that results in the weak absorption bands centred at 1.7, 2.6 and 3.7 eV in the absorption spectrum. Annealing in oxygen atmosphere resulted in decrease in the intensity of these bands. The indirect and direct band-gap energies for NSLN crystals evaluated from absorption studies are reported. The energy of the phonon involved in the indirect transition is ～85 meV (685 cm^?1). Near room temperature ac-conductivity measurements reveal lower conductivity for oxygen annealed NSLN crystal in comparison to as prepared NSLN and CLN specimens. The activation energies for ac-conductivity along the z-direction for NSLN and CLN crystals in the temperature range 500–1100 K are 1.03 eV and 0.96 eV, respectively.     

Modeling complex systems macroscopically: Case/agent-based modeling,synergetics, and the continuity equation

Recently, the continuity equation (also known as the advection equation) has been used to study stability properties of dynamical systems, where a linear transfer operator approach was used to examine the stability of a nonlinear equation both in continuous and discrete time (Vaidya and Mehta, IEEE Trans Autom Control 2008, 53, 307–323; Rajaram et al., J Math Anal Appl 2010, 368, 144–156). Our study, which conducts a series of simulations on residential patterns, demonstrates that this usage of the continuity equation can advance Haken's synergetic approach to modeling certain types of complex, self-organizing social systems macroscopically. The key to this advancement comes from employing a case-based approach that (1) treats complex systems as a set of cases and (2) treats cases as dynamical vsystems which, at the microscopic level, can be conceptualized as k dimensional row vectors; and, at the macroscopic level, as vectors with magnitude and direction, which can be modeled as population densities. Our case-based employment of the continuity equation has four benefits for agent-based and case-based modeling and, more broadly, the social scientific study of complex systems where transport or spatial mobility issues are of interest: it (1) links microscopic (agent-based) and macroscopic (structural) modeling; (2) transforms the dynamics of highly nonlinear vector fields into the linear motion of densities; (3) allows predictions to be made about future states of a complex system; and (4) mathematically formalizes the structural dynamics of these types of complex social systems.     

Propagation of wave at the boundary surface of transversely isotropic thermoelastic material with voids and isotropic elastic half-space

The purpose of this research is to study the effect of voids on the surface wave propagation in a layer of a transversely isotropic thermoelastic material with voids lying over an isotropic elastic half-space. The frequency equation is derived after developing a mathematical model for welded and smooth contact boundary conditions. The dispersion curves giving the phase velocity and attenuation coefficient via wave number are plotted graphically to depict the effects of voids and anisotropy for welded contact boundary conditions. The specific loss and amplitudes of the volume fraction field, the normal stress, and the temperature change for welded contact are obtained and shown graphically for a particular model to depict the voids and anisotropy effects. Some special cases are also deduced from the present investigation.     

A weak immersion relation on graphs and its applications

Weak immersion is a generalization of the immersion relation defined by Nash-Williams. A graph H is said to be weakly immersed in a graph G if H can be obtained from G by a sequence of these three operations: taking a subgraph, splitting a vertex, and lifting a pair of adjacent edges. The weak immersion relation has the useful property that finite graphs are well-quasi-ordered by it, which also holds for graphs with some vertices designated as terminals. As a result, any family of finite graphs that is closed under weak immersion can be characterized by a finite number of minimal forbidden graphs called obstructions. Weak immersion offers two advantages over immersion for practical applications. First, although closure under weak immersion implies closure under immersion, families can have significantly fewer obstructions under weak immersion. Hence weak immersion can provide simpler characterizations for closed families. Examples include graphs of bounded cutwidth and graphs of bounded multiway cutsize. The difference in the number of obstructions is at least exponential in the cutwidth and in the square-root of the multiway cutsize. Second, for every fixed graph H, there is a polynomial-time algorithm to decide whether H is weakly immersed in an input graph G. Consequently, there is a polynomial-time membership test for any family that is closed under weak immersion. In principle, testing for weak immersion is as fast as testing for immersion. Thus the simpler characterization provided by weak immersion may lead to faster membership algorithms.