The role of lysine-41 in RNase A catalysis - A quantum chemical study on the active site ligand complex

Several mechanisms have been proposed to explain the action of enzymes at the atomic level. Among them, the recent proposals involving short hydrogen bonds as a step in catalysis by Gerlt and Gassman [1] and proton transfer through low barrier hydrogen bonds (LBHBs) [2, 3] have attracted attention. There are several limitations to experimentally testing such hypotheses, Recent developments in computational methods facilitate the study of active site-ligand complexes to high levels of accuracy, Our previous studies, which involved the docking of the dinucleotide substrate UpA to the active site of RNase A [4, 5], enabled us to obtain a realistic model of the ligand-bound active site of RNase A. From these studies, based on empirical potential functions, we were able to obtain the molecular dynamics averaged coordinates of RNase A, bound to the ligand UpA. A quantum mechanical study is required to investigate the catalytic process which involves the cleavage and formation of covalent bonds. In the present study, we have investigated the strengths of some of the hydrogen bonds between the active site residues of RNase A and UpA at the ab initio quantum chemical level using the molecular dynamics averaged coordinates as the starting point. The 49 atom system and other model systems were optimized at the 3-21G level and the energies of the optimized systems were obtained at the 6-31G* level. The results clearly indicate the strengthening of hydrogen bonds between neutral residues due to the presence of charged species at appropriate positions. Such a strengthening manifests itself in the form of short hydrogen bonds and a low barrier for proton transfer. In the present study, the proton transfer between the 2'-OH of ribose (from the substrate) and the imidazole group from the H12 of RNase A is influenced by K41, which plays a crucial role in strengthening the neutral hydrogen bond, reducing the barrier for proton transfer.

Unsteady free convection flow in the stagnation-point region of a rotating sphere

The unsteady free convection boundary-layer flow in the forward stagnation-point region of a sphere, which is rotating with time-dependent angular velocity in an ambient fluid, has been studied. Both constant wall temperature and constant hear flux conditions have been considered. The non-linear coupled parabolic partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. The skin friction and the heat transfer are enhanced by the buoyancy force. The effect of the buoyancy force is found to be more pronounced for smaller Prandtl numbers than for larger Prandtl numbers. For a given buoyancy force, the heat transfer increases with an increase in Prandtl number, but the skin friction decreases.

Free energy landscape of a dense hard-sphere system

The topography of the free energy landscape in phase space of a dense hard-sphere system characterized by a discretized free energy functional of the Ramakishnan-Yussouff form is investigated numerically using a specially devised Monte Carlo procedure. We locate a considerable number of glassy local minima of the free energy and analyze the distributions of the free energy at a minimum and an appropriately defined phase-space "distance" between different minima. We find evidence for the existence of pairs of closely related glassy minima("two-level systems"). We also investigate the way the system makes transitions as it moves from the basin of attraction of a minimum to that of another one after a start under nonequilibrium conditions. This allows us to determine the effective height of free energy barriers that separate a glassy minimum from the others. The dependence of the height of free energy barriers on the density is investigated in detail. The general appearance of the free energy landscape resembles that of a putting green: relatively deep minima separated by a fairly flat structure. We discuss the connection of our results with the Vogel-Fulcher law and relate our observations to other work on the glass transition.

Structural and optical investigation of semiconductor CdSe/CdS core-shell quantum dot thin films

Highly luminescent CdSe/CdS core-shell nanocrystals have been assembled on indium tin oxide (ITO) coated glass substrates using a wet synthesis route. The physical properties of the quantum dots (QD) have been investigated using X-ray diffraction, transmission electron microscopy and optical absorption spectroscopy techniques. These quantum dots showed a strong enhancement in the near band edge absorption. The in situ luminescence behavior has been interpreted in the light of the quantum confinement effect and induced strain in the core-shell structure.

Working group report: Quantum chromodynamics sub-group

This is the report of the QCD working sub-group at the Tenth Workshop on High Energy Physics Phenomenology (WHEPP-X).

Probing the Neutral Edge Modes in Transport across a Point Contact via Thermal Effects in the Read-Rezayi Non-Abelian Quantum Hall States

Non-Abelian quantum Hall states are characterized by the simultaneous appearance of charge and neutral gapless edge modes, with the structure of the latter being intricately related to the existence of bulk quasiparticle excitations obeying non-Abelian statistics. Here we propose a scenario for detecting the neutral modes by having two point contacts in series separated by a distance set by the thermal equilibration length of the charge mode. We show that by using the first point contact as a heating device, the excess charge noise measured at the second point contact carries a nontrivial signature of the presence of the neutral mode. We also obtain explicit expressions for the thermal conductance and corresponding Lorentz number for transport across a quantum point contact between two edges held at different temperatures and chemical potentials.

Electroluminescence from modulation-doped pseudomorphic AlGaAs/InGaAs/GaAs quantum wells

Low-temperature electroluminescence (EL) is observed in n-type modulation-doped AlGaAs/InGaAs/GaAs quantum well samples by applying a positive voltage between the semitransparent Au gate and alloyed Au–Ge Ohmic contacts made on the top surface of the samples. We attribute impact ionization in the InGaAs QW to the observed EL from the samples. A redshift in the EL spectra is observed with increasing gate bias. The observed redshift in the EL spectra is attributed to the band gap renormalization due to many-body effects and quantum-confined Stark effect.

Prediction of a large-gap quantum-spin-Hall insulator: Diamond-like GaBi bilayer

A quantum-spin-Hall (QSH) state was achieved experimentally, albeit at a low critical temperature because of the narrow band gap of the bulk material. Twodimensional topological insulators are critically important for realizing novel topological applications. Using density functional theory (DFT), we demonstrated that hydrogenated GaBi bilayers (HGaBi) form a stable topological insulator with a large nontrivial band gap of 0.320 eV, based on the state-of-the-art hybrid functional method, which is implementable for achieving QSH states at room temperature. The nontrivial topological property of the HGaBi lattice can also be confirmed from the appearance of gapless edge states in the nanoribbon structure. Our results provide a versatile platform for hosting nontrivial topological states usable for important nanoelectronic device applications.

Investigation of the Internal Heterostructure of Highly Luminescent Quantum Dot-Quantum Well Nanocrystals

In this paper, we report on the growth and characterization of quantum dot−quantum well nanostructures with photoluminescence (PL) that is tunable over the visible range. The material exhibits a PL efficiency as high as 60% and is prepared by reacting ZnS nanocrystals in turn with precursors for CdSe and ZnS in an attempt to form a simple “ZnS/CdSe/ZnS quantum-well structure”. Through the use of synchrotron radiation-based photoelectron spectroscopy in conjunction with detailed overall compositional analysis and correlation with the size of the final composite nanostructure, the internal structure of the composite nanocrystals is shown to consist of a graded alloy core whose composition gradually changes from ZnS at the very center to CdSe at the onset of a CdSe layer. The outer shell is ZnS with a sharp interface, probably reflecting the relative thermodynamic stabilities of the parent binary phases. These contrasting aspects of the internal structure are discussed in terms of the various reactivities and are shown to be crucial for understanding the optical properties of such complex heterostructured nanomaterials.

Efficient Hg and Ag ion detection with luminescent PbS quantum dots grown in poly vinyl alcohol and capped with mercaptoethanol

PbS quantum dots capped with mercaptoethanol (C2H5OSH) have been synthesized in poly vinyl alcohol and used to investigate their photoluminescence (PL) response to various ions such as zinc (Zn), cadmium (Cd), mercury (Hg), silver (Ag), copper (Cu), iron (Fe), manganese (Mn), cobalt (Co), chromium (Cr) and nickel (Ni). The enhancement in the PL intensity was observed with specific ions namely Zn, Cd, Hg and Ag. Among these four ions, the PL response to Hg and Ag even at sub-micro-molar concentrations was quite high, compared to that of Zn and Cd. It was observed that the change in Pb and S molar ratio has profound effect on the sensitivity of these ions. These results indicate that the sensitivity of these QDs could be fine-tuned by controlling the S concentration at the surface. Contrary to the above, Cu quenched the photoluminescence. In Cd based QDs related ion probing, Hg and Cu was found to have quenching properties, however, our PbS QDs have quenching property only for Cu ions. This was attributed to the formation HgS at the surface that has bandgap higher than PbS. Another interesting property of PbS in PVA observed is photo-brightening mechanism due to the curing of the polymer with laser. However, the presence of excess ions at the surface changes its property to photo-darkening/brightening that depends on the direction of carrier transfer mechanism (from QDs to the surface adsorbed metal ions or vice-versa). which is an interesting feature for metal ion detectivity.

Quantum first-passage problem

Formulation of quantum first passage problem is attempted in terms of a restricted Feynman path integral that simulates an absorbing barrier as in the corresponding classical case. The positivity of the resulting probability density, however, remains to be demonstrated.

Quantum entanglement in a noncommutative system

We explore the effect of two-dimensional position-space noncommutativity on the bipartite entanglement of continuous-variable systems. We first extend the standard symplectic framework for studying entanglement of Gaussian states of commutative systems to the case of noncommutative systems residing in two dimensions. Using the positive partial transpose criterion for separability of bipartite states, we derive a condition on the separability of a noncommutative system that is dependent on the noncommutative parameter theta. We then consider the specific example of a bipartite Gaussian state and show the quantitative reduction in entanglement originating from noncommutative dynamics. We show that such a reduction in entanglement for a noncommutative system arising from the modification of the variances of the phase-space variables (uncertainty relations) is clearly manifested between two particles that are separated by small distances.

NMR relaxation study of disorder in the mixed system BP x GPI(1-x) and the low temperature transition from classical to quantum rotation

1H NMR spin-lattice relaxation time (T1) studies have been carried out in the temperature range 100 K to 4 K, at two Larmor frequencies 11.4 and 23.3 MHz, in the mixed system of betaine phosphate and glycine phosphite (BPxGPI(1-x)), to study the effects of disorder on the proton group dynamics. Analysis of T1 data indicates the presence of a number of inequivalent methyl groups and a gradual transition from classical reorientations to quantum tunneling rotations. At lower temperatures, microstructural disorder in the local environments of the methyl groups, result in a distribution in the activation energy (Ea) and the torsional energy gap (E01). For certain values of x, the magnetisation recovery shows biexponential behaviour at lower temperatures.

Classical Langevin dynamics of a charged particle moving on a sphere and diamagnetism: A surprise

It is generally known that the orbital diamagnetism of a classical system of charged particles in thermal equilibrium is identically zero —the Bohr-van Leeuwen theorem. Physically, this null result derives from the exact cancellation of the orbital diamagnetic moment associated with the complete cyclotron orbits of the charged particles by the paramagnetic moment subtended by the incomplete orbits skipping the boundary in the opposite sense. Motivated by this crucial but subtle role of the boundary, we have simulated here the case of a finite but unbounded system, namely that of a charged particle moving on the surface of a sphere in the presence of an externally applied uniform magnetic field. Following a real space-time approach based on the classical Langevin equation, we have computed the orbital magnetic moment that now indeed turns out to be non-zero and has the diamagnetic sign. To the best of our knowledge, this is the first report of the possibility of finite classical diamagnetism in principle, and it is due to the avoided cancellation.