Influence of phosphate ligands in abolishing the conformational difference between ribonuclease A and its acid-denatured derivative

The initial structural alteration of RNAase A due to acid denaturation (0.5 N HCl, 30 degrees C) that accompanies deamidation (without altering enzymic activity) has been dectected by spectrophotometric titration, fluorescence and ORD/CD measurements. It is shown that acid treated RNAase A has an altered conformation at neutral pH, 25 degrees C. This is characterized by the increased accessibility of buried tyrosine residue(s) towards the solvent. The most altered conformation of RNAase A is found in the 10 h acid-treated derivative. This has about 1.5 additional exposed tyrosine residues and a lesser amount of secondary structure than RNAase A. All three methods (titration, fluorescence and CD) established that the structural transition of RNAase A is biphasic. The first phase occurs within 1 h and the resulting subtle conformational change is constant up to 7 h. Following this, after the release of 0.55 mol of ammonia, the major conformational change begins. The altered conformation of the acid-denatured RNAase A could be reversed completely to the native state through a conformational change induced by substrate analogs like 2'- or 3'-CMP. Thus the monodeamidated derivative isolated from the acid-denatured RNAase A by phosphate is very similar to RNAase A in over-all conformation. The results suggest the possibility of flexibility in the RNAase A molecule that does not affect its catalytic activity, as probed through the tyrosine residues.

MIMO Precoding With X- and Y- Codes

We consider a slow fading multiple-input multiple-output (MIMO) system with channel state information at both the transmitter and receiver. A well-known precoding scheme is based upon the singular value decomposition (SVD) of the channel matrix, which transforms the MIMO channel into parallel subchannels. Despite having low maximum likelihood decoding (MLD) complexity, this SVD precoding scheme provides a diversity gain which is limited by the diversity gain of the weakest subchannel. We therefore propose X- and Y-Codes, which improve the diversity gain of the SVD precoding scheme but maintain the low MLD complexity, by jointly coding information across a pair of subchannels. In particular, subchannels with high diversity gain are paired with those having low diversity gain. A pair of subchannels is jointly encoded using a 2 2 real matrix, which is fixed a priori and does not change with each channel realization. For X-Codes, these rotation matrices are parameterized by a single angle, while for Y-Codes, these matrices are left triangular matrices. Moreover, we propose X-, Y-Precoders with the same structure as X-, Y-Codes, but with encoding matrices adapted to each channel realization. We observed that X-Codes/Precoders are good for well-conditioned channels, while Y-Codes/Precoders are good for ill-conditioned channels.

Continuum in the X-Z-Y Weak Bonds: Z= Main Group Elements

The Continuum in the variation of the X-Z bond length change from blue-shifting to red-shifting through zero-shifting in the X-Z---Y complex is inevitable. This has been analyzed by ab-initio molecular orbital calculations using Z= Hydrogen, Halogens, Chalcogens, and Pnicogens as prototypical examples. Our analysis revealed that, the competition between negative hyperconjugation within the donor (X-Z) molecule and Charge Transfer (CT) from the acceptor (Y) molecule is the primary reason for the X-Z bond length change. Here, we report that, the proper tuning of X-and Y-group for a particular Z-can change the blue-shifting nature of X-Z bond to zero-shifting and further to red-shifting. This observation led to the proposal of a continuum in the variation of the X-Z bond length during the formation of X-Z---Y complex. The varying number of orbitals and electrons available around the Z-atom differentiates various classes of weak interactions and leads to interactions dramatically different from the H-Bond. Our explanations based on the model of anti-bonding orbitals can be transferred from one class of weak interactions to another. We further take the idea of continuum to the nature of chemical bonding in general. (C) 2015 Wiley Periodicals, Inc.

Micro-mechanical stages with enhanced range

We present concepts and an optimization-based methodology for the design of micro-mechanical stages that have not only high precision but also an enhanced range. Joint-free distributed compliant designs provide high precision and easy manufacturability at macro and micro scales. The range of motion is enhanced by using displacement-amplifying compliant mechanisms (DaCMs). The main issue addressed in this paper is how to retain the decoupling between the X and Y motions in the stage when it is equipped with DaCMs. The natural frequency of the stage is also not compromised in enhancing the range. The optimized design has 2.5 times more range than the designs reported in the literature. Furthermore, the sensitivity improved by a factor of two when the stage is optimized for an accelerometer.

X-ray studies on crystalline complexes involving amino acids and peptides. XXI. Structure of a (1:1) complex between L-phenylalanine and D-valine

CsHllNO2.C9HilNO2, Mr = 282.3, P1, a = 5.245 (1), b = 5.424 (1), c = 14.414 (2) A, a = 97.86 (1), fl = 93-69 (2), y = 70-48 (2) °, V= 356 A 3, Z = 1, O m = 1-32 (2), Dx = 1.32 g cm-3, h(Mo Ka) = 0-7107 A, g = 5-9 cm-1, F(000) = 158, T= 298 K, R=0.035 for 1518 observed reflections with I>2tr(I). The molecules aggregate in double layers, one ayer made up of L-phenylalanine molecules and the other of D-valine molecules. Each double layer is stabilized by interactions involving main-chain atoms of both types of molecules. The interactions include hydrogen bonds which give rise to two head-to-tail sequences. The arrangement of molecules in the complex is almost the same as that in the structure of DL-valine (and DL-leucine and DL-isoleucine) except for the change in the side chain of L molecules. The molecules in crystals containing an equal number of L and O hydrophobic amino-acid molecules thus appear to aggregate in a similar fashion, irrespective of the precise details of the side chain.

Difference in spin state and covalence between La1-xSrxCoO3 and La2-xSrxLi0.5Co0.5O4

We present a comparative study of the spin states and electronic properties of La1-xSrxCoO3 and La2-xSrxLi0.5Co0.5O4 using X-ray absorption near-edge structure spectroscopy at both the O-K and Co-L-2.3 thresholds. In the La2-xSrxLi0.5Co0.5O4 system the CoO6 octahedra are isolated, the holes induced by Sr doping are trapped in the isolated Co(IV)O-6 octahedra, and a low-spin state is found for the Co ions, which does not change upon Sr doping. In the La1-xSrxCoO3 system, the interconnected CoO6 octahedra, with a 180degrees Co-O-Co bond angle, give rise to a transition from low-spin to intermediate-spin state with a ferromagnetic alignment of the Co spins. The double-exchange, ferromagnetic coupling between Co ions mediated by the 180degrees bond angle is responsible for suppressing the low spin-state. We find that the branching ratio of spectral intensities at the L-2 and L-3 thresholds in the Co-L-2.3 X-ray absorption spectra is sensitive to the spin state of the Co ions allowing its direct spectroscopic determination. (C) 2002 Published by Elsevier Science B.V.

The X-C---Y (X = O/F, Y = O, S, F, Cl, Br, N, P,) Carbon bond and hydrophobic interactions

While the tetrahedral face of methane has an electron rich centre and can act as a hydrogen bond acceptor, substitution of one of its hydrogens with some electron withdrawing group (such as -F/OH) can make the opposite face electron deficient. Electrostatic potential calculations confirm this and high level quantum calculations show interactions between the positive face of methanol/methyl fluoride and electron rich centers of other molecules such as H2O. Analysis of the wave functions of atoms in molecules shows the presence of an unusual C···Y interaction, which could be called 'carbon bonding'. NBO analysis and vibrational frequency shifts confirm the presence of this interaction. Given the properties of alkyl groups bonded to electronegative elements in biological molecules, such interactions could play a significant role, which is yet to be recognized. This and similar interactions could give an enthalpic contribution to what is called the 'hydrophobic interactions'.

Analysis of the evanescent field coupling between a fiber and a planar waveguide using the explicit finite difference method with a nonuniform mesh (Journal Paper)

We investigate an optical waveguide system consisting of an unclad fiber core suspended at a constant distance parallel to the surface of a planar waveguide. The coupling and propagation of light in the combined system is studied using the three-dimensional explicit finite difference beam propagation method with a nonuniform mesh configuration. The power loss in the fiber and the field distribution in the waveguide are studied as a function of various parameters, such as index changes, index profile, and propagation distance, for the combined system.

Direct evidence of redox interaction between metal ion and support oxide in Ce(0.98)Pd(0.02)O(2-delta) by a combined electrochemical and XPS study

A combined electrochemical method and X-ray photo electron spectroscopy (XPS) has been utilized to understand the Pd(2+)/CeO(2) interaction in Ce(1-x)Pd(x)O(2-delta) (x = 0.02). A constant positive potential (chronoamperometry) is applied to Ce(0.98)Pd(0.02)O(2-delta) working electrode which causes Ce(4+) to reduce to Ce(3+) to the extent of similar to 35%, while Pd remains in the +2 oxidation state. Electrochemically cycling this electrode between 0.0-1.2 V reverts back to the original state of the catalyst. This reversibility is attributed to the reversible reduction of Ce(4+) to Ce(3+) state. CeO(2) electrode with no metal component reduces to CeO(2-y) (y similar to 0.4) after applying 1.2 V which is not reversible and the original composition of CeO(2) cannot be brought back in any electrochemical condition. During the electro-catalytic oxygen evolution reaction at a constant 1.2 V for 1000 s, Ce(0.98)Pd(0.02)O(2-delta) reaches a steady state composition with Pd in the +2 states and Ce(4+) : Ce(3+) in the ratio of 0.65 : 0.35. This composition can be denoted as Ce(0.63)(4+)Ce(0.35)(4+)Pd(0.02)O(2-delta-y) (y similar to 0.17). When pure CeO(2) is put under similar electrochemical condition, it never reaches the steady state composition and reduces almost to 85%. Thus, Ce(0.98)Pd(0.02)O(2-delta) forms a stable electrode for the electro-oxidation of H(2)O to O(2) unlike CeO(2) due to the metal support interaction.

Relation between Local Structure and Glass Forming Ability of Liquid Alloys

An attempt has been made to describe the glass forming ability (GFA) of liquid alloys, using the concepts of the short range order (SRO) and middle range order (MRO) characterizing the liquid structure.A new approach to obtain good GFA of liquid alloys is based on the following four main factors: (1) formation of new SRO and competitive correlation with two or more kinds of SROs for crystallization, (2) stabilization of dense random packing by interaction between different types of SRO, (3) formation of stable cluster (SC) or middle range order (MRO) by harmonious coupling of SROs, and (4) difference between SRO characterizing the liquid structure and the near-neighbor environment in the corresponding equilibrium crystalline phases. The atomic volume mismatch estimated from the cube of the atomic radius was found to be a close relation with the minimum solute concentration for glass formation. This empirical guideline enables us to provide the optimum solute concentration for good GFA in some ternary alloys. Model structures, denoted by Bernal type and the Chemical Order type, were again tested in the novel description for the glass structure as a function of solute concentration. We illustrated the related energetics of the completion between crystal embryo and different types of SRO. Recent systematic measurements also provide that thermal diffusivity of alloys in the liquid state may be a good indicator of their GFA.

Effect of radio frequency power and thickness on the electrochemical properties of Li2-x MnO3-y thin films

In the present work, Li2-x MnO3-y (LMO) thin films have been deposited by radio frequency (RF) reactive magnetron sputtering using acid-treated Li2MnO3 powder target. Systematic investigations have been carried out to study the effect of RF power on the physicochemical properties of LMO thin films deposited on platinized silicon substrates. X-ray diffraction, electron microscopy, surface chemical analysis and electrochemical studies were carried out for the LMO films after post deposition annealing treatment at 500 A degrees C for 1 h in air ambience. Galvanostatic charge discharge studies carried out using the LMO thin film electrodes, delivered a highest discharge capacity of 139 mu Ah mu m(-1) cm(-2) in the potential window 2.0-3.5 V vs. Li/Li+ at 100 W RF power and lowest discharge capacity of 80 mu Ah mu m(-1) cm(-2) at 75 W RF power. Thereafter, the physicochemical properties of LMO films deposited using optimized RF power 100 W on stainless steel substrates has been studied in the thickness range of 70 to 300 nm as a case study. From the galvanostatic charge discharge experiments, a stable discharge capacity of 68 mu Ah mu m(-1) cm(-2) was achieved in the potential window 2.0-4.2 V vs. Li/Li+ tested up to 30 cycles. As the thickness increased, the specific discharge capacity started reducing with higher magnitude of capacity fading.

Approximate solution of u'=-A2u using a relation between exp(-tA2) and exp(itA)

Let A be a positive definite operator in a Hilbert space and consider the initial value problem for u(t) = -A(2)u. Using a representation of the semigroup exp(-A(2)t) in terms of the group exp(iAt) we express u in terms of the solution of the standard heat equation w(t) = W-yy, with initial values v solving the initial value problem for v(y) = iAv. This representation is used to construct a method for approximating u in terms of approximations of v. In the case that A is a 2(nd) order elliptic operator the method is combined with finite elements in the spatial variable and then reduces the solution of the 4(th) order equation for u to that of the 2(nd) order equation for v, followed by the solution of the heat equation in one space variable.

Synergy between tribo-oxidation and strain rate response on governing the dry sliding wear behavior of titanium.

The present work provides an insight into the dry sliding wear behavior of titanium based on synergy between tribo-oxidation and strain rate response. Pin-on-disc tribometer was used to characterize the friction and wear behavior of titanium pin in sliding contact with polycrystalline alumina disk under ambient and vacuum condition. The sliding speed was varied from 0.01 to 1.4 ms(-1), normal load was varied from 15.3 to 76 N and with a sliding distance of 1500 m. It was seen that dry sliding wear behavior of titanium was governed by combination of tribo-oxidation and strain rate response in near surface region of titanium. Strain rate response of titanium was recorded by conducting uni-axial compression tests at constant true strain rate of 100 s(-1) in the temperature range from 298 to 873 K. Coefficient of friction and wear rate were reduced with increased sliding speed from 0.01 to 1.0 ms(-1). This is attributed to the formation of in situ self lubricating oxide film (TiO) and reduction in the intensity of adiabatic shear band cracking in the near surface region. This trend was confirmed by performing series of dry sliding tests under vacuum condition of 2 x 10(-4) Torr. Characterization tools such as optical microscopy, scanning electron microscopy, and X-ray diffractometer provided evidence of such processes. These experimental findings can be applied to enhance the dry sliding wear behavior of titanium with proper choice of operating conditions such as sliding speed, normal load, and environment.

Phase relations between Al2O3---Cr2O3 and FeAl2O4---FeCr2O4 solid solutions at 1823 K

Tie-lines between the corundum and spinel solid solutions have been determined experimentally at 1823 K. Next, activities of FeCr2O4 and FeAl2O4 in the spinel solid solution were determined by combining the tie-line data with literature values for the activities of Cr2O3 and Al2O3 in the corundum phase. Activities and the Gibbs energy of mixing for the spinel solid solution were also obtained from a model based on cation distribution between nonequivalent crystallographic sites in the oxide lattice. The difference between the Gibbs energy of mixing obtained experimentally and from the model has been attributed to a strain enthalpy term which is relatively unchanged in magnitude from the reported at 1373 K. The integral enthalpy of mixing obtained from experimental data at 1373 and 1823 K using the second law is compared with the model result.

Is Human-X Chromosome Inactivation A Sex-Determining Device

The evolutionary function of X chromosome inactivation is thought to be dosage compensation. However, there is, at present, little evidence to suggest that most X chromosome-linked genes require such compensation. Another view--that X chromosome inactivation may be related to sex determination--is examined here. Consider a hypothetical DNA sequence regulating a major structural gene concerned with the determination of maleness. If this regulatory sequence occurs in both X and Y chromosomes and if its copy number in the Y chromosome is significantly greater than in the X chromosome, then the male-determining properties of the Y chromosome could be attributed to this higher copy number. On the other hand, if the Y chromosome has the same copy number of this sequence as the X chromosome, it is difficult to see how determination of two sexes would occur under such circumstances because XX and XY genomes would then be indistinguishable in this regard. Such a situation seems to occur in the human species with respect to the banded krait minor satellite, a repetitious DNA sequence associated with sex determination. This apparent difficulty may be resolved if X chromosome inactivation renders regulatory as well as structural genes nonfunctional and thereby brings about a significant reduction in the effective copy number of X chromosome-linked DNA sequences concerned with sex determination. It is suggested that X chromosome inactivation brings about, in this manner, a critical inequality between XX and XY embryos and that sex determination in humans is a consequence of this inequality. An analogous situation appears to exist in certain insects in which inactivation of a haploid set of chromosomes (and presumably, therefore, a 50% reduction in the effective copy number of most genes) is associated with maleness. If this line of reasoning is correct, it would suggest that sex determination may be the primary function of X chromosome inactivation.