Amino acid in Deep Sea Drilling Project cores

Several amino acid diagenetic reactions, which take place in the deep-sea sedimentary environment, were investigated, using various Deep Sea Drilling Project (DSDP) cores. Initially it was found that essentially all the amino acids in sediments are bound in peptide linkages; but, with increasing age, the peptide bonds undergo slow hydrolysis that results in an increasingly larger fraction of amino acids in the free state. The hydrolysis half-life in calcareous sediments was estimated to be ~1-2 million years, while in non-carbonate sediment the hydrolysis rate may be considerably slower. The amino acid compositions and the extent of racemization of several amino acids were determined in various fractions isolated from the sediments. These analyses demonstrated that the mechanism, kinetics, and rate of amino acid diagenesis are highly dependent upon the physical state (i.e., free, bound, etc.) in which the amino acids exist in the sedimentary environment. In the free state, serine and threonine were found to decompose primarily by a dehydration reaction, while in the bound state (residue or HCl-insoluble fraction) a reversible aldol-cleavage reaction is the main decomposition pathway of these amino acids. The change in amino acid composition of the residue fraction with time was suggested to be due to the hydrolysis of peptide bonds, while in foraminiferal tests the compositional changes over geological time are the result of various decomposition reactions. Reversible first-order racemization kinetics are not observed for free amino acids in sediments. The explanation for these anomalous kinetics involves a complex reaction series which includes the hydrolysis of peptide bonds and the very rapid racemization of free amino acids. The racemization rates of free amino acids in sediments were found to be many orders of magnitude faster than those predicted from elevated temperature experiments using free amino acids in aqueous solution. The racemization rate enhancement of free amino acids in sediments may be due to the catalysis of the reaction by trace metals. Reversible first-order kinetics are followed for amino acids in the residue fraction isolated from sediments; the rate of racemization in this fraction is slower than that predicted for protein-bound amino acids. Various applications of amino acid diagenetic reactions are discussed. Racemization and the decomposition reaction of serine and threonine can both be used, with certain limitations, to make rough age estimates of deep-sea sediments back to several million years. The extent of racemization in foraminiferal tests which have been dated by some other independent technique can be used to estimate geothermal gradients, and thus heat flows, and to evaluate the bottom water temperature history in certain oceanic areas.

Breakup of a multisoliton state of the linearly damped nonlinear Schrödinger equation

We address the breakup (splitting) of multisoliton solutions of the nonlinear Schrödinger equation (NLSE), occurring due to linear loss. Two different approaches are used for the study of the splitting process. The first one is based on the direct numerical solution of the linearly damped NLSE and the subsequent analysis of the eigenvalue drift for the associated Zakharov-Shabat spectral problem. The second one involves the multisoliton adiabatic perturbation theory applied for studying the evolution of the solution parameters, with the linear loss taken as a small perturbation. We demonstrate that in the case of strong nonadiabatic loss the evolution of the Zakharov-Shabat eigenvalues can be quite nontrivial. We also demonstrate that the multisoliton breakup can be correctly described within the framework of the adiabatic perturbation theory and can take place even due to small linear loss. Eventually we elucidate the occurrence of the splitting and its dependence on the phase mismatch between the solitons forming a two-soliton bound state. © 2007 The American Physical Society.

Accelerated computation of cyclic steady state for simulated-moving-bed processes

Industrial applications of the simulated-moving-bed (SMB) chromatographic technology have brought an emergent demand to improve the SMB process operation for higher efficiency and better robustness. Improved process modelling and more-efficient model computation will pave a path to meet this demand. However, the SMB unit operation exhibits complex dynamics, leading to challenges in SMB process modelling and model computation. One of the significant problems is how to quickly obtain the steady state of an SMB process model, as process metrics at the steady state are critical for process design and real-time control. The conventional computation method, which solves the process model cycle by cycle and takes the solution only when a cyclic steady state is reached after a certain number of switching, is computationally expensive. Adopting the concept of quasi-envelope (QE), this work treats the SMB operation as a pseudo-oscillatory process because of its large number of continuous switching. Then, an innovative QE computation scheme is developed to quickly obtain the steady state solution of an SMB model for any arbitrary initial condition. The QE computation scheme allows larger steps to be taken for predicting the slow change of the starting state within each switching. Incorporating with the wavelet-based technique, this scheme is demonstrated to be effective and efficient for an SMB sugar separation process. Moreover, investigations are also carried out on when the computation scheme should be activated and how the convergence of the scheme is affected by a variable stepsize.

Spin and relativistic motion of bound states

The wave functions of moving bound states may be expected to contract in the direction of motion, in analogy to a rigid rod in classical special relativity, when the constituents are at equal (ordinary) time. Indeed, the Lorentz contraction of wave functions is often appealed to in qualitative discussions. However, only few field theory studies exist of equal-time wave functions in motion. In this thesis I use the Bethe-Salpeter formalism to study the wave function of a weakly bound state such as a hydrogen atom or positronium in a general frame. The wave function of the e^-e^+ component of positronium indeed turns out to Lorentz contract both in 1+1 and in 3+1 dimensional quantum electrodynamics, whereas the next-to-leading e^-e^+\gamma Fock component of the 3+1 dimensional theory deviates from classical contraction. The second topic of this thesis concerns single spin asymmetries measured in scattering on polarized bound states. Such spin asymmetries have so far mainly been analyzed using the twist expansion of perturbative QCD. I note that QCD vacuum effects may give rise to a helicity flip in the soft rescattering of the struck quark, and that this would cause a nonvanishing spin asymmetry in \ell p^\uparrow -> \ell' + \pi + X in the Bjorken limit. An analogous asymmetry may arise in p p^\uparrow -> \pi + X from Pomeron-Odderon interference, if the Odderon has a helicity-flip coupling. Finally, I study the possibility that the large single spin asymmetry observed in p p^\uparrow -> \pi(x_F,k_\perp) + X when the pion carries a high momentum fraction x_F of the polarized proton momentum arises from coherent effects involving the entire polarized bound state.

Bound states of two spin-1/2 fermions in a synthetic non-Abelian gauge field

We study the bound states of two spin-1/2 fermions interacting via a contact attraction (characterized by a scattering length) in the singlet channel in three-dimensional space in presence of a uniform non-Abelian gauge field. The configuration of the gauge field that generates a Rashba-type spin-orbit interaction is described by three coupling parameters (lambda(x),lambda(y),lambda(z)). For a generic gauge field configuration, the critical scattering length required for the formation of a bound state is negative, i.e., shifts to the ``BCS side'' of the resonance. Interestingly, we find that there are special high-symmetry configurations (e.g., lambda(x) = lambda(y) = lambda(z)) for which there is a two-body bound state for any scattering length however small and negative. Remarkably, the bound-state wave functions obtained for such configurations have nematic spin structure similar to those found in liquid He-3. Our results show that the BCS-BEC (Bose-Einstein condensation) crossover is drastically affected by the presence of a non-Abelian gauge field. We discuss possible experimental signatures of our findings both at high and low temperatures.

Calcium/Calmodulin Dependent Protein Kinase II Bound to NMDA Receptor 2B Subunit Exhibits Increased ATP Affinity and Attenuated Dephosphorylation

Calcium/calmodulin dependent protein kinase II (CaMKII) is implicated to play a key role in learning and memory. NR2B subunit of N-methyl-D-aspartate receptor (NMDAR) is a high affinity binding partner of CaMKII at the postsynaptic membrane. NR2B binds to the T-site of CaMKII and modulates its catalysis. By direct measurement using isothermal titration calorimetry (ITC), we show that NR2B binding causes about 11 fold increase in the affinity of CaMKII for ATP gamma S, an analogue of ATP. ITC data is also consistent with an ordered binding mechanism for CaMKII with ATP binding the catalytic site first followed by peptide substrate. We also show that dephosphorylation of phospho-Thr(286)-alpha-CaMKII is attenuated when NR2B is bound to CaMKII. This favors the persistence of Thr(286) autophosphorylated state of CaMKII in a CaMKII/phosphatase conjugate system in vitro. Overall our data indicate that the NR2B- bound state of CaMKII attains unique biochemical properties which could help in the efficient functioning of the proposed molecular switch supporting synaptic memory.

Role of the loop L-4,L-5 in allosteric regulation in mtHsp70s: in vivo significance of domain communication and its implications in protein translocation

Mitochondrial Hsp70 (mtHsp70) is essential for a vast repertoire of functions, including protein import, and requires effective interdomain communication for efficient partner-protein interactions. However, the in vivo functional significance of allosteric regulation in eukaryotes is poorly defined. Using integrated biochemical and yeast genetic approaches, we provide compelling evidence that a conserved substrate-binding domain (SBD) loop, L-4,L-5, plays a critical role in allosteric communication governing mtHsp70 chaperone functions across species. In yeast, a temperature-sensitive L-4,L-5 mutation (E467A) disrupts bidirectional domain communication, leading to compromised protein import and mitochondrial function. Loop L-4,L-5 functions synergistically with the linker in modulating the allosteric interface and conformational transitions between SBD and the nucleotide-binding domain (NBD), thus regulating interdomain communication. Second-site intragenic suppressors of E467A isolated within the SBD suppress domain communication defects by conformationally altering the allosteric interface, thereby restoring import and growth phenotypes. Strikingly, the suppressor mutations highlight that restoration of communication from NBD to SBD alone is the minimum essential requirement for effective in vivo function when primed at higher basal ATPase activity, mimicking the J-protein-bound state. Together these findings provide the first mechanistic insights into critical regions within the SBD of mtHsp70s regulating interdomain communication, thus highlighting its importance in protein translocation and mitochondrial biogenesis.

I. Non-linear effects in a self-consistent calculation of SU_3 symmetry breaking in strong interaction coupling constants. II. Direct-channel reggeization of strong interaction scattering amplitudes

The thesis is divided into two parts. Part I generalizes a self-consistent calculation of residue shifts from SU₃ symmetry, originally performed by Dashen, Dothan, Frautschi, and Sharp, to include the effects of non-linear terms. Residue factorizability is used to transform an overdetermined set of equations into a variational problem, which is designed to take advantage of the redundancy of the mathematical system. The solution of this problem automatically satisfies the requirement of factorizability and comes close to satisfying all the original equations.

Part II investigates some consequences of direct channel Regge poles and treats the problem of relating Reggeized partial wave expansions made in different reaction channels. An analytic method is introduced which can be used to determine the crossed-channel discontinuity for a large class of direct-channel Regge representations, and this method is applied to some specific representations.

It is demonstrated that the multi-sheeted analytic structure of the Regge trajectory function can be used to resolve apparent difficulties arising from infinitely rising Regge trajectories. Also discussed are the implications of large collections of "daughter trajectories."

Two things are of particular interest: first, the threshold behavior in direct and crossed channels; second, the potentialities of Reggeized representations for us in self-consistent calculations. A new representation is introduced which surpasses previous formulations in these two areas, automatically satisfying direct-channel threshold constraints while being capable of reproducing a reasonable crossed channel discontinuity. A scalar model is investigated for low energies, and a relation is obtained between the mass of the lowest bound state and the slope of the Regge trajectory.

Pressure behavior of the alloy band edge and nitrogen-related centers in GaAs0.999N0.001

The photoluminescence of a GaAsN alloy with 0.1% nitrogen has been studied under pressures up to 8.5 GPa at 33, 70, and 130 K. At ambient pressure, emissions from both the GaAsN alloy conduction band edge and discrete nitrogen-related bound states are observed. Under applied pressure, these two types of emissions shift with rather different pressure coefficients: about 40 meV/GPa for the nitrogen-related features, and about 80 meV/GPa for the alloy band-edge emission. Beyond 1 GPa, these discrete nitrogen-related peaks broaden and evolve into a broad band. Three new photoluminescence bands emerge on the high-energy side of the broad band, when the pressure is above 2.5, 4.5, and 5.25 GPa, respectively, at 33 K. In view of their relative energy positions and pressure behavior, we have attributed these new emissions to the nitrogen-pair states NN3 and NN4, and the isolated nitrogen state N-x. In addition, we have attributed the high-energy component of the broad band formed above 1 GPa to resonant or near-resonant NN1 and NN2, and its main body to deeper cluster centers involving more than two nitrogen atoms. This study reveals the persistence of all the paired and isolated nitrogen-related impurity states, previously observed only in the dilute doping limit, into a rather high doping level. Additionally, we find that the responses of different N-related states to varying N-doping levels differ significantly and in a nontrivial manner.

Solitary magnon excitations in a one-dimensional antiferromagnet with Dzyaloshinsky-Moriya interactions

We investigate solitary excitations in a model of a one-dimensional antiferromagnet including a single-ion anisotropy and a Dzyaloshinsky-Moriya antisymmetric exchange interaction term. We employ the Holstein-Primakoff transformation, the coherent state ansatz and the time variational principle. We obtain two partial differential equations of motion by using the method of multiple scales and applying perturbation theory. By so doing, we show that the motion of the coherent amplitude must satisfy the nonlinear Schrodinger equation. We give the single-soliton solution.

Fundamentals of steady state, non-Newtonian rimming flow

Rimming flow on the inner surface of a horizontal rotating cylinder is investigated. Using a scale analysis, a theoretical description is obtained for steady-state non-Newtonian flow. Simple lubrication theory is applied since the Reynolds number is small and the liquid film is thin. Since the Deborah number is very small the flow is viscometric. The shear-thinning number, which characterizes the shear-thinning effect, may be small or large. A general constitutive law for this kind of flow requires only a single function relating shear stress and shear rate that corresponds to a generalized Newtonian liquid. For this case the run-off condition for rimming flow is derived. Provided the run-off condition is satisfied, the existence of a continuous steady-state solution is proved. The rheological models, which show Newtonian behavior at low shear rates with transition to power-law shear thinning at moderate shear rates, are considered. Numerical results are carried out for the Carreau and Ellis models, which exhibit Newtonian behavior near the free surface and power-law behavior near the wall of the rotating cylinder.

Structure and kinetics of phosphonopyruvate hydrolase from Variovorax sp. Pal2: New insight into the divergence of catalysis within the PEP mutase/isocitrate lyase superfamily .

Phosphonopyruvate (P-pyr) hydrolase (PPH), a member of the phosphoenolpyruvate (PEP) mutase/isocitrate lyase (PEPM/ICL) superfamily, hydrolyzes P-pyr and shares the highest sequence identity and functional similarity with PEPM. Recombinant PPH from Variovorax sp. Pal2 was expressed in Escherichia coli and purified to homogeneity. Analytical gel filtration indicated that the protein exists in solution predominantly as a tetramer. The PPH pH rate profile indicates maximal activity over a broad pH range.The steady-state kinetic constants determined for a rapid equilibrium ordered kinetic mechanism with Mg+2 binding first (Kd =140 ± 40 M), are kcat = 105 ± 2 s-1 and P-pyr Km = 5 ± 1 M. PEP (slow substrate kcat = 2 × 10-4 s-1), oxalate, and sulfopyruvate are competitive inhibitors with Ki values of 2.0 ± 0.1 mM, 17 ± 1 M, and 210 ± 10 M, respectively. Three PPH crystal structures have been determined, that of a ligand-free enzyme, the enzyme bound to Mg2+ and oxalate (inhibitor), and the enzyme bound to Mg2+ and P-pyr (substrate). The complex with the inhibitor was obtained by cocrystallization, whereas that with the substrate was obtained by briefly soaking crystals of the ligand-free enzyme with P-pyr prior to flash cooling. The PPH structure resembles that of the other members of the PEPM/ICL superfamily and is most similar to the functionally related enzyme, PEPM. Each monomer of the dimer of dimers exhibits an (/)8 barrel fold with the eighth helix swapped between two molecules of the dimer. Both P-pyr and oxalate are anchored to the active site by Mg2+. The loop capping the active site is disordered in all three structures, in contrast to PEPM, where the equivalent loop adopts an open or disordered conformation in the unbound state but sequesters the inhibitor from solvent in the bound state. Crystal packing may have favored the open conformation of PPH even when the enzyme was cocrystallized with the oxalate inhibitor. Structure alignment of PPH with other superfamily members revealed two pairs of invariant or conservatively replaced residues that anchor the flexible gating loop. The proposed PPH catalytic mechanism is analogous to that of PEPM but includes activation of a water nucleophile with the loop Thr118 residue.

R-matrix-Floquet theory of multiphoton processes:VIII. A linear equations method

A new linear equations method for calculating the R-matrix, which arises in the R-matrix-Floquet theory of multiphoton processes, is introduced. This method replaces the diagonalization of the Floquet Hamiltonian matrix by the solution of a set of linear simultaneous equations which are solved, in the present work, by the conjugate gradient method. This approach uses considerably less computer memory and can be readily ported onto parallel computers. It will thus enable much larger problems of current interest to be treated. This new method is tested by applying it to three-photon ionization of helium at frequencies where double resonances with a bound state and autoionizing states are important. Finally, an alternative linear equations method, which avoids the explicit calculation of the R-matrix by incorporating the boundary conditions directly, is described in an appendix.

Schrodinger-Poisson equations without Ambrosetti-Rabinowitz condition

We prove the existence of ground state solutions for a stationary Schrodinger-Poisson equation in R(3). The proof is based on the mountain pass theorem and it does not require the Ambrosetti-Rabinowitz condition. (C) 2010 Elsevier Inc. All rights reserved.

Bound states by a pseudoscalar Coulomb potential in one-plus-one dimensions

The Dirac equation is solved for a pseudoscalar Coulomb potential in a two-dimensional world. An infinite sequence of bounded solutions are obtained. These results are in sharp contrast with those ones obtained in 3 + 1 dimensions where no bound-state solutions are found. Next the general two-dimensional problem for pseudoscalar power-law potentials is addressed consenting us to conclude that a nonsingular potential leads to bounded solutions. The behaviour of the upper and lower components of the Dirac spinor for a confining linear potential nonconserving- as well as conserving-parity, even if the potential is unbounded from below, is discussed in some detail. (C) 2003 Elsevier B.V. All rights reserved.