Optimization of perturbative similarity renormalization group for Hamiltonians with asymptotic freedom and bound states

A model Hamiltonian that exhibits asymptotic freedom and a bound state, is used to show on example that similarity renormalization group procedure can be tuned to improve convergence of perturbative derivation of effective Hamiltonians, through adjustment of the generator of the similarity transformation. The improvement is measured by comparing the eigenvalues of perturbatively calculated renormalized Hamiltonians that couple only a relatively small number of effective basis states, with the exact bound state energy in the model. The improved perturbative calculus leads to a few-percent accuracy in a systematic expansion.Comment: 6 pages of latex, 4 eps figure

Insights Into the Carboxyltransferase Reaction of Pyruvate Carboxylase From the Structures of Bound Product and Intermediate Analogs

Pyruvate carboxylase (PC) is a biotin-dependent enzyme that catalyzes the MgATP- and bicarbonate-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in central metabolism. The carboxyltransferase (CT) domain of PC catalyzes the transfer of a carboxyl group from carboxybiotin to the accepting substrate, pyruvate. It has been hypothesized that the reactive enolpyruvate intermediate is stabilized through a bidentate interaction with the metal ion in the CT domain active site. Whereas bidentate ligands are commonly observed in enzymes catalyzing reactions proceeding through an enolpyruvate intermediate, no bidentate interaction has yet been observed in the CT domain of PC. Here, we report three X-ray crystal structures of the Rhizobium etli PC CT domain with the bound inhibitors oxalate, 3-hydroxypyruvate, and 3-bromopyruvate. Oxalate, a stereoelectronic mimic of the enolpyruvate intermediate, does not interact directly with the metal ion. Instead, oxalate is buried in a pocket formed by several positively charged amino acid residues and the metal ion. Furthermore, both 3-hydroxypyruvate and 3-bromopyruvate, analogs of the reaction product oxaloacetate, bind in an identical manner to oxalate suggesting that the substrate maintains its orientation in the active site throughout catalysis. Together, these structures indicate that the substrates, products and intermediates in the PC-catalyzed reaction are not oriented in the active site as previously assumed. The absence of a bidentate interaction with the active site metal appears to be a unique mechanistic feature among the small group of biotin-dependent enzymes that act on α-keto acid substrates

A Substrate-induced Biotin Binding Pocket in the Carboxyltransferase Domain of Pyruvate Carboxylase

Biotin-dependent enzymes catalyze carboxyl transfer reactions by efficiently coordinating multiple reactions between spatially distinct active sites. Pyruvate carboxylase (PC), a multifunctional biotin-dependent enzyme, catalyzes the bicarbonate- and MgATP-dependent carboxylation of pyruvate to oxaloacetate, an important anaplerotic reaction in mammalian tissues. To complete the overall reaction, the tethered biotin prosthetic group must first gain access to the biotin carboxylase domain and become carboxylated and then translocate to the carboxyltransferase domain, where the carboxyl group is transferred from biotin to pyruvate. Here, we report structural and kinetic evidence for the formation of a substrate-induced biotin binding pocket in the carboxyltransferase domain of PC from Rhizobium etli. Structures of the carboxyltransferase domain reveal that R. etli PC occupies a symmetrical conformation in the absence of the biotin carboxylase domain and that the carboxyltransferase domain active site is conformationally rearranged upon pyruvate binding. This conformational change is stabilized by the interaction of the conserved residues Asp590 and Tyr628 and results in the formation of the biotin binding pocket. Site-directed mutations at these residues reduce the rate of biotin-dependent reactions but have no effect on the rate of biotin-independent oxaloacetate decarboxylation. Given the conservation with carboxyltransferase domains in oxaloacetate decarboxylase and transcarboxylase, the structure-based mechanism described for PC may be applicable to the larger family of biotin-dependent enzymes

Complete phase diagram for the integrable chain with alternating spins in the sectors with competing interactions

We investigate the anisotropic integrable spin chain consisting of spins $s={1/2}$ and $s=1$ by means of thermodynamic Bethe ansatz for the anisotropy $\gamma>\pi/3$, where the analysis of the Takahashi conditions leads to a more complicated string picture. We give the phase diagram with respect to the two real coupling constants $\bar{c}$ and $\tilde{c}$, which contains a new region where the ground state is formed by strings with infinite Fermi zones. In this region the velocities of sound for the two physical excitations have been calculated from the dressed energies. This leads to an additional line of conformal invariance not known before.Comment: 13 pages, LaTeX, uses ioplppt.sty and epsfig.sty, figure 3 correcte

Study of atmospheric and AAP objectives of cross beam experiments Final report, 23 Jan. 1967 - 9 Jan. 1968

Light beam triangulation technique for atmospheric measurement

The role of wind gusts in upper ocean diurnal variability

Upper ocean processes play a key role in air-sea coupling, with variability on both short and long time scales. The diurnal cycle associated with diurnal solar insolation and nighttime cooling, may act, along with stochastic wind variability, on upper ocean temperatures and stratification resulting in a diurnal warm layer and a nonlinear rectified effect on longer time scales. This study describes diurnal changes in upper ocean temperature for a location in the equatorial Indian Ocean, using observations from the Dynamics of the Madden-Julian Oscillation field campaign, a high vertical resolution 1-D process model, and a diurnal cycling scheme. Solar forcing is the main driver of diurnal variability in upper ocean temperature and stratification. Yet except during nighttime convection, winds with variability on the order of hours (here referred to as “wind gusts”) regulate how fast surface water is mixed to greater depths when daily mean winds are weak. Wind gusts are much stronger than diurnal winds. Even using stochastic wind gusts but no diurnal winds as input in a 1-D process model yields an estimate of diurnal temperature that compares well with observations. A new version of the Large and Caron (2015) scheme (LC2015) provides an estimate of upper ocean diurnal temperature that is consistent with observations. LC2015 has the advantage of being suitable for implementation in a climate model, with the goal to improve SST estimates, hence the simulated heat flux at the air-sea interface. Yet LC2015 is not very sensitive to the inclusion or omission of the high-frequency component of the wind