Prediction of protein B-factor profiles

The polypeptide backbones and side chains of proteins are constantly moving due to thermal motion and the kinetic energy of the atoms. The B-factors of protein crystal structures reflect the fluctuation of atoms about their average positions and provide important information about protein dynamics. Computational approaches to predict thermal motion are useful for analyzing the dynamic properties of proteins with unknown structures. In this article, we utilize a novel support vector regression (SVR) approach to predict the B-factor distribution (B-factor profile) of a protein from its sequence. We explore schemes for encoding sequences and various settings for the parameters used in SVR. Based on a large dataset of high-resolution proteins, our method predicts the B-factor distribution with a Pearson correlation coefficient (CC) of 0.53. In addition, our method predicts the B-factor profile with a CC of at least 0.56 for more than half of the proteins. Our method also performs well for classifying residues (rigid vs. flexible). For almost all predicted B-factor thresholds, prediction accuracies (percent of correctly predicted residues) are greater than 70%. These results exceed the best results of other sequence-based prediction methods. (C) 2005 Wiley-Liss, Inc.

Structural Dynamics in (ND4)2[Cu(D2O)6](SO4)2

The extended X-ray absorption fine structure spectroscopy (EXAFS) of (ND4)(2)[CU(D2O)(6)](SO4)(2) at 5, 14,100, 200, and 298 K is reported. This indicates that the Cu-O bond lengths of the Cu(D2O)(6)(2+) ion do not change significantly within this temperature range, which contrasts with EPR results and X-ray and neutron diffraction experiments, which imply that two of the Cu-(D2O) bonds converge in length as the temperature is raised. The EXAFS measurements thus confirm that the bond distances yielded by the diffraction experiments refer to the average positions of ligands involved in a dynamic equilibrium in which the directions of the long and intermediate bonds of the Jahn-Teller distorted Cu(D2O)(6)(2+) ion are interchanged in the crystal lattice. Analysis of the displacement parameters is consistent with this interpretation, as are the wave functions calculated using a model involving Jahn-Teller vibronic coupling and the influence of lattice strain interactions.

Decoherence and fidelity in ion traps with fluctuating trap parameters

We consider two different kinds of fluctuations in an ion trap potential: external fluctuating electrical fields, which cause statistical movement (wobbling) of the ion relative to the center of the trap, and fluctuations of the spring constant, which an due to fluctuations of the ac component of the potential applied in the Paul trap for ions. We write down master equations for both cases and, averaging out the noise, obtain expressions for the heating of the ion. We compare our results to previous results for far-off resonance optical traps and heating in ion traps. The effect of fluctuating external electrical fields for a quantum gate operation (controlled-NOT) is determined and the fidelity for that operation derived. [S1050-2947(99)06005-9].

Atomic Latin squares of order eleven

A Latin square is pan-Hamiltonian if the permutation which defines row i relative to row j consists of a single cycle for every i j. A Latin square is atomic if all of its conjugates are pan-Hamiltonian. We give a complete enumeration of atomic squares for order 11, the smallest order for which there are examples distinct from the cyclic group. We find that there are seven main classes, including the three that were previously known. A perfect 1-factorization of a graph is a decomposition of that graph into matchings such that the union of any two matchings is a Hamiltonian cycle. Each pan-Hamiltonian Latin square of order n describes a perfect 1-factorization of Kn,n, and vice versa. Perfect 1-factorizations of Kn,n can be constructed from a perfect 1-factorization of Kn+1. Six of the seven main classes of atomic squares of order 11 can be obtained in this way. For each atomic square of order 11, we find the largest set of Mutually Orthogonal Latin Squares (MOLS) involving that square. We discuss algorithms for counting orthogonal mates, and discover the number of orthogonal mates possessed by the cyclic squares of orders up to 11 and by Parker's famous turn-square. We find that the number of atomic orthogonal mates possessed by a Latin square is not a main class invariant. We also define a new sort of Latin square, called a pairing square, which is mapped to its transpose by an involution acting on the symbols. We show that pairing squares are often orthogonal mates for symmetric Latin squares. Finally, we discover connections between our atomic squares and Franklin's diagonally cyclic self-orthogonal squares, and we correct a theorem of Longyear which uses tactical representations to identify self-orthogonal Latin squares in the same main class as a given Latin square.

Superchemistry: dynamics of coupled atomic and molecular Bose condensates

We analyze the dynamics of a dilute, trapped Bose-condensed atomic gas coupled to a diatomic molecular Bose gas by coherent Raman transitions. This system is shown to result in a new type of “superchemistry,” in which giant collective oscillations between the atomic and the molecular gas can occur. The phenomenon is caused by stimulated emission of bosonic atoms or molecules into their condensate phases.

Experimental study of the quantum driven pendulum and its classical analog in atom optics

We present experimental results for the dynamics of cold atoms in a far detuned amplitude-modulated optical standing wave. Phase-space resonances constitute distinct peaks in the atomic momentum distribution containing up to 65% of all atoms resulting from a mixed quantum chaotic phase space. We characterize the atomic behavior in classical and quantum regimes and we present the applicable quantum and classical theory, which we have developed and refined. We show experimental proof that the size and the position of the resonances in phase space can be controlled by varying several parameters, such as the modulation frequency, the scaled well depth, the modulation amplitude, and the scaled Planck’s constant of the system. We have found a surprising stability against amplitude noise. We present methods to accurately control the momentum of an ensemble of atoms using these phase-space resonances which could be used for efficient phase-space state preparation.

Quantum dynamics of three coupled atomic Bose-Einstein condensates

The simplest model of three coupled Bose-Einstein condensates is investigated using a group theoretical method. The stationary solutions are determined using the SU(3) group under the mean-field approximation. This semiclassical analysis, using system symmetries, shows a transition in the dynamics of the system from self trapping to delocalization at a critical value for the coupling between the condensates. The global dynamics are investigated by examination of the stable points, and our analysis shows that the structure of the stable points depends on the ratio of the condensate coupling to the particle-particle interaction, and undergoes bifurcations as this ratio is varied. This semiclassical model is compared to a full quantum treatment, which also displays a dynamical transition. The quantum case has collapse and revival sequences superimposed on the semiclassical dynamics, reflecting the underlying discreteness of the spectrum. Nonzero circular current states are also demonstrated as one of the higher-dimensional effects displayed in this system.

Stimulated Raman adiabatic passage from an atomic to a molecular Bose-Einstein condensate

The process of stimulated Raman adiabatic passage (STIRAP) provides a possible route for the generation of a coherent molecular Bose-Einstein condensate (BEC) from an atomic BEC. We analyze this process in a three-dimensional mean-field theory, including atom-atom interactions and nonresonant intermediate levels. We find that the process is feasible, but at larger Rabi frequencies than anticipated from a crude single-mode lossless analysis, due to two-photon dephasing caused by the atomic interactions. We then identify optimal strategies in STIRAP allowing one to maintain high conversion efficiencies with smaller Rabi frequencies and under experimentally less demanding conditions.

The relationship between plasma lactate parameters, W-peak and 1-h cycling performance in women

Purpose: The relationship between six descriptors of lactate increase, peak (V) over dot O-2,W-peak, and 1-h cycling performance were compared in 24 trained, female cyclists (peak (V) over dot O-2 = 48.11 +/- 6.32 mL . kg(-1) . min(-1)). Methods: The six descriptors of lactate increase were: 1) lactate threshold (LT; the power output at which plasma lactate concentration begins to increase above the resting level during an incremental exercise test), 2) LT1 (the power output at which plasma lactate increases by 1 mM or more), 3) LTD (the lactate threshold calculated by the D-max method), 4) LTMOD (the lactate threshold calculated by a modified D-max method), 5) L4 (the power output at which plasma lactate reaches a concentration of 4 mmol-L-1), and 6) LTLOG (the power output at which plasma lactate concentration begins to increase when the log([La-]) is plotted against the log (power output)). Subjects first completed a peak (V) over dot O-2 test on a cycle ergometer. Finger-tip capillary blood was sampled within 30 s of the end of each 3-min stage for analysis of plasma lactate. Endurance performance was assessed 7 d later using a 1-h cycle test (OHT) in which subjects were directed to achieve the highest possible average power output. Results: The mean power output (W) for the OHT (+/- SD) was 183.01 +/- 18.88, and for each lactate variable was: LT (138.54 +/- 46.61), LT1 (179.17 +/- 27.25), LTLOG (143.97 +/- 45.74), L4 (198.09 +/- 33.84), LTD (178.79 +/- 24.07), LTMOD (212.28 +/- 31.75). Average power output during the OHT was more strongly correlated with all plasma lactate parameters (0.61 < r < 0.84) and W-peak (r = 0.81) than with peak (V) over dot O-2 (r = 0.55). The six lactate parameters were strongly correlated with each other (0.54 < r < 0.91) and of the six lactate parameters, LTD correlated best with endurance performance (r = 0.84). Conclusions: It was concluded that plasma lactate parameters and W-peak provide better indices of endurance performance than peak (V) over dot O-2 and that, of the six descriptors of lactate increase measured in this study, LTD is most strongly related to 1-h cycling performance in trained, female cyclists.

On uniquely determining cell-wall material properties with the compression experiment

A finite element model (FEM) of the cell-compression experiment has been developed in dimensionless form to extract the fundamental cell-wall-material properties (i.e. the constitutive equation and its parameters) from experiment force-displacement data. The FEM simulates the compression of a thin-walled, liquid-filled sphere between two flat surfaces. The cell-wall was taken to be permeable and the FEM therefore accounts for volume loss during compression. Previous models assume an impermeable wall and hence a conserved cell volume during compression. A parametric study was conducted for structural parameters representative of yeast. It was shown that the common approach of assuming reasonable values for unmeasured parameters (e.g. cell-wall thickness, initial radial stretch) can give rise to nonunique solutions for both the form and constants in the cell-wall constitutive relationship. Similarly, measurement errors can also lead to an incorrectly defined cell-wall constitutive relationship. Unique determination of the fundamental wall properties by cell compression requires accurate and precise measurement of a minimum set of parameters (initial cell radius, initial cell-wall thickness, and the volume loss during compression). In the absence of such measurements the derived constitutive relationship may be in considerable error, and should be evaluated against its ability to predict the outcome of other mechanical experiments. (C) 1998 Elsevier Science Ltd. All rights reserved.

CXTANNEAL: an improved program for estimating solute transport parameters

CXTANNEAL is a program for analysing contaminant transport in soils. The code, written in Fortran 77, is a modified version of CXTFIT, a commonly used package for estimating solute transport parameters in soils. The improvement of the present code is that it includes simulated annealing as the optimization technique for curve fitting. Tests with hypothetical data show that CXTANNEAL performs better than the original code in searching for optimal parameter estimates. To reduce the computational time, a parallel version of CXTANNEAL (CXTANNEAL_P) was also developed. (C) 1999 Elsevier Science Ltd. All rights reserved.

Modeling of hepatic elimination and organ distribution kinetics with the extended convection-dispersion model

The conventional convection-dispersion (also called axial dispersion) model is widely used to interrelate hepatic availability (F) and clearance (Cl) with the morphology and physiology of the liver and to predict effects such as changes in liver blood flow on F and Cl. An extended form of the convection-dispersion model has been developed to adequately describe the outflow concentration-time profiles for vascular markers at both short and long times after bolus injections into perfused livers. The model, based on flux concentration and a convolution of catheters and large vessels, assumes that solute elimination in hepatocytes follows either fast distribution into or radial diffusion in hepatocytes. The model includes a secondary vascular compartment, postulated to be interconnecting sinusoids. Analysis of the mean hepatic transit time (MTT) and normalized variance (CV2) of solutes with extraction showed that the discrepancy between the predictions of MTT and CV2 for the extended and conventional models are essentially identical irrespective of the magnitude of rate constants representing permeability, volume, and clearance parameters, providing that there is significant hepatic extraction. In conclusion, the application of a newly developed extended convection-dispersion model has shown that the unweighted conventional convection-dispersion model can be used to describe the disposition of extracted solutes and, in particular, to estimate hepatic availability and clearance in booth experimental and clinical situations.

Measuring the interaction forces between protein inclusion bodies and an air bubble using an atomic force microscope

Interaction forces between protein inclusion bodies and an air bubble have been quantified using an atomic force microscope (AFM). The inclusion bodies were attached to the AFM tip by covalent bonds. Interaction forces measured in various buffer concentrations varied from 9.7 nN to 25.3 nN (+/- 4-11%) depending on pH. Hydrophobic forces provide a stronger contribution to overall interaction force than electrostatic double layer forces. It also appears that the ionic strength affects the interaction force in a complex way that cannot be directly predicted by DLVO theory. The effects of pH are significantly stronger for the inclusion body compared to the air bubble. This study provides fundamental information that will subsequently facilitate the rational design of flotation recovery system for inclusion bodies. It has also demonstrated the potential of AFM to facilitate the design of such processes from a practical viewpoint.