Analyses of Stemona alkaloids in Stemona tuberosa by liquid chromatography/tandem mass spectrometry

Alkaloid profiles in Stemona tuberosa were found to be highly variable. Six Stemona alkaloids isolated from the plant were subjected to on-line high-performance liquid chromatography/electrospray ionization mass spectrometry (HPLC/ESI-MS) and tandem mass spectrometry (MS/MS) analyses. Their fragmentation patterns and products were useful for their characterization. The LC/MS fingerprints of these alkaloids, though variable among samples, could provide an overall characterization of the authenticity and quality of this species and help to differentiate it from S. japonica and S. sessilifolia, as all three species are recognized as genuine sources of the herb Radix Stemonae in the Pharmacopoeia of the People's Republic of China.     

The midpoint method for parallelization of particle simulations

The evaluation of interactions between nearby particles constitutes the majority of the computational workload involved in classical molecular dynamics (MD) simulations. In this paper, we introduce a new method for the parallelization of range-limited particle interactions that proves particularly suitable to MD applications. Because it applies not only to pairwise interactions but also to interactions involving three or more particles, the method can be used for evaluation of both nonbonded and bonded forces in a MD simulation. It requires less interprocessor data transfer than traditional spatial decomposition methods at all but the lowest levels of parallelism. It gains an additional practical advantage in certain commonly used interprocessor communication networks by distributing the communication burden more evenly across network links and by decreasing the associated latency. When used to parallelize MD, it further reduces communication requirements by allowing the computations associated with short-range nonbonded interactions, long-range electrostatics, bonded interactions, and particle migration to use much of the same communicated data. We also introduce certain variants of this method that can significantly improve the balance of computational load across processors.     

The influence of ionic strength on the interaction of viruses with charged surfaces under environmental conditions

The influence of ionic strength on the electrostatic interaction of viruses with environmentally relevant surfaces was determined for three viruses, MS2, Q beta, and Norwalk. The virus is modeled as a particle comprised of ionizable amino acid residues in a shell surrounding a spherical RNA core of negative charge, these charges being compensated for by a Coulomb screening due to intercalated ions. A second model of the virus involving surface charges only is included for comparison. Surface potential calculations for each of the viruses show excellent agreement with electrophoretic mobility and zeta potential measurements as a function of pH. The environmental surface is modeled as a homogeneous plane held at constant potential with and without a finite region (patch) of opposite potential. The results indicate that the electrostatic interaction between the virus and the oppositely charged patch is significantly influenced by the conditions of ionic strength, pH and size of the patch. Specifically, at pH 7, the Norwalk virus interacts more strongly with the patch than MS2 (approximately 51 vs approximately 9kT) but at pH 5, the Norwalk-surface interaction is negligible while that of MS2 is approximately 5.9kT. The resulting ramifications for the use of MS2 as a surrogate for Norwalk are discussed.     

Ultrafast photoinduced deligation and ligation dynamics: DCM in micelle and micelle-enzyme complex

We report studies on diffusion controlled deligation and ligation dynamics of a probe ligand 4-(dicyanomethylene)-2-methyl-6-(p-dimethylamino-styryl) 4H-pyran (DCM) with cationic cetyltrimethylammonium bromide (CTAB) micelles. In order to investigate the effect of spatial heterogeneity on the dynamics we study the DCM labeled micelle upon complexation with an enzyme alpha-chymotrypsin (CHT). The variation of fluorescence line-width (Gamma(t)) of DCM in the complex and also in the micelle indicates the diffusion dynamics of DCM through various environments of different polarities. The temporal behavior of Gamma(t) reveals that at 50 mM CTAB concentration the excited DCM traverses 6.5 Angstrom distance from the surface of a host micelle (deligation) before entering to a stern layer of another adjacent micelle (ligation). From neutron scattering experiment the distance 6.5 Angstrom is found to be the thickness of a stern layer of CTAB micelle. No indication of ligation has been found at 2 mM CTAB concentration as the intermicellar distance is estimated to be very large (416 Angstrom) compared to the previous case. The dynamical behavior of Gamma(t) is also indicative of significantly slower diffusion of the ligand molecules (DCM) at the surface of the micelle in presence and absence of the enzyme compared to that in the bulk buffer. We have also studied the dynamics of solvation and local geometrical restriction on the probe DCM at the micellar surface with and without CHT. With picosecond time resolution, we found time constants of the solvation relaxation processes of the DCM labeled enzyme-micelle complex to be 230 ps (45%) and 870 ps (55%), which were comparable to those of the micelle without the enzyme. The time dependent anisotropy revealing local orientational motions of the probe in the complex was also found to be similar to that of DCM at the micellar surface in absence of CHT. These studies attempt to link the dynamical features for insight into the ligand mediated intercellular communication and the biological function of the enzyme alpha-chymotrypsin upon complexation with the CTAB micelle.     

Superelastic shape memory alloy cables: Part II – Subcomponent isothermal responses

This paper constitutes the second part of our experimental study of the thermo-mechanical behavior of superelastic NiTi shape memory alloy cables. Part I introduced the fundamental, room temperature, tensile responses of two cable designs (7 × 7 right regular lay, and 1 × 27 alternating lay). In Part II, each cable behavior is studied further by breaking down the response into the contributions of its hierarchical subcomponents. Selected wire strands were extracted from the two cable constructions, and their quasi-static tension responses were measured using the same experimental setup of Part I. Consistent with the shallow wire helix angles in the 7 × 7 construction, the force–elongation responses of the core wire, 1 × 7 core strand and full 7 × 7 cable were similar on a normalized basis, with only a slight decrease in transformation force plateaus and slight increase in plateau strains in this specimen sequence. By contrast, each successive 1 × 27 component (1 × 6 core strand, 1 × 15 strand, and full cable) included an additional outer layer of wires with a larger number of wires, greater helix radius, and deeper helix angle, so the normalized axial load responses became significantly more compliant. Each specimen in the sequence also exhibited progressively larger strains at failure, reaching 40% strain in the full 1 × 27 cable.Stress-induced phase transformations involved localized strain/temperature and front propagation in all of the tested 7 × 7 components but none of the 1 × 27 components aside from the 1 × 27 core wire. Stereo digital image correlation measurements revealed finer features within a global transformation front of the 1 × 7 core strand than the 7 × 7 cable, consisting of an staggered pattern of individual wire fronts that moved in lock-step during elongation. Although the 1 × 27 multi-layer strands exhibited temperature/strain localizations in a distributed pattern during transformations, the localizations did not propagate and their cause was traced back to contact indentations (stress concentrations) arising from the cable’s fabrication. The normalized axial torque responses of the multi-layer 1 × 27 components during transformation were distinctly non-monotonic and complex, due to the alternating handedness of the layers. Force and torque contributions of individual wire layers were deduced by subtracting 1 × 27 component responses, which helped to clarify the transformation kinetics within each layer and explain the unusual force and torque undulations seen in the 1 × 27 cable response of Part I.     

The effects of Coulomb friction on the performance of centrifugal pendulum vibration absorbers

We investigate analytically and experimentally the effects of Coulomb friction on the performance of centrifugal pendulum vibration absorbers (CPVAs), which are used to reduce torsional vibrations in rotating machinery. The analysis is based on perturbation methods applied to the nonlinear equations of motion for a rotor subjected to an engine order applied torque and equipped with a circular path CPVA with viscous and Coulomb damping. The experimental work is based on quantifying parameters for the damping model using free vibration measurements with a viscous and Coulomb damping identification scheme that is enhanced to better handle measurement noise, and running tests for steady-state operation under a range of loading conditions. The level of Coulomb damping is varied by adjusting the friction of the absorber connection bearing. Good agreement is found between the analytical predictions and the experimental data. It is shown that the absorber sticks up to a level of excitation that allows it to release, after which the Coulomb damping acts in the expected manner, resulting in lowered response amplitudes. The results obtained are of general use in assessing absorber performance when dry friction is present in absorber suspensions.     

Hamilton–Jacobi equation,reaction action surface and the emergence of the force concept in chemical reaction dynamics

A combination of Hamilton–Jacobi equation and fast marching algorithm can be used to study reaction dynamics by converting the potential energy surface to a reaction action surface. The reaction action surface has been found to be an important tool in theoretical chemistry, allowing us to provide a different force-based perspective of chemical reactions. Several properties such as reaction force, reaction force surface, reaction path force and reaction path force constant have been defined and calculated by using the reaction action surface. This paper investigates these newly defined properties in order to understand the role they play in chemical reaction with reference to a model 4-well potential energy surface.     

21 Tesla Fourier Transform Ion Cyclotron Resonance Mass Spectrometer Greatly Expands Mass Spectrometry Toolbox

We provide the initial performance evaluation of a 21 Tesla Fourier transform ion cyclotron resonance mass spectrometer operating at the Environmental Molecular Sciences Laboratory at the Pacific Northwest National Laboratory. The spectrometer constructed for the 21T system employs a commercial dual linear ion trap mass spectrometer coupled to a FTICR spectrometer designed and built in-house. Performance gains from moving to higher magnetic field strength are exemplified by the measurement of peptide isotopic fine structure, complex natural organic matter mixtures, and large proteins. Accurate determination of isotopic fine structure was demonstrated for doubly charged Substance P with minimal spectral averaging, and 8158 molecular formulas assigned to Suwannee River Fulvic Acid standard with root-mean-square (RMS) error of 10 ppb. We also demonstrated superior performance for intact proteins; namely, broadband isotopic resolution of the entire charge state distribution of apo-transferrin (78 kDa) and facile isotopic resolution of monoclonal antibody under a variety of acquisition parameters (e.g., 6 s time-domains with absorption mode processing yielded resolution of approximately 1 M at m/z?=?2700).

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Structure and dynamics of an unfolded protein examined by molecular dynamics simulation

The accurate characterization of the structure and dynamics of proteins in disordered states is a difficult problem at the frontier of structural biology whose solution promises to further our understanding of protein folding and intrinsically disordered proteins. Molecular dynamics (MD) simulations have added considerably to our understanding of folded proteins, but the accuracy with which the force fields used in such simulations can describe disordered proteins is unclear. In this work, using a modern force field, we performed a 200 μs unrestrained MD simulation of the acid-unfolded state of an experimentally well-characterized protein, ACBP, to explore the extent to which state-of-the-art simulation can describe the structural and dynamical features of a disordered protein. By comparing the simulation results with the results of NMR experiments, we demonstrate that the simulation successfully captures important aspects of both the local and global structure. Our simulation was ~2 orders of magnitude longer than those in previous studies of unfolded proteins, a length sufficient to observe repeated formation and breaking of helical structure, which we found to occur on a multimicrosecond time scale. We observed one structural feature that formed but did not break during the simulation, highlighting the difficulty in sampling disordered states. Overall, however, our simulation results are in reasonable agreement with the experimental data, demonstrating that MD simulations can already be useful in describing disordered proteins. Finally, our direct calculation of certain NMR observables from the simulation provides new insight into the general relationship between structural features of disordered proteins and experimental NMR relaxation properties.