Multicommutation flow techniques in the hydride generation-atomic fluorescence determination of arsenic

This review outlines automated methodologies developed for measuring arsenic in environmental samples. We report the state of the art of the most significant methods exploiting multicommutation flow techniques coupled to hydride generation-atomic fluorescence determination. We review analytical methods used and present a comparative evaluation of them. We also discuss the on-line pre-concentration procedure as being of particular interest in the development of fully automated methods.     

HPLC methods for the determination of simvastatin and atorvastatin

We review high-performance liquid chromatography (HPLC) methods for the determination of two major statins used in clinical treatment – simvastatin and atorvastatin – in various fields of application, including bio-analytical assays, pharmaceutical assays and environmental applications.

Statin molecules are known to be susceptible to interconversion of the lactone and acidic forms, so it is necessary to consider this phenomenon during method development. We highlight liquid chromatography coupled to tandem mass spectrometry (LC-MS/MS) methods, as they have become a method of choice in bio-analytical and environmental applications. We compare the methods from the point of view of sensitivity. We discuss selection of the precursor ion for performing selected reaction monitoring (SRM) in MS detection and sample preparation.     

Modeling the internal mobility of the molecule of DNA

Recent investigations of the DNA molecule showed that it has a rather moveable structure and that internal DNA mobility plays an important role in biologic activity of the molecule. We describe here one possible way of modeling the internal DNA mobility based on the Hamiltonian formalism and analytic methods of finding solutions of corresponding dynamic equations. The approach developed in this article permits us to model internal motions of both small and large amplitudes. To illustrate the algorithm, we consider in details modeling internal DNA motions associated with the process of unwinding of the DNA double helix. We discuss merits and demerits of the model obtained. Different ways to improve the model and approach by applying computer methods, databanks, and methods of visualizations are also discussed. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Engineering the surface properties of microfluidic stickers

We introduce a simple and effective method to tailor the wetting and adhesion properties of thiolene-based microfluidic devices. This one-step lithographic scheme combines most of the advantages offered by the current methods employed to pattern microchannels: (i) the channel walls can be modified in situ or ex situ, (ii) their wettability can be varied in a continuous manner, (iii) heterogeneous patterning can be easily accomplished, with contact-angle contrasts extending from 0 to 90° for pure water, (iv) the surface modification has proven to be highly stable upon aging and heating. We first characterize the wetting properties of the modified surfaces. We then provide the details of two complementary methods to achieve surface patterning. Finally, we demonstrate the two methods with three examples of applications: the capillary guiding of fluids, the production of double emulsions, and the culture of cells on adhesive micropatterns.     

Calculations of the low-lying excited states of the TiO(2) molecule

We present calculations of the lowest excited electronic states of the TiO(2) molecule. These are computed using several correlated wavefunction response based methods, as well as time-dependent density functional response theory using a range of functionals. Surprisingly lower cost wavefunction based methods, in particular the second-order CC2 and CIS(D) methods, completely fail to describe the lowest (1)B(2) and (1)A(2) states of the molecule. Density functional methods fare better but still show considerable variation amongst functionals. Thus TiO(2) provides a strenuous test for correlated excited state methods.     

Measurement of the unwinding force of a DNA double helix

The review is devoted to measurement methods of bond rupture forces in complex biological molecules, namely, the unwinding forces of a DNA double helix. Mechanical methods not affecting electromagnetically a system under study, which is especially significant for biological systems, are considered. We describe two main methods: atomic force microscopy and rupture event scanning. The latter is a new method also based on the mechanical action but it has a much simpler instrumental implementation. The capabilities of both methods are compared and they are shown to be promising to investigate chemical bond rupture forces in biological systems. The application of these methods to study the strength of chemical bonds is associated with overcoming numerous technical difficulties in both performance of measurements themselves and chemical modification of conjugated surfaces. We demonstrate the applicability of these methods not only for fundamental studies of the strength of chemical bonds determining the stability and the related possibility of functioning of three-dimensional biomolecular complexes, but also for the design of biosensors based on the mechanical effect (quartz crystal microbalance, QCM), e.g., with an opportunity of rapid analysis of DNA.     

A family of ten-step methods with vanished phase-lag and its first derivative for the numerical solution of the Schrödinger equation

A family of high algebraic order ten-step methods is obtained in this paper. The new developed methods have vanished phase-lag (the first one) and phase-lag and its first derivative (the second one). We apply the new developed methods to the resonance problem of the radial Schrödinger equation. The efficiency of the new proposed methods is shown via error analysis and numerical applications.     

Multicoefficient extrapolated density functional theory studies of pi...pi interactions: the benzene dimer

We report tests of new (2005) and established (1999-2003) multilevel methods against essentially converged benchmark results for nonbonded interactions in benzene dimers. We found that the newly developed multicoefficient extrapolated density functional theory (DFT) methods (which combine DFT with correlated wave function methods) give better performance than multilevel methods such as G3SX, G3SX(MP3), and CBS-QB3 that are based purely on wave function theory (WFT); furthermore, they have a lower computational cost. We conclude that our empirical approach for combining WFT methods with DFT methods is a very efficient and effective way for describing not only covalent interactions (as shown previously) but also nonbonded interactions.     

Quantum Monte Carlo calculations of the potential energy curve of the helium dimer

We report results of two quantum Monte Carlo methods -- variational Monte Carlo and diffusion Monte Carlo -- on the potential energy curve of the helium dimer. In contrast to previous quantum Monte Carlo calculations on this system, we have employed trial wave functions of the Slater-Jastrow form and used the fixed node approximation for the fermion nodal surface. We find both methods to be in excellent agreement with the best theoretical results at short range. In addition, the diffusion Monte Carlo results give very good agreement across the whole potential energy curve, while the Slater-Jastrow wave function fails to bind the dimer at all.     

A Family of Exponentially-fitted Runge–Kutta Methods with Exponential Order Up to Three for the Numerical Solution of the Schrödinger Equation

We have constructed three Runge–Kutta methods based on a classical method of Fehlberg with eight stages and sixth algebraic order. These methods have exponential order one, two and three. We show through the error analysis of the methods that by increasing the exponential order, the maximum power of the energy in the error expression decreases. So the higher the exponential order the smaller the local truncation error of the method compared to the corresponding classical method. The difference is higher for higher values of energy. The results confirm this, when integrating the resonance problem of the one-dimensional time-independent Schr?dinger equation.     

Moment expansion approach to the time dynamics of genetic evolution

We use moment expansion methods to analyze the time dynamics for genetic evolution under selection, mutation, and reproduction. We consider a N-allele diploid genotype reproducing randomly in a fitness landscape with either one or two maxima, and mutation is assumed to occur such that any allele can mutate into any other type. We find that the moment expansion works well, where a small number of moments can capture the general behavior toward equilibrium. Our methods allow a systematic way to capture the time dynamics of the evolutionary process efficiently using a small number of coupled equations.     

DNA序列特征的统计分析

介绍了近年来在多种学科领域对DNA碱基序列的研究中发展起来的定量分析符号序列的方法，归纳了将碱基与数字对应起来的规则和进行统计分析的方法．并给予一定的评价。DNA分子包涵了丰富的化学信息和生物信息，对于DNA序列的统计分析显得非常重要。将DNA序列表达成数字信号通常有从一维到四维4种不同维数空间的映射方式，其相应的统计方法有均方根涨落、熵近似方法、傅立叶变换和小波变换等，各种方法从多个角度多个层次来分析揭示了DNA序列的结构规律。     

Lessons learned in induced fit docking and metadynamics in the Drug Design Data Resource Grand Challenge 2

Two of the major ongoing challenges in computational drug discovery are predicting the binding pose and affinity of a compound to a protein. The Drug Design Data Resource Grand Challenge 2 was developed to address these problems and to drive development of new methods. The challenge provided the 2D structures of compounds for which the organizers help blinded data in the form of 35 X-ray crystal structures and 102 binding affinity measurements and challenged participants to predict the binding pose and affinity of the compounds. We tested a number of pose prediction methods as part of the challenge; we found that docking methods that incorporate protein flexibility (Induced Fit Docking) outperformed methods that treated the protein as rigid. We also found that using binding pose metadynamics, a molecular dynamics based method, to score docked poses provided the best predictions of our methods with an average RMSD of 2.01 Å. We tested both structure-based (e.g. docking) and ligand-based methods (e.g. QSAR) in the affinity prediction portion of the competition. We found that our structure-based methods based on docking with Smina (Spearman ρ?=?0.614), performed slightly better than our ligand-based methods (ρ?=?0.543), and had equivalent performance with the other top methods in the competition. Despite the overall good performance of our methods in comparison to other participants in the challenge, there exists significant room for improvement especially in cases such as these where protein flexibility plays such a large role.     

Up-to-date methods for the determination of rhenium

We present a review of literature on the methods for rhenium determination published from 2000 to 2010.     

Symplectic Methods for the Numerical Solution of the Radial Shrödinger Equation

In this paper new symplectic-schemes for the numerical solution of the radial Shrödinger equation are proposed. In particular, symplectic integrators for Hamiltonian systems have been developed. Based on this approach, second- and third-order methods are proposed. These methods are more accurate than the existing ones. We compare these methods not only with the existing symplectic methods, but also with a classical Runge–Kutta–Nyström method.     

Stoichiometric network analysis of the photochemical processes in the mesopause region

The mechanism of photochemistry in the mesopause region entails a chemical oscillator forced by solar short-wave radiation. A model with periodic forcing between day and night conditions produces nonlinear dynamics including period-doubling bifurcations and chaos. The photochemical mechanism represents a network involving positive and negative feedbacks that can be examined by methods of stoichiometric network analysis. We use these methods to decompose the network into irreducible subnetworks and then apply linear stability analysis to find all possible sources of oscillatory instabilities in the mesopause chemistry. These oscillators are classified according to topological features in their reaction networks and phase shifts of oscillating species. We subsequently compare phase shifts indicated by the network analysis with those from direct simulations to identify a specific subnetwork in the mechanism underlying the complex oscillatory dynamics observed in earlier simulations.     

Symplectic Methods of Fifth Order for the Numerical Solution of the Radial Shrödinger Equation

In this paper the numerical solution of the radial Shrödinger equation via new proposed symplectic-schemes is investigated. In particular, the radial Schödinger equation is transformed into Hamiltonian canonical form and is solved via symplectic integrators. Based on this approach, fifth-order methods are proposed. We compare these methods with well-known existing symplectic methods. The numerical results show the efficiency of the proposed method.     

High-level ab initio studies of the electronic excited states of the hydroxyl radical and water-hydroxyl complex

The lowest-energy electronic transitions in the hydroxyl radical and the hydrogen bound complex H(2)O.HO have been studied using ab initio methods. We have used the complete active-space self-consistent field and multireference configuration interaction (MRCI) methods to calculate vertical excitation energies and oscillator strengths. At the MRCI level the lowest-lying (2)Sigma(+)<--(2)Pi electronic transition is redshifted by about 2500 cm(-1) upon formation of the H(2)O.HO complex. We propose that this transition could be used to identify the complex in the gas phase, which in turn could be used to examine the role of H(2)O.HO in atmospheric reactions.     

Critical evaluation of mass spectrometric measurement of dissociation constants: accuracy and cross-validation against surface plasmon resonance and circular dichroism for the calmodulin-melittin system

We present a comprehensive study for determining the binding affinity of a protein-ligand complex, using mass spectrometric methods. Mass spectrometry has been used to study noncovalent interactions for a number of years. However, the use of soft ionization mass spectrometry for quantitative analysis of noncovalently bound complexes is not widely accepted. This paper reports a comparison of MS methods against established methods such as surface plasmon resonance (SPR) and circular dichroism (CD) whose suitability for the quantitative assessment of noncovalent interactions is well known. ESI titration and MALDI-SUPREX were used as representative mass spectrometric methods for this work. We chose to study the calmodulin-melittin complex that presents three challenges: (i) it exhibits a high affinity (low nanomolar KD); (ii) complexes are formed only in the presence of a coactivator, calcium ions in this case; and (iii) the protein and the complex show a different ionization efficiency. Dissociation constants were obtained from each method for the selected system and compared thoroughly to elucidate pros and cons of the selected methodologies in terms of their ability for the determination of binding constants of protein-ligand complexes. ESI titration, SPR, CD and MALDI-SUPREX yielded KD values in the low nanomolar range that are in general agreement with an older value reported in the literature. We also critically evaluated the limitations in particular of the MS methods and the associated data evaluation procedures. We present an improved evaluation of SUPREX data, as well as a detailed error analysis for all methods used.