Ferreting out gas adsorption heats: the pseudo-isobaric method

A new method is demonstrated for calculating gas adsorption heats from variable-temperature infrared spectra of adsorbed molecules. By focusing on the low coverage regime, where (at equilibrium) there is only a very small fraction of molecules adsorbed, the procedure devised yields the corresponding value of adsorption enthalpy without needing to know the equilibrium pressure. Experimental measurements can thus be highly simplified, which constitutes one of the merits of the new method. Versatility for dealing with adsorption processes occurring at a low temperature, and having a small energy balance, is another favourable feature.     

An efficient and extensible format,library, and API for binary trajectory data from molecular simulations

Molecular dynamics simulations is an important application in theoretical chemistry, and with the large high‐performance computing resources available today the programs also generate huge amounts of output data. In particular in life sciences, with complex biomolecules such as proteins, simulation projects regularly deal with several terabytes of data. Apart from the need for more cost‐efficient storage, it is increasingly important to be able to archive data, secure the integrity against disk or file transfer errors, to provide rapid access, and facilitate exchange of data through open interfaces. There is already a whole range of different formats used, but few if any of them (including our previous ones) fulfill all these goals. To address these shortcomings, we present “Trajectory Next Generation” (TNG)—a flexible but highly optimized and efficient file format designed with interoperability in mind. TNG both provides state‐of‐the‐art multiframe compression as well as a container framework that will make it possible to extend it with new compression algorithms without modifications in programs using it. TNG will be the new file format in the next major release of the GROMACS package, but it has been implemented as a separate library and API with liberal licensing to enable wide adoption both in academic and commercial codes. © 2013 Wiley Periodicals, Inc.     

High-resolution optical imaging from trajectory time distributions

Trajectory time distribution optical microscopy (TTDOM), which records the mean off-times of single molecular fluorescent indicators that light up when they collide with vesicles, is extended to record fluorescence durations or on-times. TTDOM can distinguish shapes of objects that are smaller than the diffraction limited resolution. The fluorescence duration time image can also provide high-resolution information. The effects of the threshold that separates fluorescent bursts from background signals and of two or more probes visiting the vesicles simultaneously have been investigated systematically. New experimental results along with simulations indicate that TTDOM is capable of providing the size and shape of objects and information on probe-vesicle binding.     

Interelement correlations detectable in plant samples based on data from reference materials and highly accurate research samples

Summary A correlation analysis of 45 elements from various plant standard reference materials provided a number of highly correlated element pairs (r0.9) leading to the expectation of an interelement interaction. For the elements Fe³⁺, Al³⁺, Sc³⁺ and the lanthanides, these high correlations may be attributed to the similar ionic radius of the hydrated ions or the same charge. The highly correlated occurrence of some macroelements such as P and N reflects the close association of the two elements, particularly during protein biosynthesis. Of the alkali metals, K, and the alkaline earth metals Ca, Mg and, to some extent, also Sr display high correlations amongst themselves and with the macronutrients N and P. In correlating the transition elements with each other and with the micro- and macroelements, it was only possible to find a few high correlation coefficients; only the two element pairs Co/Mo and Cr/Co display high correlation coefficients. One of the reasons for this is probably the inaccuracy of the data material. It was not possible to confirm the highly negatively correlated element pairs reported in earlier work. It was not even possible to determine a clear negative trend for typical pairs of antagonists such as Al/Ca or Mn/Ca. The highest negative correlation was found for the B/Sb element pair at r=–0.75.     

Diffusion coefficients in supercritical fluids: available data and graphical correlations

The methods for obtaining reliable data on diffusion coefficients at high pressure have received great attention over the last 15 years. This interest has been due to the importance that supercritical fluids have assumed in some industrial areas, mainly in emerging separative operations based on mass transfer mechanisms. This review includes all the available data of diffusion coefficients in supercritical fluids at infinite dilution. Revised literature includes references until 1998. Frequent types of graphical correlation were analyzed.     

Metabolic trajectory characterisation of xenobiotic-induced hepatotoxic lesions using statistical batch processing of NMR data

Multivariate statistical batch processing (BP) analysis of 1H NMR urine spectra was employed to establish time-dependent metabolic variations in animals treated with the model hepatotoxin, alpha-naphthylisothiocyanate (ANIT). ANIT (100 mg kg(-1)) was administered orally to rats (n = 5) and urine samples were collected from dosed and matching control rats at time-points up to 168 h post-dose. Urine samples were measured via 1H NMR spectroscopy and partial least squares (PLS) based batch processing analysis was used to interpret the spectral data, treating each rat as an individual batch comprising a series of timed urine samples. A model defining the mean urine profile over the 7 day study period was established, together with model confidence limits (+/-3 standard deviation), for the control group. Samples obtained from ANIT treated animals were evaluated using the control model. Time-dependent deviations from the control model were evident in all ANIT treated animals consisting of glycosuria, bile aciduria, an initial decrease in taurine levels followed by taurinuria and a reduction of tricarboxylic acid cycle intermediate excretion. BP provided an efficient means of visualising the biochemical response to ANIT in terms of both inter-animal variation and net variation in metabolite excretion profiles. BP also allowed multivariate statistical limits for normality to be established and provided a template for defining the sequence of time-dependent metabolic consequences of toxicity in NMR based metabonomic studies.     

SCOUT: A new algorithm for the inference of pseudo-time trajectory using single-cell data

Single cell technology is a powerful tool to reveal intercellular heterogeneity and discover cellular developmental processes. When analyzing the complexity of cellular dynamics and variability, it is important to construct a pseudo-time trajectory using single-cell expression data to reflect the process of cellular development. Although a number of computational and statistical methods have been developed recently for single-cell analysis, more effective and efficient methods are still strongly needed. In this work we propose a new method named SCOUT for the inference of single-cell pseudo-time ordering with bifurcation trajectories. We first propose to use the fixed-radius near neighbors algorithms based on cell densities to find landmarks to represent the cell states, and employ the minimum spanning tree (MST) to determine the developmental branches. We then propose to use the projection of Apollonian circle or a weighted distance to determine the pseudo-time trajectories of single cells. The proposed algorithm is applied to one synthetic and two realistic single-cell datasets (including single-branching and multi-branching trajectories) and the cellular developmental dynamics is recovered successfully. Compared with other popular methods, numerical results show that our proposed method is able to generate more robust and accurate pseudo-time trajectories. The code of the method is implemented in Python and available at https://github.com/statway/SCOUT.     

Extracting dominant pair correlations from many-body wave functions

The singular value decomposition of the n-particle excitation operator as determined by coupled cluster or perturbation theory is used to extract the dominant and interesting electron-electron correlations from complex molecular wave functions. As an example of the very general formalism, the decomposition of the T(2) operator obtained from coupled cluster doubles calculations is used to analyze the strength and character of pair correlations in a variety of molecules with interesting electronic structure. The magnitude of the largest singular value(s) determines the strength of the correlation(s), and the corresponding right- and left-hand singular vectors characterize the physical and spatial nature of the correlations. The primary advantage of this tool over natural orbital analysis is that it provides direct associations between the occupied and virtual geminals involved in the correlations.     

Quantum trajectory analysis of single-photon control from a single-molecule source

We investigate theory of single-photon control from a two-level single-molecule source irradiated by laser pulses of various shapes and pulse durations in terms of quantum trajectories which link stochastic dynamics of the radiating source with quantum measurement theory. Using Monte Carlo wave function simulation, we analyze the detailed dissipative dynamics of the single-molecule source and the photon statistics as revealed by repeated Gedanken photon measurement on the single radiating source. We show that much of the photon statistics from the two-level single-molecule single-photon sources, including few-photon emission probability, waiting time distribution, and two-time correlation function of the fluorescent light, can be understood qualitatively from the simple picture of Rabi nutation and pi pulse in terms of pulse areas.     

Empirical correlations between gas-chromatographic retention data and physical or topological properties of solute molecules

Kováts retention indices (I) and relative retention times (τ) using Silicone oil 550 or Bentone 34 as the stationary phase were measured for 20 hydrocarbons (mainly alkylbenzenes). Statistical analysis of repeated determinations indicated that the empirical distribution function of retention indices is not normal; the relative standard deviations decrease with increasing retention index. Several models were examined to describe the retention data as a function of boiling point (T_B) and molar refraction, molar volume, connectivity indices, etc. A universal fitting equation y_i=A exp (BT_Bi) + Cx_2i + D (where y_i=I or τ, and x_2i is one of the properties mentioned) proved to be best on the basis of statistical characteristics (examination of residuals, multiple correlation coefficient, residual mean square, variance ratio tests) which were also evaluated. The results were compared to equations recommended in the literature.     

Crystalline polysilicate magadiite with intercalated n-alkylmonoamine and some correlations involving thermochemical data

Synthesized hydrated lamellar acidic crystalline magadiite (H₂Si₁₄O₂₉·2H₂O) nanocompound was used as host for intercalation of polar n-alkylmonoamine molecules of the general formula H₃C(CH₂)_nNH₂ (n = 1–6) in aqueous solution. The original interlayer distance (d) of 1500 pm, determined by X-ray powder diffraction patterns, increases after intercalation. The values correlated with the number of aliphatic amine carbon (n_c) atoms: d = [(1312 ± 11) + (21 ± 2)]n_c. The amount of intercalated amines (N_s), decreased as n_c increased: N_s = [(5.82 ± 0.04) − (0.45 ± 0.01)]n_c. The acidic layered nanocompound was calorimetrically titrated with the amines and the thermodynamic data gave exothermic values for all guest molecules, as shown by the correlation: Δ_intH = −[(24.45 ± 0.49) − (1.91 ± 0.10)]n_c and d = [(1576 ± 16) − (10.8 ± 1.0)]Δ_intH. The negative values of the Gibbs energies and the positive entropies also presented the correlations: Δ_intG = −[(22.8 ± 0.2) − (0.2 ± 0.1)]n_c and Δ_intS = [(6 ± 1) + (5 ± 1)]n_c, respectively.     

A 500-ps molecular dynamics simulation trajectory of cardiotoxin II from Taiwan cobra venom in solution: Correlation with NMR and X-ray crystallography data

Molecular dynamics simulation of a small, basic, all β-sheet cardiotoxin, CTX II, from Taiwan cobra venom, with proper treatment of long-range electrostatic interactions, was carried out to examine the backbone mobility of CTX II in solution and aid in interpretation of order parameters of C_α H bonds obtained from NMR experiments based on the Lipari–Szabo theory. The calculated order parameters of C_α H bonds and B-factors of CTX II in solution were compared with NMR-derived backbone order parameters and the crystal structure data, respectively. An overall qualitative agreement was obtained and, quantitatively, the calculated values and experimental results of many residues were also in good agreement. The discrepancies between the results computed herein and the experimental values, physical bases, and plausible biological functions are discussed. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 546–562, 1999     

HTMoL: full-stack solution for remote access,visualization, and analysis of molecular dynamics trajectory data

Research on biology has seen significant advances with the use of molecular dynamics (MD) simulations. The MD methodology enables explanation and discovery of molecular mechanisms in a wide range of natural processes and biological systems. The need to readily share the ever-increasing amount of MD data has been hindered by the lack of specialized bioinformatic tools. The difficulty lies in the efficient management of the data, i.e., in sending and processing 3D information for its visualization. In this work, we present HTMoL, a plug-in-free, secure GPU-accelerated web application specifically designed to stream and visualize MD trajectory data on a web browser. Now, individual research labs can publish MD data on the Internet, or use HTMoL to profoundly improve scientific reports by including supplemental MD data in a journal publication. HTMoL can also be used as a visualization interface to access MD trajectories generated on a high-performance computer center directly. Furthermore, the HTMoL architecture can be leveraged with educational efforts to improve learning in the fields of biology, chemistry, and physics.     

Bond-order-bond-energy correlations

A practical procedure for determining the relative strengths of chemical bonds is presented. It is shown, for diatomic and polyatomic molecules, that bond strengths correlate directly with bond orders calculated from force constants and bond lengths. The latter two properties can be obtained either experimentally or computationally.