Structure and dynamics of liquid water with different long-range interaction truncation and temperature control methods in molecular dynamics simulations

We have used molecular dynamics simulations to study the physical properties of modified TIP3P water model included in the CHARMM program, using four different methods-the Ewald summation technique, and three different spherical truncation methods-for the treatment of the long-range interactions. Both the structure and dynamics of the liquid water model were affected by the methods used to truncate the long-range interactions. For some of the methods artificial structuring of the model liquid was observed around the cutoff radius. The model liquid properties were also affected by the commonly applied temperature control methods. Four different methods for controlling the temperature of the system were studied, and the effects of these methods on the bulk properties for liquid water were analyzed. The system size was also found to change the dynamics of the model liquid water. Two control simulations with the SPC/E water model were carried out. The self-diffusion coefficient (D), the radial distribution function (g(OO)), the distance dependent Kirkwood G-factor [G(k)(r)] and the intermolecular potential energy (E(pot)) were determined from the different trajectories and compared with the experimental data.     

Net charge changes in the calculation of relative ligand‐binding free energies via classical atomistic molecular dynamics simulation

The calculation of binding free energies of charged species to a target molecule is a frequently encountered problem in molecular dynamics studies of (bio‐)chemical thermodynamics. Many important endogenous receptor‐binding molecules, enzyme substrates, or drug molecules have a nonzero net charge. Absolute binding free energies, as well as binding free energies relative to another molecule with a different net charge will be affected by artifacts due to the used effective electrostatic interaction function and associated parameters (e.g., size of the computational box). In the present study, charging contributions to binding free energies of small oligoatomic ions to a series of model host cavities functionalized with different chemical groups are calculated with classical atomistic molecular dynamics simulation. Electrostatic interactions are treated using a lattice‐summation scheme or a cutoff‐truncation scheme with Barker–Watts reaction‐field correction, and the simulations are conducted in boxes of different edge lengths. It is illustrated that the charging free energies of the guest molecules in water and in the host strongly depend on the applied methodology and that neglect of correction terms for the artifacts introduced by the finite size of the simulated system and the use of an effective electrostatic interaction function considerably impairs the thermodynamic interpretation of guest‐host interactions. Application of correction terms for the various artifacts yields consistent results for the charging contribution to binding free energies and is thus a prerequisite for the valid interpretation or prediction of experimental data via molecular dynamics simulation. Analysis and correction of electrostatic artifacts according to the scheme proposed in the present study should therefore be considered an integral part of careful free‐energy calculation studies if changes in the net charge are involved. © 2013 The Authors Journal of Computational Chemistry Published by Wiley Periodicals, Inc.     

Isometric artifacts from polymerase chain reaction-massively parallel sequencing analysis of short tandem repeat loci: An emerging issue from a new technology?

The recent introduction of polymerase chain reaction (PCR)-massively parallel sequencing (MPS) technologies in forensics has changed the approach to allelic short tandem repeat (STR) typing because sequencing cloned PCR fragments enables alleles with identical molecular weights to be distinguished based on their nucleotide sequences. Therefore, because PCR fidelity mainly depends on template integrity, new technical issues could arise in the interpretation of the results obtained from the degraded samples. In this work, a set of DNA samples degraded in vitro was used to investigate whether PCR-MPS could generate “isometric drop-ins” (IDIs; i.e., molecular products having the same length as the original allele but with a different nucleotide sequence within the repeated units). The Precision ID GlobalFiler NGS STR panel kit was used to analyze 0.5 and 1 ng of mock samples in duplicate tests (for a total of 16 PCR-MPS analyses). As expected, several well-known PCR artifacts (such as allelic dropout, stutters above the threshold) were scored; 95 IDIs with an average occurrence of 5.9 IDIs per test (min: 1, max: 11) were scored as well. In total, IDIs represented one of the most frequent artifacts. The coverage of these IDIs reached up to 981 reads (median: 239 reads), and the ratios with the coverage of the original allele ranged from 0.069 to 7.285 (median: 0.221). In addition, approximately 5.2% of the IDIs showed coverage higher than that of the original allele. Molecular analysis of these artifacts showed that they were generated in 96.8% of cases through a single nucleotide change event, with the C > T transition being the most frequent (85.7%). Thus, in a forensic evaluation of evidence, IDIs may represent an actual issue, particularly when DNA mixtures need to be interpreted because they could mislead the operator regarding the number of contributors. Overall, the molecular features of the IDIs described in this work, as well as the performance of duplicate tests, may be useful tools for managing this new class of artifacts otherwise not detected by capillary electrophoresis technology.     

Magnetic Resonance Imaging of Electrochemical Cells Containing Bulk Metal

The development of improved energy‐storage devices, as well as corrosion prevention and metal‐electrofinishing technologies, requires knowledge of local composition and transport behaviour in electrolytes near bulk metals, in situ and in real time. It remains a challenge to acquire such data and new analytical methods are required. Recent work shows that magnetic resonance imaging (MRI) is able to map concentration gradients and visualise electrochemical processes in electrochemical cells containing bulk metals. This recent work, along with the challenges, and solutions, associated with MRI of these electrochemical cells are reviewed.     

Novel correction method for X-ray beam energy fluctuation of high energy DR system with a linear detector

A high energy digital radiography (DR) testing system has generated diverse scientific and technological interest in the field of industrial non-destructive testing. However, due to the limitations of manufacturing technology for accelerators, an energy fluctuation of the X-ray beam exists and leads to bright and dark streak artifacts in the DR image. Here we report the utilization of a new software-based method to correct the fluctuation artifacts. The correction method is performed using a high pass filtering operation to extract the high frequency information that reflects the X-ray beam energy fluctuation, and then subtracting it from the original image. Our experimental results show that this method is able to rule out the artifacts effectively and is readily implemented on a practical scanning system.     

Lingshuine,an Unexpected Passerini Product from the Hainan Sponge Axinyssa variabilis

Lingshuine ( 1 ), a novel sesquiterpene amide, along with three known N‐containing compounds, 2 – 4 , have been isolated from the Hainan sponge Axinyssa variabilis. The structure of 1 was elucidated by detailed analysis of the spectroscopic data and by chemical methods. Lingshuine represents the first example of a Passerini product formed during the isolation process.     

Nanosecond and femtosecond Laser Induced Breakdown Spectroscopic analysis of bronze alloys

In the present work we are studying the influence of pulse duration (nanosecond (ns) and femtosecond (fs)) at λ = 248 nm on the laser-induced plasma parameters and the quantitative analysis results for elements such as Sn, Zn and Pb, in different types of bronze alloys adopting LIBS in ambient atmosphere. Binary (Sn–Cu), ternary (Sn–Zn–Cu or Sn–Pb–Cu) and quaternary (Sn–Zn–Pb–Cu) reference alloys characterized by a chemical composition and metallurgical features similar to those used in Roman times, were employed in the study. Calibration curves, featuring linear regression coefficients over 98%, were obtained for tin, lead and zinc, the minor elements in the bronze alloys (using the internal standardization method) as well as for copper, the major element. The effects of laser pulse duration and energy on laser-induced plasma parameters, namely the excitation temperature and the electron density have been studied in our effort to optimize the analysis. Finally, LIBS analysis was carried on three real metal objects and the spectra obtained have been used to estimate the type and elemental composition of the alloys based on the calibration curves produced with the reference alloys. The results obtained are very useful in the future use of portable LIBS systems for in situ qualitative and quantitative elemental analysis of bronze artifacts in museums and archaeological sites.     

Suppression of ringing oscillations from high speed rubber compression curves through a detailed modal characterization of servo-hydraulic machines

System ringing is one of the most important factors affecting the quality of data obtained in high speed dynamic material tests using servo-hydraulic machines. This phenomenon is characterized by vibrations originated by the excitation of predominant modes of the machine during tests, producing distinctive waves in material curves that severely distort the required results. In the specialized literature, the quantitative study of these vibrations has mainly been carried out considering the testing machine as a single degree of freedom system, which has led to a general understanding of the variables involved in the process. However, discrepancies between analytical predictions and experimental observations have been detected using the single degree of freedom approach, so the need for further detailed study of machine dynamic characteristics has been reported. The work presented in this paper addresses this requirement by means of a detailed characterization of the dynamic behavior of a MTS 819.10 high rate testing system. Natural frequencies, mode shapes and damping factors have been obtained from an experimental modal analysis performed on the machine and a mathematical model of the process has been developed from these modal parameters. This model has been used to detect the modes that have the greatest influence in system ringing when testing rubber at high strain rates, and to predict quantitatively the amplitudes of vibrations produced in the process. Material curves have been corrected by subtracting the predicted undulations from the original measurements, obtaining smooth curves that adequately reflect the real material behavior at high strain rates and, thus, demonstrating the effectiveness of the proposed procedure. Although the research conducted in this work has been focused on rubber, the procedure can be extended equally to characterize other materials, thus constituting a valuable tool to correct experimental measurements contaminated by ringing.     

Effects of experimental imperfections on a spin counting experiment

Spin counting NMR is an experimental technique that allows a determination of the size and time evolution of networks of dipolar coupled nuclear spins. This work reports on an average Hamiltonian treatment of two spin counting sequences and compares the efficiency of the two cycles in the presence of flip errors, RF inhomogeneity, phase transients, phase errors, and offset interactions commonly present in NMR experiments. Simulations on small quantum systems performed using the two cycles reveal the effects of pulse imperfections on the resulting multiple quantum spectra, in qualitative agreement with the average Hamiltonian calculations. Experimental results on adamantane are presented, demonstrating differences in the two sequences in the presence of pulse errors.     

Learning about multiplication by comparing algorithms: “One times one,but actually they are ten times ten”

Multiplication algorithms in primary school are still frequently introduced with little attention to meaning. We present a case study focusing on a third grade class that engaged in comparing two algorithms and discussing “why they both work”. The objectives of the didactical intervention were to foster students' development of mathematical meanings concerning multiplication algorithms, and their development of an attitude to judge and compare the value and efficiency of different algorithms. Underlying hypotheses were that it is possible to promote the simultaneous unfolding of the semiotic potential of two algorithms, considered as cultural artifacts, with respect to the objectives of the didactical intervention, and to establish a fruitful synergy between the two algorithms. As results, this study sheds light onto the new theoretical construct of “bridging sign”, illuminating students’ meaning-making processes involving more than one artifact; and it provides important insight into the actual unfolding of the hypothesized potential of the algorithms.