Efficient compression of molecular dynamics trajectory files

We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: “interframe” predictors, which exploit temporal coherence between successive frames in a simulation, and more complex “intraframe” schemes, which compress each frame independently. Our interframe predictors are fast, memory‐efficient and well suited to on‐the‐fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12‐bit quantization, maximum error ≈ 10^?2 Å), we can compress a 1–2 fs trajectory file to 5–8% of its original size. For 200 fs time steps—typically used in fine grained water diffusion experiments—we can compress files to ～25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases. © 2012 Wiley Periodicals, Inc.     

Classical trajectory analysis in atom—triatom collisions: Continuous quantization and scaling behaviour

A method of analysing classical trajectory data, based on recently derived scaling principles, is applied to a model atom-triatom collinear collision system. Apart from the utility of the scaling idea in extending trajectory computations, the analysis of the scaling coefficients in terms of transition probabilities increases the scope of the classical scaling theory as a means of obtaining (at the very least) qualitative quantum-mechanical information from classical trajectories. As an useful adjunct, the method of continuous quantization is applied to generate approximate transition probabilities. These results are semiquantitative; thus a combination of classical scaling and continuous quantization affords a powerful means of modeling complex collision cases with a minimum of computational effort.     

ART‐RRT: As‐Rigid‐As‐Possible exploration of ligand unbinding pathways

This article proposes a method to efficiently generate approximate ligand unbinding pathways. It combines an efficient tree‐based exploration method with a morphing technique from Computer Graphics for dimensionality reduction. This method is computationally cheap and, unlike many existing approaches, does not require a reaction coordinate to guide the search. It can be used for finding pathways with known or unknown directions beforehand. The approach is evaluated on several benchmarks and the obtained solutions are compared with the results from other state‐of‐the‐art approaches. We show that the method is time‐efficient and produces pathways in good agreement with other state‐of‐the‐art solutions. These paths can serve as first approximations that can be used, analyzed, or improved with more specialized methods. © 2018 Wiley Periodicals, Inc.     

Estimation of Flat‐topped Gaussian distribution with application in system identification

Uniformly distributed uncertainty exists in industrial process; additive error introduced by quantization is an example. To be able to handle additive uniform and Gaussian measurement uncertainty simultaneously in system identification, the Flat‐topped Gaussian distribution is considered in this paper as an alternative to the Gaussian distribution. To incorporate this type of uncertainty in the maximum likelihood estimation framework, the explicit form of its density function is of necessity. This work proposes an approach for obtaining both the functional structure and corresponding parameter estimation of Flat‐topped Gaussian distribution by a moment fitting strategy. The performance of the proposed approximation function is verified by comparison to the Flat‐topped Gaussian distributed random variable with different Gaussian and uniform components. Results of numerical simulations and industrial applications in system identification are presented to verify the effectiveness of the Flat‐topped Gaussian distribution for noise distribution in handling additional uniform uncertainty.     

Automated error control in divide‐and‐conquer self‐consistent field calculations

In linear‐scaling divide‐and‐conquer (DC) electronic structure calculations, a buffer region is used to control the error introduced by the DC approximation. In this study, an energy‐based error estimation scheme is proposed for the DC self‐consistent field method with a two‐layer buffer region scheme. Based on this scheme, a procedure to automatically determine the appropriate buffer region in the DC method is proposed. It was confirmed that the present method works satisfactorily in calculations of water clusters and proteins, although its performance was insufficient for the calculation of a delocalized graphene system. © 2018 Wiley Periodicals, Inc.     

Critical charges of simple coulomb molecular systems: One‐two electron case

We consider some Coulomb systems with several infinitely massive centers of charge Z and one or two electrons: (Z,e), (2Z,e), (3Z,e), (4Z,e), (2Z,e,e), and (3Z,e,e). It is shown that the physical, integer charges Z = 1,2,… do not play a distinguished role for the total energy and for the equilibrium configuration of a system, giving no indication of a charge quantization. By definition, a critical charge Z_cr for a given Coulomb system (nZ,e) or (nZ,e,e) is a charge which separates the domain of the existence of bound states from the domain of unbound states (the domain of stability), the continuum (the domain of instability). For all the above‐mentioned systems critical charges Z_cr as well as equilibrium geometrical configurations are found. Furthermore, an indication to a branch point singularity at Z = Z_cr with exponent 3/2 was obtained. It is demonstrated that in the domain of the existence the optimal geometrical configuration for both (nZ,e) at n = 2,3,4 and (nZ,e,e) at n = 2,3 corresponds to the Platonic body. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

An automatic peak finding method for LC‐MS data using Gaussian second derivative filtering

A highly automated procedure for localising and characterising peaks in the chromatographic time domain of LC‐MS data has been developed. The work was initiated by an identified need to facilitate the detection and tracking of chromatographic peaks during method development for the analysis of impurities in pharmaceutical products. The algorithm is mainly based on a digital filter for which the settings are automatically adapted to the data set under study. The procedure was evaluated for synthetic data sets with various S/N levels, peak widths and baseline properties. It was found that even for the worst case tested with S/N=10 and a high variability in the baseline, 94% of the simulated analytical peaks could be detected without producing any false‐positive identifications. Furthermore, the number of correctly estimated peak heights and peak widths falling within a 10% error of the true values were 94 and 91%, respectively. For experimental data sets, peak height, and width estimations were more difficult, but the processed reconstructions showed an excellent agreement with the analytical signals of the raw data, and also a clearly improved visualisation in total ion‐ and base‐peak chromatograms.     

利用太赫兹时域光谱鉴别爆炸物2,4-DNT和 2,6-DNT

利用太赫兹时域光谱测得了2,4-DNT和 2,6-DNT在0.3-2.0THz频谱范围的吸收谱和折射谱。借助高斯03程序对2,6-DNT进行结构优化和频率计算。2,6-DNT在1.09, 1.36 and 1.55 THz有三个明显吸收并被归因于分子间的相互作用。本文使用太赫兹光谱法对2,4-DNT和 2,6-DNT混合物做了定量分析。分析的结果与实际值基本一致,相对误差约为8%。     

Extended quantization condition for constructive and destructive interferences and trajectories dominating molecular vibrational eigenstates

The role of destructive quantum interference in semiclassical quantization of molecular vibrational states is studied. This aspect is crucial for correct quantization, since failure in the appropriate treatment of destructive interference quite often results in many spurious peaks and broad background to hide the true peaks. We first study the time-Fourier transform of the autocorrelation function without performing summation over the trajectories. The resultant quantity, the prespectrum which is a function of individual classical trajectories, provides a clear view about how destructive interference among the trajectories should function. It turns out that the prespectrum is oscillatory but never a random noise. On the contrary, it bears a systematic and regular structure, which is sometimes characterized in terms of very sharp and high peaks in the energy space of the sampled classical trajectories. We have found an extended quantization condition that is responsible for generating these peaks in the prespectrum, which we call the prior quantization condition. Integration of the prespectrum over the trajectory space is supposed to give "zero" (practically a small value of the order of the Planck constant) at a noneigenvalue energy, which is actually a materialization of the destructive interference. Besides, certain finite peaks in the prespectrum survive after the integration to form the true spikes (eigenvalues) in the final spectrum, if they satisfy an additional resonance condition. For these resonance components, the prior quantization condition is reduced to the Einstein-Brillouin-Keller quantization condition. Based on these analyses, we propose a rather conventional filtering technique to efficiently handle tedious computation for destructive interference, and numerically verify that it works well even for multidimensional chaotic systems. This filtering technique is further utilized to extract a few trajectories that dominate an eigenstate of molecular vibration.     

Angular‐Resolved Magnetometry Beyond Triclinic Crystals: Out‐of‐Equilibrium Studies of Cp*ErCOT Single‐Molecule Magnet

Angular‐resolved single‐crystal magnetometry is a key tool to characterise lanthanide‐based materials with low symmetry, for which conjectures based on idealised geometries can be totally misleading. Unfortunately the technique is strictly successful only for triclinic structures, thus reducing significantly its application. By collecting out‐of‐equilibrium magnetisation data the technique was extended to the orthorhombic organometallic Cp*ErCOT single‐molecule magnet (SMM), thus allowing for the first time the reconstruction of the molecular anisotropy tensor notwithstanding the two molecular orientations in the crystal lattice. The results, flanked by state‐of‐the‐art ab initio calculations, confirmed the expected orientation of the molecular easy axis of magnetisation and thus validated the synthetic strategy based on organometallic complexes of a single lanthanide ion.     

Some aspects of data analysis of multi‐angle dynamic light scattering

In dynamic light scattering the signal to noise ratio may become very low because of short measurement times or low intensities. Then the analysis of the data becomes a central point and it is worthwhile to accept some numerical efforts and an increased calculation time caused by more sophisticated data analysis. In the following three aspects of an improved data analysis are discussed for multi‐angle dynamic light scattering. In the first part of this paper, the influence of the correlation of the errors of the autocorrelation time function is considered. With decreasing measurement time the errors of the autocorrelation time function increase. The more the errors increase, however, the more important the error model becomes. On the other hand, with increasing number of photons the correlations of the errors of the autocorrelation time function become important: The non‐diagonal elements of the covariance matrix of the data errors increase and may become of the order of the diagonal elements. In the second part the sensitivity of the nonlinear simultaneous multi‐angle regularization to aberrations in the experimental set‐up is investigated. Therefore, for a given bimodal radii distribution and different scattering angles data were simulated taking into account the finite aperture of the detector as well as the laser light backscattered at the back of the cuvette. This improved model is compared with the classical model, which neglects these aberrations in the experimental setup. Finally, the advantage of the simultaneous regularization method over averaging over single‐angle results is demonstrated. Estimating of the radii distribution from all multi‐angle data at once leads to a higher solution compared to averaging over the single‐angle results.     

Trajectory angle determination in one dimensional single molecule tracking data by orthogonal regression analysis

The quantitative assessment of single molecule diffusion trajectories by orthogonal regression analysis is reported. This analysis is broadly applicable to any single particle tracking experiments in which diffusion along one dimension (1D) is expected. It affords quantitative data on the (in plane) orientation of 1D trajectories, allowing for their absolute orientations to be determined. Histograms depicting the distribution of trajectory angles provide new physical insights into the degree of trajectory alignment, and by inference, materials order. Estimates of the errors in the trajectory angle and particle positioning along each trajectory are also obtained. The angle results are compared to those from single-step angle determinations. The advantages of the regression method include its simplicity and computational efficiency, and the ability to objectively differentiate between 1D and 2D/immobile trajectories. Its utility is demonstrated through analysis of single molecule diffusion trajectories in surfactant-templated mesoporous silica films as probed by wide-field fluorescence microscopy. The trajectory angle histograms obtained provide quantitative data on mean trajectory orientation and the degree of trajectory alignment in distinct populations and sample regions. Mesopore order was quantitatively assessed by implementation of an order parameter,

= 2-1, calculated from the individual trajectory angles in each of four representative sample regions. The results depict the presence of well-ordered domains (from microns to tens of microns in size), all having

≈ 0.9. The latter corresponds to an ≈14° average deviation of the individual trajectories from the mean trajectory (and mesopore) orientation in each domain.     

Model‐based analysis of a dielectrophoretic microfluidic device for field‐flow fractionation

We present the development of a dynamic model for predicting the trajectory of microparticles in microfluidic devices, employing dielectrophoresis, for Hyperlayer field‐flow fractionation. The electrode configuration is such that multiple finite‐sized electrodes are located on the top and bottom walls of the microchannel; the electrodes on the walls are aligned with each other. The electric potential inside the microchannel is described using the Laplace equation while the microparticles' trajectory is described using equations based on Newton's second law. All equations are solved using finite difference method. The equations of motion account for forces including inertia, buoyancy, drag, gravity, virtual mass, and dielectrophoresis. The model is used for parametric study; the geometric parameters analyzed include microparticle radius, microchannel depth, and electrode/spacing lengths while volumetric flow rate and actuation voltage are the two operating parameters considered in the study. The trajectory of microparticles is composed of transient and steady state phases; the trajectory is influenced by all parameters. Microparticle radius and volumetric flow rate, above the threshold, do not influence the steady state levitation height; microparticle levitation is not possible below the threshold of the volumetric flow rate. Microchannel depth, electrode/spacing lengths, and actuation voltage influence the steady‐state levitation height.     

Ultrafast shock compression of PDMS‐based polymers

The shock response of polymers is important for a number of commercial and defense‐related applications, but it is difficult to obtain empirical shock response data over the wide range of preparations and aging conditions typically found in such applications. Ultrafast compression is useful to characterize polymer shock response over a wide range of polymer initial conditions due to the high throughput of this method. To establish greater confidence in ultrafast compression experiments and to characterize the detailed shock response of several variations in a single base polymer, the results of sub‐nanosecond shock compression experiments in ∼5 μm thick layers of the polydimethylsiloxane (PDMS)‐based elastomeric rubbers Sylgard‐184, SE1700, and an unfilled, end‐linked model PDMS network are presented. The results of conventional ultrafast shock etalon measurements to time‐of‐flight measurements for similar thickness layers of irradiated and unirradiated SE1700 are compared. Good agreement between the shock response measured by these two ultrafast shock methods, as well as consistency between ultrafast data and long time scale gas gun data is found. From measurements across a variety of PDMS formulations, a statistically significant variation in the shock response with the quasistatic elastic modulus is presented. Published 2018.^† J. Polym. Sci., Part B: Polym. Phys. 2018 , 56, 827–832     

An Error‐in‐Variables Method for Determining Reactivity Ratios by On‐Line Monitoring of Copolymerization Reactions

Summary: A new error‐in‐variables method was developed to estimate the reactivity ratios in copolymerization systems. It brings the power of automatic, continuous, on‐line monitoring of polymerization (ACOMP) to copolymerization calculations. In ACOMP systems, monomer and polymer concentrations are measured by the monitoring of two independent properties of the system. The reactivity ratios are found by taking into account errors in the monomer concentrations determined from measurements and from calibration of the instruments. All the error sources are taken into account according to the error‐in‐variables method, and their effects are reflected in determining the confidence intervals of the reactivity ratios by the usual error propagation technique.

Distribution of concentrations [a] and [b] for the simulated experiment I. Random errors are 1% of the initial value in both observed variables.     

Proper quantization rule approach to three‐dimensional quantum dots

In this article, we develop a formalism to obtain the energy levels of the electron in a central force potential confined in a spherical quantum dot with radius r_C by the proper quantization rule and the Wentzel‐Kramers‐Brillouin approximation. It is shown that the numerical results are in good agreement with exact solutions. To illustrate this method, we consider the linear harmonic oscillator and Coulomb potential confined within an impenetrable sphere of radius r_C in three dimensions. © 2013 Wiley Periodicals, Inc.     

Changes in electrical resistance of carbon‐black‐filled silicone rubber composite during compression

We studied the changes in the electrical resistance of carbon black filled silicone rubber composite, which is the sensitive element of the flexible force sensor, as a function of time during compression. The experimental results show that there is a sudden increase of the electrical resistance along with the sudden increase of the stress immediately after the compression. When the sample strain is kept constant, the electrical resistance and the stress both decay with time. The data of the stress relaxation and the resistance relaxation both can be fitted by the linear combination of two exponential functions. Based on the shell structure theory, the experimental phenomena are explained from the view that the uniaxial pressure induces the changes in the effective conductive paths. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 2700–2706, 2007     

Plastic deformation of polyamide 6/polypropylene‐g‐acrylic acid blends

Two means of plastic deformation were applied to the poly amide 6/polypropylene‐g‐acrylic acid blends (in two composition 8:2 and 2:8): drawing and plane strain compression in a channel die. X‐ray diffraction pole figures, density measurements, SEM, DMTA were applied for studying the structure and properties of oriented blends. It is concluded that interfaces between blends components are weak elements of the blends even in presence of compatibilizing action of PP‐g‐AA.