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Exploration of NVE classical trajectories as a tool for molecular crystal structure prediction, with tests on ice polymorphs.

Following an initial Communication [Buch et al., J. Chem. Phys. 123, 051108 (2005)], a new molecular-dynamics-based approach is explored to search for candidate crystal structures of molecular solids corresponding to minima of the enthalpy. The approach is based on the observation of phase transitions in an artificial periodic system with a small unit cell and relies on the existence of an optimal energy range for observing freezing to low-lying minima in the course of classical trajectories. Tests are carried out for O structures of nine H2O-ice polymorphs. NVE trajectories for a range of preimposed box shapes display freezing to the different crystal polymorphs whenever the box dimensions approximate roughly the appropriate unit cell; the exception is ice II for which freezing requires unit cell dimensions close to the correct ones. In an alternate version of the algorithm, an initial box shape is picked at random and subsequently readjusted at short trajectory intervals by enthalpy minimization. Tests reveal the existence of ice forms which are "difficult" and "easy" to locate in this way. The former include ice IV, which is also difficult to crystallize experimentally from the liquid, and ice II, which does not interface with the liquid in the phase diagram. On the other hand, the latter crystal search procedure located successfully the remaining seven ice polymorphs, including ice V, which corresponds to the most complicated structure of all ice phases, with a monoclinic cell of 28 molecules.

Journal Article↗

Identifying reactive trajectories using a moving transition state.

A time-dependent no-recrossing dividing surface is shown to lead to a new criterion for identifying reactive trajectories well before they are evolved to infinite time. Numerical dynamics simulations of a dissipative anharmonic two-dimensional system confirm the efficiency of this approach. The results are compared to the standard fixed transition state dividing surface that is well-known to suffer from recrossings and therefore requires trajectories to be evolved over a long time interval before they can reliably be classified as reactive or nonreactive. The moving dividing surface can be used to identify reactive trajectories in harmonic or moderately anharmonic systems with considerably lower numerical effort or even without any simulation at all.

Algorithms↗

Semiclassical nonadiabatic dynamics based on quantum trajectories for the O(3P,1D) + H2 system.

The O(3P,1D) + H2 --> OH + H reaction is studied using trajectory dynamics within the approximate quantum potential approach. Calculations of the wave-packet reaction probabilities are performed for four coupled electronic states for total angular momentum J = 0 using a mixed coordinate/polar representation of the wave function. Semiclassical dynamics is based on a single set of trajectories evolving on an effective potential-energy surface and in the presence of the approximate quantum potential. Population functions associated with each trajectory are computed for each electronic state. The effective surface is a linear combination of the electronic states with the contributions of individual components defined by their time-dependent average populations. The wave-packet reaction probabilities are in good agreement with the quantum-mechanical results. Intersystem crossing is found to have negligible effect on reaction probabilities summed over final electronic states.

Journal Article↗

Quasiclassical trajectory study of the Cl+CH4 reaction dynamics on a quadratic configuration interaction with single and double excitation interpolated potential energy surface.

An ab initio interpolated potential energy surface (PES) for the Cl+CH(4) reactive system has been constructed using the interpolation method of Collins and co-workers [J. Chem. Phys. 102, 5647 (1995); 108, 8302 (1998); 111, 816 (1999); Theor. Chem. Acc. 108, 313 (2002)]. The ab initio calculations have been performed using quadratic configuration interaction with single and double excitation theory to build the PES. A simple scaling all correlation technique has been used to obtain a PES which yields a barrier height and reaction energy in good agreement with high level ab initio calculations and experimental measurements. Using these interpolated PESs, a detailed quasiclassical trajectory study of integral and differential cross sections, product rovibrational populations, and internal energy distributions has been carried out for the Cl+CH(4) and Cl+CD(4) reactions, and the theoretical results have been compared with the available experimental data. It has been shown that the calculated total reaction cross sections versus collision energy for the Cl+CH(4) and Cl+CD(4) reactions is very sensitive to the barrier height. Besides, due to the zero-point energy (ZPE) leakage of the CH(4) molecule to the reaction coordinate in the quasiclassical trajectory (QCT) calculations, the reaction threshold falls below the barrier height of the PES. The ZPE leakage leads to CH(3) and HCl coproducts with internal energy below its corresponding ZPEs. We have shown that a Gaussian binning (GB) analysis of the trajectories yields excitation functions in somehow better agreement with the experimental determinations. The HCl(v'=0) and DCl(v'=0) rotational distributions are as well very sensitive to the ZPE problem. The GB correction narrows and shifts the rotational distributions to lower values of the rotational quantum numbers. However, the present QCT rotational distributions are still hotter than the experimental distributions. In both reactions the angular distributions shift from backward peaked to sideways peaked as collision energy increases, as seen in the experiments and other theoretical calculations.

Journal Article↗

Maternal plasma corticotropin-releasing hormone trajectories vary depending on the cause of preterm delivery.

OBJECTIVE: Although second trimester maternal plasma corticotropin-releasing hormone concentrations are elevated in women who are destined to deliver preterm, the sensitivity and positive predictive value of an individual test of corticotropin-releasing hormone concentration is low. This poor screening performance may be due in part to the observation that the causes of preterm delivery are heterogenous, with potentially different effects on corticotropin-releasing hormone production. We have reanalyzed data from a previous cohort of women with multiple samplings to determine whether the trajectory of increase of placental corticotropin-releasing hormone provided more information than did a single sample. STUDY DESIGN: In this cohort, where 2 to 4 samples that had been assayed for corticotropin-releasing hormone were available on 305 women, the general form of the exponential equation y = ae(bt) was fitted to the corticotropin-releasing hormone data of each individual by the Gauss-Newton nonlinear least squares method, which generated the parameters, y-intercept and rate of rise, in corticotropin-releasing hormone concentration for each woman. Nonparametric statistical techniques, including bootstrapping, were applied to compare the results for the group of women who delivered at term with the group of women who delivered spontaneously preterm and the group of women who were delivered preterm by induction or cesarean delivery because of obstetric indication. RESULTS: The 3 clinically defined groups have significantly different parameters, y-intercept and rate of rise, which describe the corticotropin-releasing hormone trajectory. The group that delivered preterm because of obstetric indications had a similar mean y-intercept but significantly greater mean rate of rise in corticotropin-releasing hormone concentration than the term group (0.3491 vs 0.1788; 95% CI, 0.2331-0.4615 vs 0.1394-0.2330). The group that delivered spontaneously preterm had a significantly greater mean y-intercept than the group that delivered preterm because of obstetric indication (17.08 vs 1.83; 95% CI, 5.89-28.43 vs 0.03-5.19) but a similar mean rate of rise to the group that delivered at term. CONCLUSION: These data suggest that spontaneous preterm delivery is associated with an abnormal setting of the production of corticotropin-releasing hormone that is present from very early in pregnancy, although women who experience an induced preterm delivery are characterized by rapidly rising placental corticotropin-releasing hormone concentrations. These data further suggest that clinical abnormalities that are associated with preterm delivery by induction or cesarean delivery are associated with abnormalities that lead to a rapidly increasing corticotropin-releasing hormone concentrations. Trajectories for corticotropin-releasing hormone provide information beyond that obtained from a single sample.

Cesarean Section↗

The trajectory effect in intermodal temporal order judgments.

Subjects judged which one of two patterns, a visual or a tactile pattern, had been presented first. The visual and tactile displays were placed in close spatial proximity. The patterns appeared to move across their respective displays. Although irrelevant to the temporal order judgment (TOJ), the direction of motion of the patterns--the trajectory--affected the judgments. When the leading pattern was moving towards the trailing pattern (consistent movement), subjects tended to judge it, correctly, as leading. When the leading pattern was moving away from the trailing pattern (inconsistent movement), subjects tended to judge it, incorrectly, as trailing. Changing the spatial position of the arrays such that the pattern trajectories were no longer towards one another eliminated the effect of movement on TOJs. Although there was a substantial difference in performance on consistent and inconsistent trials, there were no differences in subjects' ratings of their performances. The results demonstrate that the trajectory effect can be obtained multimodally. The issues whether the effect of motion alters the perceived temporal separation between the visual and tactile patterns, and whether the visual and tactile patterns are represented by a common framework, are discussed.

Adult↗

Phylogeny of protein-folding trajectories reveals a unique pathway to native structure.

To scrutinize how a protein folds at atomic resolution, we performed 200 molecular dynamics simulations (each of 50 ns) of the miniprotein Trp-cage on the computational grid. Within the trajectories, 58 folding and 31 unfolding events were identified and subjected to extensive comparison and classification. Based on an analogy with biological sequences, the folding and unfolding trajectories (arrays of sequential snapshots of structures) were aligned by dynamic programming allowing gaps. A phylogenetic tree derived from the alignments revealed four distinct groups of the trajectories, characterized by the Trp side-chain motions and the main-chain motions. It was found that only one group attained the native structure and that the other three led to pseudonative structures having the correct main-chain trace but different nonnative Trp side-chain rotamers, indicating that those four folded structures were each attained through a unique folding pathway.

Computational Biology↗

Evaluation of mortality trajectories in evolutionary biodemography.

An important task in evolutionary biodemography is to determine the schedule of survival and reproduction as the outcome of natural selection acting on life histories. We do this by using a model in which the state of the organism is characterized by mass and accumulated damage, both of which are affected by activity and which affect the rate of mortality. Focusing on growth during the juvenile period, we determine the level of activity that maximizes reproductive value. Given this, we are able to project forward and determine the trajectory of mortality for an individual following the optimal life history, given the physiological and reproductive parameters. We show that there are two main classes of juvenile mortality trajectories: U-shaped (such as recently reported for prereproductive humans) and steadily declining and we are able to connect the shape of the mortality trajectory with the physiological and reproductive parameters characterizing the life history. Our work shows the importance of state in models of evolutionary biodemography and the power of modern computational methods to illuminate biological process.

Aging↗

Minimum Muscle-Tension Change Trajectories Predicted by Using a 17-Muscle Model of the Monkey's Arm.

Four computational problems to be solved for visually guided reaching movements, hand path, and trajectory formations, coordinate transformation, and calculations of muscle tensions are ill-posed in redundant biological control systems. These problems are ill-posed in the sense that there exist an infinite number of possible solutions. In this article, it is shown that the nervous system can solve those problems simultaneously by imposing a single global constraint: finding the smoothest muscle- tension trajectory that satisfies the desired final hand position, velocity, and acceleration. Horizontal trajectories were simulated by using a l7-muscle model of the monkey's arm as the controlled object. The simulations predicted gently curved hand paths for lateral hand movements and for movements from the side of the body to the front, and a roughly straight hand path for anterioposterior movements. The tangential hand velocities were roughly bell shaped. The simulated results were in agreement with the actual biological movements.

Journal Article↗

Adolescent alcohol-use trajectories in the transition from high school.

A cohort of 3300 students from high schools across Victoria, Australia, were surveyed regarding their patterns of alcohol consumption from mid-1993 to 1995. The first wave of data was collected halfway through the students' final year of school (year 12). Students were then resurveyed 3 months following school completion and on two subsequent occasions, each separated by 6-month intervals. Analysis of the four waves of data indicated that five longitudinal patterns (trajectories) characterized temporal trends in male and female alcohol use through the transition from high school. Stable non-use trajectories were evident for 17% of males and 16% of females. Trajectories of less than weekly use characterized 45% of females and 46% of males, and showed little tendency to escalate toward harmful use. Among those using alcohol on a weekly or more frequent basis in high school, with few exceptions, use continued with at least the same frequency, but the quantity of alcohol consumed tended to escalate over time toward harmful levels. Overall, findings indicate that patterns of alcohol use tend to be stable over time, and more frequent alcohol use during the final year of high school tends to precede potentially harmful alcohol use following high school. Encouraging those high school students who consume alcohol once per week or more often to use alcohol on a less than weekly basis may be a valuable yet neglected harm minimization strategy.

Adolescent↗

Age of acquisition persists as the main factor in picture naming when cumulative word frequency and frequency trajectory are controlled.

The aim of this study was to address the effect of objective age of acquisition (AoA) on picture-naming latencies when different measures of frequency (cumulative and adult word frequency) and frequency trajectory are taken into account. A total of 80 Spanish participants named a set of 178 pictures. Several multiple regression analyses assessed the influence of AoA, word frequency, frequency trajectory, object familiarity, name agreement, image agreement, image variability, name length, and orthographic neighbourhood density on naming times. The results revealed that AoA is the main predictor of picture-naming times. Cumulative frequency and adult word frequency (written or spoken) appeared as important factors in picture naming, but frequency trajectory and object familiarity did not. Other significant variables were image agreement, image variability, and neighbourhood density. These results (a) provide additional evidence of the predictive power of AoA in naming times independent of word-frequency and (b) suggest that image variability and neighbourhood density should also be taken into account in models of lexical production.

Adult↗

Juvenile drug use and delinquency: youths' accounts of their trajectories.

This study focuses mainly on youths' opinions about their delinquency and drug use trajectories. A qualitative approach was taken for this phenomenological research. The life account method was used to conduct a total of 62 interviews: 36 boys and 26 girls recruited in youth detention and addiction treatment centers, youth centers, high schools, and on the streets of three cities in Quebec between 1996 and 2002. Thematic analysis was used, and the deviant trajectories of the youths are broken down into five stages. Our study provides an incomplete view of these youths' more or less deviant trajectories. It would be interesting to do a follow-up study.

Adolescent↗

A shift-invariant filtered backprojection (FBP) cone-beam reconstruction algorithm for the source trajectory of two concentric circles using an equal weighting scheme.

In this paper, a shift-invariant filtered backprojection cone-beam image reconstruction algorithm is derived, based upon Katsevich's general inversion scheme, and validated for the source trajectory of two concentric circles. The source trajectory is complete according to Tuy's data sufficiency condition and is used as the basis for an exact image reconstruction algorithm. The algorithm proceeds according to the following steps. First, differentiate the cone-beam projection data with respect to the detector coordinates and with respect to the source trajectory parameter. The data are then separately filtered along three different orientations in the detector plane with a shift-invariant Hilbert kernel. Eight different filtration groups are obtained via linear combinations of weighted filtered data. Voxel-based backprojection is then carried out from eight sets of view angles, where separate filtered data are backprojected from each set according to the backprojection sets' associated filtration group. The algorithm is first derived for a scanning configuration consisting of two concentric and orthogonal circles. By performing an affine transformation on the image object, the developed image reconstruction algorithm has been generalized to the case where the two concentric circles are not orthogonal. Numerical simulations are presented to validate the reconstruction algorithm and demonstrate the dose advantage of the equal weighting scheme.

Algorithms↗

Internal models and the construction of time: generalizing from state estimation to trajectory estimation to address temporal features of perception, including temporal illusions.

The question of whether time is its own best representation is explored. Though there is theoretical debate between proponents of internal models and embedded cognition proponents concerning whether the world is its own best model, proponents of internal models are often content to let time be its own best representation. This happens via the time update of the model that simply allows the model's state to evolve along with the state of the modeled domain. I argue that this is neither necessary nor advisable. I show that this is not necessary by describing how internal modeling approaches can be generalized to schemes that explicitly represent time by maintaining trajectory estimates rather than state estimates. Though there are a variety of ways this could be done, I illustrate the proposal with a scheme that combines filtering, smoothing and prediction to maintain an estimate of the modeled domain's trajectory over time. I show that letting time be its own representation is not advisable by showing how trajectory estimation schemes can provide accounts of temporal illusions, such as apparent motion, that pose serious difficulties for any scheme that lets time be its own representation.

Brain↗

Interlocking trajectories of loss-related events and depressive symptoms among elders.

OBJECTIVES: As people age, their peers (who are also aging) become increasingly susceptible to health decline and death, implying potential growth in stressful loss-related events over time for the individual. Yet little research has examined trajectories of stress and their relationship to trajectories of depression among elders. The purpose of this research was to determine whether growth in loss-related events occurs for elders and whether stress growth is related to the well-known growth in depressive symptomatology in later life. METHODS: Three waves of National Institute on Aging Established Populations for Epidemiologic Studies of the Elderly (Duke University site) data were used in the analyses. Latent growth curve models were estimated for stress, for depressive symptoms, and for stress predicting depression net of several covariates. RESULTS: Findings include that (a) loss-events evidence clear growth across age at the aggregate level, but with much variation within the sample, and (b) variation in growth in stress is strongly related to variation in growth in depressive symptoms. DISCUSSION: The results suggest that stress in later life may be conceived of as a growth process, with strong consequences for trajectories of mental health.

Adaptation, Psychological↗

Illness trajectories in Mexican children with juvenile idiopathic arthritis and their parents.

BACKGROUND: We hypothesize that the qualitative approach of socio-cultural aspects in children with juvenile idiopathic arthritis (JIA) and their parents would improve the understanding of their illness. OBJECTIVE: To explain the phenomenon of experiencing JIA within a specific cultural context. METHODS: The theoretical position of this research was based on the substantive theories of suffering, explanatory models and illness experience. Its design was that of qualitative field, and its analysis followed the interpretative grounded theory methodology. Data were collected by in-depth interviews and notes; tape recordings were transcribed verbatim, read and imported into the ATLAS/ti 4.2 software. Data conceptualization, categorization and interpretation were based on the constant comparison method. RESULTS: A total of 16 adults and six children from 10 families were interviewed. 'Pilgrimage' (metaphorically referred by some of the parents) was a major code in the study that reflected the religious reference to the trajectory of pain, faith and hope. For children, pilgrimage was conformed by immediate concepts; for parents, by historical and immediate experiences influenced by JIA subtype. Pilgrimage was consistent with the model of the illness trajectory theory, which conceptually relates to the idea that the course of chronic diseases is variable and modifiable throughout time. CONCLUSION: The qualitative approach of JIA provides wide and deep information on the perception that children and parents have about the disease. The illness trajectory theory corresponds to pilgrimage, the theoretical model for JIA in this study.

Adolescent↗

Developmental trajectories of cocaine-and-other-drug-exposed and non-cocaine-exposed children.

Few data are available concerning the trajectories of mental and motor development across time for cocaine-exposed children compared with others. Findings are presented from individual group curve analyses of the mental and motor development measured by the Bayley Scales of Infant Development-II (BSID-II) on repeated visits from 3 through 36 months of a group of prenatally cocaine-and-other-drug-exposed children (n = 265) compared with those exposed to no drugs (n = 129) or no-cocaine-but-other-drugs (n = 66), including alcohol and/or tobacco. Across time, there was a general decline in motor performance but cocaine-exposed-infants showed a trend toward a greater decrease than children in the other two comparison groups. For mental performance, there was also a decline across age but only through 24 months and no differences in the trajectory of the cocaine-exposed group compared to the other two. And, across all assessment ages, cocaine-exposed-infants showed lower BSID-II mental performance compared to both non-drug and non-cocaine-exposed children. Results suggest that prenatally cocaine-exposed children show delayed developmental indices, particularly in their mental performance, but their trajectories across time are similar to those from impoverished, non-cocaine-exposed groups.

Child↗

Use of the anatomic trajectory for thoracic pedicle screw salvage after failure/violation using the straight-forward technique: a biomechanical analysis.

STUDY DESIGN: A biomechanical study of cadaver vertebrae to determine the feasibility of obtaining adequate thoracic pedicle screw fixation in a salvage situation. OBJECTIVE To investigate the ability to safely place a thoracic pedicle screw with adequate maximal insertional torque (MIT) using the anatomic trajectory (AT) (directed along the true anatomic axis of the pedicle) after purposeful failure/medial violation of the pedicle using the straight-forward trajectory (ST) (paralleling the vertebral endplate). SUMMARY AND BACKGROUND DATA: Failure to place a pedicle screw at an intended segment of the thoracic spine may theoretically render the level uninstrumented, because pedicle hook placement may be unsafe and the transverse process may be fractured. An alternative pedicle screw insertion technique, if biomechanically sound in this situation, may present an excellent alternative for critical instrumentation levels. MATERIALS AND METHODS: Fixed-head 5.0 mm stainless steel pedicle screws were placed using the ST and MIT was recorded after determination of bone mineral density (BMD) with dual-energy radiograph absorptiometry (DEXA) scanning. Purposeful screw malposition and critical pedicle wall failure were performed, followed by salvage placement of the screw using the AT. Insertional torque was recorded for each screw revolution with a digital torque wrench and MIT was again recorded to compare the MIT obtainable in the salvage situation. RESULTS: BMD for the vertebrae averaged 732 g/cm2 (620-884 g/cm2). The MIT for the straight-forward technique without pedicle violation was 2.61 +/- 0.19 (SE) inches per pound, whereas that of the salvage procedure after medial wall violation (AT) averaged 1.62 +/- 0.12 (SE) inches per pound. Therefore, the AT achieved 62% (P = 0.027) of the fixation strength (in terms of MIT) during salvage after failure/medial violation of the pedicle. MIT for both the ST* and AT trajectories correlated with both global BMD of the vertebrae (*P = 0.008; P = 0.004) and regional BMD of the vertebral body (*P = 0.044; P = 0.023). CONCLUSIONS: The AT achieved 62% (P = 0.027) of the MIT during salvage of a failed/violated pedicle. BMD correlated with both the initial and salvage techniques. The AT provides adequate fixation in a salvage situation and may be safely used to provide segmental fixation at critical levels.

Absorptiometry, Photon↗