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At least 883 records · Page 49Linked to original sources
PubMed2005

Influence of the nonlinearity and dipole strength on the amide I band of protein alpha-helices.

Vibrational energy storage and propagation are simulated in a fully atomic model of an alpha-helix by combining the AMBER force field for proteins with an extended version of the Davydov/Scott model for amide I vibrational transfer [A. Scott, Phys. Rep. 217, 1 (1992)]. Dipole-dipole interactions between transition dipole moments of amide I and its on-site energies are calculated from the corresponding three-dimensional atomic positions. The comparison of the theoretically calculated absorption line shapes with the experimentally measured ones leads to a putative value of the nonlinearity parameter of -30 pN.

Absorption↗
PubMed2006

Simultaneous in situ monitoring of surface and gas species and surface properties by modulation excitation polarization-modulation infrared reflection-absorption spectroscopy: CO oxidation over Pt film.

A method for in situ monitoring of surface and gas species utilizing separately the difference and sum reflectivity of two polarizations, normal and parallel to the surface, measured by polarization-modulation infrared reflection-absorption spectroscopy is presented. Surface and gas-phase spectra were separately but simultaneously obtained from the reflectivities. The technique is combined with modulation excitation spectroscopy to further enhance the sensitivity, and a small-volume cell was designed for this purpose. CO oxidation over a 40 nm Pt film on aluminum was investigated under moderate pressure (atmospheric pressure, 5% CO, and 5%-40% O2) at 373-433 K. The surface species involved in the oxidation process and the gas-phase species, both reactant (CO) and product (CO2), could be simultaneously monitored and analyzed quantitatively. In addition, the reflectivity change of the sample during the reaction was assigned to a near-surface bulk property change, that is, surface reconstruction to the oxide phase. Under an O2-rich atmosphere, two reactive phases, denoted as low- and high-activity phases, were identified. A large amount of atop CO was observed during the low-activity phase, while the adsorbed CO completely disappeared during the high-activity phase. The presence of an infrared-inactive CO2 precursor formed by the reaction between surface oxide and gaseous CO during the high-activity phase was inferred. The desorption of the CO2 precursor is facilitated under a CO-rich atmosphere, most likely, by surface reconstruction to metallic Pt and a competitive adsorption of CO on the surface.

Absorption↗
PubMed2006

Validation of Markov state models using Shannon's entropy.

Markov state models are kinetic models built from the dynamics of molecular simulation trajectories by grouping similar configurations into states and examining the transition probabilities between states. Here we present a procedure for validating the underlying Markov assumption in Markov state models based on information theory using Shannon's entropy. This entropy method is applied to a simple system and is compared with the previous eigenvalue method. The entropy method also provides a way to identify states that are least Markovian, which can then be divided into finer states to improve the model.

Bayes Theorem↗
PubMed2006

Computed lifetimes of metastable states of CO2+.

Highly correlated internally contracted multireference configuration interaction wave functions are used to calculate the potential energy and spin-orbit coupling functions for the lowest electronic states of CO2+ dication. Using these functions, the positions and lifetimes of the corresponding vibronic states are evaluated by means of log-phase-amplitude, stabilization, and complex-scaling methods within the framework of a multichannel Schrodinger analysis. For the first time in the literature, the calculated lifetimes are in good agreement with the experiment, thereby proving the reliability of the predicted characteristics and adequacy of the used theory for a theoretical study of other molecular dications.

Carbon Monoxide↗
PubMed2006

Collective Langevin dynamics of conformational motions in proteins.

Functionally relevant slow conformational motions of proteins are, at present, in most cases inaccessible to molecular dynamics (MD) simulations. The main reason is that the major part of the computational effort is spend for the accurate description of a huge number of high frequency motions of the protein and the surrounding solvent. The accumulated influence of these fluctuations is crucial for a correct treatment of the conformational dynamics; however, their details can be considered irrelevant for most purposes. To accurately describe long time protein dynamics we here propose a reduced dimension approach, collective Langevin dynamics (CLD), which evolves the dynamics of the system within a small subspace of relevant collective degrees of freedom. The dynamics within the low-dimensional conformational subspace is evolved via a generalized Langevin equation which accounts for memory effects via memory kernels also extracted from short explicit MD simulations. To determine the memory kernel with differing levels of regularization, we propose and evaluate two methods. As a first test, CLD is applied to describe the conformational motion of the peptide neurotensin. A drastic dimension reduction is achieved by considering one single curved conformational coordinate. CLD yielded accurate thermodynamical and dynamical behaviors. In particular, the rate of transitions between two conformational states agreed well with a rate obtained from a 150 ns reference molecular dynamics simulation, despite the fact that the time scale of the transition (approximately 50 ns) was much longer than the 1 ns molecular dynamics simulation from which the memory kernel was extracted.

Biophysics↗
PubMed2006

A study of density of states and ground states in hydrophobic-hydrophilic protein folding models by equi-energy sampling.

We propose an equi-energy (EE) sampling approach to study protein folding in the two-dimensional hydrophobic-hydrophilic (HP) lattice model. This approach enables efficient exploration of the global energy landscape and provides accurate estimates of the density of states, which then allows us to conduct a detailed study of the thermodynamics of HP protein folding, in particular, on the temperature dependence of the transition from folding to unfolding and on how sequence composition affects this phenomenon. With no extra cost, this approach also provides estimates on global energy minima and ground states. Without using any prior structural information of the protein the EE sampler is able to find the ground states that match the best known results in most benchmark cases. The numerical results demonstrate it as a powerful method to study lattice protein folding models.

Algorithms↗
PubMed2006

The distance-time relationship over a century of running Olympic performances: A limit on the critical speed concept.

We analyse the evolution of the slope (critical speed) and the y-intercept (anaerobic distance capacity) of the linear distance-time relationship over a century of Olympic running performances. The distance-time relationship of each Olympic Games (1920-2004) was plotted using the performances in the 800-, 1500- and 5000-m track events. Values for critical speed and anaerobic distance capacity were determined by linear modelling. Mean performances for the 800, 1500 and 5000 m were 104.9 +/- 1.5 s (1.4%), 217.2 +/- 2.8 s (1.3%) and 808.9 +/- 18.4 s (2.3%), respectively. Critical speed improved during the first three-quarters of the twentieth century to reach a plateau in 1984. This is in accordance with the literature (Peronnet & Thibault, 1989) and suggests that "human aerobic endurance" has improved within the century (+13.4%) and tends to stabilize. Anaerobic distance capacity was highly variable over the century (coefficient of variation = 9.4%) and did not show a linear improvement over the years as has previously been suggested (Peronnet & Thibault, 1989). This could be due to an artefact in the application of the two-parameter model to only three Olympic performances. A limitation to the use of this linear mathematical model to fit physiological data may have been demonstrated.

Anaerobic Threshold↗
PubMed1998

Physiological profiles of male and female taekwon-do (ITF) black belts.

Baseline physiological and kinanthropometric data were collected for 11 male and 12 female elite taekwon-do athletes from the Czech national team for evaluation of anthropometry, aerobic and anaerobic capacities, strength, visual reaction time, pulmonary function, flexibility and explosive power of the lower limbs (vertical jump). Both male and female taekwon-do black belts demonstrated low adiposity (8.2 and 15.4% fat, BMI 21.9 and 22.0 kg m(-2), respectively), normal reactivity and pulmonary function, above average muscular strength, PWC-170 (3.4 vs 2.7 W kg(-1)) and aerobic power (54 vs 42 ml min(-1) kg(-1)), and a high flexibility (37 and 38 cm) and anaerobic performance (peak power output from a 30 s Wingate test=14.7 and 10.1 W kg(-1); anaerobic capacity=334 and 242 J kg(-1), in males and females, respectively). In male athletes, competitive performance was significantly related to maximum power output and upper limb reaction time only, whereas in females, performance was related to maximum power output and ventilatory threshold level. These variables accounted for 66 and 67% of the performance rank in males and females, respectively. Time-motion analysis of competition taekwon-do fighting (two times 2 min) revealed 3-5 s bouts of maximum exercise alternating with low-intensity periods. This elicits high heart rates (100% HRmax) and lactate responses (11.4 mmol l(-1) = 81% LAmax), which agrees well with the physiological characteristics of taekwon-do black belts measured in laboratory exercise tests.

Adolescent↗
PubMed1999

Seven-year clinical follow-up after lumbar disc surgery: results and predictors of outcome.

This study evaluates the 7-year outcome of lumbar disc surgery and the predictive value of pre- and perioperative risk factors. The 7-year follow-up rate of a sample of 122 patients was 93% (n = 114). Six per cent of the patients had undergone repeat surgery. Approximately 90% reported that they were satisfied with having undergone surgery. The clinical outcome was evaluated in 96 patients (54 men and 42 women) by means of patient-scores (VAS) of low back and leg pain, and a Clinical Overall Score (COS). In multivariate regression analyses, women were shown to have poorer outcome than men. Preoperative psychological distress and impaired fibrinolytic activity were predictors of poor 7-year outcome. Age, weight, smoking habits and physical fitness had no statistically significant prognostic value. Whether the patients were operated for one or two herniated discs, or whether surgery involved a full or partial laminectomy, did not influence the outcome significantly.

Adaptation, Psychological↗
PubMed2001

Comparison of parenting stress between Malaysian mothers of four-year-old very low birthweight and normal birthweight children.

UNLABELLED: A study was carried out to compare parenting stress between 116 mothers of very low birthweight (VLBW) children and 96 mothers of normal birthweight (NBW) children at 4 y of age, using the Parenting Stress Index (PSI). Multiple regression analysis was used to determine factors associated with child-domain stress (CDS) and parent-domain stress (PDS). There was a significantly higher proportion (39.7%) of mothers of VLBW children with high CDS scores >90th percentile than mothers of NBW children (20.8%). No significant differences were observed for PDS scores. Lower intelligence quotient (IQ) scores and adverse child behaviour, as evidenced by higher Child Behavior Checklist (CBCL) scores, were significantly associated with higher CDS scores (p < 0.001). Factors associated with higher PDS scores were higher CBCL scores (p < 0.001), mothers who were the primary caregivers (p < 0.001), male sex (p = 0.018) and lower level of maternal education (p = 0.048). These factors remained statistically significant even when physically and cognitively impaired children were excluded from the analysis. CONCLUSION: Specific child characteristics and the social environment appear to have a greater impact on parenting stress than the biological risk of VLBW birth per se.

Adult↗
PubMed2005

The effect of an ergonomic intervention on musculoskeletal, psychosocial, and visual strain of VDT data entry work: the United States part of the international study.

The United States MEPS (musculoskeletal--eyestrain--psychosocial--stress) study consisted of 1 group of 28 female data entry operators. The intervention was in 3 parts: workstation redesign (including advanced ergonomic chairs, motorized adjustable workstations, advanced adjustable keyboards, adjustable copyholders, adjustable footrests, monitor support surfaces) and ergonomic training/coaching and corrective lenses. After the intervention, statistically significant reductions in physical signs (trigger points, neck and shoulder mobility), subjective reports of intensity and frequency of musculoskeletal pain, and subjective reports of visual problems were observed. Static load during the work sample, as assessed by experts, improved after the intervention as did measured postural angles of head and trunk and subjective assessment of users of ergonomic characteristics of the workplaces. For all of these measures, improvements observed 1 month after intervention were also observed in the 1-year follow-up. Trapezius load, as assessed by electromyography (EMG), decreased after intervention, but then increased in the follow-up. The increase was interpreted as a calibration problem.

Adult↗
PubMed2005

Neuropsychological functioning and MMPI-2 profiles in chronic neck pain: a comparison of whiplash and non-traumatic groups.

We measured the neuropsychological functioning in 42 patients with chronic neck pain, 21 with a whiplash trauma and 21 without previous trauma. Subjectively, the whiplash group was more forgetful and had more concentration difficulties compared with the non-traumatic group. The neuropsychological tests did not reveal any differences between the two groups and a reference group of healthy individuals. Thus, chronic neck pain did not seem to interfere with neuropsychological functioning. The personality traits assessed with MMPI-2 in our 42 patients with chronic neck pain differed significantly from the normals on several scales. We also found that the whiplash group had more divergent test results than the non-traumatic group on the MMPI-2 test. Thus, it seems that the health status in those with chronic neck pain is closely linked to separate personality traits. It is concluded that the subjective complaints and poor performance in patients with chronic neck pain may be associated to somatization and inadequate coping, especially in chronic whiplash patients.

Adult↗