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At least 991 records · Page 55Linked to original sources
PubMed2006

Probing lipid vesicles by bimolecular association and dissociation trajectories of single molecules.

Vesicles prepared by DMPC (1,2-dimyristoyl-sn-glycero-3-phosphocholine) and SOPC (1-stearoyl-2-oleoyl-sn-glycero-3-phosphocholine) lipid molecules having sizes smaller than the diffraction-limited focused laser beam have been used to confine single molecules in the laser focus. The confinement of single molecules in a volume smaller than the focused laser beam leads to a Gaussian distribution of single molecule fluorescence intensity. The interactions of single Nile Red molecules with DMPC and SOPC lipid bilayers were studied by single molecule fluorescence confocal microscopy. Nile Red molecules were observed to associate with and dissociate from individual DMPC and SOPC vesicles adsorbed on a glass surface, generating on-and-off fluctuations in a fluorescence signal representing a very low noise two-state trajectory. Off-time statistics were used to investigate the mean radius of the vesicles and the size distribution functions. The means of the on-time distributions of Nile Red in DMPC and SOPC vesicles were significantly different. The association and dissociation reactions of single Nile Red molecules with a vesicle have been studied. Features of the bimolecular interaction between the probe Nile Red and the vesicle were evaluated from the uncorrelated mean on-time and vesicle radius distributions, and the linear Nile Red concentration dependence of the mean off-time. Nile Red is shown to be a useful probe of the structural fluctuations and heterogeneity of these membrane structures, and it is a useful model with which to directly study a diffusion-influenced reversible bimolecular reaction.

Dimyristoylphosphatidylcholine↗
PubMed2005

Quasiclassical trajectory study of the O(3P) + CH4 --> OH + CH3 reaction with a specific reaction parameters semiempirical Hamiltonian.

We present a theoretical study of the O(3P) + CH4 --> OH + CH3 reaction using electronic structure, kinetics, and dynamics calculations. We calculate a grid of ab initio points at the PMP2/AUG-cc-pVDZ level to characterize the potential energy surface in regions of up to 1.3 eV above reagents. This grid of ab initio points is used to derive a set of specific reaction parameters (SRP) for the MSINDO semiempirical Hamiltonian. The resulting SRP-MSINDO Hamiltonian improves the quality of the standard Hamiltonian, particularly in regions of the potential energy surface beyond the minimum-energy reaction path. Quasiclassical-trajectory calculations are used to study the reaction dynamics with the original and the improved MSINDO semiempirical Hamiltonians, and a prior surface. The SRP-MSINDO semiempirical Hamiltonian yields OH rotational distributions in agreement with experimental results, improving over the results of the other surfaces. Thermal rate constants estimated with Variational Transition State Theory using the SRP-MSINDO Hamiltonian are also in agreement with experiments. Our results indicate that reparametrized semiempirical Hamiltonians are a good alternative to generating potential energy surfaces for accurate dynamics studies of polyatomic reactions.

Journal Article↗
PubMed2005

Biased sampling of nonequilibrium trajectories: can fast switching simulations outperform conventional free energy calculation methods?

We have investigated the maximum computational efficiency of reversible work calculations that change control parameters in a finite amount of time. Because relevant nonequilibrium averages are slow to converge, a bias on the sampling of trajectories can be beneficial. Such a bias, however, can also be employed in conventional methods for computing reversible work, such as thermodynamic integration or umbrella sampling. We present numerical results for a simple one-dimensional model and for a Widom insertion in a soft sphere liquid, indicating that, with an appropriately chosen bias, conventional methods are in fact more efficient. We describe an analogy between nonequilibrium dynamics and mappings between equilibrium ensembles, which suggests that the practical inferiority of fast switching is quite general. Finally, we discuss the relevance of adiabatic invariants in slowly driven Hamiltonian systems for the application of Jarzynski's theorem.

Chemistry, Physical↗
PubMed2005

Quasiclassical trajectory study of energy transfer and collision-induced dissociation in hyperthermal Ar + CH4 and Ar + CF4 collisions.

We present a study of energy transfer in collisions of Ar with methane and perfluoromethane at hyperthermal energies (E(coll) = 4-10 eV). Quasiclassical trajectory calculations of Ar + CX(4) (X = H, F) collisions indicate that energy transfer from reagents' translation to internal modes of the alkane molecule is greatly enhanced by fluorination. The reasons for the enhancement of energy transfer upon fluorination are shown to emerge from a decrease in the hydrocarbon vibrational frequencies of the CX(4) molecule with increasing the mass of the X atom, and to an increase of the steepness of the Ar-CX(4) intermolecular potential. At high collision energies, we find that the cross section of Ar + CF(4) collisions in which the amount of energy transfer is larger than needed to break a C-F bond is at least 1 order of magnitude larger than the cross sections of Ar + CH(4) collisions producing CH(4) with energy above the dissociation limit. In addition, collision-induced dissociation is detected in short time scales in the case of the fluorinated species at E(coll) = 10 eV. These results suggest that the cross section for degradation of fluorinated hydrocarbon polymers under the action of nonreactive hyperthermal gas-phase species might be significantly larger than that of hydrogenated hydrocarbon polymers. We also illustrate a practical way to derive intramolecular potential energy surfaces for bond-breaking collisions by improving semiempirical Hamiltonians based on grids of high-quality ab initio calculations.

Journal Article↗
PubMed2005

Quasiclassical trajectory study of the F + CH4 reaction dynamics on a dual-level interpolated potential energy surface.

An ab initio interpolated potential energy surface (PES) for the F + CH4 reactive system has been constructed using the interpolation method of Collins and co-workers. The ab initio calculations have been performed using second-order Möller-Plesset (MP2) perturbation theory to build the initial PES. Scaling all correlation (SAC) methodology has been employed to improve the ab initio calculations and to construct a dual-level PES. Using this PES, a detailed quasiclassical trajectory study of integral and differential cross sections, product rovibrational populations and internal energy distributions has been carried out for the F + CH4 and F + CD4 reactions and the theoretical results have been compared with the available experimental data.

Journal Article↗
PubMed2006

Quasiclassical trajectory study of the collision-induced dissociation dynamics of Ar + CH3SH+ using an ab initio interpolated potential energy surface.

Classical trajectory calculations have been performed to investigate the collision-induced dissociation (CID) of the CH(3)SH(+) cation with Ar atoms. A new intramolecular potential energy surface for the CH(3)SH(+) cation is evaluated by interpolation of 3000 ab initio data points calculated at the MP2/6-311G(d,p) level of theory. The new potential energy surface includes seven accessible dissociation channels of the cation. The present QCT calculations show that migration of hydrogen atoms, leading to the rearrangement CH(3)SH(+) <--> CH(2)SH(2)(+), is significant at the collision energies considered (6.5-34.7 eV) and that the formation of CH(3)(+), CH(3)S(+), and CH(2)(+) cations takes place primarily by a "shattering" mechanism in which the products are formed just after the collision. The theoretical product abundances are found to be in qualitative agreement with the experimental data. However, at high collision energies, the calculated total cross sections for the formation of CH(3)(+) and CH(2)SH(+) cations are noticeably larger than the experimental determinations. Several features of the dynamics of the CID processes are discussed.

Journal Article↗
PubMed2006

A quasiclassical trajectory study of collisional energy transfer and dissociation in He + H2(v,j) using a new potential energy surface.

Quasiclassical trajectories for He + H2 were carried out using the recent ab initio potential of Boothroyd, Martin, and Peterson (J. Chem. Phys. 2003, 119, 3187) and results for the 348 (v, j) states of H2 are compared to those of earlier calculations that used the potential of Wilson, Kapral, and Burns (Chem. Phys. Lett. 1974, 24, 4884). Examined are the cross sections for energy transfer and dissociation, the extent of threshold elevation, and the interconversion of vibrational and rotational energy. Implications for modeling the interstellar medium are discussed.

Journal Article↗
PubMed2005

Dynamics of bimolecular reactions of vibrationally highly excited molecules: quasiclassical trajectory studies.

Excitation functions from quasiclassical trajectory calculations on the H + H2O --> OH + H2, H + HF --> F + H2, and H + H'F --> H' + HF reactions indicate a different behavior at low and high vibrational excitation of the breaking bond. When the reactant tri- or diatomic molecule is in vibrational ground state or in a low vibrationally excited state, all these reactions are activated; i.e., there is a nonzero threshold energy below which there is no reaction. In contrast, at high-stretch excited-states capture-type behavior is observed; i.e., with decreasing translational energy the reactive cross-section diverges. The latter induces extreme vibrational enhancement of the thermal rate consistent with the experiments. The results indicate that the speed-up observed at high vibrational excitation is beyond the applicability of Polanyi's rules in their common form; instead, it can be interpreted in terms of an attractive potential acting on the attacking H atom when it approaches the reactant with a stretched X-H bond.

Journal Article↗
PubMed2006

Zero-point energy constraint in quasi-classical trajectory calculations.

A method to constrain the zero-point energy in quasi-classical trajectory calculations is proposed and applied to the Henon-Heiles system. The main idea of this method is to smoothly eliminate the coupling terms in the Hamiltonian as the energy of any mode falls below a specified value.

Journal Article↗
PubMed2006

Trajectory dynamics study of collision-induced dissociation of the Ar + CH4 reaction at hyperthermal conditions: vibrational excitation and isotope substitution.

We investigate the role of vibrational energy excitation of methane and two deuterated species (CD(4) and CH(2)D(2)) in the collision-induced dissociation (CID) process with argon at hyperthermal energies. The quasi-classical trajectory method has been applied, and the reactive Ar + CH(4) system has been modeled by using a modified version of the CH(4) potential energy surface of Duchovic et al. (J. Phys. Chem. 1984, 88, 1339) and the Ar-CH(4) intermolecular potential function obtained by Troya (J. Phys. Chem. A 2005, 109, 5814). This study clearly shows that CID is markedly enhanced with vibrational excitation and, to a lesser degree, with collision energy. In general, CID increases by exciting stretch vibrational modes of the reactant molecule. For the direct dissociation of CH(4), however, the CID cross sections appear to be essentially independent of which vibrational mode is initially excited. In all situations studied, the CID cross sections are always greater for the Ar + CD(4) reaction than for the Ar + CH(4) one, the Ar + CH(2)D(2) being an intermediate situation. A detailed analysis of the energy transfer processes, including their relation with CID, is also presented.

Journal Article↗
PubMed2006

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.

Dimyristoylphosphatidylcholine↗
PubMed2006

Methods to track single-molecule trajectories.

Methods are discussed to track single molecules in planar-supported phospholipid bilayers. Mainly, these methods constitute optimizations for a low signal-to-noise ratio and for the dim optical characteristics of single molecules. Algorithmic modifications to compensate and correct for misidentifications and misassignments are also described. One key advance, which exchanges the typically fragmented reconstruction of the molecules' motion for more complete trajectories, is the incorporation of information about the molecules' past and future positions into the tracking. Although the main point of these methods is to aid in extending methods of object tracking to the single-molecule regime, they may also find use in other situations where the signal-to-noise ratio is low.

Journal Article↗
PubMed2000

Sexual identity trajectories among sexual-minority youths: gender comparisons.

The present investigation explored gender differences in sexual identity development--first same-sex attractions, self-labeling, same-sex sexual contact, and disclosure--among 164 sexual-minority young adults. Based on interviews, results indicated the value of assessing gender differences in the context, timing, spacing, and sequencing of sexual identity milestones. Adolescent males had an earlier onset of all milestones except disclosure. The context for sexual identity milestones were likely to be emotionally oriented for young women and sexually oriented for young men. The gap from first same-sex attractions (8-9 years of age) to first disclosure (around 18 years) averaged 10 years for both sexes. Young women followed label-first developmental trajectories; men were more likely to pursue sex before identifying themselves as gay. In terms of achieving sexual identity milestones, gender mattered, but it was not everything.

Adolescent↗
PubMed2001

Autistic behavior, FMR1 protein, and developmental trajectories in young males with fragile X syndrome.

In the context of a longitudinal study, we assessed the relationship between ratings of autistic behavior, FMR1 protein expression (FMRP), and the developmental trajectories of 55 young males with fragile X syndrome. Autistic behavior, as measured by the Childhood Autism Rating Scale, was not related to FMRP expression. However, autistic behavior was a significant predictor of both developmental status and developmental change. Boys with both autistic behavior and fragile X syndrome functioned at significantly lower levels of development and grew at significantly slower rates than those without autistic behavior. FMRP expression accounted for less variance in developmental level than did autistic behavior, and was not significantly related to slope (developmental change over time). No autistic behavior x FMRP interaction was found.

Autistic Disorder↗
PubMed2003

Age trajectories of genetic variance in physical functioning: a longitudinal study of Danish twins aged 70 years and older.

Genetic-evolutionary theories of aging predict that the genetic variance for fitness traits increases with age, while epidemiological-gerontological theories predict an increase in the environmental variance for most traits. In this study we examine the age trajectories of the genetic and environmental variance in physical functioning in a sample of 4731 Danish twins aged 70+ who are being followed longitudinally every second year with up to four assessments completed. A biometric growth model (Neale and McArdle, 2000) was applied to a validated physical ability score. The model included an overall level effect, a rate of linear change effect, and residual effects. The best-fitting model was a sex-specific model including additive genetic and nonshared environmental factors affecting level and rate of change and only nonshared environmental factors affecting the wave-specific levels. For both sexes there is an approximate doubling of both the total variance and the genetic variance in the physical ability score over the four waves and, hence, a rather stable heritability. However, the heritability is approximately.10 for males and.30 for females in all four waves. The heritability of level and slope showed a similar pattern:.11-14 in males and.35-.39 in females. The increase in both additive genetic variance and environmental variance is in agreement with genetic-evolutionary and epidemiological-gerontological theories of aging, respectively. The present study suggests that overall level of strength may be a better phenotype for future molecular genetic studies on physical functioning in the elderly than rate of change, because rate of change is vulnerable to sample attrition due to mortality and dropout and because four waves were needed to be able to detect a heritability for rate of change of the same magnitude as the heritability for level of physical functioning.

Age Factors↗
PubMed2004

Trouble ahead: predicting antisocial trajectories with dynamic systems concepts and methods.

This paper reviews and evaluates a set of studies that utilize dynamic systems (DS) principles, and in two cases dynamic systems methods, for predicting antisocial development and other behavioral outcomes. I suggest that the emphasis of DS approaches on process and nonlinear causation is very different from the emphasis in developmental psychopathology on prediction, yet the marriage of these approaches is necessary to capture the complex interactions that give rise to problematic trajectories. The studies reviewed do indeed uncover predictive relations that would have been difficult to conceptualize or impossible to find using more traditional strategies. In discussing these studies. I suggest DS interpretations of emerging individual differences, phase-specific change, sleeper effects, mediating variables, and behavioral rigidity versus malleability, in the context of developmental prediction. I also discuss the advantages of moving from DS concepts to DS methods in clinical-developmental research.

Conduct Disorder↗
PubMed2004

Trajectories of gambling during adolescence.

This study aimed at empirically identifying groups of adolescents with distinct longitudinal trajectories of gambling involvement and validating these groups by comparing them with respect to correlates. 903 low SES boys were followed annually from age 11 to 16 years. Three groups were found: an early-onset high-level chronic group, a late-onset high-level group, and a low gambler group. The Chronic group and the Low group consistently differed on teacher-rated inhibition (i.e., anxiety) during childhood and early adolescence. They also differed on concurrent teacher and self ratings of disinhibition (i.e., impulsivity), while the Late Onset group appeared to lie in between these groups. Compared to the Low group, both high groups subsequently had elevated scores on later gambling related problems.

Adolescent↗
PubMed2006

[Consumer satisfaction trajectories of adolescents during in-patient psychiatric treatment].

OBJECTIVE: Patient satisfaction with in-patient treatment and other aspects of process quality is usually examined cross-sectionally (e.g. at discharge). Therefore, the knowledge about changes in patient satisfaction and related issues, such as participation and motivation during the treatment period, is limited. This study describes the development of a questionnaire covering these topics and the course and variability in these domains for different subgroups. METHOD: The study group comprises 88 adolescents (48 females, 40 males; aged 13 to 18 years) who delivered altogether 1,003 data points (median per person is 8). The questionnaire consisted of 16 items that were administered to them by computer twice a week at adolescent wards in two psychiatric departments. Statistical analysis was done using hierarchical linear modeling (growth curve models), which is well suited for the analysis of data with different numbers of assessment points and missing data. RESULTS: Psychometric properties of the questions were good. The trajectories for all items are very heterogeneous with regard to the level.. The trends (slope of the growth curves) are around 0 in general satisfaction, i.e. the adolescents stay on their different levels during the treatment period. Concerning participation, however, there are diverging trends, in particular between the two departments, which may reflect the difference in the treatment experience of the teams, whereas age, gender and diagnosis (internalizing vs. externalizing) play a minor role. CONCLUSION: Evaluation of process characteristics has turned out to be feasible in clinical routine and promising for further insights into process quality.

Adolescent↗