SEARCH · PubMed Health

Results for “trajectory analysis”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 163 records · Page 9Linked to original sources

PubMed1995

The essential dynamics of thermolysin: confirmation of the hinge-bending motion and comparison of simulations in vacuum and water.

Comparisons of the crystal structures of thermolysin and the thermolysin-like protease produced by B. cereus have recently led to the hypothesis that neutral proteases undergo a hinge-bending motion. We have investigated this hypothesis by analyzing molecular dynamics simulations of thermolysin in vacuum and water, using the essential dynamics method. This method is able to extract large concerted atomic motions of biological importance from a molecular dynamics trajectory. The analysis of the thermolysin trajectories indeed revealed a large rigid body hinge-bending motion of the N-terminal and C-terminal domains, similar to the motion hypothesized from the crystal structure comparisons. In addition, it appeared that the essential dynamics properties derived from the vacuum simulation were similar to those derived from the solvent simulation.

Computer Simulation↗

PubMed2000

Analysis of the three-dimensional trajectories of organisms: estimates of velocity, curvature and torsion from positional information.

Most biological motions are three-dimensional. This includes the trajectories of whole organisms and of their appendages. While recordings of three-dimensional trajectories are sometimes published, quantitative analysis of these trajectories is uncommon, primarily because there are no standard techniques or conventions in biology for the analysis of three-dimensional trajectories. This paper describes a new technique, finite helix fit (FHF), based on the geometry of three-dimensional curves, whereby a three-dimensional trajectory is completely described by its velocity, curvature and torsion. FHF estimates these parameters from discretely sampled points on a trajectory (i.e. from positional data such as x,y,z coordinates). Other measures of motion can be derived from these parameters, such as the translational and rotational (or angular) velocities of an organism. The performance of the algorithms is demonstrated using simulated trajectories and trajectories of freely swimming organisms (a flagellate, Chlamydomonas reinhardtii; a ciliate, Paramecium tetraurelia; spermatozoa of a sea urchin, Arbacia punctulata; larvae of an ascidian, Botrylloides sp.).

Algorithms↗

PubMed2006

Nonstatistical effects in the dissociation of ethyl radical: Finding order in chaos.

How does one identify order in complex dynamical systems? A Born-Oppenheimer molecular dynamics simulation of the dissociation of ethyl radical, C(2)H(5), produces an ensemble of classical trajectories which are decomposed in the time-frequency domain using wavelets. A time-dependent scalar metric, the normalized instantaneous orbital complexity, is constructed and shown to correlate not only to the more conventional Lyapunov exponents but also to the dissociation time for an individual trajectory. The analysis of the ensemble of trajectories confirms that the long-lived trajectories are associated with a low degree of ergodicity. While the analysis of molecular dissociation dynamics is the narrow focus of the present work, the method is more general for discovery and identification of ordered regimes within large sets of chaotic data.

Journal Article↗

PubMed2005

Quasiperiodic trajectories in the unimolecular dissociation of ethyl radicals by time-frequency analysis.

Direct classical trajectory calculations for ethyl radical, C2H5, at the HCTH147@6-31 +G**/6-31G** level of theory support the experimental observation that the dissociation of highly excited ethyl radicals to ethylene and and a hydrogen atom can occur much more slowly than predicted by statistical rate theories. Only 78% of the trajectories of ethyl radicals prepared in a microcanonical ensemble with 120-kcal/mol excitation energy above the zero-point energy and zero total angular momentum dissociate to form C2H4 + H. The remaining hot ground-state ethyl radicals have a lifetime of >>2 ps, during which a time-frequency analysis finds them trapped for extended periods of time in long-lived quasiperiodic trajectories.

Journal Article↗

PubMed2006

Analysis of single-molecule FRET trajectories using hidden Markov modeling.

The analysis of single-molecule fluorescence resonance energy transfer (FRET) trajectories has become one of significant biophysical interest. In deducing the transition rates between various states of a system for time-binned data, researchers have relied on simple, but often arbitrary methods of extracting rates from FRET trajectories. Although these methods have proven satisfactory in cases of well-separated, low-noise, two- or three-state systems, they become less reliable when applied to a system of greater complexity. We have developed an analysis scheme that casts single-molecule time-binned FRET trajectories as hidden Markov processes, allowing one to determine, based on probability alone, the most likely FRET-value distributions of states and their interconversion rates while simultaneously determining the most likely time sequence of underlying states for each trajectory. Together with a transition density plot and Bayesian information criterion we can also determine the number of different states present in a system in addition to the state-to-state transition probabilities. Here we present the algorithm and test its limitations with various simulated data and previously reported Holliday junction data. The algorithm is then applied to the analysis of the binding and dissociation of three RecA monomers on a DNA construct.

Algorithms↗

PubMed2026

Early-childhood temperament trajectories map onto transdiagnostic psychiatric risk.

Early-childhood temperament is associated with later mental health. Temperament continues to develop throughout the first years of life, and a single assessment cannot capture its trajectory. Whether departures from an individual's developmental trajectory carry psychiatric risk remains unknown. Using data from more than 50,000 children in the Norwegian Mother, Father and Child Cohort Study, we modeled longitudinal temperament at 1.5, 3, and 5 years of age with the FEMA-Long mixed-effects framework. We then quantified each child's departures from their predicted trajectories. Multivariate analysis revealed two transdiagnostic dimensions linking trajectory departures to psychiatric diagnoses across childhood and adolescence. Higher scores on the first dimension were associated with an increased hazard of subsequent ADHD diagnosis (hazard ratio = 1.54), and higher scores on the second with an increased hazard of Asperger syndrome (hazard ratio = 1.64). To examine the genetic basis of these associations, we performed longitudinal GWAS of temperament and conjunctional FDR analysis to detect loci shared with the associated diagnoses. The effects of these loci changed across early childhood, with some strengthening and others attenuating with age. These findings show that departures from predicted temperament trajectories reflect transdiagnostic psychiatric risk with a shared genetic basis. Longitudinal, trajectory-based monitoring could help identify children at elevated psychiatric risk.

Journal Article↗

PubMed2026

Spectral-Proteomic Integration Analysis (SPIA) Deciphers Molecular Trajectories of Breast Cancer and Enables Multitarget Therapeutic Assessment.

Raman spectroscopy and mass spectrometry-based proteomics offer deeply complementary yet largely disconnected views of cancer biology: the former provides a label-free, real-time biochemical phenotype, while the latter delivers a quantitative inventory of specific protein effectors. Bridging this gap remains a fundamental challenge in analytical biomedicine. Here, we introduce Spectral-Proteomic Integration Analysis (SPIA)─a novel, data-driven integrative framework that systematically links Raman spectroscopic phenotypes with quantitative proteomic profiles through machine learning and statistical correlation. Using a DMBA-induced rat breast cancer model with and without Toremifene (TOR) intervention, SPIA dynamically maps tumor microenvironment remodeling, capturing progressive collagen deposition and lipid metabolic reprogramming. An SVM classifier trained on Raman spectra achieves exceptional diagnostic accuracy (AUC ≥ 99.0%) and successfully predicts TOR therapeutic response. Proteomic analysis identifies 1,350 differentially expressed proteins, with convergent machine learning feature selection (LASSO, Random Forest, XGBoost) pinpointing core regulators including Luc7l2, Nucb1, Cbx3, and Csnk2a1. Crucially, Spearman correlation analysis between key Raman bands and core DEPs reveals strong, statistically robust associations (median ρ ∼ 0.75 in the 1533-1669 cm-1 region), empirically validating SPIA's core integrative logic. Leveraging this multimodal map, we elucidate a multitarget mechanism for TOR involving concurrent suppression of collagen deposition and correction of aberrant lipid metabolism. SPIA establishes a powerful, generalizable paradigm for integrating phenotypic and molecular data, with broad implications for biomarker discovery, drug mechanism elucidation, and precision oncology.

Animals↗

PubMed2006

Molecular dynamics simulations of interaction between protein-tyrosine phosphatase 1B and a bidentate inhibitor.

AIM: To investigate the dynamic properties of protein-tyrosine phosphatase (PTP) 1B and reveal the structural factors responsible for the high inhibitory potency and selectivity of the inhibitor SNA for PTP1B. METHODS: We performed molecular dynamics (MD) simulations using a long time-scale for both PTP1B and PTP1B complexed with the inhibitor SNA, the most potent and selective PTP1B inhibitor reported to date. The trajectories were analyzed by using principal component analysis. RESULTS: Trajectory analyses showed that upon binding the ligand, the flexibility of the entire PTP1B molecule decreases. The most notable change is the movement of the WPD-loop. Our simulation results also indicated that electrostatic interactions contribute more to PTP1B-SNA complex conformation than the van der Waals interactions, and that Lys41, Arg47, and Asp48 play important roles in determining the conformation of the inhibitor SNA and in the potency and selectivity of the inhibitor. Of these, Arg47 contributed most. These results were in agreement with previous experimental results. CONCLUSION: The information presented here suggests that potent and selective PTP1B inhibitors can be designed by targeting the surface residues, for example the region containing Lys41, Arg47, and Asp48, instead of the second phosphate binding site (besides the active phosphate binding site).

Binding Sites↗

PubMed2003

The academic trajectories of immigrant youths: analysis within and across cohorts.

Two nationally representative cohorts--from the National Educational Longitudinal Study (NELS) and High School and Beyond (HSB)--were used to examine the effects of generation and duration of residence on students' performance on standardized tests over a two-year period. In multivariate models, generational status predicts variation in students' performance on baseline (sophomore) tests, with effects stronger for the later age cohort (NELS) than for the earlier age cohort (HSB). With regard to the trajectory of achievement, generational status has a greatly reduced role for both cohorts. The best predictors of the trajectory of achievement are not those that are based on nativity per se, but those that reflect the social environment experienced in the United States (i.e., ethnicity and family's socioeconomic status).

Acculturation↗

PubMedDate not supplied

Root mean square deviation probability analysis of molecular dynamics trajectories on DNA.

The comparison and detection of the commonalities and differences in multiple structural ensembles is an important step in the use of molecular simulations to gain insight into the conformation and dynamics of complex biomacromolecules. While the average structure is often employed as the representative of an ensemble of structures in such comparisons, dynamic molecular systems with multiple conformational substates call for a more accurate representation that captures the complete dynamical range of the ensemble. We present a probability analysis procedure based on the root-mean-square differences among the structural ensembles that efficiently and accurately performs the relevant comparison.

Base Sequence↗

PubMed1999

Essential dynamics/factor analysis for the interpretation of molecular dynamics trajectories.

Subject of this work is the analysis of molecular dynamics (MD) trajectories of neurophysins I (NPI) and II (NPII) and their complexes with the neurophyseal nonapeptide hormones oxytocin (OT) and vasopresssin (VP), respectively, simulated in water. NPs serve in the neurosecretory granules as carrier proteins for the hormones before their release to the blood. The starting data consisted of two pairs of different trajectories for each of the (NPII/VP)2 and (NPI/OT)2 heterotetramers and two more trajectories for the NPII2 and NPI2 homodimers (six trajectories in total). Using essential dynamics which, to our judgement, is equivalent to factor analysis, we found that only about 10 degrees of freedom per trajectory are necessary and sufficient to describe in full the motions relevant for the function of the protein. This is consistent with these motions to explain about 90% of the total variance of the system. These principal degrees of freedom represent slow anharmonic motional modes, clearly pointing at distinguished mobility of the atoms involved in the protein's functionality.

Amino Acid Sequence↗

PubMed2006

Effect of finite trajectory length on the correlation function analysis of single molecule data.

The effect of finite trajectory length on single molecule rotational correlation functions has been studied by utilizing time series analysis and numerical simulations. Correlation functions obtained from the trajectories of length less than 100 times the correlation time constant (tau([script-l])) exhibit significant deviations from the true correlation function. The distributions of sample time constants (tau(F)) and stretching exponents (Beta(F)) are mapped by fitting a large number of rotational trajectories to stretched exponentials. As the trajectory length gets smaller, the distributions become broader and asymmetric and their mean values deviate from the true value predicted by pure rotational diffusion. Analysis based on higher order spherical harmonics is suggested as a method for minimizing the effect of the trajectory length. The distributions of time constants for different higher order spherical harmonics are also compared. While the focus of the paper is on rotational correlation functions, the general conclusions apply to any dynamical process that yields an exponentially decaying correlation function.

Computer Simulation↗

PubMed2004

Linear response theory: an alternative to PB and GB methods for the analysis of molecular dynamics trajectories?

We explore the use of classical Linear Response Theory (LRT) as an alternative strategy to the use of Molecular Mechanics/Poisson-Boltzmann strategies to compute the solvation free energy of macromolecules from molecular dynamics simulations using an explicit representation of solvent. The method reproduces well the free energy of solvation of standard amino acid side chains, small peptides, and proteins. The use of a fully discrete representation of solvent avoids the possible problems of continuum models to represent the solvation of systems containing tightly bound water molecules.

Alanine↗

PubMed1989

An analysis of mandibular movement trajectories and masticatory muscle EMG activity during drinking in the guinea pig.

Electromyographic (EMG) activity of the anterior digastric, lateral pterygoid, and deep masseter muscles as well as the associated jaw movements during drinking were studied in the awake guinea pig. Drinking was characterized by rhythmic, vertically directed jaw movements with little or no associated lateral movements. The jaw opening phase of each cycle was associated with bilaterally synchronized EMG activity in the digastric and lateral pterygoid muscles, and the jaw closing phase with bilaterally synchronized activity in the masseter muscles. The mean EMG burst durations (+/- 1 S.E.) in the digastric and masseter muscles were 164.2 +/- 14.93 ms and 94.3 +/- 26.44 ms, respectively. The digastric muscle EMG burst duration was significantly correlated with drinking cycle time and with masseter muscle EMG onset; on the other hand, masseter muscle EMG burst duration was not correlated with cycle time. These patterns of EMG activity and jaw movement trajectories are similar to those induced by apomorphine in the ketamine-anesthetized guinea pig.

Animals↗

PubMed1992

Kinematic analysis of upper limb trajectories in Parkinson's disease.

The purpose of this study was to analyze the kinematic properties of upper limb trajectories in Parkinson's disease (PD) patients and to investigate the role of visual feedback from the moving limb. Beyond the characteristic bradykinesia, PD patients differed from controls by generating hand trajectories with asymmetrical velocity profiles that lacked smoothness and were composed of a short initial accelerative phase, followed by a prolonged interval composed of alternating decelerative and accelerative phases. In both groups, the reaction times for movements directed away from the body were longer than for movements directed toward the body; this effect was accentuated in PD. In both groups, initial peak accelerations were significantly larger for distally as compared to proximally directed movements. In the absence of visual feedback from the limb a deterioration in the accuracy of reaching the target was observed in both control and PD patients only for distally directed movements. However, this deterioration and the effect of target location on final accuracy was substantially larger in PD. Taken together, our study suggests that in PD visual information is continuously relied upon for ongoing movement correction, therefore accentuating the bradykinesia. The deficit in final accuracy in the absence of visual feedback reflects the important role played by the basal ganglia in sensorimotor integration.

Acceleration↗

PubMed1996

Quantitative analysis of human walking trajectory on a circular path in darkness.

Thirteen normal (eight young and five older) subjects and a patient who was removed left sided acoustic neurinoma were tested to walk blindfolded along circular paths. They were asked to walk completing two revolutions and to stop when they judged they had returned to the initial position with their head faced to the initial directions. Movements of two markers on the subjects head were recorded by three dimensional motion analyzing system (ELITE system) at 50 Hz which allowed us to measure (a) total walked distance, (b) average radius of the trajectory, and (c) cumulative angle of rotation. Eight young subjects were tested on three circles with radii 0.5, 0.9, and 1.15 m, in two conditions (control, and with mental arythmetic), only to clockwise direction. Five older subjects and a patient were tested on a circle of 0.9 m radius in two conditions, but to both directions, counterclockwise and clockwise. Walked trajectories of young subjects were smooth, whereas those of older subjects tended to be polygonal. Young subjects overshot the ideal distance (6.6%) and ideal radius (9.5%), whereas they undershot the ideal angle (5.1%). There was no effect of circle size or condition on these variables. On the other hand, there was a significant effect of condition on average radius in the older group. The performance of older subjects seemed to be affected by the concurrent mental task. Comparing the counterclockwise walk, the older subjects undershot the turning angle much more than the young subjects which suggest deficits in the vestibular function with aging. The patient showed larger radius and smaller angle while she turned to the healthy side (clockwise) than to the affected side (counterclockwise). Lack of unilateral vestibular information seemed to have affected the circular walking trajectory.

Adult↗

PubMed2006

Sexual practices in youth: analysis of lifetime sexual trajectory and last sexual intercourse.

This article examines the sexual practices of young Brazilians based on data from the GRAVAD Research Project, a household survey targeting males and females from 18 to 24 years of age (n = 4,634) in three Brazilian State capitals: Porto Alegre, Rio de Janeiro, and Salvador. The set of practices experienced over the course of their sexual careers is characterized by traits of social belonging, elements from individual life histories, and prescribed rules of conduct for men and women. The authors compared the young people's range of lifetime practices and those from last sexual relations in order to discuss the spread and incorporation of practices into life histories. The data point to the hegemony of vaginal sex in both the lifetime repertoire of sexual practices and the last sexual encounters, such that vaginal sex provides the prime definition of heterosexuality.

Adolescent↗

PubMed2000

Analysis of inheritance of growth trajectories in laboratory populations of guppy-fish.

We analysed the variation of growth trajectories for body length from 40 to 90 days of age in three laboratory populations of Poecilia reticulata. The populations used were two lines of guppy-fish obtained by artificial selection for increased and decreased body length at 70 days and one line maintained under free-breeding condition. The factor analysis performed on the phenotypic correlation matrices among age-specific values of body length showed that a very large portion of the phenotypic variation is confined to a single factor. This factor corresponds to a simultaneous increase/decrease at all ages, hence representing the variation in the height of the growth trajectories. A smaller portion of the variation describes an increase/decrease at early ages followed by the reverse in the later ages, which corresponds to the variation in the shape of the trajectories. The genetic analysis performed on the height and shape of the growth curves showed a additive genetic component for the height in the free-breeding population and for the shape in the selected lines.

Animals↗