Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Precise Analysis of Polymer Rotational Dynamics.

ABSTRACT: Through the analysis of individual chain dynamics alongside the corresponding molecular structures under shear via nonequilibrium molecular dynamics simulations of C178H358 linear and short-chain branched polyethylene melts under shear flow, we observed that the conventional method based on the chain end-to-end vector (and/or the gyration tensor of chain) is susceptible to quantitatively inaccurate measurements and often misleading information in describing the rotational dynamics of polymers. Identifying the flaw as attributed to strong irregular Brownian fluctuations inherent to the chain ends associated with their large free volume and strong molecular collisions, we propose a simple, robust way based on the chain center-to-center vector connecting the two centers of mass of the bisected chain, which is shown to adequately describe polymer rotational dynamics without such shortcomings. We present further consideration that the proposed method can be useful in accurately measuring the overall chain structure and dynamics of polymeric materials with various molecular architectures, including branched and ring polymers.

SUBMITTER: Kim JM

PROVIDER: S-EPMC4705482 | biostudies-other | 2016

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Atomically precise control of rotational dynamics in charged rare-earth complexes on a metal surface.

Project description:Complexes containing rare-earth ions attract great attention for their technological applications ranging from spintronic devices to quantum information science. While charged rare-earth coordination complexes are ubiquitous in solution, they are challenging to form on materials surfaces that would allow investigations for potential solid-state applications. Here we report formation and atomically precise manipulation of rare-earth complexes on a gold surface. Although they are composed of multiple units held together by electrostatic interactions, the entire complex rotates as a single unit when electrical energy is supplied from a scanning tunneling microscope tip. Despite the hexagonal symmetry of the gold surface, a counterion at the side of the complex guides precise three-fold rotations and 100% control of their rotational directions is achieved using a negative electric field from the scanning probe tip. This work demonstrates that counterions can be used to control dynamics of rare-earth complexes on materials surfaces for quantum and nanomechanical applications.

| S-EPMC9588029 | biostudies-literature

Precise Coordination of Three-Dimensional Rotational Kinematics by Ventral Tegmental Area GABAergic Neurons.

Project description:The ventral tegmental area (VTA) is a midbrain region implicated in a variety of motivated behaviors. However, the function of VTA GABAergic (Vgat+) neurons remains poorly understood. Here, using three-dimensional motion capture, in vivo electrophysiology, calcium imaging, and optogenetics, we demonstrate a novel function of VTAVgat+ neurons. We found three distinct populations of neurons, each representing head angle about a principal axis of rotation: yaw, roll, and pitch. For each axis, opponent cell groups were found that increase firing when the head moves in one direction and decrease firing in the opposite direction. Selective excitation and inhibition of VTAVgat+ neurons generate opposite rotational movements. Thus, VTAVgat+ neurons serve a critical role in the control of rotational kinematics while pursuing a moving target. This general-purpose steering function can guide animals toward desired spatial targets in any motivated behavior.

| S-EPMC7001733 | biostudies-literature

Rotational and constitutional dynamics of caged supramolecules.

Project description:The confinement of molecular species in nanoscale environments leads to intriguing dynamic phenomena. Notably, the organization and rotational motions of individual molecules were controlled by carefully designed, fully supramolecular host architectures. Here we use an open 2D coordination network on a smooth metal surface to steer the self-assembly of discrete trimeric guest units, identified as noncovalently bound dynamers. Each caged chiral supramolecule performs concerted, chirality-preserving rotary motions within the template honeycomb pore, which are visualized and quantitatively analyzed using temperature-controlled scanning tunneling microscopy. Furthermore, with higher thermal energies, a constitutional system dynamics appears, which is revealed by monitoring repetitive switching events of the confined supramolecules' chirality signature, reflecting decay and reassembly of the caged units.

| S-EPMC3003120 | biostudies-literature

Rotational dynamics of optically trapped human spermatozoa.

Project description:IntroductionOptical trapping is a laser-based method for probing the physiological and mechanical properties of cells in a noninvasive manner. As sperm motility is an important criterion for assessing the male fertility potential, this technique is used to study sperm cell motility behavior and rotational dynamics.Methods and patientsAn integrated optical system with near-infrared laser beam has been used to analyze rotational dynamics of live sperm cells from oligozoospermic and asthenozoospermic cases and compared with controls.ResultsThe linear, translational motion of the sperm is converted into rotational motion on being optically trapped, without causing any adverse effect on spermatozoa. The rotational speed of sperm cells from infertile men is observed to be significantly less as compared to controls.ConclusionsDistinguishing normal and abnormal sperm cells on the basis of beat frequency above 5.6 Hz may be an important step in modern reproductive biology to sort and select good quality spermatozoa. The application of laser-assisted technique in biology has the potential to be a valuable tool for assessment of sperm fertilization capacity for improving assisted reproductive technology.

| S-EPMC3926395 | biostudies-literature

Light-Controlled Rotational Speed of an Acoustically Levitating Photomobile Polymer Film.

Project description:In this work, we study the light-induced changes of the rotational speed of a thin photomobile film using a single-axis acoustic levitator operating at 40 kHz. In our experiments, a 50 μm thick photomobile polymer film (PMP) is placed in one of the nodes of a stationary acoustic field. Under the action of the field, the film remains suspended in air. By externally perturbing this stable equilibrium condition, the film begins to rotate with its natural frequency. The rotations are detected in real time by monitoring the light of a low power He-Ne laser impinging on and reflected by the film itself. During the rotational motion, an external laser source is used to illuminate the PMP film; as a consequence, the film bends and the rotational speed changes by about 20 Hz. This kind of contactless long-distance interaction is an ideal platform for the development and study of many electro-optics devices in microgravity and low-friction conditions. In particular, we believe that this technology could find applications in research fields such as 3D dynamic displays and aerospace applications.

| S-EPMC9860897 | biostudies-literature

Rotational Dynamics of Proteins from Spin Relaxation Times and Molecular Dynamics Simulations.

Project description:Conformational fluctuations and rotational tumbling of proteins can be experimentally accessed with nuclear spin relaxation experiments. However, interpretation of molecular dynamics from the experimental data is often complicated, especially for molecules with anisotropic shape. Here, we apply classical molecular dynamics simulations to interpret the conformational fluctuations and rotational tumbling of proteins with arbitrarily anisotropic shape. The direct calculation of spin relaxation times from simulation data did not reproduce the experimental data. This was successfully corrected by scaling the overall rotational diffusion coefficients around the protein inertia axes with a constant factor. The achieved good agreement with experiments allowed the interpretation of the internal and overall dynamics of proteins with significantly anisotropic shape. The overall rotational diffusion was found to be Brownian, having only a short subdiffusive region below 0.12 ns. The presented methodology can be applied to interpret rotational dynamics and conformation fluctuations of proteins with arbitrary anisotropic shape. However, a water model with more realistic dynamical properties is probably required for intrinsically disordered proteins.

| S-EPMC6150695 | biostudies-literature

Rotational dynamics reduce interference between sensory and memory representations.

Project description:Cognition depends on integrating sensory percepts with the memory of recent stimuli. However, the distributed nature of neural coding can lead to interference between sensory and memory representations. Here, we show that the brain mitigates such interference by rotating sensory representations into orthogonal memory representations over time. To study how sensory inputs and memories are represented, we recorded neurons from the auditory cortex of mice as they implicitly learned sequences of sounds. We found that the neural population represented sensory inputs and the memory of recent stimuli in two orthogonal dimensions. The transformation of sensory information into a memory was facilitated by a combination of 'stable' neurons, which maintained their selectivity over time, and 'switching' neurons, which inverted their selectivity over time. Together, these neural responses rotated the population representation, transforming sensory inputs into memory. Theoretical modeling showed that this rotational dynamic is an efficient mechanism for generating orthogonal representations, thereby protecting memories from sensory interference.

| S-EPMC8102338 | biostudies-literature

Rotational dynamics and transition mechanisms of surface-adsorbed proteins.

Project description:Assembly of biomolecules at solid–water interfaces requires molecules to traverse complex orientation-dependent energy landscapes through processes that are poorly understood, largely due to the dearth of in situ single-molecule measurements and statistical analyses of the rotational dynamics that define directional selection. Emerging capabilities in high-speed atomic force microscopy and machine learning have allowed us to directly determine the orientational energy landscape and observe and quantify the rotational dynamics for protein nanorods on the surface of muscovite mica under a variety of conditions. Comparisons with kinetic Monte Carlo simulations show that the transition rates between adjacent orientation-specific energetic minima can largely be understood through traditional models of in-plane Brownian rotation across a biased energy landscape, with resulting transition rates that are exponential in the energy barriers between states. However, transitions between more distant angular states are decoupled from barrier height, with jump-size distributions showing a power law decay that is characteristic of a nonclassical Levy-flight random walk, indicating that large jumps are enabled by alternative modes of motion via activated states. The findings provide insights into the dynamics of biomolecules at solid–liquid interfaces that lead to self-assembly, epitaxial matching, and other orientationally anisotropic outcomes and define a general procedure for exploring such dynamics with implications for hybrid biomolecular–inorganic materials design.

| S-EPMC9169768 | biostudies-literature

Molecular movie of ultrafast coherent rotational dynamics of OCS.

Project description:Recording molecular movies on ultrafast timescales has been a longstanding goal for unravelling detailed information about molecular dynamics. Here we present the direct experimental recording of very-high-resolution and -fidelity molecular movies over more than one-and-a-half periods of the laser-induced rotational dynamics of carbonylsulfide (OCS) molecules. Utilising the combination of single quantum-state selection and an optimised two-pulse sequence to create a tailored rotational wavepacket, an unprecedented degree of field-free alignment, 〈cos2θ2D〉 = 0.96 (〈cos2θ〉 = 0.94) is achieved, exceeding the theoretical limit for single-pulse alignment. The very rich experimentally observed quantum dynamics is fully recovered by the angular probability distribution obtained from solutions of the time-dependent Schrödinger equation with parameters refined against the experiment. The populations and phases of rotational states in the retrieved time-dependent three-dimensional wavepacket rationalises the observed very high degree of alignment.

| S-EPMC6662765 | biostudies-literature

Precise Thermoplastic Processing of Graphene Oxide Layered Solid by Polymer Intercalation.

Project description:The processing capability is vital for the wide applications of materials to forge structures as-demand. Graphene-based macroscopic materials have shown excellent mechanical and functional properties. However, different from usual polymers and metals, graphene solids exhibit limited deformability and processibility for precise forming. Here, we present a precise thermoplastic forming of graphene materials by polymer intercalation from graphene oxide (GO) precursor. The intercalated polymer enables the thermoplasticity of GO solids by thermally activated motion of polymer chains. We detect a critical minimum containing of intercalated polymer that can expand the interlayer spacing exceeding 1.4 nm to activate thermoplasticity, which becomes the criteria for thermal plastic forming of GO solids. By thermoplastic forming, the flat GO-composite films are forged to Gaussian curved shapes and imprinted to have surface relief patterns with size precision down to 360 nm. The plastic-formed structures maintain the structural integration with outstanding electrical (3.07 × 105 S m-1) and thermal conductivity (745.65 W m-1 K-1) after removal of polymers. The thermoplastic strategy greatly extends the forming capability of GO materials and other layered materials and promises versatile structural designs for more broad applications.

| S-EPMC8643290 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data