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Biological motion

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https://www.readbyqxmd.com/read/28212034/observation-of-the-global-dynamic-collectivity-of-a-hydration-shell-around-apomyoglobin
#1
Yangzhong Qin, Luyuan Zhang, Lijuan Wang, Dongping Zhong
Protein surface hydration is critical to its structural properties and biological activities. However, it is still unknown whether the hydration shell is intrinsically connected and how its fluctuations dynamically interact with protein motions. Here, by selecting five site-specific locations with distinctly different environments around apomyoglobin surface, we used a tryptophan scan with femtosecond fluorescence spectroscopy and simultaneously detected hydration-water dynamics and tryptophan sidechain relaxations with temperature dependence...
February 17, 2017: Journal of Physical Chemistry Letters
https://www.readbyqxmd.com/read/28211526/stable-optical-trapping-and-sensitive-characterization-of-nanostructures-using-standing-wave-raman-tweezers
#2
Mu-Ying Wu, Dong-Xiong Ling, Lin Ling, William Li, Yong-Qing Li
Optical manipulation and label-free characterization of nanoscale structures open up new possibilities for assembly and control of nanodevices and biomolecules. Optical tweezers integrated with Raman spectroscopy allows analyzing a single trapped particle, but is generally less effective for individual nanoparticles. The main challenge is the weak gradient force on nanoparticles that is insufficient to overcome the destabilizing effect of scattering force and Brownian motion. Here, we present standing-wave Raman tweezers for stable trapping and sensitive characterization of single isolated nanostructures with a low laser power by combining a standing-wave optical trap with confocal Raman spectroscopy...
February 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28211184/night-time-pedestrian-conspicuity-effects-of-clothing-on-drivers-eye-movements
#3
Joanne M Wood, Richard A Tyrrell, Philippe Lacherez, Alex A Black
PURPOSE: Drivers' responses and eye movements were assessed as they approached pedestrians at night in order to explore the relative conspicuity benefits of different configurations of retroreflective markings. METHODS: Eye movements were recorded using an ASL Mobile Eye (Applied Science Technologies, www.asleyetracking.com) from 14 young licensed drivers (M = 24.1 ± 6.4 years) as they drove along a closed-road circuit at night. At two locations, pedestrians walked in place facing either towards or away from the road...
March 2017: Ophthalmic & Physiological Optics: the Journal of the British College of Ophthalmic Opticians (Optometrists)
https://www.readbyqxmd.com/read/28210337/extraction-of-knowledge-from-the-topographic-attentive-mapping-network-and-its-application-in-skill-analysis-of-table-tennis
#4
Isao Hayashi, Masanori Fujii, Toshiyuki Maeda, Jasmin Leveille, Tokio Tasaka
The Topographic Attentive Mapping (TAM) network is a biologically-inspired classifier that bears similarities to the human visual system. In case of wrong classification during training, an attentional top-down signal modulates synaptic weights in intermediate layers to reduce the difference between the desired output and the classifier's output. When used in a TAM network, the proposed pruning algorithm improves classification accuracy and allows extracting knowledge as represented by the network structure...
January 1, 2017: Journal of Human Kinetics
https://www.readbyqxmd.com/read/28208767/alternative-cdep-design-to-facilitate-cell-isolation-for-identification-by-raman-spectroscopy
#5
Cynthia Hanson, Elizabeth Vargis
Dielectrophoresis (DEP) uses non-uniform electric fields to cause motion in particles due to the particles' intrinsic properties. As such, DEP is a well-suited label-free means for cell sorting. Of the various methods of implementing DEP, contactless dielectrophoresis (cDEP) is advantageous as it avoids common problems associated with DEP, such as electrode fouling and electrolysis. Unfortunately, cDEP devices can be difficult to fabricate, replicate, and reuse. In addition, the operating parameters are limited by the dielectric breakdown of polydimethylsiloxane (PDMS)...
February 9, 2017: Sensors
https://www.readbyqxmd.com/read/28208370/emergent-pattern-formation-in-an-interstitial-biofilm
#6
Cameron Zachreson, Christian Wolff, Cynthia B Whitchurch, Milos Toth
Collective behavior of bacterial colonies plays critical roles in adaptability, survivability, biofilm expansion and infection. We employ an individual-based model of an interstitial biofilm to study emergent pattern formation based on the assumptions that rod-shaped bacteria furrow through a viscous environment and excrete extracellular polymeric substances which bias their rate of motion. Because the bacteria furrow through their environment, the substratum stiffness is a key control parameter behind the formation of distinct morphological patterns...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28205639/biological-motion-distorts-size-perception
#7
Peter Veto, Wolfgang Einhäuser, Nikolaus F Troje
Visual illusions explore the limits of sensory processing and provide an ideal testbed to study perception. Size illusions - stimuli whose size is consistently misperceived - do not only result from sensory cues, but can also be induced by cognitive factors, such as social status. Here we investigate, whether the ecological relevance of biological motion can also distort perceived size. We asked observers to judge the size of point-light walkers (PLWs), configurations of dots whose movements induce the perception of human movement, and visually matched control stimuli (inverted PLWs)...
February 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205563/geometric-tuning-of-self-propulsion-for-janus-catalytic-particles
#8
Sébastien Michelin, Eric Lauga
Catalytic swimmers have attracted much attention as alternatives to biological systems for examining collective microscopic dynamics and the response to physico-chemical signals. Yet, understanding and predicting even the most fundamental characteristics of their individual propulsion still raises important challenges. While chemical asymmetry is widely recognized as the cornerstone of catalytic propulsion, different experimental studies have reported that particles with identical chemical properties may propel in opposite directions...
February 13, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28205497/critical-motor-involvement-in-prediction-of-human-and-non-biological-motion-trajectories
#9
Matthieu M de Wit, Laurel J Buxbaum
OBJECTIVES: Adaptive interaction with the environment requires the ability to predict both human and non-biological motion trajectories. Prior accounts of the neurocognitive basis for prediction of these two motion classes may generally be divided into those that posit that non-biological motion trajectories are predicted using the same motor planning and/or simulation mechanisms used for human actions, and those that posit distinct mechanisms for each. Using brain lesion patients and healthy controls, this study examined critical neural substrates and behavioral correlates of human and non-biological motion prediction...
February 2017: Journal of the International Neuropsychological Society: JINS
https://www.readbyqxmd.com/read/28203582/indifference-to-chaotic-motion-may-be-related-to-social-disinterest-in-children-with-autism
#10
Joshua Haworth, Anastasia Kyvelidou, Wayne Fisher, Nicholas Stergiou
Children with autism spectrum disorder tend to have little interest in the presence, actions, and motives of other persons. In addition, these children tend to present with a limited and overly redundant movement repertoire, often expressing hyperfixation and aversion to novelty. We explore whether this is related to a more fundamental lack of appreciation for various temporal dynamics, including periodic, chaotic, and aperiodic motion structures. Seven children with ASD (age, gender, and height matched with children without ASD) were asked to stand and watch the motion of a visual stimulus displayed on a large (55″) video monitor...
December 2016: Journal of Motor Learning and Development
https://www.readbyqxmd.com/read/28199113/quantitative-characterization-of-domain-motions-in-molecular-machines
#11
Suvrajit Maji, Rezvan Shahoei, Klaus Schulten, Joachim Frank
The work of molecular machines such as the ribosome is accompanied by conformational changes, often characterized by relative motions of their domains. The method we have developed seeks to quantify these motions in a general way, facilitating comparisons of results obtained by different researchers. Typically there are multiple snapshots of a structure in the form of pdb coordinates resulting from flexible fitting of low-resolution density maps, from X-ray crystallography, or from molecular dynamics simulation trajectories...
February 15, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28198892/stimulated-raman-scattering-microscopy-and-spectroscopy-with-a-rapid-scanning-optical-delay-line
#12
Ruoyu He, Zhiping Liu, Yongkui Xu, Wei Huang, Hong Ma, Minbiao Ji
Stimulated Raman scattering (SRS) microscopy that is capable of both high-speed imaging and rapid spectroscopy will be advantageous for detailed chemical analysis of heterogeneous biological specimens. We have developed a system based on spectral focusing SRS technology with the integration of a rapid scanning optical delay line, which allows continuous tuning of SRS spectra by scanning a galvo mirror. We demonstrate SRS spectral measurements of dimethyl sulfoxide solution at low concentrations and multi-color imaging of rice pollens and HeLa cells with line-by-line delay tuning to reduce motion artifacts, as well as fast acquisition of SRS spectra at specific regions of interest...
February 15, 2017: Optics Letters
https://www.readbyqxmd.com/read/28195464/combining-the-martini-and-structure-based-coarse-grained-approaches-for-the-molecular-dynamics-studies-of-conformational-transitions-in-proteins
#13
Adolfo B Poma, Marek Cieplak, Panagiotis E Theodorakis
The application of coarse-grain (CG) models in biology is essential to access large length and time scales required for the description of many biological processes. The ELNEDIN protein model is based on the well-known MARTINI CG force-field and incorporates additionally harmonic bonds of a certain spring constant within a defined cutoff distance between pairs of residues, in order to preserve the native structure of the protein. In this case, the use of unbreakable harmonic bonds hinders the study of unfolded protein structures and unfolding processes...
February 14, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28192432/conformational-diversity-analysis-reveals-three-functional-mechanisms-in-proteins
#14
Alexander Miguel Monzon, Diego Javier Zea, María Silvina Fornasari, Tadeo E Saldaño, Sebastian Fernandez-Alberti, Silvio C E Tosatto, Gustavo Parisi
Protein motions are a key feature to understand biological function. Recently, a large-scale analysis of protein conformational diversity showed a positively skewed distribution with a peak at 0.5 Å C-alpha root-mean-square-deviation (RMSD). To understand this distribution in terms of structure-function relationships, we studied a well curated and large dataset of ~5,000 proteins with experimentally determined conformational diversity. We searched for global behaviour patterns studying how structure-based features change among the available conformer population for each protein...
February 13, 2017: PLoS Computational Biology
https://www.readbyqxmd.com/read/28191927/foldectures-3d-molecular-architectures-from-self-assembly-of-peptide-foldamers
#15
Sung Hyun Yoo, Hee-Seung Lee
The wide range of fascinating supramolecular architectures found in nature, from DNA double helices to giant protein shells, inspires researchers to mimic the diverse shapes and functions of natural systems. Thus, a variety of artificial molecular platforms have been developed by assembling DNA-, peptide-, and protein-based building blocks for medicinal and biological applications. There has also been a significant interest in the research of non-natural oligomers (i.e., foldamers) that fold into well-defined secondary structures analogous to those found in proteins, because the assemblies of foldamers are expected not only to form biomimetic supramolecular architectures that resemble those of nature but also to display unique functions and unprecedented topologies at the same time due to their different folding propensities from those of natural building blocks...
February 13, 2017: Accounts of Chemical Research
https://www.readbyqxmd.com/read/28190869/single-molecule-detection-thermal-fluctuation-and-life
#16
Toshio Yanagida, Yoshiharu Ishii
Single molecule detection has contributed to our understanding of the unique mechanisms of life. Unlike artificial man-made machines, biological molecular machines integrate thermal noises rather than avoid them. For example, single molecule detection has demonstrated that myosin motors undergo biased Brownian motion for stepwise movement and that single protein molecules spontaneously change their conformation, for switching to interactions with other proteins, in response to thermal fluctuation. Thus, molecular machines have flexibility and efficiency not seen in artificial machines...
2017: Proceedings of the Japan Academy. Series B, Physical and Biological Sciences
https://www.readbyqxmd.com/read/28187350/conformational-selection-and-induced-fit-as-a-useful-framework-for-molecular-motor-mechanisms
#17
REVIEW
Eric A Galburt, Eric J Tomko
The linkage between macromolecular binding and conformational change that is ubiquitous in biological molecules can be understood in the context of the mechanisms of conformational selection and induced fit. Here, we explore mappings between these mechanisms of ligand binding and those underlying the translocation of molecular motors and the nucleic acid unwinding of helicases. The mechanism of biased motion exhibited by molecular motors is typically described as either a thermal ratchet or a power-stroke and nucleic acid helicases are characterized by either active or passive unwinding mechanisms...
February 3, 2017: Biophysical Chemistry
https://www.readbyqxmd.com/read/28187128/neural-mechanisms-of-rhythm-based-temporal-prediction-delta-phase-locking-reflects-temporal-predictability-but-not-rhythmic-entrainment
#18
Assaf Breska, Leon Y Deouell
Predicting the timing of upcoming events enables efficient resource allocation and action preparation. Rhythmic streams, such as music, speech, and biological motion, constitute a pervasive source for temporal predictions. Widely accepted entrainment theories postulate that rhythm-based predictions are mediated by synchronizing low-frequency neural oscillations to the rhythm, as indicated by increased phase concentration (PC) of low-frequency neural activity for rhythmic compared to random streams. However, we show here that PC enhancement in scalp recordings is not specific to rhythms but is observed to the same extent in less periodic streams if they enable memory-based prediction...
February 2017: PLoS Biology
https://www.readbyqxmd.com/read/28186403/discretely-supported-dry-adhesive-film-inspired-by-biological-bending-behavior-for-enhanced-performance-on-rough-surface
#19
Hong Hu, Hongmiao Tian, Jinyou Shao, Xiangming Li, Yue Wang, Yan Wang, Yu Tian, Bingheng Lu
Biologically inspired dry adhesion is recently a research hot topic because of its practical significance in scientific research and instrumental technology. Yet, most of the current studies merely focus on borrowing the concept from some finer biological contact elements, but lose sight of the foundation ones that play an equally important role in the adhesion functionality. Inspired by bending behavior of the flexible foundation element of gecko (lamellar skin) in attachment motion, in this study, a new type of dry adhesive structure was proposed, wherein a mushroom-shaped micropillar array behaving as a strongly adhesive layer was engineered on a discretely-supported thin film...
February 10, 2017: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/28181798/shape-morphing-materials-from-stimuli-responsive-hydrogel-hybrids
#20
Seog-Jin Jeon, Adam W Hauser, Ryan C Hayward
The formation of well-defined and functional three-dimensional (3D) structures by buckling of thin sheets subjected to spatially nonuniform stresses is common in biological morphogenesis and has become a subject of great interest in synthetic systems, as such programmable shape-morphing materials hold promise in areas including drug delivery, biomedical devices, soft robotics, and biomimetic systems. Given their ability to undergo large changes in swelling in response to a wide variety of stimuli, hydrogels have naturally emerged as a key type of material in this field...
February 9, 2017: Accounts of Chemical Research
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