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Dynamic stretching

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https://www.readbyqxmd.com/read/28225608/time-dependent-markov-state-models-for-single-molecule-force-spectroscopy
#1
Susmita Ghosh, Abhijit Chatterjee, Swati Bhattacharya
This Letter demonstrates that using time-dependent Markov state models (TD-MSMs) one can obtain molecular-scale insights into force-extension curves for a variety of stretching experiments. A master-MSM constructed at a reference extension using a handful of molecular dynamics calculations forms the basis for generating the required TD-MSM. Changes in the network topology upon stretching is related through a thermodynamic quantity termed the mechanical disposition. Proof-of-principle is provided using a stretched alanine decapeptide under a time-varying pulling force...
February 22, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28216791/molecular-processes-leading-to-necking-in-extensional-flow-of-polymer-solutions-using-microfluidics-and-single-dna-imaging
#2
Shaurya Sachdev, Aswin Muralidharan, Pouyan E Boukany
We study the necking and pinch-off dynamics of liquid droplets that contain a semidilute polymer solution of polyacrylamide close to overlap concentration by combining microfluidics and single DNA observation. Polymeric droplets are stretched by passing them through the stagnation point of a T-shaped microfluidic junction. In contrast with the sudden breakup of Newtonian droplets, a stable neck is formed between the separating ends of the droplet which delays the breakup process. Initially, polymeric filaments experience exponential thinning by forming a stable neck with extensional flow within the filament...
December 27, 2016: Macromolecules
https://www.readbyqxmd.com/read/28214612/dynamic-organization-of-mitotic-chromosomes
#3
REVIEW
Kazuhisa Kinoshita, Tatsuya Hirano
The assembly of rod-shaped chromosomes during mitosis is an essential prerequisite for faithful segregation of genetic information into daughter cells. Despite the long history of chromosome research, it is only recently that we have acquired powerful approaches and crucial tools that help to unlock the secret of this seemingly complex process. In particular, in vitro assays, mammalian genetics, Hi-C analyses and computer simulations have provided valuable information during the past two years. These studies are now beginning to elucidate how the core components of mitotic chromosomes, namely, histones, topoisomerase IIα and condensins, cooperate with each other to convert very long stretches of DNA into rod-shaped chromosomes...
February 16, 2017: Current Opinion in Cell Biology
https://www.readbyqxmd.com/read/28212103/simulation-of-healing-threshold-in-strain-induced-inflammation-through-a-discrete-informatics-model
#4
Israr Ibrahim, Sanjay Venkata Oruganti, Ramana Pidaparti
Respiratory diseases such as asthma and acute respiratory distress syndrome as well as acute lung injury involve inflammation at the cellular level. The inflammation process is very complex and is characterized by the emergence of cytokines along with other changes in cellular processes. Due to the complexity of the various constituents that makes up the inflammation dynamics, it is necessary to develop models that can complement experiments to fully understand inflammatory diseases. In this study, we developed a discrete informatics model based on cellular automata (CA) approach to investigate the influence of elastic field (stretch/strain) on the dynamics of inflammation and account for probabilistic adaptation based on statistical interpretation of existing experimental data...
February 15, 2017: IEEE Journal of Biomedical and Health Informatics
https://www.readbyqxmd.com/read/28211708/direct-observation-of-spatiotemporal-dynamics-of-short-electron-bunches-in-storage-rings
#5
C Evain, E Roussel, M Le Parquier, C Szwaj, M-A Tordeux, J-B Brubach, L Manceron, P Roy, S Bielawski
In recent synchrotron radiation facilities, the use of short (picosecond) electron bunches is a powerful method for producing giant pulses of terahertz coherent synchrotron radiation. Here we report on the first direct observation of these pulse shapes with a few picoseconds resolution, and of their dynamics over a long time. We thus confirm in a very direct way the theories predicting an interplay between two physical processes. Below a critical bunch charge, we observe a train of identical THz pulses (a broadband Terahertz comb) stemming from the shortness of the electron bunches...
February 3, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/28208503/onset-of-shear-thinning-in-glassy-liquids-shear-induced-small-reduction-of-effective-density
#6
Akira Furukawa
We propose a simple mechanism for describing the onset of shear thinning in a high-density glassy liquid. In a shear flow, along the compression axis, the overlap between neighboring particles is more enhanced than that at equilibrium, meaning that the "effective" size is reduced along this axis. On the other hand, along the extension axis perpendicular to the compression axis, the average structural configurations are stretched, but it does not indicate the expansion of the "effective" size itself. This asymmetric shear flow effect for particles results in a small reduction of the "effective" density...
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28208388/nonequilibrium-markov-state-modeling-of-the-globule-stretch-transition
#7
Fabian Knoch, Thomas Speck
We describe a systematic approach to construct coarse-grained Markov state models from molecular dynamics data of systems driven into a nonequilibrium steady state. We apply this method to study the globule-stretch transition of a single tethered model polymer in shear flow. The folding and unfolding rates of the coarse-grained model agree with the original detailed model. We demonstrate that the folding and unfolding proceeds through the same narrow region of configuration space but along different cycles.
January 2017: Physical Review. E
https://www.readbyqxmd.com/read/28195156/finding-stable-graphene-conformations-from-pull-and-release-experiments-with-molecular-dynamics
#8
Ruslan D Yamaletdinov, Yuriy V Pershin
Here, we demonstrate that stable conformations of graphene nanoribbons can be identified using pull and release experiments, when the stretching force applied to a single-layer graphene nanoribbon is suddenly removed. As it is follows from our numerical experiments performed by means of molecular dynamics simulations, in such experiments, favorable conditions for the creation of folded structures exist. Importantly, at finite temperatures, the process of folding is probabilistic. We have calculated the transition probabilities to folded conformations for a graphene nanoribbon of a selected size...
February 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28194966/what-makes-telomeres-unique
#9
Adam Kazimierz Sieradzan, Pawel Krupa, David J Wales
Telomeres are repetitive nucleotide sequences, which are essential for protecting the termini of chromosomes. Thousands of such repetitions are necessary to maintain the stability of the whole chromosome. Several similar repeated telomeric sequences have been found in different species, but why has nature chosen them? What features do telomeres have in common? In this article we study the physical properties of human-like (TTAGGG), plant (TTTAGG), insect (TTAGG) and candida guilermondi (GGTGTAC) telomeres in comparison with seven, control, non-telomeric sequences...
February 14, 2017: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/28193505/statistical-modelling-of-ion-pgm-hid-str-10-plex-mps-data
#10
Søren B Vilsen, Torben Tvedebrink, Helle Smidt Mogensen, Niels Morling
We investigated the results of short tandem repeat (STR) markers of dilution series experiments and reference profiles generated using the Ion PGM massively parallel sequencing platform utilising the HID STR 10-plex panel. The STR markers were identified by the marker specific flanking regions of the STR region. We investigated the following: (1) the usage of quality measures for identifying substitution errors, (2) the heterozygote balance and compared it to that of capillary electrophoresis (CE), (3) the stability of the coverage and the consequence of IonExpress Barcode adapter (IBA) sampling with decreasing amounts of template DNA, (4) the hypothesis that the parental longest uninterrupted stretch (LUS) is a better linear predictor of stutter ratio than the parent allele length, (5) the use of parental allele length as a predictor of shoulder ratio, and (6) the removal of non-systematic erroneous sequences using dynamic thresholds created by fitting the distribution of the non-systematic erroneous sequences...
February 3, 2017: Forensic Science International. Genetics
https://www.readbyqxmd.com/read/28192670/metal-ion-mediated-cellulose-nanofibrils-transient-network-in-covalently-cross-linked-hydrogels-mechanistic-insight-into-morphology-and-dynamics
#11
Jun Yang, Feng Xu, Chun-Rui Han
Utilization of reversible interactions as sacrificial bonds in biopolymers is critical for the integral synthesis of mechanically superior biological materials. In this work, cellulose nanofibrils (CNFs) reinforced covalent polyacrylamide (PAAm) composite hydrogels are immersed into multivalent cation (Ca2+, Zn2+, Al3+, and Ce3+) aqueous solution to form ionic association among CNFs, leading to the ionic-covalent cross-linked hydrogels. The cations promote the formation of porous networks of nanofibrils by screening the repulsive negative charges on CNF surface and dominate the mechanical properties and self-recovery efficiency of the hydrogels, resulting in mechanically reinforced ionic hydrogels with stiff (Young's modulus 257 kPa) and tough properties (fracture toughness 386 kJ/m3)...
February 13, 2017: Biomacromolecules
https://www.readbyqxmd.com/read/28182984/study-of-cr%C3%A2-sma-phase-transition-and-hydrogen-bonding-in-four-ring-bent-core-liquid-crystal
#12
Swapnil Singh, Harshita Singh, Poonam Tandon, Nirmalangshu Chakraborty, N V S Rao, A P Ayala
A newly designed asymmetrical four-ring bent-core compound (4'-n-decyloxyphenylazo)-phenyl-4-yl-3-[N-(4'-n-octadecyloxy-2-hydroxybenzylidene) amino]-2-methyl benzoate exhibiting liquid crystalline behavior was synthesized and characterized. The thermal and textural morphology were studied using differential scanning calorimetry and polarizing optical microscopy, respectively. The study of hydrogen bonding and dynamics of the phase transition has been performed at the molecular level using temperature dependent Fourier transform infrared (FTIR) spectroscopy...
February 3, 2017: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/28178815/unfolding-dna-condensates-produced-by-dna-like-charged-depletants-a-force-spectroscopy-study
#13
C H M Lima, M S Rocha, E B Ramos
In this work, we have measured, by means of optical tweezers, forces acting on depletion-induced DNA condensates due to the presence of the DNA-like charged protein bovine serum albumin (BSA). The stretching and unfolding measurements performed on the semi-flexible DNA chain reveal (1) the softening of the uncondensed DNA contour length and (2) a mechanical behavior strikingly different from those previously observed: the force-extension curves of BSA-induced DNA condensates lack the "saw-tooth" pattern and applied external forces as high as ≈80 pN are unable to fully unfold the condensed DNA contour length...
February 7, 2017: Journal of Chemical Physics
https://www.readbyqxmd.com/read/28177634/effect-of-chain-conformation-on-the-single-molecule-melting-force-in-polymer-single-crystals-steered-molecular-dynamics-simulations-study
#14
Wei Feng, Zhigang Wang, Wenke Zhang
Understanding the relationship between polymer chain conformation as well as the chain composition within the single crystal and the mechanical properties of the corresponding single polymer chain will facilitate the rational design of high performance polymer materials. Here three model systems of polymer single crystals, namely poly(ethylene oxide) (PEO), polyethylene (PE), and nylon-66 (PA66) have been chosen to study the effects of chain conformation, helical (PEO) versus planar zigzag conformation (PE, PA66), and chain composition (PE versus PA66) on the mechanical properties of a single polymer chain...
February 15, 2017: Langmuir: the ACS Journal of Surfaces and Colloids
https://www.readbyqxmd.com/read/28177631/approximate-quantum-dynamics-using-ab-initio-classical-separable-potentials-spectroscopic-applications
#15
Barak Hirshberg, Lior Sagiv, Robert Benny Gerber
Algorithms for quantum molecular dynamics simulations which use directly ab initio methods have many potential applications. In this paper, the Ab Initio Classical Separable Potentials method (AICSP) is proposed as the basis for approximate algorithms of this type. The AICSP method assumes separability of the total time-dependent wavefunction of the nuclei, and employs mean-field potentials that govern the dynamics of each degree of freedom. In the proposed approach, the mean-field potentials are determined by classical ab initio molecular dynamics (AIMD) simulations...
February 8, 2017: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/28169506/a-combinational-effect-of-bulk-and-surface-shape-memory-transitions-on-the-regulation-of-cell-alignment
#16
Koichiro Uto, Takao Aoyagi, Cole A DeForest, Allan S Hoffman, Mitsuhiro Ebara
A novel shape-memory cell culture platform has been designed that is capable of simultaneously tuning surface topography and dimensionality to manipulate cell alignment. By crosslinking poly(ε-caprolactone) (PCL) macromonomers of precisely designed nanoarchitectures, a shape-memory PCL with switching temperature near body temperature is successfully prepared. The temporary strain-fixed PCLs are prepared by processing through heating, stretching, and cooling about the switching temperature. Temporary nanowrinkles are also formed spontaneously during the strain-fixing process with magnitudes that are dependent on the applied strain...
February 7, 2017: Advanced Healthcare Materials
https://www.readbyqxmd.com/read/28166904/difference-between-male-and-female-workers-lifting-the-same-relative-load-when-palletizing-boxes
#17
A Plamondon, C Larivière, D Denis, H Mecheri, I Nastasia
A few biomechanical studies have contrasted the work techniques of female and male workers during manual material handling (MMH). A recent study showed that female workers differed from males mostly in the strategy they used to lift 15-kg boxes from the ground, especially regarding task duration, knee and back postures and interjoint coordination. However, the lifting technique difference observed in females compared to males was perhaps due to a strength differences. The objective of this study was to test whether female workers would repeat the same lifting technique with a load adjusted to their overall strength (females: 10 kg; males: 15 kg), which can be considered a "relative load" since the overall back strength of females is 2/3 that of males...
April 2017: Applied Ergonomics
https://www.readbyqxmd.com/read/28162971/comparison-of-friction-forces-between-stainless-orthodontic-steel-brackets-and-tini-wires-in-wet-and-dry-conditions
#18
Aphinan Phukaoluan, Anak Khantachawana, Pongpan Kaewtatip, Surachai Dechkunakorn, Niwat Anuwongnukroh, Peerapong Santiwong, Julathep Kajornchaiyakul
In sliding mechanics, frictional force is an important counter-balancing element to orthodontic tooth movement, which must be controlled in order to allow application of light continuous forces. The purpose of this study was to compare the frictional forces between a stainless steel bracket and five different wire alloys under dry and wet (artificial saliva) conditions. TiNi, TiNiCu, TiNiCo, commercial wires A and commercial wires B with equal dimensions of 0.016×0.022'' were tested in this experiment. The stainless steel bracket was chosen with a slot dimension of 0...
February 2, 2017: International Orthodontics
https://www.readbyqxmd.com/read/28160525/automatic-intensity-windowing-of-mammographic-images-based-on-a-perceptual-metric
#19
Alberto Albiol, Alberto Corbi, Francisco Albiol
PURPOSE: Initial auto-adjustment of the window level WL and width WW applied to mammo-graphic images. The proposed intensity windowing (IW) method is based on the maximization of the mutual information (MI) between a perceptual decomposition of the original 12-bit sources and their screen displayed 8-bit version. Besides zoom, color inversion and panning operations, IW is the most commonly performed task in daily screening and has a direct impact on diagnosis and the time involved in the process...
February 4, 2017: Medical Physics
https://www.readbyqxmd.com/read/28155694/%C3%AE-1-integrin-signaling-in-asymmetric-migration-of-keratinocytes-under-mechanical-stretch-in-a-co-cultured-wound-repair-model
#20
Dongyuan Lü, Zhan Li, Yuxin Gao, Chunhua Luo, Fan Zhang, Lu Zheng, Jiawen Wang, Shujin Sun, Mian Long
BACKGROUND: Keratinocyte (KC) migration in re-epithelization is crucial in repairing injured skin. But the mechanisms of how mechanical stimuli regulate the migration of keratinocytes have been poorly understood. METHODS: Human immortalized keratinocyte HaCaT cells were co-cultured with skin fibroblasts on PDMS membranes and transferred to the static stretch device developed in-house for additional 6 day culture under mechanical stretch to mimic surface tension in skin...
December 28, 2016: Biomedical Engineering Online
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