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https://www.readbyqxmd.com/read/29350922/computing-curvature-sensitivity-of-biomolecules-in-membranes-by-simulated-buckling
#1
Federico Elias-Wolff, Martin Lindén, Alexander P Lyubartsev, Erik G Brandt
Membrane curvature sensing, where the binding free energies of membrane-associated molecules depend on the local membrane curvature, is a key factor to modulate and maintain the shape and organization of cell membranes. However, the microscopic mechanisms are not well understood, partly due to absence of efficient simulation methods. Here, we describe a method to compute the curvature dependence of the binding free energy of a membrane-associated probe molecule that interacts with a buckled membrane, which has been created by lateral compression of a flat bilayer patch...
January 19, 2018: Journal of Chemical Theory and Computation
https://www.readbyqxmd.com/read/29350229/aggregate-evolution-in-aqueous-solutions-of-a-gemini-surfactant-derived-from-dehydroabietic-acid
#2
Lin Feng, Danhua Xie, Binglei Song, Jiayu Zhang, Xiaomei Pei, Zhenggang Cui
Innovations in surfactant structure are a feasible way to probe molecular self-assembly principles. Herein, the solution behaviour of a newly synthesized Gemini surfactant derived from dehydroabietic acid, abbreviated R-(EO)-E-R, was investigated using surface tension, fluorescence, isothermal titration calorimetry (ITC), rheology, freeze-fracture transmission electron microscopy (FF-TEM) and cryogenic transmission electron microscopy (cryo-TEM) methods. R-(EO)-E-R has two large, rigid hydrophobic groups. At low concentrations, R-(EO)-E-R forms micelles with an aggregation number of approximately 10, which is smaller than those of Gemini surfactants containing flexible alkyl tails...
January 19, 2018: Soft Matter
https://www.readbyqxmd.com/read/29349619/1h-15n-and-13c-chemical-shift-assignments-of-the-micelle-immersed-fat-c-terminal-fatc-domains-of-the-human-protein-kinases-ataxia-telangiectasia-mutated-atm-and-dna-dependent-protein-kinase-catalytic-subunit-dna-pkcs-fused-to-the-b1-domain-of-streptococcal
#3
Munirah S Abd Rahim, Lisa A M Sommer, Anja Wacker, Martin Schaad, Sonja A Dames
FAT C-terminal (FATC) is a circa 33 residue-long domain. It controls the kinase functionality in phosphatidylinositol-3 kinase-related kinases (PIKKs). Recent NMR- and CD-monitored interaction studies indicated that the FATC domains of all PIKKs can interact with membrane mimetics albeit with different preferences for membrane properties such as surface charge and curvature. Thus they may generally act as membrane anchoring unit. Here, we present the 1H, 15N, and 13C chemical shift assignments of the DPC micelle immersed FATC domains of the human PIKKs ataxia-telangiectasia mutated (ATM, residues 3024-3056) and DNA protein kinase catalytic subunit (DNA-PKcs, residues 4096-4128), both fused to the 56 residue long B1 domain of Streptococcal protein G (GB1)...
January 18, 2018: Biomolecular NMR Assignments
https://www.readbyqxmd.com/read/29347751/surface-deformation-during-an-action-potential-in-pearled-cells
#4
Matan Mussel, Christian Fillafer, Gal Ben-Porath, Matthias F Schneider
Electric pulses in biological cells (action potentials) have been reported to be accompanied by a propagating cell-surface deformation with a nanoscale amplitude. Typically, this cell surface is covered by external layers of polymer material (extracellular matrix, cell wall material, etc.). It was recently demonstrated in excitable plant cells (Chara braunii) that the rigid external layer (cell wall) hinders the underlying deformation. When the cell membrane was separated from the cell wall by osmosis, a mechanical deformation, in the micrometer range, was observed upon excitation of the cell...
November 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347632/dynamics-of-a-thermally-driven-film-climbing-the-outside-of-a-vertical-cylinder
#5
Linda B Smolka
The dynamics of a film climbing the outside of a vertical cylinder under the competing effects of a thermally driven surface tension gradient and gravity is examined through numerical simulations of a thin-film model for the film height. The model, including boundary conditions, depends on three parameters, the scaled cylinder radius R[over ̂], the upstream film height h_{∞}, and the downstream precursor film thickness b, and reduces to the model for Marangoni driven film climbing a vertical plate in the limit R[over ̂]→∞...
October 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347458/emergent-dynamic-structures-and-statistical-law-in-spherical-lattice-gas-automata
#6
Zhenwei Yao
Various lattice gas automata have been proposed in the past decades to simulate physics and address a host of problems on collective dynamics arising in diverse fields. In this work, we employ the lattice gas model defined on the sphere to investigate the curvature-driven dynamic structures and analyze the statistical behaviors in equilibrium. Under the simple propagation and collision rules, we show that the uniform collective movement of the particles on the sphere is geometrically frustrated, leading to several nonequilibrium dynamic structures not found in the planar lattice, such as the emergent bubble and vortex structures...
December 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347242/multi-phase-field-model-for-surface-and-phase-boundary-diffusion
#7
Raphael Schiedung, Reza Darvishi Kamachali, Ingo Steinbach, Fathollah Varnik
The multi-phase-field approach is generalized to treat capillarity-driven diffusion parallel to the surfaces and phase boundaries, i.e., the boundaries between a condensed phase and its vapor and the boundaries between two or multiple condensed phases. The effect of capillarity is modeled via curvature dependence of the chemical potential whose gradient gives rise to diffusion. The model is used to study thermal grooving on the surface of a polycrystalline body. Decaying oscillations of the surface profile during thermal grooving, postulated by Hillert long ago but reported only in few studies so far, are observed and discussed...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347169/nonlinear-mechanics-of-rigidifying-curves
#8
Salem Al Mosleh, Christian Santangelo
Thin shells are characterized by a high cost of stretching compared to bending. As a result isometries of the midsurface of a shell play a crucial role in their mechanics. In turn, curves on the midsurface with zero normal curvature play a critical role in determining the number and behavior of isometries. In this paper, we show how the presence of these curves results in a decrease in the number of linear isometries. Paradoxically, shells are also known to continuously fold more easily across these rigidifying curves than other curves on the surface...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29347148/impact-of-interaction-range-and-curvature-on-crystal-growth-of-particles-confined-to-spherical-surfaces
#9
Stefan Paquay, Gert-Jan Both, Paul van der Schoot
When colloidal particles form a crystal phase on a spherical template, their packing is governed by the effective interaction between them and the elastic strain of bending the growing crystal. For example, if growth commences under appropriate conditions, and the isotropic crystal that forms reaches a critical size, growth continues via the incorporation of defects to alleviate elastic strain. Recently, it was experimentally found that, if defect formation is somehow not possible, the crystal instead continues growing in ribbons that protrude from the original crystal...
July 2017: Physical Review. E
https://www.readbyqxmd.com/read/29346890/mechanics-of-active-surfaces
#10
Guillaume Salbreux, Frank Jülicher
We derive a fully covariant theory of the mechanics of active surfaces. This theory provides a framework for the study of active biological or chemical processes at surfaces, such as the cell cortex, the mechanics of epithelial tissues, or reconstituted active systems on surfaces. We introduce forces and torques acting on a surface, and derive the associated force balance conditions. We show that surfaces with in-plane rotational symmetry can have broken up-down, chiral, or planar-chiral symmetry. We discuss the rate of entropy production in the surface and write linear constitutive relations that satisfy the Onsager relations...
September 2017: Physical Review. E
https://www.readbyqxmd.com/read/29344800/platycodon-saponins-from-platycodi-radix-platycodon-grandiflorum-for-the-green-synthesis-of-gold-and-silver-nanoparticles
#11
Yoonho Choi, Sehyeon Kang, Song-Hyun Cha, Hyun-Seok Kim, Kwangho Song, You Jeong Lee, Kyeongsoon Kim, Yeong Shik Kim, Seonho Cho, Youmie Park
A green synthesis of gold and silver nanoparticles is described in the present report using platycodon saponins from Platycodi Radix (Platycodon grandiflorum) as reducing agents. Platycodin D (PD), a major triterpenoidal platycodon saponin, was enriched by an enzymatic transformation of an aqueous extract of Platycodi Radix. This PD-enriched fraction was utilized for processing reduction reactions of gold and silver salts to synthesize gold nanoparticles (PD-AuNPs) and silver nanoparticles (PD-AgNPs), respectively...
January 17, 2018: Nanoscale Research Letters
https://www.readbyqxmd.com/read/29342869/surface-fitting-for-quasi-scattered-data-from-coordinate-measuring-systems
#12
Qing Mao, Shugui Liu, Sen Wang, Xinhui Ma
Non-uniform rational B-spline (NURBS) surface fitting from data points is wildly used in the fields of computer aided design (CAD), medical imaging, cultural relic representation and object-shape detection. Usually, the measured data acquired from coordinate measuring systems is neither gridded nor completely scattered. The distribution of this kind of data is scattered in physical space, but the data points are stored in a way consistent with the order of measurement, so it is named quasi scattered data in this paper...
January 13, 2018: Sensors
https://www.readbyqxmd.com/read/29339023/calculated-shape-dependence-of-electromagnetic-field-in-tip-enhanced-raman-scattering-by-using-a-monopole-antenna-model
#13
Yasutaka Kitahama, Tamitake Itoh, Toshiaki Suzuki
To evaluate the shape of an Ag tip with regard to tip-enhanced Raman scattering (TERS) signal, the enhanced electromagnetic (EM) field and scattering spectrum, arising from surface plasmon resonance at the apex of the tip, were calculated using a finite-difference time domain (FDTD) method. In the calculated forward scattering spectra from the smooth Ag tip, the band appeared within the visible region, similar to the experimental results and calculation for a corrugated Ag cone. In the FDTD calculation of TERS, the Ag tip acting as a monopole antenna was adopted by insertion of a perfect electric conductor between the root of the tip and a top boundary surface of the calculation space...
January 5, 2018: Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy
https://www.readbyqxmd.com/read/29328713/egalitarianism-among-bubbles-in-porous-media-an-ostwald-ripening-derived-anticoarsening-phenomenon
#14
Ke Xu, Roger Bonnecaze, Matthew Balhoff
We show that smaller gas bubbles grow at the expense of larger bubbles and all bubbles approach the same surface curvature after long times in porous media. This anticoarsening effect is contrary to typical Ostwald ripening and leads to uniformly sized bubbles in a homogeneous medium. Evolution dynamics of bubble populations were measured, and mathematical models were developed that fit the experimental data well. Ostwald ripening is shown to be the driving mechanism in this anticoarsening phenomenon; however, the relationship between surface curvature and bubble size determined by the pore-throat geometric confinement reverses the ripening direction...
December 29, 2017: Physical Review Letters
https://www.readbyqxmd.com/read/29323935/shape-related-characteristics-of-age-related-differences-in-subcortical-structures
#15
Christopher R Madan
OBJECTIVES: With an increasing aging population, it is important to understand biological markers of aging. Subcortical volume is known to differ with age; additionally considering shape-related characteristics may provide a better index of age-related differences. Fractal dimensionality is more sensitive to age-related differences, but is borne out of mathematical principles, rather than neurobiological relevance. We considered four distinct measures of shape and how they relate to aging and fractal dimensionality: surface-to-volume ratio, sphericity, long-axis curvature, and surface texture...
January 11, 2018: Aging & Mental Health
https://www.readbyqxmd.com/read/29323432/orthogonal-%C3%A2-%C3%A2-f-labeling-for-solid-state-nmr-reveals-the-conformation-and-orientation-of-short-peptaibols-in-membranes
#16
Stephan L Grage, Sezgin Kara, Andrea Bordessa, Véronique Doan, Fabio Rizzolo, Marina Putzu, Tomáš Kubař, Anna Maria Papini, Grégory Chaume, Thierry Brigaud, Sergii Afonin, Anne S Ulrich
Peptaibols are promising drug candidates in view of their interference with cellular membranes. Knowledge of their lipid interactions and membrane-bound structure is needed for understanding their activity and should be in principle accessible by solid-state NMR. However, their unusual amino acid composition and their non-canonical conformations make it very challenging to find suitable NMR labels. Especially in the case of short sequences, new strategies are required to maximize the structural information that can be obtained from each label...
January 11, 2018: Chemistry: a European Journal
https://www.readbyqxmd.com/read/29321557/haptic-shape-discrimination-and-interhemispheric-communication
#17
Catherine J Dowell, J Farley Norman, Jackie R Moment, Lindsey M Shain, Hideko F Norman, Flip Phillips, Astrid M L Kappers
In three experiments participants haptically discriminated object shape using unimanual (single hand explored two objects) and bimanual exploration (both hands were used, but each hand, left or right, explored a separate object). Such haptic exploration (one versus two hands) requires somatosensory processing in either only one or both cerebral hemispheres; previous studies related to the perception of shape/curvature found superior performance for unimanual exploration, indicating that shape comparison is more effective when only one hemisphere is utilized...
January 10, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29317999/volume-completion-between-contour-fragments-at-discrete-depths
#18
Peter Ulric Tse
Building on the modal and amodal completion work of Kanizsa, Carman and Welch showed that binocular stereo viewing of two disparate images can give rise to a percept of 3D curved, nonclosed illusory contours and surfaces. Here, it is shown that binocular presentation can also give rise to the percept of closed curved surfaces or volumes that appear to vary smoothly across discrete depths in binocularly fused images, although in fact only two binocular disparities are discretely defined between corresponding contour elements of the inducing elements...
November 2017: I-Perception
https://www.readbyqxmd.com/read/29317580/-effect-of-high-intensity-alternating-magnetic-field-%C3%A2-on-viscosity-of-sheep-blood
#19
Pengxian Tao, Xiangyang Wu, Lingzhi Zhao, Feng Wang, Qi Xia, Yan Peng, Bingren Gao
To explore the changes of blood viscosity in high-intensity alternating magnetic field and the mechanisms.
 Methods: Five adult sheep were randomly selected and the blood samples were placed in high-intensity alternating magnetic field. Before and after exposure, the blood samples were taken and divided into 2 groups: a control group and a magnetic field group. The blood rheology and transmission electron microscopy (TEM) were performed.
 Results: Compared to the control group, the high shear viscosity of whole blood was decreased in the magnetic field group (P<0...
December 28, 2017: Zhong Nan da Xue Xue Bao. Yi Xue Ban, Journal of Central South University. Medical Sciences
https://www.readbyqxmd.com/read/29314565/modelling-the-interaction-of-co-with-flexible-graphene-from-coupled-cluster-calculations-to-molecular-dynamics-simulations
#20
Jake Wilson, Noelia Faginas-Lago, Jelle Vekeman, Inmaculada García Cuesta, José Sánchez-Marín, Alfredo Sánchez de Merás
The interaction of CO with graphene has been studied at different theoretical levels. Quantum mechanical calculations on finite graphene models using coronene for coupled cluster calculations and circumcoronene for B97D calculations showed that there exists no preferential site for adsorption and that the most important factor is the orientation of CO relative to graphene. The parallel orientation is preferred, with binding energies around 9 kJ mol-1 at the CCSD(T) and B97D levels, in good agreement with experimental findings...
January 4, 2018: Chemphyschem: a European Journal of Chemical Physics and Physical Chemistry
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