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European Physical Journal. E, Soft Matter

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https://www.readbyqxmd.com/read/30014219/correlation-between-polar-surface-area-and-bioferroelectricity-in-dna-and-rna-nucleobases
#1
See-Chuan Yam, Sharifuddin Md Zain, Vannajan Sanghiran Lee, Khian-Hooi Chew
We have performed computational molecular modelling to study the polarization switching and hysteresis loop behaviours of DNA and RNA nucleobases using the PM3 semi-empirical quantum mechanical approaches. All the nucleobases: adenine (A), thymine (T), guanine (G), cytosine (C), and uracil (U) were modelled. Our study indicates that all the nucleobases exhibit a zero-field polarization due to the presence of polar atoms or molecules such as amidogen and carbonyl. The shape of polarization P versus an applied electric field E hysteresis loop is square, implying typical ferroelectrics behaviour...
July 18, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/30003353/neutron-reflectivity-measurements-at-the-oil-water-interface-for-the-study-of-stimuli-responsive-emulsions-%C3%A2
#2
M Protat, N Bodin-Thomazo, F Malloggi, J Daillant, R A Campbell, G Fragneto, E B Watkins, P Perrin, N Pantoustier, P Guenoun
Stable stimuli-responsive emulsions between oil and water are formed with an amphiphilic block copolymer bearing polystyrene (PS) and poly(dimethylaminoethyl methacrylate) (PDMAEMA) moieties. Different kinds of emulsions like direct, multiple or inverse ones are reproducibly formed as a function of chemical parameters such as p H and salt concentration. To test the correlation between the different nature of the emulsion and the conformation of the polymer chain at the interface, neutron reflectometry at the oil/water interface was carried out...
July 16, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29987441/enhancement-of-mixing-by-rodlike-polymers
#3
Stefano Musacchio, Massimo Cencini, Emmanuel L C Vi M Plan, Dario Vincenzi
We study the mixing of a passive scalar field dispersed in a solution of rodlike polymers in two dimensions, by means of numerical simulations of a rheological model for the polymer solution. The flow is driven by a parallel sinusoidal force (Kolmogorov flow). Although the Reynolds number is lower than the critical value for inertial instabilities, the rotational dynamics of the polymers generates a chaotic flow similar to the so-called elastic-turbulence regime observed in extensible polymer solutions. The temporal decay of the variance of the scalar field and its gradients shows that this chaotic flow strongly enhances mixing...
July 11, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29974276/sensing-adsorption-kinetics-through-slip-velocity-measurements-of-polymer-melts
#4
Marceau Hénot, Eric Drockenmuller, Liliane Léger, Frédéric Restagno
The evolution over time of the nonlinear slip behavior of a polydimethylsiloxane (PDMS) polymer melt on a weakly adsorbing surface made of short non-entangled PDMS chains densely end-grafted to the surface of a fused silica prism has been measured. The critical shear rate at which the melt enters the nonlinear slip regime has been shown to increase with time. The adsorption kinetics of the melt on the same surface has been determined independently using ellipsometry. We show that the evolution of slip can be explained by the slow adsorption of melt chains using the Brochard-de Gennes's model...
July 9, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29974275/controlling-breath-figure-patterns-on-pdms-by-concentration-variation-of-ethanol-methanol-binary-vapors
#5
K Nilavarasi, V Madhurima
In this paper, the self-assembly of condensed droplets on smooth and constrained surfaces under saturated vapor atmosphere of ethanol and methanol binary system is reported. Hexagonally ordered array of pores are obtained on smooth surfaces with saturated vapors of binary liquids without the assistance of any additives. The results show that the addition of a small amount of ethanol to methanol plays a role very similar to that of surface active agents in inducing the formation of a regular droplet array. The effect of constraints on a self-assembled droplet pattern such as the movement of the contact line and the depinning of the contact line is also investigated...
July 9, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29974268/sub-picosecond-proton-tunnelling-in-deformed-dna-hydrogen-bonds-under-an-asymmetric-double-oscillator-model
#6
J Luo
We present a model of proton tunnelling across DNA hydrogen bonds, compute the characteristic tunnelling time (CTT) from donor to acceptor and discuss its biological implications. The model is a double oscillator characterised by three geometry parameters describing planar deformations of the H bond, and a symmetry parameter representing the energy ratio between ground states in the individual oscillators. We discover that some values of the symmetry parameter lead to CTTs which are up to 40 orders of magnitude smaller than a previous model predicted...
July 6, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29955976/on-the-effect-of-the-thermostat-in-non-equilibrium-molecular-dynamics-simulations
#7
José Ruiz-Franco, Lorenzo Rovigatti, Emanuela Zaccarelli
The numerical investigation of the statics and dynamics of systems in non-equilibrium in general, and under shear flow in particular, has become more and more common. However, not all the numerical methods developed to simulate equilibrium systems can be successfully adapted to out-of-equilibrium cases. This is especially true for thermostats. Indeed, even though thermostats developed to work under equilibrium conditions sometimes display good agreement with rheology experiments, their performance rapidly degrades beyond weak dissipation and small shear rates...
July 2, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29934856/distinctive-diffusive-properties-of-swimming-planktonic-copepods-in-different-environmental-conditions
#8
Raffaele Pastore, Marco Uttieri, Giuseppe Bianco, Maurizio Ribera d'Alcalá, Maria Grazia Mazzocchi
Suspensions of small planktonic copepods represent a special category in the realm of active matter, as their size falls within the range of colloids, while their motion is so complex that it cannot be rationalized according to basic models of self-propelled particles. Indeed, the wide range of individual variability and swimming patterns resemble the behaviour of much larger animals. By analysing hundreds of three-dimensional trajectories of the planktonic copepod Clausocalanus furcatus, we investigate the possibility of detecting how the motion of this species is affected by different external conditions, such as the presence of food and the effect of gravity...
June 25, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29926202/translocation-of-polyampholytes-and-intrinsically-disordered-proteins-%C3%A2
#9
A Johner, J F Joanny
Polyampholytes are polymers carrying electrical charges of both signs along their backbone. We consider synthetic polyampholytes with a quenched random charge sequence and intrinsically disordered proteins, which have a well-defined charge sequence and behave like polyampholytes in the denaturated state. We study their translocation driven by an electric field through a pore. The role of disorder along the charge sequence of synthetic polyampholytes is analyzed. We show how disorder slows down the translocation dynamics...
June 21, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29926213/size-dependent-interaction-of-a-3-arm-star-poly-ethylene-glycol-with-two-biological-nanopores
#10
Monasadat Talarimoghari, Gerhard Baaken, Ralf Hanselmann, Jan C Behrends
We use two pore-forming proteins, alpha-hemolysin and aerolysin, to compare the polymer size-dependence of ionic current block by two types of ethyleneglycol polymers: 1) linear and 2) 3-arm star poly(ethylene glycol), both applied as a polydisperse mixture of average mass 1kDa under high salt conditions. The results demonstrate that monomer size sensitivity, as known for linear PEGs, is conserved for the star polymers with only subtle differences in the dependence of the residual conductance on monomer number...
June 18, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29926290/rotating-flow-of-ag-cuo-h-2-o-hybrid-nanofluid-with-radiation-and-partial-slip-boundary-effects
#11
Tanzila Hayat, S Nadeem, A U Khan
The main object of the present paper is to examine and compare the improvement of flow and heat transfer characteristics between a rotating nanofluid and a newly discovered hybrid nanofluid in the presence of velocity slip and thermal slip. The influence of thermal radiation is also included in the present study. The system after applying the similarity transformations is solved numerically by using the bvp-4c scheme. Additionally, numerical calculations for the coefficient of skin friction and local Nusselt number are introduced and perused for germane parameters...
June 14, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29926216/from-hydrodynamic-lubrication-to-many-body-interactions-in-dense-suspensions-of-active-swimmers
#12
Natsuhiko Yoshinaga, Tanniemola B Liverpool
We study how hydrodynamic interactions affect the collective behaviour of active particles suspended in a fluid at high concentrations, with particular attention to lubrication forces which appear when the particles are very close to one another. We compute exactly the limiting behaviour of the hydrodynamic interactions between two spherical (circular) active swimmers in very close proximity to one another in the general setting in both three and (two) dimensions. Combining this with far-field interactions, we develop a novel numerical scheme which allows us to study the collective behaviour of large numbers of active particles with accurate hydrodynamic interactions when close to one another...
June 14, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29884928/on-the-contribution-of-the-chain-ends-to-the-surface-tension-of-a-polymer-melt
#13
Dominique Ausserré
We propose a physical picture describing the mechanisms by which chain ends affect the surface tension of a mono-dispersed polymer melt with chain length N. The driving effect is the adsorption equilibrium of chain ends within a bulk slice adjoining the surface and acting as a confined end reservoir. The thickness of that limited space is a characteristic length of the melt. This picture conforms to a previous approach proposed years ago by de Gennes. However, the characteristic length [Formula: see text] that we consider is different from the one [Formula: see text] that he considered...
June 12, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29884922/dislocations-dynamics-during-the-nonlinear-creep-of-a-homeotropic-sample-of-smectic-a-liquid-crystal
#14
P Oswald, G Poy
New creep experiments under sinusoidal compression/dilation deformation of a homeotropic sample of smectic-A liquid crystal (8CB) show that its response is nonlinear at very small amplitude of deformation. This behavior is explained by taking into account the crossing between the edge dislocations that climb parallel to the layers and the screw dislocations joining the two surfaces limiting the sample. The activation energy of the crossing process and the density of the screw dislocations as a function of the sample thickness are estimated experimentally...
June 12, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29884956/kymoknot-a-web-server-and-software-package-to-identify-and-locate-knots-in-trajectories-of-linear-or-circular-polymers
#15
Luca Tubiana, Guido Polles, Enzo Orlandini, Cristian Micheletti
The KymoKnot software package and web server identifies and locates physical knots or proper knots in a series of polymer conformations. It is mainly intended as an analysis tool for trajectories of linear or circular polymers, but it can be used on single instances too, e.g. protein structures in PDB format. A key element of the software package is the so-called minimally interfering chain closure algorithm that is used to detect physical knots in open chains and to locate the knotted region in both open and closed chains...
June 7, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29876655/continuous-time-random-walk-approach-to-supercooled-liquids-self-part-of-the-van-hove-function-and-related-quantities
#16
J Helfferich, J Brisch, H Meyer, O Benzerara, F Ziebert, J Farago, J Baschnagel
From equilibrium molecular dynamics (MD) simulations of a bead-spring model for short-chain glass-forming polymer melts we calculate several quantities characterizing the single-monomer dynamics near the (extrapolated) critical temperature [Formula: see text] of mode-coupling theory: the mean-square displacement g0 (t), the non-Gaussian parameter [Formula: see text] and the self-part of the van Hove function [Formula: see text] which measures the distribution of monomer displacements r in time t. We also determine these quantities from a continuous-time random walk (CTRW) approach...
June 1, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29802496/binding-of-trivalent-metal-ions-al-3-in-3-la-3-with-phosphatidylcholine-liposomal-membranes-investigated-by-microelectrophoresis
#17
Joanna Kotyńska, Zbigniew A Figaszewski
Interactions between trivalent metal ions (Al3+ , In3+ , La3+ ) and phosphatidylcholine (PC) liposomes are studied by microelectrophoresis. The dependence of the PC membrane surface charge density and zeta potential on [Formula: see text] ([Formula: see text] range from 2 to 10) of the aqueous metal chloride solutions is determined. The obtained results indicate the adsorption of Al3+ , In3+ and La3+ ions on phosphatidylcholine model membranes, leading to changes in the electrical properties of the membranes...
May 29, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29802504/shear-strength-of-wet-granular-materials-macroscopic-cohesion-and-effective-stress-discrete-numerical-simulations-confronted-to-experimental-measurements
#18
Michel Badetti, Abdoulaye Fall, François Chevoir, Jean-Noël Roux
Rheometric measurements on assemblies of wet polystyrene beads, in steady uniform quasistatic shear flow, for varying liquid content within the small saturation (pendular) range of isolated liquid bridges, are supplemented with a systematic study by discrete numerical simulations. The numerical results agree quantitatively with the experimental ones provided that the intergranular friction coefficient is set to the value [Formula: see text], identified from the behaviour of the dry material. Shear resistance and solid fraction [Formula: see text] are recorded as functions of the reduced pressure [Formula: see text], which, defined as [Formula: see text], compares stress [Formula: see text], applied in the velocity gradient direction, to the tensile strength [Formula: see text] of the capillary bridges between grains of diameter a, and characterizes cohesion effects...
May 28, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29802492/surface-and-extrapolated-point-charge-renormalizations-for-charge-stabilized-colloidal-spheres
#19
Yannick Hallez, Martine Meireles
The Derjaguin-Landau-Verwey-Overbeek (DLVO) theory is widely used to model interactions between weakly charged spheres in dilute suspensions. For particles bearing a higher charge, the linearized electrostatics underlying the DLVO theory is no longer valid but it is possible to map the real colloidal system to an auxiliary one that still obeys linear electrostatics but which involves a different, effective pair potential. This procedure, termed renormalization, can be performed in various ways, the most widely used being surface charge renormalization (SCR) based on the cell model...
May 28, 2018: European Physical Journal. E, Soft Matter
https://www.readbyqxmd.com/read/29845486/compressibility-of-ferrofluids-towards-a-better-understanding-of-structural-properties
#20
Elena S Minina, Elena S Pyanzina, Ekaterina V Novak, Sofia S Kantorovich
This paper addresses a computational method aimed at obtaining the isothermal compressibility of ferrofluids by means of molecular dynamics (MD) simulations. We model ferrofluids as a system of dipolar soft spheres and carry out MD simulations in the NPT ensemble. The obtained isothermal compressibility computed via volume fluctuations provides us with a strong evidence that dipolar interactions lead to a higher compressibility of dipolar soft sphere systems: the stronger the dipolar interactions, the bigger is the deviation of the compressibility from the one of a system with no dipoles...
May 25, 2018: European Physical Journal. E, Soft Matter
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