Molecules Stretch Research Articles

Conformational Evolution of Elongated Polymer Solutions Tailors the Polarization of Light-Emission from Organic Nanofibers.

Polymer fibers are currently exploited in tremendously important technologies. Their innovative properties are mainly determined by the behavior of the polymer macromolecules under the elongation induced by external mechanical or electrostatic forces, characterizing the fiber drawing process. Although enhanced physical properties were observed in polymer fibers produced under strong stretching conditions, studies of the process-induced nanoscale organization of the polymer molecules are not available, and most of fiber properties are still obtained on an empirical basis. Here we reveal the orientational properties of semiflexible polymers in electrospun nanofibers, which allow the polarization properties of active fibers to be finely controlled. Modeling and simulations of the conformational evolution of the polymer chains during electrostatic elongation of semidilute solutions demonstrate that the molecules stretch almost fully within less than 1 mm from jet start, increasing polymer axial orientation at the jet center. The nanoscale mapping of the local dichroism of individual fibers by polarized near-field optical microscopy unveils for the first time the presence of an internal spatial variation of the molecular order, namely the presence of a core with axially aligned molecules and a sheath with almost radially oriented molecules. These results allow important and specific fiber properties to be manipulated and tailored, as here demonstrated for the polarization of emitted light.

Physiology's Impact: Applying Mathematics and Advanced Technologies

How do you measure the mechanical forces generated by single cells? What are the cues that guide cell migration? What are the interactions between cells that account for cooperative behaviors among cells? To answer these and many other basic questions about biological function, we must have the

Stability and electronic structure of covalently functionalized graphene layers

We present exemplary results of extensive studies of mechanical, electronic, and transport properties of covalent functionalization of graphene monolayers (GML) with –NH2. We report new results of ab initio studies of covalent functionalization of GML with –NH2 groups up to 12.5% concentration. Our studies are performed in the framework of the density functional theory (DFT) and non‐equilibrium Green's function (NEGF). We discuss the stability (adsorption energy), elastic moduli, electronic structure, band gaps, and effective electron masses as a function of the density of the adsorbed molecules. We also show the conductance and I(V) characteristic of these systems. Generally, the stability of the functionalized graphene layers decreases with the growing concentration of attachments and we determine the critical density of the molecules that can be chemisorbed on the surface of GLs. Because of local deformations of GLs and sp3 rehybridization of the bonds induced by fragments, elastic moduli decrease with increasing number of groups. Simultaneously, we observe that the functionalizing molecules stretch the graphene's lattice, the effect being more pronounced for higher concentration of adsorbed molecules. We find out that the GLs functionalization leads in many cases to the opening of the graphene band gap (up to 0.5302 eV for 12.5% concentration) and can be therefore utilized in graphene devices. The new HOMO and LUMO originate mostly from the impurity bands induced by the functionalization and they exhibit parabolic dispersion with electron effective masses comparable to ones in silicon or gallium nitride.

Vibrational Raman spectra of hydrogen clathrate hydrates from density functional theory

Hydrogen clathrate hydrates are promising sources of clean energy and are known to exist in a sII hydrate lattice, which consists of H2 molecules in dodecahedron (5(12)) and hexakaidecahedron (5(12)6(4)) water cages. The formation of these hydrates which occur in extreme thermodynamic conditions is known to be considerably reduced by an inclusion of tetrahydrofuran (THF) in cages of these hydrate lattice. In this present work, we employ the density functional theory with a dispersion corrected (B97-D) functional to characterize vibrational Raman modes in the cages of pure and THF doped hydrogen clathrate hydrates. Our calculations show that the symmetric stretch of the H2 molecule in the 5(12)6(4)H2·THF cage is blueshifted compared to the 5(12)6(4)H2 cage. However, all vibrational modes of water molecules are redshifted which suggest reduced interaction between the H2 molecule and water molecules in the 5(12)6(4)H2·THF cage. The symmetric and asymmetric O-H stretch of water molecules in 5(12)H2, 5(12)6(4)H2, and 5(12)6(4)H2·THF cages are redshifted compared with the corresponding guest free cages due to interactions between encapsulated H2 molecules and water molecules of the cages. The low frequency modes contain contributions from contraction and expansion of water cages and vibration of water molecules due to hydrogen bonding and these modes could possibly play an important role in the formation of the hydrate lattice.

Physico-chemical studies and emulsifying properties of N-propyl-N-methylene phosphonic chitosan

Chitosan is a modified, natural carbohydrate polymer derived by deacetylation of chitin. Due to the presence of two functional groups can undergo many chemical modifications. In a previous work we described the synthetic strategy and characterization of a novel soluble derivative: N-propyl-N-methylene phosphonic chitosan (PNMPC). In the study of some physicochemical properties, results showed that this modified chitosan aggregates in several steps when the concentration is increased. By addition of NaOH the initially coiled molecules stretch exposing more phosphonic acid groups to neutralization and finally give a cooperative reaction with OH(. PNMPC has emulsifying properties and gives O/W emulsions with quasi-monodisperse small droplets. Emulsions with 0.18% PNMPC and 30:70 o:w ratio exhibited the best emulsifying properties within the test range. This emulsion ratio showed high stability to long time storage and several successive freeze/thaw and heating/cooling cycles.

Effects of Ions on Hydrogen-Bonding Water Networks in Large Aqueous Nanodrops

Ensemble infrared photodissociation (IRPD) spectra in the hydrogen stretch region (~2800-3800 cm(-1)) are reported for aqueous nanodrops containing ~250 water molecules and either SO(4)(2-), I(-), Na(+), Ca(2+), or La(3+) at 133 K. Each spectrum has a broad feature in the bonded-OH region (~2800-3500 cm(-1)) and a sharp feature near 3700 cm(-1), corresponding to the free-OH stretch of surface water molecules that accept two hydrogen bonds and donate one hydrogen bond (AAD water molecules). A much weaker band corresponding to AD surface water molecules is observed for all ions except SO(4)(2-). The frequencies of the AAD free-OH stretch red-shift with increasingly positive charge, consistent with a Stark effect as a result of the ion's electric field at the droplet surface, and from which the corresponding frequency for water molecules at the surface of neutral nanodrops of this size is estimated to be 3699.3-3700.1 cm(-1). The intensity of the AAD band increases with increasing positive charge, consistent with a greater population of AAD water molecules for the more positively charged nanodrops. The spectra of M(H(2)O)(~250), M = Na(+) and I(-), are very similar, whereas those for Ca(2+) and SO(4)(2-) have distinct differences. These results indicate that the monovalent ions do not affect the hydrogen-bonding network of the majority of water molecules whereas this network is significantly affected in nanodrops containing the multivalent ions. The ion-induced effect on water structure propagates all the way to the surface of the nanodrops, which is located more than 1 nm from the ion.

Raman spectra of vibrational and librational modes in methane clathrate hydrates using density functional theory

The sI type methane clathrate hydrate lattice is formed during the process of nucleation where methane gas molecules are encapsulated in the form of dodecahedron (5(12)CH(4)) and tetrakaidecahedron (5(12)6(2)CH(4)) water cages. The characterization of change in the vibrational modes which occur on the encapsulation of CH(4) in these cages plays a key role in understanding the formation of these cages and subsequent growth to form the hydrate lattice. In this present work, we have chosen the density functional theory (DFT) using the dispersion corrected B97-D functional to characterize the Raman frequency vibrational modes of CH(4) and surrounding water molecules in these cages. The symmetric and asymmetric C-H stretch in the 5(12)CH(4) cage is found to shift to higher frequency due to dispersion interaction of the encapsulated CH(4) molecule with the water molecules of the cages. However, the symmetric and asymmetric O-H stretch of water molecules in 5(12)CH(4) and 5(12)6(2)CH(4) cages are shifted towards lower frequency due to hydrogen bonding, and interactions with the encapsulated CH(4) molecules. The CH(4) bending modes in the 5(12)CH(4) and 5(12)6(2)CH(4) cages are blueshifted, though the magnitude of the shifts is lower compared to modes in the high frequency region which suggests bending modes are less affected on encapsulation of CH(4). The low frequency librational modes which are collective motion of the water molecules and CH(4) in these cages show a broad range of frequencies which suggests that these modes largely contribute to the formation of the hydrate lattice.

Chemical leaching of an Indian bituminous coal and characterization of the products by vibrational spectroscopic techniques

High volatile bituminous coal was demineralized by a chemical method. The vibrations of the “aromatics” structure of graphite, crystalline or non-crystalline, were observed in the spectra at the 1600 cm−1 region. The band at 1477 cm−1 is assigned as VR band, the band at 1392 cm−1 as VL band and the band at 1540 cm−1 as GR band. Graphite structure remains after chemical leaching liberates oxygenated functional groups and mineral groups. The silicate bands between 1010 and 1100 cm−1 are active in the infrared (IR) spectrum but inactive in the Raman spectrum. Absorption arising from C-H stretching in alkenes occurs in the region of 3000 to 2840 cm−1. Raman bands because of symmetric stretch of water molecules were also observed in the spectrum at 3250 cm−1 and 3450 cm−1. Scanning electron microscopy analysis revealed the presence of a graphite layer on the surface. Leaching of the sample with hydrofluoric acid decreases the mineral phase and increases the carbon content. The ash content is reduced by 84.5wt% with leaching from its initial value by mainly removing aluminum and silicate containing minerals.

DNA conformation in nanochannels: Monte Carlo simulation studies using a primitive DNA model

We have performed canonical ensemble Monte Carlo simulations of a primitive DNA model to study the conformation of 2.56 ~ 21.8 μm long DNA molecules confined in nanochannels at various ionic concentrations with the comparison of our previous experimental findings. In the model, the DNA molecule is represented as a chain of charged hard spheres connected by fixed bond length and the nanochannels as planar hard walls. System potentials consist of explicit electrostatic potential along with short-ranged hard-sphere and angle potentials. Our primitive model system provides valuable insight into the DNA conformation, which cannot be easily obtained from experiments or theories. First, the visualization and statistical analysis of DNA molecules in various channel dimensions and ionic strengths verified the formation of locally coiled structures such as backfolding or hairpin and their significance even in highly stretched states. Although the folding events mostly occur within the region of ~0.5 μm from both chain ends, significant portion of the events still take place in the middle region. Second, our study also showed that two controlling factors such as channel dimension and ionic strength widely used in stretching DNA molecules have different influence on the local DNA structure. Ionic strength changes local correlation between neighboring monomers by controlling the strength of electrostatic interaction (and thus the persistence length of DNA), which leads to more coiled local conformation. On the other hand, channel dimension controls the overall stretch by applying the geometric constraint to the non-local DNA conformation instead of directly affecting local correlation. Third, the molecular weight dependence of DNA stretch was observed especially in low stretch regime, which is mainly due to the fact that low stretch modes observed in short DNA molecules are not readily accessible to much longer DNA molecules, resulting in the increase in the stretch of longer DNA molecules.

Streamwise variation of turbulent dynamics in boundary layer flow of drag-reducing fluid

AbstractDirect numerical simulations (DNSs) of a zero-pressure-gradient boundary layer flow of a polymeric fluid have been performed. The FENE-P model was used for the polymer stresses and a wide range of Weissenberg numbers ($\mathit{We}$) was addressed. In all cases, the streamwise variations of the level of polymer stretching and the level of drag reduction are anticorrelated. Consistent with earlier studies, the inlet condition for the flow consists of Newtonian velocity data with no polymer stretching, so in the upstream region of the boundary layer the polymer molecules stretch strongly in response, leading to an initial spatial maximum in polymer stretching. Beyond this initial region, the level of drag reduction increases with increasing downstream position, while the polymer stretch is decreasing. At sufficiently high Weissenberg numbers, these variations are monotonic with streamwise position (outside the upstream region), but at $\mathit{We}= 25$, both the polymer stretching and level of drag reduction display a decaying oscillation in the downstream position. The streamwise dependence of the velocity statistics is also shown. In addition, simulations in which the polymer stress is turned off beyond a chosen downstream position were performed; in this case the flow continues to exhibit substantial drag reduction well downstream of the cutoff position. These observations are analysed in light of other recent literature and in particular the observations of ‘active’ and ‘hibernating’ turbulence recently found in minimal channel flow by Xi and Graham. All of these observations suggest that an important role for viscoelasticity in the turbulent drag reduction phenomenon, at least near solid surfaces, is to suppress conventional turbulence, while leaving behind a much weaker form of turbulence that can persist for a substantial length of time (or downstream distance) even in the absence of viscoelastic stresses.

Thermodynamic and spectroscopic studies on binary mixtures of imidazolium ionic liquids in ethylene glycol

The thermodynamic behaviour of imidazolium based ionic liquids (ILs), 1-butyl-3-methylimidazolium chloride [C 4mim][Cl]; 1-octyl-3-methylimidazolium chloride [C 8mim][Cl], and 1-butyl-3-methylimidazolium methylsulfate [C 4mim][C 1OSO 3] in ethylene glycol [HOCH 2CH 2OH] (EG) have been investigated over the whole composition range at T = (298.15 to 318.15) K to probe the interactions in bulk. For the purpose, volumetric properties such as excess molar volume, V m E , apparent molar volume, V ϕ , i , and its limiting values at infinite dilution, V ϕ , i ∞ , have been calculated from the experimental density measurements. The molecular scale interactions between ionic liquids and EG have been investigated through Fourier transform infrared (FTIR) and 1H NMR spectroscopy. The shift in the vibrational frequency for C–H stretch of aromatic ring protons of ILs and O–H stretch of EG molecules has been analysed. The NMR chemical shifts for various protons of RTILS or EG molecules and their deviations show multiple hydrogen bonding interactions of varying strengths between RTILs and EG in their binary mixtures.

Nature of the Binding of a c(2×2)-CO Overlayer on Ag(001) and Surface Mediated Intermolecular Coupling

We present a first-principles study of the nature of the binding of a c(2×2)-CO overlayer on Ag(001) and of the origin of CO-CO interactions upon adsorption. Electronic structural changes induced by molecular adsorption provide an interpretation for earlier X-ray photoemission valence band spectra of CO/Ag(001). Our results establish that CO chemisorbs on clean Ag(001) and follows the Blyholder model of donation and back-donation between CO and metal orbitals. We analyze the origin of the dispersion of the C-O stretch mode and attest that it is caused by the metal-CO coupling. Specifically, the coupling of CO to Ag, although the weakest of those between it and transition and other noble metals, greatly enhances the intermolecular force constants. We also find that the response of the charge density around CO is much stronger and of longer range when the molecule stretches than when it rigidly vibrates against the surface. This difference explains why the C-O stretch mode disperses while the Ag-CO stretch mode does not.

Evolutionary conservation of glucocorticoids and corticotropin releasing hormone: Behavioral and physiological adaptations

Glucocorticoids and corticotropin releasing hormone (CRH) underlie the physiology of change and adaptation. Both the steroid and peptide are quite ancient. The genes that underlie the production of these information molecules stretch back millions of years. The regulatory mechanisms of glucocorticoids have both restraining and enhancing capabilities on CRH gene expression. While restraint of CRH by glucocorticoids is a fundamental physiological feature of limiting CRH expression from over-use and exhaustion, CRH is also enhanced by glucocorticoids at both the level of extra-hypothalamic CRH sites and at the level of the placenta and fetal programming in the brain. This latter function of glucocorticoids increasing CRH gene expression underlies the physiology of change that underlies diverse adaptive functions.

Large deformations in oriented polymer glasses: Experimental study and a new glass‐melt constitutive model

AbstractAn experimental study was made of the effects of prior molecular orientation on large tensile deformations of polystyrene in the glassy state. A new hybrid glass‐melt constitutive model is proposed for describing and understanding the results, achieved by parallel coupling of the ROLIEPOLY molecularly‐based melt model with a model previously proposed for polymer glasses. Monodisperse and polydisperse grades of polystyrene are considered. Comparisons between experimental results and simulations illustrate that the model captures characteristic features of both the melt and glassy states. Polystyrene was stretched in the melt state and quenched to below Tg, and then tensile tested parallel to the orientation direction near the glass transition. The degree of strain‐hardening was observed to increase with increasing prior stretch of molecules within their entanglement tubes, as predicted by the constitutive model. This was explored for varying temperature of stretching, degree of stretching, and dwell time before quenching. The model in its current form, however, lacks awareness of processes of subentanglement chain orientation. Therefore, it under‐predicts the orientation‐direction strain hardening and yield stress increase, when stretching occurs at the lowest temperatures and shortest times, where it is dominated by subentanglement orientation. © 2010 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 48: 1449–1463, 2010

紫外線照射によるナノ液体潤滑膜のパターニングに関する粗視化分子動力学シミュレーション(機械要素,潤滑,設計,生産加工,生産システムなど)

The characteristics of monolayer liquid lubricant films coated on magnetic disks are basically determined by their interactions with disk surfaces. If the strength of the interactions could be patterned by ultraviolet (UV) irradiation through a photomask, it would be possible to attain desired tribological performance by rational design of the pattern. In this research, we developed coarse-grained molecular dynamics simulations to investigate the effect of masked UV irradiation on the distribution of monolayer lubricant films coated over solid surfaces. Consistent with experimental results, the simulation results showed that masked UV irradiation induces molecular flow from non-irradiated toward irradiated areas, and thereby a patterned surface structure with thicker lubricant in the irradiated area than in the non-irradiated area. The lubricant films, however, remained monolayer even in the UV-irradiated area. Our simulation results demonstrated that, rather than stacking of lubricant molecules, the patterned surface structure is caused by the stretch of the lubricant molecules in the film thickness direction following the increase of molecule density in the irradiated area.

Conformational dynamics of DNA‐electrophoresis on cationic membranes

The conformational dynamics of DNA molecules undergoing electrophoresis on a fluid substrate-supported cationic lipid bilayer is investigated using fluorescence microscopy. At low electrophoretic velocities, drift of 2-D random coils is observed. In contrast, at velocities larger than 0.3 mum/s, the DNA molecules stretch out and assume branched configurations. The cross-over scenario is explained by the observation that cationic lipids segregate underneath the adsorbed DNA and confine the DNA to its counter charge imprint on time scales shorter than the relaxation time of the imprint. The concept of a tube-like confinement of the DNA is corroborated by the observed 1/N size dependence of the electrophoretic mobility in analogy to the biased reptation model in gels. The role of membrane defects and possible applications of membrane-based electrophoresis in microfluidic devices are discussed.

Folding of Gas-Phase Polyalanines in a Static Electric Field: Alignment, Deformations, and Polarization Effects

Monte Carlo simulations of the temperature-induced unfolding of small gas-phase polyalanines in a static, homogeneous electric field are reported, based on the AMBER ff96 force field. The peptides exhibit a structural transition from the native α-helix state to entropically favored β-sheet conformations, before eventually turning to extended coil at higher temperatures. Upon switching the electric field, the molecules undergo preferential alignment of their dipole moment vector toward the field axis and a shift of the α-β transition to higher temperatures. At higher field strengths (>108V/m) the molecules stretch and the α-β and β-coil transitions merge. A simple three-state model is shown to account for the observed behavior. Under even higher fields, density functional theory calculations and a polarizable force field both show that electronic rearrangements tend to further increase the dipole moment, polarization effects being approximately half in magnitude with respect to stretching effect. Finally a tentative (temperature, field-strength) phase diagram is sketched.

Concentration Dependence of Shear-Induced Polymer Migration in DNA Solutions near a Surface

We investigate optically the time-dependent concentration and mean fractional stretch of λ-phage DNA molecules near a solid surface in a torsional shear flow, for solutions of DNA concentrations from 0.1c* to 3.0c*. At high Weissenberg number (Wi ≥ 10), the polymer migration caused by the hydrodynamic interaction with the surface diminishes as DNA concentration increases from 0.1c* to 1.0c*, indicating that screening of wall hydrodynamics occurs to some degree in the concentration range traditionally recognized as “dilute”. In addition, the surface migration continues to exist in diminished form up to 3.0c*, implying that, while the chains are overlapping, they do not screen out the hydrodynamic interactions completely. On the time scale over which migration occurs, the apparent mean fractional stretch of DNA molecules decreases near the surface, which is probably caused by the selective retention of fragments near the surface as long chains migrate away.

Molecular Imaging of Shear-Induced Polymer Migration in Dilute Solutions near a Surface

We measure the time-dependent concentration and stretch of λ-phage DNA molecules near a glass surface in torsional shear flow using epi-fluorescence microscopy. We find that the thickness of the depletion layer increases with increasing Weissenberg number over a time scale on the order of the time for diffusion across the depletion layer, in qualitative agreement with recent theory of Ma and Graham (2005) based on a FENE-P dumbbell model. However, the steady-state experimental depletion layer at high Weissenberg number (Wi = 10) is an order of magnitude thinner than expected from these predictions. The discrepancy is reduced to a factor of 2 in Brownian dynamics simulations of 10-spring chains. The remaining discrepancy suggests that more refined models of the migration phenomenon are required to obtain quantitative predictions. Over the time scale of migration, the apparent mean fractional stretch of DNA near the surface decreases with time, which we show could be caused by a few broken DNA fragments that are left near the surface when intact DNA diffuses away.

Electronic and mechanical properties of MoS2‐Ix nanotubes and Mo6SxIy nanowires

AbstractWe present scanning probe microscopy investigations of metal dichalcogenide nanotubes and wires (MDNW) in order to explore their structure and electronic properties. Local spectroscopy shows that the electronic properties are very sensitive to the stoichiometry of the nanowires, which can be controlled by adjusting the synthesis conditions. Unlike their carbon counterparts, MDNW can be fabricated to yield mainly single‐phase material, which makes their use as devices more feasible. In addition, we find also remarkable mechanical properties, where the molecules can be cut, recombined or deformed without any loss of structural integrity. We demonstrate this by mechanically deforming Mo6SxIy nanowires to highly strained configurations without causing irreversible changes to their structures. The rupturing and/or welding process of these nanowires, using AFM manipulation, shows that the molecules stretch to more than 30% of their relaxed configuration before plastic deformation occurs. Copyright © 2006 John Wiley & Sons, Ltd.