A parallel algorithm to produce long polymer chains in molecular dynamics.

Generating initial configurations of polymer melts above the entanglement molecular weight is a challenge in molecular dynamics and Monte Carlo simulations. In this work, we adapt an algorithm mimicking a chemical polymerization to all-atom force fields. The principle of this algorithm is to start from a bath of monomers between which bonds are created and relaxed sequentially. Our implementation is parallel and efficient. The parallelization is that of a classical molecular dynamics code and enables the user to generate large systems, up to 7 × 106 atoms. The efficiency of the algorithm comes from the linear scaling between the simulation time and the chain length in the limit of very long chains. The implementation is able to produce long polymer chains, up to ∼2000 carbon atoms, with thermodynamic and local structural properties in good agreement with their experimental and numerical counterparts. Moreover, the chain conformations are close to being equilibrated right after the end of the polymerization process, corresponding to only a few hundred of picoseconds of simulation, despite a systematical drift from Gaussian-like behavior when the density of reactively available monomers decreases. Finally, the algorithm proposed in this work is versatile in nature because the bond creation can be easily modified to create copolymers, block copolymers, and mixtures of polymer melts with other material.

Anisotropic surface stresses of a solid/fluid interface: Molecular dynamics calculations for the copper/methane interface.

The full tensorial surface stress of an interface between a face-centered cubic crystal (copper) and an isotropic liquid (methane) is computed for two crystal orientations {100} and {110} using molecular dynamics simulations. The bulk crystal orientation {100} is symmetric, whereas the {110} orientation is not. Finite size effects, which can be important in the case of an interface between an isotropic solid and a liquid, are studied in detail for the two crystal orientations. We first show that the symmetry of the surface stress tensor is that of the bulk crystal orientation. In the case of the asymmetric crystal orientation {110}, the relative difference between the components of the surface stress is substantial (∼50%). Finally, we show that finite size effects persist to much larger sizes in the case of the {100} orientation compared to the case of the {110} interface, for instance, through an artificial breakdown of the symmetry of the surface stress tensor.

Granularity impact on hotspot formation and local chemistry in shocked nanostructured RDX.

The nanostructuration of energetic materials results in interesting properties. In particular, the detonation of carbon-rich explosives leads to the formation of nanodiamonds, the size of which is linked to the initial size of the explosive nanograins. This correlation could come from the role played by the granularity in the shock properties, especially the local temperature, which could be enhanced when the shock front crosses the various interfaces and nanoporosities of the material. More generally, the granularity-dependent reactivity also concerns some aspects of the sensitivity of energetic materials and subsequent inhibition or safety issues. In order to investigate this hypothesis, we perform classical and reactive molecular dynamics shock-simulations on cyclotrimethylene trinitramine (RDX), a common high-explosive. We design various nanogranular structures using the body-centered-cubic stacking of nanoparticles shaped as Kelvin cells (truncated octahedra) with slightly-bumped faces. The nanograin size and the bump radius allow to independently control the porosity value and its nanostructure. We show that the global shock properties, especially the temperature, are sensitive to the porosity value but not to the nanograin size. The porosity nanostructure has a local impact, enhancing the temperature heterogeneities between the inter- and intra-grain regions by a few hundred degrees and slowing down the thermal homogenization. For a given porosity, the larger the nanograins, the larger and the hotter the hotspots. In such hotspots, the local chemistry is significantly modified, resulting in a larger reactivity with a quicker formation of some final products. We suggest that the quicker consumption of heteroatoms (namely, H, O, and N) along with higher local temperatures is likely to impact the formation process of solid carbonaceous phases.

Dynamic formation of nanodiamond precursors from the decomposition of carbon suboxide (C3O2) under extreme conditions-A ReaxFF study.

We use molecular dynamics simulations with the ReaxFF-lg potential to model the high pressure pyrolysis of carbon suboxide (C3O2) in mixture with argon as a pressure bath. We show that the reactive simulations catch the experimental behavior of the low-pressure detonation of C3O2 (around 10 bars in shock tube experiments) and allow extrapolations to the high-pressure range of solid-state explosive detonation (up to 60 GPa). While at low pressure carbonaceous nanostructures are formed through the aggregation of species such as carbon dimers C2, it appears that the high pressure deeply modifies the process, with the aggregation of growing CxOy heterostructures, in which the oxygen amount is driven by the pressure and the temperature. Pressures in the order of 60 GPa lead to high oxygen ratios, which prevent carbon atoms to get four carbon neighbors (the first condition to get a diamond structure). But a pressure lowering leads to a substantial carbon enrichment through CO2/CO release and facilitates the formation of pure sp3-carbon phases where diamond precursors can form. These results give new insights on the conditions leading to nanodiamonds during the detonation of carbon-rich high explosives.

Calculation of a solid/liquid surface tension: A methodological study.

The surface tension of a model solid/liquid interface constituted of a graphene sheet surrounded by liquid methane has been computed using molecular dynamics in the Kirkwood-Buff formalism. We show that contrary to the fluid/fluid case, the solid/liquid case can lead to different structurations of the first fluid layer, leading to significantly different values of surface tension. Therefore we present a statistical approach that consists in running a series of molecular simulations of similar systems with different initial conditions, leading to a distribution of surface tensions from which an average value and uncertainty can be extracted. Our results suggest that these distributions converge as the system size increases. Besides we show that surface tension is not particularly sensitive to the choice of the potential energy cutoff and that long-range corrections can be neglected contrary to what we observed in the liquid/vapour interfaces. We have not observed the previously reported commensurability effect.

Impact of surface energy on the shock properties of granular explosives.

This paper presents the first part of a two-fold molecular dynamics study of the impact of the granularity on the shock properties of high explosives. Recent experimental studies show that the granularity can have a substantial impact on the properties of detonation products {i.e., variations in the size distributions of detonation nanodiamonds [V. Pichot et al., Sci. Rep. 3, 2159 (2013)]}. These variations can have two origins: the surface energy, which is a priori enhanced from micro- to nano-scale, and the porosity induced by the granular structure. In this first report, we study the impact of the surface-energy contribution on the inert shock compression of TATB, TNT, α-RDX, and ß-HMX nano-grains (triaminotrinitrobenzene, trinitrotoluene, hexogen and octogen, respectively). We compute the radius-dependent surface energy and combine it with an ab initio-based equation of state in order to obtain the resulting shock properties through the Rankine-Hugoniot relations. We find that the enhancement of the surface energy results in a moderate overheating under shock compression. This contribution is minor with respect to porosity, when compared to a simple macroscopic model. This result motivates further atomistic studies on the impact of nanoporosity networks on the shock properties.

Selective sensing of isoprene by Ti-doped ZnO for breath diagnostics.

Exhaled isoprene could enable non-invasive monitoring of cholesterol-lowering therapies. Here, we report an isoprene-selective sensor at high relative humidity (RH) for the first time (to our knowledge). It is made of nanostructured, chemo-resistive Ti-doped ZnO particles (10-20 nm crystal size) produced by flame spray pyrolysis (FSP) and directly deposited in one step onto compact sensor substrates forming highly porous films. The constituent particles consist of stable Ti-doped ZnO solid solutions for Ti levels up to 10 mol% apparently by substitutional incorporation of Ti4+ into the ZnO wurtzite lattice and dominant presence at the particle surface. These Ti4+ point defects strongly enhance the isoprene sensitivity (>15 times higher than pure ZnO) and turn ZnO isoprene-selective, while also improving its thermal stability. In situ infrared spectroscopy confirms that Ti4+ intensifies the surface interaction of Ti-doped ZnO with isoprene by providing additional sites for chemisorbed hydroxyl species. In fact, at an optimal Ti content of 2.5 mol%, this sensor shows superior isoprene responses compared to acetone, NH3 and ethanol at 90% RH. Most notably, breath-relevant isoprene concentrations can be detected accurately down to 5 ppb with high (>10) signal-to-noise ratio. As a result, an inexpensive isoprene detector has been developed that could be easily incorporated into a portable breath analyzer for non-invasive monitoring of metabolic disorders (e.g. cholesterol).

Activation of tongue-expressed GPR40 and GPR120 by non caloric agonists is not sufficient to drive preference in mice.

There is mounting evidence that, in addition to texture and olfaction, taste plays a role in the detection of long chain fatty acids. Triglycerides, the main components of oils and dietary fat, are hydrolyzed in the mouth by a lingual lipase secreted from the von Ebner gland and the released free fatty acids are detected by the taste system. GPR40 and GPR120, two fatty acid responsive G-protein-coupled receptors (GPCRs), are expressed in taste bud cells, and knockout mice lacking either of those receptors have blunted taste nerve responses to and reduced preference for fatty acids. Here we investigated whether activation of those GPCRs is sufficient to elicit fat taste and preference. Five non-fatty acid agonists of GPR40 and two non-fatty acid agonists of GPR120 activated the glossopharyngeal nerve of wild-type mice but not of knockout mice lacking the cognate receptor. In human subjects, two-alternative forced choice (2-AFC) tests, triangle tests and sensory profiling showed that non fatty acid agonists of GPR40 dissolved in water are detected in sip and spit tests and elicit a taste similar to that of linoleic acid, whereas 2-AFC tests showed that two agonists of GPR120 in water are not perceived fattier than water alone. Wild-type mice did not show any preference for five agonists of GPR40, two agonists of GPR120 and mixtures of both agonists over water in two-bottle preference tests. Together these data indicate that GPR40 mediated taste perception is not sufficient to generate preference.

Impact of crema on the aroma release and the in-mouth sensory perception of espresso coffee.

A set of six espresso coffees with different foam characteristics and similar above cup and in-mouth flavour sensory profiles was produced by combination of two varying parameters, the extraction pressure and the filtration of the coffee beverage. The coffees were subsequently evaluated in a comparative manner by a set of analytical (headspace, nose-space) and sensory (Temporal Dominance of Sensations) techniques. The presence of espresso crema in its standard quantity was demonstrated to be associated with the optimum release of pleasant high volatiles, both in the above cup headspace and in-mouth. On the other hand, the TDS study demonstrated that increasing amount of crema was associated with increasing roasted dominance along coffee consumption. Furthermore, a parallel was established between the roasted sensory dominance and the dominant release of 2-methylfuran in the nose-space. This was, however, an indirect link as 2-methylfuran was indeed a chemical marker of roasting but does not contribute to the roasted aroma. Lowering the standard amount of crema by filtration clearly decreased the release of pleasant high volatiles and the in-mouth roasted sensory dominance. On the other hand, increasing the usual crema volume by increasing the extraction pressure did not bring any added value concerning the above cup and in-mouth release of pleasant high volatiles.

Extrusion-induced changes to the chemical profile and viscosity generating properties of citrus fiber.

Each of 8 variants in extrusion conditions was applied to a commercially available citrus fiber. Extrusion under conditions where the specific mechanical energy (SME) exceeded 400 kJ·kg(-1) was able to solubilize up to 30% of the fibers. Where the SME was ∼200 kJ·kg(-1) the degree of fiber solubilization was between 8 and 12%. All extruded fibers showed a loss of water-retaining capacity compared to the reference fiber, and this was attributed to the disruption of the integrated cell wall structure during the extrusion process. Nevertheless, within the 8 extruded variants there was a wide range of viscosity generating capacity which depended on the level of SME to which the fibers were subjected. The SME also had a pronounced effect on the nature of the solubilized fibers in terms of both their monosaccharide composition and their molecular weight profile. Both pectic and hemicellulosic polysaccharides were solubilized. It is concluded that extrusion has promise as a physical process for manipulating both the technological functionality and the health promoting properties of dietary fibers.

Physical and related sensory properties of a swallowable bolus.

Rheology and water content properties of cereal boluses collected just before swallowing were investigated. No specific physical markers for swallowing were found between subjects. Each subject had his own mastication strategy leading to food boluses with different rheological and water content properties. However, for most of the subjects, similar physical properties were found for food boluses obtained from consumption of different cereals. Results showed that the food boluses from different cereals exhibited gel-like properties being in a range from 14.1 kPa to 21.2 kPa (G'(1 Hz, 0.4%)), when swallowed. The food boluses had a static yield stress varying from 1.3 kPa to 4.3 kPa. Another interesting finding was that the water content of food boluses might be an important marker for swallowing since it was similar for different cereal food boluses (around 50%). This physical property might drive the fluid sensory perception, which could also be a sensory swallowing threshold.

Variety enhances food intake in humans: role of sensory-specific satiety.

Twenty-one subjects were studied to evaluate the effect of renewal of sensory stimulations of previously eaten foods on sensory-specific satiety and intake. The subjects ate French fries then brownie cakes ad libitum in three situations: "monotonous" - fries then brownies were consumed alone; "simultaneous" - condiments (ketchup and mayonnaise for the fries, vanilla cream and whipped cream for the brownies) were added during intakes; "successive" - after intake of fries alone, ketchup then mayonnaise were available with fries and, after intake of brownies alone, vanilla cream then whipped cream were offered with brownies. The quantities eaten in the "simultaneous" and "successive" situations were higher (p<0.001) than those in the "monotonous" one (1485+/-582 and 1682+/-777 kcal vs 1195+/-552 kcal, respectively). In the "successive" situation, hedonic ratings for fries diminished during intake but increased after the introduction of ketchup, leading to additional intake of fries. Similarly, hedonic ratings for brownies diminished during intake and increased after the introduction of vanilla cream leading to additional brownie intake (mayonnaise and whipped cream had no significant effect). Food variety, obtained by adding condiments can increase food intake in the short term. The mechanism by which food consumption is increased after the addition of condiments is introduced is at least partly related to the attenuation of sensory-satiety for a given food.

Theoretical study of the nucleation/growth process of carbon clusters under pressure.

We used molecular dynamics and the empirical potential for carbon LCBOPII to simulate the nucleation/growth process of carbon clusters both in vacuum and under pressure. In vacuum, our results show that the growth process is homogeneous and yields mainly sp(2) structures such as fullerenes. We used an argon gas and Lennard-Jones potentials to mimic the high pressures and temperatures reached during the detonation of carbon-rich explosives. We found that these extreme thermodynamic conditions do not affect substantially the topologies of the clusters formed in the process. However, our estimation of the growth rates under pressure are in much better agreement with the values estimated experimentally than our vacuum simulations. The formation of sp(3) carbon was negligible both in vacuum and under pressure which suggests that larger simulation times and cluster sizes are needed to allow the nucleation of nanodiamonds.

Relaxation of hot atoms following H2 dissociation on a Pd111 surface.

We study the relaxation of hot H atoms produced by dissociation of H2 molecules on the Pd111 surface. Ab initio density-functional theory calculations and the "corrugation reducing procedure" are used to determine the interaction potential for a H atom in front of a rigid surface as well as its modification under surface-atom vibrations. A slab of 80 Pd atoms is used to model the surface together with "generalized Langevin oscillators" to account for energy dissipation to the bulk. We show that the energy relaxation is fast, about 75% of the available energy being lost by the hot atoms after 0.5 ps. As a consequence, the hot atoms do not travel more than a few angstroms along the surface before being trapped into the potential well located over the hollow site.

Proliferative actions of natriuretic peptides on neuroblastoma cells. Involvement of guanylyl cyclase and non-guanylyl cyclase pathways.

To identify neural tumor cell lines that could be used as models to study growth-related natriuretic peptide actions, we determined the effects of these peptides on the proliferation of human and rodent neuroblastoma cell lines. Subnanomolar concentrations of atrial natriuretic peptide (ANP) and type C natriuretic peptide (CNP) stimulated proliferation in all four cell lines. These actions were associated with cGMP elevation and were blocked by a protein kinase G inhibitor. These data imply the involvement of guanylyl cyclase (GC)-coupled natriuretic receptors. However, higher concentrations of ANP and CNP, and low concentrations of des-[Gln(18),Ser(19),Gly(20),Leu(21),Gly(22)]-ANP(4-23)-NH(2) (desANP(4-23)) (analog for NPR-C receptor) exerted antiproliferative actions in three of the cell lines. These effects were insensitive to a protein kinase G inhibitor and to HS-142-1, suggesting that growth-inhibitory actions involved a non-GC receptor. They did not appear to involve cAMP, protein kinase A, protein kinase C, or calcium mobilization but were abolished when constitutive mitogen-activated protein kinase activity was inhibited. Radioligand binding experiments revealed the presence of a uniform class of binding sites in NG108 cells and multiple binding sites in Neuro2a cells. Northern and reverse transcriptase-polymerase chain reaction analyses revealed differential gene expression for NPR-A/B/C in NG108 and Neuro2a cells. The results indicate that natriuretic peptides stimulate neuroblastoma cell proliferation through type NPR-A/B (GC) receptors. Higher concentrations of ANP and CNP exerted a mitogen-activated protein kinase-dependent antiproliferative action mediated by a non-GC receptor that interacts with desANP(4-23) with relatively high affinity.

The polypeptide PHI discriminates a GTP-insensitive form of VIP receptor in liver membranes.

In early reports on 125I-VIP binding experiments in liver membranes, it has been proposed that, the VIP binding sites were partially sensitive to GTP. Here we confirm that the VIP binding sites of chicken liver membranes consisted mainly in bivalent VIP/PACAP receptors and that about 50% of the 125I-VIP binding capacity was not affected by the GTP analogue GppNHp. Part of these bivalent receptors also appeared to represent PHI binding sites. In GppNHp-treated membranes, the GTP-insensitive VIP binding sites displayed a 17-fold higher relative affinity than in control membranes for the VIP analogue PHI. Such data suggested that GTP-insensitive VIP receptors may correspond to a subclass of high-affinity PHI receptors. Cross-linking of 125 I-VIP or 125 I-PHI to their receptors, revealed 2 components of 48 and 60 kDa. The radiolabelling of the 60 kDa component was strongly affected by increasing concentrations of the GTP analogue but was modestly abolished by an excess of PHI. Conversely, the radiolabelling of the 48 kDa molecular form was not affected by the GTP analogue but was efficiently abolished by increasing concentrations of PHI. Taken together, the data suggest that the 48 kDa component expressed in chicken liver membranes display the properties of a GTP-insensitive VIP/PHI receptor that can be pharmacologically discriminated from the GTP-sensitive 60 kDa form, through its much higher affinity for PHI.

Pentylenetetrazol seizures induce cell suffering but not death in the immature rat brain.

To investigate whether long-term functional consequences of status epilepticus (SE) induced by pentylenetetrazol in 10-day-old rats correlated with cell injury and/or death, acid fuchsin and TUNEL staining were performed between 4 to 144 h after SE. Acid fuchsin stained hippocampus, amygdala and cerebral cortex at 24 h but not at 72 and 144 h. No DNA fragmentation was apparent at any time. Thus, immature neurons subjected to sustained seizures suffer transiently but survive probably by activating repair processes.

Mapping of neuronal networks underlying generalized seizures induced by increasing doses of pentylenetetrazol in the immature and adult rat: a c-Fos immunohistochemical study.

Previous studies from our group have shown that pentylenetetrazol (PTZ)-induced status epilepticus (SE) leads to age-dependent acute and long-term metabolic and circulatory changes in immature rats. In order to define the neural substrates involved in PTZ seizures according to age, the purpose of the present study was to map the areas of cellular activation during seizures of increasing severity in 10-day-old (P10), 21-day-old (P21) and adult rats. Seizures were induced by repetitive injections of subconvulsive doses of PTZ. The total dose received by the animals ranged from 4 to 125 mg/kg. These doses induced a variety of seizure profiles including absence-like, clonic seizures and SE. The cellular activation was measured as the density of c-Fos immunoreactive cells in animals at 2 h after the onset of the seizures. In P10 rats receiving a behaviourally non-active dose of PTZ, c-Fos immunoreactivity appeared only in the amygdala. The dose of 40 mg/kg that induced absence-like seizures led to a weak c-Fos expression in the medial thalamus, some cortical areas and globus pallidus. Clonic seizures reinforced labelling in the previous areas and induced a spread of c-Fos immunoreactivity to other cortical areas, thalamus, hypothalamus and some brainstem nuclei. At that age, only SE led to a widespread and stronger expression of c-Fos which was, however, totally lacking in the midbrain, and remained incomplete in the brainstem and forebrain limbic system, including the hippocampus. In P21 and adult rats, the inactive dose of PTZ induced c-Fos immunoreactivity in thalamus and hypothalamus. With absence-like seizures, c-Fos labelling spread to the cerebral cortex, amygdala, septum and some brainstem regions. With clonic seizures, immunoreactivity was reinforced in all areas already activated by absence-like seizures, and appeared in the striatum, accumbens, brainstem and hippocampus, except in CA1. After SE, c-Fos was strongly expressed in all brain areas. The intensity of c-Fos labelling was higher in most regions of P21 compared to adult rats. These data are in agreement with the immaturity of cellular and synaptic connectivity in P10 rats, the known greater sensitivity of rats to various kinds of seizures during the third week of life and the nature of the neural substrates involved in PTZ seizures.

Differential effects of peptide histidine isoleucine (PHI) and related peptides on stimulation and suppression of neuroblastoma cell proliferation. A novel VIP-independent action of PHI via MAP kinase.

The growth rate of rodent embryonic neuroblasts and human neuroblastoma cell lines is regulated in part by autocrine or paracrine actions of neuropeptides of the family that includes vasoactive intestinal peptide (VIP), peptide histidine isoleucine (PHI), and pituitary adenylate cyclase-activating peptide (PACAP). These peptides act via seven transmembrane G-protein-linked receptors coupled to cAMP elevation, phospholipase C activation, intracellular Ca2+ release, and/or of mitogen-activated protein (MAP) kinase activation. Here we investigated the action of these peptides on the mouse neuroblastoma cell line Neuro2a. PHI and VIP inhibited proliferation at concentrations as low as 10(-13) M and 10(-10) M, respectively. In contrast, PACAP action was biphasic, with stimulation occurring at subnanomolar doses and inhibition at higher doses. Peptide actions were studied further by measuring cAMP and ERK1/2 MAP kinase activity and by assessing 3H-thymidine incorporation in conjunction with a panel of signal transduction pathways inhibitors. The data obtained indicated that the PHI-inhibitory and PACAP-stimulatory activities were mediated by corresponding changes in activity of the MAP kinase pathway and independent of protein kinase A (PKA) or protein kinase C (PKC). In contrast, the inhibitory actions of VIP and PACAP were specifically blocked by antagonists of PKA. Northern blot analysis revealed gene expression for only the PACAP-preferring (PAC1) receptor. However, binding experiments using 125I-labeled PACAP27, PHI, and VIP, demonstrated the presence of PACAP-preferring sites, bivalent VIP/PACAP sites, and PHI-binding sites that did not interact with VIP. The studies demonstrate potent regulatory actions of PACAP, PHI, and VIP on neuroblastoma cell proliferation which appear to be mediated by multiple subsets of receptors which differentially couple to MAP kinase and PKA signaling pathways.

The small G-proteins Rap 1 as potential targets of vasoactive intestinal peptide effects in the human clonic cancer cells HT29.

We recently reported that the vasoactive intestinal peptide (VIP) potently inhibited proliferation and induced in parallel a strong cAMP rise, in the human colonic cancer cell line HT29. In this study, we investigated whether Rap 1 proteins could be potential targets of VIP effects in HT29 cells. These Ras-related proteins in which activity was demonstrated to be regulated by PKA phosphorylation, are considered as potential modulators of the Ras / Raf / MAP kinases cascade that governs cell growth control. Our data revealed that the Rap 1a isoform is highly expressed in HT29 cells and mainly localized in a late endosomal compartment. In these cells, VIP induces Rap 1 phosphorylation and a yet unidentified modification that leads to their acidification. This latter Rap 1 acidification seems to be, at least partially, cAMP-dependent. It is concluded that in HT29 cells, Rap 1 proteins may be part of a VIP-induced signaling cascade.