Chemical memory reactions induced bursting dynamics in gene expression.

PubMed

Tian, Tianhai

2013-01-01

Memory is a ubiquitous phenomenon in biological systems in which the present system state is not entirely determined by the current conditions but also depends on the time evolutionary path of the system. Specifically, many memorial phenomena are characterized by chemical memory reactions that may fire under particular system conditions. These conditional chemical reactions contradict to the extant stochastic approaches for modeling chemical kinetics and have increasingly posed significant challenges to mathematical modeling and computer simulation. To tackle the challenge, I proposed a novel theory consisting of the memory chemical master equations and memory stochastic simulation algorithm. A stochastic model for single-gene expression was proposed to illustrate the key function of memory reactions in inducing bursting dynamics of gene expression that has been observed in experiments recently. The importance of memory reactions has been further validated by the stochastic model of the p53-MDM2 core module. Simulations showed that memory reactions is a major mechanism for realizing both sustained oscillations of p53 protein numbers in single cells and damped oscillations over a population of cells. These successful applications of the memory modeling framework suggested that this innovative theory is an effective and powerful tool to study memory process and conditional chemical reactions in a wide range of complex biological systems.

Modeling of laser induced air plasma and shock wave dynamics using 2D-hydrodynamic simulations

NASA Astrophysics Data System (ADS)

Paturi, Prem Kiran; S, Sai Shiva; Chelikani, Leela; Ikkurthi, Venkata Ramana; C. D., Sijoy; Chaturvedi, Shashank; Acrhem, University Of Hyderabad Team; Computational Analysis Division, Bhabha Atomic Research Centre, Visakhapatnam Team

2017-06-01

The laser induced air plasma dynamics and the SW evolution modeled using the two dimensional hydrodynamic code by considering two different EOS: ideal gas EOS with charge state effects taken into consideration and Chemical Equilibrium applications (CEA) EOS considering the chemical kinetics of different species will be presented. The inverse bremsstrahlung absorption process due to electron-ion and electron-neutrals is considered for the laser-air interaction process for both the models. The numerical results obtained with the two models were compared with that of the experimental observations over the time scales of 200 - 4000 ns at an input laser intensity of 2.3 ×1010 W/cm2. The comparison shows that the plasma and shock dynamics differ significantly for two EOS considered. With the ideas gas EOS the asymmetric expansion and the subsequent plasma dynamics have been well reproduced as observed in the experiments, whereas with the CEA model these processes were not reproduced due to the laser energy absorption occurring mostly at the focal volume. ACRHEM team thank DRDO, India for funding.

A swinging seesaw as a novel model mechanism for time-dependent hormesis under dose-dependent stimulatory and inhibitory effects: A case study on the toxicity of antibacterial chemicals to Aliivibrio fischeri.

PubMed

Sun, Haoyu; Calabrese, Edward J; Zheng, Min; Wang, Dali; Pan, Yongzheng; Lin, Zhifen; Liu, Ying

2018-08-01

Hormesis occurs frequently in broadly ranging biological areas (e.g. plant biology, microbiology, biogerontology), toxicology, pharmacology and medicine. While numerous mechanisms (e.g. receptor and pathway mediated pathway responses) account for stimulatory and inhibitory features of hormetic dose responses, the vast majority emphasizes the inclusion of many doses but only one timepoint or use of a single optimized dose that is assessed over a broad range of timepoints. In this paper, a toxicity study was designed using a large number of properly spaced doses with responses determined over a large number of timepoints, which could help us reveal the underlying mechanism of hormesis. We present the results of a dose-time-response study on hormesis using five antibacterial chemicals on the bioluminescence of Aliivibrio fischeri, measuring expression of protein mRNA based on quorum sensing, simulating bioluminescent reaction and analyzing toxic actions of test chemicals. The findings show dose-time-dependent responses conforming to the hormetic dose-response model, while revealing unique response dynamics between agent induced stimulatory and inhibitory effects within bacterial growth phase dynamics. These dynamic dose-time features reveal a type of biological seesaw model that integrates stimulatory and inhibitory responses within unique growth phase, dose and time features, which has faultlessly explained the time-dependent hormetic phenomenon induced by five antibacterial chemicals (characterized by low-dose stimulation and high-dose inhibition). This study offers advances in understanding cellular dynamics, the biological integration of diverse and opposing responses and their role in evolutionary adaptive strategies to chemicals, which can provide new insight into the mechanistic investigation of hormesis. Copyright © 2018 Elsevier Ltd. All rights reserved.

Manipulating and Visualizing Molecular Interactions in Customized Nanoscale Spaces

NASA Astrophysics Data System (ADS)

Stabile, Francis; Henkin, Gil; Berard, Daniel; Shayegan, Marjan; Leith, Jason; Leslie, Sabrina

We present a dynamically adjustable nanofluidic platform for formatting the conformations of and visualizing the interaction kinetics between biomolecules in solution, offering new time resolution and control of the reaction processes. This platform extends convex lens-induced confinement (CLiC), a technique for imaging molecules under confinement, by introducing a system for in situ modification of the chemical environment; this system uses a deep microchannel to diffusively exchange reagents within the nanoscale imaging region, whose height is fixed by a nanopost array. To illustrate, we visualize and manipulate salt-induced, surfactant-induced, and enzyme-induced reactions between small-molecule reagents and DNA molecules, where the conformations of the DNA molecules are formatted by the imposed nanoscale confinement. By using nanofabricated, nonabsorbing, low-background glass walls to confine biomolecules, our nanofluidic platform facilitates quantitative exploration of physiologically and biotechnologically relevant processes at the nanoscale. This device provides new kinetic information about dynamic chemical processes at the single-molecule level, using advancements in the CLiC design including a microchannel-based diffuser and postarray-based dialysis slit.

Quantitative Nuclease Protection Assays (qNPA) as Windows into Chemical-Induced Adaptive Response in Cultures of Primary Human Hepatocytes (Concentration and Time-Response)

EPA Science Inventory

Cultures of primary human hepatocytes have been shown to be dynamic in vitro model systems that retain liver-like functionality (e.g. metabolism, transport, induction). We have utilized these culture models to interrogate 309 ToxCast chemicals. The study design characterized both...

Some Sensitivity Studies of Chemical Transport Simulated in Models of the Soil-Plant-Litter System

DOE Office of Scientific and Technical Information (OSTI.GOV)

Begovich, C.L.

2002-10-28

Fifteen parameters in a set of five coupled models describing carbon, water, and chemical dynamics in the soil-plant-litter system were varied in a sensitivity analysis of model response. Results are presented for chemical distribution in the components of soil, plants, and litter along with selected responses of biomass, internal chemical transport (xylem and phloem pathways), and chemical uptake. Response and sensitivity coefficients are presented for up to 102 model outputs in an appendix. Two soil properties (chemical distribution coefficient and chemical solubility) and three plant properties (leaf chemical permeability, cuticle thickness, and root chemical conductivity) had the greatest influence onmore » chemical transport in the soil-plant-litter system under the conditions examined. Pollutant gas uptake (SO{sub 2}) increased with change in plant properties that increased plant growth. Heavy metal dynamics in litter responded to plant properties (phloem resistance, respiration characteristics) which induced changes in the chemical cycling to the litter system. Some of the SO{sub 2} and heavy metal responses were not expected but became apparent through the modeling analysis.« less

Synchronization Dynamics of Coupled Chemical Oscillators

NASA Astrophysics Data System (ADS)

Tompkins, Nathan

The synchronization dynamics of complex networks have been extensively studied over the past few decades due to their ubiquity in the natural world. Prominent examples include cardiac rhythms, circadian rhythms, the flashing of fireflies, predator/prey population dynamics, mammalian gait, human applause, pendulum clocks, the electrical grid, and of the course the brain. Detailed experiments have been done to map the topology of many of these systems and significant advances have been made to describe the mathematics of these networks. Compared to these bodies of work relatively little has been done to directly test the role of topology in the synchronization dynamics of coupled oscillators. This Dissertation develops technology to examine the dynamics due to topology within networks of discrete oscillatory components. The oscillatory system used here consists of the photo-inhibitable Belousov-Zhabotinsky (BZ) reaction water-in-oil emulsion where the oscillatory drops are diffusively coupled to one another and the topology is defined by the geometry of the diffusive connections. Ring networks are created from a close-packed 2D array of drops using the Programmable Illumination Microscope (PIM) in order to test Turing's theory of morphogenesis directly. Further technology is developed to create custom planar networks of BZ drops in more complicated topologies which can be individually perturbed using illumination from the PIM. The work presented here establishes the validity of using the BZ emulsion system with a PIM to study the topology induced effects on the synchronization dynamics of coupled chemical oscillators, tests the successes and limitations of Turing's theory of morphogenesis, and develops new technology to further probe the effects of network topology on a system of coupled oscillators. Finally, this Dissertation concludes by describing ongoing experiments which utilize this new technology to examine topology induced transitions of synchronization dynamics of diffusively coupled chemical oscillators.

Semiclassical description of hyperfine interaction in calculating chemically induced dynamic nuclear polarization in weak magnetic fields

DOE Office of Scientific and Technical Information (OSTI.GOV)

Purtov, P.A.; Salikhov, K.M.

1987-09-01

Semiclassical HFI description is applicable to calculating the integral CIDNP effect in weak fields. The HFI has been calculated for radicals with sufficiently numerous magnetically equivalent nuclei (n greater than or equal to 5) in satisfactory agreement with CIDNP calculations based on quantum-mechanical description of radical-pair spin dynamics.

Molecular Dynamics Study of Thermally Augmented Nanodroplet Motion on Chemical Energy Induced Wettability Gradient Surfaces.

PubMed

Chakraborty, Monojit; Chowdhury, Anamika; Bhusan, Richa; DasGupta, Sunando

2015-10-20

Droplet motion on a surface with chemical energy induced wettability gradient has been simulated using molecular dynamics (MD) simulation to highlight the underlying physics of molecular movement near the solid-liquid interface including the contact line friction. The simulations mimic experiments in a comprehensive manner wherein microsized droplets are propelled by the surface wettability gradient against forces opposed to motion. The liquid-wall Lennard-Jones interaction parameter and the substrate temperature are varied to explore their effects on the three-phase contact line friction coefficient. The contact line friction is observed to be a strong function of temperature at atomistic scales, confirming their experimentally observed inverse functionality. Additionally, the MD simulation results are successfully compared with those from an analytical model for self-propelled droplet motion on gradient surfaces.

Project ERIC - The search for environmental reactions induced by comets

NASA Astrophysics Data System (ADS)

Mendillo, M.; Sigwarth, J. B.; Craven, J. D.; Frank, L. A.; Holt, J.; Tetenbaum, D.

A sounding rocket experiment was conducted to release molecules of H2O and CO2 into the daytime ionosphere within the simultaneous fields of view of the Millstone Hill radar and the Dynamics Explorer UV imager. Preliminary results confirm the creation of chemically-induced F-region plasma depletions and reduced UV intensities from the modified region.

Prevalence and Mechanisms of Dynamic Chemical Defenses in Tropical Sponges

PubMed Central

Rohde, Sven; Nietzer, Samuel; Schupp, Peter J.

2015-01-01

Sponges and other sessile invertebrates are lacking behavioural escape or defense mechanisms and rely therefore on morphological or chemical defenses. Studies from terrestrial systems and marine algae demonstrated facultative defenses like induction and activation to be common, suggesting that sessile marine organisms also evolved mechanisms to increase the efficiency of their chemical defense. However, inducible defenses in sponges have not been investigated so far and studies on activated defenses are rare. We investigated whether tropical sponge species induce defenses in response to artificial predation and whether wounding triggers defense activation. Additionally, we tested if these mechanisms are also used to boost antimicrobial activity to avoid bacterial infection. Laboratory experiments with eight pacific sponge species showed that 87% of the tested species were chemically defended. Two species, Stylissa massa and Melophlus sarasinorum, induced defenses in response to simulated predation, which is the first demonstration of induced antipredatory defenses in marine sponges. One species, M. sarasinorum, also showed activated defense in response to wounding. Interestingly, 50% of the tested sponge species demonstrated induced antimicrobial defense. Simulated predation increased the antimicrobial defenses in Aplysinella sp., Cacospongia sp., M. sarasinorum, and S. massa. Our results suggest that wounding selects for induced antimicrobial defenses to protect sponges from pathogens that could otherwise invade the sponge tissue via feeding scars. PMID:26154741

Femtosecond dynamics in hydrogen-bonded solvents

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castner, E.W. Jr.; Chang, Y.J.

1993-09-01

We present results on the ultrafast dynamics of pure hydrogen-bonding solvents, obtained using femtosecond Fourier-transform optical-heterodyne-detected, Raman-induced Kerr effect spectroscopy. Solvent systems we have studied include the formamides, water, ethylene glycol, and acetic acid. Inertial and diffusive motions are clearly resolved. We comment on the effect that such ultrafast solvent motions have on chemical reactions in solution.

Evidence for charge-trapping inducing polymorphic structural-phase transition in pentacene.

PubMed

Ando, Masahiko; Kehoe, Tom B; Yoneya, Makoto; Ishii, Hiroyuki; Kawasaki, Masahiro; Duffy, Claudia M; Minakata, Takashi; Phillips, Richard T; Sirringhaus, Henning

2015-01-07

Trapped-charge-induced transformation of pentacene polymorphs is observed by using in situ Raman spectroscopy and molecular dynamics simulations reveal that the charge should be localized in pentacene molecules at the interface with static intermolecular disorder along the long axis. Quantum chemical calculations of the intermolecular transfer integrals suggest the disorder to be large enough to induce Anderson-type localization. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Electron Nuclear Dynamics Simulations of Proton Cancer Therapy Reactions: Water Radiolysis and Proton- and Electron-Induced DNA Damage in Computational Prototypes.

PubMed

Teixeira, Erico S; Uppulury, Karthik; Privett, Austin J; Stopera, Christopher; McLaurin, Patrick M; Morales, Jorge A

2018-05-06

Proton cancer therapy (PCT) utilizes high-energy proton projectiles to obliterate cancerous tumors with low damage to healthy tissues and without the side effects of X-ray therapy. The healing action of the protons results from their damage on cancerous cell DNA. Despite established clinical use, the chemical mechanisms of PCT reactions at the molecular level remain elusive. This situation prevents a rational design of PCT that can maximize its therapeutic power and minimize its side effects. The incomplete characterization of PCT reactions is partially due to the health risks associated with experimental/clinical techniques applied to human subjects. To overcome this situation, we are conducting time-dependent and non-adiabatic computer simulations of PCT reactions with the electron nuclear dynamics (END) method. Herein, we present a review of our previous and new END research on three fundamental types of PCT reactions: water radiolysis reactions, proton-induced DNA damage and electron-induced DNA damage. These studies are performed on the computational prototypes: proton + H₂O clusters, proton + DNA/RNA bases and + cytosine nucleotide, and electron + cytosine nucleotide + H₂O. These simulations provide chemical mechanisms and dynamical properties of the selected PCT reactions in comparison with available experimental and alternative computational results.

Redox Active Transition Metal ions Make Melanin Susceptible to Chemical Degradation Induced by Organic Peroxide.

PubMed

Zadlo, Andrzej; Pilat, Anna; Sarna, Michal; Pawlak, Anna; Sarna, Tadeusz

2017-12-01

With aging, retinal pigment epithelium melanosomes, by fusion with the age pigment lipofuscin, form complex granules called melanolipofuscin. Lipofuscin granules may contain oxidized proteins and lipid hydroperoxides, which in melanolipofuscin could chemically modify melanin polymer, while transition metal ions present in melanin can accelerate such oxidative modifications. The aim of this research was to examine the effect of selected transition metal ions on melanin susceptibility to chemical modification induced by the water-soluble tert-butyl hydroperoxide used as an oxidizing agent. Synthetic melanin obtained by DOPA autooxidation and melanosomes isolated from bovine retinal pigment epithelium were analyzed. To monitor tert-butyl hydroperoxide-induced oxidative changes of DMa and BMs, electron paramagnetic resonance spectroscopy, UV-vis absorption spectroscopy, dynamic light scattering, atomic force microscopy and electron paramagnetic resonance oximetry were employed. These measurements revealed that both copper and iron ions accelerated chemical degradation induced by tert-butyl hydroperoxide, while zinc ions had no effect. Strong prooxidant action was detected only in the case of melanosomes and melanin degraded in the presence of iron. It can be postulated that similar chemical processes, if they occur in situ in melanolipofuscin granules of the human retinal pigment epithelium, would modify antioxidant properties of melanin and its reactivity.

Impact of chemical plant start-up emissions on ambient ozone concentration

NASA Astrophysics Data System (ADS)

Ge, Sijie; Wang, Sujing; Xu, Qiang; Ho, Thomas

2017-09-01

Flare emissions, especially start-up flare emissions, during chemical plant operations generate large amounts of ozone precursors that may cause highly localized and transient ground-level ozone increment. Such an adverse ozone impact could be aggravated by the synergies of multiple plant start-ups in an industrial zone. In this paper, a systematic study on ozone increment superposition due to chemical plant start-up emissions has been performed. It employs dynamic flaring profiles of two olefin plants' start-ups to investigate the superposition of the regional 1-hr ozone increment. It also summaries the superposition trend by manipulating the starting time (00:00-10:00) of plant start-up operations and the plant distance (4-32 km). The study indicates that the ozone increment induced by simultaneous start-up emissions from multiple chemical plants generally does not follow the linear superposition of the ozone increment induced by individual plant start-ups. Meanwhile, the trend of such nonlinear superposition related to the temporal (starting time and operating hours of plant start-ups) and spatial (plant distance) factors is also disclosed. This paper couples dynamic simulations of chemical plant start-up operations with air-quality modeling and statistical methods to examine the regional ozone impact. It could be helpful for technical decision support for cost-effective air-quality and industrial flare emission controls.

Neuroproteomics and Environmental Chemical-induced Adverse Effects

EPA Science Inventory

Technological advances in science have aided the field of neuroproteomics with refined tools for the study of the expression, interaction, and function of proteins in the nervous system. With the aid of bioinformatics, neuroproteomics can reveal the organization of dynamic, funct...

Understanding Chemical-induced Adverse Effects with Neuroproteins

EPA Science Inventory

Technological advances in science have aided the field of neuroproteomics with refined tools for the study of the expression, interaction, and function of proteins in the nervous system. With the aid of bioinformatics, neuroproteomics can reveal the organization of dynamic, funct...

Non-linear optical techniques and optical properties of condensed molecular systems

NASA Astrophysics Data System (ADS)

Citroni, Margherita

2013-06-01

Structure, dynamics, and optical properties of molecular systems can be largely modified by the applied pressure, with remarkable consequences on their chemical stability. Several examples of selective reactions yielding technologically attractive products can be cited, which are particularly efficient when photochemical effects are exploited in conjunction with the structural conditions attained at high density. Non-linear optical techniques are a basic tool to unveil key aspects of the chemical reactivity and dynamic properties of molecules. Their application to high-pressure samples is experimentally challenging, mainly because of the small sample dimensions and of the non-linear effects generated in the anvil materials. In this talk I will present results on the electronic spectra of several aromatic crystals obtained through two-photon induced fluorescence and two-photon excitation profiles measured as a function of pressure (typically up to about 25 GPa), and discuss the relationship between the pressure-induced modifications of the electronic structure and the chemical reactivity at high pressure. I will also present the first successful pump-probe infrared measurement performed as a function of pressure on a condensed molecular system. The system under examination is liquid water, in a sapphire anvil cell, up to 1 GPa along isotherms at 298 and 363 K. These measurements give a new enlightening insight into the dynamical properties of low- and high-density water allowing a definition of the two structures.

Protonation-induced ultrafast torsional dynamics in 9-anthrylbenzimidazole: a pH activated molecular rotor.

PubMed

Nandi, Amitabha; Kushwaha, Archana; Das, Dipanwita; Ghosh, Rajib

2018-03-07

We report the photophysical properties and excited state dynamics of 9-anthrylbenzimidazole (ANBI) which exhibits protonation-induced molecular rotor properties. In contrast to the highly emissive behavior of neutral ANBI, protonation of the benzimidazole group of ANBI induces efficient nonradiative deactivation by ultrafast torsional motion around the bond connecting the anthracene and benzimidazole units, as revealed by ultrafast transient absorption and fluorescence spectroscopy. Contrary to viscosity-independent fluorescence of neutral dyes, protonated ANBI is shown to display linear variation of emission yield and lifetime with solvent viscosity. The protonation-induced molecular rotor properties in the studied system are shown to be driven by enhanced charge transfer and are corroborated by quantum chemical calculations. Potential application as a microviscosity sensor of acidic regions in a heterogeneous environment by these proton-activated molecular rotor properties of ANBI is discussed.

Targeting cell division: Small-molecule inhibitors of FtsZ GTPase perturb cytokinetic ring assembly and induce bacterial lethality

PubMed Central

Margalit, Danielle N.; Romberg, Laura; Mets, Rebecca B.; Hebert, Alan M.; Mitchison, Timothy J.; Kirschner, Marc W.; RayChaudhuri, Debabrata

2004-01-01

FtsZ, the ancestral homolog of eukaryotic tubulins, is a GTPase that assembles into a cytokinetic ring structure essential for cell division in prokaryotic cells. Similar to tubulin, purified FtsZ polymerizes into dynamic protofilaments in the presence of GTP; polymer assembly is accompanied by GTP hydrolysis. We used a high-throughput protein-based chemical screen to identify small molecules that target assembly-dependent GTPase activity of FtsZ. Here, we report the identification of five structurally diverse compounds, named Zantrins, which inhibit FtsZ GTPase either by destabilizing the FtsZ protofilaments or by inducing filament hyperstability through increased lateral association. These two classes of FtsZ inhibitors are reminiscent of the antitubulin drugs colchicine and Taxol, respectively. We also show that Zantrins perturb FtsZ ring assembly in Escherichia coli cells and cause lethality to a variety of bacteria in broth cultures, indicating that FtsZ antagonists may serve as chemical leads for the development of new broad-spectrum antibacterial agents. Our results illustrate the utility of small-molecule chemical probes to study FtsZ polymerization dynamics and the feasibility of FtsZ as a novel therapeutic target. PMID:15289600

Dynamic Chemically Driven Dewetting, Spreading, and Self-Running of Sessile Droplets on Crystalline Silicon.

PubMed

Arscott, Steve

2016-12-06

A chemically driven dewetting effect is demonstrated using sessile droplets of dilute hydrofluoric acid on chemically oxidized silicon wafers. The dewetting occurs as the thin oxide is slowly etched by the droplet and replaced by a hydrogen-terminated surface; the result of this is a gradual increase in the contact angle of the droplet with time. The time-varying work of adhesion is calculated from the time-varying contact angle; this corresponds to the changing chemical nature of the surface during dewetting and can be modeled by the well-known logistic (sigmoid) function often used for the modeling of restricted growth, in this case, the transition from an oxidized surface to a hydrogen-terminated silicon surface. The observation of the time-varying contact angle allows one to both measure the etch rate of the silicon oxide and estimate the hydrogenation rate as a function of HF concentration and wafer type. In addition to this, at a certain HF concentration, a self-running droplet effect is observed. In contrast, on hydrogen-terminated silicon wafers, a chemically induced spreading effect is observed using sessile droplets of nitric acid. The droplet spreading can also be modeled using a logistical function, where the restricted growth is the transition from hydrogen-terminated to a chemically induced oxidized silicon surface. The chemically driven dewetting and spreading observed here add to the methods available to study dynamic wetting (e.g., the moving three-phase contact line) of sessile droplets on surfaces. By slowing down chemical kinetics of the wetting, one is able to record the changing profile of the sessile droplet with time and gather information concerning the time-varying surface chemistry. The data also indicates a chemical interface hysteresis (CIH) that is compared to contact angle hysteresis (CAH). The approach can also be used to study the chemical etching and deposition behavior of thin films using liquids by monitoring the macroscopic droplet profile and relating this to the time-varying physical and chemical interface phenomena.

Chronic Nitrogen Deposition Influences the Chemical Dynamics of Leaf Litter and Fine Roots During Decomposition

EPA Science Inventory

Atmospheric nitrogen deposition induces a forest carbon sink across broad parts of the Northern Hemisphere; this carbon sink may partly result from slower litter decomposition. Although microbial responses to experimental nitrogen deposition have been well-studied, evidence linki...

Will water act as a photocatalyst for cluster phase chemical reactions? Vibrational overtone-induced dehydration reaction of methanediol

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kramer, Zeb C.; Takahashi, Kaito; Skodje, Rex T.

2012-04-28

The possibility of water catalysis in the vibrational overtone-induced dehydration reaction of methanediol is investigated using ab initio dynamical simulations of small methanediol-water clusters. Quantum chemistry calculations employing clusters with one or two water molecules reveal that the barrier to dehydration is lowered by over 20 kcal/mol because of hydrogen-bonding at the transition state. Nevertheless, the simulations of the reaction dynamics following OH-stretch excitation show little catalytic effect of water and, in some cases, even show an anticatalytic effect. The quantum yield for the dehydration reaction exhibits a delayed threshold effect where reaction does not occur until the photon energymore » is far above the barrier energy. Unlike thermally induced reactions, it is argued that competition between reaction and the irreversible dissipation of photon energy may be expected to raise the dynamical threshold for the reaction above the transition state energy. It is concluded that quantum chemistry calculations showing barrier lowering are not sufficient to infer water catalysis in photochemical reactions, which instead require dynamical modeling.« less

Fluoropolymer Microstructure and Dynamics: Influence of Molecular Orientation Induced by Uniaxial Drawing

NASA Astrophysics Data System (ADS)

Miranda, Daniel; Yin, Chaoqing; Runt, James

Fluorinated semi-crystalline polymer films are attractive for dielectric film applications due to their chemical inertness, heat resistance, and high thermal stability. In the present investigation we explore the influence of orientation induced by uniaxial drawing on the crystalline microstructure and relaxation processes of poly(ethylene-tetrafluoroethylene) (ETFE), in order to ascertain how morphological control can benefit polymer dielectric design. When drawn below or near the Tg, the crystallinity of the drawn films is unchanged, and oriented amorphous structures and crystalline microfibrils form at high draw ratios. This orientation slows segmental relaxation, reflected by an increase in the dynamic Tg, and also delays the transition to the high temperature crystalline form of ETFE. When drawing above the Tg, the films undergo strain-induced crystallization at high draw ratios. For these films an increase in the dynamic Tg is also observed, in addition to a second segmental relaxation process, appearing as a shoulder on the primary process. We propose that this represents a contribution from a rigid amorphous fraction, having slowed chain dynamics. Supported by Office of Naval Research.

Physical Processes and Real-Time Chemical Measurement of the Insect Olfactory Environment

PubMed Central

Abrell, Leif; Hildebrand, John G.

2009-01-01

Odor-mediated insect navigation in airborne chemical plumes is vital to many ecological interactions, including mate finding, flower nectaring, and host locating (where disease transmission or herbivory may begin). After emission, volatile chemicals become rapidly mixed and diluted through physical processes that create a dynamic olfactory environment. This review examines those physical processes and some of the analytical technologies available to characterize those behavior-inducing chemical signals at temporal scales equivalent to the olfactory processing in insects. In particular, we focus on two areas of research that together may further our understanding of olfactory signal dynamics and its processing and perception by insects. First, measurement of physical atmospheric processes in the field can provide insight into the spatiotemporal dynamics of the odor signal available to insects. Field measurements in turn permit aspects of the physical environment to be simulated in the laboratory, thereby allowing careful investigation into the links between odor signal dynamics and insect behavior. Second, emerging analytical technologies with high recording frequencies and field-friendly inlet systems may offer new opportunities to characterize natural odors at spatiotemporal scales relevant to insect perception and behavior. Characterization of the chemical signal environment allows the determination of when and where olfactory-mediated behaviors may control ecological interactions. Finally, we argue that coupling of these two research areas will foster increased understanding of the physicochemical environment and enable researchers to determine how olfactory environments shape insect behaviors and sensory systems. PMID:18548311

Mechano-chemical pathways to H2O and CO2 splitting

NASA Astrophysics Data System (ADS)

Vedadi, Mohammad H.; Haas, Stephan

2011-10-01

The shock-induced collapse of CO2-filled nanobubbles is investigated using molecular dynamics simulations based on a reactive force field. The energetic nanojet and high-pressure water hammer shock formed during and after collapse of the nanobubble trigger mechano-chemical H2O-CO2 reactions, some of which lead to splitting of water and formation of O2 molecules. The dominant pathways through which splitting of water molecules occur are identified.

Construction of oxygen and chemical concentration gradients in a single microfluidic device for studying tumor cell-drug interactions in a dynamic hypoxia microenvironment.

PubMed

Wang, Lei; Liu, Wenming; Wang, Yaolei; Wang, Jian-chun; Tu, Qin; Liu, Rui; Wang, Jinyi

2013-02-21

Recent microfluidic advancements in oxygen gradients have greatly promoted controllable oxygen-sensitive cellular investigations at microscale resolution. However, multi-gradient integration in a single microfluidic device for tissue-mimicking cell investigation is not yet well established. In this study, we describe a method that can generate oxygen and chemical concentration gradients in a single microfluidic device via the formation of an oxygen gradient in a chamber and a chemical concentration gradient between adjacent chambers. The oxygen gradient dynamics were systematically investigated, and were quantitatively controlled using simple exchange between the aerial oxygen and the oxygen-free conditions in the gas-permeable polydimethylsiloxane channel. Meanwhile, the chemical gradient dynamics was generated using a special channel-branched device. For potential medical applications of the established oxygen and chemical concentration gradients, a tumor cell therapy assessment was performed using two antitumor drugs (tirapazamine and bleomycin) and two tumor cell lines (human lung adenocarcinoma A549 cells and human cervical carcinoma HeLa cells). The results of the proof-of-concept experiment indicate the dose-dependent antitumor effect of the drugs and hypoxia-induced cytotoxicity of tirapazamine. We demonstrate that the integration of oxygen and chemical concentration gradients in a single device can be applied to investigating oxygen- and chemical-sensitive cell events, which can also be valuable in the development of multi-gradient generating procedures and specific drug screening.

Quantum indistinguishability in chemical reactions.

PubMed

Fisher, Matthew P A; Radzihovsky, Leo

2018-05-15

Quantum indistinguishability plays a crucial role in many low-energy physical phenomena, from quantum fluids to molecular spectroscopy. It is, however, typically ignored in most high-temperature processes, particularly for ionic coordinates, implicitly assumed to be distinguishable, incoherent, and thus well approximated classically. We explore enzymatic chemical reactions involving small symmetric molecules and argue that in many situations a full quantum treatment of collective nuclear degrees of freedom is essential. Supported by several physical arguments, we conjecture a "quantum dynamical selection" (QDS) rule for small symmetric molecules that precludes chemical processes that involve direct transitions from orbitally nonsymmetric molecular states. As we propose and discuss, the implications of the QDS rule include ( i ) a differential chemical reactivity of para- and orthohydrogen, ( ii ) a mechanism for inducing intermolecular quantum entanglement of nuclear spins, ( iii ) a mass-independent isotope fractionation mechanism, ( iv ) an explanation of the enhanced chemical activity of "reactive oxygen species", ( v ) illuminating the importance of ortho-water molecules in modulating the quantum dynamics of liquid water, and ( vi ) providing the critical quantum-to-biochemical linkage in the nuclear spin model of the (putative) quantum brain, among others.

Anti-Stokes resonant x-ray Raman scattering for atom specific and excited state selective dynamics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kunnus, Kristjan; Josefsson, Ida; Rajkovic, Ivan

Here, ultrafast electronic and structural dynamics of matter govern rate and selectivity of chemical reactions, as well as phase transitions and efficient switching in functional materials. Since x-rays determine electronic and structural properties with elemental, chemical, orbital and magnetic selectivity, short pulse x-ray sources have become central enablers of ultrafast science. Despite of these strengths, ultrafast x-rays have been poor at picking up excited state moieties from the unexcited ones. With time-resolved anti-Stokes resonant x-ray Raman scattering (AS-RXRS) performed at the LCLS, and ab initio theory we establish background free excited state selectivity in addition to the elemental, chemical, orbitalmore » and magnetic selectivity of x-rays. This unparalleled selectivity extracts low concentration excited state species along the pathway of photo induced ligand exchange of Fe(CO)5 in ethanol. Conceptually a full theoretical treatment of all accessible insights to excited state dynamics with AS-RXRS with transform-limited x-ray pulses is given—which will be covered experimentally by upcoming transform-limited x-ray sources.« less

Anti-Stokes resonant x-ray Raman scattering for atom specific and excited state selective dynamics

DOE PAGES

Kunnus, Kristjan; Josefsson, Ida; Rajkovic, Ivan; ...

2016-10-07

Here, ultrafast electronic and structural dynamics of matter govern rate and selectivity of chemical reactions, as well as phase transitions and efficient switching in functional materials. Since x-rays determine electronic and structural properties with elemental, chemical, orbital and magnetic selectivity, short pulse x-ray sources have become central enablers of ultrafast science. Despite of these strengths, ultrafast x-rays have been poor at picking up excited state moieties from the unexcited ones. With time-resolved anti-Stokes resonant x-ray Raman scattering (AS-RXRS) performed at the LCLS, and ab initio theory we establish background free excited state selectivity in addition to the elemental, chemical, orbitalmore » and magnetic selectivity of x-rays. This unparalleled selectivity extracts low concentration excited state species along the pathway of photo induced ligand exchange of Fe(CO)5 in ethanol. Conceptually a full theoretical treatment of all accessible insights to excited state dynamics with AS-RXRS with transform-limited x-ray pulses is given—which will be covered experimentally by upcoming transform-limited x-ray sources.« less

Elucidating induced plant defenses: the use of targeted metabolomics as a bridge from elicitation to response

USDA-ARS?s Scientific Manuscript database

Dynamic plant defense responses to biotic attack involve the perception of specific biochemical elicitors associated with the offending agent, activation of signaling cascades, and the production of small molecules with complex protective roles. Chemical analyses are essential empirical tools for el...

Oral dosing of chemical indicators for in vivo monitoring of Ca2+ dynamics in insect muscle.

PubMed

Ferdinandus; Arai, Satoshi; Ishiwata, Shin'ichi; Suzuki, Madoka; Sato, Hirotaka

2015-01-01

This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action) and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing). A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects.

Oral Dosing of Chemical Indicators for In Vivo Monitoring of Ca2+ Dynamics in Insect Muscle

PubMed Central

Ferdinandus; Arai, Satoshi; Ishiwata, Shin’ichi; Suzuki, Madoka; Sato, Hirotaka

2015-01-01

This paper proposes a remarkably facile staining protocol to visually investigate dynamic physiological events in insect tissues. We attempted to monitor Ca2+ dynamics during contraction of electrically stimulated living muscle. Advances in circuit miniaturization and insect neuromuscular physiology have enabled the hybridization of living insects and man-made electronic components, such as microcomputers, the result of which has been often referred as a Living Machine, Biohybrid, or Cyborg Insect. In order for Cyborg Insects to be of practical use, electrical stimulation parameters need to be optimized to induce desired muscle response (motor action) and minimize the damage in the muscle due to the electrical stimuli. Staining tissues and organs as well as measuring the dynamics of chemicals of interest in muscle should be conducted to quantitatively and systematically evaluate the effect of various stimulation parameters on the muscle response. However, existing staining processes require invasive surgery and/or arduous procedures using genetically encoded sensors. In this study, we developed a non-invasive and remarkably facile method for staining, in which chemical indicators can be orally administered (oral dosing). A chemical Ca2+ indicator was orally introduced into an insect of interest via food containing the chemical indicator and the indicator diffused from the insect digestion system to the target muscle tissue. We found that there was a positive relationship between the fluorescence intensity of the indicator and the frequency of electrical stimulation which indicates the orally dosed indicator successfully monitored Ca2+ dynamics in the muscle tissue. This oral dosing method has a potential to globally stain tissues including neurons, and investigating various physiological events in insects. PMID:25590329

Studying chemical reactions in biological systems with MBN Explorer: implementation of molecular mechanics with dynamical topology

NASA Astrophysics Data System (ADS)

Sushko, Gennady B.; Solov'yov, Ilia A.; Verkhovtsev, Alexey V.; Volkov, Sergey N.; Solov'yov, Andrey V.

2016-01-01

The concept of molecular mechanics force field has been widely accepted nowadays for studying various processes in biomolecular systems. In this paper, we suggest a modification for the standard CHARMM force field that permits simulations of systems with dynamically changing molecular topologies. The implementation of the modified force field was carried out in the popular program MBN Explorer, and, to support the development, we provide several illustrative case studies where dynamical topology is necessary. In particular, it is shown that the modified molecular mechanics force field can be applied for studying processes where rupture of chemical bonds plays an essential role, e.g., in irradiation- or collision-induced damage, and also in transformation and fragmentation processes involving biomolecular systems. Contribution to the Topical Issue "COST Action Nano-IBCT: Nano-scale Processes Behind Ion-Beam Cancer Therapy", edited by Andrey V. Solov'yov, Nigel Mason, Gustavo Garcia and Eugene Surdutovich.

Application of Graph Theory to Cost-Effective Fire Protection of Chemical Plants During Domino Effects.

PubMed

Khakzad, Nima; Landucci, Gabriele; Reniers, Genserik

2017-09-01

In the present study, we have introduced a methodology based on graph theory and multicriteria decision analysis for cost-effective fire protection of chemical plants subject to fire-induced domino effects. By modeling domino effects in chemical plants as a directed graph, the graph centrality measures such as out-closeness and betweenness scores can be used to identify the installations playing a key role in initiating and propagating potential domino effects. It is demonstrated that active fire protection of installations with the highest out-closeness score and passive fire protection of installations with the highest betweenness score are the most effective strategies for reducing the vulnerability of chemical plants to fire-induced domino effects. We have employed a dynamic graph analysis to investigate the impact of both the availability and the degradation of fire protection measures over time on the vulnerability of chemical plants. The results obtained from the graph analysis can further be prioritized using multicriteria decision analysis techniques such as the method of reference point to find the most cost-effective fire protection strategy. © 2016 Society for Risk Analysis.

Analysis of the stochastic excitability in the flow chemical reactor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Bashkirtseva, Irina

2015-11-30

A dynamic model of the thermochemical process in the flow reactor is considered. We study an influence of the random disturbances on the stationary regime of this model. A phenomenon of noise-induced excitability is demonstrated. For the analysis of this phenomenon, a constructive technique based on the stochastic sensitivity functions and confidence domains is applied. It is shown how elaborated technique can be used for the probabilistic analysis of the generation of mixed-mode stochastic oscillations in the flow chemical reactor.

Analysis of the stochastic excitability in the flow chemical reactor

NASA Astrophysics Data System (ADS)

Bashkirtseva, Irina

2015-11-01

A dynamic model of the thermochemical process in the flow reactor is considered. We study an influence of the random disturbances on the stationary regime of this model. A phenomenon of noise-induced excitability is demonstrated. For the analysis of this phenomenon, a constructive technique based on the stochastic sensitivity functions and confidence domains is applied. It is shown how elaborated technique can be used for the probabilistic analysis of the generation of mixed-mode stochastic oscillations in the flow chemical reactor.

A receptor tyrosine kinase inhibitor, Tyrphostin A9 induces cancer cell death through Drp1 dependent mitochondria fragmentation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Park, So Jung; Park, Young Jun; Shin, Ji Hyun

2011-05-13

Highlights: {yields} We screened and identified Tyrphostin A9, a receptor tyrosine kinase inhibitor as a strong mitochondria fission inducer. {yields} Tyrphostin A9 treatment promotes mitochondria dysfunction and contributes to cytotoxicity in cancer cells. {yields} Tyrphostin A9 induces apoptotic cell death through a Drp1-mediated pathway. {yields} Our studies suggest that Tyrphostin A9 induces mitochondria fragmentation and apoptotic cell death via Drp1 dependently. -- Abstract: Mitochondria dynamics controls not only their morphology but also functions of mitochondria. Therefore, an imbalance of the dynamics eventually leads to mitochondria disruption and cell death. To identify specific regulators of mitochondria dynamics, we screened a bioactivemore » chemical compound library and selected Tyrphostin A9, a tyrosine kinase inhibitor, as a potent inducer of mitochondrial fission. Tyrphostin A9 treatment resulted in the formation of fragmented mitochondria filament. In addition, cellular ATP level was decreased and the mitochondrial membrane potential was collapsed in Tyr A9-treated cells. Suppression of Drp1 activity by siRNA or over-expression of a dominant negative mutant of Drp1 inhibited both mitochondrial fragmentation and cell death induced by Tyrpohotin A9. Moreover, treatment of Tyrphostin A9 also evoked mitochondrial fragmentation in other cells including the neuroblastomas. Taken together, these results suggest that Tyrphostin A9 induces Drp1-mediated mitochondrial fission and apoptotic cell death.« less

Non-invasive detection of laser-induced retinal injury through the vitreous using dynamic light scattering (Conference Presentation)

NASA Astrophysics Data System (ADS)

Ansari, Rafat R.; Naiman, Melissa; Bouhenni, Rachida; Dunmire, Jeffery; Liu, Ying; Rafiq, Qundeel; Edward, Deepak; Gothard, David

2016-03-01

Laser radiation entering the eye has the potential of damaging the retina. As an inflammatory response, the proteins can rush to the lesion site created by laser exposure. We explore the hypothesis if these proteins can be detected non-invasively. In this preliminary study, we developed a new brief-case size dynamic light scattering instrument to detect these proteins in-vivo in the rabbit vitreous. The results were validated with bio-chemical analysis.

Internal exposure dynamics drive the Adverse Outcome Pathways of synthetic glucocorticoids in fish

NASA Astrophysics Data System (ADS)

Margiotta-Casaluci, Luigi; Owen, Stewart F.; Huerta, Belinda; Rodríguez-Mozaz, Sara; Kugathas, Subramanian; Barceló, Damià; Rand-Weaver, Mariann; Sumpter, John P.

2016-02-01

The Adverse Outcome Pathway (AOP) framework represents a valuable conceptual tool to systematically integrate existing toxicological knowledge from a mechanistic perspective to facilitate predictions of chemical-induced effects across species. However, its application for decision-making requires the transition from qualitative to quantitative AOP (qAOP). Here we used a fish model and the synthetic glucocorticoid beclomethasone dipropionate (BDP) to investigate the role of chemical-specific properties, pharmacokinetics, and internal exposure dynamics in the development of qAOPs. We generated a qAOP network based on drug plasma concentrations and focused on immunodepression, skin androgenisation, disruption of gluconeogenesis and reproductive performance. We showed that internal exposure dynamics and chemical-specific properties influence the development of qAOPs and their predictive power. Comparing the effects of two different glucocorticoids, we highlight how relatively similar in vitro hazard-based indicators can lead to different in vivo risk. This discrepancy can be predicted by their different uptake potential, pharmacokinetic (PK) and pharmacodynamic (PD) profiles. We recommend that the development phase of qAOPs should include the application of species-species uptake and physiologically-based PK/PD models. This integration will significantly enhance the predictive power, enabling a more accurate assessment of the risk and the reliable transferability of qAOPs across chemicals.

Multiple-division of self-propelled oil droplets through acetal formation.

PubMed

Banno, Taisuke; Kuroha, Rie; Miura, Shingo; Toyota, Taro

2015-02-28

We demonstrate a novel system that exhibits both self-propelled motion and division of micrometer-sized oil droplets induced by chemical conversion of the system components. Such unique dynamics were observed in an oil-in-water emulsion of a benzaldehyde derivative, an alkanol and a cationic surfactant at a low pH.

Coadsorbate-Induced Reversal of Solid-Liquid Interface Dynamics.

PubMed

Rahn, Björn; Wen, Rui; Deuchler, Lukas; Stremme, Johannes; Franke, Andreas; Pehlke, Eckhard; Magnussen, Olaf M

2018-05-22

Coadsorbed anions are well-known to influence surface reactivity and dynamics at solid-liquid interfaces. Here we demonstrate that the chemical nature of these spectator species can entirely determine the microscopic dynamic behavior. Quantitative in situ video-STM data on the surface diffusion of adsorbed sulfur atoms on Cu(100) electrodes in aqueous solution covered by bromide and chloride spectators, respectively, reveal in both cases a strong exponential potential dependence, but with opposite sign. This reversal is highly surprising in view of the isostructural adsorbate arrangement in the two systems. Detailed DFT studies suggest an anion-induced difference in the sulfur diffusion mechanism, specifically an exchange diffusion on the Br-covered surface. Experimental evidence for the latter is provided by the observation of Cu vacancy formation in the Br system, which can be rationalized by a side reaction of the sulfur exchange diffusion. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Mode Specific Electronic Friction in Dissociative Chemisorption on Metal Surfaces: H2 on Ag(111)

NASA Astrophysics Data System (ADS)

Maurer, Reinhard J.; Jiang, Bin; Guo, Hua; Tully, John C.

2017-06-01

Electronic friction and the ensuing nonadiabatic energy loss play an important role in chemical reaction dynamics at metal surfaces. Using molecular dynamics with electronic friction evaluated on the fly from density functional theory, we find strong mode dependence and a dominance of nonadiabatic energy loss along the bond stretch coordinate for scattering and dissociative chemisorption of H2 on the Ag(111) surface. Exemplary trajectories with varying initial conditions indicate that this mode specificity translates into modulated energy loss during a dissociative chemisorption event. Despite minor nonadiabatic energy loss of about 5%, the directionality of friction forces induces dynamical steering that affects individual reaction outcomes, specifically for low-incidence energies and vibrationally excited molecules. Mode-specific friction induces enhanced loss of rovibrational rather than translational energy and will be most visible in its effect on final energy distributions in molecular scattering experiments.

Experimental Study on Impact-Induced Reaction Characteristics of PTFE/Ti Composites Enhanced by W Particles.

PubMed

Li, Yan; Wang, Zaicheng; Jiang, Chunlan; Niu, Haohao

2017-02-13

Metal/fluoropolymer composites are a category of energetic structural materials that release energy through exothermic chemical reactions initiated under highly dynamic loadings. In this paper, the chemical reaction mechanism of PTFE (polytetrafluoroethylene)/Ti/W composites is investigated through thermal analysis and composition analysis. These composites undergo exothermic reactions at 510 °C to 600 °C, mainly producing TiF x . The tungsten significantly reduces the reaction heat due to its inertness. In addition, the dynamic compression properties and impact-induced reaction behaviors of PTFE/Ti/W composites with different W content prepared by pressing and sintering are studied using Split Hopkinson Pressure Bar and high speed photography. The results show that both the mechanical strength and the reaction degree are significantly improved with the increasing strain rate. Moreover, as W content increases, the mechanical strength is enhanced, but the elasticity/plasticity is decreased. The PTFE/Ti/W composites tend to become more inert with the increasing W content, which is reflected by the reduced reaction degree and the increased reaction threshold for the impact ignition.

Experimental Study on Impact-Induced Reaction Characteristics of PTFE/Ti Composites Enhanced by W Particles

PubMed Central

Li, Yan; Wang, Zaicheng; Jiang, Chunlan; Niu, Haohao

2017-01-01

Metal/fluoropolymer composites are a category of energetic structural materials that release energy through exothermic chemical reactions initiated under highly dynamic loadings. In this paper, the chemical reaction mechanism of PTFE (polytetrafluoroethylene)/Ti/W composites is investigated through thermal analysis and composition analysis. These composites undergo exothermic reactions at 510 °C to 600 °C, mainly producing TiFx. The tungsten significantly reduces the reaction heat due to its inertness. In addition, the dynamic compression properties and impact-induced reaction behaviors of PTFE/Ti/W composites with different W content prepared by pressing and sintering are studied using Split Hopkinson Pressure Bar and high speed photography. The results show that both the mechanical strength and the reaction degree are significantly improved with the increasing strain rate. Moreover, as W content increases, the mechanical strength is enhanced, but the elasticity/plasticity is decreased. The PTFE/Ti/W composites tend to become more inert with the increasing W content, which is reflected by the reduced reaction degree and the increased reaction threshold for the impact ignition. PMID:28772534

Trade-offs between constitutive and induced defences drive geographical and climatic clines in pine chemical defences.

PubMed

Moreira, Xoaquín; Mooney, Kailen A; Rasmann, Sergio; Petry, William K; Carrillo-Gavilán, Amparo; Zas, Rafael; Sampedro, Luis

2014-05-01

There is increasing evidence that geographic and climatic clines drive the patterns of plant defence allocation and defensive strategies. We quantified early growth rate and both constitutive and inducible chemical defences of 18 Pinaceae species in a common greenhouse environment and assessed their defensive allocation with respect to each species' range across climatic gradients spanning 31° latitude and 2300 m elevation. Constitutive defences traded-off with induced defences, and these defensive strategies were associated with growth rate such that slow-growing species invested more in constitutive defence, whereas fast-growing species invested more in inducible defence. The position of each pine species along this trade-off axis was in turn associated with geography; moving poleward and to higher elevations, growth rate and inducible defences decreased, while constitutive defence increased. These geographic patterns in plant defence were most strongly associated with variation in temperature. Climatic and geographical clines thus act as drivers of defence profiles by mediating the constraints imposed by trade-offs, and this dynamic underlays global patterns of defence allocation.

Dynamics of Reactive Microbial Hotspots in Concentration Gradient.

NASA Astrophysics Data System (ADS)

Hubert, A.; Farasin, J.; Tabuteau, H.; Dufresne, A.; Meheust, Y.; Le Borgne, T.

2017-12-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella capsiferriformans ES-2 as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. We measure bacterial activity and population growth locally in precisely known hydrodynamic and chemical environments. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We compare reactive microbial hotspot dynamics in our micromodels to classic growth laws and well-known growth parameters for the laboratory model bacteria Escherichia coli.We also discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Thermodiffusion as a means to manipulate liquid film dynamics on chemically patterned surfaces

PubMed Central

Kalpathy, Sreeram K.; Shreyes, Amrita Ravi

2017-01-01

The model problem examined here is the stability of a thin liquid film consisting of two miscible components, resting on a chemically patterned solid substrate and heated from below. In addition to surface tension gradients, the temperature variations also induce gradients in the concentration of the film by virtue of thermodiffusion/Soret effects. We study the stability and dewetting behaviour due to the coupled interplay between thermal gradients, Soret effects, long-range van der Waals forces, and wettability gradient-driven flows. Linear stability analysis is first employed to predict growth rates and the critical Marangoni number for chemically homogeneous surfaces. Then, nonlinear simulations are performed to unravel the interfacial dynamics and possible locations of the film rupture on chemically patterned substrates. Results suggest that appropriate tuning of the Soret parameter and its direction, in conjunction with either heating or cooling, can help manipulate the location and time scales of the film rupture. The Soret effect can either potentially aid or oppose film instability depending on whether the thermal and solutal contributions to flow are cooperative or opposed to each other. PMID:28595391

In situ analysis of chemical components induced by steaming between fresh ginseng, steamed ginseng, and red ginseng.

PubMed

In, Gyo; Ahn, Nam-Geun; Bae, Bong-Seok; Lee, Myoung-Woo; Park, Hee-Won; Jang, Kyoung Hwa; Cho, Byung-Goo; Han, Chang Kyun; Park, Chae Kyu; Kwak, Yi-Seong

2017-07-01

The chemical constituents of Panax ginseng are changed by processing methods such as steaming or sun drying. In the present study, the chemical change of Panax ginseng induced by steaming was monitored in situ . Samples were separated from the same ginseng root by incision during the steaming process, for in situ monitoring. Sampling was sequentially performed in three stages; FG (fresh ginseng) → SG (steamed ginseng) → RG (red ginseng) and 60 samples were prepared and freeze dried. The samples were then analyzed to determine 43 constituents among three stages of P. ginseng . The results showed that six malonyl-ginsenoside (Rg1, Rb1, Rb3, Rc, Rd, Rb2) and 15 amino acids were decreased in concentration during the steaming process. In contrast, ginsenoside-Rh1, 20( S )-Rg2, 20( S, R )-Rg3 and Maillard reaction product such as AF (arginine-fructose), AFG (arginine-fructose-glucose), and maltol were newly generated or their concentrations were increased. This study elucidates the dynamic changes in the chemical components of P. ginseng when the steaming process was induced. These results are thought to be helpful for quality control and standardization of herbal drugs using P. ginseng and they also provide a scientific basis for pharmacological research of processed ginseng (Red ginseng).

Direct observation of stick-slip movements of water nanodroplets induced by an electron beam

PubMed Central

Mirsaidov, Utkur M.; Zheng, Haimei; Bhattacharya, Dipanjan; Casana, Yosune; Matsudaira, Paul

2012-01-01

Dynamics of the first few nanometers of water at the interface are encountered in a wide range of physical, chemical, and biological phenomena. A simple but critical question is whether interfacial forces at these nanoscale dimensions affect an externally induced movement of a water droplet on a surface. At the bulk-scale water droplets spread on a hydrophilic surface and slip on a nonwetting, hydrophobic surface. Here we report the experimental description of the electron beam-induced dynamics of nanoscale water droplets by direct imaging the translocation of 10- to 80-nm-diameter water nanodroplets by transmission electron microscopy. These nanodroplets move on a hydrophilic surface not by a smooth flow but by a series of stick-slip steps. We observe that each step is preceded by a unique characteristic deformation of the nanodroplet into a toroidal shape induced by the electron beam. We propose that this beam-induced change in shape increases the surface free energy of the nanodroplet that drives its transition from stick to slip state. PMID:22517747

Gravity Wave Mixing and Effective Diffusivity for Minor Chemical Constituents in the Mesosphere/Lower Thermosphere

NASA Astrophysics Data System (ADS)

Grygalashvyly, M.; Becker, E.; Sonnemann, G. R.

2012-06-01

The influence of gravity waves (GWs) on the distributions of minor chemical constituents in the mesosphere-lower thermosphere (MLT) is studied on the basis of the effective diffusivity concept. The mixing ratios of chemical species used for calculations of the effective diffusivity are obtained from numerical experiments with an off-line coupled model of the dynamics and chemistry abbreviated as KMCM-MECTM (Kuehlungsborn Mechanistic general Circulation Model—MEsospheric Chemistry-Transport Model). In our control simulation the MECTM is driven with the full dynamical fields from an annual cycle simulation with the KMCM, where mid-frequency GWs down to horizontal wavelengths of 350 km are resolved and their wave-mean flow interaction is self-consistently induced by an advanced turbulence model. A perturbation simulation with the MECTM is defined by eliminating all meso-scale variations with horizontal wavelengths shorter than 1000 km from the dynamical fields by means of spectral filtering before running the MECTM. The response of the MECTM to GWs perturbations reveals strong effects on the minor chemical constituents. We show by theoretical arguments and numerical diagnostics that GWs have direct, down-gradient mixing effects on all long-lived minor chemical species that possess a mean vertical gradient in the MLT. Introducing the term wave diffusion (WD) and showing that wave mixing yields approximately the same WD coefficient for different chemical constituents, we argue that it is a useful tool for diagnostic irreversible transport processes. We also present a detailed discussion of the gravity-wave mixing effects on the photochemistry and highlight the consequences for the general circulation of the MLT.

Molecular Simulations of Shear-Induced Dynamics in Nitromethane

DTIC Science & Technology

2016-09-01

initially staggered along the y axis, and then after the crystal is sheared b), the NM molecules are rotated to orient themselves in the same... rotation of the grain. ...............................................................................8 List of Tables Table 1 Summary of the maximum...it an ideal candidate to study chemical reaction mechanisms associated with conventional explosive initiation and subsequent detonation .3,6,7

Analysis of the Electronic Structure of the Special Pair of a Bacterial Photosynthetic Reaction Center by 13 C Photochemically Induced Dynamic Nuclear Polarization Magic-Angle Spinning NMR Using a Double-Quantum Axis.

PubMed

Najdanova, Marija; Gräsing, Daniel; Alia, A; Matysik, Jörg

2018-01-01

The origin of the functional symmetry break in bacterial photosynthesis challenges since several decades. Although structurally very similar, the two branches of cofactors in the reaction center (RC) protein complex act very differently. Upon photochemical excitation, an electron is transported along one branch, while the other remains inactive. Photochemically induced dynamic nuclear polarization (photo-CIDNP) magic-angle spinning (MAS) 13 C NMR revealed that the two bacteriochlorophyll cofactors forming the "Special Pair" donor dimer are already well distinguished in the electronic ground state. These previous studies are relying solely on 13 C- 13 C correlation experiments as radio-frequency-driven recoupling (RFDR) and dipolar-assisted rotational resonance (DARR). Obviously, the chemical-shift assignment is difficult in a dimer of tetrapyrrole macrocycles, having eight pyrrole rings of similar chemical shifts. To overcome this problem, an INADEQUATE type of experiment using a POST C7 symmetry-based approach is applied to selectively isotope-labeled bacterial RC of Rhodobacter (R.) sphaeroides wild type (WT). We, therefore, were able to distinguish unresolved sites of the macromolecular dimer. The obtained chemical-shift pattern is in-line with a concentric assembly of negative charge within the common center of the Special Pair supermolecule in the electronic ground state. © 2017 The American Society of Photobiology.

Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane

NASA Astrophysics Data System (ADS)

Larentzos, James; Steele, Brad

2017-06-01

Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.

Molecular Dynamics Simulations of Shear Induced Transformations in Nitromethane

NASA Astrophysics Data System (ADS)

Larentzos, James; Steele, Brad

Recent experiments demonstrate that NM undergoes explosive chemical initiation under compressive shear stress. The atomistic dynamics of the shear response of single-crystalline and bi-crystalline nitromethane (NM) are simulated using molecular dynamics simulations under high pressure conditions to aid in interpreting these experiments. The atomic interactions are described using a recently re-optimized ReaxFF-lg potential trained specifically for NM under pressure. The simulations demonstrate that the NM crystal transforms into a disordered state upon sufficient application of shear stress; its maximum value, shear angle, and atomic-scale dynamics being highly dependent on crystallographic orientation of the applied shear. Shear simulations in bi-crystalline NM show more complex behavior resulting in the appearance of the disordered state at the grain boundary.

Patterns and Oscillations in Reaction-Diffusion Systems with Intrinsic Fluctuations

NASA Astrophysics Data System (ADS)

Giver, Michael; Goldstein, Daniel; Chakraborty, Bulbul

2013-03-01

Intrinsic or demographic noise has been shown to play an important role in the dynamics of a variety of systems including predator-prey populations, biochemical reactions within cells, and oscillatory chemical reaction systems, and is known to give rise to oscillations and pattern formation well outside the parameter range predicted by standard mean-field analysis. Initially motivated by an experimental model of cells and tissues where the cells are represented by chemical reagents isolated in emulsion droplets, we study the stochastic Brusselator, a simple activator-inhibitor chemical reaction model. Our work extends the results of recent studies on the zero and one dimensional systems with the ultimate goals of understanding the role of noise in spatially structured systems and engineering novel patterns and attractors induced by fluctuations. In the zero dimensional system, we observe a noise induced switching between small and large amplitude oscillations when a separation of time scales is present, while the spatially extended system displays a similar switching between a stationary Turing pattern and uniform oscillations.

Generation and precise control of dynamic biochemical gradients for cellular assays

NASA Astrophysics Data System (ADS)

Saka, Yasushi; MacPherson, Murray; Giuraniuc, Claudiu V.

2017-03-01

Spatial gradients of diffusible signalling molecules play crucial roles in controlling diverse cellular behaviour such as cell differentiation, tissue patterning and chemotaxis. In this paper, we report the design and testing of a microfluidic device for diffusion-based gradient generation for cellular assays. A unique channel design of the device eliminates cross-flow between the source and sink channels, thereby stabilizing gradients by passive diffusion. The platform also enables quick and flexible control of chemical concentration that makes highly dynamic gradients in diffusion chambers. A model with the first approximation of diffusion and surface adsorption of molecules recapitulates the experimentally observed gradients. Budding yeast cells cultured in a gradient of a chemical inducer expressed a reporter fluorescence protein in a concentration-dependent manner. This microfluidic platform serves as a versatile prototype applicable to a broad range of biomedical investigations.

Shape-dependent guidance of active Janus particles by chemically patterned surfaces

NASA Astrophysics Data System (ADS)

Uspal, W. E.; Popescu, M. N.; Tasinkevych, M.; Dietrich, S.

2018-01-01

Self-phoretic chemically active Janus particles move by inducing—via non-equilibrium chemical reactions occurring on their surfaces—changes in the chemical composition of the solution in which they are immersed. This process leads to gradients in chemical composition along the surface of the particle, as well as along any nearby boundaries, including solid walls. Chemical gradients along a wall can give rise to chemi-osmosis, i.e., the gradients drive surface flows which, in turn, drive flow in the volume of the solution. This bulk flow couples back to the particle, and thus contributes to its self-motility. Since chemi-osmosis strongly depends on the molecular interactions between the diffusing molecular species and the wall, the response flow induced and experienced by a particle encodes information about any chemical patterning of the wall. Here, we extend previous studies on self-phoresis of a sphere near a chemically patterned wall to the case of particles with rod-like, elongated shape. We focus our analysis on the new phenomenology potentially emerging from the coupling—which is inoperative for a spherical shape—of the elongated particle to the strain rate tensor of the chemi-osmotic flow. Via detailed numerical calculations, we show that the dynamics of a rod-like particle exhibits a novel ‘edge-following’ steady state: the particle translates along the edge of a chemical step at a steady distance from the step and with a steady orientation. Moreover, within a certain range of system parameters, the edge-following state co-exists with a ‘docking’ state (the particle stops at the step, oriented perpendicular to the step edge), i.e., a bistable dynamics occurs. These findings are rationalized as a consequence of the competition between the fluid vorticity and the rate of strain by using analytical theory based on the point-particle approximation which captures quasi-quantitatively the dynamics of the system.

Dynamic Chemical and Structural Changes of Heterogeneous Catalysts Observed in Real Time: From Catalysis-Induced Fluxionality to Catalytic Cycles

DTIC Science & Technology

2014-11-26

zeolite and showed that a step in the Ar isotherm coincides with a change in the neutron diffraction pattern. Using grand canonical Monte Carlo...the stepped Ar isotherm at 77 K for a MFI zeolite . More recently, Mallon et al. surmised that the hysteresis of the Ar 87 K adsorption isotherm of

Historical Perspective and Contribution of U.S. Researchers Into the Field of Self-Propagating High-Temperature Synthesis (SHS)/Combustion Synthesis (CS): Personal Reflections

DTIC Science & Technology

2008-07-01

Gas - Solid Systems. Chem. Eng. Comm. 1990, 92, 199. 74. Dimitriou, P.; Puszynski, J. A.; Hlavacek, V. On the Dynamic of Equations Describing...Yu, L. H.; Thadani, N. N.; Meyers, M. A.; Graham, R. A.; Hammetter , W. F. Shock-Induced Chemical Synthesis of Intermetallic Compounds. In

Hot spot formation and chemical reaction initiation in shocked HMX crystals with nanovoids: a large-scale reactive molecular dynamics study.

PubMed

Zhou, Tingting; Lou, Jianfeng; Zhang, Yangeng; Song, Huajie; Huang, Fenglei

2016-07-14

We report million-atom reactive molecular dynamic simulations of shock initiation of β-cyclotetramethylene tetranitramine (β-HMX) single crystals containing nanometer-scale spherical voids. Shock induced void collapse and subsequent hot spot formation as well as chemical reaction initiation are observed which depend on the void size and impact strength. For an impact velocity of 1 km s(-1) and a void radius of 4 nm, the void collapse process includes three stages; the dominant mechanism is the convergence of upstream molecules toward the centerline and the downstream surface of the void forming flowing molecules. Hot spot formation also undergoes three stages, and the principal mechanism is kinetic energy transforming to thermal energy due to the collision of flowing molecules on the downstream surface. The high temperature of the hot spot initiates a local chemical reaction, and the breakage of the N-NO2 bond plays the key role in the initial reaction mechanism. The impact strength and void size have noticeable effects on the shock dynamical process, resulting in a variation of the predominant mechanisms leading to void collapse and hot spot formation. Larger voids or stronger shocks result in more intense hot spots and, thus, more violent chemical reactions, promoting more reaction channels and generating more reaction products in a shorter duration. The reaction products are mainly concentrated in the developed hot spot, indicating that the chemical reactivity of the hmx crystal is greatly enhanced by void collapse. The detailed information derived from this study can aid a thorough understanding of the role of void collapse in hot spot formation and the chemical reaction initiation of explosives.

Cranberry Resistance to Dodder Parasitism: Induced Chemical Defenses and Behavior of a Parasitic Plant.

PubMed

Tjiurutue, Muvari Connie; Sandler, Hilary A; Kersch-Becker, Monica F; Theis, Nina; Adler, Lynn A

2016-02-01

Parasitic plants are common in many ecosystems, where they can structure community interactions and cause major economic damage. For example, parasitic dodder (Cuscuta spp.) can cause up to 80-100 % yield loss in heavily infested cranberry (Vaccinium macrocarpon) patches. Despite their ecological and economic importance, remarkably little is known about how parasitic plants affect, or are affected by, host chemistry. To examine chemically-mediated interactions between dodder and its cranberry host, we conducted a greenhouse experiment asking whether: (1) dodder performance varies with cranberry cultivar; (2) cultivars differ in levels of phytohormones, volatiles, or phenolics, and whether such variation correlates with dodder parasitism; (3) dodder parasitism induced changes in phytohormones, volatiles, or phenolics, and whether the level of inducible response varied among cultivars. We used five cranberry cultivars to assess host attractiveness to dodder and dodder performance. Dodder performance did not differ across cultivars, but there were marginally significant differences in host attractiveness to dodder, with fewer dodder attaching to Early Black than to any other cultivar. Dodder parasitism induced higher levels of salicylic acid (SA) across cultivars. Cultivars differed in overall levels of flavonols and volatile profiles, but not phenolic acids or proanthocyanidins, and dodder attachment induced changes in several flavonols and volatiles. While cultivars differed slightly in resistance to dodder attachment, we did not find evidence of chemical defenses that mediate these interactions. However, induction of several defenses indicates that parasitism alters traits that could influence subsequent interactions with other species, thus shaping community dynamics.

Disorder-induced amorphization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lam, N.Q.; Okamoto, P.R.; Li, Mo

1997-03-01

Many crystalline materials undergo a crystalline-to-amorphous (c-a) phase transition when subjected to energetic particle irradiation at low temperatures. By focusing on the mean-square static atomic displacement as a generic measure of chemical and topological disorder, we are led quite naturally to a generalized version of the Lindemann melting criterion as a conceptual framework for a unified thermodynamic approach to solid-state amorphizing transformations. In its simplest form, the generalized Lindemann criterion assumes that the sum of the static and dynamic mean-square atomic displacements is constant along the polymorphous melting curve so that c-a transformations can be understood simply as melting ofmore » a critically-disordered crystal at temperatures below the glass transition temperature where the supercooled liquid can persist indefinitely in a configurationally-frozen state. Evidence in support of the generalized Lindemann melting criterion for amorphization is provided by a large variety of experimental observations and by molecular dynamics simulations of heat-induced melting and of defect-induced amorphization of intermetallic compounds.« less

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

PubMed Central

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; Kong, Betty Y.; Gleber, Sophie C.; Vogt, Stefan; Chen, Si; Garwin, Seth A.; Bayer, Amanda R.; Dravid, Vinayak; Woodruff, Teresa K.; O’Halloran, Thomas V.

2015-01-01

Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes. PMID:25615666

Dynamic Responses and Initial Decomposition under Shock Loading: A DFTB Calculation Combined with MSST Method for β-HMX with Molecular Vacancy.

PubMed

He, Zheng-Hua; Chen, Jun; Ji, Guang-Fu; Liu, Li-Min; Zhu, Wen-Jun; Wu, Qiang

2015-08-20

Despite extensive efforts on studying the decomposition mechanism of HMX under extreme condition, an intrinsic understanding of mechanical and chemical response processes, inducing the initial chemical reaction, is not yet achieved. In this work, the microscopic dynamic response and initial decomposition of β-HMX with (1 0 0) surface and molecular vacancy under shock condition, were explored by means of the self-consistent-charge density-functional tight-binding method (SCC-DFTB) in conjunction with multiscale shock technique (MSST). The evolutions of various bond lengths and charge transfers were analyzed to explore and understand the initial reaction mechanism of HMX. Our results discovered that the C-N bond close to major axes had less compression sensitivity and higher stretch activity. The charge was transferred mainly from the N-NO2 group along the minor axes and H atom to C atom during the early compression process. The first reaction of HMX primarily initiated with the fission of the molecular ring at the site of the C-N bond close to major axes. Further breaking of the molecular ring enhanced intermolecular interactions and promoted the cleavage of C-H and N-NO2 bonds. More significantly, the dynamic response behavior clearly depended on the angle between chemical bond and shock direction.

Molecular Dynamics Studies of Thermal Induced Chemistry in TATB

NASA Astrophysics Data System (ADS)

Quenneville, Jason; Germann, Timothy

2007-06-01

A reactive force field (ReaxFF^2) is used with molecular dynamics to probe the chemistry induced by intense heating (accelerated `cook-off') of 1,3,5-triamino-2,4,6-trinitrobenzene (TATB). Large-system simulations are desired for TATB because of the high degree of carbon clustering expected in this material. Using small, 800-atom, simulations, we will show the reaction rate as a function of temperature and density as well as the time evolution of reaction products. A larger simulation (with 14,000 atoms) will illustrate the effect of system size on both carbon clustering and reaction rate. Insight into the mechanisms of product formation will be given, as well as the chemical structure (graphitic or diamond-like) of the carbon clusters obtained. ^2 A. C. T. Van Duin, et al, J. Phys. Chem. A, 1005, 9396 (2001).

Surface effects on the mechanical elongation of AuCu nanowires: De-alloying and the formation of mixed suspended atomic chains

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lagos, M. J.; Laboratório Nacional de Nanotecnologia-LNNANO, 13083-970 Campinas-SP; Autreto, P. A. S.

2015-03-07

We report here an atomistic study of the mechanical deformation of Au{sub x}Cu{sub (1−x)} atomic-size wires (nanowires (NWs)) by means of high resolution transmission electron microscopy experiments. Molecular dynamics simulations were also carried out in order to obtain deeper insights on the dynamical properties of stretched NWs. The mechanical properties are significantly dependent on the chemical composition that evolves in time at the junction; some structures exhibit a remarkable de-alloying behavior. Also, our results represent the first experimental realization of mixed linear atomic chains (LACs) among transition and noble metals; in particular, surface energies induce chemical gradients on NW surfacesmore » that can be exploited to control the relative LAC compositions (different number of gold and copper atoms). The implications of these results for nanocatalysis and spin transport of one-atom-thick metal wires are addressed.« less

Dynamic actuation of glassy polymersomes through isomerization of a single azobenzene unit at the block copolymer interface

NASA Astrophysics Data System (ADS)

Molla, Mijanur Rahaman; Rangadurai, Poornima; Antony, Lucas; Swaminathan, Subramani; de Pablo, Juan J.; Thayumanavan, S.

2018-06-01

Nature has engineered exquisitely responsive systems where molecular-scale information is transferred across an interface and propagated over long length scales. Such systems rely on multiple interacting, signalling and adaptable molecular and supramolecular networks that are built on dynamic, non-equilibrium structures. Comparable synthetic systems are still in their infancy. Here, we demonstrate that the light-induced actuation of a molecularly thin interfacial layer, assembled from a hydrophilic- azobenzene -hydrophobic diblock copolymer, can result in a reversible, long-lived perturbation of a robust glassy membrane across a range of over 500 chemical bonds. We show that the out-of-equilibrium actuation is caused by the photochemical trans-cis isomerization of the azo group, a single chemical functionality, in the middle of the interfacial layer. The principles proposed here are implemented in water-dispersed nanocapsules, and have implications for on-demand release of embedded cargo molecules.

Crossfit analysis: a novel method to characterize the dynamics of induced plant responses.

PubMed

Jansen, Jeroen J; van Dam, Nicole M; Hoefsloot, Huub C J; Smilde, Age K

2009-12-16

Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. This study therefore aims to describe the dynamics of the glucosinolate response, measured at three time points after induction in a feral Brassica, by a three-faceted approach, based on Principal Component Analysis. First the large-scale aspects of the response are described in a 'global model' and then each time-point in the experiment is individually described in 'local models' that focus on phenomena that occur at specific moments in time. Although each local model describes the variation among the plants at one time-point as well as possible, the response dynamics are lost. Therefore a novel method called the 'Crossfit' is described that links the local models of different time-points to each other. Each element of the described analysis approach reveals different aspects of the response. The crossfit shows that smaller dynamic changes may occur in the response that are overlooked by global models, as illustrated by the analysis of a metabolic profiling dataset of the same samples.

Crossfit analysis: a novel method to characterize the dynamics of induced plant responses

PubMed Central

2009-01-01

Background Many plant species show induced responses that protect them against exogenous attacks. These responses involve the production of many different bioactive compounds. Plant species belonging to the Brassicaceae family produce defensive glucosinolates, which may greatly influence their favorable nutritional properties for humans. Each responding compound may have its own dynamic profile and metabolic relationships with other compounds. The chemical background of the induced response is therefore highly complex and may therefore not reveal all the properties of the response in any single model. Results This study therefore aims to describe the dynamics of the glucosinolate response, measured at three time points after induction in a feral Brassica, by a three-faceted approach, based on Principal Component Analysis. First the large-scale aspects of the response are described in a 'global model' and then each time-point in the experiment is individually described in 'local models' that focus on phenomena that occur at specific moments in time. Although each local model describes the variation among the plants at one time-point as well as possible, the response dynamics are lost. Therefore a novel method called the 'Crossfit' is described that links the local models of different time-points to each other. Conclusions Each element of the described analysis approach reveals different aspects of the response. The crossfit shows that smaller dynamic changes may occur in the response that are overlooked by global models, as illustrated by the analysis of a metabolic profiling dataset of the same samples. PMID:20015363

Monitoring Ultrafast Chemical Dynamics by Time-Domain X-ray Photo- and Auger-Electron Spectroscopy.

PubMed

Gessner, Oliver; Gühr, Markus

2016-01-19

The directed flow of charge and energy is at the heart of all chemical processes. Extraordinary efforts are underway to monitor and understand the concerted motion of electrons and nuclei with ever increasing spatial and temporal sensitivity. The element specificity, chemical sensitivity, and temporal resolution of ultrafast X-ray spectroscopy techniques hold great promise to provide new insight into the fundamental interactions underlying chemical dynamics in systems ranging from isolated molecules to application-like devices. Here, we focus on the potential of ultrafast X-ray spectroscopy techniques based on the detection of photo- and Auger electrons to provide new fundamental insight into photochemical processes of systems with various degrees of complexity. Isolated nucleobases provide an excellent testing ground for our most fundamental understanding of intramolecular coupling between electrons and nuclei beyond the traditionally applied Born-Oppenheimer approximation. Ultrafast electronic relaxation dynamics enabled by the breakdown of this approximation is the major component of the nucleobase photoprotection mechanisms. Transient X-ray induced Auger electron spectroscopy on photoexcited thymine molecules provides atomic-site specific details of the extremely efficient coupling that converts potentially bond changing ultraviolet photon energy into benign heat. In particular, the time-dependent spectral shift of a specific Auger band is sensitive to the length of a single bond within the molecule. The X-ray induced Auger transients show evidence for an electronic transition out of the initially excited state within only ∼200 fs in contrast to theoretically predicted picosecond population trapping behind a reaction barrier. Photoinduced charge transfer dynamics between transition metal complexes and semiconductor nanostructures are of central importance for many emerging energy and climate relevant technologies. Numerous demonstrations of photovoltaic and photocatalytic activity have been performed based on the combination of strong light absorption in dye molecules with charge separation and transport in adjacent semiconductor nanostructures. However, a fundamental understanding of the enabling and limiting dynamics on critical atomic length- and time scales is often still lacking. Femtosecond time-resolved X-ray photoelectron spectroscopy is employed to gain a better understanding of a short-lived intermediate that may be linked to the unexpectedly limited performance of ZnO based dye-sensitized solar cells by delaying the generation of free charge carriers. The transient spectra strongly suggest that photoexcited dye molecules attached to ZnO nanocrystals inject their charges into the substrate within less than 1 ps but the electrons are then temporarily trapped at the surface of the semiconductor in direct vicinity of the injecting molecules. The experiments are extended to monitor the electronic response of the semiconductor substrate to the collective injection from a monolayer of dye molecules and the subsequent electron-ion recombination dynamics. The results indicate some qualitative similarities but quantitative differences between the recombination dynamics at molecule-semiconductor interfaces and previously studied bulk-surface electron-hole recombination dynamics in photoexcited semiconductors.

HEPES activates a MiT/TFE-dependent lysosomal-autophagic gene network in cultured cells: A call for caution.

PubMed

Tol, Marc J; van der Lienden, Martijn J C; Gabriel, Tanit L; Hagen, Jacob J; Scheij, Saskia; Veenendaal, Tineke; Klumperman, Judith; Donker-Koopman, Wilma E; Verhoeven, Arthur J; Overkleeft, Hermen; Aerts, Johannes M; Argmann, Carmen A; van Eijk, Marco

2018-01-01

In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of "master lysosomal regulators". Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated. Here, we identify HEPES, a chemical buffering agent that is broadly applied in cell culture, as a potent inducer of lysosome biogenesis. Supplementation of HEPES to cell growth media is sufficient to decouple the MiT/TFE family members-TFEB, TFE3 and MITF-from regulatory mechanisms that control their cytosolic retention. Increased MiT/TFE nuclear import in turn drives the expression of a global network of lysosomal-autophagic and innate host-immune response genes, altering lysosomal dynamics, proteolytic capacity, autophagic flux, and inflammatory signaling. In addition, siRNA-mediated MiT/TFE knockdown effectively blunted HEPES-induced lysosome biogenesis and gene expression profiles. Mechanistically, we show that MiT/TFE activation in response to HEPES requires its macropinocytic ingestion and aberrant lysosomal storage/pH, but is independent of MTORC1 signaling. Altogether, our data underscore the cautionary use of chemical buffering agents in cell culture media due to their potentially confounding effects on experimental results.

Optimization of industrial microorganisms: recent advances in synthetic dynamic regulators.

PubMed

Min, Byung Eun; Hwang, Hyun Gyu; Lim, Hyun Gyu; Jung, Gyoo Yeol

2017-01-01

Production of biochemicals by industrial fermentation using microorganisms requires maintaining cellular production capacity, because maximal productivity is economically important. High-productivity microbial strains can be developed using static engineering, but these may not maintain maximal productivity throughout the culture period as culture conditions and cell states change dynamically. Additionally, economic reasons limit heterologous protein expression using inducible promoters to prevent metabolic burden for commodity chemical and biofuel production. Recently, synthetic and systems biology has been used to design genetic circuits, precisely controlling gene expression or influencing genetic behavior toward a desired phenotype. Development of dynamic regulators can maintain cellular phenotype in a maximum production state in response to factors including cell concentration, oxygen, temperature, pH, and metabolites. Herein, we introduce dynamic regulators of industrial microorganism optimization and discuss metabolic flux fine control by dynamic regulators in response to metabolites or extracellular stimuli, robust production systems, and auto-induction systems using quorum sensing.

Dynamic control of magnetic nanowires by light-induced domain-wall kickoffs

NASA Astrophysics Data System (ADS)

Heintze, Eric; El Hallak, Fadi; Clauß, Conrad; Rettori, Angelo; Pini, Maria Gloria; Totti, Federico; Dressel, Martin; Bogani, Lapo

2013-03-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. In contrast to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiance is very low, a substantial improvement over present methods of magneto-optical switching. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to numerous fields, ranging from social evolution to neural networks and chemical reactivity.

Force-Manipulation Single-Molecule Spectroscopy Studies of Enzymatic Dynamics

NASA Astrophysics Data System (ADS)

Lu, H. Peter; He, Yufan; Lu, Maolin; Cao, Jin; Guo, Qing

2014-03-01

Subtle conformational changes play a crucial role in protein functions, especially in enzymatic reactions involving complex substrate-enzyme interactions and chemical reactions. We applied AFM-enhanced and magnetic tweezers-correlated single-molecule spectroscopy to study the mechanisms and dynamics of enzymatic reactions involved with kinase and lysozyme proteins. Enzymatic reaction turnovers and the associated structure changes of individual protein molecules were observed simultaneously in real-time by single-molecule FRET detections. Our single-molecule spectroscopy measurements of enzymatic conformational dynamics have revealed time bunching effect and intermittent coherence in conformational state change dynamics involving in enzymatic reaction cycles. The coherent conformational state dynamics suggests that the enzymatic catalysis involves a multi-step conformational motion along the coordinates of substrate-enzyme complex formation and product releasing. Our results support a multiple-conformational state model, being consistent with a complementary conformation selection and induced-fit enzymatic loop-gated conformational change mechanism in substrate-enzyme active complex formation.

Stochastic description of quantum Brownian dynamics

NASA Astrophysics Data System (ADS)

Yan, Yun-An; Shao, Jiushu

2016-08-01

Classical Brownian motion has well been investigated since the pioneering work of Einstein, which inspired mathematicians to lay the theoretical foundation of stochastic processes. A stochastic formulation for quantum dynamics of dissipative systems described by the system-plus-bath model has been developed and found many applications in chemical dynamics, spectroscopy, quantum transport, and other fields. This article provides a tutorial review of the stochastic formulation for quantum dissipative dynamics. The key idea is to decouple the interaction between the system and the bath by virtue of the Hubbard-Stratonovich transformation or Itô calculus so that the system and the bath are not directly entangled during evolution, rather they are correlated due to the complex white noises introduced. The influence of the bath on the system is thereby defined by an induced stochastic field, which leads to the stochastic Liouville equation for the system. The exact reduced density matrix can be calculated as the stochastic average in the presence of bath-induced fields. In general, the plain implementation of the stochastic formulation is only useful for short-time dynamics, but not efficient for long-time dynamics as the statistical errors go very fast. For linear and other specific systems, the stochastic Liouville equation is a good starting point to derive the master equation. For general systems with decomposable bath-induced processes, the hierarchical approach in the form of a set of deterministic equations of motion is derived based on the stochastic formulation and provides an effective means for simulating the dissipative dynamics. A combination of the stochastic simulation and the hierarchical approach is suggested to solve the zero-temperature dynamics of the spin-boson model. This scheme correctly describes the coherent-incoherent transition (Toulouse limit) at moderate dissipation and predicts a rate dynamics in the overdamped regime. Challenging problems such as the dynamical description of quantum phase transition (local- ization) and the numerical stability of the trace-conserving, nonlinear stochastic Liouville equation are outlined.

Visualizing Chemical Interaction Dynamics of Confined DNA Molecules

NASA Astrophysics Data System (ADS)

Henkin, Gilead; Berard, Daniel; Stabile, Frank; Leslie, Sabrina

We present a novel nanofluidic approach to controllably introducing reagent molecules to interact with confined biopolymers and visualizing the reaction dynamics in real time. By dynamically deforming a flow cell using CLiC (Convex Lens-induced Confinement) microscopy, we are able to tune reaction chamber dimensions from micrometer to nanometer scales. We apply this gentle deformation to load and extend DNA polymers within embedded nanotopographies and visualize their interactions with other molecules in solution. Quantifying the change in configuration of polymers within embedded nanotopographies in response to binding/unbinding of reagent molecules provides new insights into their consequent change in physical properties. CLiC technology enables an ultra sensitive, massively parallel biochemical analysis platform which can acces a broader range of interaction parameters than existing devices.

Quantification of Anti-Aggregation Activity of Chaperones: A Test-System Based on Dithiothreitol-Induced Aggregation of Bovine Serum Albumin

PubMed Central

Borzova, Vera A.; Markossian, Kira A.; Kara, Dmitriy A.; Chebotareva, Natalia A.; Makeeva, Valentina F.; Poliansky, Nikolay B.; Muranov, Konstantin O.; Kurganov, Boris I.

2013-01-01

The methodology for quantification of the anti-aggregation activity of protein and chemical chaperones has been elaborated. The applicability of this methodology was demonstrated using a test-system based on dithiothreitol-induced aggregation of bovine serum albumin at 45°C as an example. Methods for calculating the initial rate of bovine serum albumin aggregation (v agg) have been discussed. The comparison of the dependences of v agg on concentrations of intact and cross-linked α-crystallin allowed us to make a conclusion that a non-linear character of the dependence of v agg on concentration of intact α-crystallin was due to the dynamic mobility of the quaternary structure of α-crystallin and polydispersity of the α-crystallin–target protein complexes. To characterize the anti-aggregation activity of the chemical chaperones (arginine, arginine ethyl ester, arginine amide and proline), the semi-saturation concentration [L]0.5 was used. Among the chemical chaperones studied, arginine ethyl ester and arginine amide reveal the highest anti-aggregation activity ([L]0.5 = 53 and 58 mM, respectively). PMID:24058554

Biotransformation and induction: implications for toxicity, bioaccumulation and monitoring of environmental xenobiotics in fish.

PubMed Central

Kleinow, K M; Melancon, M J; Lech, J J

1987-01-01

Biotransformation of xenobiotics in fish occurs by many of the same reactions as in mammals. These reactions have been shown to affect the bioaccumulation, persistence, residue dynamics, and toxicity of select chemicals in fish. P-450-dependent monooxygenase activity of fish can be induced by polycyclic aromatic hydrocarbons, but phenobarbital-type agents induce poorly, if at all. Fish monooxygenase activity exhibits ideal temperature compensation and sex-related variation. Induction of monooxygenase activity by polycyclic aromatic hydrocarbons can result in qualitative as well as quantitative changes in the metabolic profile of a chemical. Induction can also alter toxicity. In addition, multiple P-450 isozymes have been described for several fish species. The biotransformation products of certain chemicals have been related to specific P-450 isozymes, and the formation of these products can be influenced by induction. Exposure of fish to low levels of certain environmental contaminants has resulted in induction of specific monooxygenase activities and monitoring of such activities has been suggested as a means of identifying areas of pollutant exposure in the wild. PMID:3297653

Improvement of the Correlative AFM and ToF-SIMS Approach Using an Empirical Sputter Model for 3D Chemical Characterization.

PubMed

Terlier, T; Lee, J; Lee, K; Lee, Y

2018-02-06

Technological progress has spurred the development of increasingly sophisticated analytical devices. The full characterization of structures in terms of sample volume and composition is now highly complex. Here, a highly improved solution for 3D characterization of samples, based on an advanced method for 3D data correction, is proposed. Traditionally, secondary ion mass spectrometry (SIMS) provides the chemical distribution of sample surfaces. Combining successive sputtering with 2D surface projections enables a 3D volume rendering to be generated. However, surface topography can distort the volume rendering by necessitating the projection of a nonflat surface onto a planar image. Moreover, the sputtering is highly dependent on the probed material. Local variation of composition affects the sputter yield and the beam-induced roughness, which in turn alters the 3D render. To circumvent these drawbacks, the correlation of atomic force microscopy (AFM) with SIMS has been proposed in previous studies as a solution for the 3D chemical characterization. To extend the applicability of this approach, we have developed a methodology using AFM-time-of-flight (ToF)-SIMS combined with an empirical sputter model, "dynamic-model-based volume correction", to universally correct 3D structures. First, the simulation of 3D structures highlighted the great advantages of this new approach compared with classical methods. Then, we explored the applicability of this new correction to two types of samples, a patterned metallic multilayer and a diblock copolymer film presenting surface asperities. In both cases, the dynamic-model-based volume correction produced an accurate 3D reconstruction of the sample volume and composition. The combination of AFM-SIMS with the dynamic-model-based volume correction improves the understanding of the surface characteristics. Beyond the useful 3D chemical information provided by dynamic-model-based volume correction, the approach permits us to enhance the correlation of chemical information from spectroscopic techniques with the physical properties obtained by AFM.

Using ToxCast data to reconstruct dynamic cell state ...

EPA Pesticide Factsheets

AbstractBackground. High-throughput in vitro screening is an important tool for evaluating the potential biological activity of the thousands of existing chemicals in commerce and the hundreds more introduced each year. Among the assay technologies available, high-content imaging (HCI) allows multiplexed measurements of cellular phenotypic changes induced by chemical exposures. For a large chemical inventory having limited concentration-time series data, the deconvolution of cellular response profiles into transitive or irrevocable state trajectories is an important consideration. Objectives. Our goal was to analyze temporal and concentration-related cellular changes measured using HCI to identify the “tipping point” at which the cells did not show recovery towards a normal phenotypic state. Methods. The effects of 976 chemicals (ToxCast Phase I and II) were evaluated using HCI as a function of concentration and time in HepG2 cells over a 72-hr exposure period to concentrations ranging from 0.4- to 200 µM. The cellular endpoints included nuclear p53 accumulation, JNK, markers of oxidative stress, cytoskeletal changes, mitochondrial energization and density, cell viability and cell cycle progression. A novel computational model was developed to interpret dynamic multidimensional system responses as cell-state trajectories. Results. Analysis of cell-state trajectories showed that HepG2 cells were resilient to the effects of 178 chemicals up to the highest co

Impact of Varying Wave Conditions on the Mobility of Arsenic in a Nearshore Aquifer on the Great Lakes

NASA Astrophysics Data System (ADS)

Rakhimbekova, S.; O'Carroll, D. M.; Robinson, C. E.

2017-12-01

Groundwater-coastal water interactions play an important role in controlling the behavior of inorganic chemicals in nearshore aquifers and the subsequent flux of these chemicals to receiving coastal waters. Previous studies have shown that dynamic groundwater flows and water exchange across the sediment-water interface can set up strong geochemical gradients and an important reaction zone in a nearshore aquifer that affect the fate of reactive chemicals. There is limited understanding of the impact of transient coastal forcing such as wave conditions on groundwater dynamics and geochemistry in a nearshore aquifer. The goal of this study was to assess the impact of intensified wave conditions on the behavior of arsenic in a nearshore aquifer and to determine the hydrological and geochemical factors controlling its fate and ultimate delivery to receiving coastal waters. Field investigations were conducted over the period of intensified wave conditions on a freshwater beach on Lake Erie, Canada. High spatial resolution aqueous and sediment sampling was conducted to characterize the subsurface distribution of inorganic species in the nearshore aquifer. Numerical groundwater flow and transport simulations were conducted to evaluate wave-induced perturbations in the flow dynamics including characterizing changes in the groundwater flow recirculations in the nearshore aquifer. The combination of field data and numerical simulations reveal that varying wave conditions alter groundwater flows and set up geochemical transition zones within the aquifer resulting in the release and sequestration of arsenic. Interactions between oxic surface water, mildly reducing shallow groundwater, and reducing sulfur- and iron-rich deep groundwater promote dynamic iron, sulfur and manganese cycling which control the mobility of arsenic in the aquifer. The findings of this study have potential implications for the fate and transport of other reactive chemicals (e.g. phosphorus, mercury) in nearshore marine and freshwater aquifers exposed to transient coastal forcing. Understanding the fate of chemicals and the dynamics of the reaction zone in nearshore aquifers is critical for evaluating the importance of groundwater as a pathway for delivering pollutants to coastal waters.

Low-energy electron-induced reactions in condensed matter

NASA Astrophysics Data System (ADS)

Arumainayagam, Christopher R.; Lee, Hsiao-Lu; Nelson, Rachel B.; Haines, David R.; Gunawardane, Richard P.

2010-01-01

The goal of this review is to discuss post-irradiation analysis of low-energy (≤50 eV) electron-induced processes in nanoscale thin films. Because electron-induced surface reactions in monolayer adsorbates have been extensively reviewed, we will instead focus on low-energy electron-induced reactions in multilayer adsorbates. The latter studies, involving nanoscale thin films, serve to elucidate the pivotal role that the low-energy electron-induced reactions play in high-energy radiation-induced chemical reactions in condensed matter. Although electron-stimulated desorption (ESD) experiments conducted during irradiation have yielded vital information relevant to primary or initial electron-induced processes, we wish to demonstrate in this review that analyzing the products following low-energy electron irradiation can provide new insights into radiation chemistry. This review presents studies of electron-induced reactions in nanoscale films of molecular species such as oxygen, nitrogen trifluoride, water, alkanes, alcohols, aldehydes, ketones, carboxylic acids, nitriles, halocarbons, alkane and phenyl thiols, thiophenes, ferrocene, amino acids, nucleotides, and DNA using post-irradiation techniques such as temperature-programmed desorption (TPD), reflection-absorption infrared spectroscopy (RAIRS), X-ray photoelectron spectroscopy (XPS), high-resolution electron energy loss spectroscopy (HREELS), gel electrophoresis, and microarray fluorescence. Post-irradiation temperature-programmed desorption, in particular, has been shown to be useful in identifying labile radiolysis products as demonstrated by the first identification of methoxymethanol as a reaction product of methanol radiolysis. Results of post-irradiation studies have been used not only to identify radiolysis products, but also to determine the dynamics of electron-induced reactions. For example, studies of the radiolysis yield as a function of incident electron energy have shown that dissociative electron attachment plays an important role in the electron-induced single strand breaks in DNA leading to mutagenic damage. Studies such as these not only provide insight into the fundamentals of electron-molecule interactions in the condensed phase but also may provide information valuable to (a) furthering cost-efficient destruction of hazardous chemicals, (b) understanding the electron-induced decomposition of feed gases used in the plasma processing of semiconductor devices, (c) clarifying the role, if any, of low-energy electrons, produced by cosmic rays, contributing to the formation of the ozone hole by interacting with halocarbons and producing Cl atoms, (d) illuminating the dynamics of electron-induced oligomerization and/or polymerization, and (e) explicating the astrochemistry of icy grains.

Shock initiated thermal and chemical responses of HMX crystal from ReaxFF molecular dynamics simulation.

PubMed

Zhou, Tingting; Song, Huajie; Liu, Yi; Huang, Fenglei

2014-07-21

To gain an atomistic-level understanding of the thermal and chemical responses of condensed energetic materials under thermal shock, we developed a thermal shock reactive dynamics (TS-RD) computational protocol using molecular dynamics simulation coupled with ReaxFF force field. β-Octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocane (HMX) was selected as a a target explosive due to its wide usage in the military and industry. The results show that a thermal shock initiated by a large temperature gradient between the "hot" region and the "cold" region results in thermal expansion of the particles and induces a thermal-mechanical wave propagating back and forth in the system with an averaged velocity of 3.32 km s(-1). Heat propagating along the direction of thermal shock leads to a temperature increment of the system and thus chemical reaction initiation. Applying a continuum reactive heat conduction model combined with the temperature distribution obtained from the RD simulation, a heat conduction coefficient is derived as 0.80 W m(-1) K(-1). The chemical reaction mechanisms during thermal shock were analyzed, showing that the reaction is triggered by N-NO2 bond breaking followed by HONO elimination and ring fission. The propagation rates of the reaction front and reaction center are obtained to be 0.069 and 0.038 km s(-1), based on the time and spatial distribution of NO2. The pressure effect on the thermal shock was also investigated by employing uniaxial compression before the thermal shock. We find that compression significantly accelerates thermal-mechanical wave propagation and heat conduction, resulting in higher temperature and more excited molecules and thus earlier initiation and faster propagation of chemical reactions.

Ultrafast optically induced ferromagnetic/anti-ferromagnetic phase transition in GdTiO3 from first principles

NASA Astrophysics Data System (ADS)

Khalsa, Guru; Benedek, Nicole A.

2018-03-01

Epitaxial strain and chemical substitution have been the workhorses of functional materials design. These static techniques have shown immense success in controlling properties in complex oxides through the tuning of subtle structural distortions. Recently, an approach based on the excitation of an infrared active phonon with intense midinfrared light has created an opportunity for dynamical control of structure through special nonlinear coupling to Raman phonons. We use first-principles techniques to show that this approach can dynamically induce a magnetic phase transition from the ferromagnetic ground state to a hidden antiferromagnetic phase in the rare earth titanate GdTiO3 for realistic experimental parameters. We show that a combination of a Jahn-Teller distortion, Gd displacement, and infrared phonon motion dominate this phase transition with little effect from the octahedral rotations, contrary to conventional wisdom.

Dynamically tunable electromagnetically-induced-transparency-like resonances in graphene nanoring and nanodisk hybrid metamaterials

NASA Astrophysics Data System (ADS)

Chen, De-Chao; Li, Hong-Ju; Xia, Sheng-Xuan; Qin, Meng; Zhai, Xiang; Wang, Ling-Ling

2017-08-01

A tunable electromagnetically-induced-transparency-like (EIT-like) device is proposed numerically and theoretically in the mid-infrared region, which is composed of periodically patterned ring and disk graphene. Distinguished from the commonly used three-level system, the hybridization of the plasmon mode is applied to describing and explaining the EIT-like phenomenon in the proposed systems. What is more, further researches have revealed that the spectral position of the transparency window can be tuned not only by geometrically changing the couple distance in graphene nanostructures, but also by dynamically altering the radius of the graphene nanodisk and the chemical potential of the graphene. At the transparency window, there exist large optical delays, which can slow down the speed of light in vacuum. This work may pave the way to the development of applications including tunable sensors, slow-light devices, and optical switches.

Time-resolved analysis of DNA-protein interactions in living cells by UV laser pulses.

PubMed

Nebbioso, Angela; Benedetti, Rosaria; Conte, Mariarosaria; Carafa, Vincenzo; De Bellis, Floriana; Shaik, Jani; Matarese, Filomena; Della Ventura, Bartolomeo; Gesuele, Felice; Velotta, Raffaele; Martens, Joost H A; Stunnenberg, Hendrik G; Altucci, Carlo; Altucci, Lucia

2017-09-15

Interactions between DNA and proteins are mainly studied through chemical procedures involving bi-functional reagents, mostly formaldehyde. Chromatin immunoprecipitation is used to identify the binding between transcription factors (TFs) and chromatin, and to evaluate the occurrence and impact of histone/DNA modifications. The current bottleneck in probing DNA-protein interactions using these approaches is caused by the fact that chemical crosslinkers do not discriminate direct and indirect bindings or short-lived chromatin occupancy. Here, we describe a novel application of UV laser-induced (L-) crosslinking and demonstrate that a combination of chemical and L-crosslinking is able to distinguish between direct and indirect DNA-protein interactions in a small number of living cells. The spatial and temporal dynamics of TF bindings to chromatin and their role in gene expression regulation may thus be assessed. The combination of chemical and L-crosslinking offers an exciting and unprecedented tool for biomedical applications.

Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

DOE PAGES

Chae, Jungseok; An, Sangmin; Ramer, Georg; ...

2017-08-03

The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

Nanophotonic Atomic Force Microscope Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale [Nanophotonic AFM Transducers Enable Chemical Composition and Thermal Conductivity Measurements at the Nanoscale

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chae, Jungseok; An, Sangmin; Ramer, Georg

The atomic force microscope (AFM) offers a rich observation window on the nanoscale, yet many dynamic phenomena are too fast and too weak for direct AFM detection. Integrated cavity-optomechanics is revolutionizing micromechanical sensing; however, it has not yet impacted AFM. Here, we make a groundbreaking advance by fabricating picogram-scale probes integrated with photonic resonators to realize functional AFM detection that achieve high temporal resolution (<10 ns) and picometer vertical displacement uncertainty simultaneously. The ability to capture fast events with high precision is leveraged to measure the thermal conductivity (η), for the first time, concurrently with chemical composition at the nanoscalemore » in photothermal induced resonance experiments. The intrinsic η of metal–organic-framework individual microcrystals, not measurable by macroscale techniques, is obtained with a small measurement uncertainty (8%). The improved sensitivity (50×) increases the measurement throughput 2500-fold and enables chemical composition measurement of molecular monolayer-thin samples. In conclusion, our paradigm-shifting photonic readout for small probes breaks the common trade-off between AFM measurement precision and ability to capture transient events, thus transforming the ability to observe nanoscale dynamics in materials.« less

Fast Atomic-Scale Chemical Imaging of Crystalline Materials and Dynamic Phase Transformations

DOE PAGES

Lu, Ping; Yuan, Ren Liang; Ihlefeld, Jon F.; ...

2016-03-04

Chemical imaging at the atomic-scale provides a useful real-space approach to chemically investigate solid crystal structures, and has been recently demonstrated in aberration corrected scanning transmission electron microscopy (STEM). Atomic-scale chemical imaging by STEM using energy-dispersive X-ray spectroscopy (EDS) offers easy data interpretation with a one-to-one correspondence between image and structure but has a severe shortcoming due to the poor efficiency of X-ray generation and collection. As a result, it requires a long acquisition time of typical > few 100 seconds, limiting its potential applications. Here we describe the development of an atomic-scale STEM EDS chemical imaging technique that cutsmore » the acquisition time to one or a few seconds, efficiently reducing the acquisition time by more than 100 times. This method was demonstrated using LaAlO 3 (LAO) as a model crystal. Applying this method to the study of phase transformation induced by electron-beam radiation in a layered lithium transition-metal (TM) oxide, i.e., Li[Li 0.2Ni 0.2Mn 0.6]O 2 (LNMO), a cathode materials for lithium-ion batteries, we obtained a time-series of the atomic-scale chemical imaging, showing the transformation progressing by preferably jumping of Ni atoms from the TM layers into the Li-layers. The new capability offers an opportunity for temporal, atomic-scale chemical mapping of crystal structures for the investigation of materials susceptible to electron irradiation as well as phase transformation and dynamics at the atomic-scale.« less

Spatiotemporal dynamics of DNA repair proteins following laser microbeam induced DNA damage – When is a DSB not a DSB?☆

PubMed Central

Reynolds, Pamela; Botchway, Stanley W.; Parker, Anthony W.; O’Neill, Peter

2013-01-01

The formation of DNA lesions poses a constant threat to cellular stability. Repair of endogenously and exogenously produced lesions has therefore been extensively studied, although the spatiotemporal dynamics of the repair processes has yet to be fully understood. One of the most recent advances to study the kinetics of DNA repair has been the development of laser microbeams to induce and visualize recruitment and loss of repair proteins to base damage in live mammalian cells. However, a number of studies have produced contradictory results that are likely caused by the different laser systems used reflecting in part the wavelength dependence of the damage induced. Additionally, the repair kinetics of laser microbeam induced DNA lesions have generally lacked consideration of the structural and chemical complexity of the DNA damage sites, which are known to greatly influence their reparability. In this review, we highlight the key considerations when embarking on laser microbeam experiments and interpreting the real time data from laser microbeam irradiations. We compare the repair kinetics from live cell imaging with biochemical and direct quantitative cellular measurements for DNA repair. PMID:23688615

Lab-on-a-chip platform for high throughput drug discovery with DNA-encoded chemical libraries

NASA Astrophysics Data System (ADS)

Grünzner, S.; Reddavide, F. V.; Steinfelder, C.; Cui, M.; Busek, M.; Klotzbach, U.; Zhang, Y.; Sonntag, F.

2017-02-01

The fast development of DNA-encoded chemical libraries (DECL) in the past 10 years has received great attention from pharmaceutical industries. It applies the selection approach for small molecular drug discovery. Because of the limited choices of DNA-compatible chemical reactions, most DNA-encoded chemical libraries have a narrow structural diversity and low synthetic yield. There is also a poor correlation between the ranking of compounds resulted from analyzing the sequencing data and the affinity measured through biochemical assays. By combining DECL with dynamical chemical library, the resulting DNA-encoded dynamic library (EDCCL) explores the thermodynamic equilibrium of reversible reactions as well as the advantages of DNA encoded compounds for manipulation/detection, thus leads to enhanced signal-to-noise ratio of the selection process and higher library quality. However, the library dynamics are caused by the weak interactions between the DNA strands, which also result in relatively low affinity of the bidentate interaction, as compared to a stable DNA duplex. To take advantage of both stably assembled dual-pharmacophore libraries and EDCCLs, we extended the concept of EDCCLs to heat-induced EDCCLs (hi-EDCCLs), in which the heat-induced recombination process of stable DNA duplexes and affinity capture are carried out separately. To replace the extremely laborious and repetitive manual process, a fully automated device will facilitate the use of DECL in drug discovery. Herein we describe a novel lab-on-a-chip platform for high throughput drug discovery with hi-EDCCL. A microfluidic system with integrated actuation was designed which is able to provide a continuous sample circulation by reducing the volume to a minimum. It consists of a cooled and a heated chamber for constant circulation. The system is capable to generate stable temperatures above 75 °C in the heated chamber to melt the double strands of the DNA and less than 15 °C in the cooled chamber, to reanneal the reshuffled library. In the binding chamber (the cooled chamber) specific retaining structures are integrated. These hold back beads functionalized with the target protein, while the chamber is continuously flushed with library molecules. Afterwards the whole system can be flushed with buffer to wash out unspecific bound molecules. Finally the protein-loaded beads with attached molecules can be eluted for further investigation.

Dynamic interactions between prophages induce lysis in Propionibacterium acnes.

PubMed

L Brown, Teagan; Tucci, Joseph; Dyson, Zoe A; Lock, Peter; Adda, Christopher G; Petrovski, Steve

Progress in next-generation sequencing technologies has facilitated investigations into microbial dynamics. An important bacterium in the dairy industry is Propionibacterium freudenreichii, which is exploited to manufacture Swiss cheeses. A healthy culture of these bacteria ensures a consistent cheese with formed 'eyes' and pleasant flavour profile, and the investigation of prophages and their interactions with these bacteria could assist in the maintenance of the standard of this food product. Two bacteriophages, termed PFR1 and PFR2, were chemically induced using mitomycin C from two different dairy strains of P. freudenreichii. Both phages have identical genomes; however, PFR2 was found to contain an insertion sequence, IS204. Host range characterisation showed that PFR1 was able to form plaques on a wild type Propionibacterium acnes strain, whereas PFR2 could not. The lytic plaques observed on P. acnes were a result of PFR1 inducing the lytic cycle of a pseudolysogenic phage in P. acnes. Further investigation revealed that both PFR1 and PFR2 could infect P. acnes but not replicate. This study demonstrates the dynamic interactions between phages, which may alter their lytic capacity under certain conditions. To our knowledge, this is the first report of two phages interacting to kill their host. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Effect of micro-stirring on enzymatic reaction kinetics inside a biomimetic container

NASA Astrophysics Data System (ADS)

Gozen, Irep; Horowitz, Viva; Chambers, Zachary; Manoharan, Vinothan

The intracellular environment is dynamic, influenced by the motion of active machinery such as cytoskeleton filaments and molecular motors. To understand whether and how such activity affects the rates of diffusion-limited reactions, we construct a model system consisting of a phospholipid vesicle encapsulating a small number of micro- or nanoparticles, the active motion of which can be induced by chemical or magnetic cues. We aim to determine a relation between active motion of particles and rates of enzymatic reactions in the confined volume. Our findings might illuminate how active motion influences cytoplasmic reaction dynamics, or may have played a role in protocell genetics.

Chemistry meets biology in colitis-associated carcinogenesis

PubMed Central

Mangerich, Aswin; Dedon, Peter C.; Fox, James G.; Tannenbaum, Steven R.; Wogan, Gerald N.

2015-01-01

The intestine comprises an exceptional venue for a dynamic and complex interplay of numerous chemical and biological processes. Here, multiple chemical and biological systems, including the intestinal tissue itself, its associated immune system, the gut microbiota, xenobiotics, and metabolites meet and interact to form a sophisticated and tightly regulated state of tissue homoeostasis. Disturbance of this homeostasis can cause inflammatory bowel disease (IBD) – a chronic disease of multifactorial etiology that is strongly associated with increased risk for cancer development. This review addresses recent developments in research into chemical and biological mechanisms underlying the etiology of inflammation-induced colon cancer. Beginning with a general overview of reactive chemical species generated during colonic inflammation, the mechanistic interplay between chemical and biological mediators of inflammation, the role of genetic toxicology and microbial pathogenesis in disease development are discussed. When possible, we systematically compare evidence from studies utilizing human IBD patients with experimental investigations in mice. The comparison reveals that many strong pathological and mechanistic correlates exist between mouse models of colitis-associated cancer, and the clinically relevant situation in humans. We also summarize several emerging issues in the field, such as the carcinogenic potential of novel inflammation-related DNA adducts and genotoxic microbial factors, the systemic dimension of inflammation-induced genotoxicity, and the complex role of genome maintenance mechanisms during these processes. Taken together, current evidence points to the induction of genetic and epigenetic alterations by chemical and biological inflammatory stimuli ultimately leading to cancer formation. PMID:23926919

Phytoestrogens and Mycoestrogens Induce Signature Structure Dynamics Changes on Estrogen Receptor α

PubMed Central

Chen, Xueyan; Uzuner, Ugur; Li, Man; Shi, Weibing; Yuan, Joshua S.; Dai, Susie Y.

2016-01-01

Endocrine disrupters include a broad spectrum of chemicals such as industrial chemicals, natural estrogens and androgens, synthetic estrogens and androgens. Phytoestrogens are widely present in diet and food supplements; mycoestrogens are frequently found in grains. As human beings and animals are commonly exposed to phytoestrogens and mycoestrogens in diet and environment, it is important to understand the potential beneficial or hazardous effects of estrogenic compounds. Many bioassays have been established to study the binding of estrogenic compounds with estrogen receptor (ER) and provided rich data in the literature. However, limited assays can offer structure information with regard to the ligand/ER complex. Our current study surveys the global structure dynamics changes for ERα ligand binding domain (LBD) when phytoestrogens and mycoestrogens bind. The assay is based on the structure dynamics information probed by hydrogen deuterium exchange mass spectrometry and offers a unique viewpoint to elucidate the mechanism how phytoestrogens and mycoestrogens interact with estrogen receptor. The cluster analysis based on the hydrogen deuterium exchange (HDX) assay data reveals a unique pattern when phytoestrogens and mycoestrogens bind with ERα LBD compared to that of estradiol and synthetic estrogen modulators. Our study highlights that structure dynamics could play an important role in the structure function relationship when endocrine disrupters interact with estrogen receptors. PMID:27589781

Perspective: chemical dynamics simulations of non-statistical reaction dynamics

PubMed Central

Ma, Xinyou; Hase, William L.

2017-01-01

Non-statistical chemical dynamics are exemplified by disagreements with the transition state (TS), RRKM and phase space theories of chemical kinetics and dynamics. The intrinsic reaction coordinate (IRC) is often used for the former two theories, and non-statistical dynamics arising from non-IRC dynamics are often important. In this perspective, non-statistical dynamics are discussed for chemical reactions, with results primarily obtained from chemical dynamics simulations and to a lesser extent from experiment. The non-statistical dynamical properties discussed are: post-TS dynamics, including potential energy surface bifurcations, product energy partitioning in unimolecular dissociation and avoiding exit-channel potential energy minima; non-RRKM unimolecular decomposition; non-IRC dynamics; direct mechanisms for bimolecular reactions with pre- and/or post-reaction potential energy minima; non-TS theory barrier recrossings; and roaming dynamics. This article is part of the themed issue ‘Theoretical and computational studies of non-equilibrium and non-statistical dynamics in the gas phase, in the condensed phase and at interfaces’. PMID:28320906

Transient lattice contraction in the solid to plasma transition of x-ray heated xenon clusters

NASA Astrophysics Data System (ADS)

Bostedt, C.; Ferguson, K.; Gorkhover, T.; Bucksbaum, P. H.; Boutet, S.; Koglin, J. E.; Lutman, A.; Marinelli, A.; Turner, J.; Bucher, M.; Ho, P.; Knight, C.; Young, L.; Fukuzawa, H.; Kumagai, Y.; Ueda, K.; Nagaya, K.; Messerschmidt, M.; Williams, G.

2016-05-01

Any sample in the focus of intense x-ray pulses will be transformed into a nanoplasma within femtoseconds. We have employed the novel two-color two-pulse mode available at the Linac Coherent Light Source free-electron laser to investigate the structural dynamics in nanoparticles upon x-ray exposure. We find that the nanoparticle transiently contracts within the first 80 fs following x-ray irradiation before ultimately disintegrating in a rapid hydrodynamic expansion. The contraction can be attributed to the massive x-ray induced electronic excitation that induces a collective change in the bond character of the nanoparticles. Alternative explanations for the contraction include a compression wave stemming from a rapid surface explosion of the nanoparticle. Computer simulations under way can elucidate the dominant contraction mechanism and yield further insight into the complex x-ray induced dynamics in nanoscale samples. This work is funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Division of Chemical Sciences, Geosciences, and Biosciences, under Contract No. DE-AC02-06CH11357.

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

DOE PAGES

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.; ...

2014-12-15

Fertilization of a mammalian egg induces a series of ‘zinc sparks’ that are necessary for inducing the egg-to-embryo transition. Despite the importance of these zinc efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches to resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy dispersive spectroscopy, X-ray fluorescence microscopy, and 3D elemental tomography for high resolution elemental mapping. Here we show that the zinc spark arises from a system of thousands ofmore » zinc-loaded vesicles, each of which contains, on average, 106 zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. We conclude that the discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.« less

Analysis of Aerospike Plume Induced Base-Heating Environment

NASA Technical Reports Server (NTRS)

Wang, Ten-See

1998-01-01

Computational analysis is conducted to study the effect of an aerospike engine plume on X-33 base-heating environment during ascent flight. To properly account for the effect of forebody and aftbody flowfield such as shocks and to allow for potential plume-induced flow-separation, thermo-flowfield of trajectory points is computed. The computational methodology is based on a three-dimensional finite-difference, viscous flow, chemically reacting, pressure-base computational fluid dynamics formulation, and a three-dimensional, finite-volume, spectral-line based weighted-sum-of-gray-gases radiation absorption model computational heat transfer formulation. The predicted convective and radiative base-heat fluxes are presented.

Water dynamics in protein hydration shells: the molecular origins of the dynamical perturbation.

PubMed

Fogarty, Aoife C; Laage, Damien

2014-07-17

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra.

Water Dynamics in Protein Hydration Shells: The Molecular Origins of the Dynamical Perturbation

PubMed Central

2014-01-01

Protein hydration shell dynamics play an important role in biochemical processes including protein folding, enzyme function, and molecular recognition. We present here a comparison of the reorientation dynamics of individual water molecules within the hydration shell of a series of globular proteins: acetylcholinesterase, subtilisin Carlsberg, lysozyme, and ubiquitin. Molecular dynamics simulations and analytical models are used to access site-resolved information on hydration shell dynamics and to elucidate the molecular origins of the dynamical perturbation of hydration shell water relative to bulk water. We show that all four proteins have very similar hydration shell dynamics, despite their wide range of sizes and functions, and differing secondary structures. We demonstrate that this arises from the similar local surface topology and surface chemical composition of the four proteins, and that such local factors alone are sufficient to rationalize the hydration shell dynamics. We propose that these conclusions can be generalized to a wide range of globular proteins. We also show that protein conformational fluctuations induce a dynamical heterogeneity within the hydration layer. We finally address the effect of confinement on hydration shell dynamics via a site-resolved analysis and connect our results to experiments via the calculation of two-dimensional infrared spectra. PMID:24479585

HEPES activates a MiT/TFE-dependent lysosomal-autophagic gene network in cultured cells: A call for caution

PubMed Central

Tol, Marc J.; van der Lienden, Martijn J.C.; Gabriel, Tanit L.; Hagen, Jacob J.; Scheij, Saskia; Veenendaal, Tineke; Klumperman, Judith; Donker-Koopman, Wilma E.; Verhoeven, Arthur J.; Overkleeft, Hermen; Aerts, Johannes M.; Argmann, Carmen A.; van Eijk, Marco

2018-01-01

ABSTRACT In recent years, the lysosome has emerged as a highly dynamic, transcriptionally regulated organelle that is integral to nutrient-sensing and metabolic rewiring. This is coordinated by a lysosome-to-nucleus signaling nexus in which MTORC1 controls the subcellular distribution of the microphthalmia-transcription factor E (MiT/TFE) family of “master lysosomal regulators”. Yet, despite the importance of the lysosome in cellular metabolism, the impact of traditional in vitro culture media on lysosomal dynamics and/or MiT/TFE localization has not been fully appreciated. Here, we identify HEPES, a chemical buffering agent that is broadly applied in cell culture, as a potent inducer of lysosome biogenesis. Supplementation of HEPES to cell growth media is sufficient to decouple the MiT/TFE family members–TFEB, TFE3 and MITF–from regulatory mechanisms that control their cytosolic retention. Increased MiT/TFE nuclear import in turn drives the expression of a global network of lysosomal-autophagic and innate host-immune response genes, altering lysosomal dynamics, proteolytic capacity, autophagic flux, and inflammatory signaling. In addition, siRNA-mediated MiT/TFE knockdown effectively blunted HEPES-induced lysosome biogenesis and gene expression profiles. Mechanistically, we show that MiT/TFE activation in response to HEPES requires its macropinocytic ingestion and aberrant lysosomal storage/pH, but is independent of MTORC1 signaling. Altogether, our data underscore the cautionary use of chemical buffering agents in cell culture media due to their potentially confounding effects on experimental results. PMID:29455584

Gut Dysbiosis in Animals Due to Environmental Chemical Exposures

PubMed Central

Rosenfeld, Cheryl S.

2017-01-01

The gut microbiome consists of over 103–104 microorganism inhabitants that together possess 150 times more genes that the human genome and thus should be considered an “organ” in of itself. Such communities of bacteria are in dynamic flux and susceptible to changes in host environment and body condition. In turn, gut microbiome disturbances can affect health status of the host. Gut dysbiosis might result in obesity, diabetes, gastrointestinal, immunological, and neurobehavioral disorders. Such host diseases can originate due to shifts in microbiota favoring more pathogenic species that produce various virulence factors, such as lipopolysaccharide. Bacterial virulence factors and metabolites may be transmitted to distal target sites, including the brain. Other potential mechanisms by which gut dysbiosis can affect the host include bacterial-produced metabolites, production of hormones and factors that mimic those produced by the host, and epimutations. All animals, including humans, are exposed daily to various environmental chemicals that can influence the gut microbiome. Exposure to such chemicals might lead to downstream systemic effects that occur secondary to gut microbiome disturbances. Increasing reports have shown that environmental chemical exposures can target both host and the resident gut microbiome. In this review, we will first consider the current knowledge of how endocrine disrupting chemicals (EDCs), heavy metals, air pollution, and nanoparticles can influence the gut microbiome. The second part of the review will consider how potential environmental chemical-induced gut microbiome changes might subsequently induce pathophysiological responses in the host, although definitive evidence for such effects is still lacking. By understanding how these chemicals result in gut dysbiosis, it may open up new remediation strategies in animals, including humans, exposed to such chemicals. PMID:28936425

Ultrafast Chemistry under Nonequilibrium Conditions and the Shock to Deflagration Transition at the Nanoscale

DOE PAGES

Wood, Mitchell A.; Cherukara, Mathew J.; Kober, Edward M.; ...

2015-06-13

We use molecular dynamics simulations to describe the chemical reactions following shock-induced collapse of cylindrical pores in the high-energy density material RDX. For shocks with particle velocities of 2 km/s we find that the collapse of a 40 nm diameter pore leads to a deflagration wave. Molecular collisions during the collapse lead to ultrafast, multistep chemical reactions that occur under nonequilibrium conditions. WE found that exothermic products formed during these first few picoseconds prevent the nanoscale hotspot from quenching. Within 30 ps, a local deflagration wave develops. It propagates at 0.25 km/s and consists of an ultrathin reaction zone ofmore » only ~5 nm, thus involving large temperature and composition gradients. Contrary to the assumptions in current models, a static thermal hotspot matching the dynamical one in size and thermodynamic conditions fails to produce a deflagration wave indicating the importance of nonequilibrium loading in the criticality of nanoscale hot spots. These results provide insight into the initiation of reactive decomposition.« less

Towards Cluster-Assembled Materials of True Monodispersity in Size and Chemical Environment: Synthesis, Dynamics and Activity

DTIC Science & Technology

2016-10-27

AFRL-AFOSR-UK-TR-2016-0037 Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and...Towards cluster-assembled materials of true monodispersity in size and chemical environment: synthesis, dynamics and activity 5a.  CONTRACT NUMBER 5b...report Towards cluster-assembled materials of true monodispersity in size and chemical environment: Synthesis, Dynamics and Activity Ulrich Heiz

Duplex Healing of Selectively Thiolated Guanosine Mismatches through a Cd2+ Chemical Stimulus.

PubMed

Lunn, Samantha M L; Hribesh, Samira; Whitfield, Colette J; Hall, Michael J; Houlton, Andrew; Bronowska, Agnieszka K; Tuite, Eimer M; Pike, Andrew R

2018-03-25

The on-column selective conversion of guanosine to thioguanosine (tG) yields modified oligomers that exhibit destabilisation over the fully complementary duplex. Restoration to a stabilised duplex is induced through thio-directed Cd 2+ coordination; a route for healing DNA damage. Short oligomers are G-specifically thiolated through a modified on-column protocol without the need for costly thioguanosine phosphoramidites. Addition of Cd 2+ ions to a duplex containing a highly disrupted tG central mismatch sequence, 3'-A 6 tG 4 T 6 -5', suggests a (tG) 8 Cd 2 central coordination regime, resulting in increased base stacking and duplex stability. Equilibrium molecular dynamic calculations support the hypothesis of metal-induced healing of the thiolated duplex. The 2 nm displacement of the central tG mismatched region is dramatically reduced after the addition of a chemical stimuli, Cd 2+ ions, returning to a minimized fluctuational state comparable to the unmodified fully complementary oligomer. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Metastable Superconductivity in Two-Dimensional IrTe2 Crystals.

PubMed

Yoshida, Masaro; Kudo, Kazutaka; Nohara, Minoru; Iwasa, Yoshihiro

2018-05-09

Two-dimensional (2D) materials exhibit unusual physical and chemical properties that are attributed to the thinning-induced modification of their electronic band structure. Recently, reduced thickness was found to dramatically impact not only the static electronic structure, but also the dynamic ordering kinetics. The ordering kinetics of first-order phase transitions becomes significantly slowed with decreasing thickness, and metastable supercooled states can be realized by thinning alone. We therefore focus on layered iridium ditelluride (IrTe 2 ), a charge-ordering system that is transformed into a superconductor by suppressing its first-order transition. Here, we discovered a persistent superconducting zero-resistance state in mechanically exfoliated IrTe 2 thin flakes. The maximum superconducting critical temperature ( T c ) was identical to that which is chemically optimized, and the emergent superconductivity was revealed to have a metastable nature. The discovered robust metastable superconductivity suggests that 2D material is a new platform to induce, control, and functionalize metastable electronic states that are inaccessible in bulk crystals.

The fast multipole method and point dipole moment polarizable force fields.

PubMed

Coles, Jonathan P; Masella, Michel

2015-01-14

We present an implementation of the fast multipole method for computing Coulombic electrostatic and polarization forces from polarizable force-fields based on induced point dipole moments. We demonstrate the expected O(N) scaling of that approach by performing single energy point calculations on hexamer protein subunits of the mature HIV-1 capsid. We also show the long time energy conservation in molecular dynamics at the nanosecond scale by performing simulations of a protein complex embedded in a coarse-grained solvent using a standard integrator and a multiple time step integrator. Our tests show the applicability of fast multipole method combined with state-of-the-art chemical models in molecular dynamical systems.

Modeling of hydrogen/deuterium dynamics and heat generation on palladium nanoparticles for hydrogen storage and solid-state nuclear fusion.

PubMed

Tanabe, Katsuaki

2016-01-01

We modeled the dynamics of hydrogen and deuterium adsorbed on palladium nanoparticles including the heat generation induced by the chemical adsorption and desorption, as well as palladium-catalyzed reactions. Our calculations based on the proposed model reproduce the experimental time-evolution of pressure and temperature with a single set of fitting parameters for hydrogen and deuterium injection. The model we generated with a highly generalized set of formulations can be applied for any combination of a gas species and a catalytic adsorbent/absorbent. Our model can be used as a basis for future research into hydrogen storage and solid-state nuclear fusion technologies.

Model of cohesive properties and structural phase transitions in non-metallic solids

DOE Office of Scientific and Technical Information (OSTI.GOV)

Majewski, J.A.; Vogl, P.

1986-01-01

We have developed a simple, yet microscopic and universal model for cohesive properties of solids. This model explains the physical mechanisms determining the chemical and predicts semiquantitatively static and dynamic cohesive properties. It predicts a substantial softening of the long-wavelength transverse optical phonons across the pressure induced phase transition from the zincblenda to rocksalt structure in II-VI compounds. The origin of this softening is shown to be closely related to ferroelectricity.

Photo-induced locomotion of chemo-responsive polymer gels

NASA Astrophysics Data System (ADS)

Dayal, Pratyush; Kuksenok, Olga; Balazs, Anna C.

2009-03-01

The need to translate chemical energy into a mechanical response, a characteristic of many biological processes, has motivated the study of stimuli-responsive polymer gels. Recently, it has been shown experimentally that by coupling the mechanical properties of the gel with the Belousov-Zhabotinsky (BZ) reaction it is possible to induce self-sustained oscillations in the gel. One of the means for controlling these chemical oscillations is using light as an external stimulus. To study the effect of light on the mechanical behavior of the gel, we use our recently developed a 3D gel lattice spring model (gLSM) which couples the BZ reaction kinetics to the gel dynamics. In this model, the polymer-solvent interactions were taken into account by adding a coupling term to the Flory-Huggins free energy. By virtue of this coupling term, the swelling---de-swelling behavior of the gel was captured in 3D. In order to include the effect of the polymer on the reaction kinetics, the Oregonator model for the photo-sensitive BZ reaction was also modified. Using gLSM model, we probed the effect of non-uniform light irradiation on the gel dynamics. We were able to manipulate the direction and velocity of locomotion of the gel using light as a control parameter. This ability to control the movement of the gel can be utilized in a variety of applications, ranging from bio-actuators to controlled drug release systems.

'Trophic whales' as biotic buffers: weak interactions stabilize ecosystems against nutrient enrichment.

PubMed

Schwarzmüller, Florian; Eisenhauer, Nico; Brose, Ulrich

2015-05-01

Human activities may compromise biodiversity if external stressors such as nutrient enrichment endanger overall network stability by inducing unstable dynamics. However, some ecosystems maintain relatively high diversity levels despite experiencing continuing disturbances. This indicates that some intrinsic properties prevent unstable dynamics and resulting extinctions. Identifying these 'ecosystem buffers' is crucial for our understanding of the stability of ecosystems and an important tool for environmental and conservation biologists. In this vein, weak interactions have been suggested as stabilizing elements of complex systems, but their relevance has rarely been tested experimentally. Here, using network and allometric theory, we present a novel concept for a priori identification of species that buffer against externally induced instability of increased population oscillations via weak interactions. We tested our model in a microcosm experiment using a soil food-web motif. Our results show that large-bodied species feeding at the food web's base, so called 'trophic whales', can buffer ecosystems against unstable dynamics induced by nutrient enrichment. Similar to the functionality of chemical or mechanical buffers, they serve as 'biotic buffers' that take up stressor effects and thus protect fragile systems from instability. We discuss trophic whales as common functional building blocks across ecosystems. Considering increasing stressor effects under anthropogenic global change, conservation of these network-intrinsic biotic buffers may help maintain the stability and diversity of natural ecosystems. © 2014 The Authors. Journal of Animal Ecology © 2014 British Ecological Society.

Dynamics of reactive microbial hotspots in concentration gradients

NASA Astrophysics Data System (ADS)

Hubert, Antoine; Farasin, Julien; Tabuteau, Hervé; Méheust, Yves; Le Borgne, Tanguy

2017-04-01

In subsurface environments, bacteria play a major role in controlling the kinetics of a broad range of biogeochemical reactions. In such environments, nutrients fluxes and solute concentrations needed for bacteria metabolism may be highly variable in space and intermittent in time. This can lead to the formation of reactive hotspots where and when conditions are favorable to particular microorganisms, hence inducing biogeochemical reaction kinetics that differ significantly from those measured in homogeneous model environments. To investigate the impact of chemical gradients on the spatial structure and temporal dynamics of subsurface microorganism populations, we develop microfluidic cells allowing for a precise control of flow and chemical gradient conditions, as well as a quantitative monitoring of the bacteria's spatial distribution and biofilm development. Using the non-motile Escherichia coli JW1908-1 strain and Gallionella as model organisms, we investigate the behavior and development of bacteria over a range of single and double concentration gradients in the concentrations of nutrients, electron donors and electron acceptors. To quantify bacterial activity we use Fluorescein Diacetate (FDA) hydrolysis by bacterial enzymes which transforms FDA into Fluorescein, whose local concentration is measured optically. We thus measure bacterial activity locally from the time derivative of the measured fluorescence. This approach allows time-resolved monitoring of the location and intensity of reactive hotspots in micromodels as a function of the flow and chemical gradient conditions. We discuss consequences for the formation and temporal dynamics of biofilms in the subsurface.

Optimal control of multiphoton ionization dynamics of small alkali aggregates

NASA Astrophysics Data System (ADS)

Lindinger, A.; Bartelt, A.; Lupulescu, C.; Vajda, S.; Woste, Ludger

2003-11-01

We have performed transient multi-photon ionization experiments on small alkali clusters of different size in order to probe their wave packet dynamics, structural reorientations, charge transfers and dissociative events in different vibrationally excited electronic states including their ground state. The observed processes were highly dependent on the irradiated pulse parameters like wavelength range or its phase and amplitude; an emphasis to employ a feedback control system for generating the optimum pulse shapes. Their spectral and temporal behavior reflects interesting properties about the investigated system and the irradiated photo-chemical process. First, we present the vibrational dynamics of bound electronically excited states of alkali dimers and trimers. The scheme for observing the wave packet dynamics in the electronic ground state using stimulated Raman-pumping is shown. Since the employed pulse parameters significantly influence the efficiency of the irradiated dynamic pathways photo-induced ioniziation experiments were carried out. The controllability of 3-photon ionization pathways is investigated on the model-like systems NaK and K2. A closed learning loop for adaptive feedback control is used to find the optimal fs pulse shape. Sinusoidal parameterizations of the spectral phase modulation are investigated in regard to the obtained optimal field. By reducing the number of parameters and thereby the complexity of the phase moduation, optimal pulse shapes can be generated that carry fingerprints of the molecule's dynamical properties. This enables to find "understandable" optimal pulse forms and offers the possiblity to gain insight into the photo-induced control process. Characteristic motions of the involved wave packets are proposed to explain the optimized dynamic dissociation pathways.

Light-induced nonadiabatic dynamics in molecular assemblies and nanostructures

NASA Astrophysics Data System (ADS)

Mitric, Roland

The combination of mixed quantum-classical dynamics with efficient electronic structure methods was developed in order to simulate the light-induced processes in complex molecules, multichromophoric aggregates and metallic nanostructures. We will demonstrate how the combination of nonadiabatic dynamics with experimental pump-probe techniques such as time-resolved photoelectron imaging (TRPEI) allows to fully resolve the mechanism of excited state relaxation through conical intersections in several prototype organic- and biomolecules. Specifically, the role of the solvent in the excited state relaxation in microsolvated and fully solvated systems will be addressed. Currently there is growing evidence that nonadiabatic relaxation processes also play a fundamental role in determining the efficiency of excitonic transfer or charge injection in multichromophoric assemblies. Since such systems are currently out of the reach of the state-of-the-art quantum chemistry a development of even more efficient quantum chemical approaches is necessary in order to describe the excited state dynamics in such assemblies. For this purpose we have recently developed long-range corrected time-dependent density functional tight binding (LC-TDDFTB) nonadiabatic dynamics and combined it with the QM/MM approach in order to simulate exciton relaxation in complex systems. The applications of the method to the investigation of the optical properties and dynamics in multichromophoric assemblies including stacked pi-conjugated organic chromophores, model molecular crystals as well as self-organized dye aggregates will be presented. Finally, we will address exciton transport dynamics coupled with the light propagation in hybrid exciton-plasmon nanostructures, which represent promising materials fort the development of novel light-harvesting systems.

Symmetry breaking by quantum coherence in single electron attachment

NASA Astrophysics Data System (ADS)

Krishnakumar, E.; Prabhudesai, Vaibhav S.; Mason, Nigel J.

2018-02-01

Quantum coherence-induced effects in atomic and molecular systems are the basis of several proposals for laser-based control of chemical reactions. So far, these rely on coherent photon beams inducing coherent reaction pathways that may interfere with one another, to achieve the desired outcome. This concept has been successfully exploited for removing the inversion symmetry in the dissociation of homonuclear diatomic molecules, but it remains to be seen if such quantum coherent effects can also be generated by the interaction of incoherent electrons with such molecules. Here we show that resonant electron attachment to H2 and the subsequent dissociation into H (n = 2) + H- is asymmetric about the inter-nuclear axis, whereas the asymmetry in D2 is far less pronounced. We explain this observation as due to attachment of a single electron resulting in a coherent superposition of two resonances of opposite parity. In addition to exemplifying a new quantum coherent process, our observation of coherent quantum dynamics involves the active participation of all three electrons and two nuclei, which could provide new tools for studying electron correlations as a means to control chemical processes, and demonstrates the role of coherent effects in electron-induced chemistry.

Effect of carrageenan addition on the rennet-induced gelation of skim milk.

PubMed

Wang, Fang; Zhang, Wei; Ren, Fazheng

2016-09-01

Carrageenan (CG) (κ-CG, ι-CG and λ-CG) was added to skim milk and the rennet-induced aggregation was studied. Caseinomacropeptide (CMP) release, diffusing wave spectroscopy (DWS) and rheology were used to follow the structural dynamics of casein micelles during gelation. The influence of carrageenan on the nature of protein interactions in the gels was investigated using a combination of ultracentrifugation and specific dissociating agents. For the recombined samples containing κ-CG and low concentrations of ι-CG and λ-CG, the CMP release was slowed down; however, the development of DWS and rheological parameters was similar to that of the control sample, and the increase in the incorporation of proteins through calcium bridges and hydrophobic interactions may be the most likely contributors. For the recombined samples containing high concentrations of ι-CG and λ-CG, other factors may impede the gel formation process. High concentrations of ι-CG and λ-CG strongly interfered with the rennet-induced aggregation, interrupted the interaction of caseins and therefore may contribute to good quality of low-fat cheese. © 2016 Society of Chemical Industry. © 2016 Society of Chemical Industry.

A Bacterial Quorum-Sensing Precursor Induces Mortality in the Marine Coccolithophore, Emiliania huxleyi.

PubMed

Harvey, Elizabeth L; Deering, Robert W; Rowley, David C; El Gamal, Abrahim; Schorn, Michelle; Moore, Bradley S; Johnson, Matthew D; Mincer, Tracy J; Whalen, Kristen E

2016-01-01

Interactions between phytoplankton and bacteria play a central role in mediating biogeochemical cycling and food web structure in the ocean. However, deciphering the chemical drivers of these interspecies interactions remains challenging. Here, we report the isolation of 2-heptyl-4-quinolone (HHQ), released by Pseudoalteromonas piscicida, a marine gamma-proteobacteria previously reported to induce phytoplankton mortality through a hitherto unknown algicidal mechanism. HHQ functions as both an antibiotic and a bacterial signaling molecule in cell-cell communication in clinical infection models. Co-culture of the bloom-forming coccolithophore, Emiliania huxleyi with both live P. piscicida and cell-free filtrates caused a significant decrease in algal growth. Investigations of the P. piscicida exometabolome revealed HHQ, at nanomolar concentrations, induced mortality in three strains of E. huxleyi. Mortality of E. huxleyi in response to HHQ occurred slowly, implying static growth rather than a singular loss event (e.g., rapid cell lysis). In contrast, the marine chlorophyte, Dunaliella tertiolecta and diatom, Phaeodactylum tricornutum were unaffected by HHQ exposures. These results suggest that HHQ mediates the type of inter-domain interactions that cause shifts in phytoplankton population dynamics. These chemically mediated interactions, and other like it, ultimately influence large-scale oceanographic processes.

Disorder and Chaos: Developing and Teaching an Interdisciplinary Course on Chemical Dynamics

ERIC Educational Resources Information Center

Desjardins, Steven G.

2008-01-01

In this paper we describe an interdisciplinary course on dynamics that is appropriate for nonscience majors. This course introduces ideas about mathematical modeling using examples based on pendulums, chemical kinetics, and population dynamics. The unique emphasis for a nonmajors course is on chemical reactions as dynamical systems that do more…

Impact of mixing chemically heterogeneous groundwaters on the sustainability of an open-loop groundwater heat pump

NASA Astrophysics Data System (ADS)

Burté, L.; Farasin, J.; Cravotta, C., III; Gerard, M. F.; Cotiche Baranger, C.; Aquilina, L.; Le Borgne, T.

2017-12-01

Geothermal systems using shallow aquifers are commonly used for heating and cooling. The sustainability of these systems can be severely impacted by the occurrence of clogging process. The geothermal loop operation (including pumping of groundwater, filtering and heat extraction through exchangers and cooled water injection) can lead to an unexpected biogeochemical reactivity and scaling formation that can ultimately lead to the shutdown of the geothermal doublet. Here, we report the results of investigations carried out on a shallow geothermal doublet (< 40 m depth) affected by rapid clogging processes linked to iron and manganese oxidation. Using a reactive transport model, we determine the parameters controlling clogging. To characterize the biogeochemical processes induced by the operation of the production well, we combined hydrodynamic measurements by flowmeter and in-situ chemical depth profiles. We thus investigated the chemical heterogeneity into the pumping well as a function of the operating conditions (static or dynamic). Hydrochemical data collected at the pumping well showed that groundwater was chemically heterogeneous long the 11 meters well screen. While the aquifer was dominantly oxic, a localized inflow of anoxic water was detected and evaluated to produce about 40% of the total flow . The mixture of chemically heterogeneous water induced by pumping lead to the oxidation of reductive species and thus to the formation of biogenic precipitates responsible for clogging. The impact of pumping waters of different redox potential and chemical characteristics was quantified by numerical modeling using PHREEQC. These results shows that natural chemical heterogeneity can occur at a small scale in heterogeneous aquifers and highlight the importance of their characterization during the production well testing and the geothermal loop operation in order to take preventive measures to avoid clogging.

Direct observation of spatially heterogeneous single-layer graphene oxide reduction kinetics.

PubMed

McDonald, Matthew P; Eltom, Ahmed; Vietmeyer, Felix; Thapa, Janak; Morozov, Yurii V; Sokolov, Denis A; Hodak, Jose H; Vinodgopal, Kizhanipuram; Kamat, Prashant V; Kuno, Masaru

2013-01-01

Graphene oxide (GO) is an important precursor in the production of chemically derived graphene. During reduction, GO's electrical conductivity and band gap change gradually. Doping and chemical functionalization are also possible, illustrating GO's immense potential in creating functional devices through control of its local hybridization. Here we show that laser-induced photolysis controllably reduces individual single-layer GO sheets. The reaction can be followed in real time through sizable decreases in GO's photoluminescence efficiency along with spectral blueshifts. As-produced reduced graphene oxide (rGO) sheets undergo additional photolysis, characterized by dramatic emission enhancements and spectral redshifts. Both GO's reduction and subsequent conversion to photobrightened rGO are captured through movies of their photoluminescence kinetics. Rate maps illustrate sizable spatial and temporal heterogeneities in sp(2) domain growth and reveal how reduction "flows" across GO and rGO sheets. The observed heterogeneous reduction kinetics provides mechanistic insight into GO's conversion to chemically derived graphene and highlights opportunities for overcoming its dynamic, chemical disorder.

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Que, Emily L.; Bleher, Reiner; Duncan, Francesca E.

2014-12-15

Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each ofmore » which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes« less

Quantitative mapping of zinc fluxes in the mammalian egg reveals the origin of fertilization-induced zinc sparks.

PubMed

Que, Emily L; Bleher, Reiner; Duncan, Francesca E; Kong, Betty Y; Gleber, Sophie C; Vogt, Stefan; Chen, Si; Garwin, Seth A; Bayer, Amanda R; Dravid, Vinayak P; Woodruff, Teresa K; O'Halloran, Thomas V

2015-02-01

Fertilization of a mammalian egg initiates a series of 'zinc sparks' that are necessary to induce the egg-to-embryo transition. Despite the importance of these zinc-efflux events little is known about their origin. To understand the molecular mechanism of the zinc spark we combined four physical approaches that resolve zinc distributions in single cells: a chemical probe for dynamic live-cell fluorescence imaging and a combination of scanning transmission electron microscopy with energy-dispersive spectroscopy, X-ray fluorescence microscopy and three-dimensional elemental tomography for high-resolution elemental mapping. We show that the zinc spark arises from a system of thousands of zinc-loaded vesicles, each of which contains, on average, 10(6) zinc atoms. These vesicles undergo dynamic movement during oocyte maturation and exocytosis at the time of fertilization. The discovery of these vesicles and the demonstration that zinc sparks originate from them provides a quantitative framework for understanding how zinc fluxes regulate cellular processes.

Dynamical Binding Modes Determine Agonistic and Antagonistic Ligand Effects in the Prostate-Specific G-Protein Coupled Receptor (PSGR).

PubMed

Wolf, Steffen; Jovancevic, Nikolina; Gelis, Lian; Pietsch, Sebastian; Hatt, Hanns; Gerwert, Klaus

2017-11-22

We analysed the ligand-based activation mechanism of the prostate-specific G-protein coupled receptor (PSGR), which is an olfactory receptor that mediates cellular growth in prostate cancer cells. Furthermore, it is an olfactory receptor with a known chemically near identic antagonist/agonist pair, α- and β-ionone. Using a combined theoretical and experimental approach, we propose that this receptor is activated by a ligand-induced rearrangement of a protein-internal hydrogen bond network. Surprisingly, this rearrangement is not induced by interaction of the ligand with the network, but by dynamic van der Waals contacts of the ligand with the involved amino acid side chains, altering their conformations and intraprotein connectivity. Ligand recognition in this GPCR is therefore highly stereo selective, but seemingly lacks any ligand recognition via polar contacts. A putative olfactory receptor-based drug design scheme will have to take this unique mode of protein/ligand action into account.

Modeling bubble dynamics and radical kinetics in ultrasound induced microalgal cell disruption.

PubMed

Wang, Meng; Yuan, Wenqiao

2016-01-01

Microalgal cell disruption induced by acoustic cavitation was simulated through solving the bubble dynamics in an acoustical field and their radial kinetics (chemical kinetics of radical species) occurring in the bubble during its oscillation, as well as calculating the bubble wall pressure at the collapse point. Modeling results indicated that increasing ultrasonic intensity led to a substantial increase in the number of bubbles formed during acoustic cavitation, however, the pressure generated when the bubbles collapsed decreased. Therefore, cumulative collapse pressure (CCP) of bubbles was used to quantify acoustic disruption of a freshwater alga, Scenedesmus dimorphus, and a marine alga, Nannochloropsis oculata and compare with experimental results. The strong correlations between CCP and the intracellular lipid fluorescence density, chlorophyll-a fluorescence density, and cell particle/debris concentration were found, which suggests that the developed models could accurately predict acoustic cell disruption, and can be utilized in the scale up and optimization of the process. Copyright © 2015 Elsevier B.V. All rights reserved.

Conformational and chemical selection by a trans-acting editing domain

PubMed Central

Danhart, Eric M.; Bakhtina, Marina; Cantara, William A.; Kuzmishin, Alexandra B.; Ma, Xiao; Sanford, Brianne L.; Vargas-Rodriguez, Oscar; Košutić, Marija; Goto, Yuki; Suga, Hiroaki; Nakanishi, Kotaro; Micura, Ronald; Musier-Forsyth, Karin

2017-01-01

Molecular sieves ensure proper pairing of tRNAs and amino acids during aminoacyl-tRNA biosynthesis, thereby avoiding detrimental effects of mistranslation on cell growth and viability. Mischarging errors are often corrected through the activity of specialized editing domains present in some aminoacyl-tRNA synthetases or via single-domain trans-editing proteins. ProXp-ala is a ubiquitous trans-editing enzyme that edits Ala-tRNAPro, the product of Ala mischarging by prolyl-tRNA synthetase, although the structural basis for discrimination between correctly charged Pro-tRNAPro and mischarged Ala-tRNAAla is unclear. Deacylation assays using substrate analogs reveal that size discrimination is only one component of selectivity. We used NMR spectroscopy and sequence conservation to guide extensive site-directed mutagenesis of Caulobacter crescentus ProXp-ala, along with binding and deacylation assays to map specificity determinants. Chemical shift perturbations induced by an uncharged tRNAPro acceptor stem mimic, microhelixPro, or a nonhydrolyzable mischarged Ala-microhelixPro substrate analog identified residues important for binding and deacylation. Backbone 15N NMR relaxation experiments revealed dynamics for a helix flanking the substrate binding site in free ProXp-ala, likely reflecting sampling of open and closed conformations. Dynamics persist on binding to the uncharged microhelix, but are attenuated when the stably mischarged analog is bound. Computational docking and molecular dynamics simulations provide structural context for these findings and predict a role for the substrate primary α-amine group in substrate recognition. Overall, our results illuminate strategies used by a trans-editing domain to ensure acceptance of only mischarged Ala-tRNAPro, including conformational selection by a dynamic helix, size-based exclusion, and optimal positioning of substrate chemical groups. PMID:28768811

Is chemical heating a major cause of the mesosphere inversion layer?

NASA Technical Reports Server (NTRS)

Meriwether, John W.; Mlynczak, Martin G.

1995-01-01

A region of thermal enhancement of the mesosphere has been detected on numerous occasions by in situ measurements, remote sensing from space, and lidar techniques. The source of these 'temperature inversion layers' has been attributed in the literature to the dissipation relating to dynamical forcing by gravity wave or tidal activity. However, evidence that gravity wave breaking can produce the inversion layer with amplitude as large as that observed in lidar measurements has been limited to results of numerical modeling. An alternative source for the production of the thermal inversion layer in the mesosphere is the direct deposition of heat by exothermic chemical reactions. Two-dimensional modeling combining a comprehensive model of the mesosphere photochemistry with the dynamical transport of long-lived species shows that the region from 80 to 95 km may be heated as much as 3 to 10 K/d during the night and half this rate during the day. Given the uncertainties in our understanding of the dynamics and chemistry for the mesopause region, separating the two sources by passive observations of the mesosphere thermal structure looks to be difficult. Therefore we have considered an active means for producing a mesopause thermal layer, namely the release of ozone into the upper mesosphere from a rocket payload. The induced effects would include artificial enhancements of the OH and Na airglow intensities as well as the mesopause thermal structure. The advantages of the rocket release of ozone is that detection of these effects by ground-based imaging, radar, and lidar systems and comparison of these effects with model predictions would help quantify the partition of the artificial inversion layer production into sources of dynamical and chemical forcing.

Enthalpy Distributions of Arc Jet Flow Based on Measured Laser Induced Fluorescence, Heat Flux and Stagnation Pressure Distributions

NASA Technical Reports Server (NTRS)

Suess, Leonard E.; Milhoan, James D.; Oelke, Lance; Godfrey, Dennis; Larin, Maksim Y.; Scott, Carl D.; Grinstead, Jay H.; DelPapa, Steven

2011-01-01

The centerline total enthalpy of arc jet flow is determined using laser induced fluorescence of oxygen and nitrogen atoms. Each component of the energy, kinetic, thermal, and chemical can be determined from LIF measurements. Additionally, enthalpy distributions are inferred from heat flux and pressure probe distribution measurements using an engineering formula. Average enthalpies are determined by integration over the radius of the jet flow, assuming constant mass flux and a mass flux distribution estimated from computational fluid dynamics calculations at similar arc jet conditions. The trends show favorable agreement, but there is an uncertainty that relates to the multiple individual measurements and assumptions inherent in LIF measurements.

Stratosphere-resolving CMIP5 models simulate different changes in the Southern Hemisphere

NASA Astrophysics Data System (ADS)

Rea, Gloria; Riccio, Angelo; Fierli, Federico; Cairo, Francesco; Cagnazzo, Chiara

2018-03-01

This work documents long-term changes in the Southern Hemisphere circulation in the austral spring-summer season in the Coupled Intercomparison Project Phase 5 models, showing that those changes are larger in magnitude and closer to ERA-Interim and other reanalyses if models include a dynamical representation of the stratosphere. Specifically, models with a high-top and included dynamical and—in some cases—chemical feedbacks within the stratosphere better simulate the lower stratospheric cooling observed over 1979-2001 and strongly driven by ozone depletion, when compared to the other models. This occurs because high-top models can fully capture the stratospheric large scale circulation response to the ozone-induced cooling. Interestingly, this difference is also found at the surface for the Southern Annular Mode (SAM) changes, even though all model categories tend to underestimate SAM trends over those decades. In this analysis, models including a proper dynamical stratosphere are more sensitive to lower stratospheric cooling in their tropospheric circulation response. After a brief discussion of two RCP scenarios, our study confirms that at least for large changes in the extratropical regions, stratospheric changes induced by external forcing have to be properly simulated, as they are important drivers of tropospheric climate variations.

A gratuitous β-Lactamase inducer uncovers hidden active site dynamics of the Staphylococcus aureus BlaR1 sensor domain.

PubMed

Frederick, Thomas E; Peng, Jeffrey W

2018-01-01

Increasing evidence shows that active sites of proteins have non-trivial conformational dynamics. These dynamics include active site residues sampling different local conformations that allow for multiple, and possibly novel, inhibitor binding poses. Yet, active site dynamics garner only marginal attention in most inhibitor design efforts and exert little influence on synthesis strategies. This is partly because synthesis requires a level of atomic structural detail that is frequently missing in current characterizations of conformational dynamics. In particular, while the identity of the mobile protein residues may be clear, the specific conformations they sample remain obscure. Here, we show how an appropriate choice of ligand can significantly sharpen our abilities to describe the interconverting binding poses (conformations) of protein active sites. Specifically, we show how 2-(2'-carboxyphenyl)-benzoyl-6-aminopenicillanic acid (CBAP) exposes otherwise hidden dynamics of a protein active site that binds β-lactam antibiotics. When CBAP acylates (binds) the active site serine of the β-lactam sensor domain of BlaR1 (BlaRS), it shifts the time scale of the active site dynamics to the slow exchange regime. Slow exchange enables direct characterization of inter-converting protein and bound ligand conformations using NMR methods. These methods include chemical shift analysis, 2-d exchange spectroscopy, off-resonance ROESY of the bound ligand, and reduced spectral density mapping. The active site architecture of BlaRS is shared by many β-lactamases of therapeutic interest, suggesting CBAP could expose functional motions in other β-lactam binding proteins. More broadly, CBAP highlights the utility of identifying chemical probes common to structurally homologous proteins to better expose functional motions of active sites.

Physical and mathematical modeling of antimicrobial photodynamic therapy

NASA Astrophysics Data System (ADS)

Bürgermeister, Lisa; López, Fernando Romero; Schulz, Wolfgang

2014-07-01

Antimicrobial photodynamic therapy (aPDT) is a promising method to treat local bacterial infections. The therapy is painless and does not cause bacterial resistances. However, there are gaps in understanding the dynamics of the processes, especially in periodontal treatment. This work describes the advances in fundamental physical and mathematical modeling of aPDT used for interpretation of experimental evidence. The result is a two-dimensional model of aPDT in a dental pocket phantom model. In this model, the propagation of laser light and the kinetics of the chemical reactions are described as coupled processes. The laser light induces the chemical processes depending on its intensity. As a consequence of the chemical processes, the local optical properties and distribution of laser light change as well as the reaction rates. The mathematical description of these coupled processes will help to develop treatment protocols and is the first step toward an inline feedback system for aPDT users.

Dynamics and reactivity of trapped electrons on supported ice crystallites.

PubMed

Stähler, Julia; Gahl, Cornelius; Wolf, Martin

2012-01-17

The solvation dynamics and reactivity of localized excess electrons in aqueous environments have attracted great attention in many areas of physics, chemistry, and biology. This manifold attraction results from the importance of water as a solvent in nature as well as from the key role of low-energy electrons in many chemical reactions. One prominent example is the electron-induced dissociation of chlorofluorocarbons (CFCs). Low-energy electrons are also critical in the radiation chemistry that occurs in nuclear reactors. Excess electrons in an aqueous environment are localized and stabilized by the local rearrangement of the surrounding water dipoles. Such solvated or hydrated electrons are known to play an important role in systems such as biochemical reactions and atmospheric chemistry. Despite numerous studies over many years, little is known about the microscopic details of these electron-induced chemical processes, and interest in the fundamental processes involved in the reactivity of trapped electrons continues. In this Account, we present a surface science study of the dynamics and reactivity of such localized low-energy electrons at D(2)O crystallites that are supported by a Ru(001) single crystal metal surface. This approach enables us to investigate the generation and relaxation dynamics as well as dissociative electron attachment (DEA) reaction of excess electrons under well-defined conditions. They are generated by photoexcitation in the metal template and transferred to trapping sites at the vacuum interface of crystalline D(2)O islands. In these traps, the electrons are effectively decoupled from the electronic states of the metal template, leading to extraordinarily long excited state lifetimes on the order of minutes. Using these long-lived, low-energy electrons, we study the DEA to CFCl(3) that is coadsorbed at very low concentrations (∼10(12) cm(-2)). Using rate equations and direct measurement of the change of surface dipole moment, we estimated the electron surface density for DEA, yielding cross sections that are orders of magnitude higher than the electron density measured in the gas phase.

Tropomyosin-related kinase C (TrkC) enhances podocyte migration by ERK-mediated WAVE2 activation.

PubMed

Gromnitza, Sascha; Lepa, Carolin; Weide, Thomas; Schwab, Albrecht; Pavenstädt, Hermann; George, Britta

2018-03-01

Podocyte malfunction is central to glomerular diseases and is marked by defective podocyte intercellular junctions and actin cytoskeletal dynamics. Podocytes share many morphologic features with neurons, so that similar sets of proteins appear to regulate cell process formation. One such protein is the tropomyosin-related kinase C (TrkC). TrkC deficiency in mice leads to proteinuria as a surrogate of defective kidney filter function. Activation of endogenous TrkC by its ligand neurotrophin-3 resulted in increased podocyte migration-a surrogate of podocyte actin dynamics in vivo. Employing a mutagenesis approach, we found that the Src homologous and collagen-like (Shc) binding site Tyr 516 within the TrkC cytoplasmic domain was necessary for TrkC-induced migration of podocytes. TrkC activation led to a mobility shift of Wiskott-Aldrich syndrome family verprolin-homologous protein (WAVE)-2 which is known to orchestrate Arp2/3 activation and actin polymerization. Chemical inactivation of Erk or mutagenesis of 2 of 4 known Erk target sites within WAVE2, Thr 346 and Ser 351 , abolished the TrkC-induced WAVE2 mobility shift. Knockdown of WAVE2 by shRNA abolished TrkC-induced podocyte migration. In summary, TrkC signals to the podocyte actin cytoskeleton to induce migration by phosphorylating WAVE2 Erk dependently. This signaling mechanism may be important for TrkC-mediated cytoskeletal dynamics in podocyte disease.-Gromnitza, S., Lepa, C., Weide, T., Schwab, A., Pavenstädt, H., George, B. Tropomyosin-related kinase C (TrkC) enhances podocyte migration by ERK-mediated WAVE2 activation.

Understanding the influence of solvent field and fluctuations on the stability of photo-induced charge-separated state in molecular triad

NASA Astrophysics Data System (ADS)

Balamurugan, D.; Aquino, Adelia; Lischka, Hans; Dios, Francis; Flores, Lionel; Cheung, Margaret

2013-03-01

Molecular triad composed of fullerene, porphyrin, and carotene is an artificial analogue of natural photosynthetic system and is considered for applications in solar energy conversion because of its ability to produce long-lived photo-induced charge separated state. The goal of the present multiscale simulation is to understand how the stability of photo-induced charge-separated state in molecular triad is influenced by a polar organic solvent, namely tetrahydrofuran (THF). The multiscale approach is based on combined quantum, classical molecular dynamics, and statistical physics calculations. The quantum chemical calculations were performed on the triad using the second order algebraic diagrammatic perturbation and time-dependent density functional theory. Molecular dynamics simulations were performed on triad in a box of THF solvent with the replica exchange method. The two methods on different length and time scales are bridged through an important sampling technique. We have analyzed the free energy landscape, structural fluctuations, and the long- range electrostatic interactions between triad and solvent molecules. The results suggest that the polarity and re-organization of the solvent is critical in stabilization of charge-separated state in triad. Supported by DOE (DE-FG02-10ER16175)

Tailoring graphene layer-to-layer growth

NASA Astrophysics Data System (ADS)

Li, Yongtao; Wu, Bin; Guo, Wei; Wang, Lifeng; Li, Jingbo; Liu, Yunqi

2017-06-01

A layered material grown between a substrate and the upper layer involves complex interactions and a confined reaction space, representing an unusual growth mode. Here, we show multi-layer graphene domains grown on liquid or solid Cu by the chemical vapor deposition method via this ‘double-substrate’ mode. We demonstrate the interlayer-induced coupling effect on the twist angle in bi- and multi-layer graphene. We discover dramatic growth disunity for different graphene layers, which is explained by the ideas of a chemical ‘gate’ and a material transport process within a confined space. These key results lead to a consistent framework for understanding the dynamic evolution of multi-layered graphene flakes and tailoring the layer-to-layer growth for practical applications.

Achieving high-density states through shock-wave loading of precompressed samples

PubMed Central

Jeanloz, Raymond; Celliers, Peter M.; Collins, Gilbert W.; Eggert, Jon H.; Lee, Kanani K. M.; McWilliams, R. Stewart; Brygoo, Stéphanie; Loubeyre, Paul

2007-01-01

Materials can be experimentally characterized to terapascal pressures by sending a laser-induced shock wave through a sample that is precompressed inside a diamond-anvil cell. This combination of static and dynamic compression methods has been experimentally demonstrated and ultimately provides access to the 10- to 100-TPa (0.1–1 Gbar) pressure range that is relevant to planetary science, testing first-principles theories of condensed matter, and experimentally studying a new regime of chemical bonding. PMID:17494771

Time-resolved EPR study on the photochemical reactions of benzil

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mukai, Masahiro; Yamnauchi, Seigo; Hirota, Noboru

1992-04-16

TREPR and optical studies on the photochemical reactions of benzil in 2-propanol and benzene-TEA conclude that emissive signals are due to the reaction from T{sub n} produced via the S{sub n} pointing right T{sub n} intersystem crossing process. The free-pair radical-pair mechanism can account for the main features of the slow rise component of the chemically induced dynamic electron polarization signal of the ketyl radical in 2-propanol. 27 refs., 10 figs., 2 tabs.

Competition induces allelopathy but suppresses growth and anti-herbivore defence in a chemically rich seaweed

PubMed Central

Rasher, Douglas B.; Hay, Mark E.

2014-01-01

Many seaweeds and terrestrial plants induce chemical defences in response to herbivory, but whether they induce chemical defences against competitors (allelopathy) remains poorly understood. We evaluated whether two tropical seaweeds induce allelopathy in response to competition with a reef-building coral. We also assessed the effects of competition on seaweed growth and seaweed chemical defence against herbivores. Following 8 days of competition with the coral Porites cylindrica, the chemically rich seaweed Galaxaura filamentosa induced increased allelochemicals and became nearly twice as damaging to the coral. However, it also experienced significantly reduced growth and increased palatability to herbivores (because of reduced chemical defences). Under the same conditions, the seaweed Sargassum polycystum did not induce allelopathy and did not experience a change in growth or palatability. This is the first demonstration of induced allelopathy in a seaweed, or of competitors reducing seaweed chemical defences against herbivores. Our results suggest that the chemical ecology of coral–seaweed–herbivore interactions can be complex and nuanced, highlighting the need to incorporate greater ecological complexity into the study of chemical defence. PMID:24403332

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE PAGES

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus; ...

2018-02-20

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

All-atom molecular dynamics of virus capsids as drug targets

DOE PAGES

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong; ...

2016-04-29

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Fingerprints of electronic, spin and structural dynamics from resonant inelastic soft X-ray scattering in transient photo-chemical species

DOE Office of Scientific and Technical Information (OSTI.GOV)

Norell, Jesper; Jay, Raphael M.; Hantschmann, Markus

Here, we describe how inversion symmetry separation of electronic state manifolds in resonant inelastic soft X-ray scattering (RIXS) can be applied to probe excited-state dynamics with compelling selectivity. In a case study of Fe L 3-edge RIXS in the ferricyanide complex Fe(CN) 6 3-, we demonstrate with multi-configurational restricted active space spectrum simulations how the information content of RIXS spectral fingerprints can be used to unambiguously separate species of different electronic configurations, spin multiplicities, and structures, with possible involvement in the decay dynamics of photo-excited ligand-to-metal charge-transfer. Specifically, we propose that this could be applied to confirm or reject themore » presence of a hitherto elusive transient Quartet species. Thus, RIXS offers a particular possibility to settle a recent controversy regarding the decay pathway, and we expect the technique to be similarly applicable in other model systems of photo-induced dynamics.« less

All-atom molecular dynamics of virus capsids as drug targets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Perilla, Juan R.; Hadden, Jodi A.; Goh, Boon Chong

Virus capsids are protein shells that package the viral genome. Although their morphology and biological functions can vary markedly, capsids often play critical roles in regulating viral infection pathways. A detailed knowledge of virus capsids, including their dynamic structure, interactions with cellular factors, and the specific roles that they play in the replication cycle, is imperative for the development of antiviral therapeutics. The following Perspective introduces an emerging area of computational biology that focuses on the dynamics of virus capsids and capsid–protein assemblies, with particular emphasis on the effects of small-molecule drug binding on capsid structure, stability, and allosteric pathways.more » When performed at chemical detail, molecular dynamics simulations can reveal subtle changes in virus capsids induced by drug molecules a fraction of their size. Finally, the current challenges of performing all-atom capsid–drug simulations are discussed, along with an outlook on the applicability of virus capsid simulations to reveal novel drug targets.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

DOE PAGES

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; ...

2017-05-24

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born–Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersionmore » of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.« less

Coherent structural trapping through wave packet dispersion during photoinduced spin state switching

NASA Astrophysics Data System (ADS)

Lemke, Henrik T.; Kjær, Kasper S.; Hartsock, Robert; van Driel, Tim B.; Chollet, Matthieu; Glownia, James M.; Song, Sanghoon; Zhu, Diling; Pace, Elisabetta; Matar, Samir F.; Nielsen, Martin M.; Benfatto, Maurizio; Gaffney, Kelly J.; Collet, Eric; Cammarata, Marco

2017-05-01

The description of ultrafast nonadiabatic chemical dynamics during molecular photo-transformations remains challenging because electronic and nuclear configurations impact each other and cannot be treated independently. Here we gain experimental insights, beyond the Born-Oppenheimer approximation, into the light-induced spin-state trapping dynamics of the prototypical [Fe(bpy)3]2+ compound by time-resolved X-ray absorption spectroscopy at sub-30-femtosecond resolution and high signal-to-noise ratio. The electronic decay from the initial optically excited electronic state towards the high spin state is distinguished from the structural trapping dynamics, which launches a coherent oscillating wave packet (265 fs period), clearly identified as molecular breathing. Throughout the structural trapping, the dispersion of the wave packet along the reaction coordinate reveals details of intramolecular vibronic coupling before a slower vibrational energy dissipation to the solution environment. These findings illustrate how modern time-resolved X-ray absorption spectroscopy can provide key information to unravel dynamic details of photo-functional molecules.

A Three-Wave Model of the Stratosphere with Coupled Dynamics, Radiation and Photochemistry. Appendix M

NASA Technical Reports Server (NTRS)

Shia, Run-Lie; Zhou, Shuntai; Ko, Malcolm K. W.; Sze, Nien-Dak; Salstein, David; Cady-Pereira, Karen

1997-01-01

A zonal mean chemistry transport model (2-D CTM) coupled with a semi-spectral dynamical model is used to simulate the distributions of trace gases in the present day atmosphere. The zonal-mean and eddy equations for the velocity and the geopotential height are solved in the semi-spectral dynamical model. The residual mean circulation is derived from these dynamical variables and used to advect the chemical species in the 2- D CTM. Based on a linearized wave transport equation, the eddy diffusion coefficients for chemical tracers are expressed in terms of the amplitude, frequency and growth rate of dynamical waves; local chemical loss rates; and a time constant parameterizing small scale mixing. The contributions to eddy flux are from the time varying wave amplitude (transient eddy), chemical reactions (chemical eddy) and small scale mixing. In spite of the high truncation in the dynamical module (only three longest waves are resolved), the model has simulated many observed characteristics of stratospheric dynamics and distribution of chemical species including ozone. Compared with the values commonly used in 2-D CTMs, the eddy diffusion coefficients for chemical species calculated in this model are smaller, especially in the subtropics. It is also found that the chemical eddy diffusion has only a small effects in determining the distribution of most slow species, including ozone in the stratosphere.

Variability in Benthic Exchange Rate, Depth, and Residence Time Beneath a Shallow Coastal Estuary

NASA Astrophysics Data System (ADS)

Russoniello, Christopher J.; Heiss, James W.; Michael, Holly A.

2018-03-01

Hydrodynamically driven benthic exchange of water between the water column and shallow seabed aquifer is a significant and dynamic component of coastal and estuarine fluid budgets. Associated exchange of solutes promotes ecologically important chemical reactions, so quantifying benthic exchange rates, depths, and residence times constrains coastal chemical cycling estimates. We present the first combined field, numerical, and analytical modeling investigation of wave-induced exchange. Temporal variability of exchange was calculated with data collected by instruments deployed in a shallow estuary for 11 days. Differential pressure sensors recorded pressure gradients across the seabed, and up- and down-looking ADCPs recorded currents and pressures to determine wave parameters, surface-water currents, and water depth. Wave-induced exchange was calculated (1) directly from differential pressure measurements, and indirectly with an analytical model based on wave parameters from (2) ADCP and (3) wind data. Wave-induced exchange from pressure measurements and ADCP-measured wave parameters matched well, but both exceeded wind-based values. Exchange induced by tidal pumping and current-bed form interaction—the other primary drivers in shallow coastal waters were calculated from tidal stage variation and ADCP-measured currents. Exchange from waves (mean = 20.0 cm/d; range = 1.75-92.3 cm/d) greatly exceeded exchange due to tides (mean = 3.7 cm/d) and current-bed form interaction (mean = 6.5 × 10-2 cm/d). Groundwater flow models showed aquifer properties affect wave-driven benthic exchange: residence time and depth increased and exchange rates decreased with increasing hydraulic diffusivity (ratio of aquifer permeability to compressibility). This new understanding of benthic exchange will help managers assess its control over chemical fluxes to marine systems.

Dynamical generation of Floquet Majorana flat bands in s-wave superconductors

NASA Astrophysics Data System (ADS)

Poudel, A.; Ortiz, G.; Viola, L.

2015-04-01

We present quantum control techniques to engineer flat bands of symmetry-protected Majorana edge modes in s-wave superconductors. Specifically, we show how periodic control may be employed for designing time-independent effective Hamiltonians, which support Floquet Majorana flat bands, starting from equilibrium conditions that are either topologically trivial or only support a Majorana pair per edge. In the first approach, a suitable modulation of the chemical potential simultaneously induces Majorana flat bands and dynamically activates a pre-existing chiral symmetry which is responsible for their protection. In the second approach, the application of effective parity kicks dynamically generates a desired chiral symmetry by suppressing chirality-breaking terms in the static Hamiltonian. Our results demonstrate how the use of time-dependent control enlarges the range of possibilities for realizing gapless topological superconductivity, potentially enabling access to topological states of matter that have no known equilibrium counterpart.

Activity induces traveling waves, vortices and spatiotemporal chaos in a model actomyosin layer

NASA Astrophysics Data System (ADS)

Ramaswamy, Rajesh; Jülicher, Frank

2016-02-01

Inspired by the actomyosin cortex in biological cells, we investigate the spatiotemporal dynamics of a model describing a contractile active polar fluid sandwiched between two external media. The external media impose frictional forces at the interface with the active fluid. The fluid is driven by a spatially-homogeneous activity measuring the strength of the active stress that is generated by processes consuming a chemical fuel. We observe that as the activity is increased over two orders of magnitude the active polar fluid first shows spontaneous flow transition followed by transition to oscillatory dynamics with traveling waves and traveling vortices in the flow field. In the flow-tumbling regime, the active polar fluid also shows transition to spatiotemporal chaos at sufficiently large activities. These results demonstrate that level of activity alone can be used to tune the operating point of actomyosin layers with qualitatively different spatiotemporal dynamics.

Cell-Free Optogenetic Gene Expression System.

PubMed

Jayaraman, Premkumar; Yeoh, Jing Wui; Jayaraman, Sudhaghar; Teh, Ai Ying; Zhang, Jingyun; Poh, Chueh Loo

2018-04-20

Optogenetic tools provide a new and efficient way to dynamically program gene expression with unmatched spatiotemporal precision. To date, their vast potential remains untapped in the field of cell-free synthetic biology, largely due to the lack of simple and efficient light-switchable systems. Here, to bridge the gap between cell-free systems and optogenetics, we studied our previously engineered one component-based blue light-inducible Escherichia coli promoter in a cell-free environment through experimental characterization and mathematical modeling. We achieved >10-fold dynamic expression and demonstrated rapid and reversible activation of the target gene to generate oscillatory response. The deterministic model developed was able to recapitulate the system behavior and helped to provide quantitative insights to optimize dynamic response. This in vitro optogenetic approach could be a powerful new high-throughput screening technology for rapid prototyping of complex biological networks in both space and time without the need for chemical induction.

Level crossing analysis of chemically induced dynamic nuclear polarization: Towards a common description of liquid-state and solid-state cases

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sosnovsky, Denis V.; Ivanov, Konstantin L., E-mail: ivanov@tomo.nsc.ru; Novosibirsk State University, Pirogova 2, 630090, Novosibirsk

Chemically Induced Dynamic Nuclear Polarization (CIDNP) is an efficient method of creating non-equilibrium polarization of nuclear spins by using chemical reactions, which have radical pairs as intermediates. The CIDNP effect originates from (i) electron spin-selective recombination of radical pairs and (ii) the dependence of the inter-system crossing rate in radical pairs on the state of magnetic nuclei. The CIDNP effect can be investigated by using Nuclear Magnetic Resonance (NMR) methods. The gain from CIDNP is then two-fold: it allows one to obtain considerable amplification of NMR signals; in addition, it provides a very useful tool for investigating elusive radicals andmore » radical pairs. While the mechanisms of the CIDNP effect in liquids are well established and understood, detailed analysis of solid-state CIDNP mechanisms still remains challenging; likewise a common theoretical frame for the description of CIDNP in both solids and liquids is missing. Difficulties in understanding the spin dynamics that lead to the CIDNP effect in the solid-state case are caused by the anisotropy of spin interactions, which increase the complexity of spin evolution. In this work, we propose to analyze CIDNP in terms of level crossing phenomena, namely, to attribute features in the CIDNP magnetic field dependence to Level Crossings (LCs) and Level Anti-Crossings (LACs) in a radical pair. This approach allows one to describe liquid-state CIDNP; the same holds for the solid-state case where anisotropic interactions play a significant role in CIDNP formation. In solids, features arise predominantly from LACs, since in most cases anisotropic couplings result in perturbations, which turn LCs into LACs. We have interpreted the CIDNP mechanisms in terms of the LC/LAC concept. This consideration allows one to find analytical expressions for a wide magnetic field range, where several different mechanisms are operative; furthermore, the LAC description gives a way to determine CIDNP sign rules. Thus, LCs/LACs provide a consistent description of CIDNP in both liquids and solids with the prospect of exploiting it for the analysis of short-lived radicals and for optimizing the polarization level.« less

Final Technical Report: Mathematical Foundations for Uncertainty Quantification in Materials Design

DOE Office of Scientific and Technical Information (OSTI.GOV)

Plechac, Petr; Vlachos, Dionisios G.

We developed path-wise information theory-based and goal-oriented sensitivity analysis and parameter identification methods for complex high-dimensional dynamics and in particular of non-equilibrium extended molecular systems. The combination of these novel methodologies provided the first methods in the literature which are capable to handle UQ questions for stochastic complex systems with some or all of the following features: (a) multi-scale stochastic models such as (bio)chemical reaction networks, with a very large number of parameters, (b) spatially distributed systems such as Kinetic Monte Carlo or Langevin Dynamics, (c) non-equilibrium processes typically associated with coupled physico-chemical mechanisms, driven boundary conditions, hybrid micro-macro systems,more » etc. A particular computational challenge arises in simulations of multi-scale reaction networks and molecular systems. Mathematical techniques were applied to in silico prediction of novel materials with emphasis on the effect of microstructure on model uncertainty quantification (UQ). We outline acceleration methods to make calculations of real chemistry feasible followed by two complementary tasks on structure optimization and microstructure-induced UQ.« less

XUV-induced reactions in benzene on sub-10 fs timescale: nonadiabatic relaxation and proton migration.

PubMed

Galbraith, M C E; Smeenk, C T L; Reitsma, G; Marciniak, A; Despré, V; Mikosch, J; Zhavoronkov, N; Vrakking, M J J; Kornilov, O; Lépine, F

2017-08-02

Unraveling ultrafast dynamical processes in highly excited molecular species has an impact on our understanding of chemical processes such as combustion or the chemical composition of molecular clouds in the universe. In this article we use short (<7 fs) XUV pulses to produce excited cationic states of benzene molecules and probe their dynamics using few-cycle VIS/NIR laser pulses. The excited states produced by the XUV pulses lie in an especially complex spectral region where multi-electronic effects play a dominant role. We show that very fast τ ≈ 20 fs nonadiabatic processes dominate the relaxation of these states, in agreement with the timescale expected for most excited cationic states in benzene. In the CH 3 + fragmentation channel of the doubly ionized benzene cation we identify pathways that involve structural rearrangement and proton migration to a specific carbon atom. Further, we observe non-trivial transient behavior in this fragment channel, which can be interpreted either in terms of propagation of the nuclear wavepacket in the initially excited electronic state of the cation or as a two-step electronic relaxation via an intermediate state.

Ultrafast Electron Dynamics in Solar Energy Conversion.

PubMed

Ponseca, Carlito S; Chábera, Pavel; Uhlig, Jens; Persson, Petter; Sundström, Villy

2017-08-23

Electrons are the workhorses of solar energy conversion. Conversion of the energy of light to electricity in photovoltaics, or to energy-rich molecules (solar fuel) through photocatalytic processes, invariably starts with photoinduced generation of energy-rich electrons. The harvesting of these electrons in practical devices rests on a series of electron transfer processes whose dynamics and efficiencies determine the function of materials and devices. To capture the energy of a photogenerated electron-hole pair in a solar cell material, charges of opposite sign have to be separated against electrostatic attractions, prevented from recombining and being transported through the active material to electrodes where they can be extracted. In photocatalytic solar fuel production, these electron processes are coupled to chemical reactions leading to storage of the energy of light in chemical bonds. With the focus on the ultrafast time scale, we here discuss the light-induced electron processes underlying the function of several molecular and hybrid materials currently under development for solar energy applications in dye or quantum dot-sensitized solar cells, polymer-fullerene polymer solar cells, organometal halide perovskite solar cells, and finally some photocatalytic systems.

The Dynamics of Chemical Reactions: Atomistic Visualizations of Organic Reactions, and Homage to van 't Hoff.

PubMed

Yang, Zhongyue; Houk, K N

2018-03-15

Jacobus Henricus van 't Hoff was the first Nobel Laureate in Chemistry. He pioneered in the study of chemical dynamics, which referred at that time to chemical kinetics and thermodynamics. The term has evolved in modern times to refer to the exploration of chemical transformations in a time-resolved fashion. Chemical dynamics has been driven by the development of molecular dynamics trajectory simulations, which provide atomic visualization of chemical processes and illuminate how dynamic effects influence chemical reactivity and selectivity. In homage to the legend of van 't Hoff, we review the development of the chemical dynamics of organic reactions, our area of research. We then discuss our trajectory simulations of pericyclic reactions, and our development of dynamic criteria for concerted and stepwise reaction mechanisms. We also describe a method that we call environment-perturbed transition state sampling, which enables trajectory simulations in condensed-media using quantum mechanics and molecular mechanics (QM/MM). We apply the method to reactions in solvent and in enzyme. Jacobus Henricus van 't Hoff (1852, Rotterdam-1911, Berlin) received the Nobel Prize for Chemistry in 1901 "in recognition of the extraordinary services he has rendered by the discovery of the laws of chemical dynamics and osmotic pressure in solutions". van 't Hoff was born the Netherlands, and earned his doctorate in Utrecht in 1874. In 1896 he moved to Berlin, where he was offered a position with more research and less teaching. van 't Hoff is considered one of the founders of physical chemistry. A key step in establishing this new field was the start of Zeitschrift für Physikalische Chemie in 1887. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dynamics of Protonated Peptide Ion Collisions with Organic Surfaces: Consonance of Simulation and Experiment

DOE Office of Scientific and Technical Information (OSTI.GOV)

Pratihar, Subha; Barnes, George L.; Laskin, Julia

In this Perspective mass spectrometry experiments and chemical dynamics simulations are described which have explored the atomistic dynamics of protonated peptide ions, peptide-H+, colliding with organic surfaces. These studies have investigated surface-induced dissociation (SID) for which peptide-H+ fragments upon collision with the surface, peptide-H+ physisorption on the surface, soft landing (SL), and peptide-H+ reaction with the surface, reactive landing (RL). The simulations include QM+MM and QM/MM direct dynamics. For collisions with self-assembled monolayer (SAM) surfaces there is quite good agreement between experiment and simulation in the efficiency of energy transfer to the peptide-H+ ion’s internal degrees of freedom. Both themore » experiments and simulations show two mechanisms for peptide-H+ fragmentation, i.e. shattering and statistical, RRKM dynamics. Mechanisms for SL are probed in simulations of collisions of protonated dialanine with a perfluorinated SAM surface. RL has been studied experimentally for a number of peptide-H+ + surface systems, and qualitative agreement between simulation and experiment is found for two similar systems.« less

Efficient switching of mCherry fluorescence using chemical caging.

PubMed

Cloin, Bas M C; De Zitter, Elke; Salas, Desiree; Gielen, Vincent; Folkers, Gert E; Mikhaylova, Marina; Bergeler, Maike; Krajnik, Bartosz; Harvey, Jeremy; Hoogenraad, Casper C; Van Meervelt, Luc; Dedecker, Peter; Kapitein, Lukas C

2017-07-03

Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores.

Efficient switching of mCherry fluorescence using chemical caging

PubMed Central

Cloin, Bas M. C.; Salas, Desiree; Gielen, Vincent; Folkers, Gert E.; Mikhaylova, Marina; Bergeler, Maike; Krajnik, Bartosz; Harvey, Jeremy; Hoogenraad, Casper C.; Van Meervelt, Luc; Dedecker, Peter; Kapitein, Lukas C.

2017-01-01

Fluorophores with dynamic or controllable fluorescence emission have become essential tools for advanced imaging, such as superresolution imaging. These applications have driven the continuing development of photoactivatable or photoconvertible labels, including genetically encoded fluorescent proteins. These new probes work well but require the introduction of new labels that may interfere with the proper functioning of existing constructs and therefore require extensive functional characterization. In this work we show that the widely used red fluorescent protein mCherry can be brought to a purely chemically induced blue-fluorescent state by incubation with β-mercaptoethanol (βME). The molecules can be recovered to the red fluorescent state by washing out the βME or through irradiation with violet light, with up to 80% total recovery. We show that this can be used to perform single-molecule localization microscopy (SMLM) on cells expressing mCherry, which renders this approach applicable to a very wide range of existing constructs. We performed a detailed investigation of the mechanism underlying these dynamics, using X-ray crystallography, NMR spectroscopy, and ab initio quantum-mechanical calculations. We find that the βME-induced fluorescence quenching of mCherry occurs both via the direct addition of βME to the chromophore and through βME-mediated reduction of the chromophore. These results not only offer a strategy to expand SMLM imaging to a broad range of available biological models, but also present unique insights into the chemistry and functioning of a highly important class of fluorophores. PMID:28630286

Mechanism for Si–Si Bond Rupture in Single Molecule Junctions

DOE Office of Scientific and Technical Information (OSTI.GOV)

Li, Haixing; Kim, Nathaniel T.; Su, Timothy A.

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si–Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si–Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si–Si bond is ruptured using an applied voltage. We investigate this voltage induced Si–Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation ofmore » molecular vibrational modes by tunneling electrons leads to homolytic Si–Si bond rupture.« less

Mechanism for Si-Si Bond Rupture in Single Molecule Junctions.

PubMed

Li, Haixing; Kim, Nathaniel T; Su, Timothy A; Steigerwald, Michael L; Nuckolls, Colin; Darancet, Pierre; Leighton, James L; Venkataraman, Latha

2016-12-14

The stability of chemical bonds can be studied experimentally by rupturing single molecule junctions under applied voltage. Here, we compare voltage-induced bond rupture in two Si-Si backbones: one has no alternate conductive pathway whereas the other contains an additional naphthyl pathway in parallel to the Si-Si bond. We show that in contrast to the first system, the second can conduct through the naphthyl group when the Si-Si bond is ruptured using an applied voltage. We investigate this voltage induced Si-Si bond rupture by ab initio density functional theory calculations and molecular dynamics simulations that ultimately demonstrate that the excitation of molecular vibrational modes by tunneling electrons leads to homolytic Si-Si bond rupture.

Chemically reacting fluid flow in exoplanet and brown dwarf atmospheres

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2016-11-01

In the past few decades, spectral observations of planets and brown dwarfs have demonstrated significant deviations from predictions in certain chemical abundances. Starting with Jupiter, these deviations were successfully explained to be the effect of fast dynamics on comparatively slow chemical reactions. These dynamical effects are treated using mixing length theory in what is known as the "quench" approximation. In these objects, however, both radiative and convective zones are present, and it is not clear that this approximation applies. To resolve this issue, we solve the fully compressible equations of fluid dynamics in a matched polytropic atmosphere using the state-of-the-art pseudospectral simulation framework Dedalus. Through the inclusion of passive tracers, we explore the transport properties of convective and radiative zones, and verify the classical eddy diffusion parameterization. With the addition of active tracers, we examine the interactions between dynamical and chemical processes using abstract chemical reactions. By locating the quench point (the point at which the dynamical and chemical timescales are the same) in different dynamical regimes, we test the quench approximation, and generate prescriptions for the exoplanet and brown dwarf communities.

Chemical-induced Vitiligo

PubMed Central

Harris, John E.

2016-01-01

Synopsis Chemical-induced depigmentation of the skin has been recognized for over 75 years, first as an occupational hazard but then extending to those using household commercial products as common as hair dyes. Since their discovery, these chemicals have been used therapeutically in patients with severe vitiligo to depigment their remaining skin and improve their appearance. The importance of recognizing this phenomenon was highlighted during an outbreak of vitiligo in Japan during the summer of 2013, when over 16,000 users of a new skin lightening cosmetic cream developed skin depigmentation at the site of contact with the cream and many in remote areas as well. Depigmenting chemicals appear to be analogs of the amino acid tyrosine that disrupt melanogenesis and result in autoimmunity and melanocyte destruction. Because chemical-induced depigmentation is clinically and histologically indistinguishable from non-chemically induced vitiligo, and because these chemicals appear to induce melanocyte autoimmunity, this phenomenon should be known as “chemical-induced vitiligo”, rather than less accurate terms that have been previously used. PMID:28317525

Towards validated chemistry at extreme conditions: reactive MD simulations of shocked Polyvinyl Nitrate and Nitromethane

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

A detailed atomistic-level understanding of the ultrafast chemistry of detonation processes of high energy materials is crucial to understand their performance and safety. Recent advances in laser shocks and ultra-fast spectroscopy is yielding the first direct experimental evidence of chemistry at extreme conditions. At the same time, reactive molecular dynamics (MD) in current high-performance computing platforms enable an atomic description of shock-induced chemistry with length and timescales approaching those of experiments. We use MD simulations with the reactive force field ReaxFF to investigate the shock-induced chemical decomposition mechanisms of polyvinyl nitrate (PVN) and nitromethane (NM). The effect of shock pressure on chemical reaction mechanisms and kinetics of both the materials are investigated. For direct comparison of our simulation results with experimentally derived IR absorption data, we performed spectral analysis using atomistic velocity at various shock conditions. The combination of reactive MD simulations and ultrafast spectroscopy enables both the validation of ReaxFF at extreme conditions and contributes to the interpretation of the experimental data relating changes in spectral features to atomic processes. Office of Naval Research MURI program.

Collective evolution of submicron hillocks during the early stages of anisotropic alkaline wet chemical etching of Si(1 0 0) surfaces

NASA Astrophysics Data System (ADS)

Sana, P.; Vázquez, Luis; Cuerno, Rodolfo; Sarkar, Subhendu

2017-11-01

We address experimentally the large-scale dynamics of Si(1 0 0) surfaces during the initial stages of anisotropic wet (KOH) chemical etching, which are characterized through atomic force microscopy. These systems are known to lead to the formation of characteristic pyramids, or hillocks, of typical sizes in the nanometric/micrometer scales, thus with the potential for a large number of applications that can benefit from the nanotexturing of Si surfaces. The present pattern formation process is very strongly disordered in space. We assess the space correlations in such a type of rough surface and elucidate the existence of a complex and rich morphological evolution, featuring at least three different regimes in just 10 min of etching. Such a complex time behavior cannot be consistently explained within a single formalism for dynamic scaling. The pyramidal structure reveals itself as the basic morphological motif of the surface throughout the dynamics. A detailed analysis of the surface slope distribution with etching time reveals that the texturing process induced by the KOH etching is rather gradual and progressive, which accounts for the dynamic complexity. The various stages of the morphological evolution can be accurately reproduced by computer-generated surfaces composed by uncorrelated pyramidal structures. To reach such an agreement, the key parameters are the average pyramid size, which increases with etching time, its distribution and the surface coverage by the pyramidal structures.

Methods of information geometry in computational system biology (consistency between chemical and biological evolution).

PubMed

Astakhov, Vadim

2009-01-01

Interest in simulation of large-scale metabolic networks, species development, and genesis of various diseases requires new simulation techniques to accommodate the high complexity of realistic biological networks. Information geometry and topological formalisms are proposed to analyze information processes. We analyze the complexity of large-scale biological networks as well as transition of the system functionality due to modification in the system architecture, system environment, and system components. The dynamic core model is developed. The term dynamic core is used to define a set of causally related network functions. Delocalization of dynamic core model provides a mathematical formalism to analyze migration of specific functions in biosystems which undergo structure transition induced by the environment. The term delocalization is used to describe these processes of migration. We constructed a holographic model with self-poetic dynamic cores which preserves functional properties under those transitions. Topological constraints such as Ricci flow and Pfaff dimension were found for statistical manifolds which represent biological networks. These constraints can provide insight on processes of degeneration and recovery which take place in large-scale networks. We would like to suggest that therapies which are able to effectively implement estimated constraints, will successfully adjust biological systems and recover altered functionality. Also, we mathematically formulate the hypothesis that there is a direct consistency between biological and chemical evolution. Any set of causal relations within a biological network has its dual reimplementation in the chemistry of the system environment.

The Chemistry of Shocked High-energy Materials: Connecting Atomistic Simulations to Experiments

NASA Astrophysics Data System (ADS)

Islam, Md Mahbubul; Strachan, Alejandro

2017-06-01

A comprehensive atomistic-level understanding of the physics and chemistry of shocked high energy (HE) materials is crucial for designing safe and efficient explosives. Advances in the ultrafast spectroscopy and laser shocks enabled the study of shock-induced chemistry at extreme conditions occurring at picosecond timescales. Despite this progress experiments are not without limitations and do not enable a direct characterization of chemical reactions. At the same time, large-scale reactive molecular dynamics (MD) simulations are capable of providing description of the shocked-induced chemistry but the uncertainties resulting from the use of approximate descriptions of atomistic interactions remain poorly quantified. We use ReaxFF MD simulations to investigate the shock and temperature induced chemical decomposition mechanisms of polyvinyl nitrate, RDX, and nitromethane. The effect of various shock pressures on reaction initiation mechanisms is investigated for all three materials. We performed spectral analysis from atomistic velocities at different shock pressures to enable direct comparison with experiments. The simulations predict volume-increasing reactions at the shock-to-detonation transitions and the shock vs. particle velocity data are in good agreement with available experimental data. The ReaxFF MD simulations validated against experiments enabled prediction of reaction kinetics of shocked materials, and interpretation of experimental spectroscopy data via assignment of the spectral peaks to dictate various reaction pathways at extreme conditions.

Reduction of Endoplasmic Reticulum Stress Improves Angiogenic Progenitor Cell function in a Mouse Model of Type 1 Diabetes.

PubMed

Bhatta, Maulasri; Chatpar, Krishna; Hu, Zihua; Wang, Joshua J; Zhang, Sarah X

2018-04-27

Persistent vascular injury and degeneration in diabetes are attributed in part to defective reparatory function of angiogenic cells. Our recent work implicates endoplasmic reticulum (ER) stress in high-glucose-induced bone marrow (BM) progenitor dysfunction. Herein, we investigated the in vivo role of ER stress in angiogenic abnormalities of streptozotocin-induced diabetic mice. Our data demonstrate that ER stress markers and inflammatory gene expression in BM mononuclear cells and hematopoietic progenitor cells increase dynamically with disease progression. Increased CHOP and cleaved caspase- 3 levels were observed in BM--derived early outgrowth cells (EOCs) after 3 months of diabetes. Inhibition of ER stress by ex vivo or in vivo chemical chaperone treatment significantly improved the generation and migration of diabetic EOCs while reducing apoptosis of these cells. Chemical chaperone treatment also increased the number of circulating angiogenic cells in peripheral blood, alleviated BM pathology, and enhanced retinal vascular repair following ischemia/reperfusion in diabetic mice. Mechanistically, knockdown of CHOP alleviated high-glucose-induced EOC dysfunction and mitigated apoptosis, suggesting a pivotal role of CHOP in mediating ER stress-associated angiogenic cell injury in diabetes. Together, our study suggests that targeting ER signaling may provide a promising and novel approach to enhancing angiogenic function in diabetes.

Correlation of chemical shifts predicted by molecular dynamics simulations for partially disordered proteins.

PubMed

Karp, Jerome M; Eryilmaz, Ertan; Erylimaz, Ertan; Cowburn, David

2015-01-01

There has been a longstanding interest in being able to accurately predict NMR chemical shifts from structural data. Recent studies have focused on using molecular dynamics (MD) simulation data as input for improved prediction. Here we examine the accuracy of chemical shift prediction for intein systems, which have regions of intrinsic disorder. We find that using MD simulation data as input for chemical shift prediction does not consistently improve prediction accuracy over use of a static X-ray crystal structure. This appears to result from the complex conformational ensemble of the disordered protein segments. We show that using accelerated molecular dynamics (aMD) simulations improves chemical shift prediction, suggesting that methods which better sample the conformational ensemble like aMD are more appropriate tools for use in chemical shift prediction for proteins with disordered regions. Moreover, our study suggests that data accurately reflecting protein dynamics must be used as input for chemical shift prediction in order to correctly predict chemical shifts in systems with disorder.

Insight into induced charges at metal surfaces and biointerfaces using a polarizable Lennard-Jones potential.

PubMed

Geada, Isidro Lorenzo; Ramezani-Dakhel, Hadi; Jamil, Tariq; Sulpizi, Marialore; Heinz, Hendrik

2018-02-19

Metallic nanostructures have become popular for applications in therapeutics, catalysts, imaging, and gene delivery. Molecular dynamics simulations are gaining influence to predict nanostructure assembly and performance; however, instantaneous polarization effects due to induced charges in the free electron gas are not routinely included. Here we present a simple, compatible, and accurate polarizable potential for gold that consists of a Lennard-Jones potential and a harmonically coupled core-shell charge pair for every metal atom. The model reproduces the classical image potential of adsorbed ions as well as surface, bulk, and aqueous interfacial properties in excellent agreement with experiment. Induced charges affect the adsorption of ions onto gold surfaces in the gas phase at a strength similar to chemical bonds while ions and charged peptides in solution are influenced at a strength similar to intermolecular bonds. The proposed model can be applied to complex gold interfaces, electrode processes, and extended to other metals.

Analytical modeling of drug dynamics induced by eluting stents in the coronary multi-layered curved domain.

PubMed

d'Errico, Michele; Sammarco, Paolo; Vairo, Giuseppe

2015-09-01

Pharmacokinetics induced by drug eluting stents (DES) in coronary walls is modeled by means of a one-dimensional multi-layered model, accounting for vessel curvature and non-homogeneous properties of the arterial tissues. The model includes diffusion mechanisms, advection effects related to plasma filtration through the walls, and bio-chemical drug reactions. A non-classical Sturm-Liouville problem with discontinuous coefficients is derived, whose closed-form analytical solution is obtained via an eigenfunction expansion. Soundness and consistency of the proposed approach are shown by numerical computations based on possible clinical treatments involving both hydrophilic and hydrophobic drugs. The influence of the main model parameters on drug delivery mechanisms is analyzed, highlighting the effects induced by vessel curvature and yielding comparative indications and useful insights into the concurring mechanisms governing the pharmacokinetics. Copyright © 2015. Published by Elsevier Inc.

Investigation of laser induced breakdown in liquid nitromethane using nanosecond shadowgraphy

NASA Astrophysics Data System (ADS)

Guo, Wencan; Zheng, Xianxu; Yu, Guoyang; Zhao, Jun; Zeng, Yangyang; Liu, Cangli

2016-09-01

A nanosecond time-resolved shadowgraphy is performed to observe a laser-induced breakdown in nitromethane. The digital delays are introduced between a pump beam and an illumination light to achieve a measuring range from 40 ns to 100 ms, which enable us to study the shock wave propagation, bubble dynamics, and other process of the laser-induced breakdown. Compared with distilled water, there are two obvious differences observed in nitromethane: (1) the production of a non-evaporative gas at the final stage, and (2) an absence of the secondary shock wave after the first collapse of the bubble. We also calculated the bubble energy in nitromethane and distilled water under a different incident energy. The results indicate that the bubble energy in nitromethane is more than twice as large as that in water. It is suggested that chemical reactions contribute to the releasing of energy.

Binding-Induced Fluorescence of Serotonin Transporter Ligands: A Spectroscopic and Structural Study of 4-(4-(Dimethylamino)phenyl)-1-methylpyridinium (APP+) and APP+ Analogues

PubMed Central

2014-01-01

The binding-induced fluorescence of 4-(4-(dimethylamino)-phenyl)-1-methylpyridinium (APP+) and two new serotonin transporter (SERT)-binding fluorescent analogues, 1-butyl-4-[4-(1-dimethylamino)phenyl]-pyridinium bromide (BPP+) and 1-methyl-4-[4-(1-piperidinyl)phenyl]-pyridinium (PPP+), has been investigated. Optical spectroscopy reveals that these probes are highly sensitive to their chemical microenvironment, responding to variations in polarity with changes in transition energies and responding to changes in viscosity or rotational freedom with emission enhancements. Molecular docking calculations reveal that the probes are able to access the nonpolar and conformationally restrictive binding pocket of SERT. As a result, the probes exhibit previously not identified binding-induced turn-on emission that is spectroscopically distinct from dyes that have accumulated intracellularly. Thus, binding and transport dynamics of SERT ligands can be resolved both spatially and spectroscopically. PMID:24460204

Time-resolved resonance fluorescence spectroscopy for study of chemical reactions in laser-induced plasmas.

PubMed

Liu, Lei; Deng, Leimin; Fan, Lisha; Huang, Xi; Lu, Yao; Shen, Xiaokang; Jiang, Lan; Silvain, Jean-François; Lu, Yongfeng

2017-10-30

Identification of chemical intermediates and study of chemical reaction pathways and mechanisms in laser-induced plasmas are important for laser-ablated applications. Laser-induced breakdown spectroscopy (LIBS), as a promising spectroscopic technique, is efficient for elemental analyses but can only provide limited information about chemical products in laser-induced plasmas. In this work, time-resolved resonance fluorescence spectroscopy was studied as a promising tool for the study of chemical reactions in laser-induced plasmas. Resonance fluorescence excitation of diatomic aluminum monoxide (AlO) and triatomic dialuminum monoxide (Al 2 O) was used to identify these chemical intermediates. Time-resolved fluorescence spectra of AlO and Al 2 O were used to observe the temporal evolution in laser-induced Al plasmas and to study their formation in the Al-O 2 chemistry in air.

Grain rotation and lattice deformation during photoinduced chemical reactions revealed by in situ X-ray nanodiffraction.

PubMed

Huang, Zhifeng; Bartels, Matthias; Xu, Rui; Osterhoff, Markus; Kalbfleisch, Sebastian; Sprung, Michael; Suzuki, Akihiro; Takahashi, Yukio; Blanton, Thomas N; Salditt, Tim; Miao, Jianwei

2015-07-01

In situ X-ray diffraction (XRD) and transmission electron microscopy (TEM) have been used to investigate many physical science phenomena, ranging from phase transitions, chemical reactions and crystal growth to grain boundary dynamics. A major limitation of in situ XRD and TEM is a compromise that has to be made between spatial and temporal resolution. Here, we report the development of in situ X-ray nanodiffraction to measure high-resolution diffraction patterns from single grains with up to 5 ms temporal resolution. We observed, for the first time, grain rotation and lattice deformation in chemical reactions induced by X-ray photons: Br(-) + hv → Br + e(-) and e(-) + Ag(+) → Ag(0). The grain rotation and lattice deformation associated with the chemical reactions were quantified to be as fast as 3.25 rad s(-1) and as large as 0.5 Å, respectively. The ability to measure high-resolution diffraction patterns from individual grains with a temporal resolution of several milliseconds is expected to find broad applications in materials science, physics, chemistry and nanoscience.

Real-time monitoring of metabolic function in liver-on-chip microdevices tracks the dynamics of mitochondrial dysfunction

PubMed Central

Bavli, Danny; Prill, Sebastian; Ezra, Elishai; Levy, Gahl; Cohen, Merav; Vinken, Mathieu; Vanfleteren, Jan; Jaeger, Magnus; Nahmias, Yaakov

2016-01-01

Microfluidic organ-on-a-chip technology aims to replace animal toxicity testing, but thus far has demonstrated few advantages over traditional methods. Mitochondrial dysfunction plays a critical role in the development of chemical and pharmaceutical toxicity, as well as pluripotency and disease processes. However, current methods to evaluate mitochondrial activity still rely on end-point assays, resulting in limited kinetic and prognostic information. Here, we present a liver-on-chip device capable of maintaining human tissue for over a month in vitro under physiological conditions. Mitochondrial respiration was monitored in real time using two-frequency phase modulation of tissue-embedded phosphorescent microprobes. A computer-controlled microfluidic switchboard allowed contiguous electrochemical measurements of glucose and lactate, providing real-time analysis of minute shifts from oxidative phosphorylation to anaerobic glycolysis, an early indication of mitochondrial stress. We quantify the dynamics of cellular adaptation to mitochondrial damage and the resulting redistribution of ATP production during rotenone-induced mitochondrial dysfunction and troglitazone (Rezulin)-induced mitochondrial stress. We show troglitazone shifts metabolic fluxes at concentrations previously regarded as safe, suggesting a mechanism for its observed idiosyncratic effect. Our microfluidic platform reveals the dynamics and strategies of cellular adaptation to mitochondrial damage, a unique advantage of organ-on-chip technology. PMID:27044092

Interdomain flexibility and pH-induced conformational changes of AcrA revealed by molecular dynamics simulations.

PubMed

Wang, Beibei; Weng, Jingwei; Fan, Kangnian; Wang, Wenning

2012-03-15

The membrane fusion protein (MFP) AcrA is proposed to link the inner membrane transporter AcrB and outer membrane protein TolC, forming the tripartite AcrAB-TolC efflux pump, and was shown to be functionally indispensible. Structural and EPR studies showed that AcrA has high conformational flexibility and exhibited pH-induced conformational change. In this study, we built the complete structure of AcrA through homology modeling and performed atomistic simulations of AcrA at different pH values. It was shown that the conformational flexibility of AcrA originates from the motions of α-hairpin and MP domains. The conformational dynamics of AcrA is sensitive to specific point mutations and pH values. In agreement with the EPR experiments, the interdomain motions were restrained upon lowering pH from 7.0 to 5.0 in the simulations. It was found that the protonation/deprotonation of His285 underlies the pH-regulated conformational dynamics of AcrA by disturbing the local hydrogen bond interactions, suggesting that the changes of pH in the periplasm accompanying the drug efflux could act as a signal to trigger the action of AcrA, which undergoes reversible conformational rearrangement. © 2012 American Chemical Society

Behavior of chemicals in the seawater column by shadowscopy

NASA Astrophysics Data System (ADS)

Fuhrer, Mélanie; Aprin, Laurent; Le Floch, Stéphane; Slangen, Pierre; Dusserre, Gilles

2012-10-01

Ninety percent of the Global Movement of Goods transit by ship. The transportation of HNS (Hazardous and Noxious Substances) in bulk highly increases with the tanker traffic. The huge volume capacities induce a major risk of accident involving chemicals. Among the latest accidents, many have led to vessels sinking (Ievoli Sun, 2000 - ECE, 2006). In case of floating substances, liquid release in depth entails an ascending two phase flow. The visualization of that flow is complex. Indeed, liquid chemicals have mostly a refractive index close to water, causing difficulties for the assessment of the two phase medium behavior. Several physics aspects are points of interest: droplets characterization (shape evolution and velocity), dissolution kinetics and hydrodynamic vortices. Previous works, presented in the 2010 Speckle conference in Brazil, employed Dynamic Speckle Interferometry to study Methyl Ethyl Ketone (MEK) dissolution in a 15 cm high and 1 cm thick water column. This paper deals with experiments achieved with the Cedre Experimental Column (CEC - 5 m high and 0.8 m in diameter). As the water thickness has been increased, Dynamic Speckle Interferometry results are improved by shadowscopic measurements. A laser diode is used to generate parallel light while high speed imaging records the products rising. Two measurements systems are placed at the bottom and the top of the CEC. The chemical class of pollutant like floaters, dissolvers (plume, trails or droplets) has been then identified. Physics of the two phase flow is presented and shows up the dependence on chemicals properties such as interfacial tension, viscosity and density. Furthermore, parallel light propagation through this disturbed medium has revealed trailing edges vortices for some substances (e.g. butanol) presenting low refractive index changes.

Investigate the complex process in particle-fluid based surface generation technology using reactive molecular dynamics method

NASA Astrophysics Data System (ADS)

Han, Xuesong; Li, Haiyan; Zhao, Fu

2017-07-01

Particle-fluid based surface generation process has already become one of the most important materials processing technology for many advanced materials such as optical crystal, ceramics and so on. Most of the particle-fluid based surface generation technology involves two key process: chemical reaction which is responsible for surface softening; physical behavior which is responsible for materials removal/deformation. Presently, researchers cannot give a reasonable explanation about the complex process in the particle-fluid based surface generation technology because of the small temporal-spatial scale and the concurrent influence of physical-chemical process. Molecular dynamics (MD) method has already been proved to be a promising approach for constructing effective model of atomic scale phenomenon and can serve as a predicting simulation tool in analyzing the complex surface generation mechanism and is employed in this research to study the essence of surface generation. The deformation and piles of water molecule is induced with the feeding of abrasive particle which justifies the property mutation of water at nanometer scale. There are little silica molecule aggregation or materials removal because the water-layer greatly reduce the strength of mechanical interaction between particle and materials surface and minimize the stress concentration. Furthermore, chemical effect is also observed at the interface: stable chemical bond is generated between water and silica which lead to the formation of silconl and the reaction rate changes with the amount of water molecules in the local environment. Novel ring structure is observed in the silica surface and it is justified to be favored of chemical reaction with water molecule. The siloxane bond formation process quickly strengthened across the interface with the feeding of abrasive particle because of the compressive stress resulted by the impacting behavior.

Influence of chemical reactions on the nonlinear dynamics of dissipative flows

NASA Astrophysics Data System (ADS)

Karimov, A. R.; Korshunov, A. M.; Beklemishev, V. V.

2015-08-01

The nonlinear dynamics of resistive flow with a chemical reaction is studied. Proceeding from the Lagrangian description, the influence of a chemical reaction on the development of fluid singularities is considered.

Insights into the Structural Changes Occurring upon Photoconversion in the Orange Carotenoid Protein from Broadband Two-Dimensional Electronic Spectroscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

De Re, Eleonora; Schlau-Cohen, Gabriela S.; Leverenz, Ryan L.

Carotenoids play an essential role in photoprotection, interacting with other pigments to safely dissipate excess absorbed energy as heat. In cyanobacteria, the short time scale photoprotective mechanisms involve the photoactive orange carotenoid protein (OCP), which binds a single carbonyl carotenoid. Blue-green light induces the photoswitching of OCP from its ground state form (OCPO) to a metastable photoproduct (OCPR). OCPR can bind to the phycobilisome antenna and induce fluorescence quenching. The photoswitching is accompanied by structural and functional changes at the level of the protein and of the bound carotenoid. In this study, we use broadband two-dimensional electronic spectroscopy to lookmore » at the differences in excited state dynamics of the carotenoid in the two forms of OCP. Our results provide insight into the origin of the pronounced vibrational lineshape and oscillatory dynamics observed in linear absorption and 2D electronic spectroscopy of OCPO and the large inhomogeneous broadening in OCPR, with consequences for the chemical function of the two forms.« less

Stresslets Induced by Active Swimmers.

PubMed

Lauga, Eric; Michelin, Sébastien

2016-09-30

Active particles disturb the fluid around them as force dipoles, or stresslets, which govern their collective dynamics. Unlike swimming speeds, the stresslets of active particles are rarely determined due to the lack of a suitable theoretical framework for arbitrary geometry. We propose a general method, based on the reciprocal theorem of Stokes flows, to compute stresslets as integrals of the velocities on the particle's surface, which we illustrate for spheroidal chemically active particles. Our method will allow tuning the stresslet of artificial swimmers and tailoring their collective motion in complex environments.

Irradiation-induced damage evolution in concentrated Ni-based alloys

DOE PAGES

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou; ...

2017-06-06

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

A practical approach to calculate the time evolutions of magnetic field effects on photochemical reactions in nano-structured materials.

PubMed

Yago, Tomoaki; Wakasa, Masanobu

2015-04-21

A practical method to calculate time evolutions of magnetic field effects (MFEs) on photochemical reactions involving radical pairs is developed on the basis of the theory of the chemically induced dynamic spin polarization proposed by Pedersen and Freed. In theory, the stochastic Liouville equation (SLE), including the spin Hamiltonian, diffusion motions of the radical pair, chemical reactions, and spin relaxations, is solved by using the Laplace and the inverse Laplace transformation technique. In our practical approach, time evolutions of the MFEs are successfully calculated by applying the Miller-Guy method instead of the final value theorem to the inverse Laplace transformation process. Especially, the SLE calculations are completed in a short time when the radical pair dynamics can be described by the chemical kinetics consisting of diffusions, reactions and spin relaxations. The SLE analysis with a short calculation time enables one to examine the various parameter sets for fitting the experimental date. Our study demonstrates that simultaneous fitting of the time evolution of the MFE and of the magnetic field dependence of the MFE provides valuable information on the diffusion motions of the radical pairs in nano-structured materials such as micelles where the lifetimes of radical pairs are longer than hundreds of nano-seconds and the magnetic field dependence of the spin relaxations play a major role for the generation of the MFE.

Irradiation-induced damage evolution in concentrated Ni-based alloys

DOE Office of Scientific and Technical Information (OSTI.GOV)

Velisa, Gihan; Ullah, Mohammad Wali; Xue, Haizhou

Understanding the effects of chemical complexity from the number, type and concentration of alloying elements in single-phase concentred solid-solution alloys (SP-CSAs) on defect dynamics and microstructure evolution is pivotal for developing next-generation radiation-tolerant structural alloys. A specially chosen set of SP-CSAs with different chemical complexity (Ni 80Fe 20, Ni 80Cr 20 and Ni 40Fe 40Cr 20) are investigated using 1.5 MeV Mn ions over a wide fluence range, from 2 × 10 13 to 1 × 10 16 ions cm –2 at room temperature. Based on an integrated study of Rutherford backscattering spectroscopy in channeling geometry and molecular dynamics simulations,more » the results demonstrate that Ni 40Fe 40Cr 20 is more radiation tolerant than Ni 80Fe 20, Ni 80Cr 20 and elemental Ni in the low fluence regime. While chemical complexity of this set of SP-CSAs is clearly demonstrated to affect defect evolution through suppressed defect production and enhanced recombination at early stages, the effect of the mixed ferro- and anti-ferromagnetic interactions is not the only controlling factor responsible for the improved radiation performance. As a result, the observed strong alloying effect on defect evolution is attributed to the altered defect migration mobilities of defect clusters in these alloys, an intrinsic characteristic of the complex energy landscapes in CSAs.« less

Molecular dynamics study of salt-solution interface: solubility and surface charge of salt in water.

PubMed

Kobayashi, Kazuya; Liang, Yunfeng; Sakka, Tetsuo; Matsuoka, Toshifumi

2014-04-14

The NaCl salt-solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt-solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt-solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemical potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules.

Development of a thyroperoxidase inhibition assay for high ...

EPA Pesticide Factsheets

High-throughput screening (HTPS) assays to detect inhibitors of thyroperoxidase (TPO), the enzymatic catalyst for thyroid hormone (TH) synthesis, are not currently available. Herein we describe the development of a HTPS TPO inhibition assay. Rat thyroid microsomes and a fluorescent peroxidase substrate, Amplex UltraRed (AUR, LifeTechnologies), were employed in an endpoint assay for comparison to the existing kinetic guaiacol (GUA) oxidation assay. Following optimization of assay metrics including Z’, dynamic range, and activity using methimazole (MMI), the assay was tested with a 21-chemical training set. The potency of MMI-induced TPO inhibition was greater with AUR compared to GUA. The dynamic range and Z’ score with MMI were as follows: 127-fold and 0.62 for the GUA assay, 18-fold and 0.86 for the 96-well AUR assay, and 11.5-fold and 0.93 for the 384-well AUR assay. The 384-well AUR assay drastically reduced animal use, requiring one-tenth of the rat thyroid microsomal protein needed for the GUA 96-well format assay. Fourteen chemicals inhibited TPO, with a relative potency ranking of MMI > ethylene thiourea > 6-propylthiouracil > 2,2’,4,4’-tetrahydroxy-benzophenone > 2-mercaptobenzothiazole > 3-amino-1,2,4-triazole > genistein > 4-propoxyphenol > sulfamethazine > daidzein > 4-nonylphenol > triclosan > iopanoic acid > resorcinol. These data demonstrate the capacity of this assay to detect diverse TPO inhibitors. Seven chemicals acted as negati

Large-Scale Reactive Atomistic Simulation of Shock-induced Initiation Processes in Energetic Materials

NASA Astrophysics Data System (ADS)

Thompson, Aidan

2013-06-01

Initiation in energetic materials is fundamentally dependent on the interaction between a host of complex chemical and mechanical processes, occurring on scales ranging from intramolecular vibrations through molecular crystal plasticity up to hydrodynamic phenomena at the mesoscale. A variety of methods (e.g. quantum electronic structure methods (QM), non-reactive classical molecular dynamics (MD), mesoscopic continuum mechanics) exist to study processes occurring on each of these scales in isolation, but cannot describe how these processes interact with each other. In contrast, the ReaxFF reactive force field, implemented in the LAMMPS parallel MD code, allows us to routinely perform multimillion-atom reactive MD simulations of shock-induced initiation in a variety of energetic materials. This is done either by explicitly driving a shock-wave through the structure (NEMD) or by imposing thermodynamic constraints on the collective dynamics of the simulation cell e.g. using the Multiscale Shock Technique (MSST). These MD simulations allow us to directly observe how energy is transferred from the shockwave into other processes, including intramolecular vibrational modes, plastic deformation of the crystal, and hydrodynamic jetting at interfaces. These processes in turn cause thermal excitation of chemical bonds leading to initial chemical reactions, and ultimately to exothermic formation of product species. Results will be presented on the application of this approach to several important energetic materials, including pentaerythritol tetranitrate (PETN) and ammonium nitrate/fuel oil (ANFO). In both cases, we validate the ReaxFF parameterizations against QM and experimental data. For PETN, we observe initiation occurring via different chemical pathways, depending on the shock direction. For PETN containing spherical voids, we observe enhanced sensitivity due to jetting, void collapse, and hotspot formation, with sensitivity increasing with void size. For ANFO, we examine the effect of reaction rates on shock direction, fuel oil fraction, and crystal/fuel oil/void microstructural arrangement. Sandia National Laboratories is a multi-program laboratory managed and operated by Sandia Corporation, a wholly owned subsidiary of Lockheed Martin Corporation, for the U.S. Dept. of Energy's National Nuclear Security Admin. under contract DEAC0494AL85000.

Entropic forces drive contraction of cytoskeletal networks.

PubMed

Braun, Marcus; Lansky, Zdenek; Hilitski, Feodor; Dogic, Zvonimir; Diez, Stefan

2016-05-01

The cytoskeleton is a network of interconnected protein filaments, which provide a three-dimensional scaffold for cells. Remodeling of the cytoskeleton is important for key cellular processes, such as cell motility, division, or morphogenesis. This remodeling is traditionally considered to be driven exclusively by processes consuming chemical energy, such as the dynamics of the filaments or the action of molecular motors. Here, we review two mechanisms of cytoskeletal network remodeling that are independent of the consumption of chemical energy. In both cases directed motion of overlapping filaments is driven by entropic forces, which arise from harnessing thermal energy present in solution. Entropic forces are induced either by macromolecular crowding agents or by diffusible crosslinkers confined to the regions where filaments overlap. Both mechanisms increase filament overlap length and lead to the contraction of filament networks. These force-generating mechanisms, together with the chemical energy-dependent mechanisms, need to be considered for the comprehensive quantitative picture of the remodeling of cytoskeletal networks in cells. © 2016 WILEY Periodicals, Inc.

Facilitation and inhibition: changes in plant nitrogen and secondary metabolites mediate interactions between above-ground and below-ground herbivores.

PubMed

Huang, Wei; Siemann, Evan; Yang, Xuefang; Wheeler, Gregory S; Ding, Jianqing

2013-09-22

To date, it remains unclear how herbivore-induced changes in plant primary and secondary metabolites impact above-ground and below-ground herbivore interactions. Here, we report effects of above-ground (adult) and below-ground (larval) feeding by Bikasha collaris on nitrogen and secondary chemicals in shoots and roots of Triadica sebifera to explain reciprocal above-ground and below-ground insect interactions. Plants increased root tannins with below-ground herbivory, but above-ground herbivory prevented this increase and larval survival doubled. Above-ground herbivory elevated root nitrogen, probably contributing to increased larval survival. However, plants increased foliar tannins with above-ground herbivory and below-ground herbivory amplified this increase, and adult survival decreased. As either foliar or root tannins increased, foliar flavonoids decreased, suggesting a trade-off between these chemicals. Together, these results show that plant chemicals mediate contrasting effects of conspecific larval and adult insects, whereas insects may take advantage of plant responses to facilitate their offspring performance, which may influence population dynamics.

On the Effects of Bremsstrahlung Radiation During Energetic Electron Precipitation

NASA Astrophysics Data System (ADS)

Xu, Wei; Marshall, Robert A.; Fang, Xiaohua; Turunen, Esa; Kero, Antti

2018-01-01

Precipitation of energetic particles into the Earth's atmosphere can significantly change the properties, dynamics, as well as the chemical composition of the upper and middle atmosphere. In this paper, using Monte Carlo models, we simulate, from first principles, the interaction of monoenergetic beams of precipitating electrons with the atmosphere, with particular emphasis on the process of bremsstrahlung radiation and its resultant ionization production and atmospheric effects. The pitch angle dependence of the ionization rate profile has been quantified: the altitude of peak ionization rate depends on the pitch angle by a few kilometers. We also demonstrate that the transport of precipitating electron energy in the form of bremsstrahlung photons leads to ionization at altitudes significantly lower than the direct impact ionization, as low as ˜20 km for 1 MeV precipitating electrons. Moreover, chemical modeling results suggest that the chemical effects in the atmosphere due to bremsstrahlung-induced ionization production during energetic electron precipitation are likely insignificant.

Shift in Chemical Potential of Superconducting Bi2212 Measured by Ultrafast Photoemission Spectroscopy

NASA Astrophysics Data System (ADS)

Miller, Tristan; Smallwood, Chris; Zhang, Wentao; Eisaki, Hiroshi; Lee, Dung-Hai; Lanzara, Alessandra

2015-03-01

Time- and Angle-resolved photoemission spectroscopy (tr-ARPES) has been used to directly measure the dynamics of many different properties of high-temperature superconductors, including the quasiparticle relaxation, cooper pair recombination, and many-body interactions. There have also been several intriguing results on several materials showing how laser pulses can manipulate their chemical potential on ultrafast timescales, and it's been suggested that these effects could find applications in optoelectronic devices. Studies on GaAs have also found that laser pulses may induce a surface voltage effect. Here, we extend these studies for the first time to a Bi2212 sample in the superconducting state, and disentangle the shift in chemical potential from surface voltage effects. This work was supported by Berkeley Lab's program on Quantum Materials, funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Materials Sciences and Engineering Division, under Contract No. DE-AC02-05CH11231.

Molecular Mobility of an Amorphous Chiral Pharmaceutical Compound: Impact of Chirality and Chemical Purity.

PubMed

Viel, Quentin; Delbreilh, Laurent; Coquerel, Gérard; Petit, Samuel; Dargent, Eric

2017-08-17

A dielectric relaxation spectroscopy (DRS) study was performed to investigate the molecular mobility of amorphous chiral diprophylline (DPL). For this purpose, both racemic DPL and a single enantiomer of DPL were considered. After fast cooling from the melt at very low temperature (-140 °C), progressive heating below and above the glass transition (T g ≈ 37 °C) induces two secondary relaxations (γ- and δ-) and primary relaxations (α-) for both enantiomeric compositions. After chemical purification of our samples by means of cooling recrystallization, no γ-process could be detected by DRS. Hence, it was highlighted that the molecular mobility in the glassy state is influenced by the presence of theophylline (TPH), the main impurity in DPL samples. We also proved that the dynamic behavior of a single enantiomer and the racemic mixture of the same purified compound are quasi-identical. This study demonstrates that the relative stability and the molecular mobility of chiral amorphous drugs are strongly sensitive to chemical purity.

Dynamic Processes of Conceptual Change: Analysis of Constructing Mental Models of Chemical Equilibrium.

ERIC Educational Resources Information Center

Chiu, Mei-Hung; Chou, Chin-Cheng; Liu, Chia-Ju

2002-01-01

Investigates students' mental models of chemical equilibrium using dynamic science assessments. Reports that students at various levels have misconceptions about chemical equilibrium. Involves 10th grade students (n=30) in the study doing a series of hands-on chemical experiments. Focuses on the process of constructing mental models, dynamic…

Taking the plunge: chemical reaction dynamics in liquids.

PubMed

Orr-Ewing, Andrew J

2017-12-11

The dynamics of chemical reactions in liquid solutions are now amenable to direct study using ultrafast laser spectroscopy techniques and advances in computer simulation methods. The surrounding solvent affects the chemical reaction dynamics in numerous ways, which include: (i) formation of complexes between reactants and solvent molecules; (ii) modifications to transition state energies and structures relative to the reactants and products; (iii) coupling between the motions of the reacting molecules and the solvent modes, and exchange of energy; (iv) solvent caging of reactants and products; and (v) structural changes to the solvation shells in response to the changing chemical identity of the solutes, on timescales which may be slower than the reactive events. This article reviews progress in the study of bimolecular chemical reaction dynamics in solution, concentrating on reactions which occur on ground electronic states. It illustrates this progress with reference to recent experimental and computational studies, and considers how the various ways in which a solvent affects the chemical reaction dynamics can be unravelled. Implications are considered for research in fields such as mechanistic synthetic chemistry.

Correlation between dynamic wetting behavior and chemical components of thermally modified wood

NASA Astrophysics Data System (ADS)

Wang, Wang; Zhu, Yuan; Cao, Jinzhen; Sun, Wenjing

2015-01-01

In order to investigate the dynamic wetting behavior of thermally modified wood, Cathay poplar (Populus cathayana Rehd.) and Scots pine (Pinus sylvestris L.) samples were thermally modified in an oven at 160, 180, 200, 220 or 240 °C for 4 h in this study. The dynamic contact angles and droplet volumes of water droplets on modified and unmodified wood surfaces were measured by sessile drop method, and their changing rates (expression index: K value and wetting slope) calculated by wetting models were illustrated for mapping the dynamic wetting process. The surface chemical components were also measured by X-ray photoelectron spectroscopy analysis (XPS), thus the relationship between dynamic wetting behavior and chemical components of thermally modified wood were determined. The results indicated that thermal modification was capable of decreasing the dynamic wettability of wood, expressed in lowing spread and penetration speed of water droplets on wood surfaces. This change was more obvious with the increased heating temperature. The K values varied linearly with the chemical components parameter (mass loss, O/C ratio, and C1/C2 ratio), indicating a strong correlation between dynamic wetting behavior and chemical components of thermally modified wood.

Cofilin 1-Mediated Biphasic F-Actin Dynamics of Neuronal Cells Affect Herpes Simplex Virus 1 Infection and Replication

PubMed Central

Xiang, Yangfei; Zheng, Kai; Ju, Huaiqiang; Wang, Shaoxiang; Pei, Ying; Ding, Weichao; Chen, Zhenping; Wang, Qiaoli; Qiu, Xianxiu; Zhong, Meigong; Zeng, Fanli; Ren, Zhe; Qian, Chuiwen; Liu, Ge

2012-01-01

Herpes simplex virus 1 (HSV-1) invades the nervous system and causes pathological changes. In this study, we defined the remodeling of F-actin and its possible mechanisms during HSV-1 infection of neuronal cells. HSV-1 infection enhanced the formation of F-actin-based structures in the early stage of infection, which was followed by a continuous decrease in F-actin during the later stages of infection. The disruption of F-actin dynamics by chemical inhibitors significantly reduced the efficiency of viral infection and intracellular HSV-1 replication. The active form of the actin-depolymerizing factor cofilin 1 was found to increase at an early stage of infection and then to continuously decrease in a manner that corresponded to the remodeling pattern of F-actin, suggesting that cofilin 1 may be involved in the biphasic F-actin dynamics induced by HSV-1 infection. Knockdown of cofilin 1 impaired HSV-1-induced F-actin assembly during early infection and inhibited viral entry; however, overexpression of cofilin 1 did not affect F-actin assembly or viral entry during early infection but decreased intracellular viral reproduction efficiently. Our results, for the first time, demonstrated the biphasic F-actin dynamics in HSV-1 neuronal infection and confirmed the association of F-actin with the changes in the expression and activity of cofilin 1. These results may provide insight into the mechanism by which HSV-1 productively infects neuronal cells and causes pathogenesis. PMID:22623803

Substrate Induced Structural and Dynamics Changes in Human Phosphomevalonate Kinase and Implications for Mechanism

PubMed Central

Olson, Andrew L.; Yao, Huili; Herdendorf, Timothy J.; Miziorko, Henry M.; Hannongbua, Supa; Saparpakorn, Patchareenart; Cai, Sheng; Sem, Daniel S.

2008-01-01

Phosphomevalonate kinase (PMK) catalyzes an essential step in the mevalonate pathway, which is the only pathway for synthesis of isoprenoids and steroids in humans. PMK catalyzes transfer of the γ-phosphate of ATP to mevalonate 5-phosphate (M5P) to form mevalonate 5-diphosphate. Bringing these phosphate groups in proximity to react is especially challenging, given the high negative charge density on the four phosphate groups in the active site. As such, conformational and dynamics changes needed to form the Michaelis complex are of mechanistic interest. Herein, we report the characterization of substrate induced changes (Mg-ADP, M5P, and the ternary complex) in PMK, using NMR-based dynamics and chemical shift perturbation measurements. Mg-ADP and M5P Kd's were 6-60 μM in all complexes, consistent with there being little binding synergy. Binding of M5P causes the PMK structure to compress (τc= 13.5 nsec), while subsequent binding of Mg-ADP opens the structure up (τc= 17.6 nsec). The overall complex seems to stay very rigid on the psec-nsec timescale with an average NMR order parameter of S2∼0.88. Data are consistent with addition of M5P causing movement around a hinge region to permit domain closure, which would bring the M5P domain close to ATP to permit catalysis. Dynamics data identify potential hinge residues as H55 and R93, based on their low order parameters and their location in extended regions that connect the M5P and ATP domains in the PMK homology model. Likewise, D163 may be a hinge residue for the lid region that is homologous to the adenylate kinase lid, covering the “Walker-A” catalytic loop. Binding of ATP or ADP appears to cause similar conformational changes; but, these observations do not indicate an obvious role for γ-phosphate binding interactions. Indeed, the role of γ-phosphate interactions may be more subtle than suggested by ATP/ADP comparisons, since the conservative O to NH substitution in the β-γ bridge of ATP causes a dramatic decrease in affinity and induces few chemical shift perturbations. In terms of positioning of catalytic residues, binding of M5P induces a rigidification of Gly21 (adjacent to the catalytically important Lys22), although exchange broadening in the ternary complex suggests some motion on a slower timescale does still occur. Finally, the first 9 residues of the N-terminus are highly disordered, suggesting they may be part of a cleavable signal or regulatory peptide sequence. PMID:18798562

Variability in benthic exchange rate, depth, and residence time beneath a shallow coastal estuary

NASA Astrophysics Data System (ADS)

Russoniello, C. J.; Michael, H. A.; Heiss, J.

2017-12-01

Hydrodynamically-driven exchange of water between the water column and shallow seabed aquifer, benthic exchange, is a significant and dynamic component of coastal and estuarine fluid budgets, but wave-induced benthic exchange has not been measured in the field. Mixing between surface water and groundwater solutes promotes ecologically important chemical reactions, so quantifying benthic exchange rates, depths, and residence times, constrains estimates of coastal chemical cycling. In this study, we present the first field-based direct measurements of wave-induced exchange and compare it to exchange induced by the other primary drivers of exchange - tides, and currents. We deployed instruments in a shallow estuary to measure benthic exchange and temporal variability over an 11-day period. Differential pressure sensors recorded pressure gradients across the seabed, and up-and down-looking ADCPs recorded currents and pressures from which wave parameters, surface-water currents, and water depth were determined. Wave-induced exchange was calculated directly from 1) differential pressure measurements, and indirectly with an analytical solution based on wave parameters from 2) ADCP and 3) weather station data. Groundwater flow models were used to assess the effects of aquifer properties on benthic exchange depth and residence time. Benthic exchange driven by tidal pumping or current-bedform interaction was calculated from tidal stage variation and from ADCP-measured currents at the bed, respectively. Waves were the primary benthic exchange driver (average = 20.0 cm/d, maximum = 92.3 cm/d) during the measurement period. Benthic exchange due to tides (average = 3.7 cm/d) and current-bedform interaction (average = 6.5x10-2 cm/d) was much lower. Wave-induced exchange calculated from pressure measurements and ADCP-measured wave parameters matched well, but wind-based rates underestimated wave energy and exchange. Groundwater models showed that residence time and depth increased in high-permeability, incompressible aquifers, and exchange rates increased in low-permeability, compressible aquifers. These findings support and extend the utility of existing wave-induced exchange solutions and will help managers assess the importance of benthic exchange on coastal chemical cycling.

Osmotic propulsion: the osmotic motor.

PubMed

Córdova-Figueroa, Ubaldo M; Brady, John F

2008-04-18

A model for self-propulsion of a colloidal particle--the osmotic motor--immersed in a dispersion of "bath" particles is presented. The nonequilibrium concentration of bath particles induced by a surface chemical reaction creates an osmotic pressure imbalance on the motor causing it to move. The ratio of the speed of reaction to that of diffusion governs the bath particle distribution which is employed to calculate the driving force on the motor, and from which the self-induced osmotic velocity is determined. For slow reactions, the self-propulsion is proportional to the reaction velocity. When surface reaction dominates over diffusion the osmotic velocity cannot exceed the diffusive speed of the bath particles. Implications of these features for different bath particle volume fractions and motor sizes are discussed. Theoretical predictions are compared with Brownian dynamics simulations.

Osmotic Propulsion: The Osmotic Motor

NASA Astrophysics Data System (ADS)

Córdova-Figueroa, Ubaldo M.; Brady, John F.

2008-04-01

A model for self-propulsion of a colloidal particle—the osmotic motor—immersed in a dispersion of “bath” particles is presented. The nonequilibrium concentration of bath particles induced by a surface chemical reaction creates an osmotic pressure imbalance on the motor causing it to move. The ratio of the speed of reaction to that of diffusion governs the bath particle distribution which is employed to calculate the driving force on the motor, and from which the self-induced osmotic velocity is determined. For slow reactions, the self-propulsion is proportional to the reaction velocity. When surface reaction dominates over diffusion the osmotic velocity cannot exceed the diffusive speed of the bath particles. Implications of these features for different bath particle volume fractions and motor sizes are discussed. Theoretical predictions are compared with Brownian dynamics simulations.

Superhigh moduli and tension-induced phase transition of monolayer gamma-boron at finite temperatures.

PubMed

Zhao, Junhua; Yang, Zhaoyao; Wei, Ning; Kou, Liangzhi

2016-03-16

Two dimensional (2D) gamma-boron (γ-B28) thin films have been firstly reported by the experiments of the chemical vapor deposition in the latest study. However, their mechanical properties are still not clear. Here we predict the superhigh moduli (785 ± 42 GPa at 300 K) and the tension-induced phase transition of monolayer γ-B28 along a zigzag direction for large deformations at finite temperatures using molecular dynamics (MD) simulations. The new phase can be kept stable after unloading process at these temperatures. The predicted mechanical properties are reasonable when compared with our results from density functional theory. This study provides physical insights into the origins of the new phase transition of monolayer γ-B28 at finite temperatures.

Convective Dynamics and Disequilibrium Chemistry in the Atmospheres of Giant Planets and Brown Dwarfs

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2018-02-01

Disequilibrium chemical processes significantly affect the spectra of substellar objects. To study these effects, dynamical disequilibrium has been parameterized using the quench and eddy diffusion approximations, but little work has been done to explore how these approximations perform under realistic planetary conditions in different dynamical regimes. As a first step toward addressing this problem, we study the localized, small-scale convective dynamics of planetary atmospheres by direct numerical simulation of fully compressible hydrodynamics with reactive tracers using the Dedalus code. Using polytropically stratified, plane-parallel atmospheres in 2D and 3D, we explore the quenching behavior of different abstract chemical species as a function of the dynamical conditions of the atmosphere as parameterized by the Rayleigh number. We find that in both 2D and 3D, chemical species quench deeper than would be predicted based on simple mixing-length arguments. Instead, it is necessary to employ length scales based on the chemical equilibrium profile of the reacting species in order to predict quench points and perform chemical kinetics modeling in 1D. Based on the results of our simulations, we provide a new length scale, derived from the chemical scale height, that can be used to perform these calculations. This length scale is simple to calculate from known chemical data and makes reasonable predictions for our dynamical simulations.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution.

PubMed

Wernet, Ph; Kunnus, K; Josefsson, I; Rajkovic, I; Quevedo, W; Beye, M; Schreck, S; Grübel, S; Scholz, M; Nordlund, D; Zhang, W; Hartsock, R W; Schlotter, W F; Turner, J J; Kennedy, B; Hennies, F; de Groot, F M F; Gaffney, K J; Techert, S; Odelius, M; Föhlisch, A

2015-04-02

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16 - 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Orbital-specific mapping of the ligand exchange dynamics of Fe(CO)5 in solution

NASA Astrophysics Data System (ADS)

Wernet, Ph.; Kunnus, K.; Josefsson, I.; Rajkovic, I.; Quevedo, W.; Beye, M.; Schreck, S.; Grübel, S.; Scholz, M.; Nordlund, D.; Zhang, W.; Hartsock, R. W.; Schlotter, W. F.; Turner, J. J.; Kennedy, B.; Hennies, F.; de Groot, F. M. F.; Gaffney, K. J.; Techert, S.; Odelius, M.; Föhlisch, A.

2015-04-01

Transition-metal complexes have long attracted interest for fundamental chemical reactivity studies and possible use in solar energy conversion. Electronic excitation, ligand loss from the metal centre, or a combination of both, creates changes in charge and spin density at the metal site that need to be controlled to optimize complexes for photocatalytic hydrogen production and selective carbon-hydrogen bond activation. An understanding at the molecular level of how transition-metal complexes catalyse reactions, and in particular of the role of the short-lived and reactive intermediate states involved, will be critical for such optimization. However, suitable methods for detailed characterization of electronic excited states have been lacking. Here we show, with the use of X-ray laser-based femtosecond-resolution spectroscopy and advanced quantum chemical theory to probe the reaction dynamics of the benchmark transition-metal complex Fe(CO)5 in solution, that the photo-induced removal of CO generates the 16-electron Fe(CO)4 species, a homogeneous catalyst with an electron deficiency at the Fe centre, in a hitherto unreported excited singlet state that either converts to the triplet ground state or combines with a CO or solvent molecule to regenerate a penta-coordinated Fe species on a sub-picosecond timescale. This finding, which resolves the debate about the relative importance of different spin channels in the photochemistry of Fe(CO)5 (refs 4, 16,17,18,19 and 20), was made possible by the ability of femtosecond X-ray spectroscopy to probe frontier-orbital interactions with atom specificity. We expect the method to be broadly applicable in the chemical sciences, and to complement approaches that probe structural dynamics in ultrafast processes.

Visualization of physico-chemical properties and microbial distribution in soil and root microenvironments

NASA Astrophysics Data System (ADS)

Eickhorst, Thilo; Schmidt, Hannes

2016-04-01

Plant root development is influenced by soil properties and environmental factors. In turn plant roots can also change the physico-chemical conditions in soil resulting in gradients between roots and the root-free bulk soil. By releasing a variety of substances roots facilitate microbial activities in their direct vicinity, the rhizosphere. The related microorganisms are relevant for various ecosystem functions in the root-soil interface such as nutrient cycling. It is therefore important to study the impact and dynamics of microorganisms associated to different compartments in root-soil interfaces on a biologically meaningful micro-scale. The analysis of microorganisms in their habitats requires microscopic observations of the respective microenvironment. This can be obtained by preserving the complex soil structure including the root system by resin impregnation resulting in high quality thin sections. The observation of such sections via fluorescence microscopy, SEM-EDS, and Nano-SIMS will be highlighted in this presentation. In addition, we will discuss the combination of this methodological approach with other imaging techniques such as planar optodes or non-invasive 3D X-ray CT to reveal the entire spatial structure and arrangement of soil particles and roots. When combining the preservation of soil structure via resin impregnation with 16S rRNA targeted fluorescence in situ hybridization (FISH) single microbial cells can be visualized, localized, and quantified in the undisturbed soil matrix including the root-soil interfaces. The simultaneous use of multiple oligonucleotide probes thereby provides information on the spatial distribution of microorganisms belonging to different phylogenetic groups. Results will be shown for paddy soils, where management induced physico-chemical dynamics (flooding and drying) as well as resulting microbial dynamics were visualized via correlative microscopy in resin impregnated samples.

The importance of dynamical feedback on doubled CO{sub 2}-induced changes in the thermal structure of the mesosphere

DOE Office of Scientific and Technical Information (OSTI.GOV)

Portmann, R.W.; Thomas, G.E.; Solomon, S.

The Garcia-Solomon two-dimensional model was used to study the effect of doubled carbon-dioxide on the middle atmosphere. The model has been improved to include non-LTE CO{sub 2} cooling in the 15 micron band above 70 km and new chemical heating and heating efficiencies. The effect of doubling CO{sub 2} on the temperature is found to be large at the stratopause (about 10-12K cooling) and at the mesopause (about 6-12K cooling). In the stratosphere, dynamical feedbacks on the heating rate caused by the temperature changes are small compared to the radiative changes while in the mesosphere they can be large. Inmore » fact, calculations with the present dynamical heating rate used in the doubled CO{sub 2} energy equation indicate that the radiative forcing alone could cause a temperature increase of about 10K in the polar summer mesopause region. The dynamical feedbacks which oppose this positive radiative forcing are discussed. 18 refs., 3 figs.« less

Dynamic Microenvironment Induces Phenotypic Plasticity of Esophageal Cancer Cells Under Flow

NASA Astrophysics Data System (ADS)

Calibasi Kocal, Gizem; Güven, Sinan; Foygel, Kira; Goldman, Aaron; Chen, Pu; Sengupta, Shiladitya; Paulmurugan, Ramasamy; Baskin, Yasemin; Demirci, Utkan

2016-12-01

Cancer microenvironment is a remarkably heterogeneous composition of cellular and non-cellular components, regulated by both external and intrinsic physical and chemical stimuli. Physical alterations driven by increased proliferation of neoplastic cells and angiogenesis in the cancer microenvironment result in the exposure of the cancer cells to elevated levels of flow-based shear stress. We developed a dynamic microfluidic cell culture platform utilizing eshopagael cancer cells as model cells to investigate the phenotypic changes of cancer cells upon exposure to fluid shear stress. We report the epithelial to hybrid epithelial/mesenchymal transition as a result of decreasing E-Cadherin and increasing N-Cadherin and vimentin expressions, higher clonogenicity and ALDH positive expression of cancer cells cultured in a dynamic microfluidic chip under laminar flow compared to the static culture condition. We also sought regulation of chemotherapeutics in cancer microenvironment towards phenotypic control of cancer cells. Such in vitro microfluidic system could potentially be used to monitor how the interstitial fluid dynamics affect cancer microenvironment and plasticity on a simple, highly controllable and inexpensive bioengineered platform.

Aggregation-induced chemical reactions: acid dissociation in growing water clusters.

PubMed

Forbert, Harald; Masia, Marco; Kaczmarek-Kedziera, Anna; Nair, Nisanth N; Marx, Dominik

2011-03-23

Understanding chemical reactivity at ultracold conditions, thus enabling molecular syntheses via interstellar and atmospheric processes, is a key issue in cryochemistry. In particular, acid dissociation and proton transfer reactions are ubiquitous in aqueous microsolvation environments. Here, the full dissociation of a HCl molecule upon stepwise solvation by a small number of water molecules at low temperatures, as relevant to helium nanodroplet isolation (HENDI) spectroscopy, is analyzed in mechanistic detail. It is found that upon successive aggregation of HCl with H(2)O molecules, a series of cyclic heteromolecular structures, up to and including HCl(H(2)O)(3), are initially obtained before a precursor state for dissociation, HCl(H(2)O)(3)···H(2)O, is observed upon addition of a fourth water molecule. The latter partially aggregated structure can be viewed as an "activated species", which readily leads to dissociation of HCl and to the formation of a solvent-shared ion pair, H(3)O(+)(H(2)O)(3)Cl(-). Overall, the process is mostly downhill in potential energy, and, in addition, small remaining barriers are overcome by using kinetic energy released as a result of forming hydrogen bonds due to aggregation. The associated barrier is not ruled by thermal equilibrium but is generated by athermal non-equilibrium dynamics. These "aggregation-induced chemical reactions" are expected to be of broad relevance to chemistry at ultralow temperature much beyond HENDI spectroscopy.

Divergent Mechanisms Leading to Signaling Dysfunction in Embryonic Muscle by Bisphenol A and Tetrabromobisphenol A

PubMed Central

Pessah, Isaac N.

2017-01-01

Bisphenol A (BPA) and its brominated derivative tetrabromobisphenol A (TBBPA) are high production volume chemicals used in the manufacture of various consumer products. Although regarded as endocrine disruptors, these chemicals are suspected to exert nongenomic actions on muscle function that are not well understood. Using skeletal muscle microsomes, we examined the effects of BPA and TBBPA on ryanodine receptor type 1 (RyR1), dihydropyridine receptor (DHPR), and sarcoplasmic/endoplasmic reticulum Ca2+ ATPase (SERCA). We assessed the impact of these chemicals on Ca2+ dynamics and signaling in embryonic skeletal myotubes through fluorescent Ca2+ imaging and measurement of resting membrane potential (Vm). TBBPA activated RyR1 and inhibited DHPR and SERCA, inducing a net efflux of Ca2+ from loaded microsomes, whereas BPA exhibited little or no activity at these targets. Regardless, both compounds disrupted the function of intact myotubes. TBBPA diminished and eventually abrogated Ca2+ transients, altered intracellular Ca2+ equilibrium, and caused Vm depolarization. For some cells, BPA caused rapid Ca2+ transient loss without marked changes in cytosolic and sarcoplasmic reticulum Ca2+ levels, likely owing to altered cellular excitability as a result of BPA-induced Vm hyperpolarization. BPA and TBBPA both interfere with skeletal muscle function through divergent mechanisms that impair excitation-contraction coupling and may be exemplary of their adverse outcomes in other muscle types. PMID:28143888

First-Principles Molecular Dynamics Study on the Electric-double layer Capacitance of Water-MXene interfaces

NASA Astrophysics Data System (ADS)

Ando, Yasunobu; Otani, Minoru

MXenes are a new, large family of layered materials synthesized from MAX phases by simple chemical treatments. Due to their enormous variations, MXenes have attracted great attention as promising candidates as anode materials for next-generation secondary batteries. Unfortunately, the specific capacitance of MXenes supercapacitors is lower than that of active-carbon ones. Theoretical investigation of the electric-double layer (EDL) at electrode interfaces is necessary to improve their capacitance. First-principles molecular dynamics (FPMD) simulation based on the density functional theory (DFT) is performed to estimate the EDL capacitance from a potential profile V(z) and a charge distribution q(z) induced by the ions at water-Ti2CTx (T =O, F) interfaces. Potential profiles V(z) of both Ti2CO2 and Ti2CF2 decrease about 1.0 eV steeply in a region of only 3 Å from a Ti layer, which is the same profile at the platinum interfaces. On the other hand, induced charge distribution q(z) depends on the species of surface termination. Induced electrons are introduced at Ti layers in the case of O surface termination. However, Ti2CF2 is not capable to store electrons at Ti layers because it is mono-valence anions. It indicates that effective surface-position of MXenes depends on the surface terminations. Our results are revealed that small induced charge leads the low EDL capacitance at MXene interfaces. This is because interface polarization due to strong interaction between water and Ti2CTx induces net charge. The surface net charge hinders the introduction of ion-induced charges.

Water confined in carbon nanotubes: Magnetic response and proton chemical shieldings

DOE Office of Scientific and Technical Information (OSTI.GOV)

Huang, P; Schwegler, E; Galli, G

2008-11-14

We study the proton nuclear magnetic resonance ({sup 1}H-NMR) of a model system consisting of liquid water in infinite carbon nanotubes (CNT). Chemical shieldings are evaluated from linear response theory, where the electronic structure is derived from density functional theory (DFT) with plane-wave basis sets and periodic boundary conditions. The shieldings are sampled from trajectories generated via first-principles molecular dynamics simulations at ambient conditions, for water confined in (14,0) and (19,0) CNTs with diameters d = 11 {angstrom} and 14.9 {angstrom}, respectively. We find that confinement within the CNT leads to a large ({approx} -23 ppm) upfield shift relative tomore » bulk liquid water. This shift is a consequence of strongly anisotropic magnetic fields induced in the CNT by an applied magnetic field.« less

High Pressure Oxidizer Turbopump (HPOTP) inducer dynamic design environment

NASA Technical Reports Server (NTRS)

Herda, D. A.; Gross, R. S.

1995-01-01

The dynamic environment must be known to evaluate high pressure oxidizer turbopump inducer fatigue life. This report sets the dynamic design loads for the alternate turbopump inducer as determined by water-flow rig testing. Also, guidelines are given for estimating the dynamic environment for other inducer and impeller applications.

Photoisomerization and photoionization of the photoactive yellow protein chromophore in solution.

PubMed

Larsen, Delmar S; Vengris, Mikas; van Stokkum, Ivo H M; van der Horst, Michael A; de Weerd, Frank L; Hellingwerf, Klaas J; van Grondelle, Rienk

2004-04-01

Dispersed pump-dump-probe spectroscopy has the ability to characterize and identify the underlying ultrafast dynamical processes in complicated chemical and biological systems. This technique builds on traditional pump-probe techniques by exploring both ground- and excited-state dynamics and characterizing the connectivity between constituent transient states. We have used the dispersed pump-dump-probe technique to investigate the ground-state dynamics and competing excited-state processes in the excitation-induced ultrafast dynamics of thiomethyl p-coumaric acid, a model chromophore for the photoreceptor photoactive yellow protein. Our results demonstrate the parallel formation of two relaxation pathways (with multiple transient states) that jointly lead to two different types of photochemistry: cis-trans isomerization and detachment of a hydrated electron. The relative transition rates and quantum yields of both pathways have been determined. We find that the relaxation of the photoexcited chromophores involves multiple, transient ground-state intermediates and the chromophore in solution does not generate persistent photoisomerized products, but instead undergoes photoionization resulting in the generation of detached electrons and radicals. These results are of great value in interpreting the more complex dynamical changes in the optical properties of the photoactive yellow protein.

Photoisomerization and Photoionization of the Photoactive Yellow Protein Chromophore in Solution

PubMed Central

Larsen, Delmar S.; Vengris, Mikas; van Stokkum, Ivo H. M.; van der Horst, Michael A.; de Weerd, Frank L.; Hellingwerf, Klaas J.; van Grondelle, Rienk

2004-01-01

Dispersed pump-dump-probe spectroscopy has the ability to characterize and identify the underlying ultrafast dynamical processes in complicated chemical and biological systems. This technique builds on traditional pump-probe techniques by exploring both ground- and excited-state dynamics and characterizing the connectivity between constituent transient states. We have used the dispersed pump-dump-probe technique to investigate the ground-state dynamics and competing excited-state processes in the excitation-induced ultrafast dynamics of thiomethyl p-coumaric acid, a model chromophore for the photoreceptor photoactive yellow protein. Our results demonstrate the parallel formation of two relaxation pathways (with multiple transient states) that jointly lead to two different types of photochemistry: cis-trans isomerization and detachment of a hydrated electron. The relative transition rates and quantum yields of both pathways have been determined. We find that the relaxation of the photoexcited chromophores involves multiple, transient ground-state intermediates and the chromophore in solution does not generate persistent photoisomerized products, but instead undergoes photoionization resulting in the generation of detached electrons and radicals. These results are of great value in interpreting the more complex dynamical changes in the optical properties of the photoactive yellow protein. PMID:15041690

Imaging dynamic fingerprints of competing E2 and SN2 reactions.

PubMed

Carrascosa, Eduardo; Meyer, Jennifer; Zhang, Jiaxu; Stei, Martin; Michaelsen, Tim; Hase, William L; Yang, Li; Wester, Roland

2017-06-21

The competition between bimolecular nucleophilic substitution and base-induced elimination is of fundamental importance for the synthesis of pure samples in organic chemistry. Many factors that influence this competition have been identified over the years, but the underlying atomistic dynamics have remained difficult to observe. We present product velocity distributions for a series of reactive collisions of the type X -  + RY with X and Y denoting the halogen atoms fluorine, chlorine and iodine. By increasing the size of the residue R from methyl to tert-butyl in several steps, we find that the dynamics drastically change from backward to dominant forward scattering of the leaving ion relative to the reactant RY velocity. This characteristic fingerprint is also confirmed by direct dynamics simulations for ethyl as residue and attributed to the dynamics of elimination reactions. This work opens the door to a detailed atomistic understanding of transformation reactions in even larger systems.The competition between chemical reactions critically affects our natural environment and the synthesis of new materials. Here, the authors present an approach to directly image distinct fingerprints of essential organic reactions and monitor their competition as a function of steric substitution.

Cellular Development Associated with Induced Mycotoxin Synthesis in the Filamentous Fungus Fusarium graminearum

PubMed Central

Menke, Jon; Weber, Jakob; Broz, Karen; Kistler, H. Corby

2013-01-01

Several species of the filamentous fungus Fusarium colonize plants and produce toxic small molecules that contaminate agricultural products, rendering them unsuitable for consumption. Among the most destructive of these species is F. graminearum, which causes disease in wheat and barley and often infests the grain with harmful trichothecene mycotoxins. Synthesis of these secondary metabolites is induced during plant infection or in culture in response to chemical signals. Our results show that trichothecene biosynthesis involves a complex developmental process that includes dynamic changes in cell morphology and the biogenesis of novel subcellular structures. Two cytochrome P-450 oxygenases (Tri4p and Tri1p) involved in early and late steps in trichothecene biosynthesis were tagged with fluorescent proteins and shown to co-localize to vesicles we provisionally call “toxisomes.” Toxisomes, the inferred site of trichothecene biosynthesis, dynamically interact with motile vesicles containing a predicted major facilitator superfamily protein (Tri12p) previously implicated in trichothecene export and tolerance. The immediate isoprenoid precursor of trichothecenes is the primary metabolite farnesyl pyrophosphate. Changes occur in the cellular localization of the isoprenoid biosynthetic enzyme HMG CoA reductase when cultures non-induced for trichothecene biosynthesis are transferred to trichothecene biosynthesis inducing medium. Initially localized in the cellular endomembrane system, HMG CoA reductase, upon induction of trichothecene biosynthesis, increasingly is targeted to toxisomes. Metabolic pathways of primary and secondary metabolism thus may be coordinated and co-localized under conditions when trichothecene biosynthesis occurs. PMID:23667578

Solution NMR studies of Chlorella virus DNA ligase-adenylate.

PubMed

Piserchio, Andrea; Nair, Pravin A; Shuman, Stewart; Ghose, Ranajeet

2010-01-15

DNA ligases are essential guardians of genome integrity by virtue of their ability to recognize and seal 3'-OH/5'-phosphate nicks in duplex DNA. The substrate binding and three chemical steps of the ligation pathway are coupled to global and local changes in ligase structure, involving both massive protein domain movements and subtle remodeling of atomic contacts in the active site. Here we applied solution NMR spectroscopy to study the conformational dynamics of the Chlorella virus DNA ligase (ChVLig), a minimized eukaryal ATP-dependent ligase consisting of nucleotidyltransferase, OB, and latch domains. Our analysis of backbone (15)N spin relaxation and (15)N,(1)H residual dipolar couplings of the covalent ChVLig-AMP intermediate revealed conformational sampling on fast (picosecond to nanosecond) and slow timescales (microsecond to millisecond), indicative of interdomain and intradomain flexibility. We identified local and global changes in ChVLig-AMP structure and dynamics induced by phosphate. In particular, the chemical shift perturbations elicited by phosphate were clustered in the peptide motifs that comprise the active site. We hypothesize that phosphate anion mimics some of the conformational transitions that occur when ligase-adenylate interacts with the nick 5'-phosphate. Copyright 2009 Elsevier Ltd. All rights reserved.

Hydrophobic fluorine mediated switching of the hydrogen bonding site as well as orientation of water molecules in the aqueous mixture of monofluoroethanol: IR, molecular dynamics and quantum chemical studies.

PubMed

Mondal, Saptarsi; Biswas, Biswajit; Nandy, Tonima; Singh, Prashant Chandra

2017-09-20

The local structures between water-water, alcohol-water and alcohol-alcohol have been investigated for aqueous mixtures of ethanol (ETH) and monofluoroethanol (MFE) by the deconvolution of IR bands in the OH stretching region, molecular dynamics simulation and quantum chemical calculations. It has been found that the addition of a small amount of ETH into the aqueous medium increases the strength of the hydrogen bonds between water molecules. In an aqueous mixture of MFE, the substitution of a single fluorine induces a change in the orientation as well as the hydrogen bonding site of water molecules from the oxygen to the fluorine terminal of MFE. The switching of the hydrogen bonding site of water in the aqueous mixture of MFE results in comparatively strong hydrogen bonds between MFE and water molecules as well as less clustering of water molecules, unlike the case of the aqueous mixture of ETH. These findings about the modification of a hydrogen bond network by the hydrophobic fluorine group probably make fluorinated molecules useful for pharmaceutical as well as biological applications.

Biofilm attachment reduction on bioinspired, dynamic, micro-wrinkling surfaces

NASA Astrophysics Data System (ADS)

Epstein, Alexander K.; Hong, Donggyoon; Kim, Philseok; Aizenberg, Joanna

2013-09-01

Most bacteria live in multicellular communities known as biofilms that are adherent to surfaces in our environment, from sea beds to plumbing systems. Biofilms are often associated with clinical infections, nosocomial deaths and industrial damage such as bio-corrosion and clogging of pipes. As mature biofilms are extremely challenging to eradicate once formed, prevention is advantageous over treatment. However, conventional surface chemistry strategies are either generally transient, due to chemical masking, or toxic, as in the case of leaching marine antifouling paints. Inspired by the nonfouling skins of echinoderms and other marine organisms, which possess highly dynamic surface structures that mechanically frustrate bio-attachment, we have developed and tested a synthetic platform based on both uniaxial mechanical strain and buckling-induced elastomer microtopography. Bacterial biofilm attachment to the dynamic substrates was studied under an array of parameters, including strain amplitude and timescale (1-100 mm s-1), surface wrinkle length scale, bacterial species and cell geometry, and growth time. The optimal conditions for achieving up to ˜ 80% Pseudomonas aeruginosa biofilm reduction after 24 h growth and ˜ 60% reduction after 48 h were combinatorially elucidated to occur at 20% strain amplitude, a timescale of less than ˜ 5 min between strain cycles and a topography length scale corresponding to the cell dimension of ˜ 1 μm. Divergent effects on the attachment of P. aeruginosa, Staphylococcus aureus and Escherichia coli biofilms showed that the dynamic substrate also provides a new means of species-specific biofilm inhibition, or inversely, selection for a desired type of bacteria, without reliance on any toxic or transient surface chemical treatments.

Bacteriorhodopsin as a chemical and biological sensor

NASA Astrophysics Data System (ADS)

Heeg, Bauke; Needleman, Richard; Khizhnyak, Anatoliy; L'Esperance, Drew M.; Scott, Eddie; Markov, Vladimir B.; Trolinger, James D.

2003-08-01

Bacteriorhodopsin (bR) is a small protein containing the chromophore retinal, and resides in the membrane of the Halobacterium salinarium. When the retinal absorbs a photon, a cycle of structural changes is triggered resulting in a cross-membrane proton transfer, which is used to generate energy for the organism. Many studies have been conducted to elucidate the dynamical structure - optical property relations, and the overall mechanism of photo-induced proton transport in bR is now well understood. On the other hand, site selective mutagenesis allows engineering of the original ("wild-type") bR, such that the protein can be made sensitive to specific chemicals or biological structures that consequently induce changes in the proton-transport. As such, bR provides a unique molecular platform onto which various functional elements can be built: peptide receptors for molecular recognition of pathogens (e.g. viruses, cancer cells, spores, bacteria, bio-toxins), fluorescent tags (using the inherent optical transduction mechanism of bR), and chemical anchors for capturing target cells. In particular, the stability of bR in extreme environments (pH range of 1 - 11, temperatures up to 110 °C) allows for optical detection under a large range of environmental conditions. In this paper we present and discuss experimental data of several bR mutants and their potential as chemical and biological sensors. In particular, the optical changes associated with metal ligand binding are discussed for two mutants, 170C and 169C/96N, as well as the optical changes associated with streptavidin-coated beads bound to bR with strep II tags inserted in the E/F loop.

Numerical studies from quantum to macroscopic scales of carbon nanoparticules in hydrogen plasma

NASA Astrophysics Data System (ADS)

Lombardi, Guillaume; Ngandjong, Alain; Mezei, Zsolt; Mougenot, Jonathan; Michau, Armelle; Hassouni, Khaled; Seydou, Mahamadou; Maurel, François

2016-09-01

Dusty plasmas take part in large scientific domains from Universe Science to nanomaterial synthesis processes. They are often generated by growth from molecular precursor. This growth leads to the formation of larger clusters which induce solid germs nucleation. Particle formed are described by an aerosol dynamic taking into account coagulation, molecular deposition and transport processes. These processes are controlled by the elementary particle. So there is a strong coupling between particle dynamics and plasma discharge equilibrium. This study is focused on the development of a multiscale physic and numeric model of hydrogen plasmas and carbon particles around three essential coupled axes to describe the various physical phenomena: (i) Macro/mesoscopic fluid modeling describing in an auto-coherent way, characteristics of the plasma, molecular clusters and aerosol behavior; (ii) the classic molecular dynamics offering a description to the scale molecular of the chains of chemical reactions and the phenomena of aggregation; (iii) the quantum chemistry to establish the activation barriers of the different processes driving the nanopoarticule formation.

Mesoscopic Modeling of Blood Clotting: Coagulation Cascade and Platelets Adhesion

NASA Astrophysics Data System (ADS)

Yazdani, Alireza; Li, Zhen; Karniadakis, George

2015-11-01

The process of clot formation and growth at a site on a blood vessel wall involve a number of multi-scale simultaneous processes including: multiple chemical reactions in the coagulation cascade, species transport and flow. To model these processes we have incorporated advection-diffusion-reaction (ADR) of multiple species into an extended version of Dissipative Particle Dynamics (DPD) method which is considered as a coarse-grained Molecular Dynamics method. At the continuum level this is equivalent to the Navier-Stokes equation plus one advection-diffusion equation for each specie. The chemistry of clot formation is now understood to be determined by mechanisms involving reactions among many species in dilute solution, where reaction rate constants and species diffusion coefficients in plasma are known. The role of blood particulates, i.e. red cells and platelets, in the clotting process is studied by including them separately and together in the simulations. An agonist-induced platelet activation mechanism is presented, while platelets adhesive dynamics based on a stochastic bond formation/dissociation process is included in the model.

Non-linear corrections to the time-covariance function derived from a multi-state chemical master equation.

PubMed

Scott, M

2012-08-01

The time-covariance function captures the dynamics of biochemical fluctuations and contains important information about the underlying kinetic rate parameters. Intrinsic fluctuations in biochemical reaction networks are typically modelled using a master equation formalism. In general, the equation cannot be solved exactly and approximation methods are required. For small fluctuations close to equilibrium, a linearisation of the dynamics provides a very good description of the relaxation of the time-covariance function. As the number of molecules in the system decrease, deviations from the linear theory appear. Carrying out a systematic perturbation expansion of the master equation to capture these effects results in formidable algebra; however, symbolic mathematics packages considerably expedite the computation. The authors demonstrate that non-linear effects can reveal features of the underlying dynamics, such as reaction stoichiometry, not available in linearised theory. Furthermore, in models that exhibit noise-induced oscillations, non-linear corrections result in a shift in the base frequency along with the appearance of a secondary harmonic.

Environmental-stress-induced Chromatin Regulation and its Heritability

PubMed Central

Fang, Lei; Wuptra, Kenly; Chen, Danqi; Li, Hongjie; Huang, Shau-Ku; Jin, Chunyuan; Yokoyama, Kazunari K

2014-01-01

Chromatin is subject to proofreading and repair mechanisms during the process of DNA replication, as well as repair to maintain genetic and epigenetic information and genome stability. The dynamic structure of chromatin modulates various nuclear processes, including transcription and replication, by altering the accessibility of the DNA to regulatory factors. Structural changes in chromatin are affected by the chemical modification of histone proteins and DNA, remodeling of nucleosomes, incorporation of variant histones, noncoding RNAs, and nonhistone DNA-binding proteins. Phenotypic diversity and fidelity can be balanced by controlling stochastic switching of chromatin structure and dynamics in response to the environmental disruptors and endogenous stresses. The dynamic chromatin remodeling can, therefore, serve as a sensor, through which environmental and/or metabolic agents can alter gene expression, leading to global cellular changes involving multiple interactive networks. Furthermore its recent evidence also suggests that the epigenetic changes are heritable during the development. This review will discuss the environmental sensing system for chromatin regulation and genetic and epigenetic controls from developmental perspectives. PMID:25045581

Dynamic response of phenolic resin and its carbon-nanotube composites to shock wave loading

DOE PAGES

Arman, B.; An, Q.; Luo, S. N.; ...

2011-01-04

We investigate with nonreactive molecular dynamics simulations the dynamic response of phenolic resin and its carbon-nanotube (CNT) composites to shock wave compression. For phenolic resin, our simulations yield shock states in agreement with experiments on similar polymers except the “phase change” observed in experiments, indicating that such phase change is chemical in nature. The elastic–plastic transition is characterized by shear stress relaxation and atomic-level slip, and phenolic resin shows strong strain hardening. Shock loading of the CNT-resin composites is applied parallel or perpendicular to the CNT axis, and the composites demonstrate anisotropy in wave propagation, yield and CNT deformation. Themore » CNTs induce stress concentrations in the composites and may increase the yield strength. Our simulations indicate that the bulk shock response of the composites depends on the volume fraction, length ratio, impact cross-section, and geometry of the CNT components; the short CNTs in current simulations have insignificant effect on the bulk response of resin polymer.« less

In situ imaging of the dynamics of photo-induced structural phase transition at high pressures by picosecond acoustic interferometry

NASA Astrophysics Data System (ADS)

Kuriakose, Maju; Chigarev, Nikolay; Raetz, Samuel; Bulou, Alain; Tournat, Vincent; Zerr, Andreas; Gusev, Vitalyi E.

2017-05-01

Picosecond acoustic interferometry is used to monitor in time the motion of the phase transition boundary between two water ice phases, VII and VI, coexisting at a pressure of 2.15 GPa when compressed in a diamond anvil cell at room temperature. By analyzing the time-domain Brillouin scattering signals accumulated for a single incidence direction of probe laser pulses, it is possible to access ratios of sound velocity values and of the refractive indices of the involved phases, and to distinguish between the structural phase transition and a recrystallization process. Two-dimensional spatial imaging of the phase transition dynamics indicates that it is initiated by the pump and probe laser pulses, preferentially at the diamond/ice interface. This method should find applications in three-dimensional monitoring with nanometer spatial resolution of the temporal dynamics of low-contrast material inhomogeneities caused by phase transitions or chemical reactions in optically transparent media.

Mixed Inhibition of Adenosine Deaminase Activity by 1,3-Dinitrobenzene: A Model for Understanding Cell-Selective Neurotoxicity in Chemically-Induced Energy Deprivation Syndromes in Brain

PubMed Central

Wang, Yipei; Liu, Xin; Schneider, Brandon; Zverina, Elaina A.; Russ, Kristen; Wijeyesakere, Sanjeeva J.; Fierke, Carol A.; Richardson, Rudy J.; Philbert, Martin A.

2012-01-01

Astrocytes are acutely sensitive to 1,3-dinitrobenzene (1,3-DNB) while adjacent neurons are relatively unaffected, consistent with other chemically-induced energy deprivation syndromes. Previous studies have investigated the role of astrocytes in protecting neurons from hypoxia and chemical injury via adenosine release. Adenosine is considered neuroprotective, but it is rapidly removed by extracellular deaminases such as adenosine deaminase (ADA). The present study tested the hypothesis that ADA is inhibited by 1,3-DNB as a substrate mimic, thereby preventing adenosine catabolism. ADA was inhibited by 1,3-DNB with an IC50 of 284μM, Hill slope, n = 4.8 ± 0.4. Native gel electrophoresis showed that 1,3-DNB did not denature ADA. Furthermore, adding Triton X-100 (0.01–0.05%, wt/vol), Nonidet P-40 (0.0015–0.0036%, wt/vol), or bovine serum albumin (0.05 mg/ml or changing [ADA] (0.2 and 2nM) did not substantially alter the 1,3-DNB IC50 value. Likewise, dynamic light scattering showed no particle formation over a (1,3-DNB) range of 149–1043μM. Kinetics revealed mixed inhibition with 1,3-DNB binding to ADA (KI = 520 ± 100μM, n = 1 ± 0.6) and the ADA-adenosine complex (KIS = 262 ± 7μM, n = 6 ± 0.6, indicating positive cooperativity). In accord with the kinetics, docking predicted binding of 1,3-DNB to the active site and three peripheral sites. In addition, exposure of DI TNC-1 astrocytes to 10–500μM 1,3-DNB produced concentration-dependent increases in extracellular adenosine at 24 h. Overall, the results demonstrate that 1,3-DNB is a mixed inhibitor of ADA and may thus lead to increases in extracellular adenosine. The finding may provide insights to guide future work on chemically-induced energy deprivation. PMID:22106038

Dynamic control and information processing in chemical reaction systems by tuning self-organization behavior

NASA Astrophysics Data System (ADS)

Lebiedz, Dirk; Brandt-Pollmann, Ulrich

2004-09-01

Specific external control of chemical reaction systems and both dynamic control and signal processing as central functions in biochemical reaction systems are important issues of modern nonlinear science. For example nonlinear input-output behavior and its regulation are crucial for the maintainance of the life process that requires extensive communication between cells and their environment. An important question is how the dynamical behavior of biochemical systems is controlled and how they process information transmitted by incoming signals. But also from a general point of view external forcing of complex chemical reaction processes is important in many application areas ranging from chemical engineering to biomedicine. In order to study such control issues numerically, here, we choose a well characterized chemical system, the CO oxidation on Pt(110), which is interesting per se as an externally forced chemical oscillator model. We show numerically that tuning of temporal self-organization by input signals in this simple nonlinear chemical reaction exhibiting oscillatory behavior can in principle be exploited for both specific external control of dynamical system behavior and processing of complex information.

Monte Carlo simulations of secondary electron emission due to ion beam milling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahady, Kyle; Tan, Shida; Greenzweig, Yuval

We present a Monte Carlo simulation study of secondary electron emission resulting from focused ion beam milling of a copper target. The basis of this study is a simulation code which simulates ion induced excitation and emission of secondary electrons, in addition to simulating focused ion beam sputtering and milling. This combination of features permits the simulation of the interaction between secondary electron emission, and the evolving target geometry as the ion beam sputters material. Previous ion induced SE Monte Carlo simulation methods have been restricted to predefined target geometries, while the dynamic target in the presented simulations makes thismore » study relevant to image formation in ion microscopy, and chemically assisted ion beam etching, where the relationship between sputtering, and its effects on secondary electron emission, is important. We focus on a copper target, and validate our simulation against experimental data for a range of: noble gas ions, ion energies, ion/substrate angles and the energy distribution of the secondary electrons. We then provide a detailed account of the emission of secondary electrons resulting from ion beam milling; we quantify both the evolution of the yield as high aspect ratio valleys are milled, as well as the emission of electrons within these valleys that do not escape the target, but which are important to the secondary electron contribution to chemically assisted ion induced etching.« less

Bifurcation and stability analysis of rotating chemical spirals in circular domains: Boundary-induced meandering and stabilization

NASA Astrophysics Data System (ADS)

Bär, Markus; Bangia, Anil K.; Kevrekidis, Ioannis G.

2003-05-01

Recent experimental and model studies have revealed that the domain size may strongly influence the dynamics of rotating spirals in two-dimensional pattern forming chemical reactions. Hartmann et al. [Phys. Rev. Lett. 76, 1384 (1996)], report a frequency increase of spirals in circular domains with diameters substantially smaller than the spiral wavelength in a large domain for the catalytic NO+CO reaction on a microstructured platinum surface. Accompanying simulations with a simple reaction-diffusion system reproduced the behavior. Here, we supplement these studies by a numerical bifurcation and stability analysis of rotating spirals in a simple activator-inhibitor model. The problem is solved in a corotating frame of reference. No-flux conditions are imposed at the boundary of the circular domain. At large domain sizes, eigenvalues and eigenvectors very close to those corresponding to infinite medium translational invariance are observed. Upon decrease of domain size, we observe a simultaneous change in the rotation frequency and a deviation of these eigenvalues from being neutrally stable (zero real part). The latter phenomenon indicates that the translation symmetry of the spiral solution is appreciably broken due to the interaction with the (now nearby) wall. Various dynamical regimes are found: first, the spiral simply tries to avoid the boundary and its tip moves towards the center of the circular domain corresponding to a negative real part of the “translational” eigenvalues. This effect is noticeable at a domain radius of R

Different routes to the glass transition: A comparison between chemical and physical vitrification

NASA Astrophysics Data System (ADS)

Caponi, Silvia; Corezzi, Silvia

2012-07-01

Despite the differences in the molecular processes involved in chemical and physical vitrification, surprising similarities are observed in the dynamics and in the thermodynamical properties of the resulting glasses. We report on a systematic study of reactive glass-formers undergoing a process of progressive polymerization of the constituent molecules via the formation of irreversible chemical bonds. The formation of most of the materials used in engineering plastics and the hardening of natural and synthetic resins, including epoxy resins, are based on chemical vitrification. The clear analogies characterizing the dynamic evolution of physical and chemical glass-formers, on the time scale of the structural and the low-frequency vibrational dynamics, are briefly reviewed.

75 FR 62845 - National Toxicology Program (NTP) Interagency Center for the Evaluation of Alternative...

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-13

... Eye Injuries and Chemically Induced Allergic Contact Dermatitis (ACD) AGENCY: National Institute of... Potential for Chemically Induced Allergic Contact Dermatitis,'' are planned for January 19 and 20, 2011... for Chemically Induced Allergic Contact Dermatitis'' will be held on January 20, 2011. Sessions for...

Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system

PubMed Central

Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

2016-01-01

The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion–fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies. PMID:26786848

Pulse-density modulation control of chemical oscillation far from equilibrium in a droplet open-reactor system.

PubMed

Sugiura, Haruka; Ito, Manami; Okuaki, Tomoya; Mori, Yoshihito; Kitahata, Hiroyuki; Takinoue, Masahiro

2016-01-20

The design, construction and control of artificial self-organized systems modelled on dynamical behaviours of living systems are important issues in biologically inspired engineering. Such systems are usually based on complex reaction dynamics far from equilibrium; therefore, the control of non-equilibrium conditions is required. Here we report a droplet open-reactor system, based on droplet fusion and fission, that achieves dynamical control over chemical fluxes into/out of the reactor for chemical reactions far from equilibrium. We mathematically reveal that the control mechanism is formulated as pulse-density modulation control of the fusion-fission timing. We produce the droplet open-reactor system using microfluidic technologies and then perform external control and autonomous feedback control over autocatalytic chemical oscillation reactions far from equilibrium. We believe that this system will be valuable for the dynamical control over self-organized phenomena far from equilibrium in chemical and biomedical studies.

Ab Initio Studies of Shock-Induced Chemical Reactions of Inter-Metallics

NASA Astrophysics Data System (ADS)

Zaharieva, Roussislava; Hanagud, Sathya

2009-06-01

Shock-induced and shock assisted chemical reactions of intermetallic mixtures are studied by many researchers, using both experimental and theoretical techniques. The theoretical studies are primarily at continuum scales. The model frameworks include mixture theories and meso-scale models of grains of porous mixtures. The reaction models vary from equilibrium thermodynamic model to several non-equilibrium thermodynamic models. The shock-effects are primarily studied using appropriate conservation equations and numerical techniques to integrate the equations. All these models require material constants from experiments and estimates of transition states. Thus, the objective of this paper is to present studies based on ab initio techniques. The ab inito studies, to date, use ab inito molecular dynamics. This paper presents a study that uses shock pressures, and associated temperatures as starting variables. Then intermetallic mixtures are modeled as slabs. The required shock stresses are created by straining the lattice. Then, ab initio binding energy calculations are used to examine the stability of the reactions. Binding energies are obtained for different strain components super imposed on uniform compression and finite temperatures. Then, vibrational frequencies and nudge elastic band techniques are used to study reactivity and transition states. Examples include Ni and Al.

The activation of fibroblast growth factors by heparin: synthesis, structure, and biological activity of heparin-like oligosaccharides.

PubMed

de Paz, J L; Angulo, J; Lassaletta, J M; Nieto, P M; Redondo-Horcajo, M; Lozano, R M; Giménez-Gallego, G; Martín-Lomas, M

2001-09-03

An effective strategy has been designed for the synthesis of oligosaccharides of different sizes structurally related to the regular region of heparin; this is illustrated by the preparation of hexasaccharide 1 and octasaccharide 2. This synthetic strategy provides the oligosaccharide sequence containing a D-glucosamine unit at the nonreducing end that is not available either by enzymatic or chemical degradation of heparin. It may permit, after slight modifications, the preparation of oligosaccharide fragments with different charge distribution as well. NMR spectroscopy and molecular dynamics simulations have shown that the overall structure of 1 in solution is a stable right-hand helix with four residues per turn. Hexasaccharide 1 and, most likely, octasaccharide 2 are, therefore, chemically well-defined structural models of naturally occurring heparin-like oligosaccharides for use in binding and biological activity studies. Both compounds 1 and 2 induce the mitogenic activity of acid fibroblast growth factor (FGF1), with the half-maximum activating concentration of 2 being equivalent to that of heparin. Sedimentation equilibrium analysis with compound 2 suggests that heparin-induced FGF1 dimerization is not an absolute requirement for biological activity.

Flow microcapillary plasma mass spectrometry-based investigation of new Al-Cr-Fe complex metallic alloy passivation.

PubMed

Ott, N; Beni, A; Ulrich, A; Ludwig, C; Schmutz, P

2014-03-01

Al-Cr-Fe complex metallic alloys are new intermetallic phases with low surface energy, low friction, and high corrosion resistance down to very low pH values (0-2). Flow microcapillary plasma mass spectrometry under potentiostatic control was used to characterize the dynamic aspect of passivation of an Al-Cr-Fe gamma phase in acidic electrolytes, allowing a better insight on the parameters inducing chemical stability at the oxyhydroxide-solution interface. In sulfuric acid pH 0, low element dissolution rates (in the µg cm(-2) range after 60 min) evidenced the passive state of the Al-Cr-Fe gamma phase with a preferential over-stoichiometric dissolution of Al and Fe cations. Longer air-aging was found to be beneficial for stabilizing the passive film. In chloride-containing electrolytes, ten times higher Al dissolution rates were detected at open-circuit potential (OCP), indicating that the spontaneously formed passive film becomes unstable. However, electrochemical polarization at low passive potentials induces electrical field generated oxide film modification, increasing chemical stability at the oxyhydroxide-solution interface. In the high potential passive region, localized attack is initiated with subsequent active metal dissolution. © 2013 Published by Elsevier B.V.

Phase-field modeling of chemical control of polarization stability and switching dynamics in ferroelectric thin films

DOE PAGES

Cao, Ye; Kalinin, Sergei V.

2016-12-15

Phase-field simulation (PFS) has revolutionized the understanding of domain structure and switching behavior in ferroelectric thin films and ceramics. Generally, PFS is based on the solution of (a set of) Landau-Ginzburg-Devonshire equations for a defined order parameter field(s) under physical boundary conditions (BCs) of fixed potential or charge. While well matched to the interfaces in bulk materials and devices, these BCs are generally not applicable to free ferroelectric surfaces. Here, we developed a self-consistent phase-field model with BCs based on electrochemical equilibria. We chose Pb(Zr 0.2Ti 0.8)O 3 ultrathin film consisting of (001) oriented single tetragonal domain ( Pz) asmore » a model system and systematically studied the effects of oxygen partial pressure, temperature, and surface ions on the ferroelectric state and compared it with the case of complete screening. We have further explored the polarization switching induced by the oxygen partial pressure and observed pronounced size effect induced by chemical screening. Finally, our paper thus helps to understand the emergent phenomena in ferroelectric thin films brought about by the electrochemical ionic surface compensations.« less

Phase-field modeling of chemical control of polarization stability and switching dynamics in ferroelectric thin films

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cao, Ye; Kalinin, Sergei V.

Phase-field simulation (PFS) has revolutionized the understanding of domain structure and switching behavior in ferroelectric thin films and ceramics. Generally, PFS is based on the solution of (a set of) Landau-Ginzburg-Devonshire equations for a defined order parameter field(s) under physical boundary conditions (BCs) of fixed potential or charge. While well matched to the interfaces in bulk materials and devices, these BCs are generally not applicable to free ferroelectric surfaces. Here, we developed a self-consistent phase-field model with BCs based on electrochemical equilibria. We chose Pb(Zr 0.2Ti 0.8)O 3 ultrathin film consisting of (001) oriented single tetragonal domain ( Pz) asmore » a model system and systematically studied the effects of oxygen partial pressure, temperature, and surface ions on the ferroelectric state and compared it with the case of complete screening. We have further explored the polarization switching induced by the oxygen partial pressure and observed pronounced size effect induced by chemical screening. Finally, our paper thus helps to understand the emergent phenomena in ferroelectric thin films brought about by the electrochemical ionic surface compensations.« less

Laser-induced multi-energy processing in diamond growth

NASA Astrophysics Data System (ADS)

Xie, Zhiqiang

Laser-induced multi-energy processing (MEP) introduces resonant vibrational excitations of precursor molecules to conventional chemical vapor deposition methods for material synthesis. In this study, efforts were extended to explore the capability of resonant vibrational excitations for promotion of energy efficiency in chemical reactions, for enhancement of diamond deposition, and for control of chemical reactions. The research project mainly focused on resonant vibrational excitations of precursor molecules using lasers in combustion flame deposition of diamond, which led to: 1) promotion of chemical reactions; 2) enhancement of diamond growth with higher growth rate and better crystallizations; 3) steering of chemical reactions which lead to preferential growth of {100}-oriented diamond films and crystals; and 4) mode-selective excitations of precursor molecules toward bond-selective control of chemical reactions. Diamond films and crystals were deposited in open air by combustion flame deposition through resonant vibrational excitations of precursor molecules, including ethylene (C2H4) and propylene (C3H 6). A kilowatt wavelength-tunable CO2 laser with spectral range from 9.2 to 10.9 microm was tuned to match vibrational modes of the precursor molecules. Resonant vibrational excitations of these molecules were achieved with high energy efficiency as compared with excitations using a common CO2 laser (fixed wavelength at 10.591microm). With resonant vibrational excitations, the diamond growth rate was increased; diamond quality was promoted; diamond crystals with lengths up to 5 mm were deposited in open air; preferential growth of {100}-oriented diamond films and single crystals was achieved; mode-selective excitations of precursor molecules were investigated toward control of chemical reactions. Optical emission spectroscopy (OES), mass spectrometry (MS), and molecular dynamic simulations were conducted to obtain an in-depth understanding of the resonant vibrational excitations. Species concentrations in flames without and with laser excitations under different wavelengths were investigated both experimentally and theoretically. Detection of C2, CH, and OH radicals, as well as CxHy species and their oxides (CxH yO) (x=1, 2; y=0˜5) using OES and MS, together with reaction pathway simulations, were used to explain the effect of vibrational excitations of precursor molecules on chemical reactions and on diamond depositions.

Leaching behavior and chemical stability of copper butyl xanthate complex under acidic conditions.

PubMed

Chang, Yi Kuo; Chang, Juu En; Chiang, Li Choung

2003-08-01

Although xanthate addition can be used for treating copper-containing wastewater, a better understanding of the leaching toxicity and the stability characteristics of the copper xanthate complexes formed is essential. This work was undertaken to evaluate the leaching behavior of copper xanthate complex precipitates by means of toxicity characteristics leaching procedure (TCLP) and semi-dynamic leaching test (SDLT) using 1 N acetic acid solution as the leachant. Also, the chemical stability of the copper xanthate complex during extraction has been examined with the studying of variation of chemical structure using UV-vis, Fourier transform infrared and X-ray photoelectron spectroscopies (XPS). Both TCLP and SDLT results showed that a negligible amount of copper ion was leached out from the copper xanthate complex precipitate, indicating that the complex exhibited a high degree of copper leaching stability under acidic conditions. Nevertheless, chemical structure of the copper xanthate complex precipitate varied during the leaching tests. XPS data suggested that the copper xanthate complex initially contained both cupric and cuprous xanthate, but the unstable cupric xanthate change to the cuprous form after acid extraction, indicating the cuprous xanthate to be the final stabilizing structure. Despite that, the changes of chemical structure did not induce the rapid leaching of copper from the copper xanthate complex.

Glutamate Induced Thermal Equilibrium Intermediate and Counteracting Effect on Chemical Denaturation of Proteins.

PubMed

Anumalla, Bramhini; Prabhu, N Prakash

2018-01-25

When organisms are subjected to stress conditions, one of their adaptive responses is accumulation of small organic molecules called osmolytes. These osmolytes affect the structure and stability of the biological macromolecules including proteins. The present study examines the effect of a negatively charged amino acid osmolyte, glutamate (Glu), on two model proteins, ribonuclease A (RNase A) and α-lactalbumin (α-LA), which have positive and negative surface charges at pH 7, respectively. These proteins follow two-state unfolding transitions during both heat and chemical induced denaturation processes. The addition of Glu stabilizes the proteins against temperature and induces an early equilibrium intermediate during unfolding. The stability is found to be enthalpy-driven, and the free energy of stabilization is more for α-LA compared to RNase A. The decrease in the partial molar volume and compressibility of both of the proteins in the presence of Glu suggests that the proteins attain a more compact state through surface hydration which could provide a more stable conformation. This is also supported by molecule dynamic simulation studies which demonstrate that the water density around the proteins is increased upon the addition of Glu. Further, the intermediates could be completely destabilized by lower concentrations (∼0.5 M) of guanidinium chloride and salt. However, urea subverts the Glu-induced intermediate formed by α-LA, whereas it only slightly destabilizes in the case of RNase A which has a positive surface charge and could possess charge-charge interactions with Glu. This suggests that, apart from hydration, columbic interactions might also contribute to the stability of the intermediate. Gdm-induced denaturation of RNase A and α-LA in the absence and the presence of Glu at different temperatures was carried out. These results also show the Glu-induced stabilization of both of the proteins; however, all of the unfolding transitions followed two-state transitions during chemical denaturation. The extent of stability exerted by Glu is higher for RNase A at higher temperature, whereas it provides more stability for α-LA at lower temperature. Thus, the experiments indicate that Glu induces a thermal equilibrium intermediate and increases the thermodynamic stability of proteins irrespective of their surface charges. The extent of stability varies between the proteins in a temperature-dependent manner.

Menadione Suppresses Benzo(α)pyrene-Induced Activation of Cytochromes P450 1A: Insights into a Possible Molecular Mechanism.

PubMed

Sidorova, Yulia A; Perepechaeva, Maria L; Pivovarova, Elena N; Markel, Arkady L; Lyakhovich, Vyacheslav V; Grishanova, Alevtina Y

2016-01-01

Oxidative reactions that are catalyzed by cytochromes P450 1A (CYP1A) lead to formation of carcinogenic derivatives of arylamines and polycyclic aromatic hydrocarbons (PAHs), such as the widespread environmental pollutant benzo(α)pyrene (BP). These compounds upregulate CYP1A at the transcriptional level via an arylhydrocarbon receptor (AhR)-dependent signaling pathway. Because of the involvement of AhR-dependent genes in chemically induced carcinogenesis, suppression of this signaling pathway could prevent tumor formation and/or progression. Here we show that menadione (a water-soluble analog of vitamin K3) inhibits BP-induced expression and enzymatic activity of both CYP1A1 and CYP1A2 in vivo (in the rat liver) and BP-induced activity of CYP1A1 in vitro. Coadministration of BP and menadione reduced DNA-binding activity of AhR and increased DNA-binding activity of transcription factors Oct-1 and CCAAT/enhancer binding protein (C/EBP), which are known to be involved in negative regulation of AhR-dependent genes, in vivo. Expression of another factor involved in downregulation of CYP1A-pAhR repressor (AhRR)-was lower in the liver of the rats treated with BP and menadione, indicating that the inhibitory effect of menadione on CYP1A is not mediated by this protein. Furthermore, menadione was well tolerated by the animals: no signs of acute toxicity were detected by visual examination or by assessment of weight gain dynamics or liver function. Taken together, our results suggest that menadione can be used in further studies on animal models of chemically induced carcinogenesis because menadione may suppress tumor formation and possibly progression.

Menadione Suppresses Benzo(α)pyrene-Induced Activation of Cytochromes P450 1A: Insights into a Possible Molecular Mechanism

PubMed Central

Pivovarova, Elena N.; Markel, Arkady L.; Lyakhovich, Vyacheslav V.; Grishanova, Alevtina Y.

2016-01-01

Oxidative reactions that are catalyzed by cytochromes P450 1A (CYP1A) lead to formation of carcinogenic derivatives of arylamines and polycyclic aromatic hydrocarbons (PAHs), such as the widespread environmental pollutant benzo(α)pyrene (BP). These compounds upregulate CYP1A at the transcriptional level via an arylhydrocarbon receptor (AhR)-dependent signaling pathway. Because of the involvement of AhR-dependent genes in chemically induced carcinogenesis, suppression of this signaling pathway could prevent tumor formation and/or progression. Here we show that menadione (a water-soluble analog of vitamin K3) inhibits BP-induced expression and enzymatic activity of both CYP1A1 and CYP1A2 in vivo (in the rat liver) and BP-induced activity of CYP1A1 in vitro. Coadministration of BP and menadione reduced DNA-binding activity of AhR and increased DNA-binding activity of transcription factors Oct-1 and CCAAT/enhancer binding protein (C/EBP), which are known to be involved in negative regulation of AhR-dependent genes, in vivo. Expression of another factor involved in downregulation of CYP1A—pAhR repressor (AhRR)—was lower in the liver of the rats treated with BP and menadione, indicating that the inhibitory effect of menadione on CYP1A is not mediated by this protein. Furthermore, menadione was well tolerated by the animals: no signs of acute toxicity were detected by visual examination or by assessment of weight gain dynamics or liver function. Taken together, our results suggest that menadione can be used in further studies on animal models of chemically induced carcinogenesis because menadione may suppress tumor formation and possibly progression. PMID:27167070

Matrix-isolation studies on the radiation-induced chemistry in H₂O/CO₂ systems: reactions of oxygen atoms and formation of HOCO radical.

PubMed

Ryazantsev, Sergey V; Feldman, Vladimir I

2015-03-19

The radiation-induced transformations occurring upon X-ray irradiation of solid CO2/H2O/Ng systems (Ng = Ar, Kr, Xe) at 8-10 K and subsequent annealing up to 45 K were studied by Fourier transform infrared spectroscopy. The infrared (IR) spectra of deposited matrices revealed the presence of isolated monomers, dimers, and intermolecular H2O···CO2 complexes. Irradiation resulted in effective decomposition of matrix-isolated carbon dioxide and water yielding CO molecules and OH radicals, respectively. Annealing of the irradiated samples led to formation of O3, HO2, and a number of xenon hydrides of HXeY type (in the case of xenon matrices). The formation of these species was used for monitoring of the postirradiation thermally induced chemical reactions involving O and H atoms generated by radiolysis. It was shown that the radiolysis of CO2 in noble-gas matrices produced high yields of stabilized oxygen atoms. In all cases, the temperatures at which O atoms become mobile and react are lower than those of H atoms. Dynamics and reactivity of oxygen atoms was found to be independent of the precursor nature. In addition, the formation of HOCO radicals was observed in all the noble-gas matrices at remarkably low temperatures. The IR spectra of HOCO and DOCO were first characterized in krypton and xenon matrices. It was concluded that the formation of HOCO was mainly due to the radiation-induced evolution of the weakly bound H2O···CO2 complexes. This result indicates the significance of weak intermolecular interactions in the radiation-induced chemical processes in inert low-temperature media.

Learning from Chemical Visualizations: Comparing Generation and Selection

ERIC Educational Resources Information Center

Zhang, Zhihui Helen; Linn, Marcia C.

2013-01-01

Dynamic visualizations can make unseen phenomena such as chemical reactions visible but students need guidance to benefit from them. This study explores the value of generating drawings versus selecting among alternatives to guide students to learn chemical reactions from a dynamic visualization of hydrogen combustion as part of an online inquiry…

Polychlorinated Biphenyls in a Temperate Alpine Glacier: 2. Model Results of Chemical Fate Processes.

PubMed

Steinlin, Christine; Bogdal, Christian; Pavlova, Pavlina A; Schwikowski, Margit; Lüthi, Martin P; Scheringer, Martin; Schmid, Peter; Hungerbühler, Konrad

2015-12-15

We present results from a chemical fate model quantifying incorporation of polychlorinated biphenyls (PCBs) into the Silvretta glacier, a temperate Alpine glacier located in Switzerland. Temperate glaciers, in contrast to cold glaciers, are glaciers where melt processes are prevalent. Incorporation of PCBs into cold glaciers has been quantified in previous studies. However, the fate of PCBs in temperate glaciers has never been investigated. In the model, we include melt processes, inducing elution of water-soluble substances and, conversely, enrichment of particles and particle-bound chemicals. The model is validated by comparing modeled and measured PCB concentrations in an ice core collected in the Silvretta accumulation area. We quantify PCB incorporation between 1900 and 2010, and discuss the fate of six PCB congeners. PCB concentrations in the ice core peak in the period of high PCB emissions, as well as in years with strong melt. While for lower-chlorinated PCB congeners revolatilization is important, for higher-chlorinated congeners, the main processes are storage in glacier ice and removal by particle runoff. This study gives insight into PCB fate and dynamics and reveals the effect of snow accumulation and melt processes on the fate of semivolatile organic chemicals in a temperate Alpine glacier.

Graphene production by laser shot on graphene oxide: An ab initio prediction

NASA Astrophysics Data System (ADS)

Zhang, Hong; Miyamoto, Yoshiyuki

2012-01-01

By performing the first-principles simulation of electron-ion dynamics based on the time-dependent density-functional theory, we propose a way to produce graphene from graphene oxides by means of the laser-induced reduction without using chemical species. Epoxy and hydroxyl groups on graphene sheets can be completely removed upon irradiation with femtosecond laser without damaging the graphene sheet. By comparing the simulated results with different pulse shapes and intensities, optimum conditions of the femtosecond laser for reduction of graphene oxide were determined. The current works will be useful for further experimental researches.

Genetically encoded sensors and fluorescence microscopy for anticancer research

NASA Astrophysics Data System (ADS)

Zagaynova, Elena V.; Shirmanova, Marina V.; Sergeeva, Tatiana F.; Klementieva, Natalia V.; Mishin, Alexander S.; Gavrina, Alena I.; Zlobovskay, Olga A.; Furman, Olga E.; Dudenkova, Varvara V.; Perelman, Gregory S.; Lukina, Maria M.; Lukyanov, Konstantin A.

2017-02-01

Early response of cancer cells to chemical compounds and chemotherapeutic drugs were studied using novel fluorescence tools and microscopy techniques. We applied confocal microscopy, two-photon fluorescence lifetime imaging microscopy and super-resolution localization-based microscopy to assess structural and functional changes in cancer cells in vitro. The dynamics of energy metabolism, intracellular pH, caspase-3 activation during staurosporine-induced apoptosis as well as actin cytoskeleton rearrangements under chemotherapy were evaluated. We have showed that new genetically encoded sensors and advanced fluorescence microscopy methods provide an efficient way for multiparameter analysis of cell activities

Nitric oxide, PKC-ε, and connexin43 are crucial for ischemic preconditioning-induced chemical gap junction uncoupling.

PubMed

Rong, Bing; Xie, Fei; Sun, Tao; Hao, Li; Lin, Ming-Jie; Zhong, Jing-Quan

2016-10-25

Ischemic preconditioning (IPC) maintains connexin43 (Cx43) phosphorylation and reduces chemical gap junction (GJ) coupling in cardiomyocytes to protect against ischemic damage. However, the signal transduction pathways underlying these effects are not fully understood. Here, we investigated whether nitric oxide (NO) and protein kinase C-ε (PKC-ε) contribute to IPC-induced cardioprotection by maintaining Cx43 phosphorylation and inhibiting chemical GJ coupling. IPC reduced ischemia-induced myocardial infarction and increased cardiomyocyte survival; phosphorylated Cx43, eNOS, and PKC-ε levels; and chemical GJ uncoupling. Administration of the NO donor SNAP mimicked the effects of IPC both in vivo and in vitro, maintaining Cx43 phosphorylation, promoting chemical GJ uncoupling, and reducing myocardial infarction. Preincubation with the NO synthase inhibitor L-NAME or PKC-ε translocation inhibitory peptide (PKC-ε-TIP) abolished these effects of IPC. Additionally, by inducing NO production, IPC induced translocation of PKC-ε, but not PKC-δ, from the cytosolic to the membrane fraction in primary cardiac myocytes. IPC-induced cardioprotection thus involves increased NO production, PKC-ε translocation, Cx43 phosphorylation, and chemical GJ uncoupling.

Study of the effect of gamma irradiation on a commercial polycyclooctene I. Thermal and mechanical properties

NASA Astrophysics Data System (ADS)

García-Huete, N.; Laza, J. M.; Cuevas, J. M.; Vilas, J. L.; Bilbao, E.; León, L. M.

2014-09-01

A gamma radiation process for modification of commercial polymers is a widely applied technique to promote new physical, chemical and mechanical properties. Gamma irradiation originates free radicals able to induce chain scission or recombination of radicals, which induces annihilation, branching or crosslinking processes. The aim of this work is to research the structural, thermal and mechanical changes induced on a commercial polycyclooctene (PCO) when it is irradiated with a gamma source of 60Co at different doses (25-200 kGy). After gamma irradiation, gel content was determined by Soxhlet extraction in cyclohexane. Furthermore, thermal properties were evaluated before and after Soxhlet extraction by means of Thermogravimetric Analysis (TGA) and Differential Scanning Calorimetry (DSC), as well as mechanical properties were measured by Dynamic Mechanical Thermal Analysis (DMTA). The results showed the variations of the properties depending on the irradiation dose. Finally, a first approach to evaluate qualitatively the shape memory behaviour of all irradiated PCO samples was performed by a visually monitoring shape recovery process.

Connecting G protein signaling to chemoattractant-mediated cell polarity and cytoskeletal reorganization.

PubMed

Liu, Youtao; Lacal, Jesus; Firtel, Richard A; Kortholt, Arjan

2018-07-04

The directional movement toward extracellular chemical gradients, a process called chemotaxis, is an important property of cells. Central to eukaryotic chemotaxis is the molecular mechanism by which chemoattractant-mediated activation of G-protein coupled receptors (GPCRs) induces symmetry breaking in the activated downstream signaling pathways. Studies with mainly Dictyostelium and mammalian neutrophils as experimental systems have shown that chemotaxis is mediated by a complex network of signaling pathways. Recently, several labs have used extensive and efficient proteomic approaches to further unravel this dynamic signaling network. Together these studies showed the critical role of the interplay between heterotrimeric G-protein subunits and monomeric G proteins in regulating cytoskeletal rearrangements during chemotaxis. Here we highlight how these proteomic studies have provided greater insight into the mechanisms by which the heterotrimeric G protein cycle is regulated, how heterotrimeric G proteins-induced symmetry breaking is mediated through small G protein signaling, and how symmetry breaking in G protein signaling subsequently induces cytoskeleton rearrangements and cell migration.

Nuclear spin circular dichroism.

PubMed

Vaara, Juha; Rizzo, Antonio; Kauczor, Joanna; Norman, Patrick; Coriani, Sonia

2014-04-07

Recent years have witnessed a growing interest in magneto-optic spectroscopy techniques that use nuclear magnetization as the source of the magnetic field. Here we present a formulation of magnetic circular dichroism (CD) due to magnetically polarized nuclei, nuclear spin-induced CD (NSCD), in molecules. The NSCD ellipticity and nuclear spin-induced optical rotation (NSOR) angle correspond to the real and imaginary parts, respectively, of (complex) quadratic response functions involving the dynamic second-order interaction of the electron system with the linearly polarized light beam, as well as the static magnetic hyperfine interaction. Using the complex polarization propagator framework, NSCD and NSOR signals are obtained at frequencies in the vicinity of optical excitations. Hartree-Fock and density-functional theory calculations on relatively small model systems, ethene, benzene, and 1,4-benzoquinone, demonstrate the feasibility of the method for obtaining relatively strong nuclear spin-induced ellipticity and optical rotation signals. Comparison of the proton and carbon-13 signals of ethanol reveals that these resonant phenomena facilitate chemical resolution between non-equivalent nuclei in magneto-optic spectra.

Exploration of metastability and hidden phases in correlated electron crystals visualized by femtosecond optical doping and electron crystallography

PubMed Central

Han, Tzong-Ru T.; Zhou, Faran; Malliakas, Christos D.; Duxbury, Phillip M.; Mahanti, Subhendra D.; Kanatzidis, Mercouri G.; Ruan, Chong-Yu

2015-01-01

Characterizing and understanding the emergence of multiple macroscopically ordered electronic phases through subtle tuning of temperature, pressure, and chemical doping has been a long-standing central issue for complex materials research. We report the first comprehensive studies of optical doping–induced emergence of stable phases and metastable hidden phases visualized in situ by femtosecond electron crystallography. The electronic phase transitions are triggered by femtosecond infrared pulses, and a temperature–optical density phase diagram is constructed and substantiated with the dynamics of metastable states, highlighting the cooperation and competition through which the macroscopic quantum orders emerge. These results elucidate key pathways of femtosecond electronic switching phenomena and provide an important new avenue to comprehensively investigate optical doping–induced transition states and phase diagrams of complex materials with wide-ranging applications. PMID:26601190

Matter-antimatter asymmetry induced by a running vacuum coupling

NASA Astrophysics Data System (ADS)

Lima, J. A. S.; Singleton, D.

2017-12-01

We show that a CP-violating interaction induced by a derivative coupling between the running vacuum and a non-conserving baryon current may dynamically break CPT and trigger baryogenesis through an effective chemical potential. By assuming a non-singular class of running vacuum cosmologies which provides a complete cosmic history (from an early inflationary de Sitter stage to the present day quasi-de Sitter acceleration), it is found that an acceptable baryon asymmetry is generated for many different choices of the model parameters. It is interesting that the same ingredient (running vacuum energy density) addresses several open cosmological questions/problems: avoids the initial singularity, provides a smooth exit for primordial inflation, alleviates both the coincidence and the cosmological constant problems, and, finally, is also capable of explaining the generation of matter-antimatter asymmetry in the very early Universe.

Chemical imaging of molecular changes in a hydrated single cell by dynamic secondary ion mass spectrometry and super-resolution microscopy

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hua, Xin; Szymanski, Craig; Wang, Zhaoying

2016-01-01

Chemical imaging of single cells is important in capturing biological dynamics. Single cell correlative imaging is realized between structured illumination microscopy (SIM) and time-of-flight secondary ion mass spectrometry (ToF-SIMS) using System for Analysis at the Liquid Vacuum Interface (SALVI), a multimodal microreactor. SIM characterized cells and guided subsequent ToF-SIMS analysis. Dynamic ToF-SIMS provided time- and space-resolved cell molecular mapping. Lipid fragments were identified in the hydrated cell membrane. Principal component analysis was used to elucidate chemical component differences among mouse lung cells that uptake zinc oxide nanoparticles. Our results provided submicron chemical spatial mapping for investigations of cell dynamics atmore » the molecular level.« less

Probing Seismically Melting Induced Mantle Heterogeneities in Thermal-chemical Convection Models

NASA Astrophysics Data System (ADS)

Heck, H. V.; Davies, H.; Nowacki, A.; Wookey, J. M.

2015-12-01

Two regions at the base of the Earth's mantle (the Large Low-Shear Velocity Provinces) pose a fundamental problem in understanding large-scale mantle dynamics and history. Are they dense piles of (possibly primordial) material separated from mantle circulation, or large-scale thermal features which are part of global mantle convection? Or some combination of the two? We use our numerical 3D spherical mantle convection code to perform simulations of the Earths mantle dynamical evolution. We drive the surface velocity of the model according to 200 Ma plate motion reconstructions, to arrive at Earth-like structures in the mantle at present day. Variations in bulk chemistry will be tracked in two ways: 1) by starting the calculations with a (primordial) dense layer at the base of the mantle, and 2) by tracking basalt fraction which is fractionated upon melting close to the surface. The resulting distribution of chemical heterogeneity and temperature will be converted to seismic velocities. This will be done with a thermodynamical database (Stixrude & Lithgow-Bertelloni, GJI, 2005, 2011), allowing us to compare the model with previous observations of triplications and waveform complexity near the margins of the LLSVPs. These observations have been taken as proof that strong chemical variations are present; our simulations can be used to show whether this is true, or if purely thermal convection can also cause these features. We simulate finite-frequency, 3D seismograms at ~5 s period and compare these with previous studies.

Chemistry in motion: tiny synthetic motors.

PubMed

Colberg, Peter H; Reigh, Shang Yik; Robertson, Bryan; Kapral, Raymond

2014-12-16

CONSPECTUS: Diffusion is the principal transport mechanism that controls the motion of solute molecules and other species in solution; however, the random walk process that underlies diffusion is slow and often nonspecific. Although diffusion is an essential mechanism for transport in the biological realm, biological systems have devised more efficient transport mechanisms using molecular motors. Most biological motors utilize some form of chemical energy derived from their surroundings to induce conformational changes in order to carry out specific functions. These small molecular motors operate in the presence of strong thermal fluctuations and in the regime of low Reynolds numbers, where viscous forces dominate inertial forces. Thus, their dynamical behavior is fundamentally different from that of macroscopic motors, and different mechanisms are responsible for the production of useful mechanical motion. There is no reason why our interest should be confined to the small motors that occur naturally in biological systems. Recently, micron and nanoscale motors that use chemical energy to produce directed motion by a number of different mechanisms have been made in the laboratory. These small synthetic motors also experience strong thermal fluctuations and operate in regimes where viscous forces dominate. Potentially, these motors could be directed to perform different transport tasks, analogous to those of biological motors, for both in vivo and in vitro applications. Although some synthetic motors execute conformational changes to effect motion, the majority do not, and, instead, they use other mechanisms to convert chemical energy into directed motion. In this Account, we describe how synthetic motors that operate by self-diffusiophoresis make use of a self-generated concentration gradient to drive motor motion. A description of propulsion by self-diffusiophoresis is presented for Janus particle motors comprising catalytic and noncatalytic faces. The properties of the dynamics of chemically powered motors are illustrated by presenting the results of particle-based simulations of sphere-dimer motors constructed from linked catalytic and noncatalytic spheres. The geometries of both Janus and sphere-dimer motors with asymmetric catalytic activity support the formation of concentration gradients around the motors. Because directed motion can occur only when the system is not in equilibrium, the nature of the environment and the role it plays in motor dynamics are described. Rotational Brownian motion also acts to limit directed motion, and it has especially strong effects for very small motors. We address the following question: how small can motors be and still exhibit effects due to propulsion, even if only to enhance diffusion? Synthetic motors have the potential to transform the manner in which chemical dynamical processes are carried out for a wide range of applications.

Evolution of stalk/spore ratio in a social amoeba: cell-to-cell interaction via a signaling chemical shaped by cheating risk.

PubMed

Uchinomiya, Kouki; Iwasa, Yoh

2013-11-07

The social amoeba (or cellular slime mold) is a model system for cell cooperation. When food is depleted in the environment, cells aggregate together. Some of these cells become stalks, raising spores to aid in their dispersal. Differentiation-inducing factor-1 (DIF-1) is a signaling chemical produced by prespore cells and decomposed by prestalk cells. It affects the rate of switching between prestalk and prespore cells, thereby achieving a stable stalk/spore ratio. In this study we analyzed the evolution of the stalk/spore ratio. Strains may differ in the production and decomposition rates of the signaling chemical, and in the sensitivity of cells to switch in response to the signaling chemical exposure. When two strains with the same stalk/spore ratio within their own fruiting body are combined into a single fruiting body, one strain may develop into prespores to a greater degree than the other. Direct evolutionary simulations and quantitative genetic dynamics demonstrate that if a fruiting body is always formed by a single strain, the cells evolve to produce less signaling chemical and become more sensitive to the signaling chemical due to the cost of producing the chemical. In contrast, if a fruiting body is formed by multiple strains, the cells evolve to become less sensitive to the signaling chemical and produce more signaling chemical in order to reduce the risk of being exploited. In contrast, the stalk-spore ratio is less likely to be affected by small cheating risk. Copyright © 2013 Elsevier Ltd. All rights reserved.

A review on chemical-induced inflammatory bowel disease models in rodents.

PubMed

Randhawa, Puneet Kaur; Singh, Kavinder; Singh, Nirmal; Jaggi, Amteshwar Singh

2014-08-01

Ulcerative colitis and Crohn's disease are a set of chronic, idiopathic, immunological and relapsing inflammatory disorders of the gastrointestinal tract referred to as inflammatory bowel disorder (IBD). Although the etiological factors involved in the perpetuation of IBD remain uncertain, development of various animal models provides new insights to unveil the onset and the progression of IBD. Various chemical-induced colitis models are widely used on laboratory scale. Furthermore, these models closely mimic morphological, histopathological and symptomatical features of human IBD. Among the chemical-induced colitis models, trinitrobenzene sulfonic acid (TNBS)-induced colitis, oxazolone induced-colitis and dextran sulphate sodium (DSS)-induced colitis models are most widely used. TNBS elicits Th-1 driven immune response, whereas oxazolone predominantly exhibits immune response of Th-2 phenotype. DSS-induced colitis model also induces changes in Th-1/Th-2 cytokine profile. The present review discusses the methodology and rationale of using various chemical-induced colitis models for evaluating the pathogenesis of IBD.

Framing the nano-biointeractions by proteomics

NASA Astrophysics Data System (ADS)

Sabella, S.; Maiorano, G.; Rizzello, L.; Kote, S.; Cingolani, R.; Pompa, P. P.

2012-03-01

Knowledge of the molecular mechanisms underlying the interactions between nanomaterials and living systems is fundamental for providing more effective products for nanomedicine and drug delivery. Controlling the response of cells/bacteria (such as activation of inflammatory processes or apoptosis/necrosis in tumor cells or pathogenic bacteria) by tuning specific properties of the nanomaterials is ultimately the challenging goal. Notably, this may also provide crucial information in the assessment of any toxic risks induced by nanoparticles on humans. However, in studying the nano-biointeractions, it is imperative to take into account the dynamic evolutions of nanoparticles in the biological environments (in terms of protein corona formation, size and charge changes) in synergy with the dynamic events occurring in cells, including signal transduction, metabolic processes, homeostasis and membrane trafficking. In this context, we discuss the impact of analytical technologies, especially in the field of proteomics, which can provide major insights into the processes affecting the NPs surface as well as the cells and bacteria functionalities. In particular, we show that a precise control of the chemical-physical characteristics of the interacting nanoparticles or nanostructures may impact the cells by inducing changes in the proteomic profiles with direct consequences on their viability.

Effect of heavy atoms on photochemically induced dynamic nuclear polarization in liquids

NASA Astrophysics Data System (ADS)

Okuno, Yusuke; Cavagnero, Silvia

2018-01-01

Given its short hyperpolarization time (∼10-6 s) and mostly non-perturbative nature, photo-chemically induced dynamic nuclear polarization (photo-CIDNP) is a powerful tool for sensitivity enhancement in nuclear magnetic resonance. In this study, we explore the extent of 1H-detected 13C nuclear hyperpolarization that can be gained via photo-CIDNP in the presence of small-molecule additives containing a heavy atom. The underlying rationale for this methodology is the well-known external-heavy-atom (EHA) effect, which leads to significant enhancements in the intersystem-crossing rate of selected photosensitizer dyes from photoexcited singlet to triplet. We exploited the EHA effect upon addition of moderate amounts of halogen-atom-containing cosolutes. The resulting increase in the transient triplet-state population of the photo-CIDNP sensitizer fluorescein resulted in a significant increase in the nuclear hyperpolarization achievable via photo-CIDNP in liquids. We also explored the internal-heavy-atom (IHA) effect, which is mediated by halogen atoms covalently incorporated into the photosensitizer dye. Widely different outcomes were achieved in the case of EHA and IHA, with EHA being largely preferable in terms of net hyperpolarization.

A Sense of Balance: Experimental Investigation and Modeling of a Malonyl-CoA Sensor in Escherichia coli.

PubMed

Fehér, Tamás; Libis, Vincent; Carbonell, Pablo; Faulon, Jean-Loup

2015-01-01

Production of value-added chemicals in microorganisms is regarded as a viable alternative to chemical synthesis. In the past decade, several engineered pathways producing such chemicals, including plant secondary metabolites in microorganisms have been reported; upscaling their production yields, however, was often challenging. Here, we analyze a modular device designed for sensing malonyl-CoA, a common precursor for both fatty acid and flavonoid biosynthesis. The sensor can be used either for high-throughput pathway screening in synthetic biology applications or for introducing a feedback circuit to regulate production of the desired chemical. Here, we used the sensor to compare the performance of several predicted malonyl-CoA-producing pathways, and validated the utility of malonyl-CoA reductase and malonate-CoA transferase for malonyl-CoA biosynthesis. We generated a second-order dynamic linear model describing the relation of the fluorescence generated by the sensor to the biomass of the host cell representing a filter/amplifier with a gain that correlates with the level of induction. We found the time constants describing filter dynamics to be independent of the level of induction but distinctively clustered for each of the production pathways, indicating the robustness of the sensor. Moreover, by monitoring the effect of the copy-number of the production plasmid on the dose-response curve of the sensor, we managed to coarse-tune the level of pathway expression to maximize malonyl-CoA synthesis. In addition, we provide an example of the sensor's use in analyzing the effect of inducer or substrate concentrations on production levels. The rational development of models describing sensors, supplemented with the power of high-throughput optimization provide a promising potential for engineering feedback loops regulating enzyme levels to maximize productivity yields of synthetic metabolic pathways.

CD-REST: a system for extracting chemical-induced disease relation in literature.

PubMed

Xu, Jun; Wu, Yonghui; Zhang, Yaoyun; Wang, Jingqi; Lee, Hee-Jin; Xu, Hua

2016-01-01

Mining chemical-induced disease relations embedded in the vast biomedical literature could facilitate a wide range of computational biomedical applications, such as pharmacovigilance. The BioCreative V organized a Chemical Disease Relation (CDR) Track regarding chemical-induced disease relation extraction from biomedical literature in 2015. We participated in all subtasks of this challenge. In this article, we present our participation system Chemical Disease Relation Extraction SysTem (CD-REST), an end-to-end system for extracting chemical-induced disease relations in biomedical literature. CD-REST consists of two main components: (1) a chemical and disease named entity recognition and normalization module, which employs the Conditional Random Fields algorithm for entity recognition and a Vector Space Model-based approach for normalization; and (2) a relation extraction module that classifies both sentence-level and document-level candidate drug-disease pairs by support vector machines. Our system achieved the best performance on the chemical-induced disease relation extraction subtask in the BioCreative V CDR Track, demonstrating the effectiveness of our proposed machine learning-based approaches for automatic extraction of chemical-induced disease relations in biomedical literature. The CD-REST system provides web services using HTTP POST request. The web services can be accessed fromhttp://clinicalnlptool.com/cdr The online CD-REST demonstration system is available athttp://clinicalnlptool.com/cdr/cdr.html. Database URL:http://clinicalnlptool.com/cdr;http://clinicalnlptool.com/cdr/cdr.html. © The Author(s) 2016. Published by Oxford University Press.

Nanomanufacturing of silicon surface with a single atomic layer precision via mechanochemical reactions.

PubMed

Chen, Lei; Wen, Jialin; Zhang, Peng; Yu, Bingjun; Chen, Cheng; Ma, Tianbao; Lu, Xinchun; Kim, Seong H; Qian, Linmao

2018-04-18

Topographic nanomanufacturing with a depth precision down to atomic dimension is of importance for advancement of nanoelectronics with new functionalities. Here we demonstrate a mask-less and chemical-free nanolithography process for regio-specific removal of atomic layers on a single crystalline silicon surface via shear-induced mechanochemical reactions. Since chemical reactions involve only the topmost atomic layer exposed at the interface, the removal of a single atomic layer is possible and the crystalline lattice beneath the processed area remains intact without subsurface structural damages. Molecular dynamics simulations depict the atom-by-atom removal process, where the first atomic layer is removed preferentially through the formation and dissociation of interfacial bridge bonds. Based on the parametric thresholds needed for single atomic layer removal, the critical energy barrier for water-assisted mechanochemical dissociation of Si-Si bonds was determined. The mechanochemical nanolithography method demonstrated here could be extended to nanofabrication of other crystalline materials.

Enhanced Mechanical Stability of Gold Nanotips through Carbon Nanocone Encapsulation

PubMed Central

Cano-Marquez, Abraham G.; Schmidt, Wesller G.; Ribeiro-Soares, Jenaina; Gustavo Cançado, Luiz; Rodrigues, Wagner N.; Santos, Adelina P.; Furtado, Clascidia A.; Autreto, Pedro A.S.; Paupitz, Ricardo; Galvão, Douglas S.; Jorio, Ado

2015-01-01

Gold is a noble metal that, in comparison with silver and copper, has the advantage of corrosion resistance. Despite its high conductivity, chemical stability and biocompatibility, gold exhibits high plasticity, which limits its applications in some nanodevices. Here, we report an experimental and theoretical study on how to attain enhanced mechanical stability of gold nanotips. The gold tips were fabricated by chemical etching and further encapsulated with carbon nanocones via nanomanipulation. Atomic force microscopy experiments were carried out to test their mechanical stability. Molecular dynamics simulations show that the encapsulated nanocone changes the strain release mechanisms at the nanoscale by blocking gold atomic sliding, redistributing the strain along the whole nanostructure. The carbon nanocones are conducting and can induce magnetism, thus opening new avenues on the exploitation of transport, mechanical and magnetic properties of gold covered by sp2 carbon at the nanoscale. PMID:26083864

Attomole quantitation of protein separations with accelerator mass spectrometry

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vogel, J S; Grant, P G; Buccholz, B A

2000-12-15

Quantification of specific proteins depends on separation by chromatography or electrophoresis followed by chemical detection schemes such as staining and fluorophore adhesion. Chemical exchange of short-lived isotopes, particularly sulfur, is also prevalent despite the inconveniences of counting radioactivity. Physical methods based on isotopic and elemental analyses offer highly sensitive protein quantitation that has linear response over wide dynamic ranges and is independent of protein conformation. Accelerator mass spectrometry quantifies long-lived isotopes such as 14C to sub-attomole sensitivity. We quantified protein interactions with small molecules such as toxins, vitamins, and natural biochemicals at precisions of 1-5% . Micro-proton-induced-xray-emission quantifies elemental abundancesmore » in separated metalloprotein samples to nanogram amounts and is capable of quantifying phosphorylated loci in gels. Accelerator-based quantitation is a possible tool for quantifying the genome translation into proteome.« less

Chemical Kinetics, Heat Transfer, and Sensor Dynamics Revisited in a Simple Experiment

ERIC Educational Resources Information Center

Sad, Maria E.; Sad, Mario R.; Castro, Alberto A.; Garetto, Teresita F.

2008-01-01

A simple experiment about thermal effects in chemical reactors is described, which can be used to illustrate chemical reactor models, the determination and validation of their parameters, and some simple principles of heat transfer and sensor dynamics. It is based in the exothermic reaction between aqueous solutions of sodium thiosulfate and…

Contents of chemical elements in stomach during prenatal development: different age-dependent dynamical changes and their significance

PubMed Central

Hou, Shao-Fan; Li, Hai-Rong; Wang, Li-Zhen; Li, De-Zhu; Yang, Lin-Sheng; Li, Chong-Zheng

2003-01-01

AIM: To observe dynamic of different chemical elements in stomach tissue during fetal development. METHODS: To determine contents of the 21 chemical elements in each stomach samples from fetus aging four to ten months. The content values were compared to those from adult tissue samples, and the values for each month group were also analyzed for dynamic changes. RESULTS: Three representations were found regarding the relationship between contents of the elements and ages of the fetus, including the positive correlative (K), reversely correlative (Na, Ca, P, Al, Cu, Zn, Fe, Mn, Cr, Sr, Li, Cd, Ba, Se) and irrelevant groups (Mg, Co, Ni, V, Pb, Ti). CONCLUSION: The chemical elements’ contents in stomach tissues were found to change dynamically with the stomach weights. The age-dependent representations for different chemical elements during the prenatal development may be of some significance for assessing development of fetal stomach and some chemical elements. The data may be helpful for the nutritional balance of fetus and mothers during prenatal development and even the perinatal stages. PMID:12717857

Spatio-temporal manipulation of small GTPase activity at subcellular level and on timescale of seconds in living cells.

PubMed

DeRose, Robert; Pohlmeyer, Christopher; Umeda, Nobuhiro; Ueno, Tasuku; Nagano, Tetsuo; Kuo, Scot; Inoue, Takanari

2012-03-09

Dynamic regulation of the Rho family of small guanosine triphosphatases (GTPases) with great spatiotemporal precision is essential for various cellular functions and events(1, 2). Their spatiotemporally dynamic nature has been revealed by visualization of their activity and localization in real time(3). In order to gain deeper understanding of their roles in diverse cellular functions at the molecular level, the next step should be perturbation of protein activities at a precise subcellular location and timing. To achieve this goal, we have developed a method for light-induced, spatio-temporally controlled activation of small GTPases by combining two techniques: (1) rapamycin-induced FKBP-FRB heterodimerization and (2) a photo-caging method of rapamycin. With the use of rapamycin-mediated FKBP-FRB heterodimerization, we have developed a method for rapidly inducible activation or inactivation of small GTPases including Rac(4), Cdc42(4), RhoA(4) and Ras(5), in which rapamycin induces translocation of FKBP-fused GTPases, or their activators, to the plasma membrane where FRB is anchored. For coupling with this heterodimerization system, we have also developed a photo-caging system of rapamycin analogs. A photo-caged compound is a small molecule whose activity is suppressed with a photocleavable protecting group known as a caging group. To suppress heterodimerization activity completely, we designed a caged rapamycin that is tethered to a macromolecule such that the resulting large complex cannot cross the plasma membrane, leading to virtually no background activity as a chemical dimerizer inside cells(6). Figure 1 illustrates a scheme of our system. With the combination of these two systems, we locally recruited a Rac activator to the plasma membrane on a timescale of seconds and achieved light-induced Rac activation at the subcellular level(6).

First-principles investigation of the dissociation and coupling of methane on small copper clusters: Interplay of collision dynamics and geometric and electronic effects

DOE Office of Scientific and Technical Information (OSTI.GOV)

Varghese, Jithin J.; Mushrif, Samir H., E-mail: shmushrif@ntu.edu.sg

Small metal clusters exhibit unique size and morphology dependent catalytic activity. The search for alternate minimum energy pathways and catalysts to transform methane to more useful chemicals and carbon nanomaterials led us to investigate collision induced dissociation of methane on small Cu clusters. We report here for the first time, the free energy barriers for the collision induced activation, dissociation, and coupling of methane on small Cu clusters (Cu{sub n} where n = 2–12) using ab initio molecular dynamics and metadynamics simulations. The collision induced activation of the stretching and bending vibrations of methane significantly reduces the free energy barriermore » for its dissociation. Increase in the cluster size reduces the barrier for dissociation of methane due to the corresponding increase in delocalisation of electron density within the cluster, as demonstrated using the electron localisation function topology analysis. This enables higher probability of favourable alignment of the C–H stretching vibration of methane towards regions of high electron density within the cluster and makes higher number of sites available for the chemisorption of CH{sub 3} and H upon dissociation. These characteristics contribute in lowering the barrier for dissociation of methane. Distortion and reorganisation of cluster geometry due to high temperature collision dynamics disturb electron delocalisation within them and increase the barrier for dissociation. Coupling reactions of CH{sub x} (x = 1–3) species and recombination of H with CH{sub x} have free energy barriers significantly lower than complete dehydrogenation of methane to carbon. Thus, competition favours the former reactions at high hydrogen saturation on the clusters.« less

A network dynamics approach to chemical reaction networks

NASA Astrophysics Data System (ADS)

van der Schaft, A. J.; Rao, S.; Jayawardhana, B.

2016-04-01

A treatment of a chemical reaction network theory is given from the perspective of nonlinear network dynamics, in particular of consensus dynamics. By starting from the complex-balanced assumption, the reaction dynamics governed by mass action kinetics can be rewritten into a form which allows for a very simple derivation of a number of key results in the chemical reaction network theory, and which directly relates to the thermodynamics and port-Hamiltonian formulation of the system. Central in this formulation is the definition of a balanced Laplacian matrix on the graph of chemical complexes together with a resulting fundamental inequality. This immediately leads to the characterisation of the set of equilibria and their stability. Furthermore, the assumption of complex balancedness is revisited from the point of view of Kirchhoff's matrix tree theorem. Both the form of the dynamics and the deduced behaviour are very similar to consensus dynamics, and provide additional perspectives to the latter. Finally, using the classical idea of extending the graph of chemical complexes by a 'zero' complex, a complete steady-state stability analysis of mass action kinetics reaction networks with constant inflows and mass action kinetics outflows is given, and a unified framework is provided for structure-preserving model reduction of this important class of open reaction networks.

Facilitation and inhibition: changes in plant nitrogen and secondary metabolites mediate interactions between above-ground and below-ground herbivores

PubMed Central

Huang, Wei; Siemann, Evan; Yang, Xuefang; Wheeler, Gregory S.; Ding, Jianqing

2013-01-01

To date, it remains unclear how herbivore-induced changes in plant primary and secondary metabolites impact above-ground and below-ground herbivore interactions. Here, we report effects of above-ground (adult) and below-ground (larval) feeding by Bikasha collaris on nitrogen and secondary chemicals in shoots and roots of Triadica sebifera to explain reciprocal above-ground and below-ground insect interactions. Plants increased root tannins with below-ground herbivory, but above-ground herbivory prevented this increase and larval survival doubled. Above-ground herbivory elevated root nitrogen, probably contributing to increased larval survival. However, plants increased foliar tannins with above-ground herbivory and below-ground herbivory amplified this increase, and adult survival decreased. As either foliar or root tannins increased, foliar flavonoids decreased, suggesting a trade-off between these chemicals. Together, these results show that plant chemicals mediate contrasting effects of conspecific larval and adult insects, whereas insects may take advantage of plant responses to facilitate their offspring performance, which may influence population dynamics. PMID:23902902

Counteraction of urea-induced protein denaturation by trimethylamine N-oxide: a chemical chaperone at atomic resolution.

PubMed

Bennion, Brian J; Daggett, Valerie

2004-04-27

Proteins are very sensitive to their solvent environments. Urea is a common chemical denaturant of proteins, yet some animals contain high concentrations of urea. These animals have evolved an interesting mechanism to counteract the effects of urea by using trimethylamine N-oxide (TMAO). The molecular basis for the ability of TMAO to act as a chemical chaperone remains unknown. Here, we describe molecular dynamics simulations of a small globular protein, chymotrypsin inhibitor 2, in 8 M urea and 4 M TMAO/8 M urea solutions, in addition to other control simulations, to investigate this effect at the atomic level. In 8 M urea, the protein unfolds, and urea acts in both a direct and indirect manner to achieve this effect. In contrast, introduction of 4 M TMAO counteracts the effect of urea and the protein remains well structured. TMAO makes few direct interactions with the protein. Instead, it prevents unfolding of the protein by structuring the solvent. In particular, TMAO orders the solvent and discourages it from competing with intraprotein H bonds and breaking up the hydrophobic core of the protein.

Preparation of tamarind fruit seed activated carbon by microwave heating for the adsorptive treatment of landfill leachate: A laboratory column evaluation.

PubMed

Foo, K Y; Lee, L K; Hameed, B H

2013-04-01

The preparation of tamarind fruit seed granular activated carbon (TSAC) by microwave induced chemical activation for the adsorptive treatment of semi-aerobic landfill leachate has been attempted. The chemical and physical properties of TSAC were examined. A series of column tests were performed to determine the breakthrough characteristics, by varying the operational parameters, hydraulic loading rate (5-20 mL/min) and adsorbent bed height (15-21 cm). Ammonical nitrogen and chemical oxygen demand (COD), which provide a prerequisite insight into the prediction of leachate quality was quantified. Results illustrated an encouraging performance for the adsorptive removal of ammonical nitrogen and COD, with the highest bed capacity of 84.69 and 55.09 mg/g respectively, at the hydraulic loading rate of 5 mL/min and adsorbent bed height of 21 cm. The dynamic adsorption behavior was satisfactory described by the Thomas and Yoon-Nelson models. The findings demonstrated the applicability of TSAC for the adsorptive treatment of landfill leachate. Copyright © 2013 Elsevier Ltd. All rights reserved.

Nonequilibrium Chemical Effects in Single-Molecule SERS Revealed by Ab Initio Molecular Dynamics Simulations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fischer, Sean A.; Aprà, Edoardo; Govind, Niranjan

2017-02-03

Recent developments in nanophotonics have paved the way for achieving significant advances in the realm of single molecule chemical detection, imaging, and dynamics. In particular, surface-enhanced Raman scattering (SERS) is a powerful analytical technique that is now routinely used to identify the chemical identity of single molecules. Understanding how nanoscale physical and chemical processes affect single molecule SERS spectra and selection rules is a challenging task, and is still actively debated. Herein, we explore underappreciated chemical phenomena in ultrasensitive SERS. We observe a fluctuating excited electronic state manifold, governed by the conformational dynamics of a molecule (4,4’-dimercaptostilbene, DMS) interacting withmore » a metallic cluster (Ag20). This affects our simulated single molecule SERS spectra; the time trajectories of a molecule interacting with its unique local environment dictates the relative intensities of the observable Raman-active vibrational states. Ab initio molecular dynamics of a model Ag20-DMS system are used to illustrate both concepts in light of recent experimental results.« less

Chemical unfolding of chicken villin headpiece in aqueous dimethyl sulfoxide solution: cosolvent concentration dependence, pathway, and microscopic mechanism.

PubMed

Roy, Susmita; Bagchi, Biman

2013-04-25

Unfolding of a protein often proceeds through partial unfolded intermediate states (PUIS). PUIS have been detected in several experimental and simulation studies. However, complete analyses of transitions between different PUIS and the unfolding trajectory are sparse. To understand such dynamical processes, we study chemical unfolding of a small protein, chicken villin head piece (HP-36), in aqueous dimethyl sulfoxide (DMSO) solution. We carry out molecular dynamics simulations at various solution compositions under ambient conditions. In each concentration, the initial step of unfolding involves separation of two adjacent native contacts, between phenyl alanine residues (11-18 and 7-18). This first step induces, under appropriate conditions, subsequent separation among other hydrophobic contacts, signifying a high degree of cooperativity in the unfolding process. The observed sequence of structural changes in HP-36 on increasing DMSO concentration and the observed sequence of PUIS, are in approximate agreement with earlier simulation results (in pure water) and experimental observations on unfolding of HP-36. Peculiar to water-DMSO mixture, an intervening structural transformation (around 15% of DMSO) in the binary mixture solvent retards the progression of unfolding as composition is increased. This is reflected in a remarkable nonmonotonic composition dependence of RMSD, radius of gyration and the fraction of native contacts. At 30% mole fraction of DMSO, we find the extended randomly coiled structure of the unfolded protein. The molecular mechanism of DMSO induced unfolding process is attributed to the initial preferential solvation of the hydrophobic side chain atoms through the methyl groups of DMSO, followed by the hydrogen bonding of the oxygen atom of DMSO to the exposed backbone NH groups of HP-36.

Metal Ion Binding at the Catalytic Site Induces Widely Distributed Changes in a Sequence Specific Protein–DNA Complex

PubMed Central

2016-01-01

Metal ion cofactors can alter the energetics and specificity of sequence specific protein–DNA interactions, but it is unknown if the underlying effects on structure and dynamics are local or dispersed throughout the protein–DNA complex. This work uses EcoRV endonuclease as a model, and catalytically inactive lanthanide ions, which replace the Mg2+ cofactor. Nuclear magnetic resonance (NMR) titrations indicate that four Lu3+ or two La3+ cations bind, and two new crystal structures confirm that Lu3+ binding is confined to the active sites. NMR spectra show that the metal-free EcoRV complex with cognate (GATATC) DNA is structurally distinct from the nonspecific complex, and that metal ion binding sites are not assembled in the nonspecific complex. NMR chemical shift perturbations were determined for 1H–15N amide resonances, for 1H–13C Ile-δ-CH3 resonances, and for stereospecifically assigned Leu-δ-CH3 and Val-γ-CH3 resonances. Many chemical shifts throughout the cognate complex are unperturbed, so metal binding does not induce major conformational changes. However, some large perturbations of amide and side chain methyl resonances occur as far as 34 Å from the metal ions. Concerted changes in specific residues imply that local effects of metal binding are propagated via a β-sheet and an α-helix. Both amide and methyl resonance perturbations indicate changes in the interface between subunits of the EcoRV homodimer. Bound metal ions also affect amide hydrogen exchange rates for distant residues, including a distant subdomain that contacts DNA phosphates and promotes DNA bending, showing that metal ions in the active sites, which relieve electrostatic repulsion between protein and DNA, cause changes in slow dynamics throughout the complex. PMID:27786446

Advanced and innovative wind energy concept development: Dynamic inducer system

NASA Astrophysics Data System (ADS)

Lissaman, P. B. S.; Zalay, A. D.; Hibbs, B. H.

1981-05-01

The performance benefits of the dynamic inducer tip vane system was demonstrated Tow-tests conducted on a three-bladed, 3.6-meter diameter rotor show that a dynamic inducer can achieve a power coefficient (based pon power blade swept area) of 0.5, which exceeds that of a plain rotor by about 35%. Wind tunnel tests conducted on a one-third scale model of the dynamic inducer achieved a power coefficient of 0.62 which exceeded that of a plain rotor by about 70%. The dynamic inducer substantially improves the performance of conventional rotors and indications are that higher power coefficients can be achieved through additional aerodynamic optimization.

Structural dynamics and quantum mechanical aspects of shikonin derivatives as CREBBP bromodomain inhibitors.

PubMed

Mitra, Sarmistha; Dash, Raju

2018-05-04

The Proteins involved in the chemical modification of lysine residues in histone, is currently being excessively focused as the therapeutic target for the treatment of cell related diseases like cancer. Among these proteins, the epigenetic reader, CREB-binding protein (CREBBP) bromodomain is one of the most prominent targets for effective anticancer drug design, which is responsible for the reorganization of acetylated histone lysine residues. Therefore, this study employed an integrative approach of structure based drug design, in combination with Molecular Dynamics (MD) and QM/MM study to identify as well as to describe the binding mechanism of two shikonin derivatives, acetylshikonin and propionylshikonin as inhibitors of CREBBP bromodomain. Here induced fit docking strategy was employed to explore the important intrinsic interactions of ligands with CREBBP bromodomain, consistently molecular dynamics simulation with two different methods and binding energy calculations by MM-GBSA and MM-PBSA were adopted to determine the stability of intermolecular interactions between protein and ligands. The results showed that both these derivatives made direct contacts with the important conserved residues of the active site, where propionylshikonin demonstrated stronger binding and stability than acetylshikonin, according to molecular dynamics simulation and binding free energy calculations. Further, QM/MM energy calculation was employed to study the chemical reactivity of the propionylshikonin and also to describe the mechanism of non bonded interactions between the propionylshikonin and CREBBP bromodomain. Though this study demands in vitro and in vivo experiments to evaluate the efficiency of the compound, these insights would assist to design more potent CREBBP bromodomain inhibitor, guiding the site of modification of propionylshikonin moiety for designing selective inhibitors. Copyright © 2018 Elsevier Inc. All rights reserved.

Spatiotemporal pH dynamics in concentration polarization near ion-selective membranes.

PubMed

Andersen, Mathias B; Rogers, David M; Mai, Junyu; Schudel, Benjamin; Hatch, Anson V; Rempe, Susan B; Mani, Ali

2014-07-08

We present a detailed analysis of the transient pH dynamics for a weak, buffered electrolyte subject to voltage-driven transport through an ion-selective membrane. We show that pH fronts emanate from the concentration polarization zone next to the membrane and that these propagating fronts change the pH in the system several units from its equilibrium value. The analysis is based on a 1D model using the unsteady Poisson-Nernst-Planck equations with nonequilibrium chemistry and without assumptions of electroneutrality or asymptotically thin electric double layers. Nonequilibrium chemical effects, especially for water splitting, are shown to be important for the dynamical and spatiotemporal evolution of the pH fronts. Nonetheless, the model also shows that at steady state the assumption of chemical equilibrium can still lead to good approximations of the global pH distribution. Moreover, our model shows that the transport of the hydronium ion in the extended space charge region is governed by a balance between electromigration and water self-ionization. On the basis of this observation, we present a simple model showing that the net flux of the hydronium ion is proportional to the length of the extended space charge region and the water self-ionization rate. To demonstrate these effects in practice, we have adopted the experiment of Mai et al. (Mai, J.; Miller, H.; Hatch, A. V. Spatiotemporal Mapping of Concentration Polarization Induced pH Changes at Nanoconstrictions. ACS Nano 2012, 6, 10206) as a model problem, and by including the full chemistry and transport, we show that the present model can capture the experimentally observed pH fronts. Our model can, among other things, be used to predict and engineer pH dynamics, which can be essential to the performance of membrane-based systems for biochemical separation and analysis.

Nitric oxide, PKC-ε, and connexin43 are crucial for ischemic preconditioning-induced chemical gap junction uncoupling

PubMed Central

Sun, Tao; Hao, Li; Lin, Ming-Jie; Zhong, Jing-Quan

2016-01-01

Ischemic preconditioning (IPC) maintains connexin43 (Cx43) phosphorylation and reduces chemical gap junction (GJ) coupling in cardiomyocytes to protect against ischemic damage. However, the signal transduction pathways underlying these effects are not fully understood. Here, we investigated whether nitric oxide (NO) and protein kinase C-ε (PKC-ε) contribute to IPC-induced cardioprotection by maintaining Cx43 phosphorylation and inhibiting chemical GJ coupling. IPC reduced ischemia-induced myocardial infarction and increased cardiomyocyte survival; phosphorylated Cx43, eNOS, and PKC-ε levels; and chemical GJ uncoupling. Administration of the NO donor SNAP mimicked the effects of IPC both in vivo and in vitro, maintaining Cx43 phosphorylation, promoting chemical GJ uncoupling, and reducing myocardial infarction. Preincubation with the NO synthase inhibitor L-NAME or PKC-ε translocation inhibitory peptide (PKC-ε-TIP) abolished these effects of IPC. Additionally, by inducing NO production, IPC induced translocation of PKC-ε, but not PKC-δ, from the cytosolic to the membrane fraction in primary cardiac myocytes. IPC-induced cardioprotection thus involves increased NO production, PKC-ε translocation, Cx43 phosphorylation, and chemical GJ uncoupling. PMID:27655723

Dynamic Reaction Figures: An Integrative Vehicle for Understanding Chemical Reactions

ERIC Educational Resources Information Center

Schultz, Emeric

2008-01-01

A highly flexible learning tool, referred to as a dynamic reaction figure, is described. Application of these figures can (i) yield the correct chemical equation by simply following a set of menu driven directions; (ii) present the underlying "mechanism" in chemical reactions; and (iii) help to solve quantitative problems in a number of different…

Chemotaxis in Microfluidic Devices

NASA Astrophysics Data System (ADS)

Wyatt, Danica; Nadkarni, Sharvari; Song, Loling; Voeltz, Camilla; Bodenschatz, Eberhard

2004-03-01

Dictyostelium amoebae use chemical signaling to begin starvation-induced aggregation. Cells generate a complex and dynamic pattern of cyclic AMP that drives their migration toward a central point. While this phenomenon is unique to social amoebae, the signaling pathways of chemotaxis are similar in all eukaryotic cells. Dicty serves as a model organism for imaging these intracellular protein dynamics. To date, chemotaxis has been primarily studied in diffusion-generated gradients in chambers many orders of magnitude larger than a cell. To better quantify which aspects of a gradient trigger a response, we have designed a microfluidic channel that confines cells in an environment where spatiotemporal cAMP concentration can be precisely manipulated. We report results on an early event in the signaling cascade, the translocation of PH domain-containing proteins, which test current models of chemotaxis. This work was supported by the NSF Biocomplexity program and the Nanobiotechnology Center, an STC Program of the NSF under Agreement No. ECS-9876771.

Photonic water dynamically responsive to external stimuli

PubMed Central

Sano, Koki; Kim, Youn Soo; Ishida, Yasuhiro; Ebina, Yasuo; Sasaki, Takayoshi; Hikima, Takaaki; Aida, Takuzo

2016-01-01

Fluids that contain ordered nanostructures with periodic distances in the visible-wavelength range, anomalously exhibit structural colours that can be rapidly modulated by external stimuli. Indeed, some fish can dynamically change colour by modulating the periodic distance of crystalline guanine sheets cofacially oriented in their fluid cytoplasm. Here we report that a dilute aqueous colloidal dispersion of negatively charged titanate nanosheets exhibits structural colours. In this ‘photonic water', the nanosheets spontaneously adopt a cofacial geometry with an ultralong periodic distance of up to 675 nm due to a strong electrostatic repulsion. Consequently, the photonic water can even reflect near-infrared light up to 1,750 nm. The structural colour becomes more vivid in a magnetic flux that induces monodomain structural ordering of the colloidal dispersion. The reflective colour of the photonic water can be modulated over the entire visible region in response to appropriate physical or chemical stimuli. PMID:27572806

Ultra-sensitive all-fibre photothermal spectroscopy with large dynamic range

PubMed Central

Jin, Wei; Cao, Yingchun; Yang, Fan; Ho, Hoi Lut

2015-01-01

Photothermal interferometry is an ultra-sensitive spectroscopic means for trace chemical detection in gas- and liquid-phase materials. Previous photothermal interferometry systems used free-space optics and have limitations in efficiency of light–matter interaction, size and optical alignment, and integration into photonic circuits. Here we exploit photothermal-induced phase change in a gas-filled hollow-core photonic bandgap fibre, and demonstrate an all-fibre acetylene gas sensor with a noise equivalent concentration of 2 p.p.b. (2.3 × 10−9 cm−1 in absorption coefficient) and an unprecedented dynamic range of nearly six orders of magnitude. The realization of photothermal interferometry with low-cost near infrared semiconductor lasers and fibre-based technology allows a class of optical sensors with compact size, ultra sensitivity and selectivity, applicability to harsh environment, and capability for remote and multiplexed multi-point detection and distributed sensing. PMID:25866015

Hierarchical Petascale Simulation Framework for Stress Corrosion Cracking

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vashishta, Priya

2014-12-01

Reaction Dynamics in Energetic Materials: Detonation is a prototype of mechanochemistry, in which mechanically and thermally induced chemical reactions far from equilibrium exhibit vastly different behaviors. It is also one of the hardest multiscale physics problems, in which diverse length and time scales play important roles. The CACS group has performed multimillion-atom reactive MD simulations to reveal a novel two-stage reaction mechanism during the detonation of cyclotrimethylenetrinitramine (RDX) crystal. Rapid production of N2 and H2O within ~10 ps is followed by delayed production of CO molecules within ~ 1 ns. They found that further decomposition towards the final products ismore » inhibited by the formation of large metastable C- and O-rich clusters with fractal geometry. The CACS group has also simulated the oxidation dynamics of close-packed aggregates of aluminum nanoparticles passivated by oxide shells. Their simulation results suggest an unexpectedly active role of the oxide shell as a nanoreactor.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arman, B.; An, Q.; Luo, S. N.

We investigate with nonreactive molecular dynamics simulations the dynamic response of phenolic resin and its carbon-nanotube (CNT) composites to shock wave compression. For phenolic resin, our simulations yield shock states in agreement with experiments on similar polymers except the “phase change” observed in experiments, indicating that such phase change is chemical in nature. The elastic–plastic transition is characterized by shear stress relaxation and atomic-level slip, and phenolic resin shows strong strain hardening. Shock loading of the CNT-resin composites is applied parallel or perpendicular to the CNT axis, and the composites demonstrate anisotropy in wave propagation, yield and CNT deformation. Themore » CNTs induce stress concentrations in the composites and may increase the yield strength. Our simulations indicate that the bulk shock response of the composites depends on the volume fraction, length ratio, impact cross-section, and geometry of the CNT components; the short CNTs in current simulations have insignificant effect on the bulk response of resin polymer.« less

Solute-solvent interactions and dynamics probed by THz light

NASA Astrophysics Data System (ADS)

Schwaab, Gerhard; Böhm, Fabian; Ma, Chun-Yu; Havenith, Martina

The THz range (1-12 THz, 30-400 cm-1) is especially suited to probe changes in the solvent dynamics induced by solutes of different character (hydrophobic, hydrophilic, charged, neutral). In recent years we have investigated a large variety of such solutes and found characteristic spectral fingerprints for ions, but also for uncharged solutes, such as alcohols. We will present a status report on our current understanding of the observed spectral changes and how they relate to physico-chemical parameters like hydration shell size or the lifetime of an excited intermolecular oscillation. In addition, we will show, that in some cases the spectral changes are closely related to the partition function yielding access to a microscopic understanding of macroscopic thermodynamic functions. The authors gratefully acknowledge financial support from the Cluster of Excellence RESOLV (Ruhr-Universität, EXC1069) funded by the Deutsche Forschungsgemeinschaft.

Communication: Mechanochemical fluctuation theorem and thermodynamics of self-phoretic motors

NASA Astrophysics Data System (ADS)

Gaspard, Pierre; Kapral, Raymond

2017-12-01

Microscopic dynamical aspects of the propulsion of nanomotors by self-phoretic mechanisms are considered. Propulsion by self-diffusiophoresis relies on the mechanochemical coupling between the fluid velocity field and the concentration fields induced by asymmetric catalytic reactions on the motor surface. The consistency between the thermodynamics of this coupling and the microscopic reversibility of the underlying molecular dynamics is investigated. For this purpose, a mechanochemical fluctuation theorem for the joint probability to find the motor at position r after n reactive events have occurred during the time interval t is derived, starting from coupled Langevin equations for the translational, rotational, and chemical fluctuations of self-phoretic motors. An important result that follows from this analysis is the identification of an effect that is reciprocal to self-propulsion by diffusiophoresis, which leads to a dependence of the reaction rate on the value of an externally applied force.

Hugoniot curve calculation of nitromethane decomposition mixtures: A reactive force field molecular dynamics approach

NASA Astrophysics Data System (ADS)

Guo, Feng; Zhang, Hong; Hu, Hai-Quan; Cheng, Xin-Lu; Zhang, Li-Yan

2015-11-01

We investigate the Hugoniot curve, shock-particle velocity relations, and Chapman-Jouguet conditions of the hot dense system through molecular dynamics (MD) simulations. The detailed pathways from crystal nitromethane to reacted state by shock compression are simulated. The phase transition of N2 and CO mixture is found at about 10 GPa, and the main reason is that the dissociation of the C-O bond and the formation of C-C bond start at 10.0-11.0 GPa. The unreacted state simulations of nitromethane are consistent with shock Hugoniot data. The complete pathway from unreacted to reacted state is discussed. Through chemical species analysis, we find that the C-N bond breaking is the main event of the shock-induced nitromethane decomposition. Project supported by the National Natural Science Foundation of China (Grant No. 11374217) and the Shandong Provincial Natural Science Foundation, China (Grant No. ZR2014BQ008).

Conformational free energy modeling of druglike molecules by metadynamics in the WHIM space.

PubMed

Spiwok, Vojtěch; Hlat-Glembová, Katarína; Tvaroška, Igor; Králová, Blanka

2012-03-26

Protein-ligand affinities can be significantly influenced not only by the interaction itself but also by conformational equilibrium of both binding partners, free ligand and free protein. Identification of important conformational families of a ligand and prediction of their thermodynamics is important for efficient ligand design. Here we report conformational free energy modeling of nine small-molecule drugs in explicitly modeled water by metadynamics with a bias potential applied in the space of weighted holistic invariant molecular (WHIM) descriptors. Application of metadynamics enhances conformational sampling compared to unbiased molecular dynamics simulation and allows to predict relative free energies of key conformations. Selected free energy minima and one example of transition state were tested by a series of unbiased molecular dynamics simulation. Comparison of free energy surfaces of free and target-bound Imatinib provides an estimate of free energy penalty of conformational change induced by its binding to the target. © 2012 American Chemical Society

Optical spectroscopy and photo modification of individual single-photon emitters in hexagonal boron nitride

NASA Astrophysics Data System (ADS)

Jayakumar, Harishankar; Shotan, Zav; Considine, Christopher; Mazkoit, Mažena; Fedder, Helmut; Wrachtrup, Joerg; Alkauskas, Audrius; Doherty, Marcus; Menon, Vinod; Meriles, Carlos

Fluorescent defects recently observed under ambient conditions in hexagonal boron nitride (h-BN) promise to open novel opportunities for the implementation of on-chip photonic devices that rely on identical photons from single emitters. Here we report on the room temperature photo-luminescence dynamics of individual emitters in multilayer h-BN flakes exposed to blue laser light. Comparison of optical spectra recorded at successive times reveals considerable spectral diffusion, possibly the result of slowly fluctuating, trapped-carrier-induced stark shifts. Large spectral jumps - reaching up to 100 nm - followed by bleaching are observed in most cases upon prolonged exposure to blue light, an indication of one-directional, photo-chemical changes likely taking place on the flake surface. Remarkably, only a fraction of the observed emitters also fluoresces on green illumination suggesting a more complex optical excitation dynamics than previously anticipated and raising questions on the physical nature of the atomic defect at play.

Influence of heat losses on nonlinear fingering dynamics of exothermic autocatalytic fronts

NASA Astrophysics Data System (ADS)

D'Hernoncourt, J.; De Wit, A.

2010-06-01

Across traveling exothermic autocatalytic fronts, a density jump can be observed due to changes in composition and temperature. These density changes are prone to induce buoyancy-driven convection around the front when the propagation takes place in absence of gel within the gravity field. Most recent experiments devoted to studying such reaction-diffusion-convection dynamics are performed in Hele-Shaw cells, two glass plates separated by a thin gap width and filled by the chemical solutions. We investigate here the influence of heat losses through the walls of such cells on the nonlinear fingering dynamics of exothermic autocatalytic fronts propagating in vertical Hele-Shaw cells. We show that these heat losses increase tip splittings and modify the properties of the flow field. A comparison of the differences between the dynamics in reactors with respectively insulating and conducting walls is performed as a function of the Lewis number Le, the Newton cooling coefficient α quantifying the amplitude of heat losses and the width of the system. We find that tip splitting is enhanced for intermediate values of α while coarsening towards one single finger dominates for insulated systems or large values of α leading to situations equivalent to isothermal ones.

Multivariate moment closure techniques for stochastic kinetic models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lakatos, Eszter, E-mail: e.lakatos13@imperial.ac.uk; Ale, Angelique; Kirk, Paul D. W.

2015-09-07

Stochastic effects dominate many chemical and biochemical processes. Their analysis, however, can be computationally prohibitively expensive and a range of approximation schemes have been proposed to lighten the computational burden. These, notably the increasingly popular linear noise approximation and the more general moment expansion methods, perform well for many dynamical regimes, especially linear systems. At higher levels of nonlinearity, it comes to an interplay between the nonlinearities and the stochastic dynamics, which is much harder to capture correctly by such approximations to the true stochastic processes. Moment-closure approaches promise to address this problem by capturing higher-order terms of the temporallymore » evolving probability distribution. Here, we develop a set of multivariate moment-closures that allows us to describe the stochastic dynamics of nonlinear systems. Multivariate closure captures the way that correlations between different molecular species, induced by the reaction dynamics, interact with stochastic effects. We use multivariate Gaussian, gamma, and lognormal closure and illustrate their use in the context of two models that have proved challenging to the previous attempts at approximating stochastic dynamics: oscillations in p53 and Hes1. In addition, we consider a larger system, Erk-mediated mitogen-activated protein kinases signalling, where conventional stochastic simulation approaches incur unacceptably high computational costs.« less

Effects of microsolvation on a SN2 reaction: indirect atomistic dynamics and weakened suppression of reactivity.

PubMed

Yang, Li; Liu, Xu; Zhang, Jiaxu; Xie, Jing

2017-04-12

Systematic studies of microsolvation in the gas phase have enriched our knowledge of solvent effects. Here, the dynamics of a prototype S N 2 reaction of a hydrated fluoride ion with methyl iodide is uncovered employing direct dynamics simulations that show strikingly distinct features from those determined for an unsolvated system. An indirect scattering is found to prevail, which occurs dominantly by forming hydrated F - (H 2 O)-HCH 2 I and F - (H 2 O)-CH 3 I pre-reaction complexes at low energies, but proceeds through their water-free counterparts at higher energies. This finding is in strong contrast to a general evolution from indirect to direct dynamics with enhancing energy for the unsolvated substitution reactions, and this discrepancy is understood by the substantial steric hindrance introduced by a water molecule. As established in experiments, solvation suppresses the reactivity, whereas we find that this depression is remarkably frustrated upon raising the energy given that collision-induced dehydration essentially diminishes the water block for reactive collisions. The present study sheds light on how solute-solvent interactions affect the underlying dynamics at a deeper atomic level, thereby promoting our understanding of the fundamental solvent effects on chemical reactions in solution.

The effect of VUV radiation from Ar/O2 plasmas on low-k SiOCH films

NASA Astrophysics Data System (ADS)

Lee, J.; Graves, D. B.

2011-08-01

The degradation of porous low-k materials, like SiOCH, under plasma processing continues to be a problem in the next generation of integrated-circuit fabrication. Due to the exposure of the film to many species during plasma treatment, such as photons, ions, radicals, etc, it is difficult to identify the mechanisms responsible for plasma-induced damage. Using a vacuum beam apparatus with a calibrated Xe vacuum ultraviolet (VUV) lamp, we show that 147 nm VUV photons and molecular O2 alone can damage these low-k materials. Using Fourier-transform infrared (FTIR) spectroscopy, we show that VUV/O2 exposure causes a loss of methylated species, resulting in a hydrophilic, SiOx-like layer that is susceptible to H2O absorption, leading to an increased dielectric constant. The effect of VUV radiation on chemical modification of porous SiOCH films in the vacuum beam apparatus and in Ar and O2 plasma exposure was found to be a significant contributor to dielectric damage. Measurements of dielectric constant change using a mercury probe are consistent with chemical modification inferred from FTIR analysis. Furthermore, the extent of chemical modification appears to be limited by the penetration depth of the VUV photons, which is dependent on wavelength of radiation. The creation of a SiOx-like layer near the surface of the material, which grows deeper as more methyl is extracted, introduces a dynamic change of VUV absorption throughout the material over time. As a result, the rate of methyl loss is continuously changing during the exposure. We present a model that attempts to capture this dynamic behaviour and compare the model predictions to experimental data through a fitting parameter that represents the effective photo-induced methyl removal. While this model accurately simulates the methyl loss through VUV exposure by the Xe lamp and Ar plasma, the methyl loss from VUV photons in O2 plasma are only accurately depicted at longer exposure times. We conclude that other species, such as oxygen radicals or ions, may play a major role in chemical modification at short times near the surface of the material, while VUV photons contribute to the majority of the damage in the bulk.

Coherent control of alkali cluster fragmentation dynamics

NASA Astrophysics Data System (ADS)

Lindinger, Albrecht; Lupulescu, Cosmin; Bartelt, Andreas; Vajda, Štefan; Wöste, Ludger

2003-06-01

Metal clusters exhibit extraordinary chemical and catalytic properties, which sensitively depend upon their size. This behavior makes them interesting candidates for the real-time analysis of ultrafast photo-induced processes—ultimately leading to coherent control scenarii. We have performed transient multi-photon ionization experiments on small alkali clusters of different size in order to probe their wave packet dynamics, structural reorientations, charge transfers and dissociative events in different vibrationally excited electronic states including their ground state. The observed processes were highly dependent on the irradiated pulse parameters, like its phase, amplitude and duration; an emphasis to employ a feedback control system for generating the optimum pulse shapes. Their spectral and temporal behavior reflects interesting properties about the investigated system and the irradiated photochemical process. We present first the vibrational dynamics of bound, dissociated, and pre-dissociated electronically excited states of alkali dimers and trimers. The scheme for observing the wave packet dynamics in the electronic ground state using stimulated Raman-pumping is shown. Since the employed pulse parameters significantly influence the efficiency of the irradiated dynamic pathways photo-induced fragmentation experiments on bifurcating reaction channels were carried out. In these experiments different branching ionization and fragmentation pathways of electronically excited Na 2K were investigated. By employing an evolutionary algorithm for optimizing the phase and amplitude of the applied laser field, the yield of the resulting parent or fragment ions could significantly be influenced and interesting features could be concluded from the obtained optimum pulse shapes revealing the characteristic molecular oscillation period. Moreover, the influence on the optimal pulse shape due to fragmentation from larger clusters into NaK is obtained. The substructure of the optimal pulse shape thereby offers new insight into the fragmentation channel during the control process. Characteristic motions of the involved wave packets are proposed, in order to explain the optimized dynamic dissociation pathways.

Crossed Molecular Beam Studies and Dynamics of Decomposition of Chemically Activated Radicals

DOE R&D Accomplishments Database

Lee, Y. T.

1973-09-01

The power of the crossed molecular beams method in the investigation of the dynamics of chemical reactions lies mainly in the direct observation of the consequences of single collisions of well controlled reactant molecules. The primary experimental observations which provide information on reaction dynamics are the measurements of angular and velocity distributions of reaction products.

Automatic network coupling analysis for dynamical systems based on detailed kinetic models.

PubMed

Lebiedz, Dirk; Kammerer, Julia; Brandt-Pollmann, Ulrich

2005-10-01

We introduce a numerical complexity reduction method for the automatic identification and analysis of dynamic network decompositions in (bio)chemical kinetics based on error-controlled computation of a minimal model dimension represented by the number of (locally) active dynamical modes. Our algorithm exploits a generalized sensitivity analysis along state trajectories and subsequent singular value decomposition of sensitivity matrices for the identification of these dominant dynamical modes. It allows for a dynamic coupling analysis of (bio)chemical species in kinetic models that can be exploited for the piecewise computation of a minimal model on small time intervals and offers valuable functional insight into highly nonlinear reaction mechanisms and network dynamics. We present results for the identification of network decompositions in a simple oscillatory chemical reaction, time scale separation based model reduction in a Michaelis-Menten enzyme system and network decomposition of a detailed model for the oscillatory peroxidase-oxidase enzyme system.

True Triaxial Experimental Study of Rockbursts Induced By Ramp and Cyclic Dynamic Disturbances

NASA Astrophysics Data System (ADS)

Su, Guoshao; Hu, Lihua; Feng, Xiating; Yan, Liubin; Zhang, Gangliang; Yan, Sizhou; Zhao, Bin; Yan, Zhaofu

2018-04-01

A modified rockburst testing system was utilized to reproduce rockbursts induced by ramp and cyclic dynamic disturbances with a low-intermediate strain rate of 2 × 10-3-5 × 10-3 s-1 in the laboratory. The experimental results show that both the ramp and cyclic dynamic disturbances play a significant role in inducing rockbursts. In the tests of rockbursts induced by a ramp dynamic disturbance, as the static stress before the dynamic disturbance increases, both the strength of specimens and the kinetic energy of the ejected fragments first increase and then decrease. In the tests of rockbursts induced by a cyclic dynamic disturbance, there exists a rockburst threshold of the static stress and the dynamic disturbance amplitude, and the kinetic energy of the ejected fragments first increases and then decreases as the cyclic dynamic disturbance frequency increases. The main differences between rockbursts induced by ramp dynamic disturbances and those induced by cyclic dynamic disturbances are as follows: the rockburst development process of the former is characterized by an impact failure feature, while that of the latter is characterized by a fatigue failure feature; the damage evolution curve of the specimen of the former has a leap-developing form with a significant catastrophic feature, while that of the latter has an inverted S-shape with a remarkable fatigue damage characteristic; the energy mechanism of the former involves the ramp dynamic disturbance giving extra elastic strain energy to rocks, while that of the latter involves the cyclic dynamic disturbance decreasing the ultimate energy storage capacity of rocks.

Near-field photochemical and radiation-induced chemical fabrication of nanopatterns of a self-assembled silane monolayer

PubMed Central

Hentschel, Carsten; Fontein, Florian; Stegemann, Linda; Hoeppener, Christiane; Fuchs, Harald; Hoeppener, Stefanie

2014-01-01

Summary A general concept for parallel near-field photochemical and radiation-induced chemical processes for the fabrication of nanopatterns of a self-assembled monolayer (SAM) of (3-aminopropyl)triethoxysilane (APTES) is explored with three different processes: 1) a near-field photochemical process by photochemical bleaching of a monomolecular layer of dye molecules chemically bound to an APTES SAM, 2) a chemical process induced by oxygen plasma etching as well as 3) a combined near-field UV-photochemical and ozone-induced chemical process, which is applied directly to an APTES SAM. All approaches employ a sandwich configuration of the surface-supported SAM, and a lithographic mask in form of gold nanostructures fabricated through colloidal sphere lithography (CL), which is either exposed to visible light, oxygen plasma or an UV–ozone atmosphere. The gold mask has the function to inhibit the photochemical reactions by highly localized near-field interactions between metal mask and SAM and to inhibit the radiation-induced chemical reactions by casting a highly localized shadow. The removal of the gold mask reveals the SAM nanopattern. PMID:25247126

Numerical simulation of hydrogen fluorine overtone chemical lasers

NASA Astrophysics Data System (ADS)

Chen, Jinbao; Jiang, Zhongfu; Hua, Weihong; Liu, Zejin; Shu, Baihong

1998-08-01

A two-dimensional program was applied to simulate the chemical dynamic process, gas dynamic process and lasing process of a combustion-driven CW HF overtone chemical lasers. Some important parameters in the cavity were obtained. The calculated results included HF molecule concentration on each vibration energy level while lasing, averaged pressure and temperature, zero power gain coefficient of each spectral line, laser spectrum, the averaged laser intensity, output power, chemical efficiency and the length of lasing zone.

Resistance, resilience and recovery: aquatic bacterial dynamics after water column disturbance.

PubMed

Shade, Ashley; Read, Jordan S; Welkie, David G; Kratz, Timothy K; Wu, Chin H; McMahon, Katherine D

2011-10-01

For lake microbes, water column mixing acts as a disturbance because it homogenizes thermal and chemical gradients known to define the distributions of microbial taxa. Our first objective was to isolate hypothesized drivers of lake bacterial response to water column mixing. To accomplish this, we designed an enclosure experiment with three treatments to independently test key biogeochemical changes induced by mixing: oxygen addition to the hypolimnion, nutrient addition to the epilimnion, and full water column mixing. We used molecular fingerprinting to observe bacterial community dynamics in the treatment and control enclosures, and in ambient lake water. We found that oxygen and nutrient amendments simulated the physical-chemical water column environment following mixing and resulted in similar bacterial communities to the mixing treatment, affirming that these were important drivers of community change. These results demonstrate that specific environmental changes can replicate broad disturbance effects on microbial communities. Our second objective was to characterize bacterial community stability by quantifying community resistance, recovery and resilience to an episodic disturbance. The communities in the nutrient and oxygen amendments changed quickly (had low resistance), but generally matched the control composition by the 10th day after treatment, exhibiting resilience. These results imply that aquatic bacterial assemblages are generally stable in the face of disturbance. © 2011 Society for Applied Microbiology and Blackwell Publishing Ltd.

Effects of HO-/MeO-PBDEs on androgen receptor: in vitro investigation and helix 12-involved MD simulation.

PubMed

Wang, Xiaoxiang; Yang, Huaiyu; Hu, Xinxin; Zhang, Xiaowei; Zhang, Qiansen; Jiang, Hualiang; Shi, Wei; Yu, Hongxia

2013-10-15

Hydroxylated and methoxylated polybrominated diphenyl ethers (HO-/MeO-PBDEs) have received increasing attention for their potential endocrine disrupting activities and widely environmental distribution. However, little information is available for the anti-androgenic activities, and the molecular mechanism of interactions with androgen receptor (AR) is not fully understood. In the present study, cell line assay and computational simulation were integrated to systematically explore the molecular mechanism of interactions between chemicals and AR. The metabolites with similar molecular structures exhibited different anti-androgenic activity while none of them showed androgenic activity. According to the multisystem molecular dynamics simulation, minute differences in the structure of ligands induced dramatic different conformational transition of AR-ligand binding domain (LBD). The Helix12 (H12) component of active ligands occupied AR-LBD could become stable, but this component continued to fluctuate in inactive ligands occupied AR-LBD. Settling time and reposition of H12 obtained in dynamics process are important factors governing anti-androgenic activities. The related settling times were characteristic of anti-androgenic potencies of the tested chemicals. Overall, in our study, the stable reposition of H12 is characterized as a computational mark for identifying AR antagonists from PBDE metabolites, or even other various environmental pollutants.

Ozone perturbations in the Arctic summer lower stratosphere as a reflection of NOX chemistry and planetary scale wave activity

NASA Astrophysics Data System (ADS)

Akiyoshi, H.; Sugita, T.; Kanzawa, H.; Kawamoto, N.

2004-02-01

Ozone concentration perturbations in the high-latitude lower stratosphere in the Northern Hemisphere were observed by Improved Limb Atmospheric Spectrometer (ILAS) after the polar vortex breakdown at the beginning of May 1997 and until the end of June of that same year. Simulations and a passive tracer experiment using the Center for Climate System Research/National Institute for Environmental Studies (CCSR/NIES) nudging chemical transport model (CTM) show that the low-ozone perturbations observed in May were caused by the Arctic polar vortex debris, while those after the end of May resulted from a dynamical elongation due to zonal wave number 2 planetary waves of the low-ozone region in the summer polar stratosphere, which had been developed by the catalytic ozone destruction cycle of NOX. These low-O3 air masses of different origin were advected or elongated from the polar region to the ILAS measurement points. An episodic event of a dynamical O3 perturbation in June 1997 on a chemically induced meridional O3 gradient is described. These results show that a timing of the polar vortex breakdown and activity of planetary waves after the breakdown may affect the O3 background gradient in the summer lower stratosphere at middle and high latitudes.

Exploration of bulk and interface behavior of gas molecules and 1-butyl-3-methylimidazolium tetrafluoroborate ionic liquid using equilibrium and nonequilibrium molecular dynamics simulation and quantum chemical calculation.

PubMed

Yang, Quan; Achenie, Luke E K

2018-04-18

Ionic liquids (ILs) show brilliant performance in separating gas impurities, but few researchers have performed an in-depth exploration of the bulk and interface behavior of penetrants and ILs thoroughly. In this research, we have performed a study on both molecular dynamics (MD) simulation and quantum chemical (QC) calculation to explore the transport of acetylene and ethylene in the bulk and interface regions of 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]-[BF4]). The diffusivity, solubility and permeability of gas molecules in the bulk were researched with MD simulation first. The subdiffusion behavior of gas molecules is induced by coupling between the motion of gas molecules and the ions, and the relaxation processes of the ions after the disturbance caused by gas molecules. Then, QC calculation was performed to explore the optical geometry of ions, ion pairs and complexes of ions and penetrants, and interaction potential for pairs and complexes. Finally, nonequilibrium MD simulation was performed to explore the interface structure and properties of the IL-gas system and gas molecule behavior in the interface region. The research results may be used in the design of IL separation media.

Phase Resetting Reveals Network Dynamics Underlying a Bacterial Cell Cycle

PubMed Central

Lin, Yihan; Li, Ying; Crosson, Sean; Dinner, Aaron R.; Scherer, Norbert F.

2012-01-01

Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS). PMID:23209388

Phase resetting reveals network dynamics underlying a bacterial cell cycle.

PubMed

Lin, Yihan; Li, Ying; Crosson, Sean; Dinner, Aaron R; Scherer, Norbert F

2012-01-01

Genomic and proteomic methods yield networks of biological regulatory interactions but do not provide direct insight into how those interactions are organized into functional modules, or how information flows from one module to another. In this work we introduce an approach that provides this complementary information and apply it to the bacterium Caulobacter crescentus, a paradigm for cell-cycle control. Operationally, we use an inducible promoter to express the essential transcriptional regulatory gene ctrA in a periodic, pulsed fashion. This chemical perturbation causes the population of cells to divide synchronously, and we use the resulting advance or delay of the division times of single cells to construct a phase resetting curve. We find that delay is strongly favored over advance. This finding is surprising since it does not follow from the temporal expression profile of CtrA and, in turn, simulations of existing network models. We propose a phenomenological model that suggests that the cell-cycle network comprises two distinct functional modules that oscillate autonomously and couple in a highly asymmetric fashion. These features collectively provide a new mechanism for tight temporal control of the cell cycle in C. crescentus. We discuss how the procedure can serve as the basis for a general approach for probing network dynamics, which we term chemical perturbation spectroscopy (CPS).

The Influence of Chemical Modification on Linker Rotational Dynamics in Metal-Organic Frameworks.

PubMed

Damron, Joshua T; Ma, Jialiu; Kurz, Ricardo; Saalwächter, Kay; Matzger, Adam J; Ramamoorthy, Ayyalusamy

2018-05-21

The robust synthetic flexibility of metal-organic frameworks (MOFs) offers a promising class of tailorable materials, for which the ability to tune specific physicochemical properties is highly desired. This is achievable only through a thorough description of the consequences for chemical manipulations both in structure and dynamics. Magic angle spinning solid-state NMR spectroscopy offers many modalities in this pursuit, particularly for dynamic studies. Herein, we employ a separated-local-field NMR approach to show how specific intraframework chemical modifications to MOF UiO-66 heavily modulate the dynamic evolution of the organic ring moiety over several orders of magnitude. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lagrangian Transport Calculations Using UARS Data. Part 2; Ozone

NASA Technical Reports Server (NTRS)

Manney, Gloria L.; Zurek, R. W.; Froidevaux, L.; Waters, J. W.; ONeill, A.; Swinbank, R.

1995-01-01

Trajectory calculations are used to examine ozone transport in the polar winter stratosphere during periods of the Upper Atmosphere Research Satellite (UARS) observations. The value of these calculations for determining mass transport was demonstrated previously using UARS observations of long-lived tracers, In the middle stratosphere, the overall ozone behavior observed by the Microwave Limb Sounder in the polar vortex is reproduced by this purely dynamical model. Calculations show the evolution of ozone in the lower stratosphere during early winter to be dominated by dynamics in December 1992 in the Arctic. Calculations for June 1992 in the Antarctic show evidence of chemical ozone destruction and indicate that approx. 50% of the chemical destruction may be masked by dynamical effects, mainly diabatic descent, which bring higher ozone into the lower-stratospheric vortex. Estimating differences between calculated and observed fields suggests that dynamical changes masked approx. 20% - 35% of chemical ozone loss during late February and early March 1993 in the Arctic. In the Antarctic late winter, in late August and early September 1992, below approx. 520 K, the evolution of vortex-averaged ozone is entirely dominated by chemical effects; above this level, however, chemical ozone depletion can be partially or completely masked by dynamical effects. Our calculations for 1992 showed that chemical loss was nearly completely compensated by increases due to diabatic descent at 655 K.

Identification of Potential Chemical Carcinogens in Compendia of Gene Expression Profiles

EPA Science Inventory

Chemicals induce cancer through partially characterized adverse outcome pathways (AOPs) that include molecular initiating events (MIEs) and downstream key events (KEs). Microarray profiling of chemical-induced effects is being increasingly used in medium- and high-throughput form...

Dynamics and thermodynamics of open chemical networks

NASA Astrophysics Data System (ADS)

Esposito, Massimiliano

Open chemical networks (OCN) are large sets of coupled chemical reactions where some of the species are chemostated (i.e. continuously restored from the environment). Cell metabolism is a notable example of OCN. Two results will be presented. First, dissipation in OCN operating in nonequilibrium steady-states strongly depends on the network topology (algebraic properties of the stoichiometric matrix). An application to oligosaccharides exchange dynamics performed by so-called D-enzymes will be provided. Second, at low concentration the dissipation of OCN is in general inaccurately predicted by deterministic dynamics (i.e. nonlinear rate equations for the species concentrations). In this case a description in terms of the chemical master equation is necessary. A notable exception is provided by so-called deficiency zero networks, i.e. chemical networks with no hidden cycles present in the graph of reactant complexes.

Tetrapyrrole-photosensitizers vectorization and plasma LDL: a physico-chemical approach.

PubMed

Bonneau, Stéphanie; Vever-Bizet, Christine; Mojzisova, Halina; Brault, Daniel

2007-11-01

A photosensitizer is defined as a chemical entity able to induce, under light-irradiation effect, a chemical or physical alteration of another chemical entity. Thanks to their preferential retention in proliferating tissues, some photosensitizers are therapeutically used such as in photodynamic therapy (PDT). Besides, this method has already been approved for several indications. The selectivity of photosenzitizers for cells in proliferation involves both their association with low density lipoproteins (LDLs) and their ability to cross membranes under various pH conditions. The photosensitizers used are in most cases based on the porphyrin structure, but other compounds, of which far-red-light absorption properties are most compatible with biological tissues irradiation, have been developed, such as phthalocyanines. This paper presents physico-chemical studies of the interaction of a disulfonated aluminium phthalocyanine (AlPcS2) with human LDLs. The data obtained are compared with the parameters of the interaction of these lipoproteins with deuteroporphyrin (DP) and chlorin e6 (Ce6). A close attention is paid to the dynamic aspects of these phenomena. The data obtained on these simple systems then allowed us to interpret the sub-cellular localization of the photosensitizers on a human line of fibroblasts, and to evaluate the influence of LDLs on the intracellular distribution of the compounds. This last point is of major importance because the localization of such photosensitizers (in particular AlPcS2) in endocytic vesicles and their subsequent ability to induce a release of the contents of these vesicles - including externally added macromolecules - into the cytosol is the basis for a recent method for macromolecule activation, named photochemical internalization (PCI). PCI has been shown to potentiate the biological activity of a large variety of macromolecules. The comprehension of the mechanisms governing this particular sub-cellular localization could allow the design of better candidates for PCI.

Necessary conditions for the emergence of homochirality via autocatalytic self-replication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stich, Michael; Ribó, Josep M.; Blackmond, Donna G., E-mail: blackmond@scripps.edu

We analyze a recent proposal for spontaneous mirror symmetry breaking based on the coupling of first-order enantioselective autocatalysis and direct production of the enantiomers that invokes a critical role for intrinsic reaction noise. For isolated systems, the racemic state is the unique stable outcome for both stochastic and deterministic dynamics when the system is in compliance with the constraints dictated by the thermodynamics of chemical reaction processes. In open systems, the racemic outcome also results for both stochastic and deterministic dynamics when driving the autocatalysis unidirectionally by external reagents. Nonracemic states can result in the latter only if the reversemore » reactions are strictly zero: these are kinetically controlled outcomes for small populations and volumes, and can be simulated by stochastic dynamics. However, the stability of the thermodynamic limit proves that the racemic outcome is the unique stable state for strictly irreversible externally driven autocatalysis. These findings contradict the suggestion that the inhibition requirement of the Frank autocatalytic model for the emergence of homochirality may be relaxed in a noise-induced mechanism.« less

Taple-top imaging of the non-adiabatically driven isomerization in the acetylene cation

NASA Astrophysics Data System (ADS)

Beaulieu, Samuel; Ibrahim, Heide; Wales, Benji; Schmidt, Bruno E.; Thiré, Nicolas; Bisson, Éric; Hebeisen, Christoph T.; Wanie, Vincent; Giguere, Mathieu; Kieffer, Jean-Claude; Sanderson, Joe; Schuurman, Michael S.; Légaré, François

2014-05-01

One of the primary goals of modern ultrafast science is to follow nuclear and electronic evolution of molecules as they undergo a photo-chemical reaction. Most of the interesting dynamics phenomena in molecules occur when an electronically excited state is populated. When the energy difference between electronic ground and excited states is large, Free Electron Laser (FEL) and HHG-based VUV sources were, up to date, the only light sources able to efficiently initiate those non-adiabatic dynamics. We have developed a simple table-top approach to initiate those rich dynamics via multiphoton absorption. As a proof of principle, we studied the ultrafast isomerization of the acetylene cation. We have chosen this model system for isomerization since the internal conversion mechanism which leads to proton migration is still under debate since decades. Using 266 nm multiphoton absorption as a pump and 800 nm induced Coulomb Explosion as a probe, we have shoot the first high-resolution molecular movie of the non-adiabatically driven proton migration in the acetylene cation. The experimental results are in excellent agreement with high level ab initio trajectory simulations.

Increases in intramuscular pressure raise arterial blood pressure during dynamic exercise

NASA Technical Reports Server (NTRS)

Gallagher, K. M.; Fadel, P. J.; Smith, S. A.; Norton, K. H.; Querry, R. G.; Olivencia-Yurvati, A.; Raven, P. B.

2001-01-01

This investigation was designed to determine the role of intramuscular pressure-sensitive mechanoreceptors and chemically sensitive metaboreceptors in affecting the blood pressure response to dynamic exercise in humans. Sixteen subjects performed incremental (20 W/min) cycle exercise to fatigue under four conditions: control, exercise with thigh cuff occlusion of 90 Torr (Cuff occlusion), exercise with lower body positive pressure (LBPP) of 45 Torr, and a combination of thigh cuff occlusion and LBPP (combination). Indexes of central command (heart rate, oxygen uptake, ratings of perceived exertion, and electromyographic activity), cardiac output, stroke volume, and total peripheral resistance were not significantly different between the four conditions. Mechanical stimulation during LBPP and combination conditions resulted in significant elevations in intramuscular pressure and mean arterial pressure from control at rest and throughout the incremental exercise protocol (P < 0.05). Conversely, there existed no significant changes in mean arterial pressure when the metaboreflex was stimulated by cuff occlusion. These findings suggest that under normal conditions the mechanoreflex is tonically active and is the primary mediator of exercise pressor reflex-induced alterations in arterial blood pressure during submaximal dynamic exercise in humans.

Coupled acoustic-gravity field for dynamic evaluation of ion exchange with a single resin bead.

PubMed

Kanazaki, Takahiro; Hirawa, Shungo; Harada, Makoto; Okada, Tetsuo

2010-06-01

A coupled acoustic-gravity field is efficient for entrapping a particle at the position determined by its acoustic properties rather than its size. This field has been applied to the dynamic observation of ion-exchange reactions occurring in a single resin bead. The replacement of counterions in an ion-exchange resin induces changes in its acoustic properties, such as density and compressibility. Therefore, we can visually trace the advancement of an ion-exchange reaction as a time change in the levitation position of a resin bead entrapped in the field. Cation-exchange reactions occurring in resin beads with diameters of 40-120 microm are typically completed within 100-200 s. Ion-exchange equilibrium or kinetics is often evaluated with off-line chemical analyses, which require a batch amount of ion exchangers. Measurements with a single resin particle allow us to evaluate ion-exchange dynamics and kinetics of ions including those that are difficult to measure by usual off-line analyses. The diffusion properties of ions in resins have been successfully evaluated from the time change in the levitation positions of resin beads.

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

DOE PAGES

Kern, Jan; Yachandra, Vittal K.; Yano, Junko

2015-09-02

We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

Metalloprotein structures at ambient conditions and in real-time: biological crystallography and spectroscopy using X-ray free electron lasers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kern, Jan; Yachandra, Vittal K.; Yano, Junko

We have studied the structure of enzymes and the chemistry at the catalytic sites, intensively and have acquired an understanding of the atomic-scale chemistry which requires a new approach beyond steady state X-ray crystallography and X-ray spectroscopy at cryogenic temperatures. Following the dynamic changes in the geometric and electronic structure of metallo-enzymes at ambient conditions, while overcoming the severe X-ray-induced changes to the redox active catalytic center, is key for deriving reaction mechanisms. Such studies become possible by the intense and ultra-short femtosecond (fs) X-ray pulses from an X-ray free electron laser (XFEL) by acquiring a signal before the samplemore » is destroyed. Our review describes the recent and pioneering uses of XFELs to study the protein structure and dynamics of metallo-enzymes using crystallography and scattering, as well as the chemical structure and dynamics of the catalytic complexes (charge, spin, and covalency) using spectroscopy during the reaction to understand the electron-transfer processes and elucidate the mechanism.« less

Numerical study on the thermo-chemically driven Geodynamo

NASA Astrophysics Data System (ADS)

Trümper, Tobias; Hansen, Ulrich

2014-05-01

In our numerical study we consider magneto-convection in the Earth's outer core driven by buoyancy induced by heterogeneities both in the thermal and the chemical field. The outer core is thus treated as a self-gravitating, rotating, spherical shell with unstable thermal and chemical gradients across its radius. The thermal gradient is maintained by secular cooling of the core and the release of latent heat at the inner core freezing front. Simultaneously, the concentration of the light constituents of the liquid phase increases at the inner core boundary since only a smaller fraction of the light elements can be incorporated during solidification. Thus, the inner core boundary constitutes a source of compositional buoyancy. The molecular diffusivities of the driving agents differ by some orders of magnitude so that a double-diffusive model is employed in order to study the flow dynamics of this system. We investigate the influence of different thermo-chemical driving scenarios on the structure of the flow and the internal magnetic field. A constant ratio of the diffusivities (Le=10) and a constant Ekman number (Ek=10-4) are adopted. Apart from testing different driving scenarios, the double-diffusive approach also allows to implement distinct boundary conditions on temperature and composition. Isochemical and fixed chemical flux boundary conditions are implemented in order to investigate their respective influence on the flow and magnetic field generation.

Pressure-induced phase transition of KTa1/2Nb1/2O3 solid solutions: A first-principles study

NASA Astrophysics Data System (ADS)

Zhang, Huadi; Liu, Bing; Zhang, Cong; Qiu, Chengcheng; Wang, Xuping; Zhang, Yuanyuan; Lv, Xianshun; Wei, Lei; Li, Qinggang

2018-05-01

The structures and electronic properties of KTa1/2Nb1/2O3 under high pressures have been investigated using the first-principles calculations. Three candidates with B site cation ordered along the [1 0 0], [1 1 0] and [1 1 1] directions are found stable under different pressures by thermodynamics, mechanics and dynamics stability criteria. Further electronic analysis indicates that three structures are semiconductors with different band-gap characteristics. The peculiar chemical bonds of Nb-O and Ta-O are expected to be related to the different electronegativity of the corresponding cations.

Nonlinear electromagnetic interactions in energetic materials

DOE PAGES

Wood, Mitchell Anthony; Dalvit, Diego Alejandro; Moore, David Steven

2016-01-12

We study the scattering of electromagnetic waves in anisotropic energetic materials. Nonlinear light-matter interactions in molecular crystals result in frequency-conversion and polarization changes. Applied electromagnetic fields of moderate intensity can induce these nonlinear effects without triggering chemical decomposition, offering a mechanism for the nonionizing identification of explosives. We use molecular-dynamics simulations to compute such two-dimensional THz spectra for planar slabs made of pentaerythritol tetranitrate and ammonium nitrate. Finally, we discuss third-harmonic generation and polarization-conversion processes in such materials. These observed far-field spectral features of the reflected or transmitted light may serve as an alternative tool for standoff explosive detection.

Resonance in the dynamics of chemical systems simulated by the implicit midpoint scheme

NASA Astrophysics Data System (ADS)

Mandziuk, Margaret; Schlick, Tamar

1995-05-01

The numerical behavior of the symplectic, implicit midpoint method with a wide range of integration timesteps is examined through an application to a diatomic molecule governed by a Morse potential. Our oscillator with a 12.6 fs period exhibits notable, integrator induced, timestep- ( Δt) dependent resonances and we predict approximate values of Δt where they will occur. The particular case of a third-order resonance ( Δt ≈ 7 fs here) leads to instability, and higher-order resonances ( n = 4, 5) to large energetic fluctuations and/or corrupted phase diagrams. Significantly, for Δt > 10 fs the energy errors remain bound.

Radiation damage in WC studied with MD simulations

NASA Astrophysics Data System (ADS)

Träskelin, P.; Björkas, C.; Juslin, N.; Vörtler, K.; Nordlund, K.

2007-04-01

Studying radiation damage in tungsten carbide (WC) is of importance due to its applications in fusion reactors. We have used molecular dynamics to study both deuterium induced sputtering and modification of WC surfaces and collision cascades in bulk WC. For collision cascades in bulk WC we note a massive recombination and major elemental asymmetry for the damage. Studying the erosion of WC surfaces, we find that C can erode through swift chemical sputtering, while W does not sputter more easily than from pure W. The amorphization of the surface and the D-content due to the D bombardment is important for the damage production and sputtering process.

Visualizing Molecular Diffusion through Passive Permeability Barriers in Cells: Conventional and Novel Approaches

PubMed Central

Lin, Yu-Chun; Phua, Siew Cheng; Lin, Benjamin; Inoue, Takanari

2013-01-01

Diffusion barriers are universal solutions for cells to achieve distinct organizations, compositions, and activities within a limited space. The influence of diffusion barriers on the spatiotemporal dynamics of signaling molecules often determines cellular physiology and functions. Over the years, the passive permeability barriers in various subcellular locales have been characterized using elaborate analytical techniques. In this review, we will summarize the current state of knowledge on the various passive permeability barriers present in mammalian cells. We will conclude with a description of several conventional techniques and one new approach based on chemically-inducible diffusion trap (C-IDT) for probing permeable barriers. PMID:23731778

Study on the tumor-induced angiogenesis using mathematical models.

PubMed

Suzuki, Takashi; Minerva, Dhisa; Nishiyama, Koichi; Koshikawa, Naohiko; Chaplain, Mark Andrew Joseph

2018-01-01

We studied angiogenesis using mathematical models describing the dynamics of tip cells. We reviewed the basic ideas of angiogenesis models and its numerical simulation technique to produce realistic computer graphics images of sprouting angiogenesis. We examined the classical model of Anderson-Chaplain using fundamental concepts of mass transport and chemical reaction with ECM degradation included. We then constructed two types of numerical schemes, model-faithful and model-driven ones, where new techniques of numerical simulation are introduced, such as transient probability, particle velocity, and Boolean variables. © 2017 The Authors. Cancer Science published by John Wiley & Sons Australia, Ltd on behalf of Japanese Cancer Association.

Risk evaluation of possible human hazards by chemicals, particles, and infectious units

NASA Astrophysics Data System (ADS)

Weber, Lothar W.; Spleiss, Martin

1996-12-01

Formation of laser plume by laser-tissue interaction means an inhomogeneous, pluriphasic and dynamic multicomponent system of biological material and induced modifications. While IR_laser applications often simulate processes of thermal food preservation, UV-lasers favor formation of aromatic organic compounds as VOC. Along with traces of PAH, nitriles and O-/N-containing heterocyclic compounds two classes of dialkyldiketopyrroli(di)nes are special formed VOC as laser solvents. Inhalable particles or partially dried and modified biomass contain - along with infectious particles - a lot of temperature degradation products. Ames tests and Comet-assays gave hint to some mutagenic activities present in laser smoke.

Herbivore-induced plant volatiles and tritrophic interactions across spatial scales.

PubMed

Aartsma, Yavanna; Bianchi, Felix J J A; van der Werf, Wopke; Poelman, Erik H; Dicke, Marcel

2017-12-01

Herbivore-induced plant volatiles (HIPVs) are an important cue used in herbivore location by carnivorous arthropods such as parasitoids. The effects of plant volatiles on parasitoids have been well characterised at small spatial scales, but little research has been done on their effects at larger spatial scales. The spatial matrix of volatiles ('volatile mosaic') within which parasitoids locate their hosts is dynamic and heterogeneous. It is shaped by the spatial pattern of HIPV-emitting plants, the concentration, chemical composition and breakdown of the emitted HIPV blends, and by environmental factors such as wind, turbulence and vegetation that affect transport and mixing of odour plumes. The volatile mosaic may be exploited differentially by different parasitoid species, in relation to species traits such as sensory ability to perceive volatiles and the physical ability to move towards the source. Understanding how HIPVs influence parasitoids at larger spatial scales is crucial for our understanding of tritrophic interactions and sustainable pest management in agriculture. However, there is a large gap in our knowledge on how volatiles influence the process of host location by parasitoids at the landscape scale. Future studies should bridge the gap between the chemical and behavioural ecology of tritrophic interactions and landscape ecology. © 2017 The Authors. New Phytologist © 2017 New Phytologist Trust.

Modeling of microalgal shear-induced flocculation and sedimentation using a coupled CFD-population balance approach.

PubMed

Golzarijalal, Mohammad; Zokaee Ashtiani, Farzin; Dabir, Bahram

2018-01-01

In this study, shear-induced flocculation modeling of Chlorella sp. microalgae was conducted by combination of population balance modeling and CFD. The inhomogeneous Multiple Size Group (MUSIG) and the Euler-Euler two fluid models were coupled via Ansys-CFX-15 software package to achieve both fluid and particle dynamics during the flocculation. For the first time, a detailed model was proposed to calculate the collision frequency and breakage rate during the microalgae flocculation by means of the response surface methodology as a tool for optimization. The particle size distribution resulted from the model was in good agreement with that of the jar test experiment. Furthermore, the subsequent sedimentation step was also examined by removing the shear rate in both simulations and experiments. Consequently, variation in the shear rate and its effects on the flocculation behavior, sedimentation rate and recovery efficiency were evaluated. Results indicate that flocculation of Chlorella sp. microalgae under shear rates of 37, 182, and 387 s -1 is a promising method of pre-concentration which guarantees the cost efficiency of the subsequent harvesting process by recovering more than 90% of the biomass. © 2017 American Institute of Chemical Engineers Biotechnol. Prog., 34:160-174, 2018. © 2017 American Institute of Chemical Engineers.

Clustering mechanism of oxocarboxylic acids involving hydration reaction: Implications for the atmospheric models

NASA Astrophysics Data System (ADS)

Liu, Ling; Kupiainen-Määttä, Oona; Zhang, Haijie; Li, Hao; Zhong, Jie; Kurtén, Theo; Vehkamäki, Hanna; Zhang, Shaowen; Zhang, Yunhong; Ge, Maofa; Zhang, Xiuhui; Li, Zesheng

2018-06-01

The formation of atmospheric aerosol particles from condensable gases is a dominant source of particulate matter in the boundary layer, but the mechanism is still ambiguous. During the clustering process, precursors with different reactivities can induce various chemical reactions in addition to the formation of hydrogen bonds. However, the clustering mechanism involving chemical reactions is rarely considered in most of the nucleation process models. Oxocarboxylic acids are common compositions of secondary organic aerosol, but the role of oxocarboxylic acids in secondary organic aerosol formation is still not fully understood. In this paper, glyoxylic acid, the simplest and the most abundant atmospheric oxocarboxylic acid, has been selected as a representative example of oxocarboxylic acids in order to study the clustering mechanism involving hydration reactions using density functional theory combined with the Atmospheric Clusters Dynamic Code. The hydration reaction of glyoxylic acid can occur either in the gas phase or during the clustering process. Under atmospheric conditions, the total conversion ratio of glyoxylic acid to its hydration reaction product (2,2-dihydroxyacetic acid) in both gas phase and clusters can be up to 85%, and the product can further participate in the clustering process. The differences in cluster structures and properties induced by the hydration reaction lead to significant differences in cluster formation rates and pathways at relatively low temperatures.

Collective orientational dynamics of pinned chemically-propelled nanorotors

NASA Astrophysics Data System (ADS)

Robertson, Bryan; Stark, Holger; Kapral, Raymond

2018-04-01

Collections of chemically propelled nanomotors free to move in solution can form dynamic clusters with diverse properties as a result of interactions through hydrodynamic flow and concentration fields, as well as direct intermolecular interactions between motors. Here, we study the collective rotational behavior of pinned sphere-dimer motors where direct motor-motor interactions play no role. Since the centers of mass of the motors are pinned, they cannot execute directed translational motion, but they can pump fluid and rotate; thus, the rotors remain coupled through hydrodynamic and chemical fields. Using a microscopic simulation method that accounts for coupling through both these fields, we show that different rotor configurations with a high degree of correlation exist and their forms depend on the nature of the fluid-rotor interactions. The correlations are greatly reduced or completely destroyed when the chemical interactions are removed, indicating that hydrodynamic coupling, while present, plays a lesser role in determining the collective rotor dynamics. These conclusions are supported by Langevin dynamics simulations that neglect hydrodynamics and include an approximate form of coupling through chemical fields.

Many-body dynamics of chemically propelled nanomotors

NASA Astrophysics Data System (ADS)

Colberg, Peter H.; Kapral, Raymond

2017-08-01

The collective behavior of chemically propelled sphere-dimer motors made from linked catalytic and noncatalytic spheres in a quasi-two-dimensional confined geometry is studied using a coarse-grained microscopic dynamical model. Chemical reactions at the catalytic spheres that convert fuel to product generate forces that couple to solvent degrees of freedom as a consequence of momentum conservation in the microscopic dynamics. The collective behavior of the many-body system is influenced by direct intermolecular interactions among the motors, chemotactic effects due to chemical gradients, hydrodynamic coupling, and thermal noise. Segregation into high and low density phases and globally homogeneous states with strong fluctuations are investigated as functions of the motor characteristics. Factors contributing to this behavior are discussed in the context of active Brownian models.

Systematic trends in photonic reagent induced reactions in a homologous chemical family.

PubMed

Tibbetts, Katharine Moore; Xing, Xi; Rabitz, Herschel

2013-08-29

The growing use of ultrafast laser pulses to induce chemical reactions prompts consideration of these pulses as "photonic reagents" in analogy to chemical reagents. This work explores the prospect that photonic reagents may affect systematic trends in dissociative ionization reactions of a homologous family of halomethanes, much as systematic outcomes are often observed for reactions between homologous families of chemical reagents and chemical substrates. The experiments in this work with photonic reagents of varying pulse energy and linear spectral chirp reveal systematic correlations between observable ion yields and the following set of natural variables describing the substrate molecules: the ionization energy of the parent molecule, the appearance energy of each fragment ion, and the relative strength of carbon-halogen bonds in molecules containing two different halogens. The results suggest that reactions induced by photonic reagents exhibit systematic behavior analogous to that observed in reactions driven by chemical reagents, which provides a basis to consider empirical "rules" for predicting the outcomes of photonic reagent induced reactions.

Wireless chemical sensor system based on electromagnetically energy-harvesting metamaterials (Conference Presentation)

NASA Astrophysics Data System (ADS)

Lee, Wonwoo; Jung, Yonghee; Jung, Hyunseung; Lee, Hojin

2017-02-01

In the past decade, there have been many studies on metamaterial based chemical and biological sensors due to their exotic resonance properties in microwave ranges. However, in spite of their non-destructive and highly sensitive properties, they have suffered from the use of bulky and expensive external measurement systems like a network analyzer for measuring resonance properties in the microwave regime. In this study, to increase accessibility of the metamaterial-based sensors, we propose a novel wireless chemical sensor system based on energy harvesting metamaterials at the microwave frequencies. The proposed metamaterial chemical sensor consists of a single split ring resonator and rectifier circuit to harvest the energy at the specific frequency, so that the chemical composition of the specific solution can be distinguished by the proposed metamaterial sensor by using the resonance property between the source antenna and the metamaterial which induces the variation in the energy harvesting rate of our sensor system. In our experimental setup, we used a 2.4 GHz Wi-Fi system as a source antenna. To verify the chemical sensitivity of the proposed sensor intuitively, we adopted a light emitting diode as an indicator of which luminescence is proportional to the energy harvesting rate determined by the ratio of ethanol and water in their binary mixture. With these results, it can be expected that our metamaterial-based wireless sensor can pave the way to the miniaturized wireless sensor systems and can be applied to not only for the chemical fluidic sensors but also for other dynamic environment sensing systems.

Fault Lubrication and Earthquake Propagation in Thermally Unstable Rocks

NASA Astrophysics Data System (ADS)

de Paola, Nicola; Hirose, Takehiro; Mitchell, Tom; di Toro, Giulio; Viti, Cecilia; Shimamoto, Toshiko

2010-05-01

During earthquake propagation in thermally unstable rocks, the frictional heat generated can induce thermal reactions which lead to chemical and physical changes in the slip zone. We performed laboratory friction experiments on thermally unstable minerals (gypsum, dolomite and calcite) at about 1 m/s slip velocities, more than 1 m displacements and calculated temperature rise above 500 C degrees. These conditions are typical during the propagation of large earthquakes. The main findings of our experimental work are: 1) Dramatic fault weakening is characterized by a dynamic frictional strength drop up to 90% of the initial static value in the Byerlee's range. 2) Seismic source parameters, calculated from our experimental results, match those obtained by modelling of seismological data from the 1997 Cofliorito earthquake nucleated in carbonate rocks in Italy (i.e. same rocks used in the friction experiments). Fault lubrication observed during the experiments is controlled by the superposition of multiple, thermally-activated, slip weakening mechanisms (e.g., flash heating, thermal pressurization and nanoparticle lubrication). The integration of mechanical and CO2 emission data, temperature rise calculations and XRPD analyses suggests that flash heating is not the main dynamic slip weakening process. This process was likely inhibited very soon (t < 1s) for displacements d < 0.20 m, when intense grain size reduction by both cataclastic and chemical/thermal processes took place. Conversely, most of the dynamic weakening observed was controlled by thermal pressurization and nanoparticle lubrication processes. The dynamic shear strength of experimental faults was reduced when fluids (CO2, H2O) were trapped and pressurized within the slip zone, in accord with the effective normal stress principle. The fluids were not initially present in the slip zone, but were released by decarbonation (dolomite and Mg-rich calcite) and dehydration (gypsum) reactions, both activated by frictional heating during seismic slip. The dynamic weakening effects of nanoparticles (e.g. powder lubrication) are still unclear due to the poorly understood mechanical properties of nanoparticles at high velocities and temperatures, typical of seismic slip. The experimental results improve our understanding of the controls exerted on the dynamic frictional strength of faults by the coseismic operation of chemical (mineral decomposition) and physical (grain size reduction, fluids release and pressurization) processes. The estimation of this parameter is out of the range of seismological studies, although it controls the magnitude of the stress drop, the seismic fault heat flow and the relative partitioning of the earthquake energy budget, which are all controversial and still debated issues in the scientific community.

Fault Lubrication and Earthquake Propagation in Thermally Unstable Rocks

NASA Astrophysics Data System (ADS)

de Paola, N.; Hirose, T.; Mitchell, T. M.; di Toro, G.; Viti, C.; Shimamoto, T.

2009-12-01

During earthquake propagation in thermally unstable rocks, the frictional heat generated can induce thermal reactions which lead to chemical and physical changes in the slip zone. We performed laboratory friction experiments on thermally unstable minerals (gypsum, dolomite and calcite) at about 1 m/s slip velocities, more than 1 m displacements and calculated temperature rise above 500 C degrees. These conditions are typical during the propagation of large earthquakes. The main findings of our experimental work are: 1) Dramatic fault weakening is characterized by a dynamic frictional strength drop up to 90% of the initial static value in the Byerlee’s range. 2) Seismic source parameters, calculated from our experimental results, match those obtained by modelling of seismological data from the 1997 Cofliorito earthquake nucleated in carbonate rocks in Italy (i.e. same rocks used in the friction experiments). Fault lubrication observed during the experiments is controlled by the superposition of multiple, thermally-activated, slip weakening mechanisms (e.g., flash heating, thermal pressurization and nanoparticle lubrication). The integration of mechanical and CO2 emission data, temperature rise calculations and XRPD analyses suggests that flash heating is not the main dynamic slip weakening process. This process was likely inhibited very soon (t < 1s) for displacements d < 0.20 m, when intense grain size reduction by both cataclastic and chemical/thermal processes took place. Conversely, most of the dynamic weakening observed was controlled by thermal pressurization and nanoparticle lubrication processes. The dynamic shear strength of experimental faults was reduced when fluids (CO2, H2O) were trapped and pressurized within the slip zone, in accord with the effective normal stress principle. The fluids were not initially present in the slip zone, but were released by decarbonation (dolomite and Mg-rich calcite) and dehydration (gypsum) reactions, both activated by frictional heating during seismic slip. The dynamic weakening effects of nanoparticles (e.g. powder lubrication) are still unclear due to the poorly understood mechanical properties of nanoparticles at high velocities and temperatures, typical of seismic slip. The experimental results improve our understanding of the controls exerted on the dynamic frictional strength of faults by the coseismic operation of chemical (mineral decomposition) and physical (grain size reduction, fluids release and pressurization) processes. The estimation of this parameter is out of the range of seismological studies, although it controls the magnitude of the stress drop, the seismic fault heat flow and the relative partitioning of the earthquake energy budget, which are all controversial and still debated issues in the scientific community.

Chemical structure and dynamics: Annual report 1996

DOE Office of Scientific and Technical Information (OSTI.GOV)

Colson, S.D.; McDowell, R.S.

1997-03-01

The Chemical Structure and Dynamics (CS&D) program is a major component of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) developed by Pacific Northwest National Laboratory (PNNL) to provide a state-of-the-art collaborative facility for studies of chemical structure and dynamics. We respond to the need for a fundamental, molecular-level understanding of chemistry at a wide variety of environmentally important interfaces by (1) extending the experimental characterization and theoretical description of chemical reactions to encompass the effects of condensed media and interfaces; (2) developing a multidisciplinary capability for describing interfacial chemical processes within which the new knowledge generated can bemore » brought to bear on complex phenomena in environmental chemistry and in nuclear waste processing and storage; and (3) developing state-of-the-art analytical methods for characterizing waste tanks and pollutant distributions, and for detecting and monitoring trace atmospheric species.« less

EDITORIAL: Special Issue: CAMOP MOLEC XV

NASA Astrophysics Data System (ADS)

2006-01-01

The advances in recent years in the field of molecular dynamics are numerous and impressive. In sophisticated experimental and theoretical studies it is nowadays possible to steer chemical reactions with quantum-number-prepared molecules, to study reaction products fully state-specifically, and to derive accurate potential energy surfaces with the goal of determining the pathways along which molecular interaction can take place. Both experimental and theoretical techniques have rapidly improved, and our understanding of the dynamical nature of chemical processes is continuously growing. In this special issue of CAMOP/Physica Scripta we have tried to present a snapshot of the state-of-the-art in the field of molecular dynamics. It contains a collection of papers submitted in association with the most recent MOLEC meeting (MOLEC XV) held in September 2004 in Nunspeet, The Netherlands. This biannual meeting started in 1976 in Trento and was subsequently organized in Brandbjerg Højskole (Denmark, 1978), Oxford (UK, 1980), Nijmegen (The Netherlands, 1982), Jerusalem (Israel, 1984), Aussois (France, 1986), Assissi (Italy, 1988), Bernkastel-Kues (Germany, 1990), Prague (Czech Republic, 1992), Salamanca (Spain, 1994), Nyborg Strand (Denmark, 1996), Bristol (UK, 1998), Jerusalem (Israel, 2000) and Istanbul (Turkey, 2002). Within the philosophy of CAMOP we have asked invited speakers to report on outstanding problems in their particular field. This comprises discussion of open questions, important applications, new theoretical and experimental approaches and also predictions of future developments. A good comment, in addition to being an authoritative contribution of an acknowledged expert, should also be readable by the non-expert and we have taken special care that the work presented here is introduced in an understandable way and has been placed within the context of accessible literature for the interested reader. The sequence of 16 papers that is presented in this issue is arranged according to three main topics that form a focus within the field and can be roughly summarized as induced chemical (intermolecular) dynamics, molecular spectroscopy/theory, and photo-induced uni-molecular (intramolecular) dynamics. The issue opens with a contribution by the MOLEC XV award winner Levine and his co-workers (the paper by Kornweitz et al) in which they speculate on the possibility of probing electronic rearrangement in a chemical collision using light emitted during the very collision. Banares and co-workers continue with an overview on what is and what is not understood about the dynamics of the `most simple reaction' H + H2 and prospects for future research of this prototypic system are presented. The effect of molecular structure on chemical dynamics is discussed by Pearce \\etal on the example of HCl originating from Cl atoms reacting with different organic ethers. Stereodynamical effects are discussed by Cappelletti and co-workers starting from collisional alignment in supersonic seeded molecular beams with applications ranging from (in)elastic events to selective surface scattering experiments. A laboratory controlled study of chemical reactions under interstellar conditions using temperature variable multi-electrode traps is reviewed by Gerlich and Smith. Eritt \\etal discuss a technique capable of studying the interaction of electrons with size selected molecular ions and results are presented for the electron detachment of Cn- and Aln-clusters. Ultrafast dynamical events at a conical intersection are discussed in a theoretical study by Burghardt et al and the experimental tools to study electron dynamics are presented by Vrakking in a contribution on direct and indirect methods to generate attoseconds. In four spectroscopic and theoretical contributions the latest findings are presented in interpreting and understanding complicated molecular spectra. Meerts and Smit introduce a powerful numerical assign and analysis method based upon genetic algorithms and its performance is demonstrated on the example of dense spectra of (complexed) aromatic species. Interaction potential surface calculations of rare gasses with halogens in van der Waals complexes are described by Delgado-Barrio and co-workers, and Tennyson discusses new theoretical techniques based on the use of the variational principle to guide the spectral assignment of complicated water spectra, e.g. at very high temperatures. Finally, Okumura and co-workers present NIR spectra of NO3 and in combination with new calculations these shed light on how to interpret vibronic couplings in this interesting system. The last section of this issue comprises fragmentation and photo-dissociation studies. Rubio-Lago et al discuss methods to produce high-density spin polarized hydrogen following photodissociation experiments. The photodissociation of HCl and Cl2 is taken as an example by Balint-Kurti et al to demonstrate how amplitudes and phases of the photofragmentation matrix elements are derived from experimental measurements. Directional dynamics in photodissociation processes and the derivation of molecular frame properties are discussed in detail by Van den Brom et al using laboratory oriented molecules. And the issue closes with a contribution by Chambreau et al on different reaction mechanisms in the photodissociation of formaldehyde into H2 and CO. Coming to the end of this editorial, we wish to thank all the authors who participated with their contributions in this issue. It shows what is possible nowadays in the field of molecular dynamics and where things are heading in the near future. We thank Physica Scripta for providing us with the platform for this Special Issue, and we wish you, dear reader, many new insights! Steven Solte, Vrije Universiteit Amsterdam, The Netherlands Harold Linnartz, Leiden Observatory, The Netherlands

Real-space and real-time observation of a plasmon-induced chemical reaction of a single molecule.

PubMed

Kazuma, Emiko; Jung, Jaehoon; Ueba, Hiromu; Trenary, Michael; Kim, Yousoo

2018-05-04

Plasmon-induced chemical reactions of molecules adsorbed on metal nanostructures are attracting increased attention for photocatalytic reactions. However, the mechanism remains controversial because of the difficulty of direct observation of the chemical reactions in the plasmonic field, which is strongly localized near the metal surface. We used a scanning tunneling microscope (STM) to achieve real-space and real-time observation of a plasmon-induced chemical reaction at the single-molecule level. A single dimethyl disulfide molecule on silver and copper surfaces was dissociated by the optically excited plasmon at the STM junction. The STM study combined with theoretical calculations shows that this plasmon-induced chemical reaction occurred by a direct intramolecular excitation mechanism. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Disparate roles of zinc in chemical hypoxia-induced neuronal death

PubMed Central

Kim, Sujeong; Seo, Jung-Woo; Oh, Shin Bi; Kim, So Hee; Kim, Inki; Suh, Nayoung; Lee, Joo-Yong

2015-01-01

Accumulating evidence has provided a causative role of zinc (Zn2+) in neuronal death following ischemic brain injury. Using a hypoxia model of primary cultured cortical neurons with hypoxia-inducing chemicals, cobalt chloride (1 mM CoCl2), deferoxamine (3 mM DFX), and sodium azide (2 mM NaN3), we evaluated whether Zn2+ is involved in hypoxic neuronal death. The hypoxic chemicals rapidly elicited intracellular Zn2+ release/accumulation in viable neurons. The immediate addition of the Zn2+ chelator, CaEDTA or N,N,N’N’-tetrakis-(2-pyridylmethyl) ethylenediamine (TPEN), prevented the intracellular Zn2+ load and CoCl2-induced neuronal death, but neither 3 hour later Zn2+ chelation nor a non-Zn2+ chelator ZnEDTA (1 mM) demonstrated any effects. However, neither CaEDTA nor TPEN rescued neurons from cell death following DFX- or NaN3-induced hypoxia, whereas ZnEDTA rendered them resistant to the hypoxic injury. Instead, the immediate supplementation of Zn2+ rescued DFX- and NaN3-induced neuronal death. The iron supplementation also afforded neuroprotection against DFX-induced hypoxic injury. Thus, although intracellular Zn2+ release/accumulation is common during chemical hypoxia, Zn2+ might differently influence the subsequent fate of neurons; it appears to play a neurotoxic or neuroprotective role depending on the hypoxic chemical used. These results also suggest that different hypoxic chemicals may induce neuronal death via distinct mechanisms. PMID:25667569

Disparate roles of zinc in chemical hypoxia-induced neuronal death.

PubMed

Kim, Sujeong; Seo, Jung-Woo; Oh, Shin Bi; Kim, So Hee; Kim, Inki; Suh, Nayoung; Lee, Joo-Yong

2015-01-01

Accumulating evidence has provided a causative role of zinc (Zn(2+)) in neuronal death following ischemic brain injury. Using a hypoxia model of primary cultured cortical neurons with hypoxia-inducing chemicals, cobalt chloride (1 mM CoCl2), deferoxamine (3 mM DFX), and sodium azide (2 mM NaN3), we evaluated whether Zn(2+) is involved in hypoxic neuronal death. The hypoxic chemicals rapidly elicited intracellular Zn(2+) release/accumulation in viable neurons. The immediate addition of the Zn(2+) chelator, CaEDTA or N,N,N'N'-tetrakis-(2-pyridylmethyl) ethylenediamine (TPEN), prevented the intracellular Zn(2+) load and CoCl2-induced neuronal death, but neither 3 hour later Zn(2+) chelation nor a non-Zn(2+) chelator ZnEDTA (1 mM) demonstrated any effects. However, neither CaEDTA nor TPEN rescued neurons from cell death following DFX- or NaN3-induced hypoxia, whereas ZnEDTA rendered them resistant to the hypoxic injury. Instead, the immediate supplementation of Zn(2+) rescued DFX- and NaN3-induced neuronal death. The iron supplementation also afforded neuroprotection against DFX-induced hypoxic injury. Thus, although intracellular Zn(2+) release/accumulation is common during chemical hypoxia, Zn(2+) might differently influence the subsequent fate of neurons; it appears to play a neurotoxic or neuroprotective role depending on the hypoxic chemical used. These results also suggest that different hypoxic chemicals may induce neuronal death via distinct mechanisms.

Chemical chaperones reduce ionizing radiation-induced endoplasmic reticulum stress and cell death in IEC-6 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Eun Sang; Lee, Hae-June; Lee, Yoon-Jin

Highlights: • UPR activation precedes caspase activation in irradiated IEC-6 cells. • Chemical ER stress inducers radiosensitize IEC-6 cells. • siRNAs that targeted ER stress responses ameliorate IR-induced cell death. • Chemical chaperons prevent cell death in irradiated IEC-6 cells. - Abstract: Radiotherapy, which is one of the most effective approaches to the treatment of various cancers, plays an important role in malignant cell eradication in the pelvic area and abdomen. However, it also generates some degree of intestinal injury. Apoptosis in the intestinal epithelium is the primary pathological factor that initiates radiation-induced intestinal injury, but the mechanism by whichmore » ionizing radiation (IR) induces apoptosis in the intestinal epithelium is not clearly understood. Recently, IR has been shown to induce endoplasmic reticulum (ER) stress, thereby activating the unfolded protein response (UPR) signaling pathway in intestinal epithelial cells. However, the consequences of the IR-induced activation of the UPR signaling pathway on radiosensitivity in intestinal epithelial cells remain to be determined. In this study, we investigated the role of ER stress responses in IR-induced intestinal epithelial cell death. We show that chemical ER stress inducers, such as tunicamycin or thapsigargin, enhanced IR-induced caspase 3 activation and DNA fragmentation in intestinal epithelial cells. Knockdown of Xbp1 or Atf6 with small interfering RNA inhibited IR-induced caspase 3 activation. Treatment with chemical chaperones prevented ER stress and subsequent apoptosis in IR-exposed intestinal epithelial cells. Our results suggest a pro-apoptotic role of ER stress in IR-exposed intestinal epithelial cells. Furthermore, inhibiting ER stress may be an effective strategy to prevent IR-induced intestinal injury.« less

Conservation of Dynamics Associated with Biological Function in an Enzyme Superfamily.

PubMed

Narayanan, Chitra; Bernard, David N; Bafna, Khushboo; Gagné, Donald; Chennubhotla, Chakra S; Doucet, Nicolas; Agarwal, Pratul K

2018-03-06

Enzyme superfamily members that share common chemical and/or biological functions also share common features. While the role of structure is well characterized, the link between enzyme function and dynamics is not well understood. We present a systematic characterization of intrinsic dynamics of over 20 members of the pancreatic-type RNase superfamily, which share a common structural fold. This study is motivated by the fact that the range of chemical activity as well as molecular motions of RNase homologs spans over 10 5 folds. Dynamics was characterized using a combination of nuclear magnetic resonance experiments and computer simulations. Phylogenetic clustering led to the grouping of sequences into functionally distinct subfamilies. Detailed characterization of the diverse RNases showed conserved dynamical traits for enzymes within subfamilies. These results suggest that selective pressure for the conservation of dynamical behavior, among other factors, may be linked to the distinct chemical and biological functions in an enzyme superfamily. Copyright © 2018 Elsevier Ltd. All rights reserved.

Mechanisms of plant defense against insect herbivores

PubMed Central

War, Abdul Rashid; Paulraj, Michael Gabriel; Ahmad, Tariq; Buhroo, Abdul Ahad; Hussain, Barkat; Ignacimuthu, Savarimuthu; Sharma, Hari Chand

2012-01-01

Plants respond to herbivory through various morphological, biochemicals, and molecular mechanisms to counter/offset the effects of herbivore attack. The biochemical mechanisms of defense against the herbivores are wide-ranging, highly dynamic, and are mediated both by direct and indirect defenses. The defensive compounds are either produced constitutively or in response to plant damage, and affect feeding, growth, and survival of herbivores. In addition, plants also release volatile organic compounds that attract the natural enemies of the herbivores. These strategies either act independently or in conjunction with each other. However, our understanding of these defensive mechanisms is still limited. Induced resistance could be exploited as an important tool for the pest management to minimize the amounts of insecticides used for pest control. Host plant resistance to insects, particularly, induced resistance, can also be manipulated with the use of chemical elicitors of secondary metabolites, which confer resistance to insects. By understanding the mechanisms of induced resistance, we can predict the herbivores that are likely to be affected by induced responses. The elicitors of induced responses can be sprayed on crop plants to build up the natural defense system against damage caused by herbivores. The induced responses can also be engineered genetically, so that the defensive compounds are constitutively produced in plants against are challenged by the herbivory. Induced resistance can be exploited for developing crop cultivars, which readily produce the inducible response upon mild infestation, and can act as one of components of integrated pest management for sustainable crop production. PMID:22895106

An Empirical Polarizable Force Field Based on the Classical Drude Oscillator Model: Development History and Recent Applications

PubMed Central

2016-01-01

Molecular mechanics force fields that explicitly account for induced polarization represent the next generation of physical models for molecular dynamics simulations. Several methods exist for modeling induced polarization, and here we review the classical Drude oscillator model, in which electronic degrees of freedom are modeled by charged particles attached to the nuclei of their core atoms by harmonic springs. We describe the latest developments in Drude force field parametrization and application, primarily in the last 15 years. Emphasis is placed on the Drude-2013 polarizable force field for proteins, DNA, lipids, and carbohydrates. We discuss its parametrization protocol, development history, and recent simulations of biologically interesting systems, highlighting specific studies in which induced polarization plays a critical role in reproducing experimental observables and understanding physical behavior. As the Drude oscillator model is computationally tractable and available in a wide range of simulation packages, it is anticipated that use of these more complex physical models will lead to new and important discoveries of the physical forces driving a range of chemical and biological phenomena. PMID:26815602

Photo-induced halide redistribution in organic–inorganic perovskite films

DOE PAGES

deQuilettes, Dane W.; Zhang, Wei; Burlakov, Victor M.; ...

2016-05-24

Organic-inorganic perovskites such as CH 3NH 3PbI 3 are promising materials for a variety of optoelectronic applications, with certified power conversion efficiencies in solar cells already exceeding 21%. Nevertheless, state-of-the-art films still contain performance-limiting non-radiative recombination sites and exhibit a range of complex dynamic phenomena under illumination that remain poorly understood. Here we use a unique combination of confocal photoluminescence (PL) microscopy and chemical imaging to correlate the local changes in photophysics with composition in CH 3NH 3PbI 3 films under illumination. We demonstrate that the photo-induced 'brightening' of the perovskite PL can be attributed to an order-of-magnitude reduction inmore » trap state density. By imaging the same regions with time-of-flight secondary-ion-mass spectrometry, we correlate this photobrightening with a net migration of iodine. In conclusion, our work provides visual evidence for photo-induced halide migration in triiodide perovskites and reveals the complex interplay between charge carrier populations, electronic traps and mobile halides that collectively impact optoelectronic performance.« less

The Atmospheric Scanning Electron Microscope with open sample space observes dynamic phenomena in liquid or gas.

PubMed

Suga, Mitsuo; Nishiyama, Hidetoshi; Konyuba, Yuji; Iwamatsu, Shinnosuke; Watanabe, Yoshiyuki; Yoshiura, Chie; Ueda, Takumi; Sato, Chikara

2011-12-01

Although conventional electron microscopy (EM) requires samples to be in vacuum, most chemical and physical reactions occur in liquid or gas. The Atmospheric Scanning Electron Microscope (ASEM) can observe dynamic phenomena in liquid or gas under atmospheric pressure in real time. An electron-permeable window made of pressure-resistant 100 nm-thick silicon nitride (SiN) film, set into the bottom of the open ASEM sample dish, allows an electron beam to be projected from underneath the sample. A detector positioned below captures backscattered electrons. Using the ASEM, we observed the radiation-induced self-organization process of particles, as well as phenomena accompanying volume change, including evaporation-induced crystallization. Using the electrochemical ASEM dish, we observed tree-like electrochemical depositions on the cathode. In silver nitrate solution, we observed silver depositions near the cathode forming incidental internal voids. The heated ASEM dish allowed observation of patterns of contrast in melting and solidifying solder. Finally, to demonstrate its applicability for monitoring and control of industrial processes, silver paste and solder paste were examined at high throughput. High resolution, imaging speed, flexibility, adaptability, and ease of use facilitate the observation of previously difficult-to-image phenomena, and make the ASEM applicable to various fields. Copyright © 2011 Elsevier B.V. All rights reserved.

Effect of ring rotation upon gas adsorption in SIFSIX-3-M (M = Fe, Ni) pillared square grid networks.

PubMed

Elsaidi, Sameh K; Mohamed, Mona H; Simon, Cory M; Braun, Efrem; Pham, Tony; Forrest, Katherine A; Xu, Wenqian; Banerjee, Debasis; Space, Brian; Zaworotko, Michael J; Thallapally, Praveen K

2017-03-01

Dynamic and flexible metal-organic frameworks (MOFs) that respond to external stimuli, such as stress, light, heat, and the presence of guest molecules, hold promise for applications in chemical sensing, drug delivery, gas separations, and catalysis. A greater understanding of the relationship between flexible constituents in MOFs and gas adsorption may enable the rational design of MOFs with dynamic moieties and stimuli-responsive behavior. Here, we detail the effect of subtle structural changes upon the gas sorption behavior of two "SIFSIX" pillared square grid frameworks, namely SIFSIX-3-M (M = Ni, Fe). We observe a pronounced inflection in the Xe adsorption isotherm in the Ni variant. With evidence from X-ray diffraction studies, density functional theory, and molecular simulations, we attribute the inflection to a disordered to ordered transition of the rotational configurations of the pyrazine rings induced by sorbate-sorbent interactions. We also address the effect of cage size, temperature, and sorbate on the guest-induced ring rotation and the adsorption isotherms. The absence of an inflection in the Xe adsorption isotherm in SIFSIX-3-Fe and in the Kr, N 2 , and CO 2 adsorption isotherms in SIFSIX-3-Ni suggest that the inflection is highly sensitive to the match between the size of the cage and the guest molecule.

A minimal titration model of the mammalian dynamical heat shock response

NASA Astrophysics Data System (ADS)

Sivéry, Aude; Courtade, Emmanuel; Thommen, Quentin

2016-12-01

Environmental stress, such as oxidative or heat stress, induces the activation of the heat shock response (HSR) and leads to an increase in the heat shock proteins (HSPs) level. These HSPs act as molecular chaperones to maintain cellular proteostasis. Controlled by highly intricate regulatory mechanisms, having stress-induced activation and feedback regulations with multiple partners, the HSR is still incompletely understood. In this context, we propose a minimal molecular model for the gene regulatory network of the HSR that reproduces quantitatively different heat shock experiments both on heat shock factor 1 (HSF1) and HSPs activities. This model, which is based on chemical kinetics laws, is kept with a low dimensionality without altering the biological interpretation of the model dynamics. This simplistic model highlights the titration of HSF1 by chaperones as the guiding line of the network. Moreover, by a steady states analysis of the network, three different temperature stress regimes appear: normal, acute, and chronic, where normal stress corresponds to pseudo thermal adaption. The protein triage that governs the fate of damaged proteins or the different stress regimes are consequences of the titration mechanism. The simplicity of the present model is of interest in order to study detailed modelling of cross regulation between the HSR and other major genetic networks like the cell cycle or the circadian clock.

Direct Reprogramming of Fibroblasts via a Chemically Induced XEN-like State.

PubMed

Li, Xiang; Liu, Defang; Ma, Yantao; Du, Xiaomin; Jing, Junzhan; Wang, Lipeng; Xie, Bingqing; Sun, Da; Sun, Shaoqiang; Jin, Xueqin; Zhang, Xu; Zhao, Ting; Guan, Jingyang; Yi, Zexuan; Lai, Weifeng; Zheng, Ping; Huang, Zhuo; Chang, Yanzhong; Chai, Zhen; Xu, Jun; Deng, Hongkui

2017-08-03

Direct lineage reprogramming, including with small molecules, has emerged as a promising approach for generating desired cell types. We recently found that during chemical induction of induced pluripotent stem cells (iPSCs) from mouse fibroblasts, cells pass through an extra-embryonic endoderm (XEN)-like state. Here, we show that these chemically induced XEN-like cells can also be induced to directly reprogram into functional neurons, bypassing the pluripotent state. The induced neurons possess neuron-specific expression profiles, form functional synapses in culture, and further mature after transplantation into the adult mouse brain. Using similar principles, we were also able to induce hepatocyte-like cells from the XEN-like cells. Cells in the induced XEN-like state were readily expandable over at least 20 passages and retained genome stability and lineage specification potential. Our study therefore establishes a multifunctional route for chemical lineage reprogramming and may provide a platform for generating a diverse range of cell types via application of this expandable XEN-like state. Copyright © 2017 Elsevier Inc. All rights reserved.

Can NO-indomethacin counteract the topical gastric toxicity induced by indomethacin interactions with phospholipid bilayers?

PubMed

Pereira-Leite, Catarina; Nunes, Cláudia; Bozelli, José C; Schreier, Shirley; Kamma-Lorger, Christina S; Cuccovia, Iolanda M; Reis, Salette

2018-05-23

Nitric oxide (NO)-releasing nonsteroidal anti-inflammatory drugs (NSAIDs) have been developed to overcome the gastrointestinal and cardiovascular toxicity of NSAIDs, by chemically associating a NO-releasing moiety with commercial NSAIDs. Since increasing evidence supports that NSAIDs toxicity is related to their topical actions in membrane lipids, this work aims to evaluate the impact of adding a NO-releasing moiety to parent NSAIDs regarding their effect on lipid bilayers. Thus, the interactions of NO-indomethacin and indomethacin (parent drug) with 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) bilayers were described herein at pH 3.0 and 7.4. Diverse experimental techniques were combined to characterize the partitioning and location of drugs in DMPC bilayers, and to analyze their effect on the lipid phase transition and the bilayer structure and dynamics. The partitioning of NO-indomethacin into DMPC bilayers was similar to that of charged indomethacin and smaller than that of neutral indomethacin. Both drugs were found to insert the DMPC bilayer and the membrane location of indomethacin was pH-dependent. NO-indomethacin and indomethacin induced a decrease of the main phase transition temperature of DMPC. The effect of these drugs on the bilayer structure and dynamics was dependent on diverse factors, namely drug ionization state, drug:lipid molar ratio, temperature and lipid phase. It is noteworthy that NO-indomethacin induced more pronounced alterations in the biophysical properties of DMPC bilayers than indomethacin, considering equivalent membrane concentrations. Such modifications may have in vivo implications, particularly in the gastric mucosa, where NO-NSAIDs-induced changes in the protective properties of phospholipid layers may contribute to the occurrence of adverse effects. Copyright © 2018 Elsevier B.V. All rights reserved.

Dynamic NMR under nonstationary conditions: Theoretical model, numerical calculation, and potential of application

DOE Office of Scientific and Technical Information (OSTI.GOV)

Babailov, S. P., E-mail: babajlov@niic.nsc.ru; National Research Tomsk Polytechnic University, Lenin Avenue 30, Tomsk 634050; Purtov, P. A.

An expression has been derived for the time dependence of the NMR line shape for systems with multi-site chemical exchange in the absence of spin-spin coupling, in a zero saturation limit. The dynamics of variation of the NMR line shape with time is considered in detail for the case of two-site chemical exchange. Mathematical programs have been designed for numerical simulation of the NMR spectra of chemical exchange systems. The analytical expressions obtained are useful for NMR line shape simulations for systems with photoinduced chemical exchange.

DETECTION OF LOW DOSE RADIATION-AND CHEMICALLY-INDUCED DNA DAMAGE USING TEMPERATURE DIFFERENTIAL FLUORESCENCE ASSAYS

EPA Science Inventory

Rapid, sensitive and simple assays for radiation- and chemically-induced DNA damage can be of significant benefit to a number of fields including radiation biology, clinical research, and environmental monitoring. Although temperature-induced DNA strand separation has been use...

Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment (Final Report)

EPA Science Inventory

EPA announced the release of the final report, Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment . This report provides an overview of the types of mechanisms underlying the lymphohematopoietic cancers induc...

Autophoretic locomotion from geometric asymmetry.

PubMed

Michelin, Sébastien; Lauga, Eric

2015-02-01

Among the few methods which have been proposed to create small-scale swimmers, those relying on self-phoretic mechanisms present an interesting design challenge in that chemical gradients are required to generate net propulsion. Building on recent work, we propose that asymmetries in geometry are sufficient to induce chemical gradients and swimming. We illustrate this idea using two different calculations. We first calculate exactly the self-propulsion speed of a system composed of two spheres of unequal sizes but identically chemically homogeneous. We then consider arbitrary, small-amplitude, shape deformations of a chemically homogeneous sphere, and calculate asymptotically the self-propulsion velocity induced by the shape asymmetries. Our results demonstrate how geometric asymmetries can be tuned to induce large locomotion speeds without the need of chemical patterning.

Chemically induced phospholipid translocation across biological membranes.

PubMed

Gurtovenko, Andrey A; Onike, Olajide I; Anwar, Jamshed

2008-09-02

Chemical means of manipulating the distribution of lipids across biological membranes is of considerable interest for many biomedical applications as a characteristic lipid distribution is vital for numerous cellular functions. Here we employ atomic-scale molecular simulations to shed light on the ability of certain amphiphilic compounds to promote lipid translocation (flip-flops) across membranes. We show that chemically induced lipid flip-flops are most likely pore-mediated: the actual flip-flop event is a very fast process (time scales of tens of nanoseconds) once a transient water defect has been induced by the amphiphilic chemical (dimethylsulfoxide in this instance). Our findings are consistent with available experimental observations and further emphasize the importance of transient membrane defects for chemical control of lipid distribution across cell membranes.

Micromotors for "Chemistry-on-the-Fly".

PubMed

Karshalev, Emil; Esteban-Fernández de Ávila, Berta; Wang, Joseph

2018-03-21

This perspective reviews mobile micro/nanomotor scaffolds for performing "chemistry-on-the-fly". Synthetic nano/micromotors offer great versatility and distinct advantages in diverse chemical applications owing to their efficient propulsion and facile surface functionalization that allow these mobile platforms to move and disperse reactive materials across the solution. Such dynamic microreactors have led to accelerated chemical processes, including organic pollutant degradation, metal chelation, biorecognition, redox chemistry, chemical "writing", and a variety of other chemical transformations. Representative examples of such micromotor-enhanced chemical reactions are discussed, focusing on the specific chemical role of these mobile microreactors. The advantages, gaps and limitations of using micromotors as mobile chemical platforms are discussed, concluding with the future prospects of this emerging field. We envision that artificial nano/micromotors will become attractive dynamic tools for speeding up and enhancing "on-the-fly" chemical reactions.

Dendritic cells' death induced by contact sensitizers is controlled by Nrf2 and depends on glutathione levels

DOE Office of Scientific and Technical Information (OSTI.GOV)

El Ali, Zeina

Dendritic cells (DC) are known to play a major role during contact allergy induced by contact sensitizers (CS). Our previous studies showed that Nrf2 was induced in DC and controlled allergic skin inflammation in mice in response to chemicals. In this work, we raised the question of the role of Nrf2 in response to a stress provoked by chemical sensitizers in DC. We used two well-described chemical sensitizers, dinitrochlorobenzene (DNCB) and cinnamaldehyde (CinA), known to have different chemical reactivity and mechanism of action. First, we performed a RT-qPCR array showing that CinA was a higher inducer of immune and detoxificationmore » genes compared to DNCB. Interestingly, in the absence of Nrf2, gene expression was dramatically affected in response to DNCB but was slightly affected in response to CinA. These observations prompted us to study DC's cell death in response to both chemicals. DNCB and CinA increased apoptotic cells and decreased living cells in the absence of Nrf2. The characterization of DC apoptosis induced by both CS involved the mitochondrial-dependent caspase pathway and was regulated via Nrf2 in response to both chemicals. Oxidative stress induced by DNCB, and leading to cell death, was regulated by Nrf2. Unlike CinA, DNCB treatment provoked a significant reduction of intracellular GSH levels and up-regulated bcl-2 gene expression, under the control of Nrf2. This work underlies that chemical reactivity may control Nrf2-dependent gene expression leading to different cytoprotective mechanisms in DC. - Highlights: • Nrf2 controls cell death induced by contact sensitizers in dendritic cells. • DNCB reduced GSH levels and up-regulated bcl-2 gene expression unlike CinA. • Chemical reactivity controls Nrf2-dependent genes having protective effect in DC.« less

Integrated optical sensors for 2D spatial chemical mapping (Conference Presentation)

NASA Astrophysics Data System (ADS)

Flores, Raquel; Janeiro, Ricardo; Viegas, Jaime

2017-02-01

Sensors based on optical waveguides for chemical sensing have attracted increasing interest over the last two decades, fueled by potential applications in commercial lab-on-a-chip devices for medical and food safety industries. Even though the early studies were oriented for single-point detection, progress in device size reduction and device yield afforded by photonics foundries have opened the opportunity for distributed dynamic chemical sensing at the microscale. This will allow researchers to follow the dynamics of chemical species in field of microbiology, and microchemistry, with a complementary method to current technologies based on microfluorescence and hyperspectral imaging. The study of the chemical dynamics at the surface of photoelectrodes in water splitting cells are a good candidate to benefit from such optochemical sensing devices that includes a photonic integrated circuit (PIC) with multiple sensors for real-time detection and spatial mapping of chemical species. In this project, we present experimental results on a prototype integrated optical system for chemical mapping based on the interaction of cascaded resonant optical devices, spatially covered with chemically sensitive polymers and plasmon-enhanced nanostructured metal/metal-oxide claddings offering chemical selectivity in a pixelated surface. In order to achieve a compact footprint, the prototype is based in a silicon photonics platform. A discussion on the relative merits of a photonic platform based on large bandgap metal oxides and nitrides which have higher chemical resistance than silicon is also presented.

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

PubMed Central

2018-01-01

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the properties of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Last, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site. PMID:29386401

Lymphohematopoietic Cancers Induced by Chemicals and Other Agents: Overview and Implications for Risk Assessment (External Review Draft)

EPA Science Inventory

This draft report provides an overview of the types of mechanisms underlying the lymphohematopoietic cancers induced by chemical agents and radiation in humans, with a primary emphasis on leukemia and leukemia-inducing agents. It focuses on how mechanistic information on human l...

Electro-hydrodynamics and kinetic modelling of polluted air flow activated by multi-tip-to-plane corona discharge

DOE Office of Scientific and Technical Information (OSTI.GOV)

Meziane, M.; Eichwald, O.; Ducasse, O.

The present paper is devoted to the 2D simulation of an Atmospheric Corona Discharge Reactor (ACDR) involving 10 pins powered by a DC high voltage and positioned 7 mm above a grounded metallic plane. The corona reactor is periodically crossed by thin mono filamentary streamers with a natural repetition frequency of some tens of kHz. The simulation involves the electro-dynamic, chemical kinetic, and neutral gas hydrodynamic phenomena that influence the kinetics of the chemical species transformation. Each discharge stage (including the primary and the secondary streamers development and the resulting thermal shock) lasts about one hundred nanoseconds while the post-dischargemore » stages occurring between two successive discharge phases last one hundred microseconds. The ACDR is crossed by a lateral air flow including 400 ppm of NO. During the considered time scale of 10 ms, one hundred discharge/post-discharge cycles are simulated. The simulation involves the radical formation and thermal exchange between the discharges and the background gas. The results show how the successive discharges activate the flow gas and how the induced turbulence phenomena affect the redistribution of the thermal energy and the chemical kinetics inside the ACDR.« less

Application of advanced remote sensing techniques to improve modeling estuary water quality

USDA-ARS?s Scientific Manuscript database

Estuaries, the interface between terrestrial and coastal waters are an important component of complex and dynamic coastal watersheds. They are usually characterized by abrupt chemical gradients and complex dynamics, which can result in major transformations in the amount, chemical nature and timing ...

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES

PubMed Central

Somogyi, Endre; Glazier, James A.

2017-01-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment. PMID:29303160

A MODELING AND SIMULATION LANGUAGE FOR BIOLOGICAL CELLS WITH COUPLED MECHANICAL AND CHEMICAL PROCESSES.

PubMed

Somogyi, Endre; Glazier, James A

2017-04-01

Biological cells are the prototypical example of active matter. Cells sense and respond to mechanical, chemical and electrical environmental stimuli with a range of behaviors, including dynamic changes in morphology and mechanical properties, chemical uptake and secretion, cell differentiation, proliferation, death, and migration. Modeling and simulation of such dynamic phenomena poses a number of computational challenges. A modeling language describing cellular dynamics must naturally represent complex intra and extra-cellular spatial structures and coupled mechanical, chemical and electrical processes. Domain experts will find a modeling language most useful when it is based on concepts, terms and principles native to the problem domain. A compiler must then be able to generate an executable model from this physically motivated description. Finally, an executable model must efficiently calculate the time evolution of such dynamic and inhomogeneous phenomena. We present a spatial hybrid systems modeling language, compiler and mesh-free Lagrangian based simulation engine which will enable domain experts to define models using natural, biologically motivated constructs and to simulate time evolution of coupled cellular, mechanical and chemical processes acting on a time varying number of cells and their environment.

A survey of chemicals inducing lipid peroxidation in biological systems.

PubMed

Kappus, H

1987-01-01

A great number of drugs and chemicals are reviewed which have been shown to stimulate lipid peroxidation in any biological system. The underlying mechanisms, as far as known, are also dealt with. Lipid peroxidation induced by iron ions, organic hydroperoxides, halogenated hydrocarbons, redox cycling drugs, glutathione depleting chemicals, ethanol, heavy metals, ozone, nitrogen dioxide and a number of miscellaneous compounds, e.g. hydrazines, pesticides, antibiotics, are mentioned. It is shown that lipid peroxidation is stimulated by many of these compounds. However, quantitative estimates cannot be given yet and it is still impossible to judge the biological relevance of chemical-induced lipid peroxidation.

Impact of fluorescent protein fusions on the bacterial flagellar motor.

PubMed

Heo, M; Nord, A L; Chamousset, D; van Rijn, E; Beaumont, H J E; Pedaci, F

2017-10-03

Fluorescent fusion proteins open a direct and unique window onto protein function. However, they also introduce the risk of perturbation of the function of the native protein. Successful applications of fluorescent fusions therefore rely on a careful assessment and minimization of the side effects, but such insight is still lacking for many applications. This is particularly relevant in the study of the internal dynamics of motor proteins, where both the chemical and mechanical reaction coordinates can be affected. Fluorescent proteins fused to the stator of the Bacterial Flagellar Motor (BFM) have previously been used to unveil the motor subunit dynamics. Here we report the effects on single motors of three fluorescent proteins fused to the stators, all of which altered BFM behavior. The torque generated by individual stators was reduced while their stoichiometry remained unaffected. MotB fusions decreased the switching frequency and induced a novel bias-dependent asymmetry in the speed in the two directions. These effects could be mitigated by inserting a linker at the fusion point. These findings provide a quantitative account of the effects of fluorescent fusions to the stator on BFM dynamics and their alleviation- new insights that advance the use of fluorescent fusions to probe the dynamics of protein complexes.

Control of chemical dynamics by lasers: theoretical considerations.

PubMed

Kondorskiy, Alexey; Nanbu, Shinkoh; Teranishi, Yoshiaki; Nakamura, Hiroki

2010-06-03

Theoretical ideas are proposed for laser control of chemical dynamics. There are the following three elementary processes in chemical dynamics: (i) motion of the wave packet on a single adiabatic potential energy surface, (ii) excitation/de-excitation or pump/dump of wave packet, and (iii) nonadiabatic transitions at conical intersections of potential energy surfaces. A variety of chemical dynamics can be controlled, if we can control these three elementary processes as we desire. For (i) we have formulated the semiclassical guided optimal control theory, which can be applied to multidimensional real systems. The quadratic or periodic frequency chirping method can achieve process (ii) with high efficiency close to 100%. Concerning process (iii) mentioned above, the directed momentum method, in which a predetermined momentum vector is given to the initial wave packet, makes it possible to enhance the desired transitions at conical intersections. In addition to these three processes, the intriguing phenomenon of complete reflection in the nonadiabatic-tunneling-type of potential curve crossing can also be used to control a certain class of chemical dynamics. The basic ideas and theoretical formulations are provided for the above-mentioned processes. To demonstrate the effectiveness of these controlling methods, numerical examples are shown by taking the following processes: (a) vibrational photoisomerization of HCN, (b) selective and complete excitation of the fine structure levels of K and Cs atoms, (c) photoconversion of cyclohexadiene to hexatriene, and (d) photodissociation of OHCl to O + HCl.

Enhancing Continuous Online Microdialysis Using Dexamethasone: Measurement of Dynamic Neurometabolic Changes during Spreading Depolarization.

PubMed

Varner, Erika L; Leong, Chi Leng; Jaquins-Gerstl, Andrea; Nesbitt, Kathryn M; Boutelle, Martyn G; Michael, Adrian C

2017-08-16

Microdialysis is well established in chemical neuroscience as a mainstay technology for real time intracranial chemical monitoring in both animal models and human patients. Evidence shows that microdialysis can be enhanced by mitigating the penetration injury caused during the insertion of microdialysis probes into brain tissue. Herein, we show that retrodialysis of dexamethasone in the rat cortex enhances the microdialysis detection of K + and glucose transients induced by spreading depolarization. Without dexamethasone, quantification of glucose transients was unreliable by 5 days after probe insertion. With dexamethasone, robust K + and glucose transients were readily quantified at 2 h, 5 days, and 10 days after probe insertion. The amplitudes of the K + transients declined day-to-day following probe insertion, and the amplitudes of the glucose transients exhibited a decreasing trend that did not reach statistical significance. Immunohistochemistry and fluorescence microscopy confirm that dexamethasone is highly effective at preserving a healthy probe-brain interface for at least 10 days even though retrodialysis of dexamethasone ceased after 5 days.

Chemo-mechanical modeling of tumor growth in elastic epithelial tissue

NASA Astrophysics Data System (ADS)

Bratsun, Dmitry A.; Zakharov, Andrey P.; Pismen, Len

2016-08-01

We propose a multiscale chemo-mechanical model of the cancer tumor development in the epithelial tissue. The epithelium is represented by an elastic 2D array of polygonal cells with its own gene regulation dynamics. The model allows the simulation of the evolution of multiple cells interacting via the chemical signaling or mechanically induced strain. The algorithm includes the division and intercalation of cells as well as the transformation of normal cells into a cancerous state triggered by a local failure of the spatial synchronization of the cellular rhythms driven by transcription/translation processes. Both deterministic and stochastic descriptions of the system are given for chemical signaling. The transformation of cells means the modification of their respective parameters responsible for chemo-mechanical interactions. The simulations reproduce a distinct behavior of invasive and localized carcinoma. Generally, the model is designed in such a way that it can be readily modified to take account of any newly understood gene regulation processes and feedback mechanisms affecting chemo-mechanical properties of cells.

The effect of breaking gravity waves on the dynamics and chemistry of the mesosphere and lower thermosphere (invited review)

NASA Technical Reports Server (NTRS)

Garcia, R. R.

1986-01-01

The influence of breaking gravity waves on the dynamics and chemical composition of the 60 to 110 km region is investigated with a two dimensional model that includes a parameterization of gravity wave momentum deposition and diffusion. The dynamical model is described by Garcia and Solomon (1983) and Solomon and Garcia (1983) and includes a complete chemical scheme for the mesosphere and lower thermosphere. The parameterization of Lindzen (1981) is used to calculate the momentum deposited and the turbulent diffusion produced by the gravity waves. It is found that wave momentum deposition drives a very vigorous mean meridional circulation, produces a very cold summer mesopause and reverse the zonal wind jets above about 85 km. The seasonal variation of the turbulent diffusion coefficient is consistent with the behavior of mesospheric turbulences inferred from MST radar echoes. The large degree of consistency between model results and various types of dynamical and chemical data supports very strongly the hypothesis that breaking gravity waves play a major role in determining the zonally-averaged dynamical and chemical structure of the 60 to 110 km region of the atmosphere.

Reaction Analysis of Shocked Nitromethane using Extended Lagrangian Born-Oppenheimer Molecular Dynamics

NASA Astrophysics Data System (ADS)

Perriot, Romain; Kober, Ed; Mniszewski, Sue; Martinez, Enrique; Niklasson, Anders; Yang, Ping; McGrane, Shawn; Cawkwell, Marc

2017-06-01

Characterizing the complex, rapid reactions of energetic materials under conditions of high temperatures and pressures presents strong experimental and computational challenges. The recently developed extended Lagrangian Born-Oppenheimer molecular dynamics formalism enables the long-term conservation of the total energy in microcanonical trajectories, and using a density functional tight binding formulation provides good chemical accuracy. We use this combined approach to study the evolution of temperature, pressure, and chemical species in shock-compressed liquid nitromethane over hundreds of picoseconds. The chemical species seen in nitromethane under shock compression are compared with those seen under static high temperature conditions. A reduced-order representation of the complex sequence of chemical reactions that characterize this system has been developed from the molecular dynamics simulations by focusing on classes of chemical reactions rather than specific molecular species. Time-resolved infra-red vibrational spectra were also computed from the molecular trajectories and compared to the chemical analysis. These spectra provide a time history of the species present in the system that can be compared directly with recent experiments at LANL.

Process for derivatizing carbon nanotubes with diazonium species and compositions thereof

NASA Technical Reports Server (NTRS)

Bahr, Jeffrey L. (Inventor); Tour, James M. (Inventor); Yang, Jiping (Inventor)

2011-01-01

Methods for the chemical modification of carbon nanotubes involve the derivatization of multi- and single-wall carbon nanotubes, including small diameter (ca. 0.7 nm) single-wall carbon nanotubes, with diazonium species. The method allows the chemical attachment of a variety of organic compounds to the side and ends of carbon nanotubes. These chemically modified nanotubes have applications in polymer composite materials, molecular electronic applications, and sensor devices. The methods of derivatization include electrochemical induced reactions, thermally induced reactions, and photochemically induced reactions. Moreover, when modified with suitable chemical groups, the derivatized nanotubes are chemically compatible with a polymer matrix, allowing transfer of the properties of the nanotubes (such as, mechanical strength or electrical conductivity) to the properties of the composite material as a whole. Furthermore, when modified with suitable chemical groups, the groups can be polymerized to form a polymer that includes carbon nanotubes.

The time-dependence of exchange-induced relaxation during modulated radio frequency pulses.

PubMed

Sorce, Dennis J; Michaeli, Shalom; Garwood, Michael

2006-03-01

The problem of the relaxation of identical spins 1/2 induced by chemical exchange between spins with different chemical shifts in the presence of time-dependent RF irradiation (in the first rotating frame) is considered for the fast exchange regime. The solution for the time evolution under the chemical exchange Hamiltonian in the tilted doubly rotating frame (TDRF) is presented. Detailed derivation is specified to the case of a two-site chemical exchange system with complete randomization between jumps of the exchanging spins. The derived theory can be applied to describe the modulation of the chemical exchange relaxation rate constants when using a train of adiabatic pulses, such as the hyperbolic secant pulse. Theory presented is valid for quantification of the exchange-induced time-dependent rotating frame longitudinal T1rho,ex and transverse T2rho,ex relaxations in the fast chemical exchange regime.

Incorporating zebrafish omics into chemical biology and toxicology.

PubMed

Sukardi, Hendrian; Ung, Choong Yong; Gong, Zhiyuan; Lam, Siew Hong

2010-03-01

In this communication, we describe the general aspects of omics approaches for analyses of transcriptome, proteome, and metabolome, and how they can be strategically incorporated into chemical screening and perturbation studies using the zebrafish system. Pharmacological efficacy and selectivity of chemicals can be evaluated based on chemical-induced phenotypic effects; however, phenotypic observation has limitations in identifying mechanistic action of chemicals. We suggest adapting gene-expression-based high-throughput screening as a complementary strategy to zebrafish-phenotype-based screening for mechanistic insights about the mode of action and toxicity of a chemical, large-scale predictive applications and comparative analysis of chemical-induced omics signatures, which are useful to identify conserved biological responses, signaling pathways, and biomarkers. The potential mechanistic, predictive, and comparative applications of omics approaches can be implemented in the zebrafish system. Examples of these using the omics approaches in zebrafish, including data of ours and others, are presented and discussed. Omics also facilitates the translatability of zebrafish studies across species through comparison of conserved chemical-induced responses. This review is intended to update interested readers with the current omics approaches that have been applied in chemical studies on zebrafish and their potential in enhancing discovery in chemical biology.

Molecular dynamics study of salt–solution interface: Solubility and surface charge of salt in water

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kobayashi, Kazuya; Liang, Yunfeng, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp; Matsuoka, Toshifumi, E-mail: y-liang@earth.kumst.kyoto-u.ac.jp, E-mail: matsuoka@earth.kumst.kyoto-u.ac.jp

2014-04-14

The NaCl salt–solution interface often serves as an example of an uncharged surface. However, recent laser-Doppler electrophoresis has shown some evidence that the NaCl crystal is positively charged in its saturated solution. Using molecular dynamics (MD) simulations, we have investigated the NaCl salt–solution interface system, and calculated the solubility of the salt using the direct method and free energy calculations, which are kinetic and thermodynamic approaches, respectively. The direct method calculation uses a salt–solution combined system. When the system is equilibrated, the concentration in the solution area is the solubility. In the free energy calculation, we separately calculate the chemicalmore » potential of NaCl in two systems, the solid and the solution, using thermodynamic integration with MD simulations. When the chemical potential of NaCl in the solution phase is equal to the chemical potential of the solid phase, the concentration of the solution system is the solubility. The advantage of using two different methods is that the computational methods can be mutually verified. We found that a relatively good estimate of the solubility of the system can be obtained through comparison of the two methods. Furthermore, we found using microsecond time-scale MD simulations that the positively charged NaCl surface was induced by a combination of a sodium-rich surface and the orientation of the interfacial water molecules.« less

Recent developments for realistic solar models

DOE Office of Scientific and Technical Information (OSTI.GOV)

Serenelli, Aldo M.

2014-05-02

The 'solar abundance problem' has triggered a renewed interest in revising the concept of SSM from different perspectives: 1) constituent microphysics: equation of state, nuclear rates, radiative opacities; 2) constituent macrophysics: the physical processes impact the evolution of the Sun and its present-day structure, e.g. dynamical processes induced by rotation, presence of magnetic fields; 3) challenge the hypothesis that the young Sun was chemically homogeneous: the possible interaction of the young Sun with its protoplanetary disk. Here, I briefly review and then present a (personal) view on recent advances and developments on solar modeling, part of them carried out asmore » attempts to solve the solar abundance problem.« less

Amplification of intrinsic fluctuations by the Lorenz equations

NASA Astrophysics Data System (ADS)

Fox, Ronald F.; Elston, T. C.

1993-07-01

Macroscopic systems (e.g., hydrodynamics, chemical reactions, electrical circuits, etc.) manifest intrinsic fluctuations of molecular and thermal origin. When the macroscopic dynamics is deterministically chaotic, the intrinsic fluctuations may become amplified by several orders of magnitude. Numerical studies of this phenomenon are presented in detail for the Lorenz model. Amplification to macroscopic scales is exhibited, and quantitative methods (binning and a difference-norm) are presented for measuring macroscopically subliminal amplification effects. In order to test the quality of the numerical results, noise induced chaos is studied around a deterministically nonchaotic state, where the scaling law relating the Lyapunov exponent to noise strength obtained for maps is confirmed for the Lorenz model, a system of ordinary differential equations.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2016-10-25

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Two-dimensional fourier transform spectrometer

DOEpatents

DeFlores, Lauren; Tokmakoff, Andrei

2013-09-03

The present invention relates to a system and methods for acquiring two-dimensional Fourier transform (2D FT) spectra. Overlap of a collinear pulse pair and probe induce a molecular response which is collected by spectral dispersion of the signal modulated probe beam. Simultaneous collection of the molecular response, pulse timing and characteristics permit real time phasing and rapid acquisition of spectra. Full spectra are acquired as a function of pulse pair timings and numerically transformed to achieve the full frequency-frequency spectrum. This method demonstrates the ability to acquire information on molecular dynamics, couplings and structure in a simple apparatus. Multi-dimensional methods can be used for diagnostic and analytical measurements in the biological, biomedical, and chemical fields.

Visualizing molecular diffusion through passive permeability barriers in cells: conventional and novel approaches.

PubMed

Lin, Yu-Chun; Phua, Siew Cheng; Lin, Benjamin; Inoue, Takanari

2013-08-01

Diffusion barriers are universal solutions for cells to achieve distinct organizations, compositions, and activities within a limited space. The influence of diffusion barriers on the spatiotemporal dynamics of signaling molecules often determines cellular physiology and functions. Over the years, the passive permeability barriers in various subcellular locales have been characterized using elaborate analytical techniques. In this review, we will summarize the current state of knowledge on the various passive permeability barriers present in mammalian cells. We will conclude with a description of several conventional techniques and one new approach based on chemically inducible diffusion trap (CIDT) for probing permeable barriers. Copyright © 2013 Elsevier Ltd. All rights reserved.

Automated chemical kinetic modeling via hybrid reactive molecular dynamics and quantum chemistry simulations.

PubMed

Döntgen, Malte; Schmalz, Felix; Kopp, Wassja A; Kröger, Leif C; Leonhard, Kai

2018-06-13

An automated scheme for obtaining chemical kinetic models from scratch using reactive molecular dynamics and quantum chemistry simulations is presented. This methodology combines the phase space sampling of reactive molecular dynamics with the thermochemistry and kinetics prediction capabilities of quantum mechanics. This scheme provides the NASA polynomial and modified Arrhenius equation parameters for all species and reactions that are observed during the simulation and supplies them in the ChemKin format. The ab initio level of theory for predictions is easily exchangeable and the presently used G3MP2 level of theory is found to reliably reproduce hydrogen and methane oxidation thermochemistry and kinetics data. Chemical kinetic models obtained with this approach are ready-to-use for, e.g., ignition delay time simulations, as shown for hydrogen combustion. The presented extension of the ChemTraYzer approach can be used as a basis for methodologically advancing chemical kinetic modeling schemes and as a black-box approach to generate chemical kinetic models.

Dynamic range in small-world networks of Hodgkin-Huxley neurons with chemical synapses

NASA Astrophysics Data System (ADS)

Batista, C. A. S.; Viana, R. L.; Lopes, S. R.; Batista, A. M.

2014-09-01

According to Stevens' law the relationship between stimulus and response is a power-law within an interval called the dynamic range. The dynamic range of sensory organs is found to be larger than that of a single neuron, suggesting that the network structure plays a key role in the behavior of both the scaling exponent and the dynamic range of neuron assemblies. In order to verify computationally the relationships between stimulus and response for spiking neurons, we investigate small-world networks of neurons described by the Hodgkin-Huxley equations connected by chemical synapses. We found that the dynamic range increases with the network size, suggesting that the enhancement of the dynamic range observed in sensory organs, with respect to single neurons, is an emergent property of complex network dynamics.

Atomic Resolution Imaging of Nanoscale Chemical Expansion in PrxCe1-xO2-δ during In Situ Heating.

PubMed

Swallow, Jessica G; Lee, Ja Kyung; Defferriere, Thomas; Hughes, Gareth M; Raja, Shilpa N; Tuller, Harry L; Warner, Jamie H; Van Vliet, Krystyn J

2018-02-27

Thin film nonstoichiometric oxides enable many high-temperature applications including solid oxide fuel cells, actuators, and catalysis. Large concentrations of point defects (particularly, oxygen vacancies) enable fast ionic conductivity or gas exchange kinetics in these materials but also manifest as coupling between lattice volume and chemical composition. This chemical expansion may be either detrimental or useful, especially in thin film devices that may exhibit enhanced performance through strain engineering or decreased operating temperatures. However, thin film nonstoichiometric oxides can differ from bulk counterparts in terms of operando defect concentrations, transport properties, and mechanical properties. Here, we present an in situ investigation of atomic-scale chemical expansion in Pr x Ce 1-x O 2-δ (PCO), a mixed ionic-electronic conducting oxide relevant to electrochemical energy conversion and high-temperature actuation. Through a combination of electron energy loss spectroscopy and transmission electron microscopy with in situ heating, we characterized chemical strains and changes in oxidation state in cross sections of PCO films grown on yttria-stabilized zirconia (YSZ) at temperatures reaching 650 °C. We quantified, both statically and dynamically, the nanoscale chemical expansion induced by changes in PCO redox state as a function of position and direction relative to the film-substrate interface. Additionally, we observed dislocations at the film-substrate interface, as well as reduced cation localization to threading defects within PCO films. These results illustrate several key aspects of atomic-scale structure and mechanical deformation in nonstoichiometric oxide films that clarify distinctions between films and bulk counterparts and that hold several implications for operando chemical expansion or "breathing" of such oxide films.

Abolished thermal and mechanical antinociception but retained visceral chemical antinociception induced by butorphanol in μ-opioid receptor knockout mice

PubMed Central

Ide, Soichiro; Minami, Masabumi; Ishihara, Kumatoshi; Uhl, George R.; Satoh, Masamichi; Sora, Ichiro; Ikeda, Kazutaka

2012-01-01

Butorphanol is hypothesized to induce analgesia via opioid pathways, although the precise mechanisms for its effects remain unknown. In this study, we investigated the role of the μ-opioid receptor (MOP) in thermal, mechanical, and visceral chemical antinociception induced by butorphanol using MOP knockout (KO) mice. Butorphanol-induced thermal antinociception, assessed by the hot-plate and tail-flick tests, was significantly reduced in heterozygous and abolished in homozygous MOP-KO mice compared with wildtype mice. The results obtained from our butorphanol-induced mechanical antinociception experiments, assessed by the Randall-Selitto test, were similar to the results obtained from the thermal antinociception experiments in these mice. Interestingly, however, butorphanol retained its ability to induce significant visceral chemical antinociception, assessed by the writhing test, in homozygous MOP-KO mice. The butorphanol-induced visceral chemical antinociception that was retained in homozygous MOP-KO mice was completely blocked by pretreatment with nor-binaltorphimine, a κ-opioid receptor (KOP) antagonist. In vitro binding and cyclic adenosine monophosphate assays also showed that butorphanol possessed higher affinity for KOPs and MOPs than for δ-opioid receptors. These results molecular pharmacologically confirmed previous studies implicating MOPs, and partially KOPs, in mediating butorphanol-induced analgesia. PMID:18417173

Convective dynamics and chemical disequilibrium in the atmospheres of substellar objects

NASA Astrophysics Data System (ADS)

Bordwell, Baylee; Brown, Benjamin P.; Oishi, Jeffrey S.

2017-11-01

The thousands of substellar objects now known provide a unique opportunity to test our understanding of atmospheric dynamics across a range of environments. The chemical timescales of certain species transition from being much shorter than the dynamical timescales to being much longer than them at a point in the atmosphere known as the quench point. This transition leads to a state of dynamical disequilibrium, the effects of which can be used to probe the atmospheric dynamics of these objects. Unfortunately, due to computational constraints, models that inform the interpretation of these observations are run at dynamical parameters which are far from realistic values. In this study, we explore the behavior of a disequilibrium chemical process with increasingly realistic planetary conditions, to quantify the effects of the approximations used in current models. We simulate convection in 2-D, plane-parallel, polytropically-stratified atmospheres, into which we add reactive passive tracers that explore disequilibrium behavior. We find that as we increase the Rayleigh number, and thus achieve more realistic planetary conditions, the behavior of these tracers does not conform to the classical predictions of disequilibrium chemistry.

Morphological computation and morphological control: steps toward a formal theory and applications.

PubMed

Füchslin, Rudolf M; Dzyakanchuk, Andrej; Flumini, Dandolo; Hauser, Helmut; Hunt, Kenneth J; Luchsinger, Rolf H; Reller, Benedikt; Scheidegger, Stephan; Walker, Richard

2013-01-01

Morphological computation can be loosely defined as the exploitation of the shape, material properties, and physical dynamics of a physical system to improve the efficiency of a computation. Morphological control is the application of morphological computing to a control task. In its theoretical part, this article sharpens and extends these definitions by suggesting new formalized definitions and identifying areas in which the definitions we propose are still inadequate. We go on to describe three ongoing studies, in which we are applying morphological control to problems in medicine and in chemistry. The first involves an inflatable support system for patients with impaired movement, and is based on macroscopic physics and concepts already tested in robotics. The two other case studies (self-assembly of chemical microreactors; models of induced cell repair in radio-oncology) describe processes and devices on the micrometer scale, in which the emergent dynamics of the underlying physical system (e.g., phase transitions) are dominated by stochastic processes such as diffusion.

Multimodel inference to quantify the relative importance of abiotic factors in the population dynamics of marine zooplankton

NASA Astrophysics Data System (ADS)

Everaert, Gert; Deschutter, Yana; De Troch, Marleen; Janssen, Colin R.; De Schamphelaere, Karel

2018-05-01

The effect of multiple stressors on marine ecosystems remains poorly understood and most of the knowledge available is related to phytoplankton. To partly address this knowledge gap, we tested if combining multimodel inference with generalized additive modelling could quantify the relative contribution of environmental variables on the population dynamics of a zooplankton species in the Belgian part of the North Sea. Hence, we have quantified the relative contribution of oceanographic variables (e.g. water temperature, salinity, nutrient concentrations, and chlorophyll a concentrations) and anthropogenic chemicals (i.e. polychlorinated biphenyls) to the density of Acartia clausi. We found that models with water temperature and chlorophyll a concentration explained ca. 73% of the population density of the marine copepod. Multimodel inference in combination with regression-based models are a generic way to disentangle and quantify multiple stressor-induced changes in marine ecosystems. Future-oriented simulations of copepod densities suggested increased copepod densities under predicted environmental changes.

Probing equilibrium of molecular and deprotonated water on TiO 2 (110)

DOE PAGES

Wang, Zhi-Tao; Wang, Yang-Gang; Mu, Rentao; ...

2017-02-06

Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociation barrier.more » Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. The techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.« less

Molecular Dynamics Simulations of the [2Fe-2S] Cluster-Binding Domain of NEET Proteins Reveal Key Molecular Determinants That Induce Their Cluster Transfer/Release.

PubMed

Pesce, Luca; Calandrini, Vania; Marjault, Henri-Baptiste; Lipper, Colin H; Rossetti, Gulia; Mittler, Ron; Jennings, Patricia A; Bauer, Andreas; Nechushtai, Rachel; Carloni, Paolo

2017-11-30

The NEET proteins are a novel family of iron-sulfur proteins characterized by an unusual three cysteine and one histidine coordinated [2Fe-2S] cluster. Aberrant cluster release, facilitated by the breakage of the Fe-N bond, is implicated in a variety of human diseases, including cancer. Here, the molecular dynamics in the multi-microsecond timescale, along with quantum chemical calculations, on two representative members of the family (the human NAF-1 and mitoNEET proteins), show that the loss of the cluster is associated with a dramatic decrease in secondary and tertiary structure. In addition, the calculations provide a mechanism for cluster release and clarify, for the first time, crucial differences existing between the two proteins, which are reflected in the experimentally observed difference in the pH-dependent cluster reactivity. The reliability of our conclusions is established by an extensive comparison with the NMR data of the solution proteins, in part measured in this work.

Resolving molecule-specific information in dynamic lipid membrane processes with multi-resonant infrared metasurfaces.

PubMed

Rodrigo, Daniel; Tittl, Andreas; Ait-Bouziad, Nadine; John-Herpin, Aurelian; Limaj, Odeta; Kelly, Christopher; Yoo, Daehan; Wittenberg, Nathan J; Oh, Sang-Hyun; Lashuel, Hilal A; Altug, Hatice

2018-06-04

A multitude of biological processes are enabled by complex interactions between lipid membranes and proteins. To understand such dynamic processes, it is crucial to differentiate the constituent biomolecular species and track their individual time evolution without invasive labels. Here, we present a label-free mid-infrared biosensor capable of distinguishing multiple analytes in heterogeneous biological samples with high sensitivity. Our technology leverages a multi-resonant metasurface to simultaneously enhance the different vibrational fingerprints of multiple biomolecules. By providing up to 1000-fold near-field intensity enhancement over both amide and methylene bands, our sensor resolves the interactions of lipid membranes with different polypeptides in real time. Significantly, we demonstrate that our label-free chemically specific sensor can analyze peptide-induced neurotransmitter cargo release from synaptic vesicle mimics. Our sensor opens up exciting possibilities for gaining new insights into biological processes such as signaling or transport in basic research as well as provides a valuable toolkit for bioanalytical and pharmaceutical applications.

Shock tubes and waves; Proceedings of the Sixteenth International Symposium, Rheinisch-Westfaelische Technische Hochschule, Aachen, Federal Republic of Germany, July 26-31, 1987

NASA Astrophysics Data System (ADS)

Groenig, Hans

Topics discussed in this volume include shock wave structure, propagation, and interaction; shocks in condensed matter, dusty gases, and multiphase media; chemical processes and related combustion and detonation phenomena; shock wave reflection, diffraction, and focusing; computational fluid dynamic code development and shock wave application; blast and detonation waves; advanced shock tube technology and measuring technique; and shock wave applications. Papers are presented on dust explosions, the dynamics of shock waves in certain dense gases, studies of condensation kinetics behind incident shock waves, the autoignition mechanism of n-butane behind a reflected shock wave, and a numerical simulation of the focusing process of reflected shock waves. Attention is also given to the equilibrium shock tube flow of real gases, blast waves generated by planar detonations, modern diagnostic methods for high-speed flows, and interaction between induced waves and electric discharge in a very high repetition rate excimer laser.

Dynamic light scattering as an objective noninvasive method in veterinary ophthalmic diagnosis and research

NASA Astrophysics Data System (ADS)

Dubin, Stephen; Ansari, Rafat R.; Tulp, Orien; Steinberg, Sheldon; Koch, Seth; DellaVecchia, Michael A.; Cozmi, Mihaela; Victor, Mary

1999-06-01

The absence of verbal feedback, available from most human patients, is a major limitation in veterinary diagnosis in general and in the evaluation of ophthalmic lens opacity in particular. A novel compact dynamic light scattering (DLS) instrument, developed at NASA, offers significant mitigation to this limitation. It not only yields objective repeatable non-invasive estimation of lens opacity but also provides insight into the nature of chemical and physical alternations in the lens and other eye structures. For example, DLS measurements of the cataractous lens may be interpreted in terms of alpha crystalline protein size. In contrast to most conventional methods, the examination results are numerical and readily accommodate statistical analysis. We present results of DLS measurements in laboratory rabbits with naphthalene induced cataracts, rodents with genetically conditioned hypertension and/or diabetes mellitus; as well as applications of the DLS method in clinical veterinary patients. Use of DLS in examination of phacoemulsification fluid, urine and other biological materials, and potential applications in ocular toxically will also be discussed.

Plasmonic- and dielectric-based structural coloring: from fundamentals to practical applications

NASA Astrophysics Data System (ADS)

Lee, Taejun; Jang, Jaehyuck; Jeong, Heonyeong; Rho, Junsuk

2018-01-01

Structural coloring is production of color by surfaces that have microstructure fine enough to interfere with visible light; this phenomenon provides a novel paradigm for color printing. Plasmonic color is an emergent property of the interaction between light and metallic surfaces. This phenomenon can surpass the diffraction limit and achieve near unlimited lifetime. We categorize plasmonic color filters according to their designs (hole, rod, metal-insulator-metal, grating), and also describe structures supported by Mie resonance. We discuss the principles, and the merits and demerits of each color filter. We also discuss a new concept of color filters with tunability and reconfigurability, which enable printing of structural color to yield dynamic coloring at will. Approaches for dynamic coloring are classified as liquid crystal, chemical transition and mechanical deformation. At the end of review, we highlight a scale-up of fabrication methods, including nanoimprinting, self-assembly and laser-induced process that may enable real-world application of structural coloring.

Direct evidence of two interatomic relaxation mechanisms in argon dimers ionized by electron impact

PubMed Central

Ren, Xueguang; Jabbour Al Maalouf, Elias; Dorn, Alexander; Denifl, Stephan

2016-01-01

In weakly bound systems like liquids and clusters electronically excited states can relax in inter-particle reactions via the interplay of electronic and nuclear dynamics. Here we report on the identification of two prominent examples, interatomic Coulombic decay (ICD) and radiative charge transfer (RCT), which are induced in argon dimers by electron collisions. After initial ionization of one dimer constituent ICD and RCT lead to the ionization of its neighbour either by energy transfer to or by electron transfer from the neighbour, respectively. By full quintuple-coincidence measurements, we unambiguously identify ICD and RCT, and trace the relaxation dynamics as function of the collisional excited state energies. Such interatomic processes multiply the number of electrons and shift their energies down to the critical 1–10 eV range, which can efficiently cause chemical degradation of biomolecules. Therefore, the observed relaxation channels might contribute to cause efficient radiation damage in biological systems. PMID:27000407

Dynamic Variation Patterns of Aconitum Alkaloids in Daughter Root of Aconitum Carmichaelii (Fuzi) in the Decoction Process Based on the Content Changes of Nine Aconitum Alkaloids by HPLC- MS- MS

PubMed Central

Luo, Heng; Huang, Zhifang; Tang, Xiaolong; Yi, Jinhai; Chen, Shuiying; Yang, Andong; Yang, Jun

2016-01-01

The chemical components in the decoctions of Chinese herbal medicines are not always the same as those in the crude herbs because of the insolubility or instability of some compounds. In this work, a high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) tandem mass spectrometry method was developed to explore dynamic variation patterns of aconitum alkaloids in Fuzi during the process of decocting aconite root. The fragmentation patterns of aconitum alkaloids using ESI and collision-induced dissociation (CID) techniques were reported. This assay method was validated with respect to linearity (r2 > 0.9950), precision, repeatability, and accuracy (recovery rate between 94.6 and 107.9%).The result showed that the amounts of aconitum alkaloids in the decoction at different boiling time varied significantly. In the decoction process，the diester- type alkaloids in crude aconite roots have transformed into Benzoylaconines or aconines. PMID:27610167

Dynamic Variation Patterns of Aconitum Alkaloids in Daughter Root of Aconitum Carmichaelii (Fuzi) in the Decoction Process Based on the Content Changes of Nine Aconitum Alkaloids by HPLC- MS- MS.

PubMed

Luo, Heng; Huang, Zhifang; Tang, Xiaolong; Yi, Jinhai; Chen, Shuiying; Yang, Andong; Yang, Jun

2016-01-01

The chemical components in the decoctions of Chinese herbal medicines are not always the same as those in the crude herbs because of the insolubility or instability of some compounds. In this work, a high-performance liquid chromatography (HPLC) coupled with electrospray ionization (ESI) tandem mass spectrometry method was developed to explore dynamic variation patterns of aconitum alkaloids in Fuzi during the process of decocting aconite root. The fragmentation patterns of aconitum alkaloids using ESI and collision-induced dissociation (CID) techniques were reported. This assay method was validated with respect to linearity (r(2) > 0.9950), precision, repeatability, and accuracy (recovery rate between 94.6 and 107.9%).The result showed that the amounts of aconitum alkaloids in the decoction at different boiling time varied significantly. In the decoction process，the diester- type alkaloids in crude aconite roots have transformed into Benzoylaconines or aconines.

Bioinspired design of a polymer gel sensor for the realization of extracellular Ca2+ imaging

NASA Astrophysics Data System (ADS)

Ishiwari, Fumitaka; Hasebe, Hanako; Matsumura, Satoko; Hajjaj, Fatin; Horii-Hayashi, Noriko; Nishi, Mayumi; Someya, Takao; Fukushima, Takanori

2016-04-01

Although the role of extracellular Ca2+ draws increasing attention as a messenger in intercellular communications, there is currently no tool available for imaging Ca2+ dynamics in extracellular regions. Here we report the first solid-state fluorescent Ca2+ sensor that fulfills the essential requirements for realizing extracellular Ca2+ imaging. Inspired by natural extracellular Ca2+-sensing receptors, we designed a particular type of chemically-crosslinked polyacrylic acid gel, which can undergo single-chain aggregation in the presence of Ca2+. By attaching aggregation-induced emission luminogen to the polyacrylic acid as a pendant, the conformational state of the main chain at a given Ca2+ concentration is successfully translated into fluorescence property. The Ca2+ sensor has a millimolar-order apparent dissociation constant compatible with extracellular Ca2+ concentrations, and exhibits sufficient dynamic range and excellent selectivity in the presence of physiological concentrations of biologically relevant ions, thus enabling monitoring of submillimolar fluctuations of Ca2+ in flowing analytes containing millimolar Ca2+ concentrations.

Temperature effect on the vibrational dynamics of cyclodextrin inclusion complexes: investigation by FTIR-ATR spectroscopy and numerical simulation.

PubMed

Crupi, Vincenza; Majolino, Domenico; Venuti, Valentina; Guella, Graziano; Mancini, Ines; Rossi, Barbara; Verrocchio, Paolo; Viliani, Gabriele; Stancanelli, Rosanna

2010-07-01

The vibrational dynamics of solid inclusion complexes of the nonsteroidal anti-inflammatory drug Ibuprofen (IBP) with beta-cyclodextrin (beta-CD) and methyl-beta-cyclodextrin (Me-beta-CD) has been investigated by using attenuated total reflection-Fourier transform infrared FTIR-ATR spectroscopy, in order to monitor the changes induced, as a consequence of complexation, on the vibrational spectrum of IBP, in the wavenumber range 600-4000 cm(-1). Quantum chemical calculations were performed on monomeric and dimeric structures of IBP, derived from symmetric hydrogen bonding of the two carboxylic groups, in order to unambiguously assign some characteristic IR bands in the IBP spectrum. The evolution in temperature from 250 to 340 K of the C horizontal lineO stretching vibration, described by a best-fit procedure, allowed us to extract the thermodynamic parameter DeltaH associated to the binding of IBP with betaCDs in the solid phase. By comparing these results, Me-beta-CD has been shown to be the most effective carrier for IBP.

Rethinking pattern formation in reaction-diffusion systems

NASA Astrophysics Data System (ADS)

Halatek, J.; Frey, E.

2018-05-01

The present theoretical framework for the analysis of pattern formation in complex systems is mostly limited to the vicinity of fixed (global) equilibria. Here we present a new theoretical approach to characterize dynamical states arbitrarily far from (global) equilibrium. We show that reaction-diffusion systems that are driven by locally mass-conserving interactions can be understood in terms of local equilibria of diffusively coupled compartments. Diffusive coupling generically induces lateral redistribution of the globally conserved quantities, and the variable local amounts of these quantities determine the local equilibria in each compartment. We find that, even far from global equilibrium, the system is well characterized by its moving local equilibria. We apply this framework to in vitro Min protein pattern formation, a paradigmatic model for biological pattern formation. Within our framework we can predict and explain transitions between chemical turbulence and order arbitrarily far from global equilibrium. Our results reveal conceptually new principles of self-organized pattern formation that may well govern diverse dynamical systems.

Effect of Aprotic Solvents on the Dynamics of a Room Temperature Ionic Liquid

NASA Astrophysics Data System (ADS)

Osti, Naresh; van Aken, Katherine; Thompson, Matthew; Tiet, Felix; Jiang, De-En; Cummings, Peter; Gogotsi, Yury; Mamontov, Eugene

Room temperature ionic liquids (RTILs) have attracted much attention as electrolytes in energy storage devices because of their peculiar physical and chemical characteristics. However, their remarkably high viscosity, which results in low conductivity and diffusivity, may adversely affect the charging and discharging rates. Despite changing molecular configurations, use of aprotic solvent allows to enhance the transport properties of ionic liquids by disrupting the cation-anion interactions. We explore the impact of dipole moment of aprotic solvents on the cation-anion interaction and transport in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [BMIM +][Tf2N-], RTIL using molecular dynamics (MD) simulations and quasi-elastic neutrons scattering (QENS) measurements. We observed an increase in cation diffusivity with the increasing dipole moment of the solvent. This effect is due to a decrease in the solvation free energy induced by the increasing solvent polarity. A clear nano-phase separation into ionic liquid-rich and ionic liquid-poor phases as observed by QENS will be also discussed.

Probing equilibrium of molecular and deprotonated water on TiO 2(110)

DOE PAGES

Wang, Zhi -Tao; Wang, Yang -Gang; Mu, Rentao; ...

2017-02-06

Understanding water structure and its deprotonation dynamics on oxide surfaces is key to understanding many physical and chemical processes. In this study, we directly measure the energy barriers associated with the protonation equilibrium of water on the prototypical oxide surface, rutile-TiO 2(110) by a combination of a supersonic molecular beam, scanning tunneling microscopy, and ab initio molecular dynamics simulations. We show that long-range electrostatic fields emanating from the oxide lead to steering and reorientation of the molecules approaching the surface, activating the O-H bonds and inducing deprotonation. The incident energy dependent studies allow for a direct determination of the dissociationmore » barrier. Temperature dependent imaging yields the reverse barrier and the equilibrium constant. Molecularly bound water is preferred by 0.035 eV over the surface-bound hydroxyls. In conclusion, the techniques developed in this work are readily extended to other systems where the understanding of bond-activation processes is critical.« less

Study on elucidation of bactericidal effects induced by laser beam irradiation Measurement of dynamic stress on laser irradiated surface

NASA Astrophysics Data System (ADS)

Furumoto, Tatsuaki; Kasai, Atsushi; Tachiya, Hiroshi; Hosokawa, Akira; Ueda, Takashi

2010-09-01

In dental treatment, many types of laser beams have been used for various surgical treatments, and the influences of laser beam irradiation on bactericidal effect have been investigated. However, most of the work has been performed by irradiating to an agar plate with the colony of bacteria, and very few studies have been reported on the physical mechanism of bactericidal effects induced by laser beam irradiation. This paper deals with the measurement of dynamic stress induced in extracted human enamel by irradiation with Nd:YAG laser beams. Laser beams can be delivered to the enamel surface through a quartz optical fiber. Dynamic stress induced in the specimen using elastic wave propagation in a cylindrical long bar made of aluminum alloy is measured. Laser induced stress intensity is evaluated from dynamic strain measured by small semiconductor strain gauges. Carbon powder and titanium dioxide powder were applied to the human enamel surface as absorbents. Additionally, the phenomenon of laser beam irradiation to the human enamel surface was observed with an ultrahigh speed video camera. Results showed that a plasma was generated on the enamel surface during laser beam irradiation, and the melted tissues were scattered in the vertical direction against the enamel surface with a mushroom-like wave. Averaged scattering velocity of the melted tissues was 25.2 m/s. Induced dynamic stress on the enamel surface increased with increasing laser energy in each absorbent. Induced dynamic stresses with titanium dioxide powder were superior to those with carbon powder. Induced dynamic stress was related to volume of prepared cavity, and induced stress for the removal of unit volume of human enamel was 0.03 Pa/mm 3.

Coriolis coupling and nonadiabaticity in chemical reaction dynamics.

PubMed

Wu, Emilia L

2010-12-01

The nonadiabatic quantum dynamics and Coriolis coupling effect in chemical reaction have been reviewed, with emphasis on recent progress in using the time-dependent wave packet approach to study the Coriolis coupling and nonadiabatic effects, which was done by K. L. Han and his group. Several typical chemical reactions, for example, H+D(2), F+H(2)/D(2)/HD, D(+)+H(2), O+H(2), and He+H(2)(+), have been discussed. One can find that there is a significant role of Coriolis coupling in reaction dynamics for the ion-molecule collisions of D(+)+H(2), Ne+H(2)(+), and He+H(2)(+) in both adiabatic and nonadiabatic context. © 2010 Wiley Periodicals, Inc.

AdapChem

NASA Technical Reports Server (NTRS)

Oluwole, Oluwayemisi O.; Wong, Hsi-Wu; Green, William

2012-01-01

AdapChem software enables high efficiency, low computational cost, and enhanced accuracy on computational fluid dynamics (CFD) numerical simulations used for combustion studies. The software dynamically allocates smaller, reduced chemical models instead of the larger, full chemistry models to evolve the calculation while ensuring the same accuracy to be obtained for steady-state CFD reacting flow simulations. The software enables detailed chemical kinetic modeling in combustion CFD simulations. AdapChem adapts the reaction mechanism used in the CFD to the local reaction conditions. Instead of a single, comprehensive reaction mechanism throughout the computation, a dynamic distribution of smaller, reduced models is used to capture accurately the chemical kinetics at a fraction of the cost of the traditional single-mechanism approach.

The implications of non-linear biological oscillations on human electrophysiology for electrohypersensitivity (EHS) and multiple chemical sensitivity (MCS).

PubMed

Sage, Cindy

2015-01-01

The 'informational content' of Earth's electromagnetic signaling is like a set of operating instructions for human life. These environmental cues are dynamic and involve exquisitely low inputs (intensities) of critical frequencies with which all life on Earth evolved. Circadian and other temporal biological rhythms depend on these fluctuating electromagnetic inputs to direct gene expression, cell communication and metabolism, neural development, brainwave activity, neural synchrony, a diversity of immune functions, sleep and wake cycles, behavior and cognition. Oscillation is also a universal phenomenon, and biological systems of the heart, brain and gut are dependent on the cooperative actions of cells that function according to principles of non-linear, coupled biological oscillations for their synchrony. They are dependent on exquisitely timed cues from the environment at vanishingly small levels. Altered 'informational content' of environmental cues can swamp natural electromagnetic cues and result in dysregulation of normal biological rhythms that direct growth, development, metabolism and repair mechanisms. Pulsed electromagnetic fields (PEMF) and radiofrequency radiation (RFR) can have the devastating biological effects of disrupting homeostasis and desynchronizing normal biological rhythms that maintain health. Non-linear, weak field biological oscillations govern body electrophysiology, organize cell and tissue functions and maintain organ systems. Artificial bioelectrical interference can give false information (disruptive signaling) sufficient to affect critical pacemaker cells (of the heart, gut and brain) and desynchronize functions of these important cells that orchestrate function and maintain health. Chronic physiological stress undermines homeostasis whether it is chemically induced or electromagnetically induced (or both exposures are simultaneous contributors). This can eventually break down adaptive biological responses critical to health maintenance; and resilience can be compromised. Electrohypersensitivity can be caused by successive assaults on human bioelectrochemical dynamics from exogenous electromagnetic fields (EMF) and RFR or a single acute exposure. Once sensitized, further exposures are widely reported to cause reactivity to lower and lower intensities of EMF/RFR, at which point thousand-fold lower levels can cause adverse health impacts to the electrosensitive person. Electrohypersensitivity (EHS) can be a precursor to, or linked with, multiple chemical sensitivity (MCS) based on reports of individuals who first develop one condition, then rapidly develop the other. Similarity of chemical biomarkers is seen in both conditions [histamines, markers of oxidative stress, auto-antibodies, heat shock protein (HSP), melatonin markers and leakage of the blood-brain barrier]. Low intensity pulsed microwave activation of voltage-gated calcium channels (VGCCs) is postulated as a mechanism of action for non-thermal health effects.

The impact of dissolved oxygen on sulfate radical-induced oxidation of organic micro-pollutants: A theoretical study.

PubMed

Zhang, Rui; Wang, Xiaoxiang; Zhou, Lei; Liu, Zhu; Crump, Doug

2018-05-15

Sulfate radical (SO 4 .- )-induced oxidation is an important technology in advanced oxidation processes (AOPs) for the removal of pollutants. To date, few studies have assessed the effects of dissolved oxygen (DO) on the SO 4 .- -induced oxidation of organic micro-pollutants. In the present work, a quantum chemical calculation was used to investigate the influence of the external oxygen molecule on the Gibbs free energy (G pollutant ) and HOMO-LUMO gap (ΔE) of 15 organic micro-pollutants representing four chemical categories. Several thermodynamic and statistical models were combined with the data from the quantum chemical calculation to illustrate the impact of DO on the oxidation of organic micro-pollutants by SO 4 .- . Results indicated that the external oxygen molecule increased G pollutant of all studied chemicals, which implies DO has the potential to decrease the energy barrier of the SO 4 .- -induced oxidation and shift the chemical equilibrium of the reaction towards the side of products. From the perspective of kinetics, DO can accelerate the oxidation by decreasing ΔE of organic micro-pollutants. In addition, changes of G pollutant and ΔE of the SO 4 .- -induced oxidation were both significantly different between open-chain and aromatic chemicals, and these differences were partially attributed to the difference of polarizability of these two types of chemicals. Furthermore, we revealed that all changes of G pollutant and ΔE induced by DO were dependent on the DO content. Our study emphasizes the significance of DO on the oxidation of organic micro-pollutants by SO 4 .- , and also provides a theoretical method to study the effect of components in wastewater on removal of organic pollutants in AOPs. Copyright © 2018 Elsevier Ltd. All rights reserved.

Dynamized Preparations in Cell Culture

PubMed Central

Sunila, Ellanzhiyil Surendran; Preethi, Korengath Chandran; Kuttan, Girija

2009-01-01

Although reports on the efficacy of homeopathic medicines in animal models are limited, there are even fewer reports on the in vitro action of these dynamized preparations. We have evaluated the cytotoxic activity of 30C and 200C potencies of ten dynamized medicines against Dalton's Lymphoma Ascites, Ehrlich's Ascites Carcinoma, lung fibroblast (L929) and Chinese Hamster Ovary (CHO) cell lines and compared activity with their mother tinctures during short-term and long-term cell culture. The effect of dynamized medicines to induce apoptosis was also evaluated and we studied how dynamized medicines affected genes expressed during apoptosis. Mother tinctures as well as some dynamized medicines showed significant cytotoxicity to cells during short and long-term incubation. Potentiated alcohol control did not produce any cytotoxicity at concentrations studied. The dynamized medicines were found to inhibit CHO cell colony formation and thymidine uptake in L929 cells and those of Thuja, Hydrastis and Carcinosinum were found to induce apoptosis in DLA cells. Moreover, dynamized Carcinosinum was found to induce the expression of p53 while dynamized Thuja produced characteristic laddering pattern in agarose gel electrophoresis of DNA. These results indicate that dynamized medicines possess cytotoxic as well as apoptosis-inducing properties. PMID:18955237

Diffusive Transport and Structural Properties of Liquid Iron Alloys at High Pressure

NASA Astrophysics Data System (ADS)

Posner, E.; Rubie, D. C.; Steinle-Neumann, G.; Frost, D. J.

2017-12-01

Diffusive transport properties of liquid iron alloys at high pressures (P) and temperatures (T) place important kinetic constraints on processes related to the origin and evolution of planetary cores. Earth's core composition is largely controlled by the extent of chemical equilibration achieved between liquid metal bodies and a silicate magma ocean during core formation, which can be estimated using chemical diffusion data. In order to estimate the time and length scales of metal-silicate chemical equilibration, we have measured chemical diffusion rates of Si, O and Cr in liquid iron over the P-T range of 1-18 GPa and 1873-2643 K using a multi-anvil apparatus. We have also performed first-principles molecular dynamic simulations of comparable binary liquid compositions, in addition to pure liquid Fe, over a much wider P-T range (1 bar-330 GPa, 2200-5500 K) in order to both validate the simulation results with experimental data at conditions accessible in the laboratory and to extend our dataset to conditions of the Earth's core. Over the entire P-T range studied using both methods, diffusion coefficients are described consistently and well using an exponential function of the homologous temperature relation. Si, Cr and Fe diffusivities of approximately 5 × 10-9 m2 s-1 are constant along the melting curve from ambient to core pressures, while oxygen diffusion is 2-3 times faster. Our results indicate that in order for the composition of the Earth's core to represent chemical equilibrium, impactor cores must have broken up into liquid droplet sizes no larger than a few tens of cm. Structural properties, analyzed using partial radial distribution functions from the molecular dynamics simulations, reveal a pressure-induced structural change in liquid Fe0.96O0.04 at densities of 8 g cm-3, in agreement with previous experimental studies. For densities above 8 g cm-3, the liquid is essentially close packed with a local CsCl-like (B2) packing of Fe around O under conditions of the Earth's core.

Arginine Kinase. Joint Crystallographic & NMR RDC Analyses link Substrate-Associated Motions to Intrinsic Flexibility

PubMed Central

Niu, Xiaogang; Brüschweiler-Li, Lei; Davulcu, Omar; Skalicky, Jack J.; Brüschweiler, Rafael; Chapman, Michael S.

2010-01-01

The phosphagen kinase family, including creatine and arginine kinases, catalyze the reversible transfer of a “high energy” phosphate between ATP and a phospho-guanidino substrate. They have become a model for the study of both substrate-induced conformational change and intrinsic protein dynamics. Prior crystallographic studies indicated large substrate-induced domain rotations, but differences among a recent set of arginine kinase structures was interpreted as a plastic deformation. Here, the structure of Limulus substrate-free arginine kinase is refined against high resolution crystallographic data and compared quantitatively with NMR chemical shifts and residual dipolar couplings (RDCs). This demonstrates the feasibility of this type of RDC analysis of proteins that are large by NMR standards (42 kDa), and illuminates the solution structure, free from crystal-packing constraints. Detailed comparison of the 1.7 Å resolution substrate-free crystal structure against the 1.2 Å transition state analog complex shows large substrate-induced domain motions which can be broken down into movements of smaller quasi-rigid bodies. The solution state structure of substrate-free arginine kinase is most consistent with an equilibrium of substrate-free and –bound structures, with the substrate-free form dominating, but with varying displacements of the quasi-rigid groups. Rigid-group rotations evident from the crystal structures are about axes previously associated with intrinsic millisecond dynamics using NMR relaxation dispersion. Thus, “substrate-induced” motions are along modes that are intrinsically flexible in the substrate-free enzyme, and likely involve some degree of conformational selection. PMID:21075117

Experience-induced habituation and preference towards non-host plant odors in ovipositing females of a moth.

PubMed

Wang, Hua; Guo, Wen-Fei; Zhang, Peng-Jun; Wu, Zhi-Yi; Liu, Shu-Sheng

2008-03-01

In phytophagous insects, experience can increase positive responses towards non-host plant extracts or induce oviposition on non-host plants, but the underlying chemical and behavioral mechanisms are poorly understood. By using the diamondback moth, Plutella xylostella, its host plant Chinese cabbage, and a non-host plant Chrysanthemum morifolium, as a model system, we observed the experience-altered olfactory responses of ovipositing females towards volatiles of the non-host plant, volatiles of pure chemicals (p-cymene and alpha-terpinene) found in the non-host plant, and volatiles of host plants treated with these chemicals. We assessed the experience-altered oviposition preference towards host plants treated with p-cymene. Naive females showed aversion to the odors of the non-host plant, the pure chemicals, and the pure chemical-treated host plants. In contrast, experienced females either became attracted by these non-host odors or were no longer repelled by these odors. Similarly, naive females laid a significantly lower proportion of eggs on pure chemical-treated host plants than on untreated host plants, but experienced females laid a similar or higher proportion of eggs on pure chemical-treated host plants compared to untreated host plants. Chemical analysis indicated that application of the non-host pure chemicals on Chinese cabbage induced emissions of volatiles by this host plant. We conclude that induced preference for previously repellent compounds is a major mechanism that leads to behavioral changes of this moth towards non-host plants or their extracts.

Polyamorphic Transformations in Fe-Ni-C Liquids: Implications for Chemical Evolution of Terrestrial Planets: Fe-Ni-C liquid structural change

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lai, Xiaojing; Chen, Bin; Wang, Jianwei

During the formation of the Earth's core, the segregation of metallic liquids from silicate mantle should have left behind evident geochemical imprints on both the mantle and the core. Some distinctive geochemical signatures of the mantle-derived rocks likely own their origin to the metal-silicate differentiation of the primitive Earth, setting our planet apart from undifferentiated meteorites as well as terrestrial planets or moons isotopically and compositionally. Understanding the chemical evolution of terrestrial planetary bodies requires knowledge on properties of both liquid iron alloys and silicates equilibrating under physicochemical conditions pertinent to the deep magma ocean. Here we report experimental andmore » computational results on the pressure-induced structural evolution of iron-nickel liquids alloyed with carbon. Our X-ray diffraction experiments up to 7.3 gigapascals (GPa) demonstrate that Fe-Ni (Fe90Ni10) liquids alloyed with 3 and 5 wt % carbon undergo a polyamorphic liquid structure transition at approximately 5 GPa. Corroborating the experimental observations, our first-principles molecular dynamic calculations reveal that the structural transitions result from the marked prevalence of three-atom face-sharing polyhedral connections in the liquids at >5 GPa. The structure and polyamorphic transitions of liquid iron-nickel-carbon alloys govern their physical and chemical properties and may thus cast fresh light on the chemical evolution of terrestrial planets and moons.« less

Polyamorphic Transformations in Fe-Ni-C Liquids: Implications for Chemical Evolution of Terrestrial Planets

NASA Astrophysics Data System (ADS)

Lai, Xiaojing; Chen, Bin; Wang, Jianwei; Kono, Yoshio; Zhu, Feng

2017-12-01

During the formation of the Earth's core, the segregation of metallic liquids from silicate mantle should have left behind evident geochemical imprints on both the mantle and the core. Some distinctive geochemical signatures of the mantle-derived rocks likely own their origin to the metal-silicate differentiation of the primitive Earth, setting our planet apart from undifferentiated meteorites as well as terrestrial planets or moons isotopically and compositionally. Understanding the chemical evolution of terrestrial planetary bodies requires knowledge on properties of both liquid iron alloys and silicates equilibrating under physicochemical conditions pertinent to the deep magma ocean. Here we report experimental and computational results on the pressure-induced structural evolution of iron-nickel liquids alloyed with carbon. Our X-ray diffraction experiments up to 7.3 gigapascals (GPa) demonstrate that Fe-Ni (Fe90Ni10) liquids alloyed with 3 and 5 wt % carbon undergo a polyamorphic liquid structure transition at approximately 5 GPa. Corroborating the experimental observations, our first-principles molecular dynamic calculations reveal that the structural transitions result from the marked prevalence of three-atom face-sharing polyhedral connections in the liquids at >5 GPa. The structure and polyamorphic transitions of liquid iron-nickel-carbon alloys govern their physical and chemical properties and may thus cast fresh light on the chemical evolution of terrestrial planets and moons.

Chemical and Structural Stability of Lithium-Ion Battery Electrode Materials under Electron Beam

DOE PAGES

Lin, Feng; Markus, Isaac M.; Doeff, Marca M.; ...

2014-07-16

Our investigation of chemical and structural dynamics in battery materials is essential to elucidation of structure-property relationships for rational design of advanced battery materials. Spatially resolved techniques, such as scanning/transmission electron microscopy (S/TEM), are widely applied to address this challenge. But, battery materials are susceptible to electron beam damage, complicating the data interpretation. In this study, we demonstrate that, under electron beam irradiation, the surface and bulk of battery materials undergo chemical and structural evolution equivalent to that observed during charge-discharge cycling. In a lithiated NiO nanosheet, a Li2CO3-containing surface reaction layer (SRL) was gradually decomposed during electron energy loss spectroscopy (EELS) acquisition. For cycled LiNi 0.4Mn 0.4Co 0.18Ti 0.02O 2 particles, repeated electron beam irradiation induced a phase transition from an Rmore » $$\\bar{3}$$m layered structure to an rock-salt structure, which is attributed to the stoichiometric lithium and oxygen removal from R$$\\bar{3}$$m 3a and 6c sites, respectively. Nevertheless, it is still feasible to preserve pristine chemical environments by minimizing electron beam damage, for example, in using fast electron imaging and spectroscopy. Finally, the present study provides examples of electron beam damage on lithium-ion battery materials and suggests that special attention is necessary to prevent misinterpretation of experimental results.« less

An improved molecular dynamics algorithm to study thermodiffusion in binary hydrocarbon mixtures

NASA Astrophysics Data System (ADS)

Antoun, Sylvie; Saghir, M. Ziad; Srinivasan, Seshasai

2018-03-01

In multicomponent liquid mixtures, the diffusion flow of chemical species can be induced by temperature gradients, which leads to a separation of the constituent components. This cross effect between temperature and concentration is known as thermodiffusion or the Ludwig-Soret effect. The performance of boundary driven non-equilibrium molecular dynamics along with the enhanced heat exchange (eHEX) algorithm was studied by assessing the thermodiffusion process in n-pentane/n-decane (nC5-nC10) binary mixtures. The eHEX algorithm consists of an extended version of the HEX algorithm with an improved energy conservation property. In addition to this, the transferable potentials for phase equilibria-united atom force field were employed in all molecular dynamics (MD) simulations to precisely model the molecular interactions in the fluid. The Soret coefficients of the n-pentane/n-decane (nC5-nC10) mixture for three different compositions (at 300.15 K and 0.1 MPa) were calculated and compared with the experimental data and other MD results available in the literature. Results of our newly employed MD algorithm showed great agreement with experimental data and a better accuracy compared to other MD procedures.

Altered Calcium Dynamics in Cardiac Cells Grown on Silane-Modified Surfaces

PubMed Central

Ravenscroft-Chang, Melissa S.; Stohlman, Jayna; Molnar, Peter; Natarajan, Anupama; Canavan, Heather E.; Teliska, Maggie; Stancescu, Maria; Krauthamer, Victor; Hickman, J.J.

2013-01-01

Chemically defined surfaces were created using self-assembled monolayers (SAMs) of hydrophobic and hydrophilic silanes as models for implant coatings, and the morphology and physiology of cardiac myocytes plated on these surfaces were studied in vitro. We focused on changes in intracellular Ca2+ because of its essential role in regulating heart cell function. The SAM-modified coverslips were analyzed using X-ray Photoelectron Spectroscopy to verify composition. The morphology and physiology of the cardiac cells were examined using fluorescence microscopy and intracellular Ca2+ imaging. The imaging experiments used the fluorescent ratiometric dye fura-2, AM to establish both the resting Ca2+ concentration and the dynamic responses to electrical stimulation. A significant difference in excitation-induced Ca2+ changes on the different silanated surfaces was observed. However, no significant change was noted based on the morphological analysis. This result implies a difference in internal Ca2+ dynamics, and thus cardiac function, occurs when the composition of the surface is different, and this effect is independent of cellular morphology. This finding has implications for histological examination of tissues surrounding implants, the choice of materials that could be beneficial as implant coatings and understanding of cell-surface interactions in cardiac systems. PMID:19828193

Control of dynamical self-assembly of strongly Brownian nanoparticles through convective forces induced by ultrafast laser

NASA Astrophysics Data System (ADS)

Ilday, Serim; Akguc, Gursoy B.; Tokel, Onur; Makey, Ghaith; Yavuz, Ozgun; Yavuz, Koray; Pavlov, Ihor; Ilday, F. Omer; Gulseren, Oguz

We report a new dynamical self-assembly mechanism, where judicious use of convective and strong Brownian forces enables effective patterning of colloidal nanoparticles that are almost two orders of magnitude smaller than the laser beam. Optical trapping or tweezing effects are not involved, but the laser is used to create steep thermal gradients through multi-photon absorption, and thereby guide the colloids through convective forces. Convective forces can be thought as a positive feedback mechanism that helps to form and reinforce pattern, while Brownian motion act as a competing negative feedback mechanism to limit the growth of the pattern, as well as to increase the possibilities of bifurcation into different patterns, analogous to the competition observed in reaction-diffusion systems. By steering stochastic processes through these forces, we are able to gain control over the emergent pattern such as to form-deform-reform of a pattern, to change its shape and transport it spatially within seconds. This enables us to dynamically initiate and control large patterns comprised of hundreds of colloids. Further, by not relying on any specific chemical, optical or magnetic interaction, this new method is, in principle, completely independent of the material type being assembled.

Magnetization Dynamics of Amorphous Ribbons and Wires Studied by Inductance Spectroscopy

PubMed Central

Betancourt, Israel

2010-01-01

Inductance spectroscopy is a particular formulation variant of the well known complex impedance formalism typically used for the electric characterization of dielectric, ferroelectric, and piezoelectric materials. It has been successfully exploited as a versatile tool for characterization of the magnetization dynamics in amorphous ribbons and wires by means of simple experiments involving coils for sample holding and impedance analyzer equipment. This technique affords the resolution of the magnetization processes in soft magnetic materials, in terms of reversible deformation of pinned domain walls, domain wall displacements and spin rotation, for which characteristic parameters such as the alloy initial permeability and the relaxation frequencies, indicating the dispersion of each process, can be defined. Additionally, these parameters can be correlated with chemical composition variation, size effects and induced anisotropies, leading to a more physical insight for the understanding of the frequency dependent magnetic response of amorphous alloys, which is of prime interest for the development of novel applications in the field of telecommunication and sensing technologies. In this work, a brief overview, together with recent progress on the magnetization dynamics of amorphous ribbons, wires, microwires and biphase wires, is presented and discussed for the intermediate frequency interval between 10 Hz and 13 MHz. PMID:28879975

Molecular Dynamics Simulation of Tau Peptides for the Investigation of Conformational Changes Induced by Specific Phosphorylation Patterns.

PubMed

Gandhi, Neha S; Kukic, Predrag; Lippens, Guy; Mancera, Ricardo L

2017-01-01

The Tau protein plays an important role due to its biomolecular interactions in neurodegenerative diseases. The lack of stable structure and various posttranslational modifications such as phosphorylation at various sites in the Tau protein pose a challenge for many experimental methods that are traditionally used to study protein folding and aggregation. Atomistic molecular dynamics (MD) simulations can help around deciphering relationship between phosphorylation and various intermediate and stable conformations of the Tau protein which occur on longer timescales. This chapter outlines protocols for the preparation, execution, and analysis of all-atom MD simulations of a 21-amino acid-long phosphorylated Tau peptide with the aim of generating biologically relevant structural and dynamic information. The simulations are done in explicit solvent and starting from nearly extended configurations of the peptide. The scaled MD method implemented in AMBER14 was chosen to achieve enhanced conformational sampling in addition to a conventional MD approach, thereby allowing the characterization of folding for such an intrinsically disordered peptide at 293 K. Emphasis is placed on the analysis of the simulation trajectories to establish correlations with NMR data (i.e., chemical shifts and NOEs). Finally, in-depth discussions are provided for commonly encountered problems.

Assessment of dynamic closure for premixed combustion large eddy simulation

NASA Astrophysics Data System (ADS)

Langella, Ivan; Swaminathan, Nedunchezhian; Gao, Yuan; Chakraborty, Nilanjan

2015-09-01

Turbulent piloted Bunsen flames of stoichiometric methane-air mixtures are computed using the large eddy simulation (LES) paradigm involving an algebraic closure for the filtered reaction rate. This closure involves the filtered scalar dissipation rate of a reaction progress variable. The model for this dissipation rate involves a parameter βc representing the flame front curvature effects induced by turbulence, chemical reactions, molecular dissipation, and their interactions at the sub-grid level, suggesting that this parameter may vary with filter width or be a scale-dependent. Thus, it would be ideal to evaluate this parameter dynamically by LES. A procedure for this evaluation is discussed and assessed using direct numerical simulation (DNS) data and LES calculations. The probability density functions of βc obtained from the DNS and LES calculations are very similar when the turbulent Reynolds number is sufficiently large and when the filter width normalised by the laminar flame thermal thickness is larger than unity. Results obtained using a constant (static) value for this parameter are also used for comparative evaluation. Detailed discussion presented in this paper suggests that the dynamic procedure works well and physical insights and reasonings are provided to explain the observed behaviour.

The capacity fading mechanism and improvement of cycling stability in MoS2-based anode materials for lithium-ion batteries

NASA Astrophysics Data System (ADS)

Shu, Haibo; Li, Feng; Hu, Chenli; Liang, Pei; Cao, Dan; Chen, Xiaoshuang

2016-01-01

Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance.Two-dimensional (2D) layered MoS2 nanosheets possess great potential as anode materials for lithium ion batteries (LIBs), but they still suffer from poor cycling performance. Improving the cycling stability of electrode materials depends on a deep understanding of their dynamic structural evolution and reaction kinetics in the lithiation process. Herein, thermodynamic phase diagrams and the lithiation dynamics of MoS2-based nanostructures with the intercalation of lithium ions are studied by using first-principles calculations and ab initio molecular dynamics simulations. Our results demonstrate that the continuous intercalation of Li ions induces structural destruction of 2H phase MoS2 nanosheets in the discharge process that follows a layer-by-layer dissociation mechanism. Meanwhile, the intercalation of Li ions leads to a structural transition of MoS2 nanosheets from the 2H to the 1T phase due to the ultralow transition barriers (~0.1 eV). We find that the phase transition can slow down the dissociation of MoS2 nanosheets during lithiation. The result can be applied to explain extensive experimental observation of the fast capacity fading of MoS2-based anode materials between the first and the subsequent discharges. To suppress the dissociation of MoS2 nanosheets in the lithiation process, we propose a strategy by constructing a sandwich-like graphene/MoS2/graphene structure that indicates high chemical stability, superior conductivity, and high Li-ion mobility in the charge/discharge process, implying the possibility to induce an improvement in the anode cycling performance. This work opens a new route to rational design layered transition-metal disulfide (TMD) anode materials for LIBs with superior cycling stability and electrochemical performance. Electronic supplementary information (ESI) available: Models and energetics of Li adsorption/intercalation onto MoS2 sheets, details of the phase diagram calculations, schematic illustration for the structural evolution of lithiated MoS2 nanosheets, AIMD trajectories for lithiated silicene/MoS2/silicene composites, and movies for recording the AIMD simulation results. See DOI: 10.1039/c5nr07909h

Diffusion dynamics of the Keap1–Cullin3 interaction in single live cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Baird, Liam; Dinkova-Kostova, Albena T., E-mail: a.dinkovakostova@dundee.ac.uk; Department of Pharmacology and Molecular Sciences, Johns Hopkins University School of Medicine, Baltimore, MD

2013-03-29

Highlights: ► We developed a quantitative FRAP-based system to study the Keap1–Cul3 interaction. ► We show that Keap1–EGFP and mCherry–Cul3 interact in single live cells. ► We used inducers which target distinct cysteine sensors of Keap1 and differ 4000-fold in potency. ► Inducers cause Nrf2 stabilization, nuclear translocation, and target gene expression. ► Inducers of four different types do not dissociate the Keap1–EGFP:mCherry–Cul3 complex. -- Abstract: Transcription factor NF-E2 p45-related factor 2 (Nrf2) regulates the expression of a network of genes encoding drug-detoxification, anti-inflammatory, and metabolic enzymes, as well as proteins involved in the regulation of cellular redox homeostasis. Undermore » basal conditions, Kelch-like ECH associated protein 1 (Keap1) targets Nrf2 for ubiquitination and proteasomal degradation via association with Cullin3 (Cul3)-based Rbx1 E3 ubiquitin ligase. Various small molecules (inducers) activate Nrf2 leading to upregulation of cytoprotective gene expression. Inducers chemically modify specific cysteine residues of Keap1 which ultimately loses its ability to target Nrf2 for degradation. Dissociation of the Keap1–Cul3 complex by inducers is one possible mechanism, but evidence in single live cells is lacking. To investigate the diffusion dynamics of the Keap1–Cul3 interaction and the effect of inducers, we developed a quantitative fluorescence recovery after photobleaching (FRAP)-based system using Keap1–EGFP and mCherry–Cul3 fusion proteins. We show that Keap1–EGFP and mCherry–Cul3 interact in single live cells. Exposure for 1 h to small-molecule inducers of 4 different types, the oleanane triterpenoid CDDO, the isothiocyanate sulforaphane, the sulfoxythiocarbamate STCA, and the oxidant hydrogen peroxide which target distinct cysteine sensors within Keap1 with potencies which differ by nearly 4000-fold, does not dissociate the Keap1–Cul3 complex. As inducers cause conformational changes in Keap1, we conclude that changes in conformation rather than dissociation from Cul3 inactivate the repressor function of Keap1 leading to Nrf2 stabilization.« less

Orientation dependences of atomic structures in chemically heterogeneous Cu{sub 50}Ta{sub 50}/Ta glass-crystal interfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yang, Guiqin; Gao, Xiaoze; Li, Jinfu

2015-01-07

Molecular dynamics simulations based on an angular-dependent potential were performed to examine the structural properties of chemically heterogeneous interfaces between amorphous Cu{sub 50}Ta{sub 50} and crystalline Ta. Several phenomena, namely, layering, crystallization, intermixing, and composition segregation, were observed in the Cu{sub 50}Ta{sub 50} region adjacent to the Ta layers. These interfacial behaviors are found to depend on the orientation of the underlying Ta substrate: Layering induced by Ta(110) extends the farthest into Cu{sub 50}Ta{sub 50}, crystallization in the Cu{sub 50}Ta{sub 50} region is most significant for interface against Ta(100), while inter-diffusion is most pronounced for Ta(111). It turns out thatmore » the induced layering behavior is dominated by the interlayer distances of the underlying Ta layers, while the degree of inter-diffusion is governed by the openness of the Ta crystalline layers. In addition, composition segregations are observed in all interface models, corresponding to the immiscible nature of the Cu-Ta system. Furthermore, Voronoi polyhedra 〈0,5,2,6〉 and 〈0,4,4,6〉 are found to be abundant in the vicinity of the interfaces for all models, whose presence is believed to facilitate the structural transition between amorphous and body centered cubic.« less

Genetic, structural, and chemical insights into the dual function of GRASP55 in germ cell Golgi remodeling and JAM-C polarized localization during spermatogenesis.

PubMed

Cartier-Michaud, Amandine; Bailly, Anne-Laure; Betzi, Stéphane; Shi, Xiaoli; Lissitzky, Jean-Claude; Zarubica, Ana; Sergé, Arnauld; Roche, Philippe; Lugari, Adrien; Hamon, Véronique; Bardin, Florence; Derviaux, Carine; Lembo, Frédérique; Audebert, Stéphane; Marchetto, Sylvie; Durand, Bénédicte; Borg, Jean-Paul; Shi, Ning; Morelli, Xavier; Aurrand-Lions, Michel

2017-06-01

Spermatogenesis is a dynamic process that is regulated by adhesive interactions between germ and Sertoli cells. Germ cells express the Junctional Adhesion Molecule-C (JAM-C, encoded by Jam3), which localizes to germ/Sertoli cell contacts. JAM-C is involved in germ cell polarity and acrosome formation. Using a proteomic approach, we demonstrated that JAM-C interacted with the Golgi reassembly stacking protein of 55 kDa (GRASP55, encoded by Gorasp2) in developing germ cells. Generation and study of Gorasp2-/- mice revealed that knock-out mice suffered from spermatogenesis defects. Acrosome formation and polarized localization of JAM-C in spermatids were altered in Gorasp2-/- mice. In addition, Golgi morphology of spermatocytes was disturbed in Gorasp2-/- mice. Crystal structures of GRASP55 in complex with JAM-C or JAM-B revealed that GRASP55 interacted via PDZ-mediated interactions with JAMs and induced a conformational change in GRASP55 with respect of its free conformation. An in silico pharmacophore approach identified a chemical compound called Graspin that inhibited PDZ-mediated interactions of GRASP55 with JAMs. Treatment of mice with Graspin hampered the polarized localization of JAM-C in spermatids, induced the premature release of spermatids and affected the Golgi morphology of meiotic spermatocytes.

SEQUENCE ANALYSIS OF MUTATIONS INDUCED BY N-ETHYL-N-NITROSOUREA IN THE TK AND HPRT GENES OF MOUSE LYMPHOMA CELLS.

EPA Science Inventory

The mouse lymphoma assay is widely used to identify chemicals that are capable of inducing mutational damages. The Tk+/- gene located on an autosome in mouse lymphoma cells may recover a wider range of mutational events than the X-linked Hprt locus. However, chemical-induced muta...

Nanomaterials under extreme environments: A study of structural and dynamic properties using reactive molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Shekhar, Adarsh

Nanotechnology is becoming increasingly important with the continuing advances in experimental techniques. As researchers around the world are trying to expand the current understanding of the behavior of materials at the atomistic scale, the limited resolution of equipment, both in terms of time and space, act as roadblocks to a comprehensive study. Numerical methods, in general and molecular dynamics, in particular act as able compliment to the experiments in our quest for understanding material behavior. In this research work, large scale molecular dynamics simulations to gain insight into the mechano-chemical behavior under extreme conditions of a variety of systems with many real world applications. The body of this work is divided into three parts, each covering a particular system: 1) Aggregates of aluminum nanoparticles are good solid fuel due to high flame propagation rates. Multi-million atom molecular dynamics simulations reveal the mechanism underlying higher reaction rate in a chain of aluminum nanoparticles as compared to an isolated nanoparticle. This is due to the penetration of hot atoms from reacting nanoparticles to an adjacent, unreacted nanoparticle, which brings in external heat and initiates exothermic oxidation reactions. 2) Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We use billion-atom reactive molecular dynamics simulations on a 163,840-processor BlueGene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near amorphous silica. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The pit contains a large number of silanol groups and its volume is found to be directly proportional to the volume of the nanobubble. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated. 3) The structure and dynamics of water confined in nanoporous silica are different from that of bulk water, and insight into the properties of confined water is important for our understanding of many geological and biological processes. Nanoporous silica has a wide range of technological applications because it is easy to tune the size of pores and their morphologies and to functionalize pore surfaces with a variety of molecular moieties. Nanoporous silica is used in catalysis, chromatography, anticorrosion coatings, desalination membranes, and as drug delivery vehicles. We use reactive molecular dynamics to study the structure and dynamics of nanoconfined water between 100 and 300 K

Nonadiabatic molecular dynamics simulations: synergies between theory and experiments.

PubMed

Tavernelli, Ivano

2015-03-17

Recent developments in nonadiabatic dynamics enabled ab inito simulations of complex ultrafast processes in the condensed phase. These advances have opened new avenues in the study of many photophysical and photochemical reactions triggered by the absorption of electromagnetic radiation. In particular, theoretical investigations can be combined with the most sophisticated femtosecond experimental techniques to guide the interpretation of measured time-resolved observables. At the same time, the availability of experimental data at high (spatial and time) resolution offers a unique opportunity for the benchmarking and the improvement of those theoretical models used to describe complex molecular systems in their natural environment. The established synergy between theory and experiments can produce a better understanding of new ultrafast physical and chemical processes at atomistic scale resolution. Furthermore, reliable ab inito molecular dynamics simulations can already be successfully employed as predictive tools to guide new experiments as well as the design of novel and better performing materials. In this paper, I will give a concise account on the state of the art of molecular dynamics simulations of complex molecular systems in their excited states. The principal aim of this approach is the description of a given system of interest under the most realistic ambient conditions including all environmental effects that influence experiments, for instance, the interaction with the solvent and with external time-dependent electric fields, temperature, and pressure. To this end, time-dependent density functional theory (TDDFT) is among the most efficient and accurate methods for the representation of the electronic dynamics, while trajectory surface hopping gives a valuable representation of the nuclear quantum dynamics in the excited states (including nonadiabatic effects). Concerning the environment and its effects on the dynamics, the quantum mechanics/molecular mechanics (QM/MM) approach has the advantage of providing an atomistic (even though approximated) description of the solvent molecules, which is crucial for the characterization of all ultrafast relaxation phenomena that depend on the geometrical arrangement at the interface between a molecule and the solvent, for example, the hydrogen bond network. After a short description of the TDDFT-based implementation of Ehrenfest and trajectory surface hopping dynamics, I will present applications in different domains of molecular chemistry and physics: the analysis and the understanding of (time-resolved) X-ray absorption spectra, the interpretation of the ultrafast relaxation dynamics of photoexcited dyes in solution, and the design of specific laser pulses (capable of inducing desired chemical reactions) using local control theory.

DNA-Encoded Dynamic Combinatorial Chemical Libraries.

PubMed

Reddavide, Francesco V; Lin, Weilin; Lehnert, Sarah; Zhang, Yixin

2015-06-26

Dynamic combinatorial chemistry (DCC) explores the thermodynamic equilibrium of reversible reactions. Its application in the discovery of protein binders is largely limited by difficulties in the analysis of complex reaction mixtures. DNA-encoded chemical library (DECL) technology allows the selection of binders from a mixture of up to billions of different compounds; however, experimental results often show low a signal-to-noise ratio and poor correlation between enrichment factor and binding affinity. Herein we describe the design and application of DNA-encoded dynamic combinatorial chemical libraries (EDCCLs). Our experiments have shown that the EDCCL approach can be used not only to convert monovalent binders into high-affinity bivalent binders, but also to cause remarkably enhanced enrichment of potent bivalent binders by driving their in situ synthesis. We also demonstrate the application of EDCCLs in DNA-templated chemical reactions. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Population dynamics, information transfer, and spatial organization in a chemical reaction network under spatial confinement and crowding conditions

NASA Astrophysics Data System (ADS)

Bellesia, Giovanni; Bales, Benjamin B.

2016-10-01

We investigate, via Brownian dynamics simulations, the reaction dynamics of a generic, nonlinear chemical network under spatial confinement and crowding conditions. In detail, the Willamowski-Rossler chemical reaction system has been "extended" and considered as a prototype reaction-diffusion system. Our results are potentially relevant to a number of open problems in biophysics and biochemistry, such as the synthesis of primitive cellular units (protocells) and the definition of their role in the chemical origin of life and the characterization of vesicle-mediated drug delivery processes. More generally, the computational approach presented in this work makes the case for the use of spatial stochastic simulation methods for the study of biochemical networks in vivo where the "well-mixed" approximation is invalid and both thermal and intrinsic fluctuations linked to the possible presence of molecular species in low number copies cannot be averaged out.

NMR structural and dynamical investigation of the isolated voltage-sensing domain of the potassium channel KvAP: implications for voltage gating.

PubMed

Shenkarev, Zakhar O; Paramonov, Alexander S; Lyukmanova, Ekaterina N; Shingarova, Lyudmila N; Yakimov, Sergei A; Dubinnyi, Maxim A; Chupin, Vladimir V; Kirpichnikov, Mikhail P; Blommers, Marcel J J; Arseniev, Alexander S

2010-04-28

The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein domain solubilized in DPC/LDAO (2:1) mixed micelles. Secondary and tertiary structures of the VSD were characterized using secondary chemical shifts and NOE contacts. These data indicate that the spatial structure of the VSD solubilized in micelles corresponds to the structure of the domain in an open state of the channel. NOE contacts and secondary chemical shifts of amide protons indicate the presence of tightly bound water molecule as well as hydrogen bond formation involving an interhelical salt bridge (Asp62-R133) that stabilizes the overall structure of the domain. The backbone dynamics of the VSD was studied using (15)N relaxation measurements. The loop regions S1-S2 and S2-S3 were found mobile, while the S3-S4 loop (voltage-sensor paddle) was found stable at the ps-ns time scale. The moieties of S1, S2, S3, and S4 helices sharing interhelical contacts (at the level of the Asp62-R133 salt bridge) were observed in conformational exchange on the micros-ms time scale. Similar exchange-induced broadening of characteristic resonances was observed for the VSD solubilized in the membrane of lipid-protein nanodiscs composed of DMPC, DMPG, and POPC/DOPG lipids. Apparently, the observed interhelical motions represent an inherent property of the VSD of the KvAP channel and can play an important role in the voltage gating.

Creep cavitation can establish a dynamic granular fluid pump in ductile shear zones.

PubMed

Fusseis, F; Regenauer-Lieb, K; Liu, J; Hough, R M; De Carlo, F

2009-06-18

The feedback between fluid migration and rock deformation in mid-crustal shear zones is acknowledged as being critical for earthquake nucleation, the initiation of subduction zones and the formation of mineral deposits. The importance of this poorly understood feedback is further highlighted by evidence for shear-zone-controlled advective flow of fluids in the ductile lower crust and the recognition that deformation-induced grain-scale porosity is a key to large-scale geodynamics. Fluid migration in the middle crust cannot be explained in terms of classical concepts. The environment is considered too hot for a dynamic fracture-sustained permeability as in the upper crust, and fluid pathways are generally too deformed to be controlled by equilibrium wetting angles that apply to hotter, deeper environments. Here we present evidence that mechanical and chemical potentials control a syndeformational porosity generation in mid-crustal shear zones. High-resolution synchrotron X-ray tomography and scanning electron microscopy observations allow us to formulate a model for fluid migration in shear zones where a permeable porosity is dynamically created by viscous grain-boundary sliding, creep cavitation, dissolution and precipitation. We propose that syndeformational fluid migration in our 'granular fluid pump' model is a self-sustained process controlled by the explicit role of the rate of entropy production of the underlying irreversible mechanical and chemical microprocesses. The model explains fluid transfer through the middle crust, where strain localization in the creep regime is required for plate tectonics, the formation of giant ore deposits, mantle degassing and earthquake nucleation. Our findings provide a key component for the understanding of creep instabilities in the middle crust.

Axis switching and spreading of an asymmetric jet: Role of vorticity dynamics

NASA Technical Reports Server (NTRS)

Zaman, K. B. M. Q.

1994-01-01

The effects of vortex generators and periodic excitation on vorticity dynamics and the phenomenon of axis switching in a free asymmetric jet are studied experimentally. Most of the data reported are for a 3:1 rectangular jet at a Reynolds number of 450,000 and a Mach number of 0.31. The vortex generators are in the form of 'delta tabs', triangular shaped protrusions into the flow, placed at the nozzle exit. With suitable placement of the tabs, axis switching could be either stopped or augmented. Two mechanisms are identified governing the phenomenon. One, as described by previous researchers and referred to here as the omega(sub theta)-induced dynamics, is due to difference in induced velocities for different segments of a rolled up azimuthal vortical structure. The other, omega(sub x)-induced dynamics, is due to the induced velocities of streamwise vortex pairs in the flow. Both dynamics can be active in a natural asymmetric jet; the tendency for axis switching caused by the omega(sub theta)-induced dynamics may be, depending on the streamwise vorticity distribution, either resisted or enhanced by the omega(sub x)-induced dynamics. While this simple framework qualitatively explains the various observations made on axis switching, mechanisms actually in play may be much more complex. The two dynamics are not independent as the flow field is replete with both azimuthal and streamwise vortical structures which continually interact. Phase averaged flow field data for a periodically forced case, over a volume of the flow field, are presented and discussed in an effort to gain insight into the dynamics of these vortical structures.

Theoretical studies in interstellar cloud chemistry

NASA Technical Reports Server (NTRS)

Chiu, Y. T.; Prasad, S. S.

1993-01-01

This final report represents the completion of the three tasks under the purchase order no. SCPDE5620,1,2F. Chemical composition of gravitationally contracting, but otherwise quiescent, interstellar clouds and of interstellar clouds traversed by high velocity shocks, were modeled in a comprehensive manner that represents a significant progress in modeling these objects. The evolutionary chemical modeling, done under this NASA contract, represents a notable advance over the 'classical' fixed condition equilibrium models because the evolutionary models consider not only the chemical processes but also the dynamical processes by which the dark interstellar clouds may have assumed their present state. The shock calculations, being reported here, are important because they extend the limited chemical composition derivable from dynamical calculations for the total density and temperature structures behind the shock front. In order to be tractable, the dynamical calculations must severely simplify the chemistry. The present shock calculations take the shock profiles from the dynamical calculations and derive chemical composition in a comprehensive manner. The results of the present modeling study are still to be analyzed with reference to astronomical observational data and other contemporary model predictions. As far as humanly possible, this analysis will be continued with CRE's (Creative Research Enterprises's) IR&D resources, until a sponsor is found.

Spectroscopic Observation of Chemical Interaction Between Impact-induced Vapor Clouds and the Ambient Atmosphere

NASA Technical Reports Server (NTRS)

Sugita, S.; Heineck, J. T.; Schultz, P. H.

2000-01-01

Chemical reactions within impact-induced vapor clouds were observed in laboratory experiments using a spectroscopic method. The results indicate that projectile-derived carbon-rich vapor reacts intensively with atmospheric nitrogen.

Estrogen alters gonadal soma-derived factor (Gsdf)/Foxl2 expression levels in the testes associated with testis-ova differentiation in adult medaka, Oryzias latipes.

PubMed

Kobayashi, Tohru; Chiba, Ayaka; Sato, Tadashi; Myosho, Taijun; Yamamoto, Jun; Okamura, Tetsuro; Onishi, Yuta; Sakaizumi, Mitsuru; Hamaguchi, Satoshi; Iguchi, Taisen; Horie, Yoshifumi

2017-10-01

Testis-ova differentiation in sexually mature male medaka (Oryzias latipes) is easily induced by estrogenic chemicals, indicating that spermatogonia persist in sexual bipotentiality, even in mature testes in medaka. By contrast, the effects of estrogen on testicular somatic cells associated with testis-ova differentiation in medaka remain unclear. In this study, we focused on the dynamics of sex-related genes (Gsdf, Dmrt1, and Foxl2) expressed in Sertoli cells in the mature testes of adult medaka during estrogen-induced testis-ova differentiation. When mature male medaka were exposed to estradiol benzoate (EB; 800ng/L), testis-ova first appeared after EB treatment for 14days (observed as the first oocytes of the leptotene-zygotene stage). However, the testis remained structurally unchanged, even after EB treatment for 28days. Although Foxl2 is a female-specific sex gene, EB treatment for 7days induced Foxl2/FOXL2 expression in all Sertoli cell-enclosed spermatogonia before testis-ova first appeared; however, Foxl2 was not detected in somatic cells in control testes. Conversely, Sertoli-cell-specific Gsdf mRNA expression levels significantly decreased after EB treatment for 14days, and no changes were observed in DMRT1 localization following EB treatment, whereas Dmrt1 mRNA levels increased significantly. Furthermore, after EB exposure, FOXl2 and DMRT1 were co-localized in Sertoli cells during testis-ova differentiation, although FOXL2 localization was undetectable in Sertoli-cell-enclosed apoptotic testis-ova, whereas DMRT1 remained localized in Sertoli cells. These results indicated for the first time that based on the expression of female-specific sex genes, feminization of Sertoli cells precedes testis-ova differentiation induced by estrogen in mature testes in medaka; however, complete feminization of Sertoli cells was not induced in this study. Additionally, it is suggested strongly that Foxl2 and Gsdf expression constitute potential molecular markers for evaluating the effects of estrogenic chemicals on testicular somatic cells associated with estrogen-induced testis-ova differentiation in mature male medaka. Copyright © 2017 Elsevier B.V. All rights reserved.

Relationship of CD86 surface marker expression and cytotoxicity on dendritic cells exposed to chemical allergen

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hulette, Ben C.; Ryan, Cindy A.; Gildea, Lucy A.

2005-12-01

Human peripheral blood-derived dendritic cells (DC) respond to a variety of chemical allergens by up-regulating expression of the co-stimulatory molecule CD86. It has been postulated that this measure might provide the basis for an in vitro alternative approach for the identification of skin sensitizing chemicals. We recently reported that DC, exposed in culture to the highest non-cytotoxic concentrations of various chemical allergens, displayed marginal up-regulation of membrane CD86 expression; the interpretation being that such changes were insufficiently sensitive for the purposes of hazard identification. For the work presented here, immature DC were derived from human monocytes and treated with themore » chemical allergens 2,4-dinitrobenzenesulfonic acid (DNBS), nickel sulfate (NiSO{sub 4}), p-phenylenediamine (PPD), Bandrowski's base (BB), hydroquinone (HQ) and propyl gallate (PG) for 48 h at concentrations which induced both no to slight to moderate cytotoxicity. For comparison, DC were treated with the irritants sodium dodecyl sulfate (SDS), benzoic acid (BA), and benzalkonium chloride (BZC) at concentrations resulting in comparable levels of cytotoxicity. CD86 expression, as measured by flow cytometry, was consistently up-regulated (ranging from 162 to 386% control) on DC treated with concentrations of chemical allergens that induced approximately 10-15% cytotoxicity. The irritants BA and BZC did not induce up-regulation of CD86 expression when tested at concentrations that induced similar levels of cytotoxicity. SDS, however, up-regulated CD86 expression to 125-138% of control in 2/4 preparations when tested at concentrations which induced similar toxicity. Our results confirm that chemical allergens up-regulate CD86 expression on blood-derived DC and illustrate further that up-regulation of CD86 surface marker expression is more robust when DC are treated with concentrations of chemical allergen that induce slight to moderate cytotoxicity.« less

Simultaneous effects of food limitation and inducible resistance on herbivore population dynamics.

PubMed

Abbott, Karen C; Morris, William F; Gross, Kevin

2008-02-01

Many herbivore populations fluctuate temporally, but the causes of those fluctuations remain unclear. Plant inducible resistance can theoretically cause herbivore population fluctuations, because herbivory may induce plant changes that reduce the survival or reproduction of later-feeding herbivores. Herbivory can also simply reduce the quantity of food available for later feeders and this, too, can cause population fluctuations. Inducible resistance and food limitation often occur simultaneously, yet whether they jointly facilitate or suppress herbivore fluctuations remains largely unexplored. We present models that suggest that food limitation and inducible resistance may have synergistic effects on herbivore population dynamics. The population-level response of the food plant to herbivory and the details of how inducible resistance affects herbivore performance both influence the resulting herbivore dynamics. Our results identify some biological properties of plant-herbivore systems that might determine whether or not cycles occur, and suggest that future empirical and theoretical population dynamics studies should account for the effects of both food limitation and inducible resistance.

Noise-induced symmetry breaking far from equilibrium and the emergence of biological homochirality

NASA Astrophysics Data System (ADS)

Jafarpour, Farshid; Biancalani, Tommaso; Goldenfeld, Nigel

2017-03-01

The origin of homochirality, the observed single-handedness of biological amino acids and sugars, has long been attributed to autocatalysis, a frequently assumed precursor for early life self-replication. However, the stability of homochiral states in deterministic autocatalytic systems relies on cross-inhibition of the two chiral states, an unlikely scenario for early life self-replicators. Here we present a theory for a stochastic individual-level model of autocatalytic prebiotic self-replicators that are maintained out of thermal equilibrium. Without chiral inhibition, the racemic state is the global attractor of the deterministic dynamics, but intrinsic multiplicative noise stabilizes the homochiral states. Moreover, we show that this noise-induced bistability is robust with respect to diffusion of molecules of opposite chirality, and systems of diffusively coupled autocatalytic chemical reactions synchronize their final homochiral states when the self-replication is the dominant production mechanism for the chiral molecules. We conclude that nonequilibrium autocatalysis is a viable mechanism for homochirality, without imposing additional nonlinearities such as chiral inhibition.

From in vitro to in vivo: Integration of the virtual cell based assay with physiologically based kinetic modelling.

PubMed

Paini, Alicia; Sala Benito, Jose Vicente; Bessems, Jos; Worth, Andrew P

2017-12-01

Physiologically based kinetic (PBK) models and the virtual cell based assay can be linked to form so called physiologically based dynamic (PBD) models. This study illustrates the development and application of a PBK model for prediction of estragole-induced DNA adduct formation and hepatotoxicity in humans. To address the hepatotoxicity, HepaRG cells were used as a surrogate for liver cells, with cell viability being used as the in vitro toxicological endpoint. Information on DNA adduct formation was taken from the literature. Since estragole induced cell damage is not directly caused by the parent compound, but by a reactive metabolite, information on the metabolic pathway was incorporated into the model. In addition, a user-friendly tool was developed by implementing the PBK/D model into a KNIME workflow. This workflow can be used to perform in vitro to in vivo extrapolation and forward as backward dosimetry in support of chemical risk assessment. Copyright © 2017 The Authors. Published by Elsevier Ltd.. All rights reserved.

Origin of Light Induced Photophysical Effects in Organic Metal Halide Perovskites in the Presence of Oxygen.

PubMed

Anaya, Miguel; Galisteo-López, Juan F; Calvo, Mauricio Ernesto; Espinos, Juan P; Miguez, Hernan

2018-06-21

Herein we present a combined study of the evolution of both the photoluminescence and the surface chemical structure of organic metal halide perovskites as environmental oxygen pressure rises from ultra-high vacuum up to a few thousandths of an atmosphere. Analyzing the changes occurring at the semiconductor surface upon photo-excitation under controlled oxygen atmosphere in an X-ray photoelectron spectroscopy (XPS) chamber, we can rationalize the rich variety of photophysical phenomena observed and provide a plausible explanation for light-induced ion migration, one of the most conspicuous and debated concomitant effects detected during photoexcitation. We find direct evidence of the formation of a superficial layer of negatively charged oxygen species capable of repelling the halide anions away from the surface and towards the bulk. The reported photoluminescence (PL) transient dynamics, the partial recovery of the initial state when photoexcitation stops and the eventual degradation after intense exposure times can thus be rationalized.

Capacitorless 1T-DRAM on crystallized poly-Si TFT.

PubMed

Kim, Min Soo; Cho, Won Ju

2011-07-01

The single-transistor dynamic random-access memory (1T-DRAM) using a polycrystalline-silicon thin-film transistor (poly-Si TFT) was investigated. A 100-nm amorphous silicon thin film was deposited onto a 200-nm oxidized silicon wafer via low-pressure chemical vapor deposition (LPCVD), and the amorphous silicon layer was crystallized via eximer laser annealing (ELA) with a KrF source of 248 nm wavelength and 400 mJ/cm2 power. The fabricated capacitor less 1T-DRAM on the poly-Si TFT was evaluated via impact ionization and gate-induced drain leakage (GIDL) current programming. The device showed a clear memory margin between the "1" and "0" states, and as the channel length decreased, a floating body effect which induces a kink effect increases with high mobility. Furthermore, the GIDL current programming showed improved memory properties compared to the impact ionization method. Although the sensing margins and retention times in both program methods are commercially insufficient, it was confirmed the feasibility of the application of 1T-DRAM operation to TFTs.

Asymmetric Base-Bleed Effect on Aerospike Plume-Induced Base-Heating Environment

NASA Technical Reports Server (NTRS)

Wang, Ten-See; Droege, Alan; DAgostino, Mark; Lee, Young-Ching; Williams, Robert

2004-01-01

A computational heat transfer design methodology was developed to study the dual-engine linear aerospike plume-induced base-heating environment during one power-pack out, in ascent flight. It includes a three-dimensional, finite volume, viscous, chemically reacting, and pressure-based computational fluid dynamics formulation, a special base-bleed boundary condition, and a three-dimensional, finite volume, and spectral-line-based weighted-sum-of-gray-gases absorption computational radiation heat transfer formulation. A separate radiation model was used for diagnostic purposes. The computational methodology was systematically benchmarked. In this study, near-base radiative heat fluxes were computed, and they compared well with those measured during static linear aerospike engine tests. The base-heating environment of 18 trajectory points selected from three power-pack out scenarios was computed. The computed asymmetric base-heating physics were analyzed. The power-pack out condition has the most impact on convective base heating when it happens early in flight. The source of its impact comes from the asymmetric and reduced base bleed.

Biosynthetic tailoring of existing ascaroside pheromones alters their biological function in C. elegans

PubMed Central

Zhang, Xinxing; Bhar, Subhradeep; Jones Lipinski, Rachel A; Han, Jungsoo; Feng, Likui

2018-01-01

Caenorhabditis elegans produces ascaroside pheromones to control its development and behavior. Even minor structural differences in the ascarosides have dramatic consequences for their biological activities. Here, we identify a mechanism that enables C. elegans to dynamically tailor the fatty-acid side chains of the indole-3-carbonyl (IC)-modified ascarosides it has produced. In response to starvation, C. elegans uses the peroxisomal acyl-CoA synthetase ACS-7 to activate the side chains of medium-chain IC-ascarosides for β-oxidation involving the acyl-CoA oxidases ACOX-1.1 and ACOX-3. This pathway rapidly converts a favorable ascaroside pheromone that induces aggregation to an unfavorable one that induces the stress-resistant dauer larval stage. Thus, the pathway allows the worm to respond to changing environmental conditions and alter its chemical message without having to synthesize new ascarosides de novo. We establish a new model for biosynthesis of the IC-ascarosides in which side-chain β-oxidation is critical for controlling the type of IC-ascarosides produced. PMID:29863473

Dynamic stiffness of chemically and physically ageing rubber vibration isolators in the audible frequency range: Part 2—waveguide solution

NASA Astrophysics Data System (ADS)

Kari, Leif

2017-09-01

The dynamic stiffness of a chemically and physically ageing rubber vibration isolator in the audible frequency range is modelled as a function of ageing temperature, ageing time, actual temperature, time, frequency and isolator dimension. In particular, the dynamic stiffness for an axially symmetric, homogeneously aged rubber vibration isolator is derived by waveguides where the eigenmodes given by the dispersion relation for an infinite cylinder satisfying traction free radial surface boundary condition are matched to satisfy the displacement boundary conditions at the lateral surface ends of the finite rubber cylinder. The constitutive equations are derived in a companion paper (Part 1). The dynamic stiffness is calculated over the whole audible frequency range 20-20,000 Hz at several physical ageing times for a temperature history starting at thermodynamic equilibrium at +25°C and exposed by a sudden temperature step down to -60°C and at several chemical ageing times at temperature +25°C with simultaneous molecular network scission and reformation. The dynamic stiffness results are displaying a strong frequency dependence at a short physical ageing time, showing stiffness magnitude peaks and troughs, and a strong physical ageing time dependence, showing a large stiffness magnitude increase with the increased physical ageing time, while the peaks and troughs are smoothed out. Likewise, stiffness magnitude peaks and troughs are frequency-shifted with increased chemical ageing time. The developed model is possible to apply for dynamic stiffness prediction of rubber vibration isolator over a broad audible frequency range under realistic environmental condition of chemical ageing, mainly attributed to oxygen exposure from outside and of physical ageing, primarily perceived at low-temperature steps.

A Fluorogenic TMP-tag for High Signal-to-Background Intracellular Live Cell Imaging

PubMed Central

Jing, Chaoran

2013-01-01

Developed to compliment the use of fluorescent proteins in live cell imaging, chemical tags enjoy the benefit of modular incorporation of organic fluorophores, opening the possibility of high photon output and special photophysical properties. However, the theoretical challenge in using chemical tags as opposed to fluorescent proteins for high-resolution imaging is background noise from unbound and/or non-specifically bound ligand-fluorophore. We envisioned we could overcome this limit by engineering fluorogenic trimethoprim-based chemical tags (TMP-tags) in which the fluorophore is quenched until binding with E. coli dihydrofolate reductase (eDHFR) tagged protein displaces the quencher. Thus, we began by building a non-fluorogenic, covalent TMP-tag based on a proximity-induced reaction known to achieve rapid and specific labeling both in vitro and inside of living cells. Here we take the final step and render the covalent TMP-tag fluorogenic. In brief, we designed a trimeric TMP-fluorophore-quencher molecule (TMP-Q-Atto520) with the quencher attached to a leaving group that, upon TMP binding to eDHFR, would be cleaved by a cysteine residue (Cys) installed just outside the binding pocket of eDHFR. We present the in vitro experiments showing that the eDHFR:L28C nucleophile cleaves the TMP-Q-Atto520 rapidly and efficiently, resulting in covalent labeling and remarkable fluorescence enhancement. Most significantly, while only our initial design, TMP-Q-Atto520 achieved the demanding goal of not only labeling highly abundant, localized intracellular proteins, but also less abundant, more dynamic cytoplasmic proteins. These results suggest that fluorogenic TMP-tag can significantly impact highresolution live cell imaging and further establish the potential of proximity-induced reactivity and organic chemistry more broadly as part of the growing toolbox for synthetic biology and cell engineering. PMID:23745575

Chemical reactions induced by oscillating external fields in weak thermal environments

NASA Astrophysics Data System (ADS)

Craven, Galen T.; Bartsch, Thomas; Hernandez, Rigoberto

2015-02-01

Chemical reaction rates must increasingly be determined in systems that evolve under the control of external stimuli. In these systems, when a reactant population is induced to cross an energy barrier through forcing from a temporally varying external field, the transition state that the reaction must pass through during the transformation from reactant to product is no longer a fixed geometric structure, but is instead time-dependent. For a periodically forced model reaction, we develop a recrossing-free dividing surface that is attached to a transition state trajectory [T. Bartsch, R. Hernandez, and T. Uzer, Phys. Rev. Lett. 95, 058301 (2005)]. We have previously shown that for single-mode sinusoidal driving, the stability of the time-varying transition state directly determines the reaction rate [G. T. Craven, T. Bartsch, and R. Hernandez, J. Chem. Phys. 141, 041106 (2014)]. Here, we extend our previous work to the case of multi-mode driving waveforms. Excellent agreement is observed between the rates predicted by stability analysis and rates obtained through numerical calculation of the reactive flux. We also show that the optimal dividing surface and the resulting reaction rate for a reactive system driven by weak thermal noise can be approximated well using the transition state geometry of the underlying deterministic system. This agreement persists as long as the thermal driving strength is less than the order of that of the periodic driving. The power of this result is its simplicity. The surprising accuracy of the time-dependent noise-free geometry for obtaining transition state theory rates in chemical reactions driven by periodic fields reveals the dynamics without requiring the cost of brute-force calculations.

Structure-activity relationships of pentamidine-affected ion channel trafficking and dofetilide mediated rescue.

PubMed

Varkevisser, R; Houtman, M J C; Linder, T; de Git, K C G; Beekman, H D M; Tidwell, R R; Ijzerman, A P; Stary-Weinzinger, A; Vos, M A; van der Heyden, M A G

2013-07-01

Drug interference with normal hERG protein trafficking substantially reduces the channel density in the plasma membrane and thereby poses an arrhythmic threat. The chemical substructures important for hERG trafficking inhibition were investigated using pentamidine as a model drug. Furthermore, the relationship between acute ion channel block and correction of trafficking by dofetilide was studied. hERG and K(IR)2.1 trafficking in HEK293 cells was evaluated by Western blot and immunofluorescence microscopy after treatment with pentamidine and six pentamidine analogues, and correction with dofetilide and four dofetilide analogues that displayed different abilities to inhibit IKr . Molecular dynamics simulations were used to address mode, number and type of interactions between hERG and dofetilide analogues. Structural modifications of pentamidine differentially affected plasma membrane levels of hERG and K(IR)2.1. Modification of the phenyl ring or substituents directly attached to it had the largest effect, affirming the importance of these chemical residues in ion channel binding. PA-4 had the mildest effects on both ion channels. Dofetilide corrected pentamidine-induced hERG, but not K(IR)2.1 trafficking defects. Dofetilide analogues that displayed high channel affinity, mediated by pi-pi stacks and hydrophobic interactions, also restored hERG protein levels, whereas analogues with low affinity were ineffective. Drug-induced trafficking defects can be minimized if certain chemical features are avoided or 'synthesized out'; this could influence the design and development of future drugs. Further analysis of such features in hERG trafficking correctors may facilitate the design of a non-blocking corrector for trafficking defective hERG proteins in both congenital and acquired LQTS. © 2013 The British Pharmacological Society.

Structure-activity relationships of pentamidine-affected ion channel trafficking and dofetilide mediated rescue

PubMed Central

Varkevisser, R; Houtman, M J C; Linder, T; de Git, K C G; Beekman, H D M; Tidwell, R R; IJzerman, A P; Stary-Weinzinger, A; Vos, M A; van der Heyden, M A G

2013-01-01

Background and Purpose Drug interference with normal hERG protein trafficking substantially reduces the channel density in the plasma membrane and thereby poses an arrhythmic threat. The chemical substructures important for hERG trafficking inhibition were investigated using pentamidine as a model drug. Furthermore, the relationship between acute ion channel block and correction of trafficking by dofetilide was studied. Experimental Approach hERG and KIR2.1 trafficking in HEK293 cells was evaluated by Western blot and immunofluorescence microscopy after treatment with pentamidine and six pentamidine analogues, and correction with dofetilide and four dofetilide analogues that displayed different abilities to inhibit IKr. Molecular dynamics simulations were used to address mode, number and type of interactions between hERG and dofetilide analogues. Key Results Structural modifications of pentamidine differentially affected plasma membrane levels of hERG and KIR2.1. Modification of the phenyl ring or substituents directly attached to it had the largest effect, affirming the importance of these chemical residues in ion channel binding. PA-4 had the mildest effects on both ion channels. Dofetilide corrected pentamidine-induced hERG, but not KIR2.1 trafficking defects. Dofetilide analogues that displayed high channel affinity, mediated by pi-pi stacks and hydrophobic interactions, also restored hERG protein levels, whereas analogues with low affinity were ineffective. Conclusions and Implications Drug-induced trafficking defects can be minimized if certain chemical features are avoided or ‘synthesized out’; this could influence the design and development of future drugs. Further analysis of such features in hERG trafficking correctors may facilitate the design of a non-blocking corrector for trafficking defective hERG proteins in both congenital and acquired LQTS. PMID:23586323

Quality of Life and Capsaicin Sensitivity in Patients with Airway Symptoms Induced by Chemicals and Scents: A Longitudinal Study

PubMed Central

Ternesten-Hasséus, Ewa; Lowhagen, Olle; Millqvist, Eva

2007-01-01

Objective It is common in asthma and allergy clinics to see patients presenting with upper and lower airway symptoms that are induced by chemicals and scents and not explained by allergic or asthmatic reactions. Previous studies have shown that these patients often have increased cough sensitivity to inhaled capsaicin; such sensitivity is known to reflect the airway sensory reactivity. The aim of this study was to evaluate the duration of symptoms induced by chemicals and scents and to measure health-related quality of life (HRQL) in patients with chemically induced airway symptoms. We also wished to determine and compare repeatability of the cough response to capsaicin inhalation, and to evaluate the patients’ airway sensory reactivity in a long-term perspective. Participants Seventeen patients with a history of at least 12 months of airway symptoms induced by chemicals and scents were followed over 5 years with repeated questionnaires, measurements of HRQL, and capsaicin inhalation tests. Results The symptoms persisted and did not change significantly over time, and the patients had a reduced HRQL that did not change during the 5-year period. The capsaicin sensitivity was increased at the start of the study, the cough sensitivity was long-lasting, and the repeatability of the capsaicin inhalation test was considered to be good in a long-term perspective. Conclusions Upper and lower airway symptoms induced by chemicals and scents represent an entity of chronic diseases, different from asthma or chronic obstructive pulmonary disease, with persistent symptoms, a reduced HRQL, and unchanged sensory hyperreactivity. PMID:17431493

An equation-free probabilistic steady-state approximation: dynamic application to the stochastic simulation of biochemical reaction networks.

PubMed

Salis, Howard; Kaznessis, Yiannis N

2005-12-01

Stochastic chemical kinetics more accurately describes the dynamics of "small" chemical systems, such as biological cells. Many real systems contain dynamical stiffness, which causes the exact stochastic simulation algorithm or other kinetic Monte Carlo methods to spend the majority of their time executing frequently occurring reaction events. Previous methods have successfully applied a type of probabilistic steady-state approximation by deriving an evolution equation, such as the chemical master equation, for the relaxed fast dynamics and using the solution of that equation to determine the slow dynamics. However, because the solution of the chemical master equation is limited to small, carefully selected, or linear reaction networks, an alternate equation-free method would be highly useful. We present a probabilistic steady-state approximation that separates the time scales of an arbitrary reaction network, detects the convergence of a marginal distribution to a quasi-steady-state, directly samples the underlying distribution, and uses those samples to accurately predict the state of the system, including the effects of the slow dynamics, at future times. The numerical method produces an accurate solution of both the fast and slow reaction dynamics while, for stiff systems, reducing the computational time by orders of magnitude. The developed theory makes no approximations on the shape or form of the underlying steady-state distribution and only assumes that it is ergodic. We demonstrate the accuracy and efficiency of the method using multiple interesting examples, including a highly nonlinear protein-protein interaction network. The developed theory may be applied to any type of kinetic Monte Carlo simulation to more efficiently simulate dynamically stiff systems, including existing exact, approximate, or hybrid stochastic simulation techniques.

An Equation Governing Ultralow-Velocity Zones: Implications for Holes in the ULVZ, Lateral Chemical Reactions at the Core-Mantle Boundary, and Damping of Heat Flux Variations in the Core

NASA Astrophysics Data System (ADS)

Hernlund, J. W.; Matsui, H.

2017-12-01

Ultralow-velocity zones (ULVZ) are increasingly illuminated by seismology, revealing surprising diversity in size, shape, and physical characteristics. The only viable hypotheses are that ULVZs are a compositionally distinct FeO-enriched dense material, which could have formed by fractional crystallization of a basal magma ocean, segregation of subducted banded iron formations, precipitation of solids from the outer core, partial melting and segregation of iron-rich melts from subducted basalts, or most likely a combination of many different processes. But many questions remain: Are ULVZ partially molten in some places, and not in others? Are ULVZ simply the thicker portions of an otherwise global thin layer, covering the entire CMB and thus blocking or moderating chemical interactions between the core and overlying mantle? Is such a layer inter-connected and able to conduct electrical currents that allow electro-magnetic coupling of core and mantle angular momentum? Are they being eroded and shrinking in size due to viscous entrainment, or is more material being added to ULVZ over time? Here we derive an advection-diffusion-like equation that governs the dynamical evolution of a chemically distinct ULVZ. Analysis of this equation shows that ULVZ should become readily swept aside by viscous mantle flows at the CMB, exposing "ordinary mantle" to the top of the core, thus inducing chemical heterogeneity that drives lateral CMB chemical reactions. These reactions are correlated with heat flux, thus maintaining large-scale pressure variations atop the core that induce cyclone-like flows centered around ULVZ and ponded subducted slabs. We suggest that turbulent diffusion across adjacent cyclone streams inside a stratified region atop the core readily accommodates lateral transport and re-distribution of components such as O and Si, in addition to heat. Our model implies that the deeper core is at least partly shielded from the influence of strong heat flux variations at the CMB which might otherwise cause problems for producing a geodynamo.

Analytical considerations and dimensionless analysis for a description of particle interactions in high pressure processes

NASA Astrophysics Data System (ADS)

Rauh, Cornelia; Delgado, Antonio

2010-12-01

High pressures of up to several hundreds of MPa are utilized in a wide range of applications in chemical, bio-, and food engineering, aiming at selective control of (bio-)chemical reactions. Non-uniformity of process conditions may threaten the safety and quality of the resulting products because processing conditions such as pressure, temperature, and treatment history are crucial for the course of (bio-)chemical reactions. Therefore, thermofluid-dynamical phenomena during the high pressure process have to be examined, and numerical tools to predict process uniformity and to optimize the processes have to be developed. Recently applied mathematical models and numerical simulations of laboratory and industrial scale high pressure processes investigating the mentioned crucial phenomena are based on continuum balancing models of thermofluid dynamics. Nevertheless, biological systems are complex fluids containing the relevant (bio-)chemical compounds (enzymes and microorganisms). These compounds are particles that interact with the surrounding medium and between each other. This contribution deals with thermofluid-dynamical interactions of the relevant particulate (bio-)chemical compounds (enzymes and microorganisms) with the surrounding fluid. By consideration of characteristic time and length scales and particle forces, the motion of the (bio-)chemical compounds is characterized.

Numerical study of chemically reacting viscous flow relevant to pulsed detonation engines

NASA Astrophysics Data System (ADS)

Yi, Tae-Hyeong

2005-11-01

A computational fluid dynamics code for two-dimensional, multi-species, laminar Navier-Stokes equations is developed to simulate a recently proposed engine concept for a pulsed detonation based propulsion system and to investigate the feasibility of the engine of the concept. The governing equations that include transport phenomena such as viscosity, thermal conduction and diffusion are coupled with chemical reactions. The gas is assumed to be thermally perfect and in chemically non-equilibrium. The stiffness due to coupling the fluid dynamics and the chemical kinetics is properly taken care of by using a time-operator splitting method and a variable coefficient ordinary differential equation solver. A second-order Roe scheme with a minmod limiter is explicitly used for space descretization, while a second-order, two-step Runge-Kutta method is used for time descretization. In space integration, a finite volume method and a cell-centered scheme are employed. The first-order derivatives in the equations of transport properties are discretized by a central differencing with Green's theorem. Detailed chemistry is involved in this study. Two chemical reaction mechanisms are extracted from GRI-Mech, which are forty elementary reactions with thirteen species for a hydrogen-air mixture and twenty-seven reactions with eight species for a hydrogen-oxygen mixture. The code is ported to a high-performance parallel machine with Message-Passing Interface. Code validation is performed with chemical kinetic modeling for a stoichiometric hydrogen-air mixture, an one-dimensional detonation tube, a two-dimensional, inviscid flow over a wedge and a viscous flow over a flat plate. Detonation is initiated using a numerically simulated arc-ignition or shock-induced ignition system. Various freestream conditions are utilized to study the propagation of the detonation in the proposed concept of the engine. Investigation of the detonation propagation is performed for a pulsed detonation rocket and a supersonic combustion chamber. For a pulsed detonation rocket case, the detonation tube is embedded in a mixing chamber where an initiator is added to the main detonation chamber. Propagating detonation waves in a supersonic combustion chamber is investigated for one- and two-dimensional cases. The detonation initiated by an arc and a shock wave is studied in the inviscid and viscous flow, respectively. Various features including a detonation-shock interaction, a detonation diffraction, a base flow and a vortex are observed.

The influence of projectile ion induced chemistry on surface pattern formation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Karmakar, Prasanta, E-mail: prasantak@vecc.gov.in; Satpati, Biswarup

We report the critical role of projectile induced chemical inhomogeneity on surface nanostructure formation. Experimental inconsistency is common for low energy ion beam induced nanostructure formation in the presence of uncontrolled and complex contamination. To explore the precise role of contamination on such structure formation during low energy ion bombardment, a simple and clean experimental study is performed by selecting mono-element semiconductors as the target and chemically inert or reactive ion beams as the projectile as well as the source of controlled contamination. It is shown by Atomic Force Microscopy, Cross-sectional Transmission Electron Microscopy, and Electron Energy Loss Spectroscopy measurementsmore » that bombardment of nitrogen-like reactive ions on Silicon and Germanium surfaces forms a chemical compound at impact zones. Continuous bombardment of the same ions generates surface instability due to unequal sputtering and non-uniform re-arrangement of the elemental atom and compound. This instability leads to ripple formation during ion bombardment. For Argon-like chemically inert ion bombardment, the chemical inhomogeneity induced boost is absent; as a result, no ripples are observed in the same ion energy and fluence.« less

Laser And Microwave Induced Breakdown Spectroscopy: Basis for a New Detection Technique for Chemical and Biological Agents

DTIC Science & Technology

2001-06-01

Chem. , vol. 72, pp. 721A-776A, 2000. [2] V. Majidi and M. R. Joseph, “Spectroscopic applications of laser-induced plasmas,” Crit. Rev. Analyt...Chem., vol. 23, pp. 143-162, 1992. [3] V. Majidi , “Laser-induced plasmas: A versatile tool for chemical analysis,” Spectroscopy, vol. 8, pp. 16-24

The Role of Electronic Excitations on Chemical Reaction Dynamics at Metal, Semiconductor and Nanoparticle Surfaces

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tully, John C.

Chemical reactions are often facilitated and steered when carried out on solid surfaces, essential for applications such as heterogeneous catalysis, solar energy conversion, corrosion, materials processing, and many others. A critical factor that can determine the rates and pathways of chemical reactions at surfaces is the efficiency and specificity of energy transfer; how fast does energy move around and where does it go? For reactions on insulator surfaces energy transfer generally moves in and out of vibrations of the adsorbed molecule and the underlying substrate. By contrast, on metal surfaces, metallic nanoparticles and semiconductors, another pathway for energy flow opensmore » up, excitation and de-excitation of electrons. This so-called “nonadiabatic” mechanism often dominates the transfer of energy and can directly impact the course of a chemical reaction. Conventional computational methods such as molecular dynamics simulation do not account for this nonadiabatic behavior. The current DOE-BES funded project has focused on developing the underlying theoretical foundation and the computational methodology for the prediction of nonadiabatic chemical reaction dynamics at surfaces. The research has successfully opened up new methodology and new applications for molecular simulation. In particular, over the last three years, the “Electronic Friction” theory, pioneered by the PI, has now been developed into a stable and accurate computational method that is sufficiently practical to allow first principles “on-the-fly” simulation of chemical reaction dynamics at metal surfaces.« less

Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II

DOE Office of Scientific and Technical Information (OSTI.GOV)

Amin, Muhamed; Badawi, Ashraf; Obayya, S. S.

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulsemore » in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 10 16 to 10 17 W/cm 2, but changes increase dramatically if the beam intensity is increased to 10 18 W/cm 2. Finally, in addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.« less

Radiation Damage in XFEL: Case study from the oxygen-evolving complex of Photosystem II

DOE PAGES

Amin, Muhamed; Badawi, Ashraf; Obayya, S. S.

2016-11-09

Structural changes induced by radiation damage in X-ray crystallography hinder the ability to understand the structure/function relationship in chemical reactions. Serial femtosecond crystallography overcomes this problem by exposing the sample to very short and intense laser pulse leading to measurement before destruction. Here we use molecular modeling to map the radiation damage during the 10–50 fs to the intensity, the energy and the time duration of the laser pulse on the oxygen-evolving complex (OEC) of photosystem II. In the model, the nuclei move classically in a fully quantum potential created by electron density under the effect of strong laser pulsemore » in the Ehrenfest dynamics regime. The results show that the Mn-Mn and Mn-Ca distances are less affected by radiation damage due to the their heavy masses, while one μ-oxo bridge (O5) moves significantly. The radiation damage may induce conformational changes of the water ligands but only bond elongation for the amino acids ligands. These effects are relatively intensity independent from 10 16 to 10 17 W/cm 2, but changes increase dramatically if the beam intensity is increased to 10 18 W/cm 2. Finally, in addition, the self amplified spontaneous emission (SASE) nature of the laser beam does not affect the dynamics of the ions.« less

Mode changes associated with oil droplet movement in solutions of gemini cationic surfactants.

PubMed

Banno, Taisuke; Miura, Shingo; Kuroha, Rie; Toyota, Taro

2013-06-25

Micrometer-sized self-propelled oil droplets in nonequilibrium systems have attracted much attention, since they form stable emulsions composed of oil, water, and surfactant which represent a primitive type of inanimate chemical machinery. In this work, we examined means of controlling the movement of oil droplets by studying the dynamics of n-heptyloxybenzaldehyde droplets in phosphate buffers containing alkanediyl-α,ω-bis(N-dodecyl-N,N-dimethylammonium bromide) (nG12) with either tetramethylene (4G12), octaethylene (8G12), or dodecamethylene (12G12) chains in the linker moiety. Significant differences in droplet dynamics were observed to be induced by changes in the linker structure of these gemini cationic surfactants. In a phosphate buffer containing 30 mM 4G12, self-propelled motion of droplets concurrent with the formation of molecular aggregates on their surfaces was observed, whereas the fusion of oil droplets was evident in both 8G12 and 12G12 solutions. We also determined that the surface activities and the extent of molecular self-assembly of the surfactants in phosphate buffer were strongly influenced by the alkyl chain length in the linker moiety. We therefore conclude that the surface activities of the gemini cationic surfactant have important effects on the oil-water interfacial tension of oil droplets and the formation of molecular aggregates and that both of these factors induce the unique movement of the droplets.

Improving nuclear envelope dynamics by EBV BFRF1 facilitates intranuclear component clearance through autophagy.

PubMed

Liu, Guan-Ting; Kung, Hsiu-Ni; Chen, Chung-Kuan; Huang, Cheng; Wang, Yung-Li; Yu, Cheng-Pu; Lee, Chung-Pei

2018-02-26

Although a vesicular nucleocytoplasmic transport system is believed to exist in eukaryotic cells, the features of this pathway are mostly unknown. Here, we report that the BFRF1 protein of the Epstein-Barr virus improves vesicular transport of nuclear envelope (NE) to facilitate the translocation and clearance of nuclear components. BFRF1 expression induces vesicles that selectively transport nuclear components to the cytoplasm. With the use of aggregation-prone proteins as tools, we found that aggregated nuclear proteins are dispersed when these BFRF1-induced vesicles are formed. BFRF1-containing vesicles engulf the NE-associated aggregates, exit through from the NE, and putatively fuse with autophagic vacuoles. Chemical treatment and genetic ablation of autophagy-related factors indicate that autophagosome formation and autophagy-linked FYVE protein-mediated autophagic proteolysis are involved in this selective clearance of nuclear proteins. Remarkably, vesicular transport, elicited by BFRF1, also attenuated nuclear aggregates accumulated in neuroblastoma cells. Accordingly, induction of NE-derived vesicles by BFRF1 facilitates nuclear protein translocation and clearance, suggesting that autophagy-coupled transport of nucleus-derived vesicles can be elicited for nuclear component catabolism in mammalian cells.-Liu, G.-T., Kung, H.-N., Chen, C.-K., Huang, C., Wang, Y.-L., Yu, C.-P., Lee, C.-P. Improving nuclear envelope dynamics by EBV BFRF1 facilitates intranuclear component clearance through autophagy.

The origin and dynamic evolution of chemical information transfer

PubMed Central

Steiger, Sandra; Schmitt, Thomas; Schaefer, H. Martin

2011-01-01

Although chemical communication is the most widespread form of communication, its evolution and diversity are not well understood. By integrating studies of a wide range of terrestrial plants and animals, we show that many chemicals are emitted, which can unintentionally provide information (cues) and, therefore, act as direct precursors for the evolution of intentional communication (signals). Depending on the content, design and the original function of the cue, there are predictable ways that selection can enhance the communicative function of chemicals. We review recent progress on how efficacy-based selection by receivers leads to distinct evolutionary trajectories of chemical communication. Because the original function of a cue may channel but also constrain the evolution of functional communication, we show that a broad perspective on multiple selective pressures acting upon chemicals provides important insights into the origin and dynamic evolution of chemical information transfer. Finally, we argue that integrating chemical ecology into communication theory may significantly enhance our understanding of the evolution, the design and the content of signals in general. PMID:21177681

Bicanonical ab Initio Molecular Dynamics for Open Systems.

PubMed

Frenzel, Johannes; Meyer, Bernd; Marx, Dominik

2017-08-08

Performing ab initio molecular dynamics simulations of open systems, where the chemical potential rather than the number of both nuclei and electrons is fixed, still is a challenge. Here, drawing on bicanonical sampling ideas introduced two decades ago by Swope and Andersen [ J. Chem. Phys. 1995 , 102 , 2851 - 2863 ] to calculate chemical potentials of liquids and solids, an ab initio simulation technique is devised, which introduces a fictitious dynamics of two superimposed but otherwise independent periodic systems including full electronic structure, such that either the chemical potential or the average fractional particle number of a specific chemical species can be kept constant. As proof of concept, we demonstrate that solvation free energies can be computed from these bicanonical ab initio simulations upon directly superimposing pure bulk water and the respective aqueous solution being the two limiting systems. The method is useful in many circumstances, for instance for studying heterogeneous catalytic processes taking place on surfaces where the chemical potential of reactants rather than their number is controlled and opens a pathway toward ab initio simulations at constant electrochemical potential.

Disease-induced mortality in density-dependent discrete-time S-I-S epidemic models.

PubMed

Franke, John E; Yakubu, Abdul-Aziz

2008-12-01

The dynamics of simple discrete-time epidemic models without disease-induced mortality are typically characterized by global transcritical bifurcation. We prove that in corresponding models with disease-induced mortality a tiny number of infectious individuals can drive an otherwise persistent population to extinction. Our model with disease-induced mortality supports multiple attractors. In addition, we use a Ricker recruitment function in an SIS model and obtained a three component discrete Hopf (Neimark-Sacker) cycle attractor coexisting with a fixed point attractor. The basin boundaries of the coexisting attractors are fractal in nature, and the example exhibits sensitive dependence of the long-term disease dynamics on initial conditions. Furthermore, we show that in contrast to corresponding models without disease-induced mortality, the disease-free state dynamics do not drive the disease dynamics.

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lin, Yen Ting; Buchler, Nicolas E.

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the propertiesmore » of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Finally, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site.« less

Efficient analysis of stochastic gene dynamics in the non-adiabatic regime using piecewise deterministic Markov processes

DOE PAGES

Lin, Yen Ting; Buchler, Nicolas E.

2018-01-31

Single-cell experiments show that gene expression is stochastic and bursty, a feature that can emerge from slow switching between promoter states with different activities. In addition to slow chromatin and/or DNA looping dynamics, one source of long-lived promoter states is the slow binding and unbinding kinetics of transcription factors to promoters, i.e. the non-adiabatic binding regime. Here, we introduce a simple analytical framework, known as a piecewise deterministic Markov process (PDMP), that accurately describes the stochastic dynamics of gene expression in the non-adiabatic regime. We illustrate the utility of the PDMP on a non-trivial dynamical system by analysing the propertiesmore » of a titration-based oscillator in the non-adiabatic limit. We first show how to transform the underlying chemical master equation into a PDMP where the slow transitions between promoter states are stochastic, but whose rates depend upon the faster deterministic dynamics of the transcription factors regulated by these promoters. We show that the PDMP accurately describes the observed periods of stochastic cycles in activator and repressor-based titration oscillators. We then generalize our PDMP analysis to more complicated versions of titration-based oscillators to explain how multiple binding sites lengthen the period and improve coherence. Finally, we show how noise-induced oscillation previously observed in a titration-based oscillator arises from non-adiabatic and discrete binding events at the promoter site.« less

Allosteric modulation of cardiac myosin dynamics by omecamtiv mecarbil

PubMed Central

Tiberti, Matteo

2017-01-01

New promising avenues for the pharmacological treatment of skeletal and heart muscle diseases rely on direct sarcomeric modulators, which are molecules that can directly bind to sarcomeric proteins and either inhibit or enhance their activity. A recent breakthrough has been the discovery of the myosin activator omecamtiv mecarbil (OM), which has been shown to increase the power output of the cardiac muscle and is currently in clinical trials for the treatment of heart failure. While the overall effect of OM on the mechano-chemical cycle of myosin is to increase the fraction of myosin molecules in the sarcomere that are strongly bound to actin, the molecular basis of its action is still not completely clear. We present here a Molecular Dynamics study of the motor domain of human cardiac myosin bound to OM, where the effects of the drug on the dynamical properties of the protein are investigated for the first time with atomistic resolution. We found that OM has a double effect on myosin dynamics, inducing a) an increased coupling of the motions of the converter and lever arm subdomains to the rest of the protein and b) a rewiring of the network of dynamic correlations, which produces preferential communication pathways between the OM binding site and distant functional regions. The location of the residues responsible for these effects suggests possible strategies for the future development of improved drugs and the targeting of specific cardiomyopathy-related mutations. PMID:29108014

NEUROPEPTIDE MODULATION OF CHEMICALLY INDUCED SKIN IRRITATION

EPA Science Inventory

This study was designed to demonstrate that the early symptoms of chemically-induced skin irritation are neurally mediated. everal approaches were used to affect nerve transmission in adult Balb/c female mice. hese included general anesthesia (i.e., sodium pentobarbital), systemi...

The Virtual Liver: Modeling Chemical-Induced Liver Toxicity

EPA Science Inventory

The US EPA Virtual Liver (v-Liver) project is aimed at modeling chemical-induced processes in hepatotoxicity and simulating their dose-dependent perturbations. The v-Liver embodies an emerging field of research in computational tissue modeling that integrates molecular and cellul...

Probing local bias-induced transitions using photothermal excitation contact resonance atomic force microscopy and voltage spectroscopy

DOE PAGES

Li, Qian; Jesse, Stephen; Tselev, Alexander; ...

2015-01-05

In this paper, nanomechanical properties are closely related to the states of matter, including chemical composition, crystal structure, mesoscopic domain configuration, etc. Investigation of these properties at the nanoscale requires not only static imaging methods, e.g., contact resonance atomic force microscopy (CR-AFM), but also spectroscopic methods capable of revealing their dependence on various external stimuli. Here we demonstrate the voltage spectroscopy of CR-AFM, which was realized by combining photothermal excitation (as opposed to the conventional piezoacoustic excitation method) with the band excitation technique. We applied this spectroscopy to explore local bias-induced phenomena ranging from purely physical to surface electromechanical andmore » electrochemical processes. Our measurements show that the changes in the surface properties associated with these bias-induced transitions can be accurately assessed in a fast and dynamic manner, using resonance frequency as a signature. Finally, with many of the advantages offered by photothermal excitation, contact resonance voltage spectroscopy not only is expected to find applications in a broader field of nanoscience but also will provide a basis for future development of other nanoscale elastic spectroscopies.« less

From hydration repulsion to dry adhesion between asymmetric hydrophilic and hydrophobic surfaces

PubMed Central

Kanduč, Matej; Netz, Roland R.

2015-01-01

Using all-atom molecular dynamics (MD) simulations at constant water chemical potential in combination with basic theoretical arguments, we study hydration-induced interactions between two overall charge-neutral yet polar planar surfaces with different wetting properties. Whether the water film between the two surfaces becomes unstable below a threshold separation and cavitation gives rise to long-range attraction, depends on the sum of the two individual surface contact angles. Consequently, cavitation-induced attraction also occurs for a mildly hydrophilic surface interacting with a very hydrophobic surface. If both surfaces are very hydrophilic, hydration repulsion dominates at small separations and direct attractive force contribution can—if strong enough—give rise to wet adhesion in this case. In between the regimes of cavitation-induced attraction and hydration repulsion we find a narrow range of contact angle combinations where the surfaces adhere at contact in the absence of cavitation. This dry adhesion regime is driven by direct surface–surface interactions. We derive simple laws for the cavitation transition as well as for the transition between hydration repulsion and dry adhesion, which favorably compare with simulation results in a generic adhesion state diagram as a function of the two surface contact angles. PMID:26392526

Effect of urea on heat-induced gelation of bovine serum albumin (BSA) studied by rheology and small angle neutron scattering (SANS)

NASA Astrophysics Data System (ADS)

Nnyigide, Osita Sunday; Oh, Yuna; Song, Hyeong Yong; Park, Eun-kyoung; Choi, Soo-Hyung; Hyun, Kyu

2017-05-01

This paper reports the effects of urea on the heat-induced gelation of bovine serum albumin (BSA), which was studied by the tube inversion method, rheological measurements, and small-angle neutron scattering (SANS). An increase in the urea concentration accelerated the rate of gelation because the protein molecules have already been unfolded to some extent during sample preparation in the urea solution. In addition, the BSA solution in the presence of urea underwent a sol-gel-sol transition during the time sweep test at a constant temperature of 80oC. On the other hand, the BSA solution without urea turned into a hard and brittle gel that did not return to the solution state during isothermal heating at a constant temperature of 80oC. Aggregation and re-bonding of the denatured and unfolded protein chains led to gel formation. Urea added to the protein denatures its tertiary and secondary structures by simultaneously disrupting the hydrogen bonds, hydrophobic interactions, and altering the solvent properties. Furthermore, urea induces thermoreversible chemical interactions in BSA solutions leading to the formation of a gel with dynamic properties under these experimental conditions.

Anomalous transport from holography: part II

NASA Astrophysics Data System (ADS)

Bu, Yanyan; Lublinsky, Michael; Sharon, Amir

2017-03-01

This is a second study of chiral anomaly-induced transport within a holographic model consisting of anomalous U(1)_V× U(1)_A Maxwell theory in Schwarzschild-AdS_5 spacetime. In the first part, chiral magnetic/separation effects (CME/CSE) are considered in the presence of a static spatially inhomogeneous external magnetic field. Gradient corrections to CME/CSE are analytically evaluated up to third order in the derivative expansion. Some of the third order gradient corrections lead to an anomaly-induced negative B^2-correction to the diffusion constant. We also find modifications to the chiral magnetic wave nonlinear in B. In the second part, we focus on the experimentally interesting case of the axial chemical potential being induced dynamically by a constant magnetic and time-dependent electric fields. Constitutive relations for the vector/axial currents are computed employing two different approximations: (a) derivative expansion (up to third order) but fully nonlinear in the external fields, and (b) weak electric field limit but resuming all orders in the derivative expansion. A non-vanishing nonlinear axial current (CSE) is found in the first case. The dependence on magnetic field and frequency of linear transport coefficient functions is explored in the second.

Light induced kickoff of magnetic domain walls in Ising chains

NASA Astrophysics Data System (ADS)

Bogani, Lapo

2012-02-01

Controlling the speed at which systems evolve is a challenge shared by all disciplines, and otherwise unrelated areas use common theoretical frameworks towards this goal. A particularly widespread model is Glauber dynamics, which describes the time evolution of the Ising model and can be applied to any binary system. Here we show, using molecular nanowires under irradiation, that Glauber dynamics can be controlled by a novel domain-wall kickoff mechanism. Contrary to known processes, the kickoff has unambiguous fingerprints, slowing down the spin-flip attempt rate by several orders of magnitude, and following a scaling law. The required irradiation power is very low, a substantial improvement over present methods of magnetooptical switching: in our experimental demonstration we switched molecular nanowires with light, using powers thousands of times lower than in previous optical switching methods. This manipulation of stochastic dynamic processes is extremely clean, leading to fingerprint signatures and scaling laws. These observations can be used, in material science, to better study domain-wall displacements and solitons in discrete lattices. These results provide a new way to control and study stochastic dynamic processes. Being general for Glauber dynamics, they can be extended to different kinds of magnetic nanowires and to a myriad of fields, ranging from social evolution to neural networks and chemical reactivity. For nanoelectronics and molecular spintronics the kickoff affords external control of molecular spin-valves and a magnetic fingerprint in single molecule measurements. It can also be applied to the dynamics of mechanical switches and the related study of phasons and order-disorder transitions.

Personal Chemical Exposure informatics

EPA Science Inventory

Chemical Exposure science is the study of human contact with chemicals (from manufacturing facilities, everyday products, waste) occurring in their environments and advances knowledge of the mechanisms and dynamics of events that cause or prevent adverse health outcomes. (adapted...

Dynamics and linear stability of thermocapillary spreading films on homogeneous and micropatterned surfaces

NASA Astrophysics Data System (ADS)

Davis, Jeffrey Michael

The recent focus on microfluidic devices has generated substantial interest in small-scale transport phenomena. Because the surface to volume ratio scales inversely with the characteristic length scale, surface forces dominate in microscale systems. In particular, these forces can be manipulated to regulate the motion of thin liquid films. The dynamics and stability of thermocapillary spreading films are theoretically investigated in this dissertation for flow on homogeneous and chemically or topographically patterned substrates. Because the governing equations for spreading films driven by other forces are analogous, the approach and results are valid for general lubrication flows. Experiments have shown that films spreading on homogeneous substrates can undergo a flow transition from a uniform front at the advancing solid-liquid-vapor contact line to an array of parallel rivulets. This instability is investigated via a non-modal, transient analysis because the relevant linearized disturbance operators for spatially inhomogeneous thin films are nonnormal. Stability results for three different contact line models are compared. This investigation of thermocapillary driven spreading is also pursued in the context of characterizing a novel, open-architecture microfluidic device based on flow confinement to completely wetting microstripes through chemical micropatterning of the substrate. The resulting lateral curvature of the fluid significantly influences the dynamics of the liquid. Applied to the dip coating of these patterned substrates, hydrodynamic scaling arguments are used to derive a replacement for the classical Landau-Levich result for homogeneous substrates. Thermocapillary flow along wetting microstripes is then characterized. The lateral curvature modifies the expected spreading velocity and film profile and also suppresses the capillary ridge and instability observed at the advancing contact line on homogeneous surfaces. In addition, a lubrication-based model is derived to quantify the significant effects of lateral film curvature and fluid confinement on the transverse diffusive broadening in two microstreams merging at a ⋎ -junction. Finally, the analysis is extended to lubrication flow over chemically uniform but topographically patterned substrates. A transient analysis is employed to determine the evolution of disturbances to the capillary ridges induced by the substrate topography.

Melting and Reactive Flow of Carbonated Peridotite Beneath Mid-Ocean Ridges

NASA Astrophysics Data System (ADS)

Keller, T.; Katz, R. F.

2015-12-01

The mantle carbon reservoir is four orders of magnitude more massive than that of the atmosphere and ocean combined. The behaviour of carbon in the mantle, especially its transport and extraction, is thus of crucial importance to understanding the coupling between the deep interior and the surface environment of Earth. Laboratory experiments indicate that even small concentrations of carbon dioxide (and other volatiles like H2O) in the upper mantle significantly affect silicate melting [HK96,DH06] by stabilising carbon-rich melt at high pressure. The presence of carbon in the mantle substantially extends the region where partial melt is stable and has important consequences for the dynamics of magma transport and chemical differentiation [H10,DH10]. We have developed theory and numerical implementation to simulate thermo-chemically coupled magma/mantle dynamics in terms of a two-phase (rock+melt), three component (dunite+MORB+carbonated MORB) physical model. The fluid dynamics is based on McKenzie's equations [McK84]. The thermo-chemical formulation of the system is represented by a novel, disequilibrium, multi-component melting model based on thermodynamic theory [RBS11]. This physical model is implemented as a parallel, two-dimensional, finite-volume code that leverages tools from the PETSc toolkit. First results show that carbon and other volatiles cause a qualitative difference to the style of melt transport, potentially enhancing its extraction efficiency - measured in the carbon mass flux arriving at the mid-ocean ridge axis - by at least an order of magnitude. The process that controls magma transport in our models is a volatile flux-induced reactive infiltration instability, causing carbonated melt to rise from depth in localized channels. These results add to our understanding of melt formation and transport at mid-ocean ridges (the most important magmatic system in the mantle) and may have important implications for subduction zones. REFERENCESHK96 Hirth & Kohlstedt (1996), EPSLDH06 Dasgupta & Hirschmann (2006), NatureH10 Hirschmann (2010), PEPI DH10 Dasgupta & Hirschmann (2010), EPSLMcK84 McKenzie (1984), J PetKW12 Katz & Weatherley (2012), EPSLRBS11 Rudge, Bercovici & Spiegelman (2011), GJI

Hydrophilic CeO2 nanocubes protect pancreatic β-cell line INS-1 from H2O2-induced oxidative stress

NASA Astrophysics Data System (ADS)

Lyu, Guang-Ming; Wang, Yan-Jie; Huang, Xue; Zhang, Huai-Yuan; Sun, Ling-Dong; Liu, Yan-Jun; Yan, Chun-Hua

2016-04-01

Oxidative stress plays a key role in the occurrence and development of diabetes. With their unique redox properties, CeO2 nanoparticles (nanoceria) exhibit promising potential for the treatment of diabetes resulting from oxidative stress. Here, we develop a novel preparation of hydrophilic CeO2 nanocubes (NCs) with two different sizes (5 nm and 25 nm) via an acetate assisted hydrothermal method. Dynamic light scattering, zeta potential measurements and thermogravimetric analyses were utilized to investigate the changes in the physico-chemical characteristics of CeO2 NCs when exposed to in vitro cell culture conditions. CCK-8 assays revealed that the CeO2 NCs did not impair cell proliferation in the pancreatic β-cell line INS-1 at the highest dose of 200 μg mL-1 over the time scale of 72 h, while being able to protect INS-1 cells from H2O2-induced cytotoxicity even after protein adsorption. It is also noteworthy that nanoceria with a smaller hydrodynamic radius exhibit stronger antioxidant and anti-apoptotic effects, which is consistent with their H2O2 quenching capability in biological systems. These findings suggest that nanoceria can be used as an excellent antioxidant for controlling oxidative stress-induced pancreatic β-cell damage.Oxidative stress plays a key role in the occurrence and development of diabetes. With their unique redox properties, CeO2 nanoparticles (nanoceria) exhibit promising potential for the treatment of diabetes resulting from oxidative stress. Here, we develop a novel preparation of hydrophilic CeO2 nanocubes (NCs) with two different sizes (5 nm and 25 nm) via an acetate assisted hydrothermal method. Dynamic light scattering, zeta potential measurements and thermogravimetric analyses were utilized to investigate the changes in the physico-chemical characteristics of CeO2 NCs when exposed to in vitro cell culture conditions. CCK-8 assays revealed that the CeO2 NCs did not impair cell proliferation in the pancreatic β-cell line INS-1 at the highest dose of 200 μg mL-1 over the time scale of 72 h, while being able to protect INS-1 cells from H2O2-induced cytotoxicity even after protein adsorption. It is also noteworthy that nanoceria with a smaller hydrodynamic radius exhibit stronger antioxidant and anti-apoptotic effects, which is consistent with their H2O2 quenching capability in biological systems. These findings suggest that nanoceria can be used as an excellent antioxidant for controlling oxidative stress-induced pancreatic β-cell damage. Electronic supplementary information (ESI) available. See DOI: 10.1039/c6nr00826g