Microdialysis unit for molecular weight separation

DOEpatents

Smith, Richard D.; Liu, Chuanliang

1999-01-01

The present invention relates generally to an apparatus and method for separating high molecular weight molecules from low molecular weight molecules. More specifically, the invention relates to the use of microdialysis for removal of the salt (low molecular weight molecules) from a nucleotide sample (high molecular weight molecules) for ESI-MS analysis. The dialysis or separation performance of the present invention is improved by (1) increasing dialysis temperature thereby increasing desalting efficiency and improving spectrum quality; (2) adding piperidine and imidazole to the dialysis buffer solution and reducing charge states and further increasing detection sensitivity for DNA; (3) using low concentrations (0-2.5 mM NH4OAc) of dialysis buffer and shifting the DNA negative ions to higher charge states, producing a nearly 10-fold increase in detection sensitivity and a slightly decreased desalting efficiency, or (4) any combination of (1), (2), and (3).

Design of magnetic polyplexes taken up efficiently by dendritic cell for enhanced DNA vaccine delivery.

PubMed

Nawwab Al-Deen, F M; Selomulya, C; Kong, Y Y; Xiang, S D; Ma, C; Coppel, R L; Plebanski, M

2014-02-01

Dendritic cells (DC) targeting vaccines require high efficiency for uptake, followed by DC activation and maturation. We used magnetic vectors comprising polyethylenimine (PEI)-coated superparamagnetic iron oxide nanoparticles, with hyaluronic acid (HA) of different molecular weights (<10 and 900 kDa) to reduce cytotoxicity and to facilitate endocytosis of particles into DCs via specific surface receptors. DNA encoding Plasmodium yoelii merozoite surface protein 1-19 and a plasmid encoding yellow fluorescent gene were added to the magnetic complexes with various % charge ratios of HA: PEI. The presence of magnetic fields significantly enhanced DC transfection and maturation. Vectors containing a high-molecular-weight HA with 100% charge ratio of HA: PEI yielded a better transfection efficiency than others. This phenomenon was attributed to their longer molecular chains and higher mucoadhesive properties aiding DNA condensation and stability. Insights gained should improve the design of more effective DNA vaccine delivery systems.

Accelerated molecular dynamics: A promising and efficient simulation method for biomolecules

NASA Astrophysics Data System (ADS)

Hamelberg, Donald; Mongan, John; McCammon, J. Andrew

2004-06-01

Many interesting dynamic properties of biological molecules cannot be simulated directly using molecular dynamics because of nanosecond time scale limitations. These systems are trapped in potential energy minima with high free energy barriers for large numbers of computational steps. The dynamic evolution of many molecular systems occurs through a series of rare events as the system moves from one potential energy basin to another. Therefore, we have proposed a robust bias potential function that can be used in an efficient accelerated molecular dynamics approach to simulate the transition of high energy barriers without any advance knowledge of the location of either the potential energy wells or saddle points. In this method, the potential energy landscape is altered by adding a bias potential to the true potential such that the escape rates from potential wells are enhanced, which accelerates and extends the time scale in molecular dynamics simulations. Our definition of the bias potential echoes the underlying shape of the potential energy landscape on the modified surface, thus allowing for the potential energy minima to be well defined, and hence properly sampled during the simulation. We have shown that our approach, which can be extended to biomolecules, samples the conformational space more efficiently than normal molecular dynamics simulations, and converges to the correct canonical distribution.

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence.

PubMed

Schneider, Thomas D

2010-10-01

The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is [Formula in text] joules per bit (kB is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2=0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal.

70% efficiency of bistate molecular machines explained by information theory, high dimensional geometry and evolutionary convergence

PubMed Central

Schneider, Thomas D.

2010-01-01

The relationship between information and energy is key to understanding biological systems. We can display the information in DNA sequences specifically bound by proteins by using sequence logos, and we can measure the corresponding binding energy. These can be compared by noting that one of the forms of the second law of thermodynamics defines the minimum energy dissipation required to gain one bit of information. Under the isothermal conditions that molecular machines function this is joules per bit ( is Boltzmann's constant and T is the absolute temperature). Then an efficiency of binding can be computed by dividing the information in a logo by the free energy of binding after it has been converted to bits. The isothermal efficiencies of not only genetic control systems, but also visual pigments are near 70%. From information and coding theory, the theoretical efficiency limit for bistate molecular machines is ln 2 = 0.6931. Evolutionary convergence to maximum efficiency is limited by the constraint that molecular states must be distinct from each other. The result indicates that natural molecular machines operate close to their information processing maximum (the channel capacity), and implies that nanotechnology can attain this goal. PMID:20562221

High-efficiency GaAs and GaInP solar cells grown by all solid-state molecular-beam-epitaxy

PubMed Central

2011-01-01

We report the initial results of GaAs and GaInP solar cells grown by all solid-state molecular-beam-epitaxy (MBE) technique. For GaAs single-junction solar cell, with the application of AlInP as the window layer and GaInP as the back surface field layer, the photovoltaic conversion efficiency of 26% at one sun concentration and air mass 1.5 global (AM1.5G) is realized. The efficiency of 16.4% is also reached for GaInP solar cell. Our results demonstrate that the MBE-grown phosphide-contained III-V compound semiconductor solar cell can be quite comparable to the metal-organic-chemical-vapor-deposition-grown high-efficiency solar cell. PMID:22040124

High-Efficiency Multiscale Modeling of Cell Deformations in Confined Microenvironments in Microcirculation and Microfluidics

NASA Astrophysics Data System (ADS)

Lu, Huijie; Peng, Zhangli

2017-11-01

We developed a high-efficiency multiscale modeling method to predict the stress and deformation of cells during the interactions with their microenvironments in microcirculation and microfluidics, including red blood cells (RBCs) and circulating tumor cells (CTCs). There are more than 1 billion people in the world suffering from RBC diseases. The mechanical properties of RBCs are changed in these diseases due to molecular structure alternations, which is not only important for understanding the disease pathology but also provides an opportunity for diagnostics. On the other hand, the mechanical properties of cancer cells are also altered compared to healthy cells. This can lead to acquired ability to cross the narrow capillary networks and endothelial gaps, which is crucial for metastasis, the leading cause of cancer mortality. Therefore, it is important to predict the deformation and stress of RBCs and CTCs in microcirculations. We develop a high-efficiency multiscale model of cell-fluid interaction. We pass the information from our molecular scale models to the cell scale to study the effect of molecular mutations. Using our high-efficiency boundary element methods of fluids, we will be able to run 3D simulations using a single CPU within several hours, which will enable us to run extensive parametric studies and optimization.

New Molecular Design Concurrently Providing Superior Pure Blue, Thermally Activated Delayed Fluorescence and Optical Out-Coupling Efficiencies.

PubMed

Rajamalli, P; Senthilkumar, N; Huang, P-Y; Ren-Wu, C-C; Lin, H-W; Cheng, C-H

2017-08-16

Simultaneous enhancement of out-coupling efficiency, internal quantum efficiency, and color purity in thermally activated delayed fluorescence (TADF) emitters is highly desired for the practical application of these materials. We designed and synthesized two isomeric TADF emitters, 2DPyM-mDTC and 3DPyM-pDTC, based on di(pyridinyl)methanone (DPyM) cores as the new electron-accepting units and di(tert-butyl)carbazole (DTC) as the electron-donating units. 3DPyM-pDTC, which is structurally nearly planar with a very small ΔE ST , shows higher color purity, horizontal ratio, and quantum yield than 2DPyM-mDTC, which has a more flexible structure. An electroluminescence device based on 3DPyM-pDTC as the dopant emitter can reach an extremely high external quantum efficiency of 31.9% with a pure blue emission. This work also demonstrates a way to design materials with a high portion of horizontal molecular orientation to realize a highly efficient pure-blue device based on TADF emitters.

Efficient L1 regularization-based reconstruction for fluorescent molecular tomography using restarted nonlinear conjugate gradient.

PubMed

Shi, Junwei; Zhang, Bin; Liu, Fei; Luo, Jianwen; Bai, Jing

2013-09-15

For the ill-posed fluorescent molecular tomography (FMT) inverse problem, the L1 regularization can protect the high-frequency information like edges while effectively reduce the image noise. However, the state-of-the-art L1 regularization-based algorithms for FMT reconstruction are expensive in memory, especially for large-scale problems. An efficient L1 regularization-based reconstruction algorithm based on nonlinear conjugate gradient with restarted strategy is proposed to increase the computational speed with low memory consumption. The reconstruction results from phantom experiments demonstrate that the proposed algorithm can obtain high spatial resolution and high signal-to-noise ratio, as well as high localization accuracy for fluorescence targets.

Poly(ethylenimine) conjugated bioreducible dendrimer for efficient gene delivery.

PubMed

Nam, Kihoon; Jung, Simhyun; Nam, Joung-Pyo; Kim, Sung Wan

2015-12-28

Branched poly(ethylenimine) (PEI) 25 kDa is an efficient gene delivery vector with outstanding gene condensation ability and great endosome escape activity. However, it also induces higher cytotoxicity. Transfection efficiency and toxicity of PEI are highly dependent upon their molecular weight and structure. We developed a bioreducible poly(ethylenimine) (PEI (-s-s-)) derived from low molecular weight PEI (1.8 kDa) for efficient gene delivery. Bioreducible core molecule is expected to increase molecular weight and reduce the cytotoxicity of the copolymer. PEI (-s-s-) polyplexes showed higher transfection efficiency and lower cytotoxicity compared to branched PEI 25 kDa, Lipofectamine® 2000 and, FuGENE® 6. In addition, PEI (-s-s-) derivative (16 kDa) formed stable polyplexes with a zeta-potential value of +34 mV and polyplex size of 61 nm. PEI (-s-s-) derivative (16 kDa) showed excellent transfection efficiency: 3.6 times higher than branched PEI 25 kDa in HeLa cells and 7.4 times higher than Lipofectamine® 2000 in H9C2 cell. The derivatives also showed lower cytotoxicity compared with Lipofectamine® 2000 and PEI 25 kDa in various cell types. In addition, newly synthesized PEI (-s-s-) derivatives have high reproducibility. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular design of photovoltaic materials for polymer solar cells: toward suitable electronic energy levels and broad absorption.

PubMed

Li, Yongfang

2012-05-15

Bulk heterojunction (BHJ) polymer solar cells (PSCs) sandwich a blend layer of conjugated polymer donor and fullerene derivative acceptor between a transparent ITO positive electrode and a low work function metal negative electrode. In comparison with traditional inorganic semiconductor solar cells, PSCs offer a simpler device structure, easier fabrication, lower cost, and lighter weight, and these structures can be fabricated into flexible devices. But currently the power conversion efficiency (PCE) of the PSCs is not sufficient for future commercialization. The polymer donors and fullerene derivative acceptors are the key photovoltaic materials that will need to be optimized for high-performance PSCs. In this Account, I discuss the basic requirements and scientific issues in the molecular design of high efficiency photovoltaic molecules. I also summarize recent progress in electronic energy level engineering and absorption spectral broadening of the donor and acceptor photovoltaic materials by my research group and others. For high-efficiency conjugated polymer donors, key requirements are a narrower energy bandgap (E(g)) and broad absorption, relatively lower-lying HOMO (the highest occupied molecular orbital) level, and higher hole mobility. There are three strategies to meet these requirements: D-A copolymerization for narrower E(g) and lower-lying HOMO, substitution with electron-withdrawing groups for lower-lying HOMO, and two-dimensional conjugation for broad absorption and higher hole mobility. Moreover, better main chain planarity and less side chain steric hindrance could strengthen π-π stacking and increase hole mobility. Furthermore, the molecular weight of the polymers also influences their photovoltaic performance. To produce high efficiency photovoltaic polymers, researchers should attempt to increase molecular weight while maintaining solubility. High-efficiency D-A copolymers have been obtained by using benzodithiophene (BDT), dithienosilole (DTS), or indacenodithiophene (IDT) donor unit and benzothiadiazole (BT), thienopyrrole-dione (TPD), or thiazolothiazole (TTz) acceptor units. The BDT unit with two thienyl conjugated side chains is a highly promising unit in constructing high-efficiency copolymer donor materials. The electron-withdrawing groups of ester, ketone, fluorine, or sulfonyl can effectively tune the HOMO energy levels downward. To improve the performance of fullerene derivative acceptors, researchers will need to strengthen absorption in the visible spectrum, upshift the LUMO (the lowest unoccupied molecular orbital) energy level, and increase the electron mobility. [6,6]-Phenyl-C(71)-butyric acid methyl ester (PC(70)BM) is superior to [6,6]-phenyl-C(61)-butyric acid methyl ester (PCBM) because C(70) absorbs visible light more efficiently. Indene-C(60) bisadduct (ICBA) and Indene-C(70) bisadduct (IC(70)BA) show 0.17 and 0.19 eV higher LUMO energy levels, respectively, than PCBM, due to the electron-rich character of indene and the effect of bisadduct. ICBA and IC(70)BA are excellent acceptors for the P3HT-based PSCs.

Combination of molecular, morphological, and interfacial engineering to achieve highly efficient and stable plastic solar cells.

PubMed

Chang, Chih-Yu; Cheng, Yen-Ju; Hung, Shih-Hsiu; Wu, Jhong-Sian; Kao, Wei-Shun; Lee, Chia-Hao; Hsu, Chain-Shu

2012-01-24

A flexible solar device showing exceptional air and mechanical stability is produced by simultaneously optimizing molecular structure, active layer morphology, and interface characteristics. The PFDCTBT-C8-based devices with inverted architecture exhibited excellent power conversion efficiencies of 7.0% and 6.0% on glass and flexible substrates, respectively. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Current development and patents on high-brightness white LED for illumination.

PubMed

Pang, Wen-Yuan; Lo, Ikai; Hsieh, Chia-Ho; Hsu, Yu-Chi; Chou, Ming-Chi; Shih, Cheng-Hung

2010-01-01

In this paper, we reviewed the current development and patents for the application of high-brightness and high-efficiency white light-emitting diode (LED). The high-efficiency GaN nanostructures, such as disk, pyramid, and rod were grown on LiAlO(2) substrate by plasma-assisted molecular-beam epitaxy, and a model was developed to demonstrate the growth of the GaN nanostructures. Based on the results, the GaN disk p-n junction was designed for the application of high brightness and high efficiency white LED.

Molecularly imprinted polymers based stir bar sorptive extraction for determination of cefaclor and cefalexin in environmental water.

PubMed

Peng, Jun; Liu, Donghao; Shi, Tian; Tian, Huairu; Hui, Xuanhong; He, Hua

2017-07-01

Although stir bar sportive extraction was thought to be a highly efficiency and simple pretreatment approach, its wide application was limited by low selectivity, short service life, and relatively high cost. In order to improve the performance of the stir bar, molecular imprinted polymers and magnetic carbon nanotubes were combined in the present study. In addition, two monomers were utilized to intensify the selectivity of molecularly imprinted polymers. Fourier transform infrared spectroscopy, scanning electron microscopy, and selectivity experiments showed that the molecularly imprinted polymeric stir bar was successfully prepared. Then micro-extraction based on the obtained stir bar was coupled with HPLC for determination of trace cefaclor and cefalexin in environmental water. This approach had the advantages of stir bar sportive extraction, high selectivity of molecular imprinted polymers, and high sorption efficiency of carbon nanotubes. To utilize this pretreatment approach, pH, extraction time, stirring speed, elution solvent, and elution time were optimized. The LOD and LOQ of cefaclor were found to be 3.5 ng · mL -1 and 12.0 ng · mL -1 , respectively; the LOD and LOQ of cefalexin were found to be 3.0 ng · mL -1 and 10.0 ng · mL -1 , respectively. The recoveries of cefaclor and cefalexin were 86.5 ~ 98.6%. The within-run precision and between-run precision were acceptable (relative standard deviation <7%). Even when utilized in more than 14 cycles, the performance of the stir bar did not decrease dramatically. This demonstrated that the molecularly imprinted polymeric stir bar based micro-extraction was a convenient, efficient, low-cost, and a specific method for enrichment of cefaclor and cefalexin in environmental samples.

Molecularly Imprinted Polymer Enables High-Efficiency Recognition and Trapping Lithium Polysulfides for Stable Lithium Sulfur Battery.

PubMed

Liu, Jie; Qian, Tao; Wang, Mengfan; Liu, Xuejun; Xu, Na; You, Yizhou; Yan, Chenglin

2017-08-09

Using molecularly imprinted polymer to recognize various target molecules emerges as a fascinating research field. Herein, we applied this strategy for the first time to efficiently recognize and trap long-chain polysulfides (Li 2 S x , x = 6-8) in lithium sulfur battery to minimize the polysulfide shuttling between anode and cathode, which enables us to achieve remarkable electrochemical performance including a high specific capacity of 1262 mAh g -1 at 0.2 C and superior capacity retention of over 82.5% after 400 cycles at 1 C. The outstanding performance is attributed to the significantly reduced concentration of long-chain polysulfides in electrolyte as evidenced by in situ UV/vis spectroscopy and Li 2 S nucleation tests, which were further confirmed by density functional theory calculations. The molecular imprinting is demonstrated as a promising approach to effectively prevent the free diffusion of long-chain polysulfides, providing a new avenue to efficiently recognize and trap lithium polysulfides for high-performance lithium sulfur battery with greatly suppressed shuttle effect.

Experimental thermodynamics of single molecular motor.

PubMed

Toyabe, Shoichi; Muneyuki, Eiro

2013-01-01

Molecular motor is a nano-sized chemical engine that converts chemical free energy to mechanical motions. Hence, the energetics is as important as kinetics in order to understand its operation principle. We review experiments to evaluate the thermodynamic properties of a rotational F1-ATPase motor (F1-motor) at a single-molecule level. We show that the F1-motor achieves 100% thermo dynamic efficiency at the stalled state. Furthermore, the motor reduces the internal irreversible heat inside the motor to almost zero and achieves a highly-efficient free energy transduction close to 100% during rotations far from quasistatic process. We discuss the mechanism of how the F1-motor achieves such a high efficiency, which highlights the remarkable property of the nano-sized engine F1-motor.

How molecular motors work in the crowded environment of living cells: coexistence and efficiency of normal and anomalous transport.

PubMed

Goychuk, Igor; Kharchenko, Vasyl O; Metzler, Ralf

2014-01-01

Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included.

How Molecular Motors Work in the Crowded Environment of Living Cells: Coexistence and Efficiency of Normal and Anomalous Transport

PubMed Central

Goychuk, Igor; Kharchenko, Vasyl O.; Metzler, Ralf

2014-01-01

Recent experiments reveal both passive subdiffusion of various nanoparticles and anomalous active transport of such particles by molecular motors in the molecularly crowded environment of living biological cells. Passive and active microrheology reveals that the origin of this anomalous dynamics is due to the viscoelasticity of the intracellular fluid. How do molecular motors perform in such a highly viscous, dissipative environment? Can we explain the observed co-existence of the anomalous transport of relatively large particles of 100 to 500 nm in size by kinesin motors with the normal transport of smaller particles by the same molecular motors? What is the efficiency of molecular motors in the anomalous transport regime? Here we answer these seemingly conflicting questions and consistently explain experimental findings in a generalization of the well-known continuous diffusion model for molecular motors with two conformational states in which viscoelastic effects are included. PMID:24626511

The unlikely high efficiency of a molecular motor based on active motion

NASA Astrophysics Data System (ADS)

Ebeling, W.

2015-07-01

The efficiency of a simple model of a motor converting chemical into mechanical energy is studied analytically. The model motor shows interesting properties corresponding qualitatively to motors investigated in experiments. The efficiency increases with the load and may for low loss reach high values near to 100 percent in a narrow regime of optimal load. It is shown that the optimal load and the maximal efficiency depend by universal power laws on the dimensionless loss parameter. Stochastic effects decrease the stability of motor regimes with high efficiency and make them unlikely. Numerical studies show efficiencies below the theoretical optimum and demonstrate that special ratchet profiles my stabilize efficient regimes.

Beating the thermodynamic limit with photo-activation of n-doping in organic semiconductors

NASA Astrophysics Data System (ADS)

Lin, Xin; Wegner, Berthold; Lee, Kyung Min; Fusella, Michael A.; Zhang, Fengyu; Moudgil, Karttikay; Rand, Barry P.; Barlow, Stephen; Marder, Seth R.; Koch, Norbert; Kahn, Antoine

2017-12-01

Chemical doping of organic semiconductors using molecular dopants plays a key role in the fabrication of efficient organic electronic devices. Although a variety of stable molecular p-dopants have been developed and successfully deployed in devices in the past decade, air-stable molecular n-dopants suitable for materials with low electron affinity are still elusive. Here we demonstrate that photo-activation of a cleavable air-stable dimeric dopant can result in kinetically stable and efficient n-doping of host semiconductors, whose reduction potentials are beyond the thermodynamic reach of the dimer’s effective reducing strength. Electron-transport layers doped in this manner are used to fabricate high-efficiency organic light-emitting diodes. Our strategy thus enables a new paradigm for using air-stable molecular dopants to improve conductivity in, and provide ohmic contacts to, organic semiconductors with very low electron affinity.

Rhenium-phthalocyanine molecular nanojunction with high magnetic anisotropy and high spin filtering efficiency

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

Li, J.; Institute of Nanomaterial and Nanostructure, Changsha University of Science and Technology, Changsha 410114; Hu, J.

2015-07-20

Using the density functional and non-equilibrium Green's function approaches, we studied the magnetic anisotropy and spin-filtering properties of various transition metal-Phthalocyanine molecular junctions across two Au electrodes. Our important finding is that the Au-RePc-Au junction has both large spin filtering efficiency (>80%) and large magnetic anisotropy energy, which makes it suitable for device applications. To provide insights for the further experimental work, we discussed the correlation between the transport property, magnetic anisotropy, and wave function features of the RePc molecule, and we also illustrated the possibility of controlling its magnetic state.

Learning Kinetic Monte Carlo Models of Condensed Phase High Temperature Chemistry from Molecular Dynamics

NASA Astrophysics Data System (ADS)

Yang, Qian; Sing-Long, Carlos; Chen, Enze; Reed, Evan

2017-06-01

Complex chemical processes, such as the decomposition of energetic materials and the chemistry of planetary interiors, are typically studied using large-scale molecular dynamics simulations that run for weeks on high performance parallel machines. These computations may involve thousands of atoms forming hundreds of molecular species and undergoing thousands of reactions. It is natural to wonder whether this wealth of data can be utilized to build more efficient, interpretable, and predictive models. In this talk, we will use techniques from statistical learning to develop a framework for constructing Kinetic Monte Carlo (KMC) models from molecular dynamics data. We will show that our KMC models can not only extrapolate the behavior of the chemical system by as much as an order of magnitude in time, but can also be used to study the dynamics of entirely different chemical trajectories with a high degree of fidelity. Then, we will discuss three different methods for reducing our learned KMC models, including a new and efficient data-driven algorithm using L1-regularization. We demonstrate our framework throughout on a system of high-temperature high-pressure liquid methane, thought to be a major component of gas giant planetary interiors.

Highly Efficient Computation of the Basal kon using Direct Simulation of Protein-Protein Association with Flexible Molecular Models.

PubMed

Saglam, Ali S; Chong, Lillian T

2016-01-14

An essential baseline for determining the extent to which electrostatic interactions enhance the kinetics of protein-protein association is the "basal" kon, which is the rate constant for association in the absence of electrostatic interactions. However, since such association events are beyond the milliseconds time scale, it has not been practical to compute the basal kon by directly simulating the association with flexible models. Here, we computed the basal kon for barnase and barstar, two of the most rapidly associating proteins, using highly efficient, flexible molecular simulations. These simulations involved (a) pseudoatomic protein models that reproduce the molecular shapes, electrostatic, and diffusion properties of all-atom models, and (b) application of the weighted ensemble path sampling strategy, which enhanced the efficiency of generating association events by >130-fold. We also examined the extent to which the computed basal kon is affected by inclusion of intermolecular hydrodynamic interactions in the simulations.

Enhanced Efficiency in Fullerene-Free Polymer Solar Cell by Incorporating Fine-designed Donor and Acceptor Materials.

PubMed

Ye, Long; Sun, Kai; Jiang, Wei; Zhang, Shaoqing; Zhao, Wenchao; Yao, Huifeng; Wang, Zhaohui; Hou, Jianhui

2015-05-06

Among the diverse nonfullerene acceptors, perylene bisimides (PBIs) have been attracting much attention due to their excellent electron mobility and tunable molecular and electronic properties by simply engineering the bay and head linkages. Herein, guided by two efficient small molecular acceptors, we designed, synthesized, and characterized a new nonfullerene small molecule PPDI with fine-tailored alkyl chains. Notably, a certificated PCE of 5.40% is realized in a simple structured fullerene-free polymer solar cell comprising PPDI as the electron acceptor and a fine-tailored 2D-conjugated polymer PBDT-TS1 as the electron donor. Moreover, the device behavior, morphological feature, and origin of high efficiency in PBDT-TS1/PPDI-based fullerene-free PSC were investigated. The synchronous selection and design of donor and acceptor materials reported here offer a feasible strategy for realizing highly efficient fullerene-free organic photovoltaics.

Molecularly imprinted polymeric stir bar: Preparation and application for the determination of naftopidil in plasma and urine samples.

PubMed

Peng, Jun; Xiao, Deli; He, Hua; Zhao, Hongyan; Wang, Cuixia; Shi, Tian; Shi, Kexin

2016-01-01

In this study, molecularly imprinting technology and stir bar absorption technology were combined to develop a microextraction approach based on a molecularly imprinted polymeric stir bar. The molecularly imprinted polymer stir bar has a high performance, is specific, economical, and simple to prepare. The obtained naftopidil-imprinted polymer-coated bars could simultaneously agitate and adsorb naftopidil in the sample solution. The ratio of template/monomer/cross-linker and conditions of template removal were optimized to prepare a stir bar with highly efficient adsorption. Fourier transform infrared spectroscopy, scanning electron microscopy, selectivity, and extraction capacity experiments showed that the molecularly imprinted polymer stir bar was prepared successfully. To utilize the molecularly imprinted polymer stir bar for the determination of naftopidil in complex body fluid matrices, the extraction time, stirring speed, eluent, and elution time were optimized. The limits of detection of naftopidil in plasma and urine sample were 7.5 and 4.0 ng/mL, respectively, and the recoveries were in the range of 90-112%. The within-run precision and between-run precision were acceptable (relative standard deviation <7%). These data demonstrated that the molecularly imprinted polymeric stir bar based microextraction with high-performance liquid chromatography was a convenient, rapid, efficient, and specific method for the precise determination of trace naftopidil in clinical analysis. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Experimental thermodynamics of single molecular motor

PubMed Central

Toyabe, Shoichi; Muneyuki, Eiro

2013-01-01

Molecular motor is a nano-sized chemical engine that converts chemical free energy to mechanical motions. Hence, the energetics is as important as kinetics in order to understand its operation principle. We review experiments to evaluate the thermodynamic properties of a rotational F1-ATPase motor (F1-motor) at a single-molecule level. We show that the F1-motor achieves 100% thermo dynamic efficiency at the stalled state. Furthermore, the motor reduces the internal irreversible heat inside the motor to almost zero and achieves a highly-efficient free energy transduction close to 100% during rotations far from quasistatic process. We discuss the mechanism of how the F1-motor achieves such a high efficiency, which highlights the remarkable property of the nano-sized engine F1-motor. PMID:27493546

Immobilization of a molecular catalyst on carbon nanotubes for highly efficient electro-catalytic water oxidation.

PubMed

Li, Fusheng; Li, Lin; Tong, Lianpeng; Daniel, Quentin; Göthelid, Mats; Sun, Licheng

2014-11-21

Electrochemically driven water oxidation has been performed using a molecular water oxidation catalyst immobilized on hybrid carbon nanotubes and nano-material electrodes. A high turnover frequency (TOF) of 7.6 s(-1) together with a high catalytic current density of 2.2 mA cm(-2) was successfully obtained at an overpotential of 480 mV after 1 h of bulk electrolysis.

The dependence of efficiency of transmembrane molecular transfer using electroporation on medium viscosity.

PubMed

Sungailaitė, Sandra; Ruzgys, Paulius; Šatkauskienė, Ingrida; Čepurnienė, Karolina; Šatkauskas, Saulius

2015-01-01

In the present study, we aimed to evaluate the efficiency of drug and gene electrotransfer into cells in vitro depending on medium viscosity. Experiments were performed using Chinese hamster ovary cells. Efficiency of molecular electrotransfer depending of medium viscosity was evaluated using two different electroporation conditions: a high-voltage (HV) pulse and a combination of a high-voltage pulse and a low-voltage pulse (HV + LV). To evaluate the efficiency of molecular electrotransfer, anticancer drug bleomycin and two different plasmids coding for green fluorescent protein and luciferase were used. We found that a slight increase in medium viscosity from 1.3-1.4 mPa·s significantly decreased the transfection efficiency, both in terms of transfected cells and total protein production, which was abolished completely with an increase in medium viscosity to 6.1 mPa·s. Notably, at this medium viscosity, electrotransfer of the small anticancer drug was still efficient. Using HV and HV + LV pulse combinations, we showed that a decrease of DNA electrotransfer, especially at lower medium viscosities, can be compensated for by the LV pulse to some extent. On the other hand, the addition of the LV pulse after the HV pulse did not have any positive effect on the efficiency of bleomycin electrotransfer. These findings demonstrate that transfection is very susceptible to medium viscosity and highlights the importance of the electrophoretic component in experiments when a considerable transfection level is needed. Copyright © 2015 John Wiley & Sons, Ltd.

Molecular characterization of an endornavirus from Cucumis spp

USDA-ARS?s Scientific Manuscript database

Endornaviruses infect hosts in the kingdoms Plantae, Fungi and Chromista. They are efficiently transmitted vertically and generally do not induce visible symptoms. In this investigation high molecular weight dsRNA, representing the genome of an endornavirus, was isolated from an unknown melon (Cucum...

Functional Comparison for Lipid Metabolism and Intestinal and Fecal Microflora Enzyme Activities between Low Molecular Weight Chitosan and Chitosan Oligosaccharide in High-Fat-Diet-Fed Rats.

PubMed

Chiu, Chen-Yuan; Feng, Shih-An; Liu, Shing-Hwa; Chiang, Meng-Tsan

2017-07-24

The present study investigated and compared the regulatory effects on the lipid-related metabolism and intestinal disaccharidase/fecal bacterial enzyme activities between low molecular weight chitosan and chitosan oligosaccharide in high-fat-diet-fed rats. Diet supplementation of low molecular weight chitosan showed greater efficiency than chitosan oligosaccharide in suppressing the increased weights in body and in liver and adipose tissues of high-fat-diet-fed rats. Supplementation of low molecular weight chitosan also showed a greater improvement than chitosan oligosaccharide in imbalance of plasma, hepatic, and fecal lipid profiles, and intestinal disaccharidase activities in high-fat-diet-fed rats. Moreover, both low molecular weight chitosan and chitosan oligosaccharide significantly decreased the fecal microflora mucinase and β-glucuronidase activities in high-fat-diet-fed rats. These results suggest that low molecular weight chitosan exerts a greater positive improvement than chitosan oligosaccharide in lipid metabolism and intestinal disaccharidase activity in high-fat-diet-induced obese rats.

Precise control of molecular dynamics with a femtosecond frequency comb.

PubMed

Pe'er, Avi; Shapiro, Evgeny A; Stowe, Matthew C; Shapiro, Moshe; Ye, Jun

2007-03-16

We present a general and highly efficient scheme for performing narrow-band Raman transitions between molecular vibrational levels using a coherent train of weak pump-dump pairs of shaped ultrashort pulses. The use of weak pulses permits an analytic description within the framework of coherent control in the perturbative regime, while coherent accumulation of many pulse pairs enables near unity transfer efficiency with a high spectral selectivity, thus forming a powerful combination of pump-dump control schemes and the precision of the frequency comb. Simulations verify the feasibility and robustness of this concept, with the aim to form deeply bound, ultracold molecules.

Computer aided drug discovery of highly ligand efficient, low molecular weight imidazopyridine analogs as FLT3 inhibitors

PubMed Central

Frett, Brendan; McConnell, Nick; Smith, Catherine C.; Wang, Yuanxiang; Shah, Neil P.; Li, Hong-yu

2015-01-01

The FLT3 kinase represents an attractive target to effectively treat AML. Unfortunately, no FLT3 targeted therapeutic is currently approved. In line with our continued interests in treating kinase related disease for anti-FLT3 mutant activity, we utilized pioneering synthetic methodology in combination with computer aided drug discovery and identified low molecular weight, highly ligand efficient, FLT3 kinase inhibitors. Compounds were analyzed for biochemical inhibition, their ability to selectively inhibit cell proliferation, for FLT3 mutant activity, and preliminary aqueous solubility. Validated hits were discovered that can serve as starting platforms for lead candidates. PMID:25765758

Interaction sorting method for molecular dynamics on multi-core SIMD CPU architecture.

PubMed

Matvienko, Sergey; Alemasov, Nikolay; Fomin, Eduard

2015-02-01

Molecular dynamics (MD) is widely used in computational biology for studying binding mechanisms of molecules, molecular transport, conformational transitions, protein folding, etc. The method is computationally expensive; thus, the demand for the development of novel, much more efficient algorithms is still high. Therefore, the new algorithm designed in 2007 and called interaction sorting (IS) clearly attracted interest, as it outperformed the most efficient MD algorithms. In this work, a new IS modification is proposed which allows the algorithm to utilize SIMD processor instructions. This paper shows that the improvement provides an additional gain in performance, 9% to 45% in comparison to the original IS method.

Diffusion pump modification promotes self-cleansing and high efficiency

NASA Technical Reports Server (NTRS)

Buggele, A. E.

1975-01-01

Modifications eliminate contaminant substances from pump fluid during operation, which are principal causes of torpidity on evaporative surface. Diffusion pump is also acting as still. Resulting 100 percent vigorous working surface provides much greater molecular throughput and greatly improved efficiency.

Efficient spin filter and spin valve in a single-molecule magnet Fe{sub 4} between two graphene electrodes

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

Zu, Feng-Xia; School of Physics and Wuhan National High Magnetic Field Center, Huazhong University of Science and Technology, Wuhan 430074; Gao, Guo-Ying

2015-12-21

We propose a magnetic molecular junction consisting of a single-molecule magnet Fe{sub 4} connected two graphene electrodes and investigate transport properties, using the nonequilibrium Green's function method in combination with spin-polarized density-functional theory. The results show that the device can be used as a nearly perfect spin filter with efficiency approaching 100%. Our calculations provide crucial microscopic information how the four iron cores of the chemical structure are responsible for the spin-resolved transmissions. Moreover, it is also found that the device behaves as a highly efficient spin valve, which is an excellent candidate for spintronics of molecular devices. The ideamore » of combining single-molecule magnets with graphene provides a direction in designing a new class of molecular spintronic devices.« less

Using microwave heating to improve the desorption efficiency of high molecular weight VOC from beaded activated carbon.

PubMed

Fayaz, Mohammadreza; Shariaty, Pooya; Atkinson, John D; Hashisho, Zaher; Phillips, John H; Anderson, James E; Nichols, Mark

2015-04-07

Incomplete regeneration of activated carbon loaded with organic compounds results in heel build-up that reduces the useful life of the adsorbent. In this study, microwave heating was tested as a regeneration method for beaded activated carbon (BAC) loaded with n-dodecane, a high molecular weight volatile organic compound. Energy consumption and desorption efficiency for microwave-heating regeneration were compared with conductive-heating regeneration. The minimum energy needed to completely regenerate the adsorbent (100% desorption efficiency) using microwave regeneration was 6% of that needed with conductive heating regeneration, owing to more rapid heating rates and lower heat loss. Analyses of adsorbent pore size distribution and surface chemistry confirmed that neither heating method altered the physical/chemical properties of the BAC. Additionally, gas chromatography (with flame ionization detector) confirmed that neither regeneration method detectably altered the adsorbate composition during desorption. By demonstrating improvements in energy consumption and desorption efficiency and showing stable adsorbate and adsorbent properties, this paper suggests that microwave heating is an attractive method for activated carbon regeneration particularly when high-affinity VOC adsorbates are present.

Molecular Dynamics Characterization of the Conformational Landscape of Small Peptides: A Series of Hands-On Collaborative Practical Sessions for Undergraduate Students

ERIC Educational Resources Information Center

Rodrigues, João P. G. L. M.; Melquiond, Adrien S. J.; Bonvin, Alexandre M. J. J.

2016-01-01

Molecular modelling and simulations are nowadays an integral part of research in areas ranging from physics to chemistry to structural biology, as well as pharmaceutical drug design. This popularity is due to the development of high-performance hardware and of accurate and efficient molecular mechanics algorithms by the scientific community. These…

Controlling chitosan-based encapsulation for protein and vaccine delivery

PubMed Central

Koppolu, Bhanu prasanth; Smith, Sean G.; Ravindranathan, Sruthi; Jayanthi, Srinivas; Kumar, Thallapuranam K.S.; Zaharoff, David A.

2014-01-01

Chitosan-based nano/microencapsulation is under increasing investigation for the delivery of drugs, biologics and vaccines. Despite widespread interest, the literature lacks a defined methodology to control chitosan particle size and drug/protein release kinetics. In this study, the effects of precipitation-coacervation formulation parameters on chitosan particle size, protein encapsulation efficiency and protein release were investigated. Chitosan particle sizes, which ranged from 300 nm to 3 μm, were influenced by chitosan concentration, chitosan molecular weight and addition rate of precipitant salt. The composition of precipitant salt played a significant role in particle formation with upper Hofmeister series salts containing strongly hydrated anions yielding particles with a low polydispersity index (PDI) while weaker anions resulted in aggregated particles with high PDIs. Sonication power had minimal effect on mean particle size, however, it significantly reduced polydispersity. Protein loading efficiencies in chitosan nano/microparticles, which ranged from 14.3% to 99.2%, was inversely related to the hydration strength of precipitant salts, protein molecular weight and directly related to the concentration and molecular weight of chitosan. Protein release rates increased with particle size and were generally inversely related to protein molecular weight. This study demonstrates that chitosan nano/microparticles with high protein loading efficiencies can be engineered with well-defined sizes and controllable release kinetics through manipulation of specific formulation parameters. PMID:24560459

Open-Shell-Character-Based Molecular Design Principles: Applications to Nonlinear Optics and Singlet Fission.

PubMed

Nakano, Masayoshi

2017-01-01

Open-shell character, e. g., diradical character, is a quantum chemically well-defined quantity in ground-state molecular systems, which is not an observable but can quantify the degree of effective bond weakness in the chemical sense or electron correlation strength in the physical sense. Because this quantity also correlates to specific excited states, physicochemical properties concerned with those states are expected to strongly correlate to the open-shell character. This feature enables us to open a new path to revealing the mechanism of these properties as well as to realizing new design principles for efficient functional molecular systems. This account explains the open-shell-character-based molecular design principles and introduces their applications to the rational design of highly efficient nonlinear optical and singlet fission molecular systems. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Nano-electro-mechanical pump: Giant pumping of water in carbon nanotubes

PubMed Central

Farimani, Amir Barati; Heiranian, Mohammad; Aluru, Narayana R.

2016-01-01

A fully controllable nano-electro-mechanical device that can pump fluids at nanoscale is proposed. Using molecular dynamics simulations, we show that an applied electric field to an ion@C60 inside a water-filled carbon nanotube can pump water with excellent efficiency. The key physical mechanism governing the fluid pumping is the conversion of electrical energy into hydrodynamic flow with efficiencies as high as 64%. Our results show that water can be compressed up to 7% higher than its bulk value by applying electric fields. High flux of water (up to 13,000 molecules/ns) is obtained by the electro-mechanical, piston-cylinder-like moving mechanism of the ion@C60 in the CNT. This large flux results from the piston-like mechanism, compressibility of water (increase in density of water due to molecular ordering), orienting dipole along the electric field and efficient electrical to mechanical energy conversion. Our findings can pave the way towards efficient energy conversion, pumping of fluids at nanoscale, and drug delivery. PMID:27193507

Nano-electro-mechanical pump: Giant pumping of water in carbon nanotubes

NASA Astrophysics Data System (ADS)

Farimani, Amir Barati; Heiranian, Mohammad; Aluru, Narayana R.

2016-05-01

A fully controllable nano-electro-mechanical device that can pump fluids at nanoscale is proposed. Using molecular dynamics simulations, we show that an applied electric field to an ion@C60 inside a water-filled carbon nanotube can pump water with excellent efficiency. The key physical mechanism governing the fluid pumping is the conversion of electrical energy into hydrodynamic flow with efficiencies as high as 64%. Our results show that water can be compressed up to 7% higher than its bulk value by applying electric fields. High flux of water (up to 13,000 molecules/ns) is obtained by the electro-mechanical, piston-cylinder-like moving mechanism of the ion@C60 in the CNT. This large flux results from the piston-like mechanism, compressibility of water (increase in density of water due to molecular ordering), orienting dipole along the electric field and efficient electrical to mechanical energy conversion. Our findings can pave the way towards efficient energy conversion, pumping of fluids at nanoscale, and drug delivery.

Nano-electro-mechanical pump: Giant pumping of water in carbon nanotubes.

PubMed

Farimani, Amir Barati; Heiranian, Mohammad; Aluru, Narayana R

2016-05-19

A fully controllable nano-electro-mechanical device that can pump fluids at nanoscale is proposed. Using molecular dynamics simulations, we show that an applied electric field to an ion@C60 inside a water-filled carbon nanotube can pump water with excellent efficiency. The key physical mechanism governing the fluid pumping is the conversion of electrical energy into hydrodynamic flow with efficiencies as high as 64%. Our results show that water can be compressed up to 7% higher than its bulk value by applying electric fields. High flux of water (up to 13,000 molecules/ns) is obtained by the electro-mechanical, piston-cylinder-like moving mechanism of the ion@C60 in the CNT. This large flux results from the piston-like mechanism, compressibility of water (increase in density of water due to molecular ordering), orienting dipole along the electric field and efficient electrical to mechanical energy conversion. Our findings can pave the way towards efficient energy conversion, pumping of fluids at nanoscale, and drug delivery.

Characterization of nanoparticle mediated laser transfection by femtosecond laser pulses for applications in molecular medicine.

PubMed

Schomaker, Markus; Heinemann, Dag; Kalies, Stefan; Willenbrock, Saskia; Wagner, Siegfried; Nolte, Ingo; Ripken, Tammo; Murua Escobar, Hugo; Meyer, Heiko; Heisterkamp, Alexander

2015-02-03

In molecular medicine, the manipulation of cells is prerequisite to evaluate genes as therapeutic targets or to transfect cells to develop cell therapeutic strategies. To achieve these purposes it is essential that given transfection techniques are capable of handling high cell numbers in reasonable time spans. To fulfill this demand, an alternative nanoparticle mediated laser transfection method is presented herein. The fs-laser excitation of cell-adhered gold nanoparticles evokes localized membrane permeabilization and enables an inflow of extracellular molecules into cells. The parameters for an efficient and gentle cell manipulation are evaluated in detail. Efficiencies of 90% with a cell viability of 93% were achieved for siRNA transfection. The proof for a molecular medical approach is demonstrated by highly efficient knock down of the oncogene HMGA2 in a rapidly proliferating prostate carcinoma in vitro model using siRNA. Additionally, investigations concerning the initial perforation mechanism are conducted. Next to theoretical simulations, the laser induced effects are experimentally investigated by spectrometric and microscopic analysis. The results indicate that near field effects are the initial mechanism of membrane permeabilization. This methodical approach combined with an automated setup, allows a high throughput targeting of several 100,000 cells within seconds, providing an excellent tool for in vitro applications in molecular medicine. NIR fs lasers are characterized by specific advantages when compared to lasers employing longer (ps/ns) pulses in the visible regime. The NIR fs pulses generate low thermal impact while allowing high penetration depths into tissue. Therefore fs lasers could be used for prospective in vivo applications.

Surface similarity-based molecular query-retrieval

PubMed Central

Singh, Rahul

2007-01-01

Background Discerning the similarity between molecules is a challenging problem in drug discovery as well as in molecular biology. The importance of this problem is due to the fact that the biochemical characteristics of a molecule are closely related to its structure. Therefore molecular similarity is a key notion in investigations targeting exploration of molecular structural space, query-retrieval in molecular databases, and structure-activity modelling. Determining molecular similarity is related to the choice of molecular representation. Currently, representations with high descriptive power and physical relevance like 3D surface-based descriptors are available. Information from such representations is both surface-based and volumetric. However, most techniques for determining molecular similarity tend to focus on idealized 2D graph-based descriptors due to the complexity that accompanies reasoning with more elaborate representations. Results This paper addresses the problem of determining similarity when molecules are described using complex surface-based representations. It proposes an intrinsic, spherical representation that systematically maps points on a molecular surface to points on a standard coordinate system (a sphere). Molecular surface properties such as shape, field strengths, and effects due to field super-positioningcan then be captured as distributions on the surface of the sphere. Surface-based molecular similarity is subsequently determined by computing the similarity of the surface-property distributions using a novel formulation of histogram-intersection. The similarity formulation is not only sensitive to the 3D distribution of the surface properties, but is also highly efficient to compute. Conclusion The proposed method obviates the computationally expensive step of molecular pose-optimisation, can incorporate conformational variations, and facilitates highly efficient determination of similarity by directly comparing molecular surfaces and surface-based properties. Retrieval performance, applications in structure-activity modeling of complex biological properties, and comparisons with existing research and commercial methods demonstrate the validity and effectiveness of the approach. PMID:17634096

Computer aided drug discovery of highly ligand efficient, low molecular weight imidazopyridine analogs as FLT3 inhibitors.

PubMed

Frett, Brendan; McConnell, Nick; Smith, Catherine C; Wang, Yuanxiang; Shah, Neil P; Li, Hong-yu

2015-04-13

The FLT3 kinase represents an attractive target to effectively treat AML. Unfortunately, no FLT3 targeted therapeutic is currently approved. In line with our continued interests in treating kinase related disease for anti-FLT3 mutant activity, we utilized pioneering synthetic methodology in combination with computer aided drug discovery and identified low molecular weight, highly ligand efficient, FLT3 kinase inhibitors. Compounds were analyzed for biochemical inhibition, their ability to selectively inhibit cell proliferation, for FLT3 mutant activity, and preliminary aqueous solubility. Validated hits were discovered that can serve as starting platforms for lead candidates. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Biodegradable poly(amine-co-ester) terpolymers for targeted gene delivery

PubMed Central

Zhou, Jiangbing; Liu, Jie; Cheng, Christopher J.; Patel, Toral R.; Weller, Caroline E.; Piepmeier, Joseph M.; Jiang, Zhaozhong; Saltzman, W. Mark

2014-01-01

Many synthetic polycationic vectors for non-viral gene delivery show high efficiency in vitro, but their usually excessive charge density makes them toxic for in vivo applications. Here we describe the synthesis of a series of high molecular weight terpolymers with low charge density, and show that they exhibit efficient gene delivery, some surpassing the efficiency of the commercial transfection reagents Polyethylenimine and Lipofectamine 2000. The terpolymers were synthesized via enzyme-catalyzed copolymerization of lactone with dialkyl diester and amino diol, and their hydrophobicity adjusted by varying the lactone content and by selecting a lactone comonomer of specific ring size. Targeted delivery of the pro-apoptotic TRAIL gene to tumour xenografts by one of the terpolymers results in significant inhibition of tumour growth, with minimal toxicity both in vitro and in vivo. Our findings suggest that the gene delivery ability of the terpolymers stems from their high molecular weight and increased hydrophobicity, which compensates for their low charge density. PMID:22138789

Control of nitromethane photoionization efficiency with shaped femtosecond pulses.

PubMed

Roslund, Jonathan; Shir, Ofer M; Dogariu, Arthur; Miles, Richard; Rabitz, Herschel

2011-04-21

The applicability of adaptive femtosecond pulse shaping is studied for achieving selectivity in the photoionization of low-density polyatomic targets. In particular, optimal dynamic discrimination (ODD) techniques exploit intermediate molecular electronic resonances that allow a significant increase in the photoionization efficiency of nitromethane with shaped near-infrared femtosecond pulses. The intensity bias typical of high-photon number, nonresonant ionization is accounted for by reference to a strictly intensity-dependent process. Closed-loop adaptive learning is then able to discover a pulse form that increases the ionization efficiency of nitromethane by ∼150%. The optimally induced molecular dynamics result from entry into a region of parameter space inaccessible with intensity-only control. Finally, the discovered pulse shape is demonstrated to interact with the molecular system in a coherent fashion as assessed from the asymmetry between the response to the optimal field and its time-reversed counterpart.

The influence of the cluster environment on the star formation efficiency of 12 Virgo spiral galaxies

NASA Astrophysics Data System (ADS)

Vollmer, B.; Wong, O. I.; Braine, J.; Chung, A.; Kenney, J. D. P.

2012-07-01

The influence of the environment on gas surface density and star formation efficiency of cluster spiral galaxies is investigated. We extend previous work on radial profiles by a pixel-to pixel analysis looking for asymmetries due to environmental interactions. The star formation rate is derived from GALEX UV and Spitzer total infrared data based on the 8, 24, 70, and 160 μm data. As in field galaxies, the star formation rate for most Virgo galaxies is approximately proportional to the molecular gas mass. Except for NGC 4438, the cluster environment does not affect the star formation efficiency with respect to the molecular gas. Gas truncation is not associated with major changes in the total gas surface density distribution of the inner disk of Virgo spiral galaxies. In three galaxies (NGC 4430, NGC 4501, and NGC 4522), possible increases in the molecular fraction and the star formation efficiency with respect to the total gas, of factors of 1.5 to 2, are observed on the windward side of the galactic disk. A significant increase of the star formation efficiency with respect to the molecular gas content on the windward side of ram pressure-stripped galaxies is not observed. The ram-pressure stripped extraplanar gas of 3 highly inclined spiral galaxies (NGC 4330, NGC 4438, and NGC 4522) shows a depressed star formation efficiency with respect to the total gas, and one of them (NGC 4438) shows a depressed rate even with respect to the molecular gas. The interpretation is that stripped gas loses the gravitational confinement and associated pressure of the galactic disk, and the gas flow is diverging, so the gas density decreases and the star formation rate drops. We found two such regions of low star formation efficiency in the more face-on galaxies NGC 4501 and NGC 4654 which are both undergoing ram pressure stripping. These regions show low radio continuum emission or unusually steep radio spectral index. However, the stripped extraplanar gas in one highly inclined galaxy (NGC 4569) shows a normal star formation efficiency with respect to the total gas. We propose this galaxy is different because it is observed long after peak pressure, and its extraplanar gas is now in a converging flow as it resettles back into the disk. Appendices are available in electronic form http://www.aanda.org

Molecular implementation of molecular shift register memories

NASA Technical Reports Server (NTRS)

Beratan, David N. (Inventor); Onuchic, Jose N. (Inventor)

1991-01-01

An electronic shift register memory (20) at the molecular level is described. The memory elements are based on a chain of electron transfer molecules (22) and the information is shifted by photoinduced (26) electron transfer reactions. Thus, multi-step sequences of charge transfer reactions are used to move charge with high efficiency down a molecular chain. The device integrates compositions of the invention onto a VLSI substrate (36), providing an example of a molecular electronic device which may be fabricated. Three energy level schemes, molecular implementation of these schemes, optical excitation strategies, charge amplification strategies, and error correction strategies are described.

Bioreducible Zinc(II)-Coordinative Polyethylenimine with Low Molecular Weight for Robust Gene Delivery of Primary and Stem Cells.

PubMed

Liu, Shuai; Zhou, Dezhong; Yang, Jixiang; Zhou, Hao; Chen, Jiatong; Guo, Tianying

2017-03-30

To transform common low-molecular-weight (LMW) cationic polymers, such as polyethylenimine (PEI), to highly efficient gene vectors would be of great significance but remains challenging. Because LMW cationic polymers perform far less efficiently than their high-molecular-weight counterparts, mainly due to weaker nucleic acid encapsulation, herein we report the design and synthesis of a dipicolylamine-based disulfide-containing zinc(II) coordinative module (Zn-DDAC), which is used to functionalize LMW PEI (M w ≈ 1800 Da) to give a non-viral vector (Zn-PD) with high efficiency and safety in primary and stem cells. Given its high phosphate binding affinity, Zn-DDAC can significantly promote the DNA packaging functionality of PEI 1.8k and improve the cellular uptake of formulated polyplexes, which is particularly critical for hard-to-transfect cell types. Furthermore, Zn-PD polymer can be cleaved by glutathione in cytoplasm to facilitate DNA release post internalization and diminish the cytotoxicity. Consequently, the optimal Zn-PD mediates 1-2 orders of magnitude higher gluciferase activity than commercial transfection reagents, Xfect and PEI 25k , across diverse cell types, including primary and stem cells. Our findings provide a valuable insight into the exploitation of LMW cationic polymers for gene delivery and demonstrate great promise for the development of next-generation non-viral vectors for clinically viable gene therapy.

Vacuum MOCVD fabrication of high efficience cells

NASA Technical Reports Server (NTRS)

Partain, L. D.; Fraas, L. M.; Mcleod, P. S.; Cape, J. A.

1985-01-01

Vacuum metal-organic-chemical-vapor-deposition (MOCVD) is a new fabrication process with improved safety and easier scalability due to its metal rather than glass construction and its uniform multiport gas injection system. It uses source materials more efficiently than other methods because the vacuum molecular flow conditions allow the high sticking coefficient reactants to reach the substrates as undeflected molecular beams and the hot chamber walls cause the low sticking coefficient reactants to bounce off the walls and interact with the substrates many times. This high source utilization reduces the materials costs power device and substantially decreases the amounts of toxic materials that must be handled as process effluents. The molecular beams allow precise growth control. With improved source purifications, vacuum MOCVD has provided p GaAs layers with 10-micron minority carrier diffusion lengths and GaAs and GaAsSb solar cells with 20% AMO efficiencies at 59X and 99X sunlight concentration ratios. Mechanical stacking has been identified as the quickest, most direct and logical path to stacked multiple-junction solar cells that perform better than the best single-junction devices. The mechanical stack is configured for immediate use in solar arrays and allows interconnections that improve the system end-of-life performance in space.

Recent Developments in Hydrogen Evolving Molecular Cobalt(II)-Polypyridyl Catalysts

PubMed Central

Queyriaux, N.; Jane, R. T.; Massin, J.; Artero, V.; Chavarot-Kerlidou, M.

2015-01-01

The search for efficient noble metal-free hydrogen-evolving catalysts is the subject of intense research activity. A new family of molecular cobalt(II)-polypyridyl catalysts has recently emerged. These catalysts prove more robust under reductive conditions than other cobalt-based systems and display high activities under fully aqueous conditions. This review discusses the design, characterization, and evaluation of these catalysts for electrocatalytic and light-driven hydrogen production. Mechanistic considerations are addressed and structure-catalytic activity relationships identified in order to guide the future design of more efficient catalytic systems. PMID:26688590

Preparation of ellagic acid molecularly imprinted polymeric microspheres based on distillation-precipitation polymerization for the efficient purification of a crude extract.

PubMed

Zhang, Hua; Zhao, Shangge; Zhang, Lu; Han, Bo; Yao, Xincheng; Chen, Wen; Hu, Yanli

2016-08-01

Molecularly imprinted polymeric microspheres with a high recognition ability toward the template molecule, ellagic acid, were synthesized based on distillation-precipitation polymerization. The as-obtained polymers were characterized by scanning electron microscopy, infrared spectroscopy, and thermogravimetric analysis. Static, dynamic, and selective binding tests were adopted to study the binding properties and the molecular recognition ability of the prepared polymers for ellagic acid. The results indicated that the maximum static adsorption capacity of the prepared polymers toward ellagic acid was 37.07 mg/g and the adsorption equilibrium time was about 100 min when the concentration of ellagic acid was 40 mg/mL. Molecularly imprinted polymeric microspheres were also highly selective toward ellagic acid compared with its analogue quercetin. It was found that the content of ellagic acid in the pomegranate peel extract was enhanced from 23 to 86% after such molecularly imprinted solid-phase extraction process. This work provides an efficient way for effective separation and enrichment of ellagic acid from complex matrix, which is especially valuable in industrial production. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Supramolecularly Engineered Circular Bivalent Aptamer for Enhanced Functional Protein Delivery.

PubMed

Jiang, Ying; Pan, Xiaoshu; Chang, Jin; Niu, Weijia; Hou, Weijia; Kuai, Hailan; Zhao, Zilong; Liu, Ji; Wang, Ming; Tan, Weihong

2018-06-06

Circular bivalent aptamers (cb-apt) comprise an emerging class of chemically engineered aptamers with substantially improved stability and molecular recognition ability. Its therapeutic application, however, is challenged by the lack of functional modules to control the interactions of cb-apt with therapeutics. We present the design of a β-cyclodextrin-modified cb-apt (cb-apt-βCD) and its supramolecular interaction with molecular therapeutics via host-guest chemistry for targeted intracellular delivery. The supramolecular ensemble exhibits high serum stability and enhanced intracellular delivery efficiency compared to a monomeric aptamer. The cb-apt-βCD ensemble delivers green fluorescent protein into targeted cells with efficiency as high as 80%, or cytotoxic saporin to efficiently inhibit tumor cell growth. The strategy of conjugating βCD to cb-apt, and subsequently modulating the supramolecular chemistry of cb-apt-βCD, provides a general platform to expand and diversify the function of aptamers, enabling new biological and therapeutic applications.

Universal bound on the efficiency of molecular motors

NASA Astrophysics Data System (ADS)

Pietzonka, Patrick; Barato, Andre C.; Seifert, Udo

2016-12-01

The thermodynamic uncertainty relation provides an inequality relating any mean current, the associated dispersion and the entropy production rate for arbitrary non-equilibrium steady states. Applying it here to a general model of a molecular motor running against an external force or torque, we show that the thermodynamic efficiency of such motors is universally bounded by an expression involving only experimentally accessible quantities. For motors pulling cargo through a viscous fluid, a universal bound for the corresponding Stokes efficiency follows as a variant. A similar result holds if mechanical force is used to synthesize molecules of high chemical potential. Crucially, no knowledge of the detailed underlying mechano-chemical mechanism is required for applying these bounds.

Medium Bandgap Conjugated Polymer for High Performance Polymer Solar Cells Exceeding 9% Power Conversion Efficiency.

PubMed

Jung, Jae Woong; Liu, Feng; Russell, Thomas P; Jo, Won Ho

2015-12-02

Two medium-bandgap polymers composed of benzo[1,2-b:4,5-b']dithiohpene and 2,1,3-benzothiadiazole with 6-octyl-thieno[3,2-b]thiophene as a π-bridge unit are synthesized and their photovoltaic properties are analyzed. The two polymers have deep highest occupied molecular orbital energy levels, high crystallinity, optimal bulk-heterojunction morphology, and efficient charge transport, resulting in a power conversion efficiency of as high as 9.44% for a single-junction polymer solar-cell device. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

NASA Astrophysics Data System (ADS)

Guerrero, Carlo L.; Perlado, Jose M.

2016-03-01

In systems of inertial confinement fusion targets Deuterium-Tritium are manufactured with a solid layer, it must have specific properties to increase the efficiency of ignition. Currently there have been some proposals to model the phases of hydrogen isotopes and hence their high pressure, but these works do not allow explaining some of the structures present at the solid phase change effect of increased pressure. By means of simulation with first principles methods and Quantum Molecular Dynamics, we compare the structural difference of solid molecular hydrogen pure and solid molecular hydrogen with beryllium, watching beryllium inclusion in solid hydrogen matrix, we obtain several differences in mechanical properties, in particular elastic constants. For C11 the difference between hydrogen and hydrogen with beryllium is 37.56%. This may produce a non-uniform initial compression and decreased efficiency of ignition.

Multidisciplinary approaches to solar hydrogen

PubMed Central

Bren, Kara L.

2015-01-01

This review summarizes three different approaches to engineering systems for the solar-driven evolution of hydrogen fuel from water: molecular, nanomaterials and biomolecular. Molecular systems have the advantage of being highly amenable to modification and detailed study and have provided great insight into photophysics, electron transfer and catalytic mechanism. However, they tend to display poor stability. Systems based on nanomaterials are more robust but also are more difficult to synthesize in a controlled manner and to modify and study in detail. Biomolecular systems share many properties with molecular systems and have the advantage of displaying inherently high efficiencies for light absorption, electron–hole separation and catalysis. However, biological systems must be engineered to couple modules that capture and convert solar photons to modules that produce hydrogen fuel. Furthermore, biological systems are prone to degradation when employed in vitro. Advances that use combinations of these three tactics also are described. Multidisciplinary approaches to this problem allow scientists to take advantage of the best features of biological, molecular and nanomaterials systems provided that the components can be coupled for efficient function. PMID:26052425

The Harvard Clean Energy Project: High-throughput screening of organic photovoltaic materials using cheminformatics, machine learning, and pattern recognition

NASA Astrophysics Data System (ADS)

Olivares-Amaya, Roberto; Hachmann, Johannes; Amador-Bedolla, Carlos; Daly, Aidan; Jinich, Adrian; Atahan-Evrenk, Sule; Boixo, Sergio; Aspuru-Guzik, Alán

2012-02-01

Organic photovoltaic devices have emerged as competitors to silicon-based solar cells, currently reaching efficiencies of over 9% and offering desirable properties for manufacturing and installation. We study conjugated donor polymers for high-efficiency bulk-heterojunction photovoltaic devices with a molecular library motivated by experimental feasibility. We use quantum mechanics and a distributed computing approach to explore this vast molecular space. We will detail the screening approach starting from the generation of the molecular library, which can be easily extended to other kinds of molecular systems. We will describe the screening method for these materials which ranges from descriptor models, ubiquitous in the drug discovery community, to eventually reaching first principles quantum chemistry methods. We will present results on the statistical analysis, based principally on machine learning, specifically partial least squares and Gaussian processes. Alongside, clustering methods and the use of the hypergeometric distribution reveal moieties important for the donor materials and allow us to quantify structure-property relationships. These efforts enable us to accelerate materials discovery in organic photovoltaics through our collaboration with experimental groups.

Utilizing fast multipole expansions for efficient and accurate quantum-classical molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Schwörer, Magnus; Lorenzen, Konstantin; Mathias, Gerald; Tavan, Paul

2015-03-01

Recently, a novel approach to hybrid quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations has been suggested [Schwörer et al., J. Chem. Phys. 138, 244103 (2013)]. Here, the forces acting on the atoms are calculated by grid-based density functional theory (DFT) for a solute molecule and by a polarizable molecular mechanics (PMM) force field for a large solvent environment composed of several 103-105 molecules as negative gradients of a DFT/PMM hybrid Hamiltonian. The electrostatic interactions are efficiently described by a hierarchical fast multipole method (FMM). Adopting recent progress of this FMM technique [Lorenzen et al., J. Chem. Theory Comput. 10, 3244 (2014)], which particularly entails a strictly linear scaling of the computational effort with the system size, and adapting this revised FMM approach to the computation of the interactions between the DFT and PMM fragments of a simulation system, here, we show how one can further enhance the efficiency and accuracy of such DFT/PMM-MD simulations. The resulting gain of total performance, as measured for alanine dipeptide (DFT) embedded in water (PMM) by the product of the gains in efficiency and accuracy, amounts to about one order of magnitude. We also demonstrate that the jointly parallelized implementation of the DFT and PMM-MD parts of the computation enables the efficient use of high-performance computing systems. The associated software is available online.

Exploring high dimensional free energy landscapes: Temperature accelerated sliced sampling

NASA Astrophysics Data System (ADS)

Awasthi, Shalini; Nair, Nisanth N.

2017-03-01

Biased sampling of collective variables is widely used to accelerate rare events in molecular simulations and to explore free energy surfaces. However, computational efficiency of these methods decreases with increasing number of collective variables, which severely limits the predictive power of the enhanced sampling approaches. Here we propose a method called Temperature Accelerated Sliced Sampling (TASS) that combines temperature accelerated molecular dynamics with umbrella sampling and metadynamics to sample the collective variable space in an efficient manner. The presented method can sample a large number of collective variables and is advantageous for controlled exploration of broad and unbound free energy basins. TASS is also shown to achieve quick free energy convergence and is practically usable with ab initio molecular dynamics techniques.

Nano-siRNA Particles and Combination Therapies for Ovarian Tumor Targeting

DTIC Science & Technology

2015-08-01

stable complexes than siRNA for systemic delivery. Our preliminary tests suggest that low molecular weight , biodegradable polymers give higher...transfection efficiencies for csiRNA or T1-csiRNA than polymers that have higher molecular weight or are not degradable. We will therefore design and screen...combinations of chemotherapy drugs with siRNA and molecular inhibitors shown to be effective in ovarian cancer, thus providing the opportunity for highly

PMG: online generation of high-quality molecular pictures and storyboarded animations

PubMed Central

Autin, Ludovic; Tufféry, Pierre

2007-01-01

The Protein Movie Generator (PMG) is an online service able to generate high-quality pictures and animations for which one can then define simple storyboards. The PMG can therefore efficiently illustrate concepts such as molecular motion or formation/dissociation of complexes. Emphasis is put on the simplicity of animation generation. Rendering is achieved using Dino coupled to POV-Ray. In order to produce highly informative images, the PMG includes capabilities of using different molecular representations at the same time to highlight particular molecular features. Moreover, sophisticated rendering concepts including scene definition, as well as modeling light and materials are available. The PMG accepts Protein Data Bank (PDB) files as input, which may include series of models or molecular dynamics trajectories and produces images or movies under various formats. PMG can be accessed at http://bioserv.rpbs.jussieu.fr/PMG.html. PMID:17478496

High Sulfation and a High Molecular Weight Are Important for Anti-hepcidin Activity of Heparin

PubMed Central

Asperti, Michela; Naggi, Annamaria; Esposito, Emiliano; Ruzzenenti, Paola; Di Somma, Margherita; Gryzik, Magdalena; Arosio, Paolo; Poli, Maura

2016-01-01

Heparins are efficient inhibitors of hepcidin expression even in vivo, where they induce an increase of systemic iron availability. Heparins seem to act by interfering with BMP6 signaling pathways that control the expression of liver hepcidin, causing the suppression of SMAD1/5/8 phosphorylation. The anti-hepcidin activity persists also when the heparin anticoagulant property is abolished or reduced by chemical reactions of oxidation/reduction (glycol-split, Gs-Heparins) or by high sulfation (SS-Heparins), but the structural characteristics needed to optimize this inhibitory activity have not been studied in detail. To this aim we analyzed three different heparins (Mucosal Heparin, the Glycol split RO-82, the partially desulfated glycol-split RO-68 and the oversulfated SSLMWH) and separated them in fractions of molecular weight in the range 4–16 kD. Since the distribution of the negative charges in heparins contributes to the activity, we produced 2-O- and 6-O-desulfated heparins. These derivatives were analyzed for the capacity to inhibit hepcidin expression in hepatic HepG2 cells and in mice. The two approaches produced consistent results and showed that the anti-hepcidin activity strongly decreases with molecular weight below 7 kD, with high N-acetylation and after 2-O and 6-O desulfation. The high sulfation and high molecular weight properties for efficient anti-hepcidin activity suggest that heparin is involved in multiple binding sites. PMID:26955355

Polyelectrolyte Complexes of Low Molecular Weight PEI and Citric Acid as Efficient and Nontoxic Vectors for in Vitro and in Vivo Gene Delivery.

PubMed

Giron-Gonzalez, M Dolores; Salto-Gonzalez, Rafael; Lopez-Jaramillo, F Javier; Salinas-Castillo, Alfonso; Jodar-Reyes, Ana Belen; Ortega-Muñoz, Mariano; Hernandez-Mateo, Fernando; Santoyo-Gonzalez, Francisco

2016-03-16

Gene transfection mediated by the cationic polymer polyethylenimine (PEI) is considered a standard methodology. However, while highly branched PEIs form smaller polyplexes with DNA that exhibit high transfection efficiencies, they have significant cell toxicity. Conversely, low molecular weight PEIs (LMW-PEIs) with favorable cytotoxicity profiles display minimum transfection activities as a result of inadequate DNA complexation and protection. To solve this paradox, a novel polyelectrolyte complex was prepared by the ionic cross-linking of branched 1.8 kDa PEI with citric acid (CA). This system synergistically exploits the good cytotoxicity profile exhibited by LMW-PEI with the high transfection efficiencies shown by highly branched and high molecular weight PEIs. The polyectrolyte complex (1.8 kDa-PEI@CA) was obtained by a simple synthetic protocol based on the microwave irradiation of a solution of 1.8 kDa PEI and CA. Upon complexation with DNA, intrinsic properties of the resulting particles (size and surface charge) were measured and their ability to form stable polyplexes was determined. Compared with unmodified PEIs the new complexes behave as efficient gene vectors and showed enhanced DNA binding capability associated with facilitated intracellular DNA release and enhanced DNA protection from endonuclease degradation. In addition, while transfection values for LMW-PEIs are almost null, transfection efficiencies of the new reagent range from 2.5- to 3.8-fold to those of Lipofectamine 2000 and 25 kDa PEI in several cell lines in culture such as CHO-k1, FTO2B hepatomas, L6 myoblasts, or NRK cells, simultaneously showing a negligible toxicity. Furthermore, the 1.8 kDa-PEI@CA polyelectrolyte complexes retained the capability to transfect eukaryotic cells in the presence of serum and exhibited the capability to promote in vivo transfection in mouse (as an animal model) with an enhanced efficiency compared to 25 kDa PEI. Results support the polyelectrolyte complex of LMW-PEI and CA as promising generic nonviral gene carriers.

Regulating Molecular Aggregations of Polymers via Ternary Copolymerization Strategy for Efficient Solar Cells.

PubMed

Wang, Qian; Wang, Yingying; Zheng, Wei; Shahid, Bilal; Qiu, Meng; Wang, Di; Zhu, Dangqiang; Yang, Renqiang

2017-09-20

For many high-performance photovoltaic materials in polymer solar cells (PSCs), the active layers usually need to be spin-coated at high temperature due to the strong intermolecular aggregation of donor polymers, which is unfavorable in device repeatability and large-scale PSC printing. In this work, we adopted a ternary copolymerization strategy to regulate polymer solubility and molecular aggregation. A series of D-A 1 -D-A 2 random polymers based on different acceptors, strong electron-withdrawing unit ester substituted thieno[3,4-b]thiophene (TT-E), and highly planar dithiazole linked TT-E (DTzTT) were constructed to realize the regulation of molecular aggregation and simplification of device fabrication. The results showed that as the relative proportion of TT-E segment in the backbone increased, the absorption evidently red-shifted with a gradually decreased aggregation in solution, eventually leading to the active layers that can be fabricated at low temperature. Furthermore, due to the excellent phase separation and low recombination, the optimized solar cells based on the terpolymer P1 containing 30% of TT-E segment exhibit high power conversion efficiency (PCE) of 9.09% with a significantly enhanced fill factor up to 72.86%. Encouragingly, the photovoltaic performance is insensitive to the fabrication temperature of the active layer, and it still could maintain high PCE of 8.82%, even at room temperature. This work not only develops the highly efficient photovoltaic materials for low temperature processed PSCs through ternary copolymerization strategy but also preliminarily constructs the relationship between aggregation and photovoltaic performance.

Strategies to enhance the excitation energy-transfer efficiency in a light-harvesting system using the intra-molecular charge transfer character of carotenoids

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

Yukihira, Nao; Sugai, Yuko; Fujiwara, Masazumi

Fucoxanthin is a carotenoid that is mainly found in light-harvesting complexes from brown algae and diatoms. Due to the presence of a carbonyl group attached to polyene chains in polar environments, excitation produces an excited intra-molecular charge transfer. This intra-molecular charge transfer state plays a key role in the highly efficient (~95%) energy-transfer from fucoxanthin to chlorophyllain the light-harvesting complexes from brown algae. In purple bacterial light-harvesting systems the efficiency of excitation energy-transfer from carotenoids to bacteriochlorophylls depends on the extent of conjugation of the carotenoids. In this study we were successful, for the first time, in incorporating fucoxanthin intomore » a light-harvesting complex 1 from the purple photosynthetic bacterium,Rhodospirillum rubrumG9+ (a carotenoidless strain). Femtosecond pump-probe spectroscopy was applied to this reconstituted light-harvesting complex in order to determine the efficiency of excitation energy-transfer from fucoxanthin to bacteriochlorophyllawhen they are bound to the light-harvesting 1 apo-proteins.« less

Experimental and theoretical studies of Schiff bases as corrosion inhibitors.

PubMed

Jamil, Dalia M; Al-Okbi, Ahmed K; Al-Baghdadi, Shaimaa B; Al-Amiery, Ahmed A; Kadhim, Abdulhadi; Gaaz, Tayser Sumer; Kadhum, Abdul Amir H; Mohamad, Abu Bakar

2018-02-05

Relatively inexpensive, stable Schiff bases, namely 3-((4-hydroxybenzylidene)amino)-2-methylquinazolin-4(3H)-one (BZ3) and 3-((4-(dimethylamino)benzylidene)amino)-2-methylquinazolin-4(3H)-one (BZ4), were employed as highly efficient inhibitors of mild steel corrosion by corrosive acid. The inhibition efficiencies were estimated based on weight loss method. Moreover, scanning electron microscopy was used to investigate the inhibition mechanism. The synthesized Schiff bases were characterized by Fourier transform infrared spectroscopy, nuclear magnetic resonance spectroscopy and micro-elemental analysis. The inhibition efficiency depends on three factors: the amount of nitrogen in the inhibitor, the inhibitor concentration and the inhibitor molecular weight. Inhibition efficiencies of 96 and 92% were achieved with BZ4 and BZ3, respectively, at the maximum tested concentration. Density functional theory calculations of BZ3 and BZ4 were performed to compare the effects of hydroxyl and N,N-dimethylamino substituents on the inhibition efficiency, providing insight for designing new molecular structures that exhibit enhanced inhibition efficiencies.

Molecular machines operating on the nanoscale: from classical to quantum

PubMed Central

2016-01-01

Summary The main physical features and operating principles of isothermal nanomachines in the microworld, common to both classical and quantum machines, are reviewed. Special attention is paid to the dual, constructive role of dissipation and thermal fluctuations, the fluctuation–dissipation theorem, heat losses and free energy transduction, thermodynamic efficiency, and thermodynamic efficiency at maximum power. Several basic models are considered and discussed to highlight generic physical features. This work examines some common fallacies that continue to plague the literature. In particular, the erroneous beliefs that one should minimize friction and lower the temperature for high performance of Brownian machines, and that the thermodynamic efficiency at maximum power cannot exceed one-half are discussed. The emerging topic of anomalous molecular motors operating subdiffusively but very efficiently in the viscoelastic environment of living cells is also discussed. PMID:27335728

Probing molecular dynamics in solution with x-ray valence-to-core spectroscopy

NASA Astrophysics Data System (ADS)

Doumy, Gilles; March, Anne Marie; Tu, Ming-Feng; Al Haddad, Andre; Southworth, Stephen; Young, Linda; Walko, Donald; Bostedt, Christoph

2017-04-01

Hard X-ray spectroscopies are powerful tools for probing the electronic and geometric structure of molecules in complex or disordered systems and have been particularly useful for studying molecules in the solution phase. They are element specific, sensitive to the electronic structure and the local arrangements of surrounding atoms of the element being selectively probed. When combined in a pump-probe scheme with ultrafast lasers, X-ray spectroscopies can be used to track the evolution of structural changes that occur after photoexcitation. Efficient use of hard x-ray radiation coming from high brilliance synchrotrons and upcoming high repetition rate X-ray Free Electron Lasers requires MHz repetition rate lasers and data acquisition systems. High information content Valence-to-Core x-ray emission is directly sensitive to the molecular orbitals involved in photochemistry. We report on recent progress towards fully enabling this photon-hungry technique for the study of time-resolved molecular dynamics, including efficient detection and use of polychromatic x-ray micro-probe at the Advanced Photon Source. Work was supported by the U.S. Department of Energy, Office of Science, Chemical Sciences, Geosciences, and Biosciences Division.

Molecularly imprinted fluorescent hollow nanoparticles as sensors for rapid and efficient detection λ-cyhalothrin in environmental water.

PubMed

Wang, Jixiang; Qiu, Hao; Shen, Hongqiang; Pan, Jianming; Dai, Xiaohui; Yan, Yongsheng; Pan, Guoqing; Sellergren, Börje

2016-11-15

Molecularly imprinted fluorescent polymers have shown great promise in biological or chemical separations and detections, due to their high stability, selectivity and sensitivity. In this work, molecularly imprinted fluorescent hollow nanoparticles, which could rapidly and efficiently detect λ-cyhalothrin (a toxic insecticide) in water samples, was reported. The molecularly imprinted fluorescent sensor showed excellent sensitivity (the limit of detection low to 10.26nM), rapid detection rate (quantitative detection of λ-cyhalothrin within 8min), regeneration ability (maintaining good fluorescence properties after 8 cycling operation) and appreciable selectivity over several structural analogs. Moreover, the fluorescent sensor was further used to detect λ-cyhalothrin in real samples form the Beijing-Hangzhou Grand Canal Water. Despite the relatively complex components of the environmental water, the molecularly imprinted fluorescent hollow nanosensor still showed good recovery, clearly demonstrating the potential value of this smart sensor nanomaterial in environmental monitoring. Copyright © 2016 Elsevier B.V. All rights reserved.

Communication: Adaptive boundaries in multiscale simulations

NASA Astrophysics Data System (ADS)

Wagoner, Jason A.; Pande, Vijay S.

2018-04-01

Combined-resolution simulations are an effective way to study molecular properties across a range of length and time scales. These simulations can benefit from adaptive boundaries that allow the high-resolution region to adapt (change size and/or shape) as the simulation progresses. The number of degrees of freedom required to accurately represent even a simple molecular process can vary by several orders of magnitude throughout the course of a simulation, and adaptive boundaries react to these changes to include an appropriate but not excessive amount of detail. Here, we derive the Hamiltonian and distribution function for such a molecular simulation. We also design an algorithm that can efficiently sample the boundary as a new coordinate of the system. We apply this framework to a mixed explicit/continuum simulation of a peptide in solvent. We use this example to discuss the conditions necessary for a successful implementation of adaptive boundaries that is both efficient and accurate in reproducing molecular properties.

Sequence-controlled methacrylic multiblock copolymers via sulfur-free RAFT emulsion polymerization

NASA Astrophysics Data System (ADS)

Engelis, Nikolaos G.; Anastasaki, Athina; Nurumbetov, Gabit; Truong, Nghia P.; Nikolaou, Vasiliki; Shegiwal, Ataulla; Whittaker, Michael R.; Davis, Thomas P.; Haddleton, David M.

2017-02-01

Translating the precise monomer sequence control achieved in nature over macromolecular structure (for example, DNA) to whole synthetic systems has been limited due to the lack of efficient synthetic methodologies. So far, chemists have only been able to synthesize monomer sequence-controlled macromolecules by means of complex, time-consuming and iterative chemical strategies such as solid-state Merrifield-type approaches or molecularly dissolved solution-phase systems. Here, we report a rapid and quantitative synthesis of sequence-controlled multiblock polymers in discrete stable nanoscale compartments via an emulsion polymerization approach in which a vinyl-terminated macromolecule is used as an efficient chain-transfer agent. This approach is environmentally friendly, fully translatable to industry and thus represents a significant advance in the development of complex macromolecule synthesis, where a high level of molecular precision or monomer sequence control confers potential for molecular targeting, recognition and biocatalysis, as well as molecular information storage.

Evaluation of 3M molecular detection system and ANSR pathogen detection system for rapid detection of salmonella from egg products

USDA-ARS?s Scientific Manuscript database

Loop-mediated isothermal amplification (LAMP) is a novel simple detection technology that amplifies DNA with high speed, efficiency, and specificity under isothermal conditions. The objective of this study was to evaluate the effectiveness of 3M Molecular Detection System (MDS) and ANSR Pathogen Det...

Cell specific aptamer-photosensitizer conjugates as a molecular tool in photodynamic therapy

PubMed Central

Mallikaratchy, Prabodhika; Tang, Zhiwen

2010-01-01

This paper describes the application of a molecular construct of a photosensitizer and an aptamer for photo-therapeutically targeting tumor cells. The key step in increasing selectivity in chemotherapeutic drugs is to create effective molecular platforms that could target cancer cells but not normal cells. Recently, we have developed a strategy via cell-SELEX (Systematic Evolution of Ligands by Exponential Enrichment) to obtain cell specific aptamers using intact viable cells as targets to select aptamers that can recognize cell membrane proteins with high selectivity and excellent affinity. We have identified an aptamer TD05 that only recognizes Ramos cells, a Burkitt’s lymphoma cell line. Here, the high specificity of aptamers in target cell binding and an efficient phototherapy reagent, Ce6, are molecularly engineered to construct a highly selective Aptamer-photosensitizer conjugates (APS) to effectively destroy target cancer cells. Introduction of the APS conjugates followed by irradiation of light selectively destroyed target Ramos cells but not acute lymphoblastic leukemia and myeloid leukemia cell lines. This study demonstrates that the use of cancer specific aptamers conjugated to a photosensitizer will enhance the selectivity of photodynamic therapy. Coupled with the advantages of the cell-SELEX in generating multiple effective aptamers for diseased cell recognition, we will be able to develop highly efficient photosensitizer based therapeutical reagents for clinical applications. PMID:18058891

Fine-Tuning of Molecular Packing and Energy Level through Methyl Substitution Enabling Excellent Small Molecule Acceptors for Nonfullerene Polymer Solar Cells with Efficiency up to 12.54.

PubMed

Luo, Zhenghui; Bin, Haijun; Liu, Tao; Zhang, Zhi-Guo; Yang, Yankang; Zhong, Cheng; Qiu, Beibei; Li, Guanghao; Gao, Wei; Xie, Dongjun; Wu, Kailong; Sun, Yanming; Liu, Feng; Li, Yongfang; Yang, Chuluo

2018-03-01

A novel small molecule acceptor MeIC with a methylated end-capping group is developed. Compared to unmethylated counterparts (ITCPTC), MeIC exhibits a higher lowest unoccupied molecular orbital (LUMO) level value, tighter molecular packing, better crystallites quality, and stronger absorption in the range of 520-740 nm. The MeIC-based polymer solar cells (PSCs) with J71 as donor, achieve high power conversion efficiency (PCE), up to 12.54% with a short-circuit current (J SC ) of 18.41 mA cm -2 , significantly higher than that of the device based on J71:ITCPTC (11.63% with a J SC of 17.52 mA cm -2 ). The higher J SC of the PSC based on J71:MeIC can be attributed to more balanced μ h /μ e , higher charge dissociation and charge collection efficiency, better molecular packing, and more proper phase separation features as indicated by grazing incident X-ray diffraction and resonant soft X-ray scattering results. It is worth mentioning that the as-cast PSCs based on MeIC also yield a high PCE of 11.26%, which is among the highest value for the as-cast nonfullerene PSCs so far. Such a small modification that leads to so significant an improvement of the photovoltaic performance is a quite exciting finding, shining a light on the molecular design of the nonfullerene acceptors. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Recent Developments and Applications of the MMPBSA Method

PubMed Central

Wang, Changhao; Greene, D'Artagnan; Xiao, Li; Qi, Ruxi; Luo, Ray

2018-01-01

The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been widely applied as an efficient and reliable free energy simulation method to model molecular recognition, such as for protein-ligand binding interactions. In this review, we focus on recent developments and applications of the MMPBSA method. The methodology review covers solvation terms, the entropy term, extensions to membrane proteins and high-speed screening, and new automation toolkits. Recent applications in various important biomedical and chemical fields are also reviewed. We conclude with a few future directions aimed at making MMPBSA a more robust and efficient method. PMID:29367919

Design and synthesis of molecular donors for solution-processed high-efficiency organic solar cells.

PubMed

Coughlin, Jessica E; Henson, Zachary B; Welch, Gregory C; Bazan, Guillermo C

2014-01-21

Organic semiconductors incorporated into solar cells using a bulk heterojunction (BHJ) construction show promise as a cleaner answer to increasing energy needs throughout the world. Organic solar cells based on the BHJ architecture have steadily increased in their device performance over the past two decades, with power conversion efficiencies reaching 10%. Much of this success has come with conjugated polymer/fullerene combinations, where optimized polymer design strategies, synthetic protocols, device fabrication procedures, and characterization methods have provided significant advancements in the technology. More recently, chemists have been paying particular attention to well-defined molecular donor systems due to their ease of functionalization, amenability to standard organic purification and characterization methods, and reduced batch-to-batch variability compared to polymer counterparts. There are several critical properties for efficient small molecule donors. First, broad optical absorption needs to extend towards the near-IR region to achieve spectral overlap with the solar spectrum. Second, the low lying highest occupied molecular orbital (HOMO) energy levels need to be between -5.2 and -5.5 eV to ensure acceptable device open circuit voltages. Third, the structures need to be relatively planar to ensure close intermolecular contacts and high charge carrier mobilities. And last, the small molecule donors need to be sufficiently soluble in organic solvents (≥10 mg/mL) to facilitate solution deposition of thin films of appropriate uniformity and thickness. Ideally, these molecules should be constructed from cost-effective, sustainable building blocks using established, high yielding reactions in as few steps as possible. The structures should also be easy to functionalize to maximize tunability for desired properties. In this Account, we present a chronological description of our thought process and design strategies used in the development of highly efficient molecular donors that achieve power conversion efficiencies greater than 7%. The molecules are based on a modular D(1)-A-D(2)-A-D(1) architecture, where A is an asymmetric electron deficient heterocycle, which allowed us to quickly access a library of compounds and develop structure-property-performance relationships. Modifications to the D1 and D2 units enable spectral coverage throughout the entire visible region and control of HOMO energy levels, while adjustments to the pendant alkyl substituents dictate molecular solubility, thermal transition temperatures, and solid-state organizational tendencies. Additionally, we discuss regiochemical considerations that highlight how individual atom placements can significantly influence molecular and subsequently device characteristics. Our results demonstrate the utility of this architecture for generating promising materials to be integrated into organic photovoltaic devices, call attention to areas for improvement, and provide guiding principles to sustain the steady increases necessary to move this technology forward.

Doping-free white organic light-emitting diodes without blue molecular emitter: An unexplored approach to achieve high performance via exciplex emission

NASA Astrophysics Data System (ADS)

Luo, Dongxiang; Xiao, Ye; Hao, Mingming; Zhao, Yu; Yang, Yibin; Gao, Yuan; Liu, Baiquan

2017-02-01

Doping-free white organic light-emitting diodes (DF-WOLEDs) are promising for the low-cost commercialization because of their simplified device structures. However, DF-WOLEDs reported thus far in the literature are based on the use of blue single molecular emitters, whose processing can represent a crucial point in device manufacture. Herein, DF-WOLEDs without the blue single molecular emitter have been demonstrated by managing a blue exciplex system. For the single-molecular-emitter (orange or yellow emitter) DF-WOLEDs, (i) a color rendering index (CRI) of 81 at 1000 cd/m2 can be obtained, which is one of the highest for the single-molecular-emitter WOLEDs, or (ii) a high efficiency of 35.4 lm/W can be yielded. For the dual-molecular-emitter (yellow/red emitters) DF-WOLED, a high CRI of 85 and low correlated color temperature of 2376 K at 1000 cd/m2 have been simultaneously achieved, which has not been reported by previous DF-WOLEDs. Such presented findings may unlock an alternative avenue to the simplified but high-performance WOLEDs.

Perylene-diimide-based nanoparticles as highly efficient photoacoustic agents for deep brain tumor imaging in living mice

DOE PAGES

Fan, Quli; Cheng, Kai; Yang, Zhen; ...

2014-11-06

In order to promote preclinical and clinical applications of photoacoustic imaging, novel photoacoustic contrast agents are highly desired for molecular imaging of diseases, especially for deep tumor imaging. In this paper, perylene-3,4,9,10-tetracarboxylic diiimide-based near-infrared-absorptive organic nanoparticles are reported as an efficient agent for photoacoustic imaging of deep brain tumors in living mice with enhanced permeability and retention effect

Controllable production of low molecular weight heparins by combinations of heparinase I/II/III.

PubMed

Wu, Jingjun; Zhang, Chong; Mei, Xiang; Li, Ye; Xing, Xin-Hui

2014-01-30

Enzymatic depolymerization of heparin by heparinases is promising for production of low molecular weight heparins (LMWHs) as anticoagulants, due to its mild reaction conditions and high selectivity. Here, different heparinase combinations were used to depolymerize heparin. Heparinase I and heparinase II can depolymerize heparin more efficiently than heparinase III, respectively, but heparinase III was the best able to protect the anticoagulant activities of LMWHs. Heparinase III and heparinase I/II combinations were able to efficiently depolymerize heparin to LMWHs with higher anticoagulant activity than the LMWHs produced by the respective heparinase I and heparinase II. HepIII and HepI is the best combination for maintaining high anti-IIa activity (75.7 ± 4.21 IU/mg) at the same Mw value. Furthermore, considering both the changes in molecular weight and anticoagulant activity, the action patterns of heparinase I and heparinase II were found not to follow the exolytic and processive depolymerizing mechanism from the reducing end of heparin. Copyright © 2013 Elsevier Ltd. All rights reserved.

GROMACS 4:  Algorithms for Highly Efficient, Load-Balanced, and Scalable Molecular Simulation.

PubMed

Hess, Berk; Kutzner, Carsten; van der Spoel, David; Lindahl, Erik

2008-03-01

Molecular simulation is an extremely useful, but computationally very expensive tool for studies of chemical and biomolecular systems. Here, we present a new implementation of our molecular simulation toolkit GROMACS which now both achieves extremely high performance on single processors from algorithmic optimizations and hand-coded routines and simultaneously scales very well on parallel machines. The code encompasses a minimal-communication domain decomposition algorithm, full dynamic load balancing, a state-of-the-art parallel constraint solver, and efficient virtual site algorithms that allow removal of hydrogen atom degrees of freedom to enable integration time steps up to 5 fs for atomistic simulations also in parallel. To improve the scaling properties of the common particle mesh Ewald electrostatics algorithms, we have in addition used a Multiple-Program, Multiple-Data approach, with separate node domains responsible for direct and reciprocal space interactions. Not only does this combination of algorithms enable extremely long simulations of large systems but also it provides that simulation performance on quite modest numbers of standard cluster nodes.

Molecular ligand modulation of palladium nanocatalysts for highly efficient and robust heterogeneous oxidation of cyclohexenone to phenol

DOE PAGES

Xue, Teng; Lin, Zhaoyang; Chiu, Chin-Yi; ...

2017-01-06

Metallic nanoparticles are emerging as an exciting class of heterogeneous catalysts with the potential advantages of exceptional activity, stability, recyclability, and easier separation than homogeneous catalysts. The traditional colloid nanoparticle syntheses usually involve strong surface binding ligands that could passivate the surface active sites and result in poor catalytic activity. The subsequent removal of surface ligands could reactivate the surface but often leads to metal ion leaching and/or severe Ostwald ripening with diminished catalytic activity or poor stability. Molecular ligand engineering represents a powerful strategy for the design of homogeneous molecular catalysts but is insufficiently explored for nanoparticle catalysts tomore » date. We report a systematic investigation on molecular ligand modulation of palladium (Pd) nanoparticle catalysts. Our studies show that β-functional groups of butyric acid ligand on Pd nanoparticles can significantly modulate the catalytic reaction process to modify the catalytic activity and stability for important aerobic reactions. With a β-hydroxybutyric acid ligand, the Pd nanoparticle catalysts exhibit exceptional catalytic activity and stability with an unsaturated turnover number (TON) >3000 for dehydrogenative oxidation of cyclohexenone to phenol, greatly exceeding that of homogeneous Pd(II) catalysts (TON, ~30). This study presents a systematic investigation of molecular ligand modulation of nanoparticle catalysts and could open up a new pathway toward the design and construction of highly efficient and robust heterogeneous catalysts through molecular ligand engineering.« less

Interfacial engineering of pyridinium gemini surfactants for the generation of synthetic transfection systems.

PubMed

Sharma, Vishnu D; Aifuwa, Eronmwon O; Heiney, Paul A; Ilies, Marc A

2013-09-01

Pyridinium gemini surfactants possess a soft charge, a high charge/mass ratio and a high molecular flexibility - all key parameters that recommend their use in synthetic gene delivery systems with in vitro and in vivo efficiency. In present study we generated a DNA delivery system through interfacial engineering of pyridinium gemini surfactants at the level of linker, hydrophobic chains and counterions. The self-assembling of the pyridinium amphiphiles and the physicochemical properties of the resultant supra-molecular assemblies were studied in bulk and in solution through a combination of techniques that included DSC, X-ray diffraction, polarized microscopy, CMC, dynamic light scattering and zeta potential measurements. We assessed the impact of different structural elements and formulation parameters of these pyridinium amphiphiles on their DNA compaction properties, transfection efficiency, cytotoxicity, in a complete structure-activity relationship study. This interfacial engineering process generated transfection systems with reduced cytotoxicity and high transfection efficiency in media containing elevated levels of serum that mimic the in vivo conditions. Copyright © 2013 Elsevier Ltd. All rights reserved.

Computation of Dielectric Response in Molecular Solids for High Capacitance Organic Dielectrics.

PubMed

Heitzer, Henry M; Marks, Tobin J; Ratner, Mark A

2016-09-20

The dielectric response of a material is central to numerous processes spanning the fields of chemistry, materials science, biology, and physics. Despite this broad importance across these disciplines, describing the dielectric environment of a molecular system at the level of first-principles theory and computation remains a great challenge and is of importance to understand the behavior of existing systems as well as to guide the design and synthetic realization of new ones. Furthermore, with recent advances in molecular electronics, nanotechnology, and molecular biology, it has become necessary to predict the dielectric properties of molecular systems that are often difficult or impossible to measure experimentally. In these scenarios, it is would be highly desirable to be able to determine dielectric response through efficient, accurate, and chemically informative calculations. A good example of where theoretical modeling of dielectric response would be valuable is in the development of high-capacitance organic gate dielectrics for unconventional electronics such as those that could be fabricated by high-throughput printing techniques. Gate dielectrics are fundamental components of all transistor-based logic circuitry, and the combination high dielectric constant and nanoscopic thickness (i.e., high capacitance) is essential to achieving high switching speeds and low power consumption. Molecule-based dielectrics offer the promise of cheap, flexible, and mass producible electronics when used in conjunction with unconventional organic or inorganic semiconducting materials to fabricate organic field effect transistors (OFETs). The molecular dielectrics developed to date typically have limited dielectric response, which results in low capacitances, translating into poor performance of the resulting OFETs. Furthermore, the development of better performing dielectric materials has been hindered by the current highly empirical and labor-intensive pace of synthetic progress. An accurate and efficient theoretical computational approach could drastically decrease this time by screening potential dielectric materials and providing reliable design rules for future molecular dielectrics. Until recently, accurate calculation of dielectric responses in molecular materials was difficult and highly approximate. Most previous modeling efforts relied on classical formalisms to relate molecular polarizability to macroscopic dielectric properties. These efforts often vastly overestimated polarizability in the subject materials and ignored crucial material properties that can affect dielectric response. Recent advances in first-principles calculations via density functional theory (DFT) with periodic boundary conditions have allowed accurate computation of dielectric properties in molecular materials. In this Account, we outline the methodology used to calculate dielectric properties of molecular materials. We demonstrate the validity of this approach on model systems, capturing the frequency dependence of the dielectric response and achieving quantitative accuracy compared with experiment. This method is then used as a guide to new high-capacitance molecular dielectrics by determining what materials and chemical properties are important in maximizing dielectric response in self-assembled monolayers (SAMs). It will be seen that this technique is a powerful tool for understanding and designing new molecular dielectric systems, the properties of which are fundamental to many scientific areas.

Polyethyleneimine Capped Silver Nanoclusters as Efficient Antibacterial Agents.

PubMed

Xu, Dong; Wang, Qingyun; Yang, Tao; Cao, Jianzhong; Lin, Qinlu; Yuan, Zhiqin; Li, Le

2016-03-18

Development of efficient antibacterial agents is critical for human health. In the present study, we investigated the antibacterial activity of polyethyleneimine (PEI)-capped silver nanoclusters (PEI-AgNCs), based on the fact that nanoclusters normally have higher surface-to-volume ratios than traditional nanomaterials and PEI itself has a strong antimicrobial capacity. We synthesized stable silver nanoclusters by altering PEI molecular weight from 0.6 kDa to 25 kDa and characterized them by UV-Vis absorption and fluorescence spectroscopy and high resolution transmission electron microscopy. The sizes of AgNCs were around 2 nm in diameter and were little influenced by the molecular weight of PEIs. The antibacterial abilities of the four PEI-AgNCs were explored on agar plate and in liquid systems. Our results revealed that the antibacterial activity of PEI-AgNCs is excellent and the reduction of PEI molecular weight could result in the increased antibacterial capacity of PEI-AgNCs. Such proposed new materials might be useful as efficient antibacterial agents in practical clinical applications.

Full Quantum Dynamics Simulation of a Realistic Molecular System Using the Adaptive Time-Dependent Density Matrix Renormalization Group Method.

PubMed

Yao, Yao; Sun, Ke-Wei; Luo, Zhen; Ma, Haibo

2018-01-18

The accurate theoretical interpretation of ultrafast time-resolved spectroscopy experiments relies on full quantum dynamics simulations for the investigated system, which is nevertheless computationally prohibitive for realistic molecular systems with a large number of electronic and/or vibrational degrees of freedom. In this work, we propose a unitary transformation approach for realistic vibronic Hamiltonians, which can be coped with using the adaptive time-dependent density matrix renormalization group (t-DMRG) method to efficiently evolve the nonadiabatic dynamics of a large molecular system. We demonstrate the accuracy and efficiency of this approach with an example of simulating the exciton dissociation process within an oligothiophene/fullerene heterojunction, indicating that t-DMRG can be a promising method for full quantum dynamics simulation in large chemical systems. Moreover, it is also shown that the proper vibronic features in the ultrafast electronic process can be obtained by simulating the two-dimensional (2D) electronic spectrum by virtue of the high computational efficiency of the t-DMRG method.

De Novo Design of Boron-Based Host Materials for Highly Efficient Blue and White Phosphorescent OLEDs with Low Efficiency Roll-Off.

PubMed

Xue, Miao-Miao; Huang, Chen-Chao; Yuan, Yi; Cui, Lin-Song; Li, Yong-Xi; Wang, Bo; Jiang, Zuo-Quan; Fung, Man-Keung; Liao, Liang-Sheng

2016-08-10

Borane is an excellent electron-accepting species, and its derivatives have been widely used in a variety of fields. However, the use of borane derivatives as host materials in OLEDs has rarely reported because the device performance is generally not satisfactory. In this work, two novel spiro-bipolar hosts with incorporated borane were designed and synthesized. The strategies used in preparing these materials were to increase the spatial separation of the highest occupied molecular orbitals (HOMOs) and lowest unoccupied molecular orbitals (LUMOs) in the molecules, tune the connecting positions of functional groups, and incorporate specific functional groups with desirable thermal stability. Based on these designs, phosphorescent OLEDs with borane derivatives as hosts and with outstanding device performances were obtained. In particular, devices based on SAF-3-DMB/FIrpic exhibited an external quantum efficiency (EQE) of >25%. More encouragingly, the device was found to have quite a low efficiency roll-off, giving an efficiency of >20% even at a high brightness of 10000 cd/m(2). Furthermore, the EQE of the three-color-based (R + G + B) white OLED employing SAF-3-DMB as a host was also as high as 22.9% with CIE coordinates of (x, y) = (0.40, 0.48). At a brightness of 5000 cd/m(2), there was only a 3% decrease in EQE from its maximum value, implying a very low efficiency roll-off.

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach.

PubMed

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D; Duvenaud, David; Maclaurin, Dougal; Blood-Forsythe, Martin A; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

Design of efficient molecular organic light-emitting diodes by a high-throughput virtual screening and experimental approach

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Duvenaud, David; MacLaurin, Dougal; Blood-Forsythe, Martin A.; Chae, Hyun Sik; Einzinger, Markus; Ha, Dong-Gwang; Wu, Tony; Markopoulos, Georgios; Jeon, Soonok; Kang, Hosuk; Miyazaki, Hiroshi; Numata, Masaki; Kim, Sunghan; Huang, Wenliang; Hong, Seong Ik; Baldo, Marc; Adams, Ryan P.; Aspuru-Guzik, Alán

2016-10-01

Virtual screening is becoming a ground-breaking tool for molecular discovery due to the exponential growth of available computer time and constant improvement of simulation and machine learning techniques. We report an integrated organic functional material design process that incorporates theoretical insight, quantum chemistry, cheminformatics, machine learning, industrial expertise, organic synthesis, molecular characterization, device fabrication and optoelectronic testing. After exploring a search space of 1.6 million molecules and screening over 400,000 of them using time-dependent density functional theory, we identified thousands of promising novel organic light-emitting diode molecules across the visible spectrum. Our team collaboratively selected the best candidates from this set. The experimentally determined external quantum efficiencies for these synthesized candidates were as large as 22%.

Molecular modeling of the process of reversible dissolution of the collagen protein under the action of tissue-clearing agents

NASA Astrophysics Data System (ADS)

Dvoretsky, K. N.; Berezin, K. V.; Chernavina, M. L.; Likhter, A. M.; Shagautdinova, I. T.; Antonova, E. M.; Rybakov, A. V.; Grechukhina, O. N.; Tuchin, V. V.

2018-04-01

The interaction of glycerol immersion agent with collagen mimetic peptide ((GPH)9)3 and a fragment of the microfibril 5((GPH)12)3 was studied by the classical molecular dynamics method using the GROMACS software. The change in geometric parameters of collagen α-chains at various concentrations of an aqueous solution of glycerol is analyzed. It is shown that these changes nonlinearly depend on the concentration and are limited to a certain level, which correlates with the experimental data on optical clearing efficiency of human skin. A hypothesis on the cause of the decreased efficiency of optical skin clearing at high immersion agent concentrations is put forward. The molecular mechanism of immersion optical clearing of biological tissues is discussed.

Efficient triplet harvesting by fluorescent molecules through exciplexes for high efficiency organic light-emitting diodes

NASA Astrophysics Data System (ADS)

Park, Young-Seo; Kim, Kwon-Hyeon; Kim, Jang-Joo

2013-04-01

Efficient triplet harvesting from exciplexes by reverse intersystem crossing (RISC) is reported using a fluorescent molecular system composed of the 4,4',4″-tris(N-carbazolyl)-triphenylamine and bis-4,6-(3,5-di-3-pyridylphenyl)-2-methylpyrimidine. The exciplex forming material system shows the efficient delayed fluorescence emission. As a result, almost 100% PL efficiency at 35 K and 10% external quantum efficiency at 195 K are achieved from the exciplex. The delayed fluorescence of the exciplex clearly demonstrates that a significant proportion of the triplet exciplexes is harvested through the RISC.

Broadband Light-Harvesting Molecular Triads with High FRET Efficiency Based on the Coumarin-Rhodamine-BODIPY Platform.

PubMed

He, Longwei; Zhu, Sasa; Liu, Yong; Xie, Yinan; Xu, Qiuyan; Wei, Haipeng; Lin, Weiying

2015-08-17

Broadband capturing and FRET-based light-harvesting molecular triads, CRBs, based on the coumarin-rhodamine-BODIPY platform were rationally designed and synthesized. The absorption band of CRBs starts from blue-green to yellow-orange regions (330-610 nm), covering the strong radiation scope of sunlight. The peripheral coumarin and BODIPY chromophore energy could transfer to the central acceptor rhodamine by a one-step direct way. The energy of the coumarin moiety could also transfer to the BODIPY unit, subsequently transferring to the rhodamine core by two-step sequential ways. Both the efficiencies of the coumarin moiety and the BODIPY unit to the rhodamine core in CRBs, determined by two different ways, are very high. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

SELF-HEALING NANOMATERIALS: MULTIMILLION-ATOM REACTIVE MOLECULAR DYNAMICS SIMULATIONS

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

Hakamata, Tomoya; Shimamura, Kohei; Shimojo, Fuyuki

Organometal halide perovskites are attracting great attention as promising material for solar cells because of their high power conversion efficiency. The high performance has been attributed to the existence of free charge carriers and their large diffusion lengths, but the nature of carrier transport at the atomistic level remains elusive. Here, nonadiabatic quantum molecular dynamics simulations elucidate the mechanisms underlying the excellent free-carrier transport in CH 3NH 3PbI 3. Pb and I sublattices act as disjunct pathways for rapid and balanced transport of photoexcited electrons and holes, respectively, while minimizing efficiency-degrading charge recombination. On the other hand, CH 3NH 3more » sublattice quickly screens out electrostatic electron-hole attraction to generate free carriers within 1 ps. Together this nano-architecture lets photoexcited electrons and holes dissociate instantaneously and travel far away to be harvested before dissipated as heat. As a result, this work provides much needed structure-property relationships and time-resolved information that potentially lead to rational design of efficient solar cells.« less

An Efficient Method for Genomic DNA Extraction from Different Molluscs Species

PubMed Central

Pereira, Jorge C.; Chaves, Raquel; Bastos, Estela; Leitão, Alexandra; Guedes-Pinto, Henrique

2011-01-01

The selection of a DNA extraction method is a critical step when subsequent analysis depends on the DNA quality and quantity. Unlike mammals, for which several capable DNA extraction methods have been developed, for molluscs the availability of optimized genomic DNA extraction protocols is clearly insufficient. Several aspects such as animal physiology, the type (e.g., adductor muscle or gills) or quantity of tissue, can explain the lack of efficiency (quality and yield) in molluscs genomic DNA extraction procedure. In an attempt to overcome these aspects, this work describes an efficient method for molluscs genomic DNA extraction that was tested in several species from different orders: Veneridae, Ostreidae, Anomiidae, Cardiidae (Bivalvia) and Muricidae (Gastropoda), with different weight sample tissues. The isolated DNA was of high molecular weight with high yield and purity, even with reduced quantities of tissue. Moreover, the genomic DNA isolated, demonstrated to be suitable for several downstream molecular techniques, such as PCR sequencing among others. PMID:22174651

Separation and purification of thymopentin with molecular imprinting membrane by solid phase extraction disks.

PubMed

Wang, Chaoli; Hu, Xiaoling; Guan, Ping; Wu, Danfeng; Qian, Liwei; Li, Ji; Song, Renyuan

2015-01-01

The synthesis and performance of molecularly imprinted membranes (MIMs) as a solid phase extraction packing materials for the separation and purification of thymopentin from crude samples was described. In order to increase structural selectivity and imprinting efficiency, surface-initiated ATRP and ionic liquid (1-vinyl-3-ethyl acetate imidazolium chloride) were used to prepare molecularly imprinting membranes. The results demonstrated that solid phase extraction disks stuffed by MIMs with ionic liquids as functional monomer demonstrated high isolation and purification of performance to the thymopentin. The molecular recognition of thymopentin was analyzed by using molecular modeling software. Copyright © 2014 Elsevier B.V. All rights reserved.

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with the associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3-8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.

A naphthodithiophene-diketopyrrolopyrrole donor molecule for efficient solution-processed solar cells.

PubMed

Loser, Stephen; Bruns, Carson J; Miyauchi, Hiroyuki; Ortiz, Rocío Ponce; Facchetti, Antonio; Stupp, Samuel I; Marks, Tobin J

2011-06-01

We report the synthesis, characterization, and first implementation of a naphtho[2,3-b:6,7-b']dithiophene (NDT)-based donor molecule in highly efficient organic photovoltaics (OPVs). When NDT(TDPP)(2) (TDPP = thiophene-capped diketopyrrolopyrrole) is combined with the electron acceptor PC(61)BM, a power conversion efficiency (PCE) of 4.06 ± 0.06% is achieved-a record for a PC(61)BM-based small-molecule OPV. The substantial PCE is attributed to the broad, high oscillator strength visible absorption, the ordered molecular packing, and an exceptional hole mobility of NDT(TDPP)(2). © 2011 American Chemical Society

Comparative transcriptome analysis reveals a global insight into molecular processes regulating citrate accumulation in sweet orange (Citrus sinensis).

PubMed

Lu, Xiaopeng; Cao, Xiongjun; Li, Feifei; Li, Jing; Xiong, Jiang; Long, Guiyou; Cao, Shangyin; Xie, Shenxi

2016-12-01

Citrate, the predominant organic acid in citrus, determines the taste of these fruits. However, little is known about the synergic molecular processes regulating citrate accumulation. Using 'Dahongtiancheng' (Citrus sinensis) and 'Bingtangcheng' (C. sinensis) with significant difference in citrate, the objectives of this study were to understand the global mechanisms of high-citrate accumulation in sweet orange. 'Dahongtiancheng' and 'Bingtangcheng' exhibit significantly different patterns in citrate accumulation throughout fruit development, with the largest differences observed at 50-70 days after full bloom (DAFB). Comparative transcriptome profiling was performed for the endocarps of both cultivars at 50 and 70 DAFB. Over 34.5 million clean reads per library were successfully mapped to the reference database and 670-2630 differentially expressed genes (DEGs) were found in four libraries. Among the genes, five transcription factors were ascertained to be the candidates regulating citrate accumulation. Functional assignments of the DEGs indicated that photosynthesis, the citrate cycle and amino acid metabolism were significantly altered in 'Dahongtiancheng'. Physiological and molecular analyses suggested that high photosynthetic efficiency and partial impairment of citrate catabolism were crucial for the high-citrate trait, and amino acid biosynthesis was one of the important directions for citrate flux. The results reveal a global insight into the gene expression changes in a high-citrate compared with a low-citrate sweet orange. High accumulating efficiency and impaired degradation of citrate may be associated with the high-citrate trait of 'Dahongtiancheng'. Findings in this study increase understanding of the molecular processes regulating citrate accumulation in sweet orange. © 2016 Scandinavian Plant Physiology Society.

An episomal vector-based CRISPR/Cas9 system for highly efficient gene knockout in human pluripotent stem cells.

PubMed

Xie, Yifang; Wang, Daqi; Lan, Feng; Wei, Gang; Ni, Ting; Chai, Renjie; Liu, Dong; Hu, Shijun; Li, Mingqing; Li, Dajin; Wang, Hongyan; Wang, Yongming

2017-05-24

Human pluripotent stem cells (hPSCs) represent a unique opportunity for understanding the molecular mechanisms underlying complex traits and diseases. CRISPR/Cas9 is a powerful tool to introduce genetic mutations into the hPSCs for loss-of-function studies. Here, we developed an episomal vector-based CRISPR/Cas9 system, which we called epiCRISPR, for highly efficient gene knockout in hPSCs. The epiCRISPR system enables generation of up to 100% Insertion/Deletion (indel) rates. In addition, the epiCRISPR system enables efficient double-gene knockout and genomic deletion. To minimize off-target cleavage, we combined the episomal vector technology with double-nicking strategy and recent developed high fidelity Cas9. Thus the epiCRISPR system offers a highly efficient platform for genetic analysis in hPSCs.

LyP-1 ultrasonic microbubbles targeting to cancer cell as tumor bio-acoustics markers or drug carriers: targeting efficiency evaluation in, microfluidic channels.

PubMed

Li, Xiang; Jin, Qiaofeng; Chen, Tan; Zhang, Baoyue; Zheng, Rongqin; Wang, Zhanhui; Zheng, Hairong

2009-01-01

Using ultrasonic contrast microbubbles as acoustic biomarkers and drug carrier vehicles by conjugating tumor specific antibody to microbubbles has shown great potential in ultrasonic tumor molecular imaging or drug-delivery and therapy. Microbubble probe targeting efficiency is one of the major challenges. In this study, we developed a novel method to evaluate the targeting capability and efficiency of microbubbles to cells, and more specifically, microbubbles binding LyP-1 (a cyclic nonapeptide acid peptide) target to cancer cell within a microfluidic system. The micro cell sieves within the microfludic channels could trap the tumor cells and enhance the microbubble's interaction with the cell. Assisted with the controllable fluid shear stress, the microbubble's targeting to the cell and the corresponding affinity efficiency could be quantitatively evaluated under a florescent microscope. The system provides a useful low-cost high efficient in vitro platform for studying microbubble-cell interaction for ultrasonic tumor molecular imaging or drug-delivery and therapy.

Optically (solar) pumped oxygen-iodine lasers

NASA Astrophysics Data System (ADS)

Danilov, O. B.; Zhevlakov, A. P.; Yur'ev, M. S.

2014-07-01

We present the results of theoretical and experimental studies demonstrating the possibility of developing an oxygen-iodine laser (OIL) with direct optical pumping of molecular oxygen involving inter-molecular interaction with charge transfer from donor molecule (buffer gas) to acceptor molecule (oxygen). This interaction lifts degeneracy of the lower energy states of molecular oxygen and increases its absorption cross section in the visible spectral region and the UV Herzberg band, where high quantum yield of singlet oxygen is achieved (QY ˜ 1 and QY ˜ 2, respectively) at the same time. A pulse-periodic optical pump sources with pulse energy of ˜50 kJ, pulse duration of ˜25 μs, and repetition rate of ˜10 Hz, which are synchronized with the mechanism of singlet oxygen generation, are developed. This allows implementation of a pulse-periodic oxygen-iodine laser with an efficiency of ˜25%, optical efficiency of ˜40%, and parameter L/ T ˜ 1/1.5, where T is the thermal energy released in the laser active medium upon generation of energy L. It is demonstrated that, under direct solar pumping of molecular oxygen, the efficiency parameter of the OIL can reach L/ T ˜ 1/0.8 in a wide range of scaling factors.

Triplet Tellurophene-Based Acceptors for Organic Solar Cells.

PubMed

Yang, Lei; Gu, Wenxing; Lv, Lei; Chen, Yusheng; Yang, Yufei; Ye, Pan; Wu, Jianfei; Hong, Ling; Peng, Aidong; Huang, Hui

2018-01-22

Triplet materials have been employed to achieve high-performing organic solar cells (OSCs) by extending the exciton lifetime and diffusion distances, while the triplet non-fullerene acceptor materials have never been reported for bulk heterojunction OSCs. Herein, for the first time, three triplet molecular acceptors based on tellurophene with different degrees of ring fusing were designed and synthesized for OSCs. Significantly, these molecules have long exciton lifetime and diffusion lengths, leading to efficient power conversion efficiency (7.52 %), which is the highest value for tellurophene-based OSCs. The influence of the extent of ring fusing on molecular geometry and OSCs performance was investigated to show the power conversion efficiencies (PCEs) continuously increased along with increasing the extent of ring fusing. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient and Flexible Computation of Many-Electron Wave Function Overlaps.

PubMed

Plasser, Felix; Ruckenbauer, Matthias; Mai, Sebastian; Oppel, Markus; Marquetand, Philipp; González, Leticia

2016-03-08

A new algorithm for the computation of the overlap between many-electron wave functions is described. This algorithm allows for the extensive use of recurring intermediates and thus provides high computational efficiency. Because of the general formalism employed, overlaps can be computed for varying wave function types, molecular orbitals, basis sets, and molecular geometries. This paves the way for efficiently computing nonadiabatic interaction terms for dynamics simulations. In addition, other application areas can be envisaged, such as the comparison of wave functions constructed at different levels of theory. Aside from explaining the algorithm and evaluating the performance, a detailed analysis of the numerical stability of wave function overlaps is carried out, and strategies for overcoming potential severe pitfalls due to displaced atoms and truncated wave functions are presented.

Efficient synthesis of molecularly imprinted polymers with bio-recognition sites for the selective separation of bovine hemoglobin.

PubMed

Zhang, Zulei; Li, Lei

2018-06-01

We developed a facile approach to the construction of bio-recognition sites in silica nanoparticles for efficient separation of bovine hemoglobin based on amino-functionalized silica nanoparticles grafting by 3-aminopropyltriethoxylsilane providing hydrogen bonds with bovine hemoglobin through surface molecularly imprinting technology. The resulting amino-functionalized silica surface molecularly imprinted polymers were characterized using scanning electron microscope, transmission electronic microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and thermogravimetric analysis. Results showed that the as-synthesized imprinted polymers exhibited spherical morphology and favorable thermal stability. The binding adsorption experiments showed that the imprinted polymers can reach equilibrium within 1 h. The Langmuir isotherm and pseudo-second-order kinetic model fitted the adsorption data well. Meanwhile, the imprinted polymers possessed a maximum binding capacity up to 90.3 mg/g and highly selectivity for the recognition of bovine hemoglobin. Moreover, such high binding capacity and selectivity retained after eight cycles, indicating the good stability and reusability of the imprinted polymers. Finally, successful application in the selective recognition of bovine hemoglobin from a real bovine blood sample indicated that the imprinted polymers displayed great potentials in efficient purification and separation of target proteins. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Highly nonlinear organic crystal OHQ-T for efficient ultra-broadband terahertz wave generation beyond 10 THz.

PubMed

Kang, Bong Joo; Baek, In Hyung; Lee, Seung-Heon; Kim, Won Tae; Lee, Seung-Jun; Jeong, Young Uk; Kwon, O-Pil; Rotermund, Fabian

2016-05-16

We report on efficient generation of ultra-broadband terahertz (THz) waves via optical rectification in a novel nonlinear organic crystal with acentric core structure, i.e. 2-(4-hydroxystyryl)-1-methylquinolinium 4-methylbenzenesulfonate (OHQ-T), which possesses an ideal molecular structure leading to a maximized nonlinear optical response for near-infrared-pumped THz wave generation. By systematic studies on wavelength-dependent phase-matching conditions in OHQ-T crystals of different thicknesses we are able to generate coherent THz waves with a high peak-to-peak electric field amplitude of up to 650 kV/cm and an upper cut-off frequency beyond 10 THz. High optical-to-THz conversion efficiency of 0.31% is achieved by efficient index matching with a selective pumping at 1300 nm.

Surface Polarity and Self-Structured Nanogrooves Collaboratively Oriented Molecular Packing for High Crystallinity toward Efficient Charge Transport.

PubMed

Ji, Deyang; Xu, Xiaomin; Jiang, Longfeng; Amirjalayer, Saeed; Jiang, Lang; Zhen, Yonggang; Zou, Ye; Yao, Yifan; Dong, Huanli; Yu, Junsheng; Fuchs, Harald; Hu, Wenping

2017-02-22

Efficient charge transport in organic semiconductors is essential for construction of high performance optoelectronic devices. Herein, for the first time, we demonstrate that poly(amic acid) (PAA), a facilely deposited and annealing-free dielectric layer, can tailor the growth of organic semiconductor films with large area and high crystallinity toward efficient charge transport and high mobility in their thin film transistors. Pentacene is used as a model system to demonstrate the concept with mobility up to 30.6 cm 2 V -1 s -1 , comparable to its high quality single crystal devices. The structure of PAA has corrugations with OH groups pointing out of the surface, and the presence of an amide bond further allows adjacent polymer strands to interact via hydrogen bonding, leading to a self-rippled surface perpendicular to the corrugation. On the other hand, the strong polar groups (-COOH/-CONH) of PAA could provide repulsive forces between PAA and pentacene, which results in the vertical orientation of pentacene on the dielectric surface. Indeed, in comparison with its imidized counterpart polyimide (PI), PAA dielectric significantly enhances the film crystallinity, drastically increases the domain size, and decreases the interface trap density, giving rise to superior device performance with high mobility. This concept can be extended to more organic semiconducting systems, e.g., 2,6-diphenylanthracene (DPA), tetracene, copper phthalocyanine (CuPc), and copper hexadecafluorophthalocyanine (F 16 CuPc), demonstrating the general applicability. The results show the importance of combining surface nanogrooves with the strong polarity in orienting the molecular arrangement for high crystallinity toward efficient charge transport in organic semiconductors.

Perspective: Rapid synthesis of complex oxides by combinatorial molecular beam epitaxy

DOE PAGES

A. T. Bollinger; Wu, J.; Bozovic, I.

2016-03-15

In this study, the molecular beam epitaxy(MBE) technique is well known for producing atomically smooth thin films as well as impeccable interfaces in multilayers of many different materials. In particular, molecular beam epitaxy is well suited to the growth of complex oxides, materials that hold promise for many applications. Rapid synthesis and high throughput characterization techniques are needed to tap into that potential most efficiently. We discuss our approach to doing that, leaving behind the traditional one-growth-one-compound scheme and instead implementing combinatorial oxide molecular beam epitaxy in a custom built system.

Essential energy space random walk via energy space metadynamics method to accelerate molecular dynamics simulations

NASA Astrophysics Data System (ADS)

Li, Hongzhi; Min, Donghong; Liu, Yusong; Yang, Wei

2007-09-01

To overcome the possible pseudoergodicity problem, molecular dynamic simulation can be accelerated via the realization of an energy space random walk. To achieve this, a biased free energy function (BFEF) needs to be priori obtained. Although the quality of BFEF is essential for sampling efficiency, its generation is usually tedious and nontrivial. In this work, we present an energy space metadynamics algorithm to efficiently and robustly obtain BFEFs. Moreover, in order to deal with the associated diffusion sampling problem caused by the random walk in the total energy space, the idea in the original umbrella sampling method is generalized to be the random walk in the essential energy space, which only includes the energy terms determining the conformation of a region of interest. This essential energy space generalization allows the realization of efficient localized enhanced sampling and also offers the possibility of further sampling efficiency improvement when high frequency energy terms irrelevant to the target events are free of activation. The energy space metadynamics method and its generalization in the essential energy space for the molecular dynamics acceleration are demonstrated in the simulation of a pentanelike system, the blocked alanine dipeptide model, and the leucine model.

Watershed processing of atmospheric polychlorinated biphenyl inputs.

PubMed

Rowe, Amy A; Totten, Lisa A; Cavallo, Gregory I; Yagecic, John R

2007-04-01

Indirect atmospheric deposition of PCBs was examined in subwatersheds of the Delaware River Estuary. Tributary PCB loads and atmospheric PCB concentrations were used to understand the pass-through efficiencies for nine rivers/ creeks for which PCB inputs appeared to be dominated by atmospheric deposition. The pass-through efficiency, E, was calculated from tributary loads and atmospheric deposition fluxes. Unfortunately, uncertainties in the gaseous and dry particle deposition velocities, vg and vd, respectively, render the calculated atmospheric deposition fluxes highly uncertain. In order to circumvent this problem, export of PCBs from the watershed was related directly to atmospheric PCB concentrations via a new mass transfer coefficient, the watershed delivery rate or vws, which describes the process by which the watershed transfers PCBs from the airto the River's main stem. vws increases with increasing chlorination and is significantly correlated with vapor pressure. This trend suggests that the transfer of PCBs from the atmosphere to the River via the watershed is more efficient for high molecular weight PCBs than for low molecular weight PCBs. This may indicate that the selected watersheds are at or close to equilibrium with respect to gaseous exchange of PCBs, such that lower molecular weight congeners undergo substantial revolatilization after deposition. The magnitude of the pass-through efficiency, E, depends on the deposition velocities used to calculate the atmospheric deposition flux, but when congener-specific deposition velocities are used, E is independent of vapor pressure and is relatively constant at about 3%.

Application of a molecular beacon based real-time isothermal amplification (MBRTIA) technology for simultaneous detection of Bacillus cereus and Staphylococcus aureus.

PubMed

Mandappa, I M; Joglekar, Prasanna; Manonmani, H K

2015-07-01

A multiplex real-time isothermal amplification assay was developed using molecular beacons for the detection of Bacillus cereus and Staphylococcus aureus by targeting four important virulence genes. A correlation between targeting highly accessible DNA sequences and isothermal amplification based molecular beacon efficiency and sensitivity was demonstrated using phi(Φ)29 DNA polymerase at a constant isothermal temperature of 30 °C. It was very selective and consistently detected down to 10(1) copies of DNA. The specificity and sensitivity of this assay, when tested with pure culture were high, surpassing those of currently used PCR assays for the detection of these organisms. The molecular beacon based real-time isothermal amplification (MBRTIA) assay could be carried out entirely in 96 well plates or well strips, enabling a rapid and high-throughput detection of food borne pathogens.

High sensitivity optical molecular imaging system

NASA Astrophysics Data System (ADS)

An, Yu; Yuan, Gao; Huang, Chao; Jiang, Shixin; Zhang, Peng; Wang, Kun; Tian, Jie

2018-02-01

Optical Molecular Imaging (OMI) has the advantages of high sensitivity, low cost and ease of use. By labeling the regions of interest with fluorescent or bioluminescence probes, OMI can noninvasively obtain the distribution of the probes in vivo, which play the key role in cancer research, pharmacokinetics and other biological studies. In preclinical and clinical application, the image depth, resolution and sensitivity are the key factors for researchers to use OMI. In this paper, we report a high sensitivity optical molecular imaging system developed by our group, which can improve the imaging depth in phantom to nearly 5cm, high resolution at 2cm depth, and high image sensitivity. To validate the performance of the system, special designed phantom experiments and weak light detection experiment were implemented. The results shows that cooperated with high performance electron-multiplying charge coupled device (EMCCD) camera, precision design of light path system and high efficient image techniques, our OMI system can simultaneously collect the light-emitted signals generated by fluorescence molecular imaging, bioluminescence imaging, Cherenkov luminance and other optical imaging modality, and observe the internal distribution of light-emitting agents fast and accurately.

Interaction Entropy: A New Paradigm for Highly Efficient and Reliable Computation of Protein-Ligand Binding Free Energy.

PubMed

Duan, Lili; Liu, Xiao; Zhang, John Z H

2016-05-04

Efficient and reliable calculation of protein-ligand binding free energy is a grand challenge in computational biology and is of critical importance in drug design and many other molecular recognition problems. The main challenge lies in the calculation of entropic contribution to protein-ligand binding or interaction systems. In this report, we present a new interaction entropy method which is theoretically rigorous, computationally efficient, and numerically reliable for calculating entropic contribution to free energy in protein-ligand binding and other interaction processes. Drastically different from the widely employed but extremely expensive normal mode method for calculating entropy change in protein-ligand binding, the new method calculates the entropic component (interaction entropy or -TΔS) of the binding free energy directly from molecular dynamics simulation without any extra computational cost. Extensive study of over a dozen randomly selected protein-ligand binding systems demonstrated that this interaction entropy method is both computationally efficient and numerically reliable and is vastly superior to the standard normal mode approach. This interaction entropy paradigm introduces a novel and intuitive conceptual understanding of the entropic effect in protein-ligand binding and other general interaction systems as well as a practical method for highly efficient calculation of this effect.

Enabling High Efficiency Nanoplasmonics with Novel Nanoantenna Architectures

PubMed Central

Cohen, Moshik; Shavit, Reuven; Zalevsky, Zeev

2015-01-01

Surface plasmon polaritons (SPPs) are propagating excitations that arise from coupling of light with collective electron oscillations. Characterized by high field intensity and nanometric dimensions, SPPs fashion rapid expansion of interest from fundamental and applicative perspectives. However, high metallic losses at optical frequencies still make nanoplasmonics impractical when high absolute efficiency is paramount, with major challenge is efficient plasmon generation in deep nanoscale. Here we introduce the Plantenna, the first reported nanodevice with the potential of addressing these limitations utilizing novel plasmonic architecture. The Plantenna has simple 2D structure, ultracompact dimensions and is fabricated on Silicon chip for future CMOS integration. We design the Plantenna to feed channel (20 nm × 20 nm) nanoplasmonic waveguides, achieving 52% coupling efficiency with Plantenna dimensions of λ3/17,000. We theoretically and experimentally show that the Plantenna enormously outperforms dipole couplers, achieving 28 dB higher efficiency with broad polarization diversity and huge local field enhancement. Our findings confirm the Plantenna as enabling device for high efficiency plasmonic technologies such as quantum nanoplasmonics, molecular strong coupling and plasmon nanolasers. PMID:26620270

Oligomer Molecules for Efficient Organic Photovoltaics.

PubMed

Lin, Yuze; Zhan, Xiaowei

2016-02-16

Solar cells, a renewable, clean energy technology that efficiently converts sunlight into electricity, are a promising long-term solution for energy and environmental problems caused by a mass of production and the use of fossil fuels. Solution-processed organic solar cells (OSCs) have attracted much attention in the past few years because of several advantages, including easy fabrication, low cost, lightweight, and flexibility. Now, OSCs exhibit power conversion efficiencies (PCEs) of over 10%. In the early stage of OSCs, vapor-deposited organic dye materials were first used in bilayer heterojunction devices in the 1980s, and then, solution-processed polymers were introduced in bulk heterojunction (BHJ) devices. Relative to polymers, vapor-deposited small molecules offer potential advantages, such as a defined molecular structure, definite molecular weight, easy purification, mass-scale production, and good batch-to-batch reproducibility. However, the limited solubility and high crystallinity of vapor-deposited small molecules are unfavorable for use in solution-processed BHJ OSCs. Conversely, polymers have good solution-processing and film-forming properties and are easily processed into flexible devices, whereas their polydispersity of molecular weights and difficulty in purification results in batch to batch variation, which may hamper performance reproducibility and commercialization. Oligomer molecules (OMs) are monodisperse big molecules with intermediate molecular weights (generally in the thousands), and their sizes are between those of small molecules (generally with molecular weights <1000) and polymers (generally with molecular weights >10000). OMs not only overcome shortcomings of both vapor-deposited small molecules and solution-processed polymers, but also combine their advantages, such as defined molecular structure, definite molecular weight, easy purification, mass-scale production, good batch-to-batch reproducibility, good solution processability, and film-forming properties. Therefore, OMs are a good choice for solution-processed reproducible OSCs toward scalable commercialized applications. Considerable efforts have been dedicated to developing new OM electron donors and electron acceptors for OSCs. So far, the highest PCEs of solution-processed OSCs based on OM donors and acceptors are 9-10% and 6-7%, respectively. OM materials have become promising alternatives to polymer and/or fullerene materials for efficient and stable OSCs. In this Account, we present a brief survey of the recent developments in solution-processable OM electron donors and acceptors and their application in OSCs. Rational design of OMs with star- and linear-shaped structures based on triphenylamine, benzodithiophene, and indacenodithiophene units and their impacts on device performance are discussed. Structure-property relationships are also proposed. Furthermore, the remaining challenges and the key research directions in the near future are also addressed. In the next years, an interdisciplinary approach involving novel OM materials, especially electron acceptor materials, accurate morphology optimization, and advanced device technologies will probably bring high-efficiency and stable OSCs to final commercialization.

Nanoscale tailor-made membranes for precise and rapid molecular sieve separation.

PubMed

Wang, Jing; Zhu, Junyong; Zhang, Yatao; Liu, Jindun; Van der Bruggen, Bart

2017-03-02

The precise and rapid separation of different molecules from aqueous, organic solutions and gas mixtures is critical to many technologies in the context of resource-saving and sustainable development. The strength of membrane-based technologies is well recognized and they are extensively applied as cost-effective, highly efficient separation techniques. Currently, empirical-based approaches, lacking an accurate nanoscale control, are used to prepare the most advanced membranes. In contrast, nanoscale control renders the membrane molecular specificity (sub-2 nm) necessary for efficient and rapid molecular separation. Therefore, as a growing trend in membrane technology, the field of nanoscale tailor-made membranes is highlighted in this review. An in-depth analysis of the latest advances in tailor-made membranes for precise and rapid molecule sieving is given, along with an outlook to future perspectives of such membranes. Special attention is paid to the established processing strategies, as well as the application of molecular dynamics (MD) simulation in nanoporous membrane design. This review will provide useful guidelines for future research in the development of nanoscale tailor-made membranes with a precise and rapid molecular sieve separation property.

The Chromosome Microdissection and Microcloning Technique.

PubMed

Zhang, Ying-Xin; Deng, Chuan-Liang; Hu, Zan-Min

2016-01-01

Chromosome microdissection followed by microcloning is an efficient tool combining cytogenetics and molecular genetics that can be used for the construction of the high density molecular marker linkage map and fine physical map, the generation of probes for chromosome painting, and the localization and cloning of important genes. Here, we describe a modified technique to microdissect a single chromosome, paint individual chromosomes, and construct single-chromosome DNA libraries.

Efficient multidimensional free energy calculations for ab initio molecular dynamics using classical bias potentials

NASA Astrophysics Data System (ADS)

VandeVondele, Joost; Rothlisberger, Ursula

2000-09-01

We present a method for calculating multidimensional free energy surfaces within the limited time scale of a first-principles molecular dynamics scheme. The sampling efficiency is enhanced using selected terms of a classical force field as a bias potential. This simple procedure yields a very substantial increase in sampling accuracy while retaining the high quality of the underlying ab initio potential surface and can thus be used for a parameter free calculation of free energy surfaces. The success of the method is demonstrated by the applications to two gas phase molecules, ethane and peroxynitrous acid, as test case systems. A statistical analysis of the results shows that the entire free energy landscape is well converged within a 40 ps simulation at 500 K, even for a system with barriers as high as 15 kcal/mol.

Introduction of Molecular Building Blocks to Improve the Stability of Metal-Organic Frameworks for Efficient Mercury Removal.

PubMed

Jiang, Shu-Yi; He, Wen-Wen; Li, Shun-Li; Su, Zhong-Min; Lan, Ya-Qian

2018-05-21

With expanding human needs, many heavy metals were mined, smelted, processed, and manufactured for commercialization, which caused serious environmental pollutions. Currently, many adsorption materials are applied in the field of adsorption of heavy metals. Among them, the principle of many mercury adsorbents is based on the interaction between mercury and sulfur. Here, a S-containing metal-organic framework NENU-400 was synthesized for effective mercury extraction. Unfortunately, the skeleton of NENU-400 collapsed easily when exposed to the mercury liquid solution. To improve the stability, a synthetic strategy installing molecular building blocks (MBBs) into the channels was used. Modified by the MBBs, a more stable nanoporous framework was synthesized, which not only exhibits a high capacity of saturation mercury uptake but also shows high selectivity and efficient recyclability.

Molecular Identification of Date Palm Cultivars Using Random Amplified Polymorphic DNA (RAPD) Markers.

PubMed

Al-Khalifah, Nasser S; Shanavaskhan, A E

2017-01-01

Ambiguity in the total number of date palm cultivars across the world is pointing toward the necessity for an enumerative study using standard morphological and molecular markers. Among molecular markers, DNA markers are more suitable and ubiquitous to most applications. They are highly polymorphic in nature, frequently occurring in genomes, easy to access, and highly reproducible. Various molecular markers such as restriction fragment length polymorphism (RFLP), amplified fragment length polymorphism (AFLP), simple sequence repeats (SSR), inter-simple sequence repeats (ISSR), and random amplified polymorphic DNA (RAPD) markers have been successfully used as efficient tools for analysis of genetic variation in date palm. This chapter explains a stepwise protocol for extracting total genomic DNA from date palm leaves. A user-friendly protocol for RAPD analysis and a table showing the primers used in different molecular techniques that produce polymorphisms in date palm are also provided.

Stability of high-mass molecular libraries: the role of the oligoporphyrin core

PubMed Central

Sezer, Uĝur; Schmid, Philipp; Felix, Lukas; Mayor, Marcel; Arndt, Markus

2015-01-01

Molecular beam techniques are a key to many experiments in physical chemistry and quantum optics. In particular, advanced matter-wave experiments with high-mass molecules profit from the availability of slow, neutral and mass-selected molecular beams that are sufficiently stable to remain intact during laser heating and photoionization mass spectrometry. We present experiments on the photostability with molecular libraries of tailored oligoporphyrins with masses up to 25 000 Da. We compare two fluoroalkylsulfanyl-functionalized libraries based on two different molecular cores that offer the same number of anchor points for functionalization but differ in their geometry and electronic properties. A pentaporphyrin core stabilizes a library of chemically well-defined molecules with more than 1600 atoms. They can be neutrally desorbed with velocities as low as 20 m/s and efficiently analyzed in photoionization mass spectrometry. Copyright © 2015 John Wiley & Sons, Ltd. PMID:25601698

Molecular imaging needles: dual-modality optical coherence tomography and fluorescence imaging of labeled antibodies deep in tissue

PubMed Central

Scolaro, Loretta; Lorenser, Dirk; Madore, Wendy-Julie; Kirk, Rodney W.; Kramer, Anne S.; Yeoh, George C.; Godbout, Nicolas; Sampson, David D.; Boudoux, Caroline; McLaughlin, Robert A.

2015-01-01

Molecular imaging using optical techniques provides insight into disease at the cellular level. In this paper, we report on a novel dual-modality probe capable of performing molecular imaging by combining simultaneous three-dimensional optical coherence tomography (OCT) and two-dimensional fluorescence imaging in a hypodermic needle. The probe, referred to as a molecular imaging (MI) needle, may be inserted tens of millimeters into tissue. The MI needle utilizes double-clad fiber to carry both imaging modalities, and is interfaced to a 1310-nm OCT system and a fluorescence imaging subsystem using an asymmetrical double-clad fiber coupler customized to achieve high fluorescence collection efficiency. We present, to the best of our knowledge, the first dual-modality OCT and fluorescence needle probe with sufficient sensitivity to image fluorescently labeled antibodies. Such probes enable high-resolution molecular imaging deep within tissue. PMID:26137379

ls1 mardyn: The Massively Parallel Molecular Dynamics Code for Large Systems.

PubMed

Niethammer, Christoph; Becker, Stefan; Bernreuther, Martin; Buchholz, Martin; Eckhardt, Wolfgang; Heinecke, Alexander; Werth, Stephan; Bungartz, Hans-Joachim; Glass, Colin W; Hasse, Hans; Vrabec, Jadran; Horsch, Martin

2014-10-14

The molecular dynamics simulation code ls1 mardyn is presented. It is a highly scalable code, optimized for massively parallel execution on supercomputing architectures and currently holds the world record for the largest molecular simulation with over four trillion particles. It enables the application of pair potentials to length and time scales that were previously out of scope for molecular dynamics simulation. With an efficient dynamic load balancing scheme, it delivers high scalability even for challenging heterogeneous configurations. Presently, multicenter rigid potential models based on Lennard-Jones sites, point charges, and higher-order polarities are supported. Due to its modular design, ls1 mardyn can be extended to new physical models, methods, and algorithms, allowing future users to tailor it to suit their respective needs. Possible applications include scenarios with complex geometries, such as fluids at interfaces, as well as nonequilibrium molecular dynamics simulation of heat and mass transfer.

Subtle Monte Carlo Updates in Dense Molecular Systems.

PubMed

Bottaro, Sandro; Boomsma, Wouter; E Johansson, Kristoffer; Andreetta, Christian; Hamelryck, Thomas; Ferkinghoff-Borg, Jesper

2012-02-14

Although Markov chain Monte Carlo (MC) simulation is a potentially powerful approach for exploring conformational space, it has been unable to compete with molecular dynamics (MD) in the analysis of high density structural states, such as the native state of globular proteins. Here, we introduce a kinetic algorithm, CRISP, that greatly enhances the sampling efficiency in all-atom MC simulations of dense systems. The algorithm is based on an exact analytical solution to the classic chain-closure problem, making it possible to express the interdependencies among degrees of freedom in the molecule as correlations in a multivariate Gaussian distribution. We demonstrate that our method reproduces structural variation in proteins with greater efficiency than current state-of-the-art Monte Carlo methods and has real-time simulation performance on par with molecular dynamics simulations. The presented results suggest our method as a valuable tool in the study of molecules in atomic detail, offering a potential alternative to molecular dynamics for probing long time-scale conformational transitions.

Machine learning of accurate energy-conserving molecular force fields.

PubMed

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E; Poltavsky, Igor; Schütt, Kristof T; Müller, Klaus-Robert

2017-05-01

Using conservation of energy-a fundamental property of closed classical and quantum mechanical systems-we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol -1 for energies and 1 kcal mol -1 Å̊ -1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

Machine learning of accurate energy-conserving molecular force fields

PubMed Central

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel E.; Poltavsky, Igor; Schütt, Kristof T.; Müller, Klaus-Robert

2017-01-01

Using conservation of energy—a fundamental property of closed classical and quantum mechanical systems—we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio molecular dynamics (AIMD) trajectories. The GDML implementation is able to reproduce global potential energy surfaces of intermediate-sized molecules with an accuracy of 0.3 kcal mol−1 for energies and 1 kcal mol−1 Å̊−1 for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative molecular dynamics simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods. PMID:28508076

Unexpectedly high pressure for molecular dissociation in liquid hydrogen by electronic simulation.

PubMed

Mazzola, Guglielmo; Yunoki, Seiji; Sorella, Sandro

2014-03-19

The study of the high pressure phase diagram of hydrogen has continued with renewed effort for about one century as it remains a fundamental challenge for experimental and theoretical techniques. Here we employ an efficient molecular dynamics based on the quantum Monte Carlo method, which can describe accurately the electronic correlation and treat a large number of hydrogen atoms, allowing a realistic and reliable prediction of thermodynamic properties. We find that the molecular liquid phase is unexpectedly stable, and the transition towards a fully atomic liquid phase occurs at much higher pressure than previously believed. The old standing problem of low-temperature atomization is, therefore, still far from experimental reach.

Measuring molecular biomarkers in epidemiologic studies: laboratory techniques and biospecimen considerations.

PubMed

Erickson, Heidi S

2012-09-28

The future of personalized medicine depends on the ability to efficiently and rapidly elucidate a reliable set of disease-specific molecular biomarkers. High-throughput molecular biomarker analysis methods have been developed to identify disease risk, diagnostic, prognostic, and therapeutic targets in human clinical samples. Currently, high throughput screening allows us to analyze thousands of markers from one sample or one marker from thousands of samples and will eventually allow us to analyze thousands of markers from thousands of samples. Unfortunately, the inherent nature of current high throughput methodologies, clinical specimens, and cost of analysis is often prohibitive for extensive high throughput biomarker analysis. This review summarizes the current state of high throughput biomarker screening of clinical specimens applicable to genetic epidemiology and longitudinal population-based studies with a focus on considerations related to biospecimens, laboratory techniques, and sample pooling. Copyright © 2012 John Wiley & Sons, Ltd.

Divalent cation interactions with oligogalacturonides.

PubMed

Cescutti, P; Rizzo, R

2001-07-01

The conformational properties of high and low molecular weight galacturonides were investigated in relation to the ability of oligomers with degree of polymerization >10 to act as elicitors of plant defense mechanisms. Oligomers from polygalacturonate were obtained by means of enzymatic hydrolysis. Two fractions exhibiting high and low average degrees of polymerization were isolated by solvent fractionation and characterized by means of electrospray mass spectrometry. The conformational behaviors of the two fractions were investigated in the presence of different divalent cations using circular dichroism. Calcium, copper, and zinc ions were able to induce a conformational transition in both fractions. When in the presence of the high molecular weight fraction, copper and zinc ions were much more effective than calcium ions, whereas the efficiency was much reduced with low molecular weight oligomers.

Highly Polarized Fluorescent Illumination Using Liquid Crystal Phase.

PubMed

Gim, Min-Jun; Turlapati, Srikanth; Debnath, Somen; Rao, Nandiraju V S; Yoon, Dong Ki

2016-02-10

Liquid crystal (LC) materials are currently the dominant electronic materials in display technology because of the ease of control of molecular orientation using an electric field. However, this technology requires the fabrication of two polarizers to create operational displays, reducing light transmission efficiency below 10%. It is therefore desirable to develop new technologies to enhance the light efficiency while maintaining or improving other properties such as the modulation speed of the molecular orientation. Here we report a uniaxial-oriented B7 smectic liquid crystalline film, using fluorescent bent-core LC molecules, a chemically modified substrate, and an in-plane electric field. A LC droplet under homeotropic boundary conditions of air/LC as well as LC/substrate exhibits large focal conic like optical textures. The in-plane electric field induced uniaxial orientation of the LC molecules, in which molecular polar directors are aligned in the direction of the electric field. This highly oriented LC film exhibits linearly polarized luminescence and microsecond time-scale modulation characteristics. The resultant device is both cheap and easy to fabricate and thus has great potential for electro-optic applications, including LC displays, bioimaging systems, and optical communications.

Efficient Conformational Sampling in Explicit Solvent Using a Hybrid Replica Exchange Molecular Dynamics Method

DTIC Science & Technology

2011-12-01

REMD while reproducing the energy landscape of explicit solvent simulations . ’ INTRODUCTION Molecular dynamics (MD) simulations of proteins can pro...Mongan, J.; McCammon, J. A. Accelerated molecular dynamics : a promising and efficient simulation method for biomolecules. J. Chem. Phys. 2004, 120 (24...Chemical Theory and Computation ARTICLE (8) Abraham,M. J.; Gready, J. E. Ensuringmixing efficiency of replica- exchange molecular dynamics simulations . J

One-Step Borylation of 1,3-Diaryloxybenzenes Towards Efficient Materials for Organic Light-Emitting Diodes.

PubMed

Hirai, Hiroki; Nakajima, Kiichi; Nakatsuka, Soichiro; Shiren, Kazushi; Ni, Jingping; Nomura, Shintaro; Ikuta, Toshiaki; Hatakeyama, Takuji

2015-11-09

The development of a one-step borylation of 1,3-diaryloxybenzenes, yielding novel boron-containing polycyclic aromatic compounds, is reported. The resulting boron-containing compounds possess high singlet-triplet excitation energies as a result of localized frontier molecular orbitals induced by boron and oxygen. Using these compounds as a host material, we successfully prepared phosphorescent organic light-emitting diodes exhibiting high efficiency and adequate lifetimes. Moreover, using the present one-step borylation, we succeeded in the synthesis of an efficient, thermally activated delayed fluorescence emitter and boron-fused benzo[6]helicene. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Inductively coupled plasma mass spectrometry (ICP MS): a versatile tool.

PubMed

Ammann, Adrian A

2007-04-01

Inductively coupled plasma (ICP) mass spectrometry (MS) is routinely used in many diverse research fields such as earth, environmental, life and forensic sciences and in food, material, chemical, semiconductor and nuclear industries. The high ion density and the high temperature in a plasma provide an ideal atomizer and element ionizer for all types of samples and matrices introduced by a variety of specialized devices. Outstanding properties such as high sensitivity (ppt-ppq), relative salt tolerance, compound-independent element response and highest quantitation accuracy lead to the unchallenged performance of ICP MS in efficiently detecting, identifying and reliably quantifying trace elements. The increasing availability of relevant reference compounds and high separation selectivity extend the molecular identification capability of ICP MS hyphenated to species-specific separation techniques. While molecular ion source MS is specialized in determining the structure of unknown molecules, ICP MS is an efficient and highly sensitive tool for target-element orientated discoveries of relevant and unknown compounds. This special-feature, tutorial article presents the principle and advantages of ICP MS, highlighting these using examples from recently published investigations. Copyright 2007 John Wiley & Sons, Ltd.

Design of Ultrathin Pt-Based Multimetallic Nanostructures for Efficient Oxygen Reduction Electrocatalysis.

PubMed

Lai, Jianping; Guo, Shaojun

2017-12-01

Nanocatalysts with high platinum (Pt) utilization efficiency are attracting extensive attention for oxygen reduction reactions (ORR) conducted at the cathode of fuel cells. Ultrathin Pt-based multimetallic nanostructures show obvious advantages in accelerating the sluggish cathodic ORR due to their ultrahigh Pt utilization efficiency. A focus on recent important developments is provided in using wet chemistry techniques for making/tuning the multimetallic nanostructures with high Pt utilization efficiency for boosting ORR activity and durability. First, new synthetic methods for multimetallic core/shell nanoparticles with ultrathin shell sizes for achieving highly efficient ORR catalysts are reviewed. To obtain better ORR activity and stability, multimetallic nanowires or nanosheets with well-defined structure and surface are further highlighted. Furthermore, ultrathin Pt-based multimetallic nanoframes that feature 3D molecularly accessible surfaces for achieving more efficient ORR catalysis are discussed. Finally, the remaining challenges and outlooks for the future will be provided for this promising research field. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Light Extraction From Solution-Based Processable Electrophosphorescent Organic Light-Emitting Diodes

NASA Astrophysics Data System (ADS)

Krummacher, Benjamin C.; Mathai, Mathew; So, Franky; Choulis, Stelios; Choong, And-En, Vi

2007-06-01

Molecular dye dispersed solution processable blue emitting organic light-emitting devices have been fabricated and the resulting devices exhibit efficiency as high as 25 cd/A. With down-conversion phosphors, white emitting devices have been demonstrated with peak efficiency of 38 cd/A and luminous efficiency of 25 lm/W. The high efficiencies have been a product of proper tuning of carrier transport, optimization of the location of the carrier recombination zone and, hence, microcavity effect, efficient down-conversion from blue to white light, and scattering/isotropic remission due to phosphor particles. An optical model has been developed to investigate all these effects. In contrast to the common misunderstanding that light out-coupling efficiency is about 22% and independent of device architecture, our device data and optical modeling results clearly demonstrated that the light out-coupling efficiency is strongly dependent on the exact location of the recombination zone. Estimating the device internal quantum efficiencies based on external quantum efficiencies without considering the device architecture could lead to erroneous conclusions.

Machine Learning of Accurate Energy-Conserving Molecular Force Fields

NASA Astrophysics Data System (ADS)

Chmiela, Stefan; Tkatchenko, Alexandre; Sauceda, Huziel; Poltavsky, Igor; Schütt, Kristof; Müller, Klaus-Robert; GDML Collaboration

Efficient and accurate access to the Born-Oppenheimer potential energy surface (PES) is essential for long time scale molecular dynamics (MD) simulations. Using conservation of energy - a fundamental property of closed classical and quantum mechanical systems - we develop an efficient gradient-domain machine learning (GDML) approach to construct accurate molecular force fields using a restricted number of samples from ab initio MD trajectories (AIMD). The GDML implementation is able to reproduce global potential-energy surfaces of intermediate-size molecules with an accuracy of 0.3 kcal/mol for energies and 1 kcal/mol/Å for atomic forces using only 1000 conformational geometries for training. We demonstrate this accuracy for AIMD trajectories of molecules, including benzene, toluene, naphthalene, malonaldehyde, ethanol, uracil, and aspirin. The challenge of constructing conservative force fields is accomplished in our work by learning in a Hilbert space of vector-valued functions that obey the law of energy conservation. The GDML approach enables quantitative MD simulations for molecules at a fraction of cost of explicit AIMD calculations, thereby allowing the construction of efficient force fields with the accuracy and transferability of high-level ab initio methods.

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

Lee, Jongbok; Li, Huanbin; Kalin, Alexander J.

Well-defined, fused-ring aromatic oligomers represent promising candidates for the fundamental understanding and application of advanced carbon-rich materials, though bottom-up synthesis and structure–property correlation of these compounds remain challenging. In this work, an efficient synthetic route was employed to construct extended benzo[k]tetraphene-derived oligomers with up to 13 fused rings. The molecular and electronic structures of these compounds were clearly elucidated. Precise correlation of molecular sizes and crystallization dynamics was established, thus demonstrating the pivotal balance between intermolecular interaction and molecular mobility for optimized processing of highly ordered solids of these extended conjugated molecules.

Polyethylenimine Interfacial Layers in Inverted Organic Photovoltaic Devices: Effects of Ethoxylation and Molecular Weight on Efficiency and Temporal Stability.

PubMed

Courtright, Brett A E; Jenekhe, Samson A

2015-12-02

We report a comparative study of polyethylenimine (PEI) and ethoxylated-polyethylenimine (PEIE) cathode buffer layers in high performance inverted organic photovoltaic devices. The work function of the indium-tin oxide (ITO)/zinc oxide (ZnO) cathode was reduced substantially (Δφ = 0.73-1.09 eV) as the molecular weight of PEI was varied from 800 g mol(-1) to 750 000 g mol(-1) compared with the observed much smaller reduction when using a PEIE thin film (Δφ = 0.56 eV). The reference inverted polymer solar cells based on the small band gap polymer PBDTT-FTTE (ITO/ZnO/PBDTT-FTTE:PC70BM/MoO3/Ag), without a cathode buffer layer, had an average power conversion efficiency (PCE) of 6.06 ± 0.22%. Incorporation of a PEIE cathode buffer layer in the same PBDTT-FTTE:PC70BM blend devices gave an enhanced performance with a PCE of 7.37 ± 0.53%. In contrast, an even greater photovoltaic efficiency with a PCE of 8.22 ± 0.10% was obtained in similar PBDTT-FTTE:PC70BM blend solar cells containing a PEI cathode buffer layer. The temporal stability of the inverted polymer solar cells was found to increase with increasing molecular weight of the cathode buffer layer. The results show that PEI is superior to PEIE as a cathode buffer layer in high performance organic photovoltaic devices and that the highest molecular weight PEI interlayer provides the highest temporal stability.

Design considerations for highly effective fluorescence excitation and detection optical systems for molecular diagnostics

NASA Astrophysics Data System (ADS)

Kasper, Axel; Van Hille, Herbert; Kuk, Sola

2018-02-01

Modern instruments for molecular diagnostics are continuously optimized for diagnostic accuracy, versatility and throughput. The latest progress in LED technology together with tailored optics solutions allows developing highly efficient photonics engines perfectly adapted to the sample under test. Super-bright chip-on-board LED light sources are a key component for such instruments providing maximum luminous intensities in a multitude of narrow spectral bands. In particular the combination of white LEDs with other narrow band LEDs allows achieving optimum efficiency outperforming traditional Xenon light sources in terms of energy consumption, heat dissipation in the system, and switching time between spectral channels. Maximum sensitivity of the diagnostic system can only be achieved with an optimized optics system for the illumination and imaging of the sample. The illumination beam path must be designed for optimum homogeneity across the field while precisely limiting the angular distribution of the excitation light. This is a necessity for avoiding spill-over to the detection beam path and guaranteeing the efficiency of the spectral filtering. The imaging optics must combine high spatial resolution, high light collection efficiency and optimized suppression of excitation light for good signal-to-noise ratio. In order to achieve minimum cross-talk between individual wells in the sample, the optics design must also consider the generation of stray light and the formation of ghost images. We discuss what parameters and limitations have to be considered in an integrated system design approach covering the full path from the light source to the detector.

Highly efficient pseudomorphic InGaAs/GaAs/AlGaAs single quantum well lasers for monolithic integration

NASA Technical Reports Server (NTRS)

Larsson, A.; Cody, J.; Forouhar, S.; Lang, R. J.

1990-01-01

Highly efficient ridge waveguide pseudomorphic single quantum well lasers, emitting at 980 nm, have been fabricated from an In(0.2)Ga(0.8)As/GaAs/AlGaAs graded-index separate confinement heterostructure grown by molecular beam epitaxy. The laterial index guiding provided by the ridge reduces the anomalously large lateral loss of optical power found in gain-guided structures, thereby reducing the internal loss by more than 50 percent. The low threshold current (7.6 mA) and high differential quantum efficiency (79 percent) obtained under continuous operation as well as the transparency of the GaAs substrate to the emitted radiation render these lasers attractive for Ga-As-based optoelectronic integration.

Strained-layer InGaAs/GaAs/AlGaAs single quantum well lasers with high internal quantum efficiency

NASA Technical Reports Server (NTRS)

Larsson, Anders; Cody, Jeffrey; Lang, Robert J.

1989-01-01

Low threshold current density strained-layer In(0.2)Ga(0.8)As/GaAs/AlGaAs single quantum well lasers, emitting at 980 nm, have been grown by molecular beam epitaxy. Contrary to what has been reported for broad-area lasers with pseudomorphic InGaAs active layers grown by metalorganic chemical vapor deposition, these layers exhibit a high internal quantum efficiency (about 90 percent). The maximum external differential quantum efficiency is 70 percent, limited by an anomalously high internal loss possibly caused by a large lateral spreading of the optical mode. In addition, experimental results supporting the theoretically predicted strain-induced reduction of the valence-band nonparabolicity and density of states are presented.

ChemTS: an efficient python library for de novo molecular generation.

PubMed

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

Solar-pumped electronic-to-vibrational energy transfer lasers

NASA Technical Reports Server (NTRS)

Harries, W. L.; Wilson, J. W.

1981-01-01

The possibility of using solar-pumped lasers as solar energy converters is examined. The absorbing media considered are halogens or halogen compounds, which are dissociated to yield excited atoms, which then hand over energy to a molecular lasing medium. Estimates of the temperature effects for a Br2-CO2-He system with He as the cooling gas are given. High temperatures can cause the lower energy levels of the CO2 laser transition to be filled. The inverted populations are calculated and lasing should be possible. However, the efficiency is less than 0.001. Examination of other halogen-molecular lasant combinations (where the rate coefficients are known) indicate efficiencies in all cases of less than 0.005.

ChemTS: an efficient python library for de novo molecular generation

NASA Astrophysics Data System (ADS)

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-12-01

Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS.

A Molecular Ni-complex Containing Tetrahedral Nickel Selenide Core as Highly Efficient Electrocatalyst for Water Oxidation.

PubMed

Masud, Jahangir; Ioannou, Polydoros-Chrysovalantis; Levesanos, Nikolaos; Kyritsis, Panayotis; Nath, Manashi

2016-11-23

We report the highly efficient catalytic activity of a transition metal selenide-based coordination complex, [Ni{(SeP i Pr 2 ) 2 N} 2 ], (1) for oxygen evolution and hydrogen evolution reactions (OER and HER, respectively) in alkaline solution. Very low overpotentials of 200 mV and 310 mV were required to achieve 10 mA cm -2 for OER and HER, respectively. The overpotential for OER is one of the lowest that has been reported up to now, making this one of the best OER electrocatalysts. In addition, this molecular complex exhibits an exceptionally high mass activity (111.02 A g -1 ) and a much higher TOF value (0.26 s -1 ) at a overpotential of 300 mV. This bifunctional electrocatalyst enables water electrolysis in alkaline solutions at a cell voltage of 1.54 V. © 2016 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Advances in algal-prokaryotic wastewater treatment: A review of nitrogen transformations, reactor configurations and molecular tools.

PubMed

Wang, Meng; Keeley, Ryan; Zalivina, Nadezhda; Halfhide, Trina; Scott, Kathleen; Zhang, Qiong; van der Steen, Peter; Ergas, Sarina J

2018-07-01

The synergistic activity of algae and prokaryotic microorganisms can be used to improve the efficiency of biological wastewater treatment, particularly with regards to nitrogen removal. For example, algae can provide oxygen through photosynthesis needed for aerobic degradation of organic carbon and nitrification and harvested algal-prokaryotic biomass can be used to produce high value chemicals or biogas. Algal-prokaryotic consortia have been used to treat wastewater in different types of reactors, including waste stabilization ponds, high rate algal ponds and closed photobioreactors. This review addresses the current literature and identifies research gaps related to the following topics: 1) the complex interactions between algae and prokaryotes in wastewater treatment; 2) advances in bioreactor technologies that can achieve high nitrogen removal efficiencies in small reactor volumes, such as algal-prokaryotic biofilm reactors and enhanced algal-prokaryotic treatment systems (EAPS); 3) molecular tools that have expanded our understanding of the activities of algal and prokaryotic communities in wastewater treatment processes. Copyright © 2018 Elsevier Ltd. All rights reserved.

Abnormal strong burn-in degradation of highly efficient polymer solar cells caused by spinodal donor-acceptor demixing

PubMed Central

Li, Ning; Perea, José Darío; Kassar, Thaer; Richter, Moses; Heumueller, Thomas; Matt, Gebhard J.; Hou, Yi; Güldal, Nusret S.; Chen, Haiwei; Chen, Shi; Langner, Stefan; Berlinghof, Marvin; Unruh, Tobias; Brabec, Christoph J.

2017-01-01

The performance of organic solar cells is determined by the delicate, meticulously optimized bulk-heterojunction microstructure, which consists of finely mixed and relatively separated donor/acceptor regions. Here we demonstrate an abnormal strong burn-in degradation in highly efficient polymer solar cells caused by spinodal demixing of the donor and acceptor phases, which dramatically reduces charge generation and can be attributed to the inherently low miscibility of both materials. Even though the microstructure can be kinetically tuned for achieving high-performance, the inherently low miscibility of donor and acceptor leads to spontaneous phase separation in the solid state, even at room temperature and in the dark. A theoretical calculation of the molecular parameters and construction of the spinodal phase diagrams highlight molecular incompatibilities between the donor and acceptor as a dominant mechanism for burn-in degradation, which is to date the major short-time loss reducing the performance and stability of organic solar cells. PMID:28224984

IV INTERNATIONAL CONFERENCE ON ATOM AND MOLECULAR PULSED LASERS (AMPL'99): Efficiency of an H2—SF6 laser with electron-beam initiation of chemical reactions

NASA Astrophysics Data System (ADS)

Erofeev, M. V.; Orlovskii, Viktor M.; Skakun, V. S.; Sosnin, E. A.; Tarasenko, Viktor F.

2000-06-01

The spectral and amplitude—time characteristics of HF lasers pumped by a nonchain chemical reaction and initiated by radially convergent and planar electron beams were investigated. The principal channels leading to the formation of vibrationally excited HF molecules were analysed. It was confirmed that high efficiencies (~10%) of a nonchain HF laser may be attained only as a result of the simultaneous formation of atomic and molecular fluorine when the active mixture is acted upon by an electron beam and of the participation of molecular fluorine in population inversion. It was shown that a laser pulse has a complex spectral—temporal profile caused by the successive generation of P-lines and the overlap during the radiation pulse of both the rotational lines of the same vibrational band and of individual vibrational bands.

A combined thermal dissociation and electron impact ionization source for RIB generation

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

Alton, G.D.; Williams, C.

1995-12-31

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for RIB applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, in principle, overcome thismore » handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility (HRIBF), now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article.« less

Purely organic electroluminescent material realizing 100% conversion from electricity to light

PubMed Central

Kaji, Hironori; Suzuki, Hajime; Fukushima, Tatsuya; Shizu, Katsuyuki; Suzuki, Katsuaki; Kubo, Shosei; Komino, Takeshi; Oiwa, Hajime; Suzuki, Furitsu; Wakamiya, Atsushi; Murata, Yasujiro; Adachi, Chihaya

2015-01-01

Efficient organic light-emitting diodes have been developed using emitters containing rare metals, such as platinum and iridium complexes. However, there is an urgent need to develop emitters composed of more abundant materials. Here we show a thermally activated delayed fluorescence material for organic light-emitting diodes, which realizes both approximately 100% photoluminescence quantum yield and approximately 100% up-conversion of the triplet to singlet excited state. The material contains electron-donating diphenylaminocarbazole and electron-accepting triphenyltriazine moieties. The typical trade-off between effective emission and triplet-to-singlet up-conversion is overcome by fine-tuning the highest occupied molecular orbital and lowest unoccupied molecular orbital distributions. The nearly zero singlet–triplet energy gap, smaller than the thermal energy at room temperature, results in an organic light-emitting diode with external quantum efficiency of 29.6%. An external quantum efficiency of 41.5% is obtained when using an out-coupling sheet. The external quantum efficiency is 30.7% even at a high luminance of 3,000 cd m−2. PMID:26477390

Molecular engineering and sequential cosensitization for preventing the "trade-off" effect with photovoltaic enhancement.

PubMed

Zhang, Weiwei; Wu, Yongzhen; Li, Xin; Li, Erpeng; Song, Xiongrong; Jiang, Huiyun; Shen, Chao; Zhang, Hao; Tian, He; Zhu, Wei-Hong

2017-03-01

In dye-sensitized solar cells (DSSCs), it is essential to use rational molecular design to obtain promising photosensitizers with well-matched energy levels and narrow optical band gaps. However, the "trade-off" effect between the photocurrent and photovoltage is still a challenge. Here we report four benzoxidazole based D-A-π-A metal-free organic dyes ( WS-66 , WS-67 , WS-68 and WS-69 ) with different combinations of π-spacer units and anchoring-acceptor groups. Either extending the π-spacer or enhancing the electron acceptor can efficiently modulate the molecular energy levels, leading to a red-shift in the absorption spectra. The optimal dye, WS-69 , containing a cyclopentadithiophene (CPDT) spacer and cyanoacetic acid acceptor, shows the narrowest energy band gap, which displays a very high photocurrent density of 19.39 mA cm -2 , but suffers from a relatively low photovoltage of 696 mV, along with the so-called deleterious "trade-off" effect. A cosensitization strategy is further adopted for enhancing the device performance. Optimization of the dye loading sequence is found to be capable of simultaneously improving the photocurrent and photovoltage, and distinctly preventing the "trade-off" effect. The superior cosensitized cell exhibits an excellent power-conversion efficiency (PCE) of 10.09% under one-sun irradiation, and 11.12% under 0.3 sun irradiation, which constitutes a great achievement in that the efficiency of a pure metal-free organic dye with iodine electrolyte can exceed 11% even under relatively weak light irradiation. In contrast with the previous cosensitization strategy which mostly focused on compensation of light-harvesting, we propose a novel cosensitization architecture, in which the large molecular-sized, high photocurrent dye WS-69 takes charge of broadening the light-harvesting region to generate a high short-circuit current ( J SC ) while the small molecular-sized, high photovoltage dye WS-5 is responsible for retarding charge recombination to generate a high open-circuit voltage ( V OC ). In addition, adsorption amount and photo-stability studies suggest that the cyano group in the anchoring acceptor is important for the stability since it is beneficial towards decreasing the LUMO levels and enhancing the binding of dyes onto TiO 2 nanocrystals.

Insight into D-A-π-A Structured Sensitizers: A Promising Route to Highly Efficient and Stable Dye-Sensitized Solar Cells.

PubMed

Wu, Yongzhen; Zhu, Wei-Hong; Zakeeruddin, Shaik M; Grätzel, Michael

2015-05-13

The dye-sensitized solar cell (DSSC) is one of the most promising photovoltaic technologies with potential of low cost, light weight, and good flexibility. The practical application of DSSCs requires further improvement in power conversion efficiency and long-term stability. Recently, significant progress has been witnessed in DSSC research owing to the novel concept of the D-A-π-A motif for the molecular engineering of organic photosensitizers. New organic and porphyrin dyes based on the D-A-π-A motif can not only enhance photovoltaic performance, but also improve durability in DSSC applications. This Spotlight on Applications highlights recent advances in the D-A-π-A-based photosensitizers, specifically focusing on the mechanism of efficiency and stability enhancements. Also, we find insight into the additional acceptor as well as the trade-off of long wavelength response. The basic principles are involved in molecular engineering of efficient D-A-π-A sensitizers, providing a clear road map showing how to modulate the energy bands, rationally extending the response wavelength, and optimizing photovoltaic efficiency step by step.

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

Li, Yang; Tu, Xingchen; Wang, Hao

The electronic efficiency and binding energy of contacts formed between graphene electrodes and poly-aromatic hydrocarbon (PAH) anchoring groups have been investigated by the non-equilibrium Green’s function formalism combined with density functional theory. Our calculations show that PAH molecules always bind in the interior and at the edge of graphene in the AB stacking manner, and that the binding energy increases following the increase of the number of carbon and hydrogen atoms constituting the PAH molecule. When we move to analyzing the electronic transport properties of molecular junctions with a six-carbon alkyne chain as the central molecule, the electronic efficiency ofmore » the graphene-PAH contacts is found to depend on the energy gap between the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of the corresponding PAH anchoring group, rather than its size. To be specific, the smaller is the HOMO-LUMO gap of the PAH anchoring group, the higher is the electronic efficiency of the graphene-PAH contact. Although the HOMO-LUMO gap of a PAH molecule depends on its specific configuration, PAH molecules with similar atomic structures show a decreasing trend for their HOMO-LUMO gap as the number of fused benzene rings increases. Therefore, graphene-conjugated molecule-graphene junctions with high-binding and high-conducting graphene-PAH contacts can be realized by choosing appropriate PAH anchor groups with a large area and a small HOMO-LUMO gap.« less

Virtual Tissues in Toxicology

EPA Science Inventory

New approaches are vital for efficiently evaluating human health risk of thousands of chemicals in commerce. In vitro models offer a high-throughput approach for assaying chemical-induced molecular and cellular changes; however, bridging these perturbations to in vivo effects acr...

Synthetic Zeolites and Other Microporous Oxide Molecular Sieves

NASA Astrophysics Data System (ADS)

Sherman, John D.

1999-03-01

Use of synthetic zeolites and other microporous oxides since 1950 has improved insulated windows, automobile air-conditioning, refrigerators, air brakes on trucks, laundry detergents, etc. Their large internal pore volumes, molecular-size pores, regularity of crystal structures, and the diverse framework chemical compositions allow "tailoring" of structure and properties. Thus, highly active and selective catalysts as well as adsorbents and ion exchangers with high capacities and selectivities were developed. In the petroleum refining and petrochemical industries, zeolites have made possible cheaper and lead-free gasoline, higher performance and lower-cost synthetic fibers and plastics, and many improvements in process efficiency and quality and in performance. Zeolites also help protect the environment by improving energy efficiency, reducing automobile exhaust and other emissions, cleaning up hazardous wastes (including the Three Mile Island nuclear power plant and other radioactive wastes), and, as specially tailored desiccants, facilitating the substitution of new refrigerants for the ozone-depleting chlorofluorocarbons banned by the Montreal Protocol.

Enzymatic and acidic degradation of high molecular weight dextran into low molecular weight and its characterizations using novel Diffusion-ordered NMR spectroscopy.

PubMed

Iqbal, Samina; Marchetti, Roberta; Aman, Afsheen; Silipo, Alba; Qader, Shah Ali Ul; Molinaro, Antonio

2017-10-01

Low molecular weight fractions were derived from native high molecular weight dextran produced by Leuconostoc mesenteroides KIBGE-IB26. Structural characterization of native and low molecular weight fractions obtained after acidic and enzymatic hydrolysis was done using FTIR and NMR spectroscopy. The molecular weight was estimated using Diffusion Ordered NMR spectroscopy. Native dextran (892kDa) is composed of α-(1→6) glycosidic linkage along with α-(1→3) branching. Major proportion of 528kDa dextran was obtained after prolong enzymatic hydrolysis however, an effective acidic treatment at pH-1.4 up to 02 and 04h of exposure resulted in the formation of 77kDa and 57kDa, respectively. The increment in pH from 1.4 to 1.8 lowered the hydrolysis efficiency and resulted in the formation of 270kDa dextran fraction. The results suggest that derived low molecular weight water soluble fractions can be utilized as a drug delivery carrier along with multiple application relating pharmaceutical industries. Copyright © 2017 Elsevier B.V. All rights reserved.

Photoprecursor Approach Enables Preparation of Well-Performing Bulk-Heterojunction Layers Comprising a Highly Aggregating Molecular Semiconductor.

PubMed

Suzuki, Mitsuharu; Yamaguchi, Yuji; Takahashi, Kohei; Takahira, Katsuya; Koganezawa, Tomoyuki; Masuo, Sadahiro; Nakayama, Ken-ichi; Yamada, Hiroko

2016-04-06

Active-layer morphology critically affects the performance of organic photovoltaic cells, and thus its optimization is a key toward the achievement of high-efficiency devices. However, the optimization of active-layer morphology is sometimes challenging because of the intrinsic properties of materials such as strong self-aggregating nature or low miscibility. This study postulates that the "photoprecursor approach" can serve as an effective means to prepare well-performing bulk-heterojunction (BHJ) layers containing highly aggregating molecular semiconductors. In the photoprecursor approach, a photoreactive precursor compound is solution-deposited and then converted in situ to a semiconducting material. This study employs 2,6-di(2-thienyl)anthracene (DTA) and [6,6]-phenyl-C71-butyric acid methyl ester as p- and n-type materials, respectively, in which DTA is generated by the photoprecursor approach from the corresponding α-diketone-type derivative DTADK. When only chloroform is used as a cast solvent, the photovoltaic performance of the resulting BHJ films is severely limited because of unfavorable film morphology. The addition of a high-boiling-point cosolvent, o-dichlorobenzene (o-DCB), to the cast solution leads to significant improvement such that the resulting active layers afford up to approximately 5 times higher power conversion efficiencies. The film structure is investigated by two-dimensional grazing-incident wide-angle X-ray diffraction, atomic force microscopy, and fluorescence microspectroscopy to demonstrate that the use of o-DCB leads to improvement in film crystallinity and increase in charge-carrier generation efficiency. The change in film structure is assumed to originate from dynamic molecular motion enabled by the existence of solvent during the in situ photoreaction. The unique features of the photoprecursor approach will be beneficial in extending the material and processing scopes for the development of organic thin-film devices.

A polymer tandem solar cell with 10.6% power conversion efficiency.

PubMed

You, Jingbi; Dou, Letian; Yoshimura, Ken; Kato, Takehito; Ohya, Kenichiro; Moriarty, Tom; Emery, Keith; Chen, Chun-Chao; Gao, Jing; Li, Gang; Yang, Yang

2013-01-01

An effective way to improve polymer solar cell efficiency is to use a tandem structure, as a broader part of the spectrum of solar radiation is used and the thermalization loss of photon energy is minimized. In the past, the lack of high-performance low-bandgap polymers was the major limiting factor for achieving high-performance tandem solar cell. Here we report the development of a high-performance low bandgap polymer (bandgap <1.4 eV), poly[2,7-(5,5-bis-(3,7-dimethyloctyl)-5H-dithieno[3,2-b:2',3'-d]pyran)-alt-4,7-(5,6-difluoro-2,1,3-benzothia diazole)] with a bandgap of 1.38 eV, high mobility, deep highest occupied molecular orbital. As a result, a single-junction device shows high external quantum efficiency of >60% and spectral response that extends to 900 nm, with a power conversion efficiency of 7.9%. The polymer enables a solution processed tandem solar cell with certified 10.6% power conversion efficiency under standard reporting conditions (25 °C, 1,000 Wm(-2), IEC 60904-3 global), which is the first certified polymer solar cell efficiency over 10%.

A polymer tandem solar cell with 10.6% power conversion efficiency

PubMed Central

You, Jingbi; Dou, Letian; Yoshimura, Ken; Kato, Takehito; Ohya, Kenichiro; Moriarty, Tom; Emery, Keith; Chen, Chun-Chao; Gao, Jing; Li, Gang; Yang, Yang

2013-01-01

An effective way to improve polymer solar cell efficiency is to use a tandem structure, as a broader part of the spectrum of solar radiation is used and the thermalization loss of photon energy is minimized. In the past, the lack of high-performance low-bandgap polymers was the major limiting factor for achieving high-performance tandem solar cell. Here we report the development of a high-performance low bandgap polymer (bandgap <1.4 eV), poly[2,7-(5,5-bis-(3,7-dimethyloctyl)-5H-dithieno[3,2-b:2′,3′-d]pyran)-alt-4,7-(5,6-difluoro-2,1,3-benzothia diazole)] with a bandgap of 1.38 eV, high mobility, deep highest occupied molecular orbital. As a result, a single-junction device shows high external quantum efficiency of >60% and spectral response that extends to 900 nm, with a power conversion efficiency of 7.9%. The polymer enables a solution processed tandem solar cell with certified 10.6% power conversion efficiency under standard reporting conditions (25 °C, 1,000 Wm−2, IEC 60904-3 global), which is the first certified polymer solar cell efficiency over 10%. PMID:23385590

Amyloodiniosis in cultured Dicentrarchus labrax: parasitological and molecular diagnosis, and an improved treatment protocol.

PubMed

Bessat, Mohamed; Fadel, Amr

2018-06-19

Amyloodinium ocellatum, the causative agent of amyloodiniosis (marine velvet, velvet disease), affects marine and brackish fish in various warm and temperate habitats. We recorded disease outbreaks with high morbidity and mortality rates in marine-cultured European seabass Dicentrarchus labrax fry at 2 locations in northwest Egypt. The sudden outbreak, high morbidity and mortality rates, and skin lesions with a velvety appearance in affected fish all indicated A. ocellatum infection. This was further confirmed by microscopic findings of the parasitic stage (trophonts) in skin and gill smears. While ecological factors including water temperature and salinity were all amenable to parasite establishment and propagation, mortality rates differed between the 2 farms, with rates of mortality well correlated with prevalence and intensity of A. ocellatum infections. Characterization by PCR targeting rDNA gene fragments and subsequent DNA sequencing and phylogenetic analysis further confirmed the molecular identity of the A. ocellatum isolate, which was genetically similar to isolates from other geographical locations. Finally, an improved treatment method using dual hyposalination and copper sulfate exposure to increase the efficiency and decrease the toxicity of copper sulfate was tested. The gradual reduction in water salinity coupled with copper sulfate treatment was more efficient at controlling the disease than only applying copper sulfate. To our knowledge, this is the first parasitological and molecular characterization of A. ocellatum in marine cultures in Egypt. The high molecular identity and close phylogenetic relationship further confirmed the monophyletic nature of A. ocellatum isolates.

High Throughput, High Yield Fabrication of High Quantum Efficiency Back-Illuminated Photon Counting, Far UV, UV, and Visible Detector Arrays

NASA Technical Reports Server (NTRS)

Nikzad, Shouleh; Hoenk, M. E.; Carver, A. G.; Jones, T. J.; Greer, F.; Hamden, E.; Goodsall, T.

2013-01-01

In this paper we discuss the high throughput end-to-end post fabrication processing of high performance delta-doped and superlattice-doped silicon imagers for UV, visible, and NIR applications. As an example, we present our results on far ultraviolet and ultraviolet quantum efficiency (QE) in a photon counting, detector array. We have improved the QE by nearly an order of magnitude over microchannel plates (MCPs) that are the state-of-the-art UV detectors for many NASA space missions as well as defense applications. These achievements are made possible by precision interface band engineering of Molecular Beam Epitaxy (MBE) and Atomic Layer Deposition (ALD).

A nanoscale study of charge extraction in organic solar cells: the impact of interfacial molecular configurations.

PubMed

Tang, Fu-Ching; Wu, Fu-Chiao; Yen, Chia-Te; Chang, Jay; Chou, Wei-Yang; Gilbert Chang, Shih-Hui; Cheng, Horng-Long

2015-01-07

In the optimization of organic solar cells (OSCs), a key problem lies in the maximization of charge carriers from the active layer to the electrodes. Hence, this study focused on the interfacial molecular configurations in efficient OSC charge extraction by theoretical investigations and experiments, including small molecule-based bilayer-heterojunction (sm-BLHJ) and polymer-based bulk-heterojunction (p-BHJ) OSCs. We first examined a well-defined sm-BLHJ model system of OSC composed of p-type pentacene, an n-type perylene derivative, and a nanogroove-structured poly(3,4-ethylenedioxythiophene) (NS-PEDOT) hole extraction layer. The OSC with NS-PEDOT shows a 230% increment in the short circuit current density compared with that of the conventional planar PEDOT layer. Our theoretical calculations indicated that small variations in the microscopic intermolecular interaction among these interfacial configurations could induce significant differences in charge extraction efficiency. Experimentally, different interfacial configurations were generated between the photo-active layer and the nanostructured charge extraction layer with periodic nanogroove structures. In addition to pentacene, poly(3-hexylthiophene), the most commonly used electron-donor material system in p-BHJ OSCs was also explored in terms of its possible use as a photo-active layer. Local conductive atomic force microscopy was used to measure the nanoscale charge extraction efficiency at different locations within the nanogroove, thus highlighting the importance of interfacial molecular configurations in efficient charge extraction. This study enriches understanding regarding the optimization of the photovoltaic properties of several types of OSCs by conducting appropriate interfacial engineering based on organic/polymer molecular orientations. The ultimate power conversion efficiency beyond at least 15% is highly expected when the best state-of-the-art p-BHJ OSCs are combined with present arguments.

Turbocharged molecular discovery of OLED emitters: from high-throughput quantum simulation to highly efficient TADF devices

NASA Astrophysics Data System (ADS)

Gómez-Bombarelli, Rafael; Aguilera-Iparraguirre, Jorge; Hirzel, Timothy D.; Ha, Dong-Gwang; Einzinger, Markus; Wu, Tony; Baldo, Marc A.; Aspuru-Guzik, Alán.

2016-09-01

Discovering new OLED emitters requires many experiments to synthesize candidates and test performance in devices. Large scale computer simulation can greatly speed this search process but the problem remains challenging enough that brute force application of massive computing power is not enough to successfully identify novel structures. We report a successful High Throughput Virtual Screening study that leveraged a range of methods to optimize the search process. The generation of candidate structures was constrained to contain combinatorial explosion. Simulations were tuned to the specific problem and calibrated with experimental results. Experimentalists and theorists actively collaborated such that experimental feedback was regularly utilized to update and shape the computational search. Supervised machine learning methods prioritized candidate structures prior to quantum chemistry simulation to prevent wasting compute on likely poor performers. With this combination of techniques, each multiplying the strength of the search, this effort managed to navigate an area of molecular space and identify hundreds of promising OLED candidate structures. An experimentally validated selection of this set shows emitters with external quantum efficiencies as high as 22%.

Star cluster formation in a turbulent molecular cloud self-regulated by photoionization feedback

NASA Astrophysics Data System (ADS)

Gavagnin, Elena; Bleuler, Andreas; Rosdahl, Joakim; Teyssier, Romain

2017-12-01

Most stars in the Galaxy are believed to be formed within star clusters from collapsing molecular clouds. However, the complete process of star formation, from the parent cloud to a gas-free star cluster, is still poorly understood. We perform radiation-hydrodynamical simulations of the collapse of a turbulent molecular cloud using the RAMSES-RT code. Stars are modelled using sink particles, from which we self-consistently follow the propagation of the ionizing radiation. We study how different feedback models affect the gas expulsion from the cloud and how they shape the final properties of the emerging star cluster. We find that the star formation efficiency is lower for stronger feedback models. Feedback also changes the high-mass end of the stellar mass function. Stronger feedback also allows the establishment of a lower density star cluster, which can maintain a virial or sub-virial state. In the absence of feedback, the star formation efficiency is very high, as well as the final stellar density. As a result, high-energy close encounters make the cluster evaporate quickly. Other indicators, such as mass segregation, statistics of multiple systems and escaping stars confirm this picture. Observations of young star clusters are in best agreement with our strong feedback simulation.

Implementing Molecular Dynamics on Hybrid High Performance Computers - Particle-Particle Particle-Mesh

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

Brown, W Michael; Kohlmeyer, Axel; Plimpton, Steven J

The use of accelerators such as graphics processing units (GPUs) has become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high-performance computers, machines with nodes containing more than one type of floating-point processor (e.g. CPU and GPU), are now becoming more prevalent due to these advantages. In this paper, we present a continuation of previous work implementing algorithms for using accelerators into the LAMMPS molecular dynamics software for distributed memory parallel hybrid machines. In our previous work, we focused on acceleration for short-range models with anmore » approach intended to harness the processing power of both the accelerator and (multi-core) CPUs. To augment the existing implementations, we present an efficient implementation of long-range electrostatic force calculation for molecular dynamics. Specifically, we present an implementation of the particle-particle particle-mesh method based on the work by Harvey and De Fabritiis. We present benchmark results on the Keeneland InfiniBand GPU cluster. We provide a performance comparison of the same kernels compiled with both CUDA and OpenCL. We discuss limitations to parallel efficiency and future directions for improving performance on hybrid or heterogeneous computers.« less

Quantum Dot-Fullerene Based Molecular Beacon Nanosensors for Rapid, Highly Sensitive Nucleic Acid Detection.

PubMed

Liu, Ye; Kannegulla, Akash; Wu, Bo; Cheng, Li-Jing

2018-05-15

Spherical fullerene (C 60 ) can quench the fluorescence of a quantum dot (QD) through energy transfer and charge transfer processes, with the quenching efficiency regulated by the number of proximate C 60 on each QD. With the quenching property and its small size compared with other nanoparticle-based quenchers, it is advantageous to group a QD reporter and multiple C 60 -labeled oligonucleotide probes to construct a molecular beacon (MB) probe for sensitive, robust nucleic acid detection. We demonstrated a rapid, high-sensitivity DNA detection method using the nanosensors composed of QD-C 60 based MBs carried by magnetic nanoparticles (MNPs). The assay was accelerated by first dispersing the nanosensors in analytes for highly efficient DNA capture resulting from short-distance 3-dimensional diffusion of targets to the sensor surface and then concentrating the nanosensors to a substrate by magnetic force to amplify the fluorescence signal for target quantification. The enhanced mass transport enabled a rapid detection (< 10 min) with a small sample volume (1-10 µl). The high signal-to-noise ratio produced by the QD-C 60 pairs and magnetic concentration yielded a detection limit of 100 fM (~106 target DNA copies for a 10 µl analyte). The rapid, sensitive, label-free detection method will benefit the applications in point-of-care molecular diagnostic technologies.

Adaptive sampling strategies with high-throughput molecular dynamics

NASA Astrophysics Data System (ADS)

Clementi, Cecilia

Despite recent significant hardware and software developments, the complete thermodynamic and kinetic characterization of large macromolecular complexes by molecular simulations still presents significant challenges. The high dimensionality of these systems and the complexity of the associated potential energy surfaces (creating multiple metastable regions connected by high free energy barriers) does not usually allow to adequately sample the relevant regions of their configurational space by means of a single, long Molecular Dynamics (MD) trajectory. Several different approaches have been proposed to tackle this sampling problem. We focus on the development of ensemble simulation strategies, where data from a large number of weakly coupled simulations are integrated to explore the configurational landscape of a complex system more efficiently. Ensemble methods are of increasing interest as the hardware roadmap is now mostly based on increasing core counts, rather than clock speeds. The main challenge in the development of an ensemble approach for efficient sampling is in the design of strategies to adaptively distribute the trajectories over the relevant regions of the systems' configurational space, without using any a priori information on the system global properties. We will discuss the definition of smart adaptive sampling approaches that can redirect computational resources towards unexplored yet relevant regions. Our approaches are based on new developments in dimensionality reduction for high dimensional dynamical systems, and optimal redistribution of resources. NSF CHE-1152344, NSF CHE-1265929, Welch Foundation C-1570.

Implementing Molecular Dynamics for Hybrid High Performance Computers - 1. Short Range Forces

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

Brown, W Michael; Wang, Peng; Plimpton, Steven J

The use of accelerators such as general-purpose graphics processing units (GPGPUs) have become popular in scientific computing applications due to their low cost, impressive floating-point capabilities, high memory bandwidth, and low electrical power requirements. Hybrid high performance computers, machines with more than one type of floating-point processor, are now becoming more prevalent due to these advantages. In this work, we discuss several important issues in porting a large molecular dynamics code for use on parallel hybrid machines - 1) choosing a hybrid parallel decomposition that works on central processing units (CPUs) with distributed memory and accelerator cores with shared memory,more » 2) minimizing the amount of code that must be ported for efficient acceleration, 3) utilizing the available processing power from both many-core CPUs and accelerators, and 4) choosing a programming model for acceleration. We present our solution to each of these issues for short-range force calculation in the molecular dynamics package LAMMPS. We describe algorithms for efficient short range force calculation on hybrid high performance machines. We describe a new approach for dynamic load balancing of work between CPU and accelerator cores. We describe the Geryon library that allows a single code to compile with both CUDA and OpenCL for use on a variety of accelerators. Finally, we present results on a parallel test cluster containing 32 Fermi GPGPUs and 180 CPU cores.« less

Ultra-Fast RAFT-HDA Click Conjugation: An Efficient Route to High Molecular Weight Block Copolymers.

PubMed

Inglis, Andrew J; Stenzel, Martina H; Barner-Kowollik, Christopher

2009-11-02

The use of the reversible addition fragmentation chain transfer-hetero Diels-Alder (RAFT-HDA) click reaction for the modular construction of block copolymers is extended to the generation of high molecular weight materials. Cyclopentadienyl end-functionalized polystyrene (PS-Cp) prepared via both atom transfer radical polymerization (ATRP) and the RAFT process are conjugated to poly(isobornyl acrylate) (PiBoA) (also prepared via RAFT polymerization) to achieve well-defined block copolymers with molecular weights ranging from 34 000 to over 100 000 g · mol(-1) and with small polydispersities (PDI < 1.2). The conjugation reactions proceeded in a very rapid fashion (less than 10 min in the majority of cases) under ambient conditions of temperature and atmosphere. The present study demonstrates-for the first time-that RAFT-HDA click chemistry can provide access to high molecular weight block copolymers in a simple and straight-forward fashion. Copyright © 2009 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Benchmarking of HPCC: A novel 3D molecular representation combining shape and pharmacophoric descriptors for efficient molecular similarity assessments.

PubMed

Karaboga, Arnaud S; Petronin, Florent; Marchetti, Gino; Souchet, Michel; Maigret, Bernard

2013-04-01

Since 3D molecular shape is an important determinant of biological activity, designing accurate 3D molecular representations is still of high interest. Several chemoinformatic approaches have been developed to try to describe accurate molecular shapes. Here, we present a novel 3D molecular description, namely harmonic pharma chemistry coefficient (HPCC), combining a ligand-centric pharmacophoric description projected onto a spherical harmonic based shape of a ligand. The performance of HPCC was evaluated by comparison to the standard ROCS software in a ligand-based virtual screening (VS) approach using the publicly available directory of useful decoys (DUD) data set comprising over 100,000 compounds distributed across 40 protein targets. Our results were analyzed using commonly reported statistics such as the area under the curve (AUC) and normalized sum of logarithms of ranks (NSLR) metrics. Overall, our HPCC 3D method is globally as efficient as the state-of-the-art ROCS software in terms of enrichment and slightly better for more than half of the DUD targets. Since it is largely admitted that VS results depend strongly on the nature of the protein families, we believe that the present HPCC solution is of interest over the current ligand-based VS methods. Copyright © 2013 Elsevier Inc. All rights reserved.

Sequencing small genomic targets with high efficiency and extreme accuracy

PubMed Central

Schmitt, Michael W.; Fox, Edward J.; Prindle, Marc J.; Reid-Bayliss, Kate S.; True, Lawrence D.; Radich, Jerald P.; Loeb, Lawrence A.

2015-01-01

The detection of minority variants in mixed samples demands methods for enrichment and accurate sequencing of small genomic intervals. We describe an efficient approach based on sequential rounds of hybridization with biotinylated oligonucleotides, enabling more than one-million fold enrichment of genomic regions of interest. In conjunction with error correcting double-stranded molecular tags, our approach enables the quantification of mutations in individual DNA molecules. PMID:25849638

Linking the mobilization of dissolved organic matter in catchments and its removal in drinking water treatment to its molecular characteristics.

PubMed

Raeke, Julia; Lechtenfeld, Oliver J; Tittel, Jörg; Oosterwoud, Marieke R; Bornmann, Katrin; Reemtsma, Thorsten

2017-04-15

Drinking water reservoirs in the Northern Hemisphere are largely affected by the decadal-long increase in riverine dissolved organic carbon (DOC) concentrations. The removal of DOC in drinking water treatment is costly and predictions are needed to link DOC removal efficiency to its mobilization in catchments, both of which are determined by the molecular composition. To study the effect of hydrological events and land use on the molecular characteristics of dissolved organic matter (DOM), 36 samples from three different catchment areas in the German low mountain ranges, with DOC concentrations ranging from 3 to 32 mg L -1 , were examined. Additionally, nine pairs of samples from downstream drinking water reservoirs were analyzed before and after flocculation. The molecular composition and the age of DOM were analyzed using ultrahigh resolution Fourier transform ion cyclotron resonance mass spectrometry (FTICR-MS) and radiocarbon ( 14 C) analysis. At elevated discharge in a forested catchment comparatively younger, more oxygenated and unsaturated molecules of higher molecular weight were preferentially mobilized, likely linked to the reductive mobilization of iron. DOM with highly similar molecular characteristics (O/C ratio > 0.5, m/z > 500) could also be efficiently removed through flocculation in drinking water treatment. The proportion of DOM removed through flocculation ranged between 43% and 73% of DOC and was highest at elevated discharge. In catchment areas with a higher percentage of grassland and agriculture a higher proportion of DOM molecules containing sulfur and nitrogen was detected, which in turn could be less efficiently flocculated. Altogether, it was shown that DOM that is released during large hydrological events can be efficiently flocculated again, suggesting a reversal of similar chemical mechanisms in both processes. Since the occurrence of heavy rainfall events is predicted to increase in the future, event-driven mobilization of DOC may continue to challenge drinking water production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Effect of Aggregation on Squaraine Fullerene Bulk-Heterojunction Organic Photovoltaic Devices

NASA Astrophysics Data System (ADS)

Jalan, Ishita

Organic photovoltaics (OPV) offer great promise as a low-cost renewable energy source, the relative low efficiency still challenges its commercialization potential. Small conjugated molecules like Squaraine (SQ) molecules show promising advancement in organic photovoltaics (OPV). Advantages of SQ over other materials is that it has a high extinction coefficient (>105), decent photo-stability, good synthetic reproducibility, and tunable molecular structure. With small chemical modifications, the squaraines can have substantial impact on photophysical properties and aggregation pattern, and thus on operational OPV efficiency. The squaraine molecule that will be studied in this work is a symmetric aniline-based squaraine with n-hexyl chain on the molecular arm with di hydroxyl substituents on the aniline, this will be referred to DHSQ(OH) 2. In this work, the assignment of the monomer and aggregate peak is discussed. It is known that crystallinity is important for efficient charge transport and exciton diffusion in the BHJ, this thesis focuses on thermal and solvent vapor annealing the as-cast films to reduce the amorphous regions. It is observed that crystallinity is improved but often at the expense of larger crystal size. Therefore, to achieve optimal OPV efficiency, this tradeoff is controlled to improve the crystallinity while maintaining a small, highly mixed BHJ morphology.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics.

PubMed

Yang, Qian; Sing-Long, Carlos A; Reed, Evan J

2017-08-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

PubMed Central

Sing-Long, Carlos A.

2017-01-01

We propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. In contrast, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our method on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. The framework described in this work paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates. PMID:28989618

Learning reduced kinetic Monte Carlo models of complex chemistry from molecular dynamics

DOE PAGES

Yang, Qian; Sing-Long, Carlos A.; Reed, Evan J.

2017-06-19

Here, we propose a novel statistical learning framework for automatically and efficiently building reduced kinetic Monte Carlo (KMC) models of large-scale elementary reaction networks from data generated by a single or few molecular dynamics simulations (MD). Existing approaches for identifying species and reactions from molecular dynamics typically use bond length and duration criteria, where bond duration is a fixed parameter motivated by an understanding of bond vibrational frequencies. Conversely, we show that for highly reactive systems, bond duration should be a model parameter that is chosen to maximize the predictive power of the resulting statistical model. We demonstrate our methodmore » on a high temperature, high pressure system of reacting liquid methane, and show that the learned KMC model is able to extrapolate more than an order of magnitude in time for key molecules. Additionally, our KMC model of elementary reactions enables us to isolate the most important set of reactions governing the behavior of key molecules found in the MD simulation. We develop a new data-driven algorithm to reduce the chemical reaction network which can be solved either as an integer program or efficiently using L1 regularization, and compare our results with simple count-based reduction. For our liquid methane system, we discover that rare reactions do not play a significant role in the system, and find that less than 7% of the approximately 2000 reactions observed from molecular dynamics are necessary to reproduce the molecular concentration over time of methane. Furthermore, we describe a framework in this work that paves the way towards a genomic approach to studying complex chemical systems, where expensive MD simulation data can be reused to contribute to an increasingly large and accurate genome of elementary reactions and rates.« less

High-Flux Carbon Molecular Sieve Membranes for Gas Separation.

PubMed

Richter, Hannes; Voss, Hartwig; Kaltenborn, Nadine; Kämnitz, Susanne; Wollbrink, Alexander; Feldhoff, Armin; Caro, Jürgen; Roitsch, Stefan; Voigt, Ingolf

2017-06-26

Carbon membranes have great potential for highly selective and cost-efficient gas separation. Carbon is chemically stable and it is relative cheap. The controlled carbonization of a polymer coating on a porous ceramic support provides a 3D carbon material with molecular sieving permeation performance. The carbonization of the polymer blend gives turbostratic carbon domains of randomly stacked together sp 2 hybridized carbon sheets as well as sp 3 hybridized amorphous carbon. In the evaluation of the carbon molecular sieve membrane, hydrogen could be separated from propane with a selectivity of 10 000 with a hydrogen permeance of 5 m 3 (STP)/(m 2 hbar). Furthermore, by a post-synthesis oxidative treatment, the permeation fluxes are increased by widening the pores, and the molecular sieve carbon membrane is transformed from a molecular sieve carbon into a selective surface flow carbon membrane with adsorption controlled performance and becomes selective for carbon dioxide. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

On the enhanced sampling over energy barriers in molecular dynamics simulations.

PubMed

Gao, Yi Qin; Yang, Lijiang

2006-09-21

We present here calculations of free energies of multidimensional systems using an efficient sampling method. The method uses a transformed potential energy surface, which allows an efficient sampling of both low and high energy spaces and accelerates transitions over barriers. It allows efficient sampling of the configuration space over and only over the desired energy range(s). It does not require predetermined or selected reaction coordinate(s). We apply this method to study the dynamics of slow barrier crossing processes in a disaccharide and a dipeptide system.

Reductive Bis-addition of Aromatic Aldehydes to α,β-Unsaturated Esters via the Use of Sm/Cu(I) in Air: A Route to the Construction of Furofuran Lignans.

PubMed

Liu, Yongjun; Tian, Guang; Li, Jingjing; Qi, Yan; Wen, Yonghong; Du, Feng

2017-06-02

The novel bis-addition of benzaldehydes to acrylates or maleates was achieved by the direct use of samarium metal with the assistance of CuI under mild conditions under dry air, and the useful 2-hydroxylalkyl-γ-butyrolactons and lignan derivatives were thus constructed with high efficiency. The key factors that influence the reaction efficiency were investigated. The use of potassium iodide and molecular sieves as additives can improve the reaction efficiency remarkably.

IONIZED GAS KINEMATICS AT HIGH RESOLUTION. V. [Ne ii], MULTIPLE CLUSTERS, HIGH EFFICIENCY STAR FORMATION, AND BLUE FLOWS IN HE 2–10

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

Beck, Sara; Turner, Jean; Lacy, John

2015-11-20

We measured the 12.8 μm [Ne ii] line in the dwarf starburst galaxy He 2–10 with the high-resolution spectrometer TEXES on the NASA IRTF. The data cube has a diffraction-limited spatial resolution of ∼1″ and a total velocity resolution, including thermal broadening, of ∼5 km s{sup −1}. This makes it possible to compare the kinematics of individual star-forming clumps and molecular clouds in the three dimensions of space and velocity, and allows us to determine star formation efficiencies. The kinematics of the ionized gas confirm that the starburst contains multiple dense clusters. From the M/R of the clusters and themore » ≃30%–40% star formation efficiencies, the clusters are likely to be bound and long lived, like globulars. Non-gravitational features in the line profiles show how the ionized gas flows through the ambient molecular material, as well as a narrow velocity feature, which we identify with the interface of the H ii region and a cold dense clump. These data offer an unprecedented view of the interaction of embedded H ii regions with their environment.« less

Highly Efficient Plastic Crystal Ionic Conductors for Solid-state Dye-sensitized Solar Cells

PubMed Central

Hwang, Daesub; Kim, Dong Young; Jo, Seong Mu; Armel, Vanessa; MacFarlane, Douglas R.; Kim, Dongho; Jang, Sung-Yeon

2013-01-01

We have developed highly efficient, ambient temperature, solid-state ionic conductors (SSICs) for dye-sensitized solar cells (DSSCs) by doping a molecular plastic crystal, succinonitrile (SN), with trialkyl-substituted imidazolium iodide salts. High performance SSICs with enhanced ionic conductivity (2–4 mScm−1) were obtained. High performance solid-state DSSCs with power conversion efficiency of 7.8% were fabricated using our SSICs combined with unique hierarchically nanostructured TiO2 sphere (TiO2-SP) photoelectrodes; these electrodes have significant macroporosity, which assists penetration of the solid electrolyte into the electrode. The performance of our solid-state DSSCs is, to the best of our knowledge, the highest reported thus far for cells using plastic crystal-based SSICs, and is comparable to that of the state-of-the-art DSSCs which use ionic liquid type electrolytes. This report provides a logical strategy for the development of efficient plastic crystal-based SSICs for DSSCs and other electrochemical devices. PMID:24343425

ChemTS: an efficient python library for de novo molecular generation

PubMed Central

Yang, Xiufeng; Zhang, Jinzhe; Yoshizoe, Kazuki; Terayama, Kei; Tsuda, Koji

2017-01-01

Abstract Automatic design of organic materials requires black-box optimization in a vast chemical space. In conventional molecular design algorithms, a molecule is built as a combination of predetermined fragments. Recently, deep neural network models such as variational autoencoders and recurrent neural networks (RNNs) are shown to be effective in de novo design of molecules without any predetermined fragments. This paper presents a novel Python library ChemTS that explores the chemical space by combining Monte Carlo tree search and an RNN. In a benchmarking problem of optimizing the octanol-water partition coefficient and synthesizability, our algorithm showed superior efficiency in finding high-scoring molecules. ChemTS is available at https://github.com/tsudalab/ChemTS. PMID:29435094

OH megamasers in high-luminosity IRAS galaxies

NASA Technical Reports Server (NTRS)

Mirabel, I. F.; Sanders, D. B.

1987-01-01

OH megamaser emission and H I and CO profiles from the distant infrared galaxies IRAS 10173 + 0828, III Zw 035, and Zw 475.056 are reported. The OH isotropic luminosities at 1667 MHz are 463, 534, and 6.6 solar luminosities, respectively. Far-infrared pumping efficiencies of the OH greater than 1 percent are found in IRAS 10173 + 0828 and III Zw 035. These two galaxies show anomalously large 1667/1665 MHz emission line ratios. OH megamasers reside in the nuclei of superluminous far-infrared galaxies that have a high content of molecular gas, high efficiency of star formation, and in some instances, a striking deficiency of atomic hydrogen.

A mechanistic approach to explore novel HDAC1 inhibitor using pharmacophore modeling, 3D- QSAR analysis, molecular docking, density functional and molecular dynamics simulation study.

PubMed

Choubey, Sanjay K; Jeyaraman, Jeyakanthan

2016-11-01

Deregulated epigenetic activity of Histone deacetylase 1 (HDAC1) in tumor development and carcinogenesis pronounces it as promising therapeutic target for cancer treatment. HDAC1 has recently captured the attention of researchers owing to its decisive role in multiple types of cancer. In the present study a multistep framework combining ligand based 3D-QSAR, molecular docking and Molecular Dynamics (MD) simulation studies were performed to explore potential compound with good HDAC1 binding affinity. Four different pharmacophore hypotheses Hypo1 (AADR), Hypo2 (AAAH), Hypo3 (AAAR) and Hypo4 (ADDR) were obtained. The hypothesis Hypo1 (AADR) with two hydrogen bond acceptors (A), one hydrogen bond donor (D) and one aromatics ring (R) was selected to build 3D-QSAR model on the basis of statistical parameter. The pharmacophore hypothesis produced a statistically significant QSAR model, with co-efficient of correlation r 2 =0.82 and cross validation correlation co-efficient q 2 =0.70. External validation result displays high predictive power with r 2 (o) value of 0.88 and r 2 (m) value of 0.58 to carry out further in silico studies. Virtual screening result shows ZINC70450932 as the most promising lead where HDAC1 interacts with residues Asp99, His178, Tyr204, Phe205 and Leu271 forming seven hydrogen bonds. A high docking score (-11.17kcal/mol) and lower docking energy -37.84kcal/mol) displays the binding efficiency of the ligand. Binding free energy calculation was done using MM/GBSA to access affinity of ligands towards protein. Density Functional Theory was employed to explore electronic features of the ligands describing intramolcular charge transfer reaction. Molecular dynamics simulation studies at 50ns display metal ion (Zn)-ligand interaction which is vital to inhibit the enzymatic activity of the protein. Copyright © 2016 Elsevier Inc. All rights reserved.

High Efficiency Molecular Delivery with Sequential Low-Energy Sonoporation Bursts

PubMed Central

Song, Kang-Ho; Fan, Alexander C.; Brlansky, John T.; Trudeau, Tammy; Gutierrez-Hartmann, Arthur; Calvisi, Michael L.; Borden, Mark A.

2015-01-01

Microbubbles interact with ultrasound to induce transient microscopic pores in the cellular plasma membrane in a highly localized thermo-mechanical process called sonoporation. Theranostic applications of in vitro sonoporation include molecular delivery (e.g., transfection, drug loading and cell labeling), as well as molecular extraction for measuring intracellular biomarkers, such as proteins and mRNA. Prior research focusing mainly on the effects of acoustic forcing with polydisperse microbubbles has identified a “soft limit” of sonoporation efficiency at 50% when including dead and lysed cells. We show here that this limit can be exceeded with the judicious use of monodisperse microbubbles driven by a physiotherapy device (1.0 MHz, 2.0 W/cm2, 10% duty cycle). We first examined the effects of microbubble size and found that small-diameter microbubbles (2 µm) deliver more instantaneous power than larger microbubbles (4 & 6 µm). However, owing to rapid fragmentation and a short half-life (0.7 s for 2 µm; 13.3 s for 6 µm), they also deliver less energy over the sonoporation time. This translates to a higher ratio of FITC-dextran (70 kDa) uptake to cell death/lysis (4:1 for 2 µm; 1:2 for 6 µm) in suspended HeLa cells after a single sonoporation. Sequential sonoporations (up to four) were consequently employed to increase molecular delivery. Peak uptake was found to be 66.1 ± 1.2% (n=3) after two sonoporations when properly accounting for cell lysis (7.0 ± 5.6%) and death (17.9 ± 2.0%), thus overcoming the previously reported soft limit. Substitution of TRITC-dextran (70 kDa) on the second sonoporation confirmed the effects were multiplicative. Overall, this study demonstrates the possibility of utilizing monodisperse small-diameter microbubbles as a means to achieve multiple low-energy sonoporation bursts for efficient in vitro cellular uptake and sequential molecular delivery. PMID:26681986

Elucidating the role of surface chemistry on cationic phosphorus dendrimer-siRNA complexation.

PubMed

Deriu, Marco A; Tsapis, Nicolas; Noiray, Magali; Grasso, Gianvito; El Brahmi, Nabil; Mignani, Serge; Majoral, Jean-Pierre; Fattal, Elias; Danani, Andrea

2018-06-14

In the field of dendrimers targeting small interfering RNA (siRNA) delivery, dendrimer structural properties, such as the flexibility/rigidity ratio, play a crucial role in the efficiency of complexation. However, advances in organic chemistry have enabled the development of dendrimers that differ only by a single atom on their surface terminals. This is the case for cationic phosphorus dendrimers functionalized with either pyrrolidinium (DP) or morpholinium (DM) terminal groups. This small change was shown to strongly affect the dendrimer-siRNA complexation, leading to more efficient anti-inflammatory effects in the case of DP. Reasons for this different behavior can hardly be inferred only by biological in vitro and in vivo experiments due to the high number of variables and complexity of the investigated biological system. However, an understanding of how small chemical surface changes may completely modify the overall dendrimer-siRNA complexation is a significant breakthrough towards the design of efficient dendrimers for nucleic acid delivery. Herein, we present experimental and computational approaches based on isothermal titration calorimetry and molecular dynamics simulations to elucidate the molecular reasons behind different efficiencies and activities of DP and DM. Results of the present research highlight how chemical surface modifications may drive the overall dendrimer-siRNA affinity by influencing enthalpic and entropic contributions of binding free energy. Moreover, this study elucidates molecular reasons related to complexation stoichiometry that may be crucial in determining the dendrimer complexation efficiency.

CO observations of nearby galaxies and the efficiency of star formation

NASA Technical Reports Server (NTRS)

Young, Judith S.

1987-01-01

The CO distributions and total molecular content of 160 galaxies were observed using the 14 meter millimeter telescope of the FCRAO. For the luminous, relatively face-on Sc galaxies, the azimuthally averaged CO distributions are centrally peaked, while for the Sb and Sa galaxies the Co distributions often exhibit central CO holes up to 5 kpc across. None of the Sc galaxies have CO distributions which resemble the Milky Way. A general correlation was found between total CO and IR luminosities in galaxies. The scatter in this relation is highly correlated with dust temperature. No strong correlation of IR luminosities was found with HI masses, and it was thereby concluded that the infrared emission is more directly tied to the molecular content of galaxies. It is suggested that galaxies which have high Star Formation Effiencies (SFEs) produce more stars per unit molecular mass, thereby increasing the average temperature of the dust in the star forming regions. Irregular galaxies and galaxies previously identified as mergers have the highest observed star formation efficiencies. For the mergers, evidence was found that the IR/CO luminosity ratio increases with the merger age estimated by Joseph and Wright (1985).

High efficiency Raman memory by suppressing radiation trapping

NASA Astrophysics Data System (ADS)

Thomas, S. E.; Munns, J. H. D.; Kaczmarek, K. T.; Qiu, C.; Brecht, B.; Feizpour, A.; Ledingham, P. M.; Walmsley, I. A.; Nunn, J.; Saunders, D. J.

2017-06-01

Raman interactions in alkali vapours are used in applications such as atomic clocks, optical signal processing, generation of squeezed light and Raman quantum memories for temporal multiplexing. To achieve a strong interaction the alkali ensemble needs both a large optical depth and a high level of spin-polarisation. We implement a technique known as quenching using a molecular buffer gas which allows near-perfect spin-polarisation of over 99.5 % in caesium vapour at high optical depths of up to ˜ 2× {10}5; a factor of 4 higher than can be achieved without quenching. We use this system to explore efficient light storage with high gain in a GHz bandwidth Raman memory.

Analog synthetic biology.

PubMed

Sarpeshkar, R

2014-03-28

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog-digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA-protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations.

Analog synthetic biology

PubMed Central

Sarpeshkar, R.

2014-01-01

We analyse the pros and cons of analog versus digital computation in living cells. Our analysis is based on fundamental laws of noise in gene and protein expression, which set limits on the energy, time, space, molecular count and part-count resources needed to compute at a given level of precision. We conclude that analog computation is significantly more efficient in its use of resources than deterministic digital computation even at relatively high levels of precision in the cell. Based on this analysis, we conclude that synthetic biology must use analog, collective analog, probabilistic and hybrid analog–digital computational approaches; otherwise, even relatively simple synthetic computations in cells such as addition will exceed energy and molecular-count budgets. We present schematics for efficiently representing analog DNA–protein computation in cells. Analog electronic flow in subthreshold transistors and analog molecular flux in chemical reactions obey Boltzmann exponential laws of thermodynamics and are described by astoundingly similar logarithmic electrochemical potentials. Therefore, cytomorphic circuits can help to map circuit designs between electronic and biochemical domains. We review recent work that uses positive-feedback linearization circuits to architect wide-dynamic-range logarithmic analog computation in Escherichia coli using three transcription factors, nearly two orders of magnitude more efficient in parts than prior digital implementations. PMID:24567476

Non-adiabatic molecular dynamics by accelerated semiclassical Monte Carlo

DOE PAGES

White, Alexander J.; Gorshkov, Vyacheslav N.; Tretiak, Sergei; ...

2015-07-07

Non-adiabatic dynamics, where systems non-radiatively transition between electronic states, plays a crucial role in many photo-physical processes, such as fluorescence, phosphorescence, and photoisomerization. Methods for the simulation of non-adiabatic dynamics are typically either numerically impractical, highly complex, or based on approximations which can result in failure for even simple systems. Recently, the Semiclassical Monte Carlo (SCMC) approach was developed in an attempt to combine the accuracy of rigorous semiclassical methods with the efficiency and simplicity of widely used surface hopping methods. However, while SCMC was found to be more efficient than other semiclassical methods, it is not yet as efficientmore » as is needed to be used for large molecular systems. Here, we have developed two new methods: the accelerated-SCMC and the accelerated-SCMC with re-Gaussianization, which reduce the cost of the SCMC algorithm up to two orders of magnitude for certain systems. In many cases shown here, the new procedures are nearly as efficient as the commonly used surface hopping schemes, with little to no loss of accuracy. This implies that these modified SCMC algorithms will be of practical numerical solutions for simulating non-adiabatic dynamics in realistic molecular systems.« less

Graphene defects induced by ion beam

NASA Astrophysics Data System (ADS)

Gawlik, Grzegorz; Ciepielewski, Paweł; Baranowski, Jacek; Jagielski, Jacek

2017-10-01

The CVD graphene deposited on the glass substrate was bombarded by molecular carbon ions C3+ C6+ hydrocarbon ions C3H4+ and atomic ions He+, C+, N+, Ar+, Kr+ Yb+. Size and density of ion induced defects were estimated from evolution of relative intensities of Raman lines D (∼1350 1/cm), G (∼1600 1/cm), and D‧ (∼1620 1/cm) with ion fluence. The efficiency of defect generation by atomic ions depend on ion mass and energy similarly as vacancy generation directly by ion predicted by SRIM simulations. However, efficiency of defect generation in graphene by molecular carbon ions is essentially higher than summarized efficiency of similar group of separate atomic carbon ions of the same energy that each carbon ion in a cluster. The evolution of the D/D‧ ratio of Raman lines intensities with ion fluence was observed. This effect may indicate evolution of defect nature from sp3-like at low fluence to a vacancy-like at high fluence. Observed ion graphene interactions suggest that the molecular ion interacts with graphene as single integrated object and should not be considered as a group of atomic ions with partial energy.

Photocatalytic oxidation of organic compounds in a hybrid system composed of a molecular catalyst and visible light-absorbing semiconductor.

PubMed

Zhou, Xu; Li, Fei; Li, Xiaona; Li, Hua; Wang, Yong; Sun, Licheng

2015-01-14

Photocatalytic oxidation of organic compounds proceeded efficiently in a hybrid system with ruthenium aqua complexes as catalysts, BiVO4 as a light absorber, [Co(NH3)5Cl](2+) as a sacrificial electron acceptor and water as an oxygen source. The photogenerated holes in the semiconductor are used to oxidize molecular catalysts into the high-valent Ru(IV)=O intermediates for 2e(-) oxidation.

Analytical applications of MIPs in diagnostic assays: future perspectives.

PubMed

Bedwell, Thomas S; Whitcombe, Michael J

2016-03-01

Many efforts have been made to produce artificial materials with biomimetic properties for applications in binding assays. Among these efforts, the technique of molecular imprinting has received much attention because of the high selectivity obtainable for molecules of interest, robustness of the produced polymers, simple and short synthesis, and excellent cost efficiency. In this review, progress in the field of molecularly imprinted sorbent assays is discussed-with a focus on work conducted from 2005 to date.

The dissection and SSR mapping of a high-temperature adult-plant stripe rust resistance gene in American spring wheat cultivar Alturas

USDA-ARS?s Scientific Manuscript database

Stripe rust is one of major diseases in wheat production worldwide. The best economic and efficient method is to utilize resistant varieties. Alturas has high-temperature adult-plant resistance. In order to determine stripe rust resistance characteristics, resistance gene combination and molecular m...

Probe molecules (PrM) approach in adverse outcome pathway (AOP) based high throughput screening (HTS): in vivo discovery for developing in vitro target methods

EPA Science Inventory

Efficient and accurate adverse outcome pathway (AOP) based high-throughput screening (HTS) methods use a systems biology based approach to computationally model in vitro cellular and molecular data for rapid chemical prioritization; however, not all HTS assays are grounded by rel...

Highly parallel single-molecule amplification approach based on agarose droplet polymerase chain reaction for efficient and cost-effective aptamer selection.

PubMed

Zhang, Wei Yun; Zhang, Wenhua; Liu, Zhiyuan; Li, Cong; Zhu, Zhi; Yang, Chaoyong James

2012-01-03

We have developed a novel method for efficiently screening affinity ligands (aptamers) from a complex single-stranded DNA (ssDNA) library by employing single-molecule emulsion polymerase chain reaction (PCR) based on the agarose droplet microfluidic technology. In a typical systematic evolution of ligands by exponential enrichment (SELEX) process, the enriched library is sequenced first, and tens to hundreds of aptamer candidates are analyzed via a bioinformatic approach. Possible candidates are then chemically synthesized, and their binding affinities are measured individually. Such a process is time-consuming, labor-intensive, inefficient, and expensive. To address these problems, we have developed a highly efficient single-molecule approach for aptamer screening using our agarose droplet microfluidic technology. Statistically diluted ssDNA of the pre-enriched library evolved through conventional SELEX against cancer biomarker Shp2 protein was encapsulated into individual uniform agarose droplets for droplet PCR to generate clonal agarose beads. The binding capacity of amplified ssDNA from each clonal bead was then screened via high-throughput fluorescence cytometry. DNA clones with high binding capacity and low K(d) were chosen as the aptamer and can be directly used for downstream biomedical applications. We have identified an ssDNA aptamer that selectively recognizes Shp2 with a K(d) of 24.9 nM. Compared to a conventional sequencing-chemical synthesis-screening work flow, our approach avoids large-scale DNA sequencing and expensive, time-consuming DNA synthesis of large populations of DNA candidates. The agarose droplet microfluidic approach is thus highly efficient and cost-effective for molecular evolution approaches and will find wide application in molecular evolution technologies, including mRNA display, phage display, and so on. © 2011 American Chemical Society

Small molecular glasses based on multiposition encapsulated phenyl benzimidazole iridium(III) complexes: toward efficient solution-processable host-free electrophosphorescent diodes.

PubMed

Xu, Hui; Yu, Dong-Hui; Liu, Le-Le; Yan, Peng-Fei; Jia, Li-Wei; Li, Guang-Ming; Yue, Zheng-Yu

2010-01-14

Three electrophosphorescent small molecular Ir(3+) complexes, Ir(HexPhBI)(3) 1 (HexPhBI = 1-Hexyl-2-phenyl-1H-benzo[d]imidazole), Ir(CzPhBI)(3) 2 (CzPhBI = 9-(6-(2-phenyl-1H-benzo[d]imidazol-1-yl)hexyl)-9H-carbazole), and Ir(Cz(2)PhBI)(3) 3 (Cz(2)PhBI = 9-(6-(4-(1-(6-(9H-carbazol-9-yl)hexyl)-1H-benzo[d]imidazol-2-yl)phenoxy)hexyl)-9H-carbazole), were synthesized in which 3 was designed with the structure of multiposition encapsulation. Compared to the hexyl-substituted 1, 2 and 3 end-capped with the conjugated carbazole moieties have improved thermal stability. X-ray diffraction analysis proved the amorphous state of 2 and 3. High-photoluminescent efficiencies of 3 are achieved as 72% in solution and 61% in solid. It indicates that the peripheral carbazoles not only facilitate the separation of triplet-emission cores and reduce the intermolecular aggregation but also supply a routine for the intermolecular energy transfer. Electrochemical analysis showed the more oxidation states of 3, which might be anticipated to make it superior to 1 and 2 in hole injection and transporting. The important role of the peripheral carbazole moieties in carrier injection/transporting and the optical properties of the complexes were further investigated by Gaussian simulation. A dramatic electroluminescent (EL) performance, including external quantum efficiency of nearly 6%, low turn-on voltage of 2.5 V, and high brightness over 6000 cd m(-2), from the host-free spin-coated device of 3 was achieved. The superiority of multiencapsulation in EL was proved by comparing the EL performance of 2 and 3. By making comparison between the host-free and phosphor-doping devices, it indicated that the combined modification of the aliphatic chains and functional groups in multipositions is a feasible approach to realize the high-efficiency small molecular phosphorescent materials.

Nanowire array chips for molecular typing of rare trafficking leukocytes with application to neurodegenerative pathology

NASA Astrophysics Data System (ADS)

Kwak, Minsuk; Kim, Dong-Joo; Lee, Mi-Ri; Wu, Yu; Han, Lin; Lee, Sang-Kwon; Fan, Rong

2014-05-01

Despite the presence of the blood-brain barrier (BBB) that restricts the entry of immune cells and mediators into the central nervous system (CNS), a small number of peripheral leukocytes can traverse the BBB and infiltrate into the CNS. The cerebrospinal fluid (CSF) is one of the major routes through which trafficking leukocytes migrate into the CNS. Therefore, the number of leukocytes and their phenotypic compositions in the CSF may represent important sources to investigate immune-to-brain interactions or diagnose and monitor neurodegenerative diseases. Due to the paucity of trafficking leucocytes in the CSF, a technology capable of efficient isolation, enumeration, and molecular typing of these cells in the clinical settings has not been achieved. In this study, we report on a biofunctionalized silicon nanowire array chip for highly efficient capture and multiplexed phenotyping of rare trafficking leukocytes in small quantities (50 microliters) of clinical CSF specimens collected from neurodegenerative disease patients. The antibody coated 3D nanostructured materials exhibited vastly improved rare cell capture efficiency due to high-affinity binding and enhanced cell-substrate interactions. Moreover, our platform creates multiple cell capture interfaces, each of which can selectively isolate specific leukocyte phenotypes. A comparison with the traditional immunophenotyping using flow cytometry demonstrated that our novel silicon nanowire-based rare cell analysis platform can perform rapid detection and simultaneous molecular characterization of heterogeneous immune cells. Multiplexed molecular typing of rare leukocytes in CSF samples collected from Alzheimer's disease patients revealed the elevation of white blood cell counts and significant alterations in the distribution of major leukocyte phenotypes. Our technology represents a practical tool for potentially diagnosing and monitoring the pathogenesis of neurodegenerative diseases by allowing an effective hematological analysis of the CSF from patients.Despite the presence of the blood-brain barrier (BBB) that restricts the entry of immune cells and mediators into the central nervous system (CNS), a small number of peripheral leukocytes can traverse the BBB and infiltrate into the CNS. The cerebrospinal fluid (CSF) is one of the major routes through which trafficking leukocytes migrate into the CNS. Therefore, the number of leukocytes and their phenotypic compositions in the CSF may represent important sources to investigate immune-to-brain interactions or diagnose and monitor neurodegenerative diseases. Due to the paucity of trafficking leucocytes in the CSF, a technology capable of efficient isolation, enumeration, and molecular typing of these cells in the clinical settings has not been achieved. In this study, we report on a biofunctionalized silicon nanowire array chip for highly efficient capture and multiplexed phenotyping of rare trafficking leukocytes in small quantities (50 microliters) of clinical CSF specimens collected from neurodegenerative disease patients. The antibody coated 3D nanostructured materials exhibited vastly improved rare cell capture efficiency due to high-affinity binding and enhanced cell-substrate interactions. Moreover, our platform creates multiple cell capture interfaces, each of which can selectively isolate specific leukocyte phenotypes. A comparison with the traditional immunophenotyping using flow cytometry demonstrated that our novel silicon nanowire-based rare cell analysis platform can perform rapid detection and simultaneous molecular characterization of heterogeneous immune cells. Multiplexed molecular typing of rare leukocytes in CSF samples collected from Alzheimer's disease patients revealed the elevation of white blood cell counts and significant alterations in the distribution of major leukocyte phenotypes. Our technology represents a practical tool for potentially diagnosing and monitoring the pathogenesis of neurodegenerative diseases by allowing an effective hematological analysis of the CSF from patients. Electronic supplementary information (ESI) available: Additional data are available in the supplementary tables and supplementary figures. See DOI: 10.1039/c3nr06465d

Efficiently sampling conformations and pathways using the concurrent adaptive sampling (CAS) algorithm

NASA Astrophysics Data System (ADS)

Ahn, Surl-Hee; Grate, Jay W.; Darve, Eric F.

2017-08-01

Molecular dynamics simulations are useful in obtaining thermodynamic and kinetic properties of bio-molecules, but they are limited by the time scale barrier. That is, we may not obtain properties' efficiently because we need to run microseconds or longer simulations using femtosecond time steps. To overcome this time scale barrier, we can use the weighted ensemble (WE) method, a powerful enhanced sampling method that efficiently samples thermodynamic and kinetic properties. However, the WE method requires an appropriate partitioning of phase space into discrete macrostates, which can be problematic when we have a high-dimensional collective space or when little is known a priori about the molecular system. Hence, we developed a new WE-based method, called the "Concurrent Adaptive Sampling (CAS) algorithm," to tackle these issues. The CAS algorithm is not constrained to use only one or two collective variables, unlike most reaction coordinate-dependent methods. Instead, it can use a large number of collective variables and adaptive macrostates to enhance the sampling in the high-dimensional space. This is especially useful for systems in which we do not know what the right reaction coordinates are, in which case we can use many collective variables to sample conformations and pathways. In addition, a clustering technique based on the committor function is used to accelerate sampling the slowest process in the molecular system. In this paper, we introduce the new method and show results from two-dimensional models and bio-molecules, specifically penta-alanine and a triazine trimer.

Lambda Red recombinase-mediated integration of the high molecular weight DNA into the Escherichia coli chromosome.

PubMed

Juhas, Mario; Ajioka, James W

2016-10-05

Escherichia coli K-12 is a frequently used host for a number of synthetic biology and biotechnology applications and chassis for the development of the minimal cell factories. Novel approaches for integrating high molecular weight DNA into the E. coli chromosome would therefore greatly facilitate engineering efforts in this bacterium. We developed a reliable and flexible lambda Red recombinase-based system, which utilizes overlapping DNA fragments for integration of the high molecular weight DNA into the E. coli chromosome. Our chromosomal integration strategy can be used to integrate high molecular weight DNA of variable length into any non-essential locus in the E. coli chromosome. Using this approach we integrated 15 kb DNA encoding sucrose catabolism and lactose metabolism and transport operons into the fliK locus of the flagellar region 3b in the E. coli K12 MG1655 chromosome. Furthermore, with this system we integrated 50 kb of Bacillus subtilis 168 DNA into two target sites in the E. coli K12 MG1655 chromosome. The chromosomal integrations into the fliK locus occurred with high efficiency, inhibited motility, and did not have a negative effect on the growth of E. coli. In addition to the rational design of synthetic biology devices, our high molecular weight DNA chromosomal integration system will facilitate metabolic and genome-scale engineering of E. coli.

Toxicology and drug delivery by cucurbit[n]uril type molecular containers.

PubMed

Hettiarachchi, Gaya; Nguyen, Duc; Wu, Jing; Lucas, Derick; Ma, Da; Isaacs, Lyle; Briken, Volker

2010-05-06

Many drug delivery systems are based on the ability of certain macrocyclic compounds - such as cyclodextrins (CDs) - to act as molecular containers for pharmaceutical agents in water. Indeed beta-CD and its derivatives have been widely used in the formulation of hydrophobic pharmaceuticals despite their poor abilities to act as a molecular container (e.g., weak binding (K(a)<10(4) M(-1)) and their challenges toward chemical functionalization. Cucurbit[n]urils (CB[n]) are a class of molecular containers that bind to a variety of cationic and neutral species with high affinity (K(a)>10(4) M(-1)) and therefore show great promise as a drug delivery system. In this study we investigated the toxicology, uptake, and bioactivity of two cucurbit[n]urils (CB[5] and CB[7]) and three CB[n]-type containers (Pentamer 1, methyl hexamer 2, and phenyl hexamer 3). All five containers demonstrated high cell tolerance at concentrations of up to 1 mM in cell lines originating from kidney, liver or blood tissue using assays for metabolic activity and cytotoxicity. Furthermore, the CB[7] molecular container was efficiently internalized by macrophages indicating their potential for the intracellular delivery of drugs. Bioactivity assays showed that the first-line tuberculosis drug, ethambutol, was as efficient in treating mycobacteria infected macrophages when loaded into CB[7] as when given in the unbound form. This result suggests that CB[7]-bound drug molecules can be released from the container to find their intracellular target. Our study reveals very low toxicity of five members of the cucurbit[n]uril family of nanocontainers. It demonstrates the uptake of containers by cells and intracellular release of container-loaded drugs. These results provide initial proof-of-concept towards the use of CB[n] molecular containers as an advanced drug delivery system.

Poly(ethyleneoxide) functionalization through alkylation

DOEpatents

Sivanandan, Kulandaivelu; Eitouni, Hany Basam; Li, Yan; Pratt, Russell Clayton

2015-04-21

A new and efficient method of functionalizing high molecular weight polymers through alkylation using a metal amide base is described. This novel procedure can also be used to synthesize polymer-based macro-initiators containing radical initiating groups at the chain-ends for synthesis of block copolymers.

Design principles and optimal performance for molecular motors under realistic constraints

NASA Astrophysics Data System (ADS)

Tu, Yuhai; Cao, Yuansheng

2018-02-01

The performance of a molecular motor, characterized by its power output and energy efficiency, is investigated in the motor design space spanned by the stepping rate function and the motor-track interaction potential. Analytic results and simulations show that a gating mechanism that restricts forward stepping in a narrow window in configuration space is needed for generating high power at physiologically relevant loads. By deriving general thermodynamics laws for nonequilibrium motors, we find that the maximum torque (force) at stall is less than its theoretical limit for any realistic motor-track interactions due to speed fluctuations. Our study reveals a tradeoff for the motor-track interaction: while a strong interaction generates a high power output for forward steps, it also leads to a higher probability of wasteful spontaneous back steps. Our analysis and simulations show that this tradeoff sets a fundamental limit to the maximum motor efficiency in the presence of spontaneous back steps, i.e., loose-coupling. Balancing this tradeoff leads to an optimal design of the motor-track interaction for achieving a maximum efficiency close to 1 for realistic motors that are not perfectly coupled with the energy source. Comparison with existing data and suggestions for future experiments are discussed.

Design of biomimetic catalysts by molecular imprinting in synthetic polymers: the role of transition state stabilization.

PubMed

Wulff, Günter; Liu, Junqiu

2012-02-21

The impressive efficiency and selectivity of biological catalysts has engendered a long-standing effort to understand the details of enzyme action. It is widely accepted that enzymes accelerate reactions through their steric and electronic complementarity to the reactants in the rate-determining transition states. Thus, tight binding to the transition state of a reactant (rather than to the corresponding substrate) lowers the activation energy of the reaction, providing strong catalytic activity. Debates concerning the fundamentals of enzyme catalysis continue, however, and non-natural enzyme mimics offer important additional insight in this area. Molecular structures that mimic enzymes through the design of a predetermined binding site that stabilizes the transition state of a desired reaction are invaluable in this regard. Catalytic antibodies, which can be quite active when raised against stable transition state analogues of the corresponding reaction, represent particularly successful examples. Recently, synthetic chemistry has begun to match nature's ability to produce antibody-like binding sites with high affinities for the transition state. Thus, synthetic, molecularly imprinted polymers have been engineered to provide enzyme-like specificity and activity, and they now represent a powerful tool for creating highly efficient catalysts. In this Account, we review recent efforts to develop enzyme models through the concept of transition state stabilization. In particular, models for carboxypeptidase A were prepared through the molecular imprinting of synthetic polymers. On the basis of successful experiments with phosphonic esters as templates to arrange amidinium groups in the active site, the method was further improved by combining the concept of transition state stabilization with the introduction of special catalytic moieties, such as metal ions in a defined orientation in the active site. In this way, the imprinted polymers were able to provide both an electrostatic stabilization for the transition state through the amidinium group as well as a synergism of transition state recognition and metal ion catalysis. The result was an excellent catalyst for carbonate hydrolysis. These enzyme mimics represent the most active catalysts ever prepared through the molecular imprinting strategy. Their catalytic activity, catalytic efficiency, and catalytic proficiency clearly surpass those of the corresponding catalytic antibodies. The active structures in natural enzymes evolve within soluble proteins, typically by the refining of the folding of one polypeptide chain. To incorporate these characteristics into synthetic polymers, we used the concept of transition state stabilization to develop soluble, nanosized carboxypeptidase A models using a new polymerization method we term the "post-dilution polymerization method". With this methodology, we were able to prepare soluble, highly cross-linked, single-molecule nanoparticles. These particles have controlled molecular weights (39 kDa, for example) and, on average, one catalytically active site per particle. Our strategies have made it possible to obtain efficient new enzyme models and further advance the structural and functional analogy with natural enzymes. Moreover, this bioinspired design based on molecular imprinting in synthetic polymers offers further support for the concept of transition state stabilization in catalysis.

Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller.

PubMed

Xu, Chang; Nezami Ranjbar, Mohammad R; Wu, Zhong; DiCarlo, John; Wang, Yexun

2017-01-03

Detection of DNA mutations at very low allele fractions with high accuracy will significantly improve the effectiveness of precision medicine for cancer patients. To achieve this goal through next generation sequencing, researchers need a detection method that 1) captures rare mutation-containing DNA fragments efficiently in the mix of abundant wild-type DNA; 2) sequences the DNA library extensively to deep coverage; and 3) distinguishes low level true variants from amplification and sequencing errors with high accuracy. Targeted enrichment using PCR primers provides researchers with a convenient way to achieve deep sequencing for a small, yet most relevant region using benchtop sequencers. Molecular barcoding (or indexing) provides a unique solution for reducing sequencing artifacts analytically. Although different molecular barcoding schemes have been reported in recent literature, most variant calling has been done on limited targets, using simple custom scripts. The analytical performance of barcode-aware variant calling can be significantly improved by incorporating advanced statistical models. We present here a highly efficient, simple and scalable enrichment protocol that integrates molecular barcodes in multiplex PCR amplification. In addition, we developed smCounter, an open source, generic, barcode-aware variant caller based on a Bayesian probabilistic model. smCounter was optimized and benchmarked on two independent read sets with SNVs and indels at 5 and 1% allele fractions. Variants were called with very good sensitivity and specificity within coding regions. We demonstrated that we can accurately detect somatic mutations with allele fractions as low as 1% in coding regions using our enrichment protocol and variant caller.

Novel Solid-State Solar Cell Based on Hole-Conducting MOF-Sensitizer Demonstrating Power Conversion Efficiency of 2.1.

PubMed

Ahn, Do Young; Lee, Deok Yeon; Shin, Chan Yong; Bui, Hoa Thi; Shrestha, Nabeen K; Giebeler, Lars; Noh, Yong-Young; Han, Sung-Hwan

2017-04-19

This work reports on designing of first successful MOF-sensitizer based solid-state photovoltaic device, perticularly with a meaningful output power conversion efficiency. In this study, an intrinsically conductive cobalt-based MOFs (Co-DAPV) formed by the coordination between Co (II) ions and a redox active di(3-diaminopropyl)-viologen (i.e., DAPV) ligand is investigated as sensitizer. Hall-effect measurement shows p-type conductivity of the Co-DAPV film with hole mobility of 0.017 cm 2 V -1 s -1 , suggesting its potential application as hole transporting sensitizer. Further, the energy levels of the highest occupied molecular orbital (HOMO) and the lowest unoccupied molecular orbital (LUMO) of Co-DAPV are well-matched to be suitably employed for sensitizing TiO 2 . Thus, by layer-by-layer deposition of hole conducting MOF-sensitizer onto mesoporous TiO 2 film, a power conversion efficiency of as high as 2.1% is achieved, which exceeds the highest efficiency values of MOF-sensitized liquid-junction solar cells reported so far.

Perovskite Solar Cells: Influence of Hole Transporting Materials on Power Conversion Efficiency.

PubMed

Ameen, Sadia; Rub, Malik Abdul; Kosa, Samia A; Alamry, Khalid A; Akhtar, M Shaheer; Shin, Hyung-Shik; Seo, Hyung-Kee; Asiri, Abdullah M; Nazeeruddin, Mohammad Khaja

2016-01-08

The recent advances in perovskite solar cells (PSCs) created a tsunami effect in the photovoltaic community. PSCs are newfangled high-performance photovoltaic devices with low cost that are solution processable for large-scale energy production. The power conversion efficiency (PCE) of such devices experienced an unprecedented increase from 3.8 % to a certified value exceeding 20 %, demonstrating exceptional properties of perovskites as solar cell materials. A key advancement in perovskite solar cells, compared with dye-sensitized solar cells, occurred with the replacement of liquid electrolytes with solid-state hole-transporting materials (HTMs) such as 2,2',7,7'-tetrakis-(N,N-di-4-methoxyphenylamino)-9,9'-spirobifluorene (Spiro-OMeTAD), which contributed to enhanced PCE values and improved the cell stability. Following improvements in the perovskite crystallinity to produce a smooth, uniform morphology, the selective and efficient extraction of positive and negative charges in the device dictated the PCE of PSCs. In this Review, we focus mainly on the HTMs responsible for hole transport and extraction in PSCs, which is one of the essential components for efficient devices. Here, we describe the current state-of-the-art in molecular engineering of hole-transporting materials that are used in PSCs and highlight the requisites for market-viability of this technology. Finally, we include an outlook on molecular engineering of new functional HTMs for high efficiency PSCs. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The application of high efficient yellow phosphorescent material to white OLEDs

NASA Astrophysics Data System (ADS)

Lin, Jin-Sheng; Ku, Chun-Neng; Huang, Pang-Chi; Wu, Cheng-An; Chang, Meng-Hao; Liou, Jia-Lun; Tseng, Mei-Rurng

2014-10-01

A new type of thiopyridinyl-based iridium molecule (POT) was used as the yellow phosphorescent material in our research. On fabricating a yellow PHOLED by doping POT-02 with host as the emitter, the device achieved a high power efficiency of 66.0 lm/W and an external quantum efficiency of 23.2%. On the other hand, a white organic lightemitting diode (WOLED) with a high power efficiency has been demonstrated by dispersing a host-free, yellow phosphorescent material in-between double blue phosphorescent emitters. In this study, we introduce a simple process for generating yellow emission of a WOLED by using the B/Y/B EML configuration. The B/Y/B EML configuration can achieve a higher efficiency and a smaller color shift with various operational brightness values. Based on the concept of this device, the molecular engineering of the blue phosphorescent host material as well as the light-extraction film, a WOLED with a power efficiency of 103 lm/W and an external quantum efficiency of 38.2% at a practical brightness of 1000 cd/m2 with CIE coordinates (CIEx, y) of (0.36, 0.48) can be achieved.

High-performance light-emitting diodes based on carbene-metal-amides

NASA Astrophysics Data System (ADS)

Di, Dawei; Romanov, Alexander S.; Yang, Le; Richter, Johannes M.; Rivett, Jasmine P. H.; Jones, Saul; Thomas, Tudor H.; Abdi Jalebi, Mojtaba; Friend, Richard H.; Linnolahti, Mikko; Bochmann, Manfred; Credgington, Dan

2017-04-01

Organic light-emitting diodes (OLEDs) promise highly efficient lighting and display technologies. We introduce a new class of linear donor-bridge-acceptor light-emitting molecules, which enable solution-processed OLEDs with near-100% internal quantum efficiency at high brightness. Key to this performance is their rapid and efficient utilization of triplet states. Using time-resolved spectroscopy, we establish that luminescence via triplets occurs within 350 nanoseconds at ambient temperature, after reverse intersystem crossing to singlets. We find that molecular geometries exist at which the singlet-triplet energy gap (exchange energy) is close to zero, so that rapid interconversion is possible. Calculations indicate that exchange energy is tuned by relative rotation of the donor and acceptor moieties about the bridge. Unlike other systems with low exchange energy, substantial oscillator strength is sustained at the singlet-triplet degeneracy point.

Synthesis of molecularly imprinted dye-silica nanocomposites with high selectivity and sensitivity: Fluorescent imprinted sensor for rapid and efficient detection of τ-fluvalinate in vodka.

PubMed

Wang, Yunyun; Wang, Jixiang; Cheng, Rujia; Sun, Lin; Dai, Xiaohui; Yan, Yongsheng

2018-04-01

An imprinted fluorescent sensor was fabricated based on SiO 2 nanoparticles encapsulated with a molecularly imprinted polymer containing allyl fluorescein. High fluorine cypermethirin as template molecules, methyl methacrylate as functional monomer, and allyl fluorescein as optical materials synthesized a core-shell fluorescent molecular imprinted sensor, which showed a high and rapid sensitivity and selectivity for the detection of τ-fluvalinate. The sensor presented appreciable sensitivity with a limit of 13.251 nM, rapid detection that reached to equilibrium within 3 min, great linear relationship in the relevant concentration range from 0 to 150 nM, and excellent selectivity over structural analogues. In addition, the fluorescent sensor demonstrated desirable regeneration ability (eight cycling operations). The molecularly imprinted polymers ensured specificity, while the fluorescent dyes provided the stabile sensitivity. Finally, an effective application of the sensor was implemented by the detection of τ-fluvalinate in real samples from vodka. The molecularly imprinted fluorescent sensor showed a promising potential in environmental monitoring and food safety. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A combined thermal dissociation and electron impact ionization source for radioactive ion beam generation{sup a}

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

Alton, G.D.; Williams, C.

1996-04-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, inmore » principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. {copyright} {ital 1996 American Institute of Physics.}« less

A combined thermal dissociation and electron impact ionization source for radioactive ion beam generation (abstract){sup a}

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

Alton, G.D.; Williams, C.

1996-03-01

The probability for simultaneously dissociating and efficiently ionizing the individual atomic constituents of molecular feed materials with conventional, hot-cathode, electron-impact ion sources is low and consequently, the ion beams from these sources often appear as mixtures of several molecular sideband beams. This fragmentation process leads to dilution of the intensity of the species of interest for radioactive ion beam (RIB) applications where beam intensity is at a premium. We have conceived an ion source that combines the excellent molecular dissociation properties of a thermal dissociator and the high ionization efficiency characteristics of an electron impact ionization source that will, inmore » principle, overcome this handicap. The source concept will be evaluated as a potential candidate for use for RIB generation at the Holifield Radioactive Ion Beam Facility, now under construction at the Oak Ridge National Laboratory. The design features and principles of operation of the source are described in this article. {copyright} {ital 1996 American Institute of Physics.}« less

The Use of Molecular Oxygen in Pharmaceutical Manufacturing: Is Flow the Way to Go?

PubMed

Hone, Christopher A; Roberge, Dominique M; Kappe, C Oliver

2017-01-10

Molecular oxygen is arguably the greenest reagent available to the organic chemist. Most commonly, a diluted form of oxygen gas, consisting of less than 10 % O 2 in N 2 ("synthetic air"), is used in pharmaceutical and fine chemical batch manufacturing to effectively address safety concerns when handling molecular oxygen. Concentrations of O 2 in N 2 below 10 % are generally required to prevent the risk of combustions in the presence of flammable organic solvents ("limiting oxygen concentration"). Nonetheless, the use of pure oxygen is more efficient than using O 2 diluted with N 2 and can often provide enhanced reaction rates, resulting in significant improvements in product quality and process efficiency. This Concept takes into account recent studies to make the argument that, for liquid-phase aerobic oxidations, pure oxygen can indeed be handled safely on large scale by employing continuous-flow reactors, while also providing highly convincing synthetic and manufacturing benefits. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Development of gel-filter method for high enrichment of low-molecular weight proteins from serum.

PubMed

Chen, Lingsheng; Zhai, Linhui; Li, Yanchang; Li, Ning; Zhang, Chengpu; Ping, Lingyan; Chang, Lei; Wu, Junzhu; Li, Xiangping; Shi, Deshun; Xu, Ping

2015-01-01

The human serum proteome has been extensively screened for biomarkers. However, the large dynamic range of protein concentrations in serum and the presence of highly abundant and large molecular weight proteins, make identification and detection changes in the amount of low-molecular weight proteins (LMW, molecular weight ≤ 30kDa) difficult. Here, we developed a gel-filter method including four layers of different concentration of tricine SDS-PAGE-based gels to block high-molecular weight proteins and enrich LMW proteins. By utilizing this method, we identified 1,576 proteins (n = 2) from 10 μL serum. Among them, 559 (n = 2) proteins belonged to LMW proteins. Furthermore, this gel-filter method could identify 67.4% and 39.8% more LMW proteins than that in representative methods of glycine SDS-PAGE and optimized-DS, respectively. By utilizing SILAC-AQUA approach with labeled recombinant protein as internal standard, the recovery rate for GST spiked in serum during the treatment of gel-filter, optimized-DS, and ProteoMiner was 33.1 ± 0.01%, 18.7 ± 0.01% and 9.6 ± 0.03%, respectively. These results demonstrate that the gel-filter method offers a rapid, highly reproducible and efficient approach for screening biomarkers from serum through proteomic analyses.

Electrospray Ionization Efficiency Is Dependent on Different Molecular Descriptors with Respect to Solvent pH and Instrumental Configuration

PubMed Central

Kiontke, Andreas; Oliveira-Birkmeier, Ariana; Opitz, Andreas

2016-01-01

Over the past decades, electrospray ionization for mass spectrometry (ESI-MS) has become one of the most commonly employed techniques in analytical chemistry, mainly due to its broad applicability to polar and semipolar compounds and the superior selectivity which is achieved in combination with high resolution separation techniques. However, responsiveness of an analytical method also determines its suitability for the quantitation of chemical compounds; and in electrospray ionization for mass spectrometry, it can vary significantly among different analytes with identical solution concentrations. Therefore, we investigated the ESI-response behavior of 56 nitrogen-containing compounds including aromatic amines and pyridines, two compound classes of high importance to both, synthetic organic chemistry as well as to pharmaceutical sciences. These compounds are increasingly analyzed employing ESI mass spectrometry detection due to their polar, basic character. Signal intensities of the peaks from the protonated molecular ion (MH+) were acquired under different conditions and related to compound properties such as basicity, polarity, volatility and molecular size exploring their quantitative impact on ionization efficiency. As a result, we found that though solution basicity of a compound is the main factor initially determining the ESI response of the protonated molecular ion, other factors such as polarity and vaporability become more important under acidic solvent conditions and may nearly outweigh the importance of basicity under these conditions. Moreover, we show that different molecular descriptors may become important when using different types of instruments for such investigations, a fact not detailed so far in the available literature. PMID:27907110

Molecular engineering and sequential cosensitization for preventing the “trade-off” effect with photovoltaic enhancement† †Electronic supplementary information (ESI) available: Synthesis and characterization, and additional photovoltaic data. See DOI: 10.1039/c6sc03938c Click here for additional data file.

PubMed Central

Zhang, Weiwei; Wu, Yongzhen; Li, Xin; Li, Erpeng; Song, Xiongrong; Jiang, Huiyun; Shen, Chao; Zhang, Hao; Tian, He

2017-01-01

In dye-sensitized solar cells (DSSCs), it is essential to use rational molecular design to obtain promising photosensitizers with well-matched energy levels and narrow optical band gaps. However, the “trade-off” effect between the photocurrent and photovoltage is still a challenge. Here we report four benzoxidazole based D–A–π–A metal-free organic dyes (WS-66, WS-67, WS-68 and WS-69) with different combinations of π-spacer units and anchoring-acceptor groups. Either extending the π-spacer or enhancing the electron acceptor can efficiently modulate the molecular energy levels, leading to a red-shift in the absorption spectra. The optimal dye, WS-69, containing a cyclopentadithiophene (CPDT) spacer and cyanoacetic acid acceptor, shows the narrowest energy band gap, which displays a very high photocurrent density of 19.39 mA cm–2, but suffers from a relatively low photovoltage of 696 mV, along with the so-called deleterious “trade-off” effect. A cosensitization strategy is further adopted for enhancing the device performance. Optimization of the dye loading sequence is found to be capable of simultaneously improving the photocurrent and photovoltage, and distinctly preventing the “trade-off” effect. The superior cosensitized cell exhibits an excellent power-conversion efficiency (PCE) of 10.09% under one-sun irradiation, and 11.12% under 0.3 sun irradiation, which constitutes a great achievement in that the efficiency of a pure metal-free organic dye with iodine electrolyte can exceed 11% even under relatively weak light irradiation. In contrast with the previous cosensitization strategy which mostly focused on compensation of light-harvesting, we propose a novel cosensitization architecture, in which the large molecular-sized, high photocurrent dye WS-69 takes charge of broadening the light-harvesting region to generate a high short-circuit current (J SC) while the small molecular-sized, high photovoltage dye WS-5 is responsible for retarding charge recombination to generate a high open-circuit voltage (V OC). In addition, adsorption amount and photo-stability studies suggest that the cyano group in the anchoring acceptor is important for the stability since it is beneficial towards decreasing the LUMO levels and enhancing the binding of dyes onto TiO2 nanocrystals. PMID:28507663

An Efficient, Rapid, and Recyclable System for CRISPR-Mediated Genome Editing in Candida albicans.

PubMed

Nguyen, Namkha; Quail, Morgan M F; Hernday, Aaron D

2017-01-01

Candida albicans is the most common fungal pathogen of humans. Historically, molecular genetic analysis of this important pathogen has been hampered by the lack of stable plasmids or meiotic cell division, limited selectable markers, and inefficient methods for generating gene knockouts. The recent development of clustered regularly interspaced short palindromic repeat(s) (CRISPR)-based tools for use with C. albicans has opened the door to more efficient genome editing; however, previously reported systems have specific limitations. We report the development of an optimized CRISPR-based genome editing system for use with C. albicans . Our system is highly efficient, does not require molecular cloning, does not leave permanent markers in the genome, and supports rapid, precise genome editing in C. albicans . We also demonstrate the utility of our system for generating two independent homozygous gene knockouts in a single transformation and present a method for generating homozygous wild-type gene addbacks at the native locus. Furthermore, each step of our protocol is compatible with high-throughput strain engineering approaches, thus opening the door to the generation of a complete C. albicans gene knockout library. IMPORTANCE Candida albicans is the major fungal pathogen of humans and is the subject of intense biomedical and discovery research. Until recently, the pace of research in this field has been hampered by the lack of efficient methods for genome editing. We report the development of a highly efficient and flexible genome editing system for use with C. albicans . This system improves upon previously published C. albicans CRISPR systems and enables rapid, precise genome editing without the use of permanent markers. This new tool kit promises to expedite the pace of research on this important fungal pathogen.

Fabrication, Physicochemical Characterization, and Performance Evaluation of Biodegradable Polymeric Microneedle Patch System for Enhanced Transcutaneous Flux of High Molecular Weight Therapeutics.

PubMed

Shah, Viral; Choudhury, Bijaya Krushna

2017-11-01

A revolutionary paradigm shift is being observed currently, towards the use of therapeutic biologics for disease management. The present research was focused on designing an efficient dosage form for transdermal delivery of α-choriogonadotropin (high molecular weight biologic), through biodegradable polymeric microneedles. Polyvinylpyrrolidone-based biodegradable microneedle arrays loaded with high molecular weight polypeptide, α-choriogonadotropin, were fabricated for its systemic delivery via transdermal route. Varied process and formulation parameters were optimized for fabricating microneedle array, which in turn was expected to temporally rupture the stratum corneum layer of the skin, acting as a major barrier to drug delivery through transdermal route. The developed polymeric microneedles were optimized on the basis of quality attributes like mechanical strength, axial strength, insertion ratio, and insertion force analysis. The optimized polymeric microneedle arrays were characterized for in vitro drug release studies, ex vivo drug permeation studies, skin resealing studies, and in vivo pharmacokinetic studies. Results depicted that fabricated polymeric microneedle arrays with mechanical strength of above 5 N and good insertion ratio exhibited similar systemic bioavailability of α-choriogonadotropin in comparison to marketed subcutaneous injection formulation of α-choriogonadotropin. Thus, it was ultimately concluded that the designed drug delivery system can serve as an efficient tool for systemic delivery of therapeutic biologics, with an added benefit of overcoming the limitations of parenteral delivery, achieving better patient acceptability and compliance.

Timing Embryo Segmentation: Dynamics and Regulatory Mechanisms of the Vertebrate Segmentation Clock

PubMed Central

Resende, Tatiana P.; Andrade, Raquel P.; Palmeirim, Isabel

2014-01-01

All vertebrate species present a segmented body, easily observed in the vertebrate column and its associated components, which provides a high degree of motility to the adult body and efficient protection of the internal organs. The sequential formation of the segmented precursors of the vertebral column during embryonic development, the somites, is governed by an oscillating genetic network, the somitogenesis molecular clock. Herein, we provide an overview of the molecular clock operating during somite formation and its underlying molecular regulatory mechanisms. Human congenital vertebral malformations have been associated with perturbations in these oscillatory mechanisms. Thus, a better comprehension of the molecular mechanisms regulating somite formation is required in order to fully understand the origin of human skeletal malformations. PMID:24895605

Well-tempered metadynamics as a tool for characterizing multi-component, crystalline molecular machines.

PubMed

Ilott, Andrew J; Palucha, Sebastian; Hodgkinson, Paul; Wilson, Mark R

2013-10-10

The well-tempered, smoothly converging form of the metadynamics algorithm has been implemented in classical molecular dynamics simulations and used to obtain an estimate of the free energy surface explored by the molecular rotations in the plastic crystal, octafluoronaphthalene. The biased simulations explore the full energy surface extremely efficiently, more than 4 orders of magnitude faster than unbiased molecular dynamics runs. The metadynamics collective variables used have also been expanded to include the simultaneous orientations of three neighboring octafluoronaphthalene molecules. Analysis of the resultant three-dimensional free energy surface, which is sampled to a very high degree despite its significant complexity, demonstrates that there are strong correlations between the molecular orientations. Although this correlated motion is of limited applicability in terms of exploiting dynamical motion in octafluoronaphthalene, the approach used is extremely well suited to the investigation of the function of crystalline molecular machines.

Effect of horizontal molecular orientation on triplet-exciton diffusion in amorphous organic films

NASA Astrophysics Data System (ADS)

Sawabe, T.; Takasu, I.; Yonehara, T.; Ono, T.; Yoshida, J.; Enomoto, S.; Amemiya, I.; Adachi, C.

2012-09-01

Triplet harvesting is a candidate technology for highly efficient and long-life white OLEDs, where green or red phosphorescent emitters are activated by the triplet-excitons diffused from blue fluorescent emitters. We examined two oxadiazole-based electron transport materials with different horizontal molecular orientation as a triplet-exciton diffusion layer (TDL) in triplet-harvesting OLEDs. The device characteristics and the transient electroluminescent analyses of the red phosphorescent emitter showed that the triplet-exciton diffusion was more effective in the highly oriented TDL. The results are ascribed to the strong orbital overlap between the oriented molecules, which provides rapid electron exchange (Dexter energy transfer) in the TDL.

Synthetic zeolites and other microporous oxide molecular sieves

PubMed Central

Sherman, John D.

1999-01-01

Use of synthetic zeolites and other microporous oxides since 1950 has improved insulated windows, automobile air-conditioning, refrigerators, air brakes on trucks, laundry detergents, etc. Their large internal pore volumes, molecular-size pores, regularity of crystal structures, and the diverse framework chemical compositions allow “tailoring” of structure and properties. Thus, highly active and selective catalysts as well as adsorbents and ion exchangers with high capacities and selectivities were developed. In the petroleum refining and petrochemical industries, zeolites have made possible cheaper and lead-free gasoline, higher performance and lower-cost synthetic fibers and plastics, and many improvements in process efficiency and quality and in performance. Zeolites also help protect the environment by improving energy efficiency, reducing automobile exhaust and other emissions, cleaning up hazardous wastes (including the Three Mile Island nuclear power plant and other radioactive wastes), and, as specially tailored desiccants, facilitating the substitution of new refrigerants for the ozone-depleting chlorofluorocarbons banned by the Montreal Protocol. PMID:10097059

Highly efficient solar vapour generation via hierarchically nanostructured gels.

PubMed

Zhao, Fei; Zhou, Xingyi; Shi, Ye; Qian, Xin; Alexander, Megan; Zhao, Xinpeng; Mendez, Samantha; Yang, Ronggui; Qu, Liangti; Yu, Guihua

2018-04-02

Solar vapour generation is an efficient way of harvesting solar energy for the purification of polluted or saline water. However, water evaporation suffers from either inefficient utilization of solar energy or relies on complex and expensive light-concentration accessories. Here, we demonstrate a hierarchically nanostructured gel (HNG) based on polyvinyl alcohol (PVA) and polypyrrole (PPy) that serves as an independent solar vapour generator. The converted energy can be utilized in situ to power the vaporization of water contained in the molecular meshes of the PVA network, where water evaporation is facilitated by the skeleton of the hydrogel. A floating HNG sample evaporated water with a record high rate of 3.2 kg m -2  h -1 via 94% solar energy from 1 sun irradiation, and 18-23 litres of water per square metre of HNG was delivered daily when purifying brine water. These values were achievable due to the reduced latent heat of water evaporation in the molecular mesh under natural sunlight.

Highly efficient solar vapour generation via hierarchically nanostructured gels

NASA Astrophysics Data System (ADS)

Zhao, Fei; Zhou, Xingyi; Shi, Ye; Qian, Xin; Alexander, Megan; Zhao, Xinpeng; Mendez, Samantha; Yang, Ronggui; Qu, Liangti; Yu, Guihua

2018-06-01

Solar vapour generation is an efficient way of harvesting solar energy for the purification of polluted or saline water. However, water evaporation suffers from either inefficient utilization of solar energy or relies on complex and expensive light-concentration accessories. Here, we demonstrate a hierarchically nanostructured gel (HNG) based on polyvinyl alcohol (PVA) and polypyrrole (PPy) that serves as an independent solar vapour generator. The converted energy can be utilized in situ to power the vaporization of water contained in the molecular meshes of the PVA network, where water evaporation is facilitated by the skeleton of the hydrogel. A floating HNG sample evaporated water with a record high rate of 3.2 kg m-2 h-1 via 94% solar energy from 1 sun irradiation, and 18-23 litres of water per square metre of HNG was delivered daily when purifying brine water. These values were achievable due to the reduced latent heat of water evaporation in the molecular mesh under natural sunlight.

Bioconjugation of luminescent Eu-BDC-NH2 MOFs for highly efficient sensing of BSA

NASA Astrophysics Data System (ADS)

Kukkar, Preeti; Sammi, Heena; Rawat, Mohit; Singh, Pritpal; Basu, Soumen; Kukkar, Deepak

2018-05-01

Luminescent metal organic frameworks (MOFs) have emerged as an exciting prospect for molecular sensing applications owing to their tunable porosity and optical properties. In this study, we have reported the synthesis of luminescent Europium-amino terephthalic acid (Eu-BDC-NH2) MOFs through solvothermal approach subsequently followed by their bioconjugation with anti-Bovine serum albumin (BSA) antibody using standard carbodiimide linkage chemistry. Subsequently nanocomposite of the bioconjugate and Zeolotic Imidazole Frameworks -8(ZIF-8) nanoparticles was prepared by adding varying volumes of ZIF-8 NPs to check the variation in photoluminescence (PL) intensity. Finally, optimized nanocomposites with increased PL intensity were treated with different concentrations of BSA to show a turn on effect on the PL intensity. The prepared nanocomposites were able to screen 0.1 ppm concentration of the BSA thus showing their high efficiency as a molecular sensor. This fluorescent platform would be further utilized for sensitive detection of pesticides in solution.

Synthesis of molecular imprinting polymers for extraction of gallic acid from urine.

PubMed

Bhawani, Showkat Ahmad; Sen, Tham Soon; Ibrahim, Mohammad Nasir Mohammad

2018-02-21

The molecularly imprinted polymers for gallic acid were synthesized by precipitation polymerization. During the process of synthesis a non-covalent approach was used for the interaction of template and monomer. In the polymerization process, gallic acid was used as a template, acrylic acid as a functional monomer, ethylene glycol dimethacrylate as a cross-linker and 2,2'-azobisisobutyronitrile as an initiator and acetonitrile as a solvent. The synthesized imprinted and non-imprinted polymer particles were characterized by using Fourier-transform infrared spectroscopy and scanning electron microscopy. The rebinding efficiency of synthesized polymer particles was evaluated by batch binding assay. The highly selective imprinted polymer for gallic acid was MIPI1 with a composition (molar ratio) of 1:4:20, template: monomer: cross-linker, respectively. The MIPI1 showed highest binding efficiency (79.50%) as compared to other imprinted and non-imprinted polymers. The highly selective imprinted polymers have successfully extracted about 80% of gallic acid from spiked urine sample.

Active Cocatalysts for Photocatalytic Hydrogen Evolution Derived from Nickel or Cobalt Amine Complexes.

PubMed

Huang, Yi; Zhang, Bin

2017-11-20

A cost-effective and robust strategy for the anchoring of molecular hydrogen evolution cocatalysts onto semiconductors has recently been reported. The composite materials were highly efficient and stable towards photocatalytic H 2 evolution. This study provides guidance for the design and construction of highly active heterogeneous photocatalysts. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Ternary Polymer Solar Cells based on Two Acceptors and One Donor for Achieving 12.2% Efficiency.

PubMed

Zhao, Wenchao; Li, Sunsun; Zhang, Shaoqing; Liu, Xiaoyu; Hou, Jianhui

2017-01-01

Ternary polymer solar cells are fabricated based on one donor PBDB-T and two acceptors (a methyl-modified small-molecular acceptor (IT-M) and a bis-adduct of Bis[70]PCBM). A high power conversion efficiency of 12.2% can be achieved. The photovoltaic performance of the ternary polymer solar cells is not sensitive to the composition of the blend. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Modification on C217 by auxiliary acceptor toward efficient sensitiser for dye-sensitised solar cells: a theoretical study

NASA Astrophysics Data System (ADS)

Zhao, Caibin; Jin, Lingxia; Ge, Hongguang; Guo, Xiaohua; Zhang, Qiang; Wang, Wenliang

2018-02-01

In this work, to develop efficient organic dye sensitisers, a series of novel donor-acceptor-π-acceptor metal-free dyes were designed based on the C217 dye by means of modifying different auxiliary acceptors, and their photovoltaic performances were theoretically investigated with systematic density functional theory calculations coupled with the incoherent charge-hopping model. Results showed that the designed dyes possess lower highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) levels as well as narrower HOMO-LUMO gaps compared to C217, which indicate their higher light-harvesting efficiency. In addition, using the (TiO2)38 cluster and bidentate bridging model, we predicted that the photoelectric conversion efficiency (PCE) for the C217 dye is as high as 9.92% under air mass (AM) 1.5 illumination (100 mW.cm-2), which is in good agreement with its experimental value (9.60%-9.90%). More interestingly, the cell sensitised by the dye 7 designed in this work exhibits a middle-sized open-circuit voltage of 0.737 V, large short-circuit photocurrent density of 21.16 mAˑcm-2 and a fill factor of 0.801, corresponding to a quite high PCE of 12.49%, denoting the dye 7 is a more promising sensitiser candidate than the C217, and is worth further experimental study.

Crucial role of molecular planarity on the second order nonlinear optical property of pyridine based chalcone single crystals

NASA Astrophysics Data System (ADS)

Menezes, Anthoni Praveen; Jayarama, A.; Ng, Seik Weng

2015-05-01

An efficient nonlinear optical material 2E-3-(4-bromophenyl)-1-(pyridin-3-yl) prop-2-en-1-one (BPP) was synthesized and single crystals were grown using slow evaporation solution growth technique at room temperature. Grown crystal had prismatic morphology and its structure was confirmed by various spectroscopic studies, elemental analysis, and single crystal X-ray diffraction (XRD) technique. The single crystal XRD of the crystal showed that BPP crystallizes in monoclinic system with noncentrosymmetric space group P21 and the cell parameters are a = 5.6428(7) Å, b = 3.8637(6) Å, c = 26.411(2) Å, β = 97.568(11) deg and v = 575.82(12) Å3. The UV-Visible spectrum reveals that the crystal is optically transparent and has high optical energy band gap of 3.1 eV. The powder second harmonic generation efficiency (SHG) of BPP is 6.8 times that of KDP. From thermal analysis it is found that the crystal melts at 139 °C and decomposes at 264 °C. High optical transparency down to blue region, higher powder SHG efficiency and better thermal stability than that of urea makes this chalcone derivative a promising candidate for SHG applications. Furthermore, effect of molecular planarity on SHG efficiency and role of pyridine ring adjacent to carbonyl group in forming noncentrosymmetric crystal systems of chalcone family is also discussed.

Exploring the free energy surface using ab initio molecular dynamics

DOE PAGES

Samanta, Amit; Morales, Miguel A.; Schwegler, Eric

2016-04-22

Efficient exploration of the configuration space and identification of metastable structures are challenging from both computational as well as algorithmic perspectives. Here, we extend the recently proposed orderparameter aided temperature accelerated sampling schemes to efficiently and systematically explore free energy surfaces, and search for metastable states and reaction pathways within the framework of density functional theory based molecular dynamics. The sampling method is applied to explore the relevant parts of the configuration space in prototypical materials SiO 2 and Ti to identify the different metastable structures corresponding to different phases in these materials. In addition, we use the string methodmore » in collective variables to study the melting pathways in the high pressure cotunnite phase of SiO 2 and the hcp to fcc phase transition in Ti.« less

Efficiency bounds of molecular motors under a trade-off figure of merit

NASA Astrophysics Data System (ADS)

Zhang, Yanchao; Huang, Chuankun; Lin, Guoxing; Chen, Jincan

2017-05-01

On the basis of the theory of irreversible thermodynamics and an elementary model of the molecular motors converting chemical energy by ATP hydrolysis to mechanical work exerted against an external force, the efficiencies of the molecular motors at two different optimization configurations for trade-off figure of merit representing a best compromise between the useful energy and the lost energy are calculated. The upper and lower bounds for the efficiency at two different optimization configurations are determined. It is found that the optimal efficiencies at the two different optimization configurations are always larger than 1 / 2.

Submillimetre flux as a probe of molecular ISM mass in high-z galaxies

NASA Astrophysics Data System (ADS)

Liang, Lichen; Feldmann, Robert; Faucher-Giguère, Claude-André; Kereš, Dušan; Hopkins, Philip F.; Hayward, Christopher C.; Quataert, Eliot; Scoville, Nick Z.

2018-07-01

Recent long-wavelength observations on the thermal dust continuum suggest that the Rayleigh-Jeans tail can be used as a time-efficient quantitative probe of the dust and interstellar medium (ISM) mass in high-z galaxies. We use high-resolution cosmological simulations from the Feedback in Realistic Environment (FIRE) project to analyse the dust emission of M* ≳ 1010 M⊙ galaxies at z= 2-4. Our simulations (MASSIVEFIRE) explicitly include various forms of stellar feedback, and they produce the stellar masses and star formation rates of high-z galaxies in agreement with observations. Using radiative transfer modelling, we show that sub-millimetre (sub-mm) luminosity and molecular ISM mass are tightly correlated and that the overall normalization is in quantitative agreement with observations. Notably, sub-mm luminosity traces molecular ISM mass even during starburst episodes as dust mass and mass-weighted temperature evolve only moderately between z = 4 and z = 2, including during starbursts. Our finding supports the empirical approach of using broadband sub-mm flux as a proxy for molecular gas content in high-z galaxies. We thus expect single-band sub-mm observations with ALMA to dramatically increase the sample size of high-z galaxies with reliable ISM masses in the near future.

Submillimeter flux as a probe of molecular ISM mass in high-z galaxies

NASA Astrophysics Data System (ADS)

Liang, Lichen; Feldmann, Robert; Faucher-Giguère, Claude-André; Kereš, Dušan; Hopkins, Philip F.; Hayward, Christopher C.; Quataert, Eliot; Scoville, Nick Z.

2018-04-01

Recent long wavelength observations on the thermal dust continuum suggest that the Rayleigh-Jeans (RJ) tail can be used as a time-efficient quantitative probe of the dust and ISM mass in high-z galaxies. We use high-resolution cosmological simulations from the Feedback in Realistic Environment (FIRE) project to analyze the dust emission of M* ≳ 1010M⊙ galaxies at z = 2 - 4. Our simulations (MassiveFIRE) explicitly include various forms of stellar feedback, and they produce the stellar masses and star formation rates of high-z galaxies in agreement with observations. Using radiative transfer modelling, we show that sub-millimeter (sub-mm) luminosity and molecular ISM mass are tightly correlated and that the overall normalization is in quantitative agreement with observations. Notably, sub-mm luminosity traces molecular ISM mass even during starburst episodes as dust mass and mass-weighted temperature evolve only moderately between z = 4 and z = 2, including during starbursts. Our finding supports the empirical approach of using broadband sub-mm flux as a proxy for molecular gas content in high-z galaxies. We thus expect single-band sub-mm observations with ALMA to dramatically increase the sample size of high-z galaxies with reliable ISM masses in the near future.

Achieving Highly Efficient Nonfullerene Organic Solar Cells with Improved Intermolecular Interaction and Open-Circuit Voltage

DOE PAGES

Yao, Huifeng; Ye, Long; Hou, Junxian; ...

2017-03-29

Here, a new acceptor–donor–acceptor-structured nonfullerene acceptor ITCC (3,9-bis(4-(1,1-dicyanomethylene)-3-methylene-2-oxo-cyclopenta[b]thiophen)-5,5,11,11-tetrakis(4-hexylphenyl)-dithieno[2,3- d':2,3- d'] -s-indaceno[1,2- b:5,6- b']-dithiophene) is designed and synthesized via simple end-group modification. ITCC shows improved electron-transport properties and a high-lying lowest unoccupied molecular orbital level. A power conversion efficiency of 11.4% with an impressive V OC of over 1 V is recorded in photovoltaic devices, suggesting that ITCC has great potential for applications in tandem organic solar cells.

[Molecular typing methods for Pasteurella multocida-A review].

PubMed

Peng, Zhong; Liang, Wan; Wu, Bin

2016-10-04

Pasteurella multocida is an important gram-negative pathogenic bacterium that could infect wide ranges of animals. Humans could also be infected by P. multocida via animal bite or scratching. Current typing methods for P. multocida include serological typing methods and molecular typing methods. Of them, serological typing methods are based on immunological assays, which are too complicated for clinical bacteriological studies. However, the molecular methods including multiple PCRs and multilocus sequence typing (MLST) methods are more suitable for bacteriological studies of P. multocida in clinic, with their simple operation, high efficiency and accurate detection compared to the traditional serological typing methods, they are therefore widely used. In the current review, we briefly describe the molecular typing methods for P. multocida. Our aim is to provide a knowledge-foundation for clinical bacteriological investigation especially the molecular investigation for P. multocida.

Highly sensitive and rapid bacteria detection using molecular beacon-Au nanoparticles hybrid nanoprobes.

PubMed

Cao, Jing; Feng, Chao; Liu, Yan; Wang, Shouyu; Liu, Fei

2014-07-15

Since many diseases are caused by pathogenic bacterial infections, accurate and rapid detection of pathogenic bacteria is in urgent need to timely apply appropriate treatments and to reduce economic costs. To end this, we designed molecular beacon-Au nanoparticle hybrid nanoprobes to improve the bacterial detection efficiency and sensitivity. Here, we show that the designed molecular beacon modified Au nanoparticles could specifically recognize synthetic DNAs targets and can readily detect targets in clinical samples. Moreover, the hybrid nanoprobes can recognize Escherichia coli within an hour at a concentration of 10(2) cfu/ml, which is 1000-folds sensitive than using molecular beacon directly. Our results show that the molecular beacon-Au nanoparticle hybrid nanoprobes have great potential in medical and biological applications. Copyright © 2014 Elsevier B.V. All rights reserved.

Molecularly imprinted solid-phase extraction in the analysis of agrochemicals.

PubMed

Yi, Ling-Xiao; Fang, Rou; Chen, Guan-Hua

2013-08-01

The molecular imprinting technique is a highly predeterminative recognition technology. Molecularly imprinted polymers (MIPs) can be applied to the cleanup and preconcentration of analytes as the selective adsorbent of solid-phase extraction (SPE). In recent years, a new type of SPE has formed, molecularly imprinted polymer solid-phase extraction (MISPE), and has been widely applied to the extraction of agrochemicals. In this review, the mechanism of the molecular imprinting technique and the methodology of MIP preparations are explained. The extraction modes of MISPE, including offline and online, are discussed, and the applications of MISPE in the analysis of agrochemicals such as herbicides, fungicides and insecticides are summarized. It is concluded that MISPE is a powerful tool to selectively isolate agrochemicals from real samples with higher extraction and cleanup efficiency than commercial SPE and that it has great potential for broad applications.

EPDM polymers with intermolecular asymmetrical molecular weight, crystallinity and diene distribution

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

Datta, S.; Cheremishinoff, N.P.; Kresge, E.N.

1993-12-31

Rapid extrusion of EPDM elastomers require low viscosity and thus low molecular weights for the polymer. Efficient vulcanization of these elastomers requires network perfection and thus high molecular weights for the polymer. The benefits of these apparently mutually exclusive goals is important in uses of EPDM elastomers which require extrusion of profiles which are later cured. This paper shows that by introducing simultaneously asymmetry in the distribution of molecular weights, crystallinity and vulcanizable sites these apparently contradictory goals can be resolved. While these polymers cannot be made from a single Ziegler polymerization catalyst, the authors show the synthesis of thesemore » model EPDM polymers by blending polymers with very different molecular weights, ethylene and ENB contents. These blends can be rapidly extruded without melt fracture and can be cured to vulcanizates which have excellent tensile properties.« less

A novel superparamagnetic surface molecularly imprinted nanoparticle adopting dummy template: an efficient solid-phase extraction adsorbent for bisphenol A.

PubMed

Lin, Zhenkun; Cheng, Wenjing; Li, Yanyan; Liu, Zhiren; Chen, Xiangping; Huang, Changjiang

2012-03-30

Leakage of the residual template molecules is one of the biggest challenges for application of molecularly imprinted polymer (MIP) in solid-phase extraction (SPE). In this study, bisphenol F (BPF) was adopted as a dummy template to prepare MIP of bisphenol A (BPA) with a superparamagnetic core-shell nanoparticle as the supporter, aiming to avoid residual template leakage and to increase the efficiency of SPE. Characterization and test of the obtained products (called mag-DMIP beads) revealed that these novel nanoparticles not only had excellent magnetic property but also displayed high selectivity to the target molecule BPA. As mag-DMIP beads were adopted as the adsorbents of solid-phase extraction for detecting BPA in real water samples, the recoveries of spiked samples ranged from 84.7% to 93.8% with the limit of detection of 2.50 pg mL(-1), revealing that mag-DMIP beads were efficient SPE adsorbents. Copyright © 2012 Elsevier B.V. All rights reserved.

Sieving polymer synthesis by reversible addition fragmentation chain transfer polymerization.

PubMed

Nai, Yi Heng; Jones, Roderick C; Breadmore, Michael C

2013-12-01

Replaceable sieving polymers are the fundamental component for high resolution nucleic acids separation in CE. The choice of polymer and its physical properties play significant roles in influencing separation performance. Recently, reversible addition fragmentation chain transfer (RAFT) polymerization has been shown to be a versatile polymerization technique capable of yielding well defined polymers previously unattainable by conventional free radical polymerization. In this study, a high molecular weight PDMA at 765 000 gmol-1 with a PDI of 1.55 was successfully synthesized with the use of chain transfer agent - 2-propionic acidyl butyl trithiocarbonate (PABTC) in a multi-step sequential RAFT polymerization approach. This study represents the first demonstration of RAFT polymerization for synthesizing polymers with the molecular weight range suitable for high resolution DNA separation in sieving electrophoresis. Adjustment of pH in the reaction was found to be crucial for the successful RAFT polymerization of high molecular weight polymer as the buffered condition minimizes the effect of hydrolysis and aminolysis commonly associated with trithiocarbonate chain transfer agents. The separation efficiency of PABTC-PDMA was found to have marginally superior separation performance compared to a commercial PDMA formulation, POP™-CAP, of similar molecular weight range.

Poly[n]catenanes: Synthesis of molecular interlocked chains

NASA Astrophysics Data System (ADS)

Wu, Qiong; Rauscher, Phillip M.; Lang, Xiaolong; Wojtecki, Rudy J.; de Pablo, Juan J.; Hore, Michael J. A.; Rowan, Stuart J.

2017-12-01

As the macromolecular version of mechanically interlocked molecules, mechanically interlocked polymers are promising candidates for the creation of sophisticated molecular machines and smart soft materials. Poly[n]catenanes, where the molecular chains consist solely of interlocked macrocycles, contain one of the highest concentrations of topological bonds. We report, herein, a synthetic approach toward this distinctive polymer architecture in high yield (~75%) via efficient ring closing of rationally designed metallosupramolecular polymers. Light-scattering, mass spectrometric, and nuclear magnetic resonance characterization of fractionated samples support assignment of the high-molar mass product (number-average molar mass ~21.4 kilograms per mole) to a mixture of linear poly[7-26]catenanes, branched poly[13-130]catenanes, and cyclic poly[4-7]catenanes. Increased hydrodynamic radius (in solution) and glass transition temperature (in bulk materials) were observed upon metallation with Zn2+.

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

PubMed Central

Pronk, Sander; Páll, Szilárd; Schulz, Roland; Larsson, Per; Bjelkmar, Pär; Apostolov, Rossen; Shirts, Michael R.; Smith, Jeremy C.; Kasson, Peter M.; van der Spoel, David; Hess, Berk; Lindahl, Erik

2013-01-01

Motivation: Molecular simulation has historically been a low-throughput technique, but faster computers and increasing amounts of genomic and structural data are changing this by enabling large-scale automated simulation of, for instance, many conformers or mutants of biomolecules with or without a range of ligands. At the same time, advances in performance and scaling now make it possible to model complex biomolecular interaction and function in a manner directly testable by experiment. These applications share a need for fast and efficient software that can be deployed on massive scale in clusters, web servers, distributed computing or cloud resources. Results: Here, we present a range of new simulation algorithms and features developed during the past 4 years, leading up to the GROMACS 4.5 software package. The software now automatically handles wide classes of biomolecules, such as proteins, nucleic acids and lipids, and comes with all commonly used force fields for these molecules built-in. GROMACS supports several implicit solvent models, as well as new free-energy algorithms, and the software now uses multithreading for efficient parallelization even on low-end systems, including windows-based workstations. Together with hand-tuned assembly kernels and state-of-the-art parallelization, this provides extremely high performance and cost efficiency for high-throughput as well as massively parallel simulations. Availability: GROMACS is an open source and free software available from http://www.gromacs.org. Contact: erik.lindahl@scilifelab.se Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23407358

Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

NASA Astrophysics Data System (ADS)

Qiu, Liming; Vaughn, Mark; Cheng, Kelvin

2012-10-01

Early events of human beta-amyloid protein interactions with cholesterol-containing membranes are critical to understanding the pathogenesis of Alzheimer's disease (AD) and to exploring new therapeutic interventions of AD. Atomistic molecular dynamics (AMD) simulations have been extensively used to study the protein-lipid interaction at high atomic resolutions. However, traditional MD simulations are not efficient in sampling the phase space of complex lipid/protein systems with rugged free energy landscapes. Meanwhile, coarse-grained MD (CGD) simulations are efficient in the phase space sampling but suffered from low spatial resolutions and from the fact that the energy landscapes are not identical to those of the AMD. Here, a multiscale approach was employed to simulate the protein-lipid interactions of beta-amyloid upon its release from proteolysis residing in the neuronal membranes. We utilized a forward (AMD to CGD) and reverse (CGD-AMD) strategy to explore new transmembrane and surface protein configuration and evaluate the stabilization mechanisms by measuring the residue-specific protein-lipid or protein conformations. The detailed molecular interactions revealed in this multiscale MD approach will provide new insights into understanding the early molecular events leading to the pathogenesis of AD.

Electrosprayed chitosan nanoparticles: facile and efficient approach for bacterial transformation

NASA Astrophysics Data System (ADS)

Abyadeh, Morteza; Sadroddiny, Esmaeil; Ebrahimi, Ammar; Esmaeili, Fariba; Landi, Farzaneh Saeedi; Amani, Amir

2017-12-01

A rapid and efficient procedure for DNA transformation is a key prerequisite for successful cloning and genomic studies. While there are efforts to develop a facile method, so far obtained efficiencies for alternative methods have been unsatisfactory (i.e. 105-106 CFU/μg plasmid) compared with conventional method (up to 108 CFU/μg plasmid). In this work, for the first time, we prepared chitosan/pDNA nanoparticles by electrospraying methods to improve transformation process. Electrospray method was used for chitosan/pDNA nanoparticles production to investigate the non-competent bacterial transformation efficiency; besides, the effect of chitosan molecular weight, N/P ratio and nanoparticle size on non-competent bacterial transformation efficiency was evaluated too. The results showed that transformation efficiency increased with decreasing the molecular weight, N/P ratio and nanoparticles size. In addition, transformation efficiency of 1.7 × 108 CFU/μg plasmid was obtained with chitosan molecular weight, N/P ratio and nanoparticles size values of 30 kDa, 1 and 125 nm. Chitosan/pDNA electrosprayed nanoparticles were produced and the effect of molecular weight, N/P and size of nanoparticles on transformation efficiency was evaluated. In total, we present a facile and rapid method for bacterial transformation, which has comparable efficiency with the common method.

U.S. EPA computational toxicology programs: Central role of chemical-annotation efforts and molecular databases

EPA Science Inventory

EPA’s National Center for Computational Toxicology is engaged in high-profile research efforts to improve the ability to more efficiently and effectively prioritize and screen thousands of environmental chemicals for potential toxicity. A central component of these efforts invol...

Effects of Toluene, Acrolein and Vinyl Chloride on Motor Activity of Drosophila Melanogaster

EPA Science Inventory

The data generated by current high-throughput assays for chemical toxicity require information to link effects at molecular targets to adverse outcomes in whole animals. In addition, more efficient methods for testing volatile chemicals are needed. Here we begin to address these ...

The ToxCast Chemical Prioritization Program at the US EPA (UCLA Molecular Toxicology Program)

EPA Science Inventory

To meet the needs of chemical regulators reviewing large numbers of data-poor chemicals for safety, the EPA's National Center for Computational Toxicology is developing a means of efficiently testing thousands of compounds for potential toxicity. High-throughput bioactivity profi...

Irrelevance of the Power Stroke for the Directionality, Stopping Force, and Optimal Efficiency of Chemically Driven Molecular Machines

PubMed Central

Astumian, R. Dean

2015-01-01

A simple model for a chemically driven molecular walker shows that the elastic energy stored by the molecule and released during the conformational change known as the power-stroke (i.e., the free-energy difference between the pre- and post-power-stroke states) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Further, the apportionment of the dependence on the externally applied force between the forward and reverse rate constants of the power-stroke (or indeed among all rate constants) is irrelevant for determining the directionality, stopping force, and efficiency of the motor. Arguments based on the principle of microscopic reversibility demonstrate that this result is general for all chemically driven molecular machines, and even more broadly that the relative energies of the states of the motor have no role in determining the directionality, stopping force, or optimal efficiency of the machine. Instead, the directionality, stopping force, and optimal efficiency are determined solely by the relative heights of the energy barriers between the states. Molecular recognition—the ability of a molecular machine to discriminate between substrate and product depending on the state of the machine—is far more important for determining the intrinsic directionality and thermodynamics of chemo-mechanical coupling than are the details of the internal mechanical conformational motions of the machine. In contrast to the conclusions for chemical driving, a power-stroke is very important for the directionality and efficiency of light-driven molecular machines and for molecular machines driven by external modulation of thermodynamic parameters. PMID:25606678

MIMO: an efficient tool for molecular interaction maps overlap

PubMed Central

2013-01-01

Background Molecular pathways represent an ensemble of interactions occurring among molecules within the cell and between cells. The identification of similarities between molecular pathways across organisms and functions has a critical role in understanding complex biological processes. For the inference of such novel information, the comparison of molecular pathways requires to account for imperfect matches (flexibility) and to efficiently handle complex network topologies. To date, these characteristics are only partially available in tools designed to compare molecular interaction maps. Results Our approach MIMO (Molecular Interaction Maps Overlap) addresses the first problem by allowing the introduction of gaps and mismatches between query and template pathways and permits -when necessary- supervised queries incorporating a priori biological information. It then addresses the second issue by relying directly on the rich graph topology described in the Systems Biology Markup Language (SBML) standard, and uses multidigraphs to efficiently handle multiple queries on biological graph databases. The algorithm has been here successfully used to highlight the contact point between various human pathways in the Reactome database. Conclusions MIMO offers a flexible and efficient graph-matching tool for comparing complex biological pathways. PMID:23672344

In vitro and in vivo gene delivery using chitosan/hyaluronic acid nanoparticles: Influences of molecular mass of hyaluronic acid and lyophilization on transfection efficiency.

PubMed

Sato, Toshinori; Nakata, Mitsuhiro; Yang, Zhihong; Torizuka, Yu; Kishimoto, Satoko; Ishihara, Masayuki

2017-08-01

Lyophilization is an effective method for preserving nonviral gene vectors. To improve the stability and transgene expression of lyophilized plasmid DNA (pDNA) complexes, we coated the surfaces of pDNA/chitosan complexes with hyaluronic acid (HA) of varying molecular masses. The transgene expression of pDNA/chitosan/HA ternary complexes was characterized in vitro and in vivo. pDNA complexes were lyophilized overnight and the resultant products with spongy, porous consistencies were stored at -30, 4 or 25°C for 2 weeks. Rehydrated complexes were characterized using gel retardation assays, aiming to confirm complex formation, measure particle size and evaluate zeta potential, as well as conduct luciferase gene reporter assays. The anti-tumor effects of pDNA ternary complexes were evaluated using suicide gene (pTK) coding thymidine kinase in Huh7-implanted mice. Transfection efficiencies of pDNA/chitosan/HA ternary complexes were dependent on the average molecular masses of HA. The coating of pDNA/chitosan complexes with HA maintained the cellular transfection efficiencies of lyophilized pDNA ternary complexes. Furthermore, intratumoral injection of lyophilized, rehydrated pDNA ternary complexes into tumor-bearing mice showed a significant suppression of tumor growth. The coating of pDNA/chitosan complexes with high-molecular-weight HA augmented the stability and cellular transfection ability of the complexes after lyophilization-rehydration. Copyright © 2017 John Wiley & Sons, Ltd.

Inorganic-Organic Coating via Molecular Layer Deposition Enables Long Life Sodium Metal Anode.

PubMed

Zhao, Yang; Goncharova, Lyudmila V; Zhang, Qian; Kaghazchi, Payam; Sun, Qian; Lushington, Andrew; Wang, Biqiong; Li, Ruying; Sun, Xueliang

2017-09-13

Metallic Na anode is considered as a promising alternative candidate for Na ion batteries (NIBs) and Na metal batteries (NMBs) due to its high specific capacity, and low potential. However, the unstable solid electrolyte interphase layer caused by serious corrosion and reaction in electrolyte will lead to big challenges, including dendrite growth, low Coulombic efficiency and even safety issues. In this paper, we first demonstrate the inorganic-organic coating via advanced molecular layer deposition (alucone) as a protective layer for metallic Na anode. By protecting Na anode with controllable alucone layer, the dendrites and mossy Na formation have been effectively suppressed and the lifetime has been significantly improved. Moreover, the molecular layer deposition alucone coating shows better performances than the atomic layer deposition Al 2 O 3 coating. The novel design of molecular layer deposition protected Na metal anode may bring in new opportunities to the realization of the next-generation high energy-density NIBs and NMBs.

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds.

PubMed

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R J D; Giacomini, Elisa; Hansen, Mette R; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F; Spring, David R

2015-04-21

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity.

High- to low-dose extrapolation: critical determinants involved in the dose response of carcinogenic substances.

PubMed

Swenberg, J A; Richardson, F C; Boucheron, J A; Deal, F H; Belinsky, S A; Charbonneau, M; Short, B G

1987-12-01

Recent investigations on mechanism of carcinogenesis have demonstrated important quantitative relationships between the induction of neoplasia, the molecular dose of promutagenic DNA adducts and their efficiency for causing base-pair mismatch, and the extent of cell proliferation in target organ. These factors are involved in the multistage process of carcinogenesis, including initiation, promotion, and progression. The molecular dose of DNA adducts can exhibit supralinear, linear, or sublinear relationships to external dose due to differences in absorption, biotransformation, and DNA repair at high versus low doses. In contrast, increased cell proliferation is a common phenomena that is associated with exposures to relatively high doses of toxic chemicals. As such, it enhances the carcinogenic response at high doses, but has little effect at low doses. Since data on cell proliferation can be obtained for any exposure scenario and molecular dosimetry studies are beginning to emerge on selected chemical carcinogens, methods are needed so that these critical factors can be utilized in extrapolation from high to low doses and across species. The use of such information may provide a scientific basis for quantitative risk assessment.

High- to low-dose extrapolation: critical determinants involved in the dose response of carcinogenic substances.

PubMed Central

Swenberg, J A; Richardson, F C; Boucheron, J A; Deal, F H; Belinsky, S A; Charbonneau, M; Short, B G

1987-01-01

Recent investigations on mechanism of carcinogenesis have demonstrated important quantitative relationships between the induction of neoplasia, the molecular dose of promutagenic DNA adducts and their efficiency for causing base-pair mismatch, and the extent of cell proliferation in target organ. These factors are involved in the multistage process of carcinogenesis, including initiation, promotion, and progression. The molecular dose of DNA adducts can exhibit supralinear, linear, or sublinear relationships to external dose due to differences in absorption, biotransformation, and DNA repair at high versus low doses. In contrast, increased cell proliferation is a common phenomena that is associated with exposures to relatively high doses of toxic chemicals. As such, it enhances the carcinogenic response at high doses, but has little effect at low doses. Since data on cell proliferation can be obtained for any exposure scenario and molecular dosimetry studies are beginning to emerge on selected chemical carcinogens, methods are needed so that these critical factors can be utilized in extrapolation from high to low doses and across species. The use of such information may provide a scientific basis for quantitative risk assessment. PMID:3447904

A novel high resolution, high sensitivity SPECT detector for molecular imaging of cardiovascular diseases

NASA Astrophysics Data System (ADS)

Cusanno, F.; Argentieri, A.; Baiocchi, M.; Colilli, S.; Cisbani, E.; De Vincentis, G.; Fratoni, R.; Garibaldi, F.; Giuliani, F.; Gricia, M.; Lucentini, M.; Magliozzi, M. L.; Majewski, S.; Marano, G.; Musico, P.; Musumeci, M.; Santavenere, F.; Torrioli, S.; Tsui, B. M. W.; Vitelli, L.; Wang, Y.

2010-05-01

Cardiovascular diseases are the most common cause of death in western countries. Understanding the rupture of vulnerable atherosclerotic plaques and monitoring the effect of innovative therapies of heart failure is of fundamental importance. A flexible, high resolution, high sensitivity detector system for molecular imaging with radionuclides on small animal models has been designed for this aim. A prototype has been built using tungsten pinhole and LaBr3(Ce) scintillator coupled to Hamamatsu Flat Panel PMTs. Compact individual-channel readout has been designed, built and tested. Measurements with phantoms as well as pilot studies on mice have been performed, the results show that the myocardial perfusion in mice can be determined with sufficient precision. The detector will be improved replacing the Hamamatsu Flat Panel with Silicon Photomultipliers (SiPMs) to allow integration of the system with MRI scanners. Application of LaBr3(Ce) scintillator coupled to photosensor with high photon detection efficiency and excellent energy resolution will allow dual-label imaging to monitor simultaneously the cardiac perfusion and the molecular targets under investigation during the heart therapy.

Photocatalytic Conversion of CO2 to CO by a Copper(II) Quaterpyridine Complex.

PubMed

Guo, Zhenguo; Yu, Fei; Yang, Ying; Leung, Chi-Fai; Ng, Siu-Mui; Ko, Chi-Chiu; Cometto, Claudio; Lau, Tai-Chu; Robert, Marc

2017-10-23

The invention of efficient systems for the photocatalytic reduction of CO 2 comprising earth-abundant metal catalysts is a promising approach for the production of solar fuels. One bottleneck is to design highly selective and robust molecular complexes that are able to transform the CO 2 gas. The Cu II quaterpyridine complex [Cu(qpy)] 2+ (1) is found to be a highly efficient and selective catalyst for visible-light driven CO 2 reduction in CH 3 CN using [Ru(bpy) 3 ] 2+ (bpy: bipyridine) as photosensitizer and BIH/TEOA (1,3-dimethyl-2-phenyl-2,3-dihydro-1H-benzo[d]imidazole/triethanolamine) as sacrificial reductant. The photocatalytic reaction is greatly enhanced by the presence of H 2 O (1-4 % v/v), and a turnover number of >12 400 for CO production can be achieved with 97 % selectivity, which is among the highest of molecular 3d CO 2 reduction catalysts. Results from Hg poisoning and dynamic light scattering experiments suggest that this photocatalyst is homogenous. To the best of our knowledge, 1 is the first example of molecular Cu-based catalyst for the photoreduction of CO 2 . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Online molecular characterization of fine particulate matter in Port Angeles, WA: Evidence for a major impact from residential wood smoke

NASA Astrophysics Data System (ADS)

Gaston, Cassandra J.; Lopez-Hilfiker, Felipe D.; Whybrew, Lauren E.; Hadley, Odelle; McNair, Fran; Gao, Honglian; Jaffe, Daniel A.; Thornton, Joel A.

2016-08-01

We present on-line molecular composition measurements of wintertime particulate matter (PM) during 2014 using an iodide-adduct high-resolution, time-of-flight chemical ionization mass spectrometer (HR-TOF-CIMS) coupled to a Filter Inlet for Gases and AEROsols (FIGAERO). These measurements were part of an intensive effort to characterize PM in the region with a focus on ultrafine particle sources. The technique was used to detect and quantify different classes of wood burning tracers, including levoglucosan, methoxyphenols, and nitrocatechols, among other compounds in near real-time. During the campaign, particulate mass concentrations of compounds with the same molecular composition as levoglucosan ranged from 0.002 to 19 μg/m3 with a median mass concentration of 0.9 μg/m3. Wood burning markers, in general, showed a strong diurnal pattern peaking at night and in the early morning. This diurnal profile combined with cold, stagnant conditions, wind directions from predominantly residential areas, and observations of lower combustion efficiency at night support residential wood burning as a dominant source of wintertime PM in Port Angeles. This finding has implications for improving wintertime air quality in the region by encouraging the use of high efficiency wood-burning stoves or other cleaner home heating options throughout the relevant domain.

Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions.

PubMed

Paliwal, Himanshu; Shirts, Michael R

2013-11-12

Multistate reweighting methods such as the multistate Bennett acceptance ratio (MBAR) can predict free energies and expectation values of thermodynamic observables at poorly sampled or unsampled thermodynamic states using simulations performed at only a few sampled states combined with single point energy reevaluations of these samples at the unsampled states. In this study, we demonstrate the power of this general reweighting formalism by exploring the effect of simulation parameters controlling Coulomb and Lennard-Jones cutoffs on free energy calculations and other observables. Using multistate reweighting, we can quickly identify, with very high sensitivity, the computationally least expensive nonbonded parameters required to obtain a specified accuracy in observables compared to the answer obtained using an expensive "gold standard" set of parameters. We specifically examine free energy estimates of three molecular transformations in a benchmark molecular set as well as the enthalpy of vaporization of TIP3P. The results demonstrates the power of this multistate reweighting approach for measuring changes in free energy differences or other estimators with respect to simulation or model parameters with very high precision and/or very low computational effort. The results also help to identify which simulation parameters affect free energy calculations and provide guidance to determine which simulation parameters are both appropriate and computationally efficient in general.

Molecular Mechanisms of Phosphorus Metabolism and Transport during Leaf Senescence

PubMed Central

Stigter, Kyla A.; Plaxton, William C.

2015-01-01

Leaf senescence, being the final developmental stage of the leaf, signifies the transition from a mature, photosynthetically active organ to the attenuation of said function and eventual death of the leaf. During senescence, essential nutrients sequestered in the leaf, such as phosphorus (P), are mobilized and transported to sink tissues, particularly expanding leaves and developing seeds. Phosphorus recycling is crucial, as it helps to ensure that previously acquired P is not lost to the environment, particularly under the naturally occurring condition where most unfertilized soils contain low levels of soluble orthophosphate (Pi), the only form of P that roots can directly assimilate from the soil. Piecing together the molecular mechanisms that underpin the highly variable efficiencies of P remobilization from senescing leaves by different plant species may be critical for devising effective strategies for improving overall crop P-use efficiency. Maximizing Pi remobilization from senescing leaves using selective breeding and/or biotechnological strategies will help to generate P-efficient crops that would minimize the use of unsustainable and polluting Pi-containing fertilizers in agriculture. This review focuses on the molecular mechanisms whereby P is remobilized from senescing leaves and transported to sink tissues, which encompasses the action of hormones, transcription factors, Pi-scavenging enzymes, and Pi transporters. PMID:27135351

Noncovalent interaction-assisted drug delivery system with highly efficient uptake and release of paclitaxel for anticancer therapy.

PubMed

Wei, Yuping; Ma, Liang; Zhang, Liang; Xu, Xia

2017-01-01

An effective drug delivery system requires efficient drug uptake and release inside cancer cells. Here, we report a novel drug delivery system, in which paclitaxel (PTX) interacts with a novel cell penetrating peptide (CPP) through noncovalent interaction designed based on molecular simulations. This CPP/PTX complex confers high efficiency in delivering PTX into cancer cells not by endocytosis but by an energy-independent pathway. Once inside cells, the noncovalent interaction between PTX and the CPP may allow fast release of PTX within cells due to the direct translocation of CPP/PTX. This drug delivery system exhibits strong capacity for inhibition of tumor growth and offers a new avenue for the development of advanced drug delivery systems for anticancer therapy.

Simultaneous extraction and determination of phthalate esters in aqueous solution by yolk-shell magnetic mesoporous carbon-molecularly imprinted composites based on solid-phase extraction coupled with gas chromatography-mass spectrometry.

PubMed

Yang, Rui; Liu, Yuxin; Yan, Xiangyang; Liu, Shaomin

2016-12-01

A rapid, sensitive and accurate method for the simultaneous extraction and determination of five types of trace phthalate esters (PAEs) in environmental water and beverage samples using magnetic molecularly imprinted solid-phase extraction (MMIP-SPE) coupled with gas chromatography-mass spectrometry (GC-MS) was developed. A novel type of molecularly imprinted polymers on the surface of yolk-shell magnetic mesoporous carbon (Fe 3 O 4 @void@C-MIPs) was used as an efficient adsorbent for selective adsorption of phthalate esters based on magnetic solid-phase extraction (MSPE). The real samples were first preconcentrated by Fe 3 O 4 @void@C-MIPs, subsequently extracted by eluent and finally determined by GC-MS after magnetic separation. Several variables affecting the extraction efficiency of the analytes, including the type and volume of the elution solvent, amount of adsorbent, extraction time, desorption time and pH of the sample solution, were investigated and optimized. Validation experiments indicated that the developed method presented good linearity (R 2 >0.9961), satisfactory precision (RSD<6.7%), and high recovery (86.1-103.1%). The limits of detection ranged from 1.6ng/L to 5.2ng/L and the enrichment factor was in the range of 822-1423. The results indicated that the novel method had the advantages of convenience, good sensitivity, and high efficiency, and it could also be successfully applied to the analysis of PAEs in real samples. Copyright © 2016. Published by Elsevier B.V.

A Nonfullerene Small Molecule Acceptor with 3D Interlocking Geometry Enabling Efficient Organic Solar Cells.

PubMed

Lee, Jaewon; Singh, Ranbir; Sin, Dong Hun; Kim, Heung Gyu; Song, Kyu Chan; Cho, Kilwon

2016-01-06

A new 3D nonfullerene small-molecule acceptor is reported. The 3D interlocking geometry of the small-molecule acceptor enables uniform molecular conformation and strong intermolecular connectivity, facilitating favorable nanoscale phase separation and electron charge transfer. By employing both a novel polymer donor and a nonfullerene small-molecule acceptor in the solution-processed organic solar cells, a high-power conversion efficiency of close to 6% is demonstrated. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effects of Molecular Stresses on Energy Transfer Pathways in Opto- and Electro-Excited Conjugated Polymers for High-Efficiency Optoelectronic Devices

DTIC Science & Technology

2014-10-20

unless it hops, and lead to obstructed recombination for PL or charge separation for solar cells and the reduced quantum efficiencies of the...excitons (Fig. 1a and 1b). For the free-moving delocalized states of the Wannier-Mott excitons, the binding energy in silicon , for example, is around...typically encompass many unit cells and typically exist in materials of small bandgap and large dielectric constant. In converse, the the tightly

A transcriptome multi-tissue analysis identifies biological pathways and genes associated with variations in feed efficiency of growing pigs.

PubMed

Gondret, Florence; Vincent, Annie; Houée-Bigot, Magalie; Siegel, Anne; Lagarrigue, Sandrine; Causeur, David; Gilbert, Hélène; Louveau, Isabelle

2017-03-21

Animal's efficiency in converting feed into lean gain is a critical issue for the profitability of meat industries. This study aimed to describe shared and specific molecular responses in different tissues of pigs divergently selected over eight generations for residual feed intake (RFI). Pigs from the low RFI line had an improved gain-to-feed ratio during the test period and displayed higher leanness but similar adiposity when compared with pigs from the high RFI line at 132 days of age. Transcriptomics data were generated from longissimus muscle, liver and two adipose tissues using a porcine microarray and analyzed for the line effect (n = 24 pigs per line). The most apparent effect of the line was seen in muscle, whereas subcutaneous adipose tissue was the less affected tissue. Molecular data were analyzed by bioinformatics and subjected to multidimensional statistics to identify common biological processes across tissues and key genes participating to differences in the genetics of feed efficiency. Immune response, response to oxidative stress and protein metabolism were the main biological pathways shared by the four tissues that distinguished pigs from the low or high RFI lines. Many immune genes were under-expressed in the four tissues of the most efficient pigs. The main genes contributing to difference between pigs from the low vs high RFI lines were CD40, CTSC and NTN1. Different genes associated with energy use were modulated in a tissue-specific manner between the two lines. The gene expression program related to glycogen utilization was specifically up-regulated in muscle of pigs from the low RFI line (more efficient). Genes involved in fatty acid oxidation were down-regulated in muscle but were promoted in adipose tissues of the same pigs when compared with pigs from the high RFI line (less efficient). This underlined opposite line-associated strategies for energy use in skeletal muscle and adipose tissue. Genes related to cholesterol synthesis and efflux in liver and perirenal fat were also differentially regulated in pigs from the low vs high RFI lines. Non-productive functions such as immunity, defense against pathogens and oxidative stress contribute likely to inter-individual variations in feed efficiency.

Nanostructured organosilicon luminophores as a new concept of nanomaterials for highly efficient down-conversion of light

NASA Astrophysics Data System (ADS)

Ponomarenko, Sergey A.; Surin, Nikolay M.; Borshchev, Oleg V.; Skorotetcky, Maxim S.; Muzafarov, Aziz M.

2015-10-01

Nanostructured organosilicon luminophores (NOLs) are branched molecular structures having two types of covalently bonded via silicon atoms organic luminophores with efficient Förster energy transfer between them. They combine the best properties of organic luminophores and inorganic quantum dots: high absorption cross-section, excellent photoluminescence quantum yield, fast luminescence decay time, good processability and low toxicity. A smart choice of organic luminophores allowed us to design and synthesize a library of NOLs, absorbing from VUV to visible region and emitting at the desired wavelengths from 390 to 650 nm. They can be used as unique wavelength shifters in plastic scintillators and other applications.

Organic Solar Cells Based on a 2D Benzo[1,2-b:4,5-b']difuran-Conjugated Polymer with High-Power Conversion Efficiency.

PubMed

Huo, Lijun; Liu, Tao; Fan, Bingbing; Zhao, Zhiyuan; Sun, Xiaobo; Wei, Donghui; Yu, Mingming; Liu, Yunqi; Sun, Yanming

2015-11-18

A novel 2D benzodifuran (BDF)-based copolymer (PBDF-T1) is synthesized. Polymer solar cells fabricated with PBDF-T1 show high power conversion efficiency of 9.43% and fill factor of 77.4%, which is higher than the performance of its benzothiophene (BDT) counterpart (PBDT-T1). These results provide important progress for BDF-based copolymers and demonstrate that BDF-based copolymers can be competitive with the well-studied BDT counterparts via molecular structure design and device optimization. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Subtype-independent near full-length HIV-1 genome sequencing and assembly to be used in large molecular epidemiological studies and clinical management.

PubMed

Grossmann, Sebastian; Nowak, Piotr; Neogi, Ujjwal

2015-01-01

HIV-1 near full-length genome (HIV-NFLG) sequencing from plasma is an attractive multidimensional tool to apply in large-scale population-based molecular epidemiological studies. It also enables genotypic resistance testing (GRT) for all drug target sites allowing effective intervention strategies for control and prevention in high-risk population groups. Thus, the main objective of this study was to develop a simplified subtype-independent, cost- and labour-efficient HIV-NFLG protocol that can be used in clinical management as well as in molecular epidemiological studies. Plasma samples (n=30) were obtained from HIV-1B (n=10), HIV-1C (n=10), CRF01_AE (n=5) and CRF01_AG (n=5) infected individuals with minimum viral load >1120 copies/ml. The amplification was performed with two large amplicons of 5.5 kb and 3.7 kb, sequenced with 17 primers to obtain HIV-NFLG. GRT was validated against ViroSeq™ HIV-1 Genotyping System. After excluding four plasma samples with low-quality RNA, a total of 26 samples were attempted. Among them, NFLG was obtained from 24 (92%) samples with the lowest viral load being 3000 copies/ml. High (>99%) concordance was observed between HIV-NFLG and ViroSeq™ when determining the drug resistance mutations (DRMs). The N384I connection mutation was additionally detected by NFLG in two samples. Our high efficiency subtype-independent HIV-NFLG is a simple and promising approach to be used in large-scale molecular epidemiological studies. It will facilitate the understanding of the HIV-1 pandemic population dynamics and outline effective intervention strategies. Furthermore, it can potentially be applicable in clinical management of drug resistance by evaluating DRMs against all available antiretrovirals in a single assay.

Highly Disordered Amyloid-β Monomer Probed by Single-Molecule FRET and MD Simulation.

PubMed

Meng, Fanjie; Bellaiche, Mathias M J; Kim, Jae-Yeol; Zerze, Gül H; Best, Robert B; Chung, Hoi Sung

2018-02-27

Monomers of amyloid-β (Aβ) protein are known to be disordered, but there is considerable controversy over the existence of residual or transient conformations that can potentially promote oligomerization and fibril formation. We employed single-molecule Förster resonance energy transfer (FRET) spectroscopy with site-specific dye labeling using an unnatural amino acid and molecular dynamics simulations to investigate conformations and dynamics of Aβ isoforms with 40 (Aβ40) and 42 residues (Aβ42). The FRET efficiency distributions of both proteins measured in phosphate-buffered saline at room temperature show a single peak with very similar FRET efficiencies, indicating there is apparently only one state. 2D FRET efficiency-donor lifetime analysis reveals, however, that there is a broad distribution of rapidly interconverting conformations. Using nanosecond fluorescence correlation spectroscopy, we measured the timescale of the fluctuations between these conformations to be ∼35 ns, similar to that of disordered proteins. These results suggest that both Aβ40 and Aβ42 populate an ensemble of rapidly reconfiguring unfolded states, with no long-lived conformational state distinguishable from that of the disordered ensemble. To gain molecular-level insights into these observations, we performed molecular dynamics simulations with a force field optimized to describe disordered proteins. We find, as in experiments, that both peptides populate configurations consistent with random polymer chains, with the vast majority of conformations lacking significant secondary structure, giving rise to very similar ensemble-averaged FRET efficiencies. Published by Elsevier Inc.

Gas Phase Probe Molecules for Assessing In vitro Metabolism to Infer an In vivo Response

EPA Science Inventory

Efficient and accurate in vitro high-throughput screening (HTS) methods use cellular and molecular based adverse outcome pathways (AOPs) as central elements for exposure assessment and chemical prioritization. However, not all AOPs are based on human or animal systems biology, bu...

Advancing polymers of intrinsic microporosity by mechanochemistry

DOE PAGES

Zhang, Pengfei; Jiang, Xueguang; Wan, Shun; ...

2015-02-20

Herein, we report a fast (15 min) and solvent-free mechanochemical approach to construct polymers of intrinsic microporosity (PIMs) with high molecular mass and low polydispersity by solid grinding. The enhanced reaction efficiency results from the instantaneous frictional heating and continuous exposure of active sites within those solid reactants.

Manipulating the Electronic Excited State Energies of Pyrimidine-Based Thermally Activated Delayed Fluorescence Emitters To Realize Efficient Deep-Blue Emission.

PubMed

Komatsu, Ryutaro; Ohsawa, Tatsuya; Sasabe, Hisahiro; Nakao, Kohei; Hayasaka, Yuya; Kido, Junji

2017-02-08

The development of efficient and robust deep-blue emitters is one of the key issues in organic light-emitting devices (OLEDs) for environmentally friendly, large-area displays or general lighting. As a promising technology that realizes 100% conversion from electrons to photons, thermally activated delayed fluorescence (TADF) emitters have attracted considerable attention. However, only a handful of examples of deep-blue TADF emitters have been reported to date, and the emitters generally show large efficiency roll-off at practical luminance over several hundreds to thousands of cd m -2 , most likely because of the long delayed fluorescent lifetime (τ d ). To overcome this problem, we molecularly manipulated the electronic excited state energies of pyrimidine-based TADF emitters to realize deep-blue emission and reduced τ d . We then systematically investigated the relationships among the chemical structure, properties, and device performances. The resultant novel pyrimidine emitters, called Ac-XMHPMs (X = 1, 2, and 3), contain different numbers of bulky methyl substituents at acceptor moieties, increasing the excited singlet (E S ) and triplet state (E T ) energies. Among them, Ac-3MHPM, with a high E T of 2.95 eV, exhibited a high external quantum efficiency (η ext,max ) of 18% and an η ext of 10% at 100 cd m -2 with Commission Internationale de l'Eclairage chromaticity coordinates of (0.16, 0.15). These efficiencies are among the highest values to date for deep-blue TADF OLEDs. Our molecular design strategy provides fundamental guidance to design novel deep-blue TADF emitters.

High-Flow-Rate Impinger for the Study of Concentration, Viability, Metabolic Activity, and Ice-Nucleation Activity of Airborne Bacteria.

PubMed

Šantl-Temkiv, Tina; Amato, Pierre; Gosewinkel, Ulrich; Thyrhaug, Runar; Charton, Anaïs; Chicot, Benjamin; Finster, Kai; Bratbak, Gunnar; Löndahl, Jakob

2017-10-03

The study of airborne bacteria relies on a sampling strategy that preserves their integrity and in situ physiological state, e.g. viability, cultivability, metabolic activity, and ice-nucleation activity. Because ambient air harbors low concentrations of bacteria, an effective bioaerosol sampler should have a high sampling efficiency and a high airflow. We characterize a high-flow-rate impinger with respect to particle collection and retention efficiencies in the range 0.5-3.0 μm, and we investigated its ability to preserve the physiological state of selected bacterial species and seawater bacterial community in comparison with four commercial bioaerosol samplers. The collection efficiency increased with particle size and the cutoff diameter was between 0.5 and 1 μm. During sampling periods of 120-300 min, the impinger retained the cultivability, metabolic activity, viability, and ice-nucleation activity of investigated bacteria. Field studies in semiurban, high-altitude, and polar environments included periods of low bacterial air concentrations, thus demonstrating the benefits of the impinger's high flow rate. In conclusion, the impinger described here has many advantages compared with other bioaerosol samplers currently on the market: a potential for long sampling time, a high flow rate, a high sampling and retention efficiency, low costs, and applicability for diverse downstream microbiological and molecular analyses.

Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

NASA Astrophysics Data System (ADS)

Zhan, Aibin; Bao, Zhenmin; Hu, Xiaoli; Lu, Wei; Hu, Jingjie

2009-06-01

Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time- and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop ( Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time- and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

Genetic control of functional traits related to photosynthesis and water use efficiency in Pinus pinaster Ait. drought response: integration of genome annotation, allele association and QTL detection for candidate gene identification.

PubMed

de Miguel, Marina; Cabezas, José-Antonio; de María, Nuria; Sánchez-Gómez, David; Guevara, María-Ángeles; Vélez, María-Dolores; Sáez-Laguna, Enrique; Díaz, Luis-Manuel; Mancha, Jose-Antonio; Barbero, María-Carmen; Collada, Carmen; Díaz-Sala, Carmen; Aranda, Ismael; Cervera, María-Teresa

2014-06-12

Understanding molecular mechanisms that control photosynthesis and water use efficiency in response to drought is crucial for plant species from dry areas. This study aimed to identify QTL for these traits in a Mediterranean conifer and tested their stability under drought. High density linkage maps for Pinus pinaster were used in the detection of QTL for photosynthesis and water use efficiency at three water irrigation regimes. A total of 28 significant and 27 suggestive QTL were found. QTL detected for photochemical traits accounted for the higher percentage of phenotypic variance. Functional annotation of genes within the QTL suggested 58 candidate genes for the analyzed traits. Allele association analysis in selected candidate genes showed three SNPs located in a MYB transcription factor that were significantly associated with efficiency of energy capture by open PSII reaction centers and specific leaf area. The integration of QTL mapping of functional traits, genome annotation and allele association yielded several candidate genes involved with molecular control of photosynthesis and water use efficiency in response to drought in a conifer species. The results obtained highlight the importance of maintaining the integrity of the photochemical machinery in P. pinaster drought response.

Preparation of magnetic molecularly imprinted polymers by atom transfer radical polymerization for the rapid extraction of avermectin from fish samples.

PubMed

You, Xiaoxiao; Gao, Lei; Qin, Dongli; Chen, Ligang

2017-01-01

A novel and highly efficient approach to obtain magnetic molecularly imprinted polymers is described to detect avermectin in fish samples. The magnetic molecularly imprinted polymers were synthesized by surface imprinting polymerization using magnetic multiwalled carbon nanotubes as the support materials, atom transfer radical polymerization as the polymerization method, avermectin as template, acrylamide as functional monomer, and ethylene glycol dimethacrylate as crosslinker. The characteristics of the magnetic molecularly imprinted polymers were assessed by using transmission electron microscopy, Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, vibrating sample magnetometry, X-ray diffraction, and thermogravimetric analysis. The binding characteristics of magnetic molecularly imprinted polymers were researched through isothermal adsorption experiment, kinetics adsorption experiment, and the selectivity experiment. Coupled with ultra high performance liquid chromatography and tandem mass spectrometry, the extraction conditions of the magnetic molecularly imprinted polymers as adsorbents for avermectin were investigated in detail. The recovery of avermectin was 84.2-97.0%, and the limit of detection was 0.075 μg/kg. Relative standard deviations of intra- and inter-day precisions were in the range of 1.7-2.9% and 3.4-5.6%, respectively. The results demonstrated that the extraction method not only has high selectivity and accuracy, but also is convenient for the determination of avermectin in fish samples. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

High-order-harmonic generation from H2+ molecular ions near plasmon-enhanced laser fields

NASA Astrophysics Data System (ADS)

Yavuz, I.; Tikman, Y.; Altun, Z.

2015-08-01

Simulations of plasmon-enhanced high-order-harmonic generation are performed for a H2+ molecular cation near the metallic nanostructures. We employ the numerical solution of the time-dependent Schrödinger equation in reduced coordinates. We assume that the main axis of H2+ is aligned perfectly with the polarization direction of the plasmon-enhanced field. We perform systematic calculations on plasmon-enhanced harmonic generation based on an infinite-mass approximation, i.e., pausing nuclear vibrations. Our simulations show that molecular high-order-harmonic generation from plasmon-enhanced laser fields is possible. We observe the dispersion of a plateau of harmonics when the laser field is plasmon enhanced. We find that the maximum kinetic energy of the returning electron follows 4 Up . We also find that when nuclear vibrations are enabled, the efficiency of the harmonics is greatly enhanced relative to that of static nuclei. However, the maximum kinetic energy 4 Up is largely maintained.

Mechanochemical Ring-Opening Polymerization of Lactide: Liquid-Assisted Grinding for the Green Synthesis of Poly(lactic acid) with High Molecular Weight.

PubMed

Ohn, Nuri; Shin, Jihoon; Kim, Sung Sik; Kim, Jeung Gon

2017-09-22

Mechanochemical polymerization of lactide is carried out by using ball milling. Mechanical energy from collisions between the balls and the vessel efficiently promotes an organic-base-mediated metal- and solvent-free solid-state polymerization. Investigation of the parameters of the ball-milling synthesis revealed that the degree of lactide ring-opening polymerization could be modulated by the ball-milling time, vibration frequency, mass of the ball media, and liquid-assisted grinding. Liquid-assisted grinding was found to be an especially important factor for achieving a high degree of mechanochemical polymerization. Although polymer-chain scission from the strong collision energy prevented mechanical-force-driven high-molecular-weight polymer synthesis, the addition of only a small amount of liquid enabled sufficient energy dissipation and poly(lactic acid) was thereby obtained with a molecular weight of over 1×10 5  g mol -1 . © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Bright Photon Upconversion on Composite Organic Lanthanide Molecules through Localized Thermal Radiation.

PubMed

Ye, Huanqing; Bogdanov, Viktor; Liu, Sheng; Vajandar, Saumitra; Osipowicz, Thomas; Hernández, Ignacio; Xiong, Qihua

2017-12-07

Converting low-energy photons via thermal radiation can be a potential approach for utilizing infrared (IR) photons to improve photovoltaic efficiency. Lanthanide-containing materials have achieved great progress in IR-to-visible photon upconversion (UC). Herein, we first report bright photon, tunable wavelength UC through localized thermal radiation at the molecular scale with low excitation power density (<10 W/cm 2 ) realized on lanthanide complexes of perfluorinated organic ligands. This is enabled by engineering the pathways of nonradiative de-excitation and energy transfer in a composite of ytterbium and terbium perfluoroimidodiphosphinates. The IR-excited thermal UC and wavelength control is realized through the terbium activators sensitized by the ytterbium sensitizers having high luminescence efficiency. The metallic molecular composite thus can be a potential energy material in the use of the IR solar spectrum for thermal photovoltaic applications.

Geometric integration in Born-Oppenheimer molecular dynamics.

PubMed

Odell, Anders; Delin, Anna; Johansson, Börje; Cawkwell, Marc J; Niklasson, Anders M N

2011-12-14

Geometric integration schemes for extended Lagrangian self-consistent Born-Oppenheimer molecular dynamics, including a weak dissipation to remove numerical noise, are developed and analyzed. The extended Lagrangian framework enables the geometric integration of both the nuclear and electronic degrees of freedom. This provides highly efficient simulations that are stable and energy conserving even under incomplete and approximate self-consistent field (SCF) convergence. We investigate three different geometric integration schemes: (1) regular time reversible Verlet, (2) second order optimal symplectic, and (3) third order optimal symplectic. We look at energy conservation, accuracy, and stability as a function of dissipation, integration time step, and SCF convergence. We find that the inclusion of dissipation in the symplectic integration methods gives an efficient damping of numerical noise or perturbations that otherwise may accumulate from finite arithmetics in a perfect reversible dynamics. © 2011 American Institute of Physics

Coupled wave-packets for non-adiabatic molecular dynamics: a generalization of Gaussian wave-packet dynamics to multiple potential energy surfaces

DOE PAGES

White, Alexander James; Tretiak, Sergei; Mozyrsky, Dima V.

2016-04-25

Accurate simulation of the non-adiabatic dynamics of molecules in excited electronic states is key to understanding molecular photo-physical processes. Here we present a novel method, based on a semiclassical approximation, that is as efficient as the commonly used mean field Ehrenfest or ad hoc surface hopping methods and properly accounts for interference and decoherence effects. This novel method is an extension of Heller's thawed Gaussian wave-packet dynamics that includes coupling between potential energy surfaces. By studying several standard test problems we demonstrate that the accuracy of the method can be systematically improved while maintaining high efficiency. The method is suitablemore » for investigating the role of quantum coherence in the non-adiabatic dynamics of many-atom molecules.« less

ECUT: Energy Conversion and Utilization Technologies program - Biocatalysis research activity

NASA Technical Reports Server (NTRS)

Wilcox, R.

1984-01-01

The activities of the Biocatalysis Research Activity are organized into the Biocatalysis and Molecular Modeling work elements and a supporting planning and analysis function. In the Biocatalysis work element, progress is made in developing a method for stabilizing genetically engineered traits in microorganisms, refining a technique for monitoring cells that are genetically engineered, and identifying strains of fungi for highly efficient preprocessing of biomass for optimizing the efficiency of bioreactors. In the Molecular Modeling work element, a preliminary model of the behavior of enzymes is developed. A preliminary investigation of the potential for synthesizing enzymes for use in electrochemical processes is completed. Contact with industry and universities is made to define key biocatalysis technical issues and to broaden the range of potential participants in the activity. Analyses are conducted to identify and evaluate potential concepts for future research funding.

Polymer-fullerene miscibility: a metric for screening new materials for high-performance organic solar cells.

PubMed

Treat, Neil D; Varotto, Alessandro; Takacs, Christopher J; Batara, Nicolas; Al-Hashimi, Mohammed; Heeney, Martin J; Heeger, Alan J; Wudl, Fred; Hawker, Craig J; Chabinyc, Michael L

2012-09-26

The improvement of the power conversion efficiency (PCE) of polymer bulk heterojunction (BHJ) solar cells has generally been achieved through synthetic design to control frontier molecular orbital energies and molecular ordering of the electron-donating polymer. An alternate approach to control the PCE of a BHJ is to tune the miscibility of the fullerene and a semiconducting polymer by varying the structure of the fullerene. The miscibility of a series of 1,4-fullerene adducts in the semiconducting polymer, poly(3-hexylselenophene), P3HS, was measured by dynamic secondary ion mass spectrometry using a model bilayer structure. The microstructure of the bilayer was investigated using high-angle annular dark-field scanning transmission microscopy and linked to the polymer-fullerene miscibility. Finally, P3HS:fullerene BHJ solar cells were fabricated from each fullerene derivative, enabling the correlation of the active layer microstructure to the charge collection efficiency and resulting PCE of each system. The volume fraction of polymer-rich, fullerene-rich, and polymer-fullerene mixed domains can be tuned using the miscibility leading to improvement in the charge collection efficiency and PCE in P3HS:fullerene BHJ solar cells. These results suggest a rational approach to the design of fullerenes for improved BHJ solar cells.

Molecular Doping the Topological Dirac Semimetal Na3Bi across the Charge Neutrality Point with F4-TCNQ.

PubMed

Edmonds, Mark T; Hellerstedt, Jack; O'Donnell, Kane M; Tadich, Anton; Fuhrer, Michael S

2016-06-29

We perform low-temperature transport and high-resolution photoelectron spectroscopy on 20 nm thin film topological Dirac semimetal Na3Bi grown by molecular beam epitaxy. We demonstrate efficient electron depletion ∼10(13) cm(-2) of Na3Bi via vacuum deposition of molecular F4-TCNQ without degrading the sample mobility. For samples with low as-grown n-type doping (1 × 10(12) cm(-2)), F4-TCNQ doping can achieve charge neutrality and even a net p-type doping. Photoelectron spectroscopy and density functional theory are utilized to investigate the behavior of F4-TCNQ on the Na3Bi surface.

Virtual Screening of Receptor Sites for Molecularly Imprinted Polymers.

PubMed

Bates, Ferdia; Cela-Pérez, María Concepción; Karim, Kal; Piletsky, Sergey; López-Vilariño, José Manuel

2016-08-01

Molecularly Imprinted Polymers (MIPs) are highly advantageous in the field of analytical chemistry. However, interference from secondary molecules can also impede capture of a target by a MIP receptor. This greatly complicates the design process and often requires extensive laboratory screening which is time consuming, costly, and creates substantial waste products. Herein, is presented a new technique for screening of "virtually imprinted receptors" for rebinding of the molecular template as well as secondary structures, correlating the virtual predictions with experimentally acquired data in three case studies. This novel technique is particularly applicable to the evaluation and prediction of MIP receptor specificity and efficiency in complex aqueous systems. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Photodynamic Efficiency: From Molecular Photochemistry to Cell Death

PubMed Central

Bacellar, Isabel O. L.; Tsubone, Tayana M.; Pavani, Christiane; Baptista, Mauricio S.

2015-01-01

Photodynamic therapy (PDT) is a clinical modality used to treat cancer and infectious diseases. The main agent is the photosensitizer (PS), which is excited by light and converted to a triplet excited state. This latter species leads to the formation of singlet oxygen and radicals that oxidize biomolecules. The main motivation for this review is to suggest alternatives for achieving high-efficiency PDT protocols, by taking advantage of knowledge on the chemical and biological processes taking place during and after photosensitization. We defend that in order to obtain specific mechanisms of cell death and maximize PDT efficiency, PSes should oxidize specific molecular targets. We consider the role of subcellular localization, how PS photochemistry and photophysics can change according to its nanoenvironment, and how can all these trigger specific cell death mechanisms. We propose that in order to develop PSes that will cause a breakthrough enhancement in the efficiency of PDT, researchers should first consider tissue and intracellular localization, instead of trying to maximize singlet oxygen quantum yields in in vitro tests. In addition to this, we also indicate many open questions and challenges remaining in this field, hoping to encourage future research. PMID:26334268

Exploring Hamiltonian dielectric solvent molecular dynamics

NASA Astrophysics Data System (ADS)

Bauer, Sebastian; Tavan, Paul; Mathias, Gerald

2014-09-01

Hamiltonian dielectric solvent (HADES) is a recent method [7,25], which enables Hamiltonian molecular dynamics (MD) simulations of peptides and proteins in dielectric continua. Sample simulations of an α-helical decapeptide with and without explicit solvent demonstrate the high efficiency of HADES-MD. Addressing the folding of this peptide by replica exchange MD we study the properties of HADES by comparing melting curves, secondary structure motifs and salt bridges with explicit solvent results. Despite the unoptimized ad hoc parametrization of HADES, calculated reaction field energies correlate well with numerical grid solutions of the dielectric Poisson equation.

Shaping a screening file for maximal lead discovery efficiency and effectiveness: elimination of molecular redundancy.

PubMed

Bakken, Gregory A; Bell, Andrew S; Boehm, Markus; Everett, Jeremy R; Gonzales, Rosalia; Hepworth, David; Klug-McLeod, Jacquelyn L; Lanfear, Jeremy; Loesel, Jens; Mathias, John; Wood, Terence P

2012-11-26

High Throughput Screening (HTS) is a successful strategy for finding hits and leads that have the opportunity to be converted into drugs. In this paper we highlight novel computational methods used to select compounds to build a new screening file at Pfizer and the analytical methods we used to assess their quality. We also introduce the novel concept of molecular redundancy to help decide on the density of compounds required in any region of chemical space in order to be confident of running successful HTS campaigns.

Technical Desiderata for the Integration of Genomic Data into Electronic Health Records

PubMed Central

Masys, Daniel R.; Jarvik, Gail P.; Abernethy, Neil F.; Anderson, Nicholas R.; Papanicolaou, George J.; Paltoo, Dina N.; Hoffman, Mark A.; Kohane, Isaac S.; Levy, Howard P.

2012-01-01

The era of “Personalized Medicine,” guided by individual molecular variation in DNA, RNA, expressed proteins and other forms of high volume molecular data brings new requirements and challenges to the design and implementation of Electronic Health Records (EHRs). In this article we describe the characteristics of biomolecular data that differentiate it from other classes of data commonly found in EHRs, enumerate a set of technical desiderata for its management in healthcare settings, and offer a candidate technical approach to its compact and efficient representation in operational systems. PMID:22223081

A highly efficient silole-containing dithienylethene with excellent thermal stability and fatigue resistance: a promising candidate for optical memory storage materials.

PubMed

Chan, Jacky Chi-Hung; Lam, Wai Han; Yam, Vivian Wing-Wah

2014-12-10

Diarylethene compounds are potential candidates for applications in optical memory storage systems and photoswitchable molecular devices; however, they usually show low photocycloreversion quantum yields, which result in ineffective erasure processes. Here, we present the first highly efficient photochromic silole-containing dithienylethene with excellent thermal stability and fatigue resistance. The photochemical quantum yields for photocyclization and photocycloreversion of the compound are found to be high and comparable to each other; the latter of which is rarely found in diarylethene compounds. These would give rise to highly efficient photoswitchable material with effective writing and erasure processes. Incorporation of the silole moiety as a photochromic dithienylethene backbone also was demonstrated to enhance the thermal stability of the closed form, in which the thermal backward reaction to the open form was found to be negligible even at 100 °C, which leads to a promising candidate for use as photoswitchable materials and optical memory storage.

Treatment of high ethanol concentration wastewater by biological sand filters: enhanced COD removal and bacterial community dynamics.

PubMed

Rodriguez-Caballero, A; Ramond, J-B; Welz, P J; Cowan, D A; Odlare, M; Burton, S G

2012-10-30

Winery wastewater is characterized by its high chemical oxygen demand (COD), seasonal occurrence and variable composition, including periodic high ethanol concentrations. In addition, winery wastewater may contain insufficient inorganic nutrients for optimal biodegradation of organic constituents. Two pilot-scale biological sand filters (BSFs) were used to treat artificial wastewater: the first was amended with ethanol and the second with ethanol, inorganic nitrogen (N) and phosphorus (P). A number of biochemical parameters involved in the removal of pollutants through BSF systems were monitored, including effluent chemistry and bacterial community structures. The nutrient supplemented BSF showed efficient COD, N and P removal. Comparison of the COD removal efficiencies of the two BSFs showed that N and P addition enhanced COD removal efficiency by up to 16%. Molecular fingerprinting of BSF sediment samples using denaturing gradient gel electrophoresis (DGGE) showed that amendment with high concentrations of ethanol destabilized the microbial community structure, but that nutrient supplementation countered this effect. Copyright © 2012 Elsevier Ltd. All rights reserved.

Boron doped graphene wrapped silver nanowires as an efficient electrocatalyst for molecular oxygen reduction

NASA Astrophysics Data System (ADS)

Nair, Anju K.; Thazhe Veettil, Vineesh; Kalarikkal, Nandakumar; Thomas, Sabu; Kala, M. S.; Sahajwalla, Veena; Joshi, Rakesh K.; Alwarappan, Subbiah

2016-12-01

Metal nanowires exhibit unusually high catalytic activity towards oxygen reduction reaction (ORR) due to their inherent electronic structures. However, controllable synthesis of stable nanowires still remains as a daunting challenge. Herein, we report the in situ synthesis of silver nanowires (AgNWs) over boron doped graphene sheets (BG) and demonstrated its efficient electrocatalytic activity towards ORR for the first time. The electrocatalytic ORR efficacy of BG-AgNW is studied using various voltammetric techniques. The BG wrapped AgNWs shows excellent ORR activity, with very high onset potential and current density and it followed four electron transfer mechanism with high methanol tolerance and stability towards ORR. The results are comparable to the commercially available 20% Pt/C in terms of performance.

Active Site Flexibility as a Hallmark for Efficient PET Degradation by I. sakaiensis PETase.

PubMed

Fecker, Tobias; Galaz-Davison, Pablo; Engelberger, Felipe; Narui, Yoshie; Sotomayor, Marcos; Parra, Loreto P; Ramírez-Sarmiento, César A

2018-03-27

Polyethylene terephthalate (PET) is one of the most-consumed synthetic polymers, with an annual production of 50 million tons. Unfortunately, PET accumulates as waste and is highly resistant to biodegradation. Recently, fungal and bacterial thermophilic hydrolases were found to catalyze PET hydrolysis with optimal activities at high temperatures. Strikingly, an enzyme from Ideonella sakaiensis, termed PETase, was described to efficiently degrade PET at room temperature, but the molecular basis of its activity is not currently understood. Here, a crystal structure of PETase was determined at 2.02 Å resolution and employed in molecular dynamics simulations showing that the active site of PETase has higher flexibility at room temperature than its thermophilic counterparts. This flexibility is controlled by a novel disulfide bond in its active site, with its removal leading to destabilization of the catalytic triad and reduction of the hydrolase activity. Molecular docking of a model substrate predicts that PET binds to PETase in a unique and energetically favorable conformation facilitated by several residue substitutions within its active site when compared to other enzymes. These computational predictions are in excellent agreement with recent mutagenesis and PET film degradation analyses. Finally, we rationalize the increased catalytic activity of PETase at room temperature through molecular dynamics simulations of enzyme-ligand complexes for PETase and other thermophilic PET-degrading enzymes at 298, 323, and 353 K. Our results reveal that both the binding pose and residue substitutions within PETase favor proximity between the catalytic residues and the labile carbonyl of the substrate at room temperature, suggesting a more favorable hydrolytic reaction. These results are valuable for enabling detailed evolutionary analysis of PET-degrading enzymes and for rational design endeavors aiming at increasing the efficiency of PETase and similar enzymes toward plastic degradation. Copyright © 2018 Biophysical Society. Published by Elsevier Inc. All rights reserved.

A new assay based on terminal restriction fragment length polymorphism of homocitrate synthase gene fragments for Candida species identification.

PubMed

Szemiako, Kasjan; Śledzińska, Anna; Krawczyk, Beata

2017-08-01

Candida sp. have been responsible for an increasing number of infections, especially in patients with immunodeficiency. Species-specific differentiation of Candida sp. is difficult in routine diagnosis. This identification can have a highly significant association in therapy and prophylaxis. This work has shown a new application of the terminal restriction fragment length polymorphism (t-RFLP) method in the molecular identification of six species of Candida, which are the most common causes of fungal infections. Specific for fungi homocitrate synthase gene was chosen as a molecular target for amplification. The use of three restriction enzymes, DraI, RsaI, and BglII, for amplicon digestion can generate species-specific fluorescence labeled DNA fragment profiles, which can be used to determine the diagnostic algorithm. The designed method can be a cost-efficient high-throughput molecular technique for the identification of six clinically important Candida species.

Efficiency of High Molecular Weight Backbone Degradable HPMA Copolymer – Prostaglandin E1 Conjugate in Promotion of Bone Formation in Ovariectomized Rats

PubMed Central

Pan, Huaizhong; Sima, Monika; Miller, Scott C.; Kopečková, Pavla; Yang, Jiyuan; Kopeček, Jindřich

2013-01-01

Multiblock, high molecular weight, linear, backbone degradable HPMA copolymer-prostaglandin E1 (PGE1) conjugate has been synthesized by RAFT polymerization mediated by a new bifunctional chain transfer agent (CTA), which contains an enzymatically degradable oligopeptide sequence flanked by two dithiobenzoate groups, followed by post-polymerization aminolysis and thiol-ene chain extension. The multiblock conjugate contains Asp8 as the bone-targeting moiety and enzymatically degradable bonds in the polymer backbone; in vivo degradation produces cleavage products that are below the renal threshold. Using an ovariectomized (OVX) rat model, the accumulation in bone and efficacy to promote bone formation was evaluated; low molecular weight conjugates served as control. The results indicated a higher accumulation in bone, greater enhancement of bone density, and higher plasma osteocalcin levels for the backbone degradable conjugate. PMID:23731780

Experimental and computational studies on molecularly imprinted solid-phase extraction for gonyautoxins 2,3 from dinoflagellate Alexandrium minutum.

PubMed

Lian, Ziru; Li, Hai-Bei; Wang, Jiangtao

2016-08-01

An innovative and effective extraction procedure based on molecularly imprinted solid-phase extraction (MISPE) was developed for the isolation of gonyautoxins 2,3 (GTX2,3) from Alexandrium minutum sample. Molecularly imprinted polymer microspheres were prepared by suspension polymerization and and were employed as sorbents for the solid-phase extraction of GTX2,3. An off-line MISPE protocol was optimized. Subsequently, the extract samples from A. minutum were analyzed. The results showed that the interference matrices in the extract were obviously cleaned up by MISPE procedures. This outcome enabled the direct extraction of GTX2,3 in A. minutum samples with extraction efficiency as high as 83 %, rather significantly, without any need for a cleanup step prior to the extraction. Furthermore, computational approach also provided direct evidences of the high selective isolation of GTX2,3 from the microalgal extracts.

Crystal MD: The massively parallel molecular dynamics software for metal with BCC structure

NASA Astrophysics Data System (ADS)

Hu, Changjun; Bai, He; He, Xinfu; Zhang, Boyao; Nie, Ningming; Wang, Xianmeng; Ren, Yingwen

2017-02-01

Material irradiation effect is one of the most important keys to use nuclear power. However, the lack of high-throughput irradiation facility and knowledge of evolution process, lead to little understanding of the addressed issues. With the help of high-performance computing, we could make a further understanding of micro-level-material. In this paper, a new data structure is proposed for the massively parallel simulation of the evolution of metal materials under irradiation environment. Based on the proposed data structure, we developed the new molecular dynamics software named Crystal MD. The simulation with Crystal MD achieved over 90% parallel efficiency in test cases, and it takes more than 25% less memory on multi-core clusters than LAMMPS and IMD, which are two popular molecular dynamics simulation software. Using Crystal MD, a two trillion particles simulation has been performed on Tianhe-2 cluster.

Bottom-up synthesis of multifunctional nanoporous graphene

NASA Astrophysics Data System (ADS)

Moreno, César; Vilas-Varela, Manuel; Kretz, Bernhard; Garcia-Lekue, Aran; Costache, Marius V.; Paradinas, Markos; Panighel, Mirko; Ceballos, Gustavo; Valenzuela, Sergio O.; Peña, Diego; Mugarza, Aitor

2018-04-01

Nanosize pores can turn semimetallic graphene into a semiconductor and, from being impermeable, into the most efficient molecular-sieve membrane. However, scaling the pores down to the nanometer, while fulfilling the tight structural constraints imposed by applications, represents an enormous challenge for present top-down strategies. Here we report a bottom-up method to synthesize nanoporous graphene comprising an ordered array of pores separated by ribbons, which can be tuned down to the 1-nanometer range. The size, density, morphology, and chemical composition of the pores are defined with atomic precision by the design of the molecular precursors. Our electronic characterization further reveals a highly anisotropic electronic structure, where orthogonal one-dimensional electronic bands with an energy gap of ∼1 electron volt coexist with confined pore states, making the nanoporous graphene a highly versatile semiconductor for simultaneous sieving and electrical sensing of molecular species.

Cleavable DNA-protein hybrid molecular beacon: A novel efficient signal translator for sensitive fluorescence anisotropy bioassay.

PubMed

Hu, Pan; Yang, Bin

2016-01-15

Due to its unique features such as high sensitivity, homogeneous format, and independence on fluorescent intensity, fluorescence anisotropy (FA) assay has become a hotspot of study in oligonucleotide-based bioassays. However, until now most FA probes require carefully customized structure designs, and thus are neither generalizable for different sensing systems nor effective to obtain sufficient signal response. To address this issue, a cleavable DNA-protein hybrid molecular beacon was successfully engineered for signal amplified FA bioassay, via combining the unique stable structure of molecular beacon and the large molecular mass of streptavidin. Compared with single DNA strand probe or conventional molecular beacon, the DNA-protein hybrid molecular beacon exhibited a much higher FA value, which was potential to obtain high signal-background ratio in sensing process. As proof-of-principle, this novel DNA-protein hybrid molecular beacon was further applied for FA bioassay using DNAzyme-Pb(2+) as a model sensing system. This FA assay approach could selectively detect as low as 0.5nM Pb(2+) in buffer solution, and also be successful for real samples analysis with good recovery values. Compatible with most of oligonucleotide probes' designs and enzyme-based signal amplification strategies, the molecular beacon can serve as a novel signal translator to expand the application prospect of FA technology in various bioassays. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular approaches towards development of purified natural products and their structurally known derivatives as efficient anti-cancer drugs: current trends.

PubMed

Saha, Santu Kumar; Khuda-Bukhsh, Anisur Rahman

2013-08-15

Several natural products and their derivatives, either in purified or structurally identified form, exhibit immense pharmacological and biological properties, some of them showing considerable anticancer potential. Although the molecular mechanisms of action of some of these products are yet to be elucidated, extensive research in this area continues to generate new data that are clinically exploitable. Recent advancement in molecular biology, high throughput screening, biomarker identifications, target selection and genomic approaches have enabled us to understand salient interactions of natural products and their derivatives with cancer cells vis-à-vis normal cells. In this review we highlight the recent approaches and application of innovative technologies made to improve quality as well as efficiency of structurally identified natural products and their derivatives, particularly in small molecular forms capable of being used in "targeted therapies" in oncology. These products preferentially involve multiple mechanistic pathways and overcome chemo-resistance in tumor types with cumulative action. We also mention briefly a few physico-chemical features that compare natural products with drugs in recent natural product discovery approaches. We further report here a few purified natural products as examples that provide molecular interventions in cancer therapeutics to give the reader a glimpse of the current trends of approach for discovering useful anticancer drugs. © 2013 Elsevier B.V. All rights reserved.

Guanidine: A Highly Efficient Stabilizer in Atmospheric New-Particle Formation.

PubMed

Myllys, Nanna; Ponkkonen, Tuomo; Passananti, Monica; Elm, Jonas; Vehkamäki, Hanna; Olenius, Tinja

2018-05-24

The role of a strong organobase, guanidine, in sulfuric acid-driven new-particle formation is studied using state-of-the-art quantum chemical methods and molecular cluster formation simulations. Cluster formation mechanisms at the molecular level are resolved, and theoretical results on cluster stability are confirmed with mass spectrometer measurements. New-particle formation from guanidine and sulfuric acid molecules occurs without thermodynamic barriers under studied conditions, and clusters are growing close to a 1:1 composition of acid and base. Evaporation rates of the most stable clusters are extremely low, which can be explained by the proton transfers and symmetrical cluster structures. We compare the ability of guanidine and dimethylamine to enhance sulfuric acid-driven particle formation and show that more than 2000-fold concentration of dimethylamine is needed to yield as efficient particle formation as in the case of guanidine. At similar conditions, guanidine yields 8 orders of magnitude higher particle formation rates compared to dimethylamine. Highly basic compounds such as guanidine may explain experimentally observed particle formation events at low precursor vapor concentrations, whereas less basic and more abundant bases such as ammonia and amines are likely to explain measurements at high concentrations.

High performance of a unique mesoporous polystyrene-based adsorbent for blood purification

PubMed Central

Chen, Jian; Han, Wenyan; Chen, Jie; Zong, Wenhui; Wang, Weichao; Wang, Yue; Cheng, Guanghui; Li, Chunran; Ou, Lailiang; Yu, Yaoting

2017-01-01

A multi-functional polystyrene based adsorbent (NKU-9) with a unique mesoporous and a high surface area was prepared by suspension polymerization for removal of therapeutic toxins in blood purification. The adsorbent produced had an almost equal amount of mesopore distribution in the range from 2 to 50 nm. The adsorption of serum toxins with different molecular weights were examined by in vitro adsorption assays and compared with some clinical currently used adsorbents such as HA-330, Cytosorb and BL-300 which are produced by China, America and Japan, respectively. Test results indicated that the adsorption rate for pentobarbital by NKU-9 was 81.24% which is nearly as high as HA-330 (81.44%). The latter adsorbent is currently used for acute detoxification treatment in China. To reach adsorption equilibrium, NKU-9 was faster than HA-330, which implies short treatment time. For the removal of middle molecular toxins such as β2-microglobulin (98.88%), NKU-9 performed better adsorptive selectivity than Cytosorb (92.80%). In addition, NKU-9 showed high performance for the removal of albumin-bound toxins (e.g., bilirubin), and its adsorption rate for total bilirubin (80.79%) in plasma was 8.4% higher than that of anion exchange resin BL-300 which is currently used to eliminate bilirubin in clinic. Therefore, our results indicate that the newly developed adsorbent with a wide distribution and almost equal amount of mesopores is a multifunctional adsorbent for high efficient removal of serum toxins with different molecular weights which might be an excellent blood purification adsorbent especially to treat diseases that conventional medical methods are low or not efficient. PMID:28149527

High performance of a unique mesoporous polystyrene-based adsorbent for blood purification.

PubMed

Chen, Jian; Han, Wenyan; Chen, Jie; Zong, Wenhui; Wang, Weichao; Wang, Yue; Cheng, Guanghui; Li, Chunran; Ou, Lailiang; Yu, Yaoting

2017-02-01

A multi-functional polystyrene based adsorbent (NKU-9) with a unique mesoporous and a high surface area was prepared by suspension polymerization for removal of therapeutic toxins in blood purification. The adsorbent produced had an almost equal amount of mesopore distribution in the range from 2 to 50 nm. The adsorption of serum toxins with different molecular weights were examined by in vitro adsorption assays and compared with some clinical currently used adsorbents such as HA-330, Cytosorb and BL-300 which are produced by China, America and Japan, respectively. Test results indicated that the adsorption rate for pentobarbital by NKU-9 was 81.24% which is nearly as high as HA-330 (81.44%). The latter adsorbent is currently used for acute detoxification treatment in China. To reach adsorption equilibrium, NKU-9 was faster than HA-330, which implies short treatment time. For the removal of middle molecular toxins such as β2-microglobulin (98.88%), NKU-9 performed better adsorptive selectivity than Cytosorb (92.80%). In addition, NKU-9 showed high performance for the removal of albumin-bound toxins (e.g., bilirubin), and its adsorption rate for total bilirubin (80.79%) in plasma was 8.4% higher than that of anion exchange resin BL-300 which is currently used to eliminate bilirubin in clinic. Therefore, our results indicate that the newly developed adsorbent with a wide distribution and almost equal amount of mesopores is a multifunctional adsorbent for high efficient removal of serum toxins with different molecular weights which might be an excellent blood purification adsorbent especially to treat diseases that conventional medical methods are low or not efficient.

Record figure of merit values of highly stoichiometric Sb 2Te 3 porous bulk synthesized from tailor-made molecular precursors in ionic liquids

DOE PAGES

Heimann, Stefan; Schulz, Stephan; Schaumann, Julian; ...

2015-08-06

We report on the synthesis of Sb 2Te 3 nanoparticles with record-high figure of merit values of up to 1.5. The central thermoelectric parameters, electrical conductivity, thermal conductivity and Seebeck coefficient, were independently optimized. Critical influence of porosity for the fabrication of highly efficient thermoelectric materials is firstly demonstrated, giving a strong guidance for the optimization of other thermoelectric materials.

A Force Balanced Fragmentation Method for ab Initio Molecular Dynamic Simulation of Protein.

PubMed

Xu, Mingyuan; Zhu, Tong; Zhang, John Z H

2018-01-01

A force balanced generalized molecular fractionation with conjugate caps (FB-GMFCC) method is proposed for ab initio molecular dynamic simulation of proteins. In this approach, the energy of the protein is computed by a linear combination of the QM energies of individual residues and molecular fragments that account for the two-body interaction of hydrogen bond between backbone peptides. The atomic forces on the caped H atoms were corrected to conserve the total force of the protein. Using this approach, ab initio molecular dynamic simulation of an Ace-(ALA) 9 -NME linear peptide showed the conservation of the total energy of the system throughout the simulation. Further a more robust 110 ps ab initio molecular dynamic simulation was performed for a protein with 56 residues and 862 atoms in explicit water. Compared with the classical force field, the ab initio molecular dynamic simulations gave better description of the geometry of peptide bonds. Although further development is still needed, the current approach is highly efficient, trivially parallel, and can be applied to ab initio molecular dynamic simulation study of large proteins.

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

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

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

DOE PAGES

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; ...

2016-04-20

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp 2 carbons with pentagonalmore » and heptagonal defects. Furthermore, this work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites.« less

Nanocarbon synthesis by high-temperature oxidation of nanoparticles

PubMed Central

Nomura, Ken-ichi; Kalia, Rajiv K.; Li, Ying; Nakano, Aiichiro; Rajak, Pankaj; Sheng, Chunyang; Shimamura, Kohei; Shimojo, Fuyuki; Vashishta, Priya

2016-01-01

High-temperature oxidation of silicon-carbide nanoparticles (nSiC) underlies a wide range of technologies from high-power electronic switches for efficient electrical grid and thermal protection of space vehicles to self-healing ceramic nanocomposites. Here, multimillion-atom reactive molecular dynamics simulations validated by ab initio quantum molecular dynamics simulations predict unexpected condensation of large graphene flakes during high-temperature oxidation of nSiC. Initial oxidation produces a molten silica shell that acts as an autocatalytic ‘nanoreactor’ by actively transporting oxygen reactants while protecting the nanocarbon product from harsh oxidizing environment. Percolation transition produces porous nanocarbon with fractal geometry, which consists of mostly sp2 carbons with pentagonal and heptagonal defects. This work suggests a simple synthetic pathway to high surface-area, low-density nanocarbon with numerous energy, biomedical and mechanical-metamaterial applications, including the reinforcement of self-healing composites. PMID:27095061

Organic Light-Emitting Devices (OLEDS) and Their Optically Detected Magnetic Resonance (ODMR)

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

Li, Gang

2003-01-01

Organic Light-Emitting Devices (OLEDs), both small molecular and polymeric have been studied extensively since the first efficient small molecule OLED was reported by Tang and VanSlyke in 1987. Burroughes' report on conjugated polymer-based OLEDs led to another track in OLED development. These developments have resulted in full color, highly efficient (up to {approx} 20% external efficiency 60 lm/W power efficiency for green emitters), and highly bright (> 140,000 Cd/m{sup 2} DC, {approx}2,000,000 Cd/m{sup 2} AC), stable (>40,000 hr at 5 mA/cm{sup 2}) devices. OLEDs are Lambertian emitters, which intrinsically eliminates the view angle problem of liquid crystal displays (LCDs). Thusmore » OLEDs are beginning to compete with the current dominant LCDs in information display. Numerous companies are now active in this field, including large companies such as Pioneer, Toyota, Estman Kodak, Philipps, DuPont, Samsung, Sony, Toshiba, and Osram, and small companies like Cambridge Display Technology (CDT), Universal Display Corporation (UDC), and eMagin. The first small molecular display for vehicular stereos was introduced in 1998, and polymer OLED displays have begun to appear in commercial products. Although displays are the major application for OLEDs at present, they are also candidates for nest generation solid-state lighting. In this case the light source needs to be white in most cases. Organic transistors, organic solar cells, etc. are also being developed vigorously.« less

Cu-catalyzed multicomponent polymerization to synthesize a library of poly(N-sulfonylamidines).

PubMed

Lee, In-Hwan; Kim, Hyunseok; Choi, Tae-Lim

2013-03-13

We report a versatile Cu-catalyzed multicomponent polymerization (MCP) technique that enables the synthesis of high-molecular-weight, defect-free poly(N-sulfonylamidines) from monomers of diynes, sulfonyl azides, and diamines. Through a series of optimizations, we discovered that the addition of excess triethylamine and the use of N,N'-dimethylformamide as a solvent are key factors to ensure efficient MCP. Formation of cyclic polyamidines was a side reaction during polymerization, but it was readily controlled by using diynes or diamines with long or rigid moieties. In addition, this polymerization is highly selective for three-component reactions over click reactions. The combination of the above factors enables the synthesis of high-molecular-weight polymers, which was challenging in previous MCPs. All three kinds of monomers (diynes, sulfonyl azides, and diamines) are readily accessible and stable under the reaction conditions, with various monomers undergoing successful polymerization regardless of their steric and electronic properties. Thus, we synthesized various high-molecular-weight, defect-free polyamidines from a broad range of monomers while overcoming the limitations of previous MCPs, such as low conversion and defects in the polymer structures.

Saccharification efficiencies of multi-enzyme complexes produced by aerobic fungi.

PubMed

Badhan, Ajay; Huang, Jiangli; Wang, Yuxi; Abbott, D Wade; Di Falco, Marcos; Tsang, Adrian; McAllister, Tim

2018-05-24

In the present study, we have characterized high molecular weight multi-enzyme complexes in two commercial enzymes produced by Trichoderma reesei (Spezyme CP) and Penicillium funiculosum (Accellerase XC). We successfully identified 146-1000 kDa complexes using Blue native polyacrylamide gel electrophoresis (BN-PAGE) to fractionate the protein profile in both preparations. Identified complexes dissociated into lower molecular weight constituents when loaded on SDS PAGE. Unfolding of the secondary structure of multi-enzyme complexes with trimethylamine (pH >10) suggested that they were not a result of unspecific protein aggregation. Cellulase (CMCase) profiles of extracts of BN-PAGE fractionated protein bands confirmed cellulase activity within the multi-enzyme complexes. A microassay was used to identify protein bands that promoted high levels of glucose release from barley straw. Those with high saccharification yield were subjected to LC-MS analysis to identify the principal enzymatic activities responsible. The results suggest that secretion of proteins by aerobic fungi leads to the formation of high molecular weight multi-enzyme complexes that display activity against carboxymethyl cellulose and barley straw. Copyright © 2018. Published by Elsevier B.V.

Sharp organic interface of molecular C60 chains and a pentacene derivative SAM on Au(788): A combined STM & DFT study

NASA Astrophysics Data System (ADS)

Wang, Jun; Tang, Jian-Ming; Larson, Amanda M.; Miller, Glen P.; Pohl, Karsten

2013-12-01

Controlling the molecular structure of the donor-acceptor interface is essential to overcoming the efficiency bottleneck in organic photovoltaics. We present a study of self-assembled fullerene (C60) molecular chains on perfectly ordered 6,13-dichloropentacene (DCP) monolayers forming on a vicinal Au(788) surface using scanning tunneling microscopy in conjunction with density functional theory calculations. DCP is a novel pentacene derivative optimized for photovoltaic applications. The molecules form a brick-wall patterned centered rectangular lattice with the long axis parallel to the monatomic steps that separate the 3.9 nm wide Au(111) terraces. The strong interaction between the C60 molecules and the gold substrate is well screened by the DCP monolayer. At submonolayer C60 coverage, the fullerene molecules form long parallel chains, 1.1 nm apart, with a rectangular arrangement instead of the expected close-packed configuration along the upper step edges. The perfectly ordered DCP structure is unaffected by the C60 chain formation. The controlled sharp highly-ordered organic interface has the potential to improve the conversion efficiency in organic photovoltaics.

Rational design of a molecularly imprinted polymer for dinotefuran: theoretical and experimental studies aimed at the development of an efficient adsorbent for microextraction by packed sorbent.

PubMed

Silva, Camilla Fonseca; Borges, Keyller Bastos; do Nascimento, Clebio Soares

2017-12-18

In this work, we studied theoretically the formation process of a molecularly imprinted polymer (MIP) for dinotefuran (DNF), testing distinct functional monomers (FM) in various solvents through density functional theory calculations. The results revealed that the best conditions for MIP synthesis were established with methacrylic acid (MAA) as FM in a 1 : 4 stoichiometry and with chloroform as the solvent. This protocol showed the most favourable stabilization energies for the pre-polymerization complexes. Furthermore, the formation of the FM/template complex is enthalpy driven and the occurrence of hydrogen bonds between the DNF and MAA plays a major role in the complex stability. To confirm the theoretical results, MIP was experimentally synthesized considering the best conditions found at the molecular level and characterized by scanning electron microscopy and thermogravimetric analysis. After that, the synthesized material was efficiently employed in microextraction by packed sorbent combined with high-performance liquid chromatography in a preliminary study of the recovery of DNF from water and artificial saliva samples.

High efficiency and stable white OLED using a single emitter

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

Li, Jian

2016-01-18

The ultimate objective of this project was to demonstrate an efficient and stable white OLED using a single emitter on a planar glass substrate. The focus of the project is on the development of efficient and stable square planar phosphorescent emitters and evaluation of such class of materials in the device settings. Key challenges included improving the emission efficiency of molecular dopants and excimers, controlling emission color of emitters and their excimers, and improving optical and electrical stability of emissive dopants. At the end of this research program, the PI has made enough progress to demonstrate the potential of excimer-basedmore » white OLED as a cost-effective solution for WOLED panel in the solid state lighting applications.« less

An Efficient Variable Screening Method for Effective Surrogate Models for Reliability-Based Design Optimization

DTIC Science & Technology

2014-04-01

surrogate model generation is difficult for high -dimensional problems, due to the curse of dimensionality. Variable screening methods have been...a variable screening model was developed for the quasi-molecular treatment of ion-atom collision [16]. In engineering, a confidence interval of...for high -level radioactive waste [18]. Moreover, the design sensitivity method can be extended to the variable screening method because vital

Top-down approach for the direct characterization of low molecular weight heparins using LC-FT-MS.

PubMed

Li, Lingyun; Zhang, Fuming; Zaia, Joseph; Linhardt, Robert J

2012-10-16

Low molecular heparins (LMWHs) are structurally complex, heterogeneous, polydisperse, and highly negatively charged mixtures of polysaccharides. The direct characterization of LMWH is a major challenge for currently available analytical technologies. Electrospray ionization (ESI) liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for the characterization complex biological samples in the fields of proteomics, metabolomics, and glycomics. LC-MS has been applied to the analysis of heparin oligosaccharides, separated by size exclusion, reversed phase ion-pairing chromatography, and chip-based amide hydrophilic interaction chromatography (HILIC). However, there have been limited applications of ESI-LC-MS for the direct characterization of intact LMWHs (top-down analysis) due to their structural complexity, low ionization efficiency, and sulfate loss. Here we present a simple and reliable HILIC-Fourier transform (FT)-ESI-MS platform to characterize and compare two currently marketed LMWH products using the top-down approach requiring no special sample preparation steps. This HILIC system relies on cross-linked diol rather than amide chemistry, affording highly resolved chromatographic separations using a relatively high percentage of acetonitrile in the mobile phase, resulting in stable and high efficiency ionization. Bioinformatics software (GlycReSoft 1.0) was used to automatically assign structures within 5-ppm mass accuracy.

Synthesis of mesoporous SAPO-34 molecular sieves and their applications in dehydration of butanols and ethanol.

PubMed

Jun, Jong Won; Jeon, Jaewoo; Kim, Chul-Ung; Jeong, Kwang-Eun; Jeong, Soon-Yong; Jhung, Sung Hwa

2013-04-01

Microporous SAPO-34 molecular sieves were hydrothermally synthesized with microwave irradiation in the presence of tetraethylammonium hydroxide (TEAOH) as a template. SAPO-34 molecular sieves with mesoporosity were also prepared in the presence of carbon black as a hard template. By increasing the content of the carbon black template in the synthesis, the mesopore volume increased. Dehydration of alcohols (butanols and ethanol) was carried out with the synthesized SAPO-34 molecular sieves, and the lifetime of the catalysts for the dehydration reaction increased as the mesoporosity increased. Moreover, the performance of the microporous catalyst synthesized with microwave was better than that of the catalyst obtained with conventional electric heating. The relative performance of the catalytic dehydration may be explained by the mesoporosity and the crystal size. Therefore, it may be concluded that small-sized SAPO-34 molecular sieves with high mesoporosity can be produced efficiently with microwave irradiation in the presence of carbon black template, and the molecular sieves are effective in the stable dehydration of alcohols.

A Hadoop-based Molecular Docking System

NASA Astrophysics Data System (ADS)

Dong, Yueli; Guo, Quan; Sun, Bin

2017-10-01

Molecular docking always faces the challenge of managing tens of TB datasets. It is necessary to improve the efficiency of the storage and docking. We proposed the molecular docking platform based on Hadoop for virtual screening, it provides the preprocessing of ligand datasets and the analysis function of the docking results. A molecular cloud database that supports mass data management is constructed. Through this platform, the docking time is reduced, the data storage is efficient, and the management of the ligand datasets is convenient.

A search for the double-beta decay of Xenon-136 to an excited state of Barium-136 with exo-200

NASA Astrophysics Data System (ADS)

Yee, Shannon Koa

While greater than 80% of all electricity continues to be generated by heat engines, methods of directly converting heat into electricity will remain appealing. Thermoelectric generators are one technology that is capable of doing this but the low efficiency and high cost has limited their terrestrial deployment. Thermoelectrics are compact, solid state devices, without moving parts that directly convert a temperature difference into a voltage. Developing better thermoelectric materials is challenging and requires that materials be engineered with new transport physics. The interface between organic and inorganic materials is one example where new transport physics manifests. Therefore, it is possible that improvements in thermoelectrics can be made by engineering organic-inorganic hybrid thermoelectric materials. Composite materials exhibit characteristics of their constituents where hybrid materials possess new properties that are distinctly different from their constituents. At the interface between organic and inorganic materials, hybrid properties manifest. One ideal system to understand this interface is in a metal-molecule-metal junction commonly referred to as a molecular junction. This is often a result of the discrete electronic energy levels of the organic hybridizing with the continuum of electronic states in the inorganic. Herein, new transport phenomenon is observed in molecular junctions, which have great promise for thermoelectrics. It is observed that the transport property are positively correlated breaking the historic trends to improving thermoelectric efficiency. Towards the goal of higher efficiency thermoelectrics, the fundamental science of interfaces is first investigated in molecular junctions. Guiding principles from these fundamental studies are then applied to engineer a bulk, polymer-based, thermoelectric materials with high efficiency. These improvements are encouraging and motivated a cost analysis to evaluate their current market potential against competing thermoelectric materials. In all, this dissertation marks the progress in developing a new class of hybrid organic-inorganic materials for thermoelectric applications.

Molecularly imprinted polymer cartridges coupled on-line with high performance liquid chromatography for simple and rapid analysis of dextromethorphan in human plasma samples.

PubMed

Moein, Mohammad Mahdi; Javanbakht, Mehran; Akbari-Adergani, Behrouz

2011-04-01

In this paper, a novel method is described for automated determination of dextromethorphan in biological fluids using molecularly imprinted solid-phase extraction (MISPE) as a sample clean-up technique combined with high performance liquid chromatography (HPLC). The water-compatible molecularly imprinted polymers (MIPs) were prepared using methacrylic acid as functional monomer, ethylene glycol dimethacrylate as cross-linker, chloroform as porogen and dextromethorphan as template molecule. These imprinted polymers were used as solid-phase extraction sorbent for the extraction of dextromethorphan from human plasma samples. Various parameters affecting the extraction efficiency of the MIP cartridges were evaluated. The high selectivity of the sorbent coupled to the high performance liquid chromatographic system permitted a simple and rapid analysis of this drug in plasma samples with limits of detection (LOD) and quantification (LOQ) of 0.12 ng/mL and 0.35 ng/mL, respectively. The MIP selectivity was evaluated by analyzing of the dextromethorphan in presence of several substances with similar molecular structures and properties. Results from the HPLC analyses showed that the recoveries of dextromethorphan using MIP cartridges from human plasma samples in the range of 1-50 ng/mL were higher than 87%. Copyright © 2011 Elsevier B.V. All rights reserved.

Early Estrogen Action: Stimulation of the Metabolism of High Molecular Weight and Ribosomal RNAs

PubMed Central

Luck, Dennis N.; Hamilton, Terrell H.

1972-01-01

Samples of RNA, isolated from uteri of ovariectomized adult rats treated with estrogen, have been analyzed on sucrose gradients. Treatment with estrogen either for 20 min or 2 hr increased the specific activity of all classes of uterine RNA, but produced no significant alteration in the distribution of radioactivity in the gradients, when animals received [3H]uridine intraperitoneally 15 min before they were killed. After labeling periods of 30 min, 1 hr, or 2 hr, however, the RNAs isolated from animals treated with estrogen had a smaller percentage of rapidly sedimenting (faster than 28S) species of RNA than did RNA from animals not treated with the hormone. The decreased percentage of high molecular weight RNA correlated with increases in both the specific activity of 28S and 18S RNA and the concentration of RNA in the whole organ. The labeled RNA of high molecular weight was also demonstrated, by the use of actinomycin D in vivo, to have a more rapid turnover rate in the estrogen-stimulated uterus. Our results indicate that estrogen increases not only the rate of synthesis of ribosomal RNA in the uterus of the ovariectomized adult rat, but also the rate or efficiency of processing of precursor RNA species of high molecular weight. PMID:4500546

Efficient implementation of the many-body Reactive Bond Order (REBO) potential on GPU

NASA Astrophysics Data System (ADS)

Trędak, Przemysław; Rudnicki, Witold R.; Majewski, Jacek A.

2016-09-01

The second generation Reactive Bond Order (REBO) empirical potential is commonly used to accurately model a wide range hydrocarbon materials. It is also extensible to other atom types and interactions. REBO potential assumes complex multi-body interaction model, that is difficult to represent efficiently in the SIMD or SIMT programming model. Hence, despite its importance, no efficient GPGPU implementation has been developed for this potential. Here we present a detailed description of a highly efficient GPGPU implementation of molecular dynamics algorithm using REBO potential. The presented algorithm takes advantage of rarely used properties of the SIMT architecture of a modern GPU to solve difficult synchronizations issues that arise in computations of multi-body potential. Techniques developed for this problem may be also used to achieve efficient solutions of different problems. The performance of proposed algorithm is assessed using a range of model systems. It is compared to highly optimized CPU implementation (both single core and OpenMP) available in LAMMPS package. These experiments show up to 6x improvement in forces computation time using single processor of the NVIDIA Tesla K80 compared to high end 16-core Intel Xeon processor.

Depleting high-abundant and enriching low-abundant proteins in human serum: An evaluation of sample preparation methods using magnetic nanoparticle, chemical depletion and immunoaffinity techniques.

PubMed

de Jesus, Jemmyson Romário; da Silva Fernandes, Rafael; de Souza Pessôa, Gustavo; Raimundo, Ivo Milton; Arruda, Marco Aurélio Zezzi

2017-08-01

The efficiency of three different depletion methods to remove the most abundant proteins, enriching those human serum proteins with low abundance is checked to make more efficient the search and discovery of biomarkers. These methods utilize magnetic nanoparticles (MNPs), chemical reagents (sequential application of dithiothreitol and acetonitrile, DTT/ACN), and commercial apparatus based on immunoaffinity (ProteoMiner, PM). The comparison between methods shows significant removal of abundant protein, remaining in the supernatant at concentrations of 4.6±0.2, 3.6±0.1, and 3.3±0.2µgµL -1 (n=3) for MNPs, DTT/ACN and PM respectively, from a total protein content of 54µgµL -1 . Using GeLC-MS/MS analysis, MNPs depletion shows good efficiency in removing high molecular weight proteins (>80kDa). Due to the synergic effect between the reagents DTT and ACN, DTT/ACN-based depletion offers good performance in the depletion of thiol-rich proteins, such as albumin and transferrin (DTT action), as well as of high molecular weight proteins (ACN action). Furthermore, PM equalization confirms its efficiency in concentrating low-abundant proteins, decreasing the dynamic range of protein levels in human serum. Direct comparison between the treatments reveals 72 proteins identified when using MNP depletion (43 of them exclusively by this method), but only 20 proteins using DTT/ACN (seven exclusively by this method). Additionally, after PM treatment 30 proteins were identified, seven exclusively by this method. Thus, MNPs and DTT/ACN depletion can be simple, quick, cheap, and robust alternatives for immunochemistry-based protein depletion, providing a potential strategy in the search for disease biomarkers. Copyright © 2017 Elsevier B.V. All rights reserved.

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

Biyikli, Emre; To, Albert C., E-mail: albertto@pitt.edu

Atomistic/continuum coupling methods combine accurate atomistic methods and efficient continuum methods to simulate the behavior of highly ordered crystalline systems. Coupled methods utilize the advantages of both approaches to simulate systems at a lower computational cost, while retaining the accuracy associated with atomistic methods. Many concurrent atomistic/continuum coupling methods have been proposed in the past; however, their true computational efficiency has not been demonstrated. The present work presents an efficient implementation of a concurrent coupling method called the Multiresolution Molecular Mechanics (MMM) for serial, parallel, and adaptive analysis. First, we present the features of the software implemented along with themore » associated technologies. The scalability of the software implementation is demonstrated, and the competing effects of multiscale modeling and parallelization are discussed. Then, the algorithms contributing to the efficiency of the software are presented. These include algorithms for eliminating latent ghost atoms from calculations and measurement-based dynamic balancing of parallel workload. The efficiency improvements made by these algorithms are demonstrated by benchmark tests. The efficiency of the software is found to be on par with LAMMPS, a state-of-the-art Molecular Dynamics (MD) simulation code, when performing full atomistic simulations. Speed-up of the MMM method is shown to be directly proportional to the reduction of the number of the atoms visited in force computation. Finally, an adaptive MMM analysis on a nanoindentation problem, containing over a million atoms, is performed, yielding an improvement of 6.3–8.5 times in efficiency, over the full atomistic MD method. For the first time, the efficiency of a concurrent atomistic/continuum coupling method is comprehensively investigated and demonstrated.« less

ALMA CO Observations of Shocks and Star Formation in the Interacting Galaxies IC 2163 and NGC 2207

NASA Astrophysics Data System (ADS)

Elmegreen, Debra M.; Elmegreen, Bruce; Kaufman, Michele; Brinks, Elias; Struck, Curtis; Bournaud, Frederic; Sheth, Kartik; Juneau, Stephanie

2017-01-01

The spiral galaxies IC 2163 and NGC 2207 are a well-studied pair undergoing a grazing collision. ALMA CO observations of masses, column densities, and velocities are combined with HI, Hα, optical, and 24 micron data to study the star formation rates and efficiencies. The close encounter of the galaxies produced in-plane tidal forces in IC 2163, resulting in a large shock with high molecular velocity gradients and both radial and azimuthal streaming (100 km/s) that formed a pile-up of molecular gas in the resulting cuspy-oval or ``eyelid'' structure at mid-radius. The encounter also produced forces nearly orthogonal to the plane of NGC 2207, resulting in a warp. By comparing with the Kennicutt-Schmidt relation for star formation, we find that some regions of NGC 2207 with unusually high turbulent speeds (40-50 km/s) and high star formation rates (>0.01 Mo/pc2/Myr) have gas that is predominantly atomic with high density cores. Half of the CO mass is in 300 clouds each more massive than 4.0x105 Mo. The mass distribution functions for the CO clouds and star complexes in the eyelid in IC 2163 both have a slope similar to what is observed in Milky Way clouds; the CO slope is steeper in NGC 2207. The CO distribution in NGC 2207 also includes a nuclear ring, a mini-bar, and a mini-starburst region that dominates the 24 micron, radio, and Hα emission in both galaxies. Dust extinction, molecular column densities, and slightly negative molecular velocities indicate the mini-starburst region has ejected a jet of molecular gas nearly perpendicular to the plane of NGC 2207 on the near side with a kinetic energy of 1052 ergs. The large scale star formation efficiency, measured as the ratio of the summed masses of the star complexes near molecular clouds to the combined star complex and cloud masses, is 7% overall; it is 23% in the mini-starburst. The maximum age of star complexes in the galactic-scale shock front at the eyelid is about the same as the time since closest approach of the galaxies, suggesting a triggering process related to tidal compression.

Photocatalytic water splitting: Materials design and high-throughput screening of molecular compositions

NASA Astrophysics Data System (ADS)

Khnayzer, Rony S.

Due to the expected increases on energy demand in the near future, the development of new catalytic molecular compositions and materials capable of directly converting water, with the aid of solar photons, into hydrogen becomes obviated. Hydrogen is a combustible fuel and precious high-energy feedstock chemical. However, for the water-splitting reaction to proceed efficiently and economically enough for large-scale application, efficient light-absorbing sensitizers and water splitting catalysts are required. To study the kinetics of the water reduction reaction, we have used titania (TiO2) nanoparticles as a robust scaffold to photochemically grow platinum (Pt) nanoparticles from a unique surface-anchored molecular precursor Pt(dcbpy)Cl2 [dcbpy = 4,4'-dicarboxylic acid-2,2'-bipyridine]. The hybrid Pt/TiO 2 nanomaterials obtained were shown to be a superior water reduction catalyst (WRC) in aqueous suspensions when compared with the benchmark platinized TiO2. In addition, cobalt phosphate (CoPi) water oxidation catalyst (WOC) was photochemically assembled on the surface of TiO2, and its structure and mechanism of activity showed resemblance to the established electrochemically grown CoPi material. Both WRC and WOC described above possessed near unity Faradaic efficiency for hydrogen and oxygen production respectively, and were fully characterized by electron microscopy, x-ray absorption spectroscopy, electrochemistry and photochemistry. While there are established materials and molecules that are able to drive water splitting catalysis, some of these efficient semiconductors, including titanium dioxide (TiO2) and tungsten trioxide (WO3), are only able to absorb high-energy (ultraviolet or blue) photons. This high-energy light represents merely a fraction of the solar spectrum that strikes the earth and the energy content of those remaining photons is simply wasted. A strategy to mitigate this problem has been developed over the years in our laboratory. Briefly, photons of low energy are converted into higher energy light using a process termed photon upconversion. Using this technique, low energy photons supplied by the sun can be converted into light of appropriate energy to trigger electronic transitions in high energy absorbing photoactive materials without any chemical modification of the latter. We have shown, that this technology is capable of upconverting visible sunlight to sensitize wide-bandgap semiconductors such as WO3, subsequently extending the photoaction of these materials to cover a larger portion of the solar spectrum. Besides the engineering of different compositions that serve as either sensitizers or catalysts in these solar energy conversion schemes, we have designed an apparatus for parallel high-throughput screening of these photocatalytic compositions. This combinatorial approach to solar fuels photocatalysis has already led to unprecedented fundamental understanding of the generation of hydrogen gas from pure water. The activity of a series of new Ru(II) sensitizers along with Co(II) molecular WRCs were optimized under visible light excitation utilizing different experimental conditions. The multi-step mechanism of activity of selected compositions was further elucidated by pump-probe transient absorption spectroscopy.

High density genetic linkage map and bin mapping for disease resistance QTLs in peanut

USDA-ARS?s Scientific Manuscript database

Mapping and identification of QTLs are important for efficient marker-assisted breeding and for analysis of the molecular mechanisms regulating traits. Diseases, such as early and late leaf spots, Tomato spotted wilt virus (TSWV), cause significant loses to peanut growers. Our goal is to develop a h...

Organic Optoelectronic Devices Employing Small Molecules

NASA Astrophysics Data System (ADS)

Fleetham, Tyler Blain

Organic optoelectronic devices have remained a research topic of great interest over the past two decades, particularly in the development of efficient organic photovoltaics (OPV) and organic light emitting diodes (OLED). In order to improve the efficiency, stability, and materials variety for organic optoelectronic devices a number of emitting materials, absorbing materials, and charge transport materials were developed and employed in a device setting. Optical, electrical, and photophysical studies of the organic materials and their corresponding devices were thoroughly carried out. Two major approaches were taken to enhance the efficiency of small molecule based OPVs: developing material with higher open circuit voltages or improved device structures which increased short circuit current. To explore the factors affecting the open circuit voltage (VOC) in OPVs, molecular structures were modified to bring VOC closer to the effective bandgap, DeltaE DA, which allowed the achievement of 1V VOC for a heterojunction of a select Ir complex with estimated exciton energy of only 1.55eV. Furthermore, the development of anode interfacial layer for exciton blocking and molecular templating provide a general approach for enhancing the short circuit current. Ultimately, a 5.8% PCE was achieved in a single heterojunction of C60 and a ZnPc material prepared in a simple, one step, solvent free, synthesis. OLEDs employing newly developed deep blue emitters based on cyclometalated complexes were demonstrated. Ultimately, a peak EQE of 24.8% and nearly perfect blue emission of (0.148,0.079) was achieved from PtON7dtb, which approaches the maximum attainable performance from a blue OLED. Furthermore, utilizing the excimer formation properties of square-planar Pt complexes, highly efficient and stable white devices employing a single emissive material were demonstrated. A peak EQE of over 20% for pure white color (0.33,0.33) and 80 CRI was achieved with the tridentate Pt complex, Pt-16. Furthermore, the development of a series of tetradentate Pt complexes yielded highly efficient and stable single doped white devices due to their halogen free tetradentate design. In addition to these benchmark achievements, the systematic molecular modification of both emissive and absorbing materials provides valuable structure-property relationship information that should help guide further developments in the field.

Visible-light-driven methane formation from CO2 with a molecular iron catalyst.

PubMed

Rao, Heng; Schmidt, Luciana C; Bonin, Julien; Robert, Marc

2017-08-03

Converting CO 2 into fuel or chemical feedstock compounds could in principle reduce fossil fuel consumption and climate-changing CO 2 emissions. One strategy aims for electrochemical conversions powered by electricity from renewable sources, but photochemical approaches driven by sunlight are also conceivable. A considerable challenge in both approaches is the development of efficient and selective catalysts, ideally based on cheap and Earth-abundant elements rather than expensive precious metals. Of the molecular photo- and electrocatalysts reported, only a few catalysts are stable and selective for CO 2 reduction; moreover, these catalysts produce primarily CO or HCOOH, and catalysts capable of generating even low to moderate yields of highly reduced hydrocarbons remain rare. Here we show that an iron tetraphenylporphyrin complex functionalized with trimethylammonio groups, which is the most efficient and selective molecular electro- catalyst for converting CO 2 to CO known, can also catalyse the eight-electron reduction of CO 2 to methane upon visible light irradiation at ambient temperature and pressure. We find that the catalytic system, operated in an acetonitrile solution containing a photosensitizer and sacrificial electron donor, operates stably over several days. CO is the main product of the direct CO 2 photoreduction reaction, but a two-pot procedure that first reduces CO 2 and then reduces CO generates methane with a selectivity of up to 82 per cent and a quantum yield (light-to-product efficiency) of 0.18 per cent. However, we anticipate that the operating principles of our system may aid the development of other molecular catalysts for the production of solar fuels from CO 2 under mild conditions.

Visible-light-driven methane formation from CO2 with a molecular iron catalyst

NASA Astrophysics Data System (ADS)

Rao, Heng; Schmidt, Luciana C.; Bonin, Julien; Robert, Marc

2017-08-01

Converting CO2 into fuel or chemical feedstock compounds could in principle reduce fossil fuel consumption and climate-changing CO2 emissions. One strategy aims for electrochemical conversions powered by electricity from renewable sources, but photochemical approaches driven by sunlight are also conceivable. A considerable challenge in both approaches is the development of efficient and selective catalysts, ideally based on cheap and Earth-abundant elements rather than expensive precious metals. Of the molecular photo- and electrocatalysts reported, only a few catalysts are stable and selective for CO2 reduction; moreover, these catalysts produce primarily CO or HCOOH, and catalysts capable of generating even low to moderate yields of highly reduced hydrocarbons remain rare. Here we show that an iron tetraphenylporphyrin complex functionalized with trimethylammonio groups, which is the most efficient and selective molecular electro- catalyst for converting CO2 to CO known, can also catalyse the eight-electron reduction of CO2 to methane upon visible light irradiation at ambient temperature and pressure. We find that the catalytic system, operated in an acetonitrile solution containing a photosensitizer and sacrificial electron donor, operates stably over several days. CO is the main product of the direct CO2 photoreduction reaction, but a two-pot procedure that first reduces CO2 and then reduces CO generates methane with a selectivity of up to 82 per cent and a quantum yield (light-to-product efficiency) of 0.18 per cent. However, we anticipate that the operating principles of our system may aid the development of other molecular catalysts for the production of solar fuels from CO2 under mild conditions.

Synthesis of surface molecular imprinted TiO2/graphene photocatalyst and its highly efficient photocatalytic degradation of target pollutant under visible light irradiation

NASA Astrophysics Data System (ADS)

Lai, Cui; Wang, Man-Man; Zeng, Guang-Ming; Liu, Yun-Guo; Huang, Dan-Lian; Zhang, Chen; Wang, Rong-Zhong; Xu, Piao; Cheng, Min; Huang, Chao; Wu, Hai-Peng; Qin, Lei

2016-12-01

The molecular imprinted TiO2/graphene photocatalyst (MIP-TiO2/GR) was successfully prepared with bisphenol A (BPA) as the template molecule (target pollutant) and o-phenylenediamine (OPDA) as functional monomers by the surface molecular imprinting method. The combination between BPA and OPDA led to the formation of the precursor, and the subsequent polymerization of OPDA initiated by ultraviolet radiation can ensure the realization of MIP-TiO2/GR. The samples were characterized by SEM, EDS, XRD, BET, UV-vis DRS and Zeta potential. In addition, adsorption capacities, adsorption selectivity and visible light photocatalytic performances of MIP-TiO2/GR and non-imprinted TiO2/graphene (NIP-TiO2/GR) were evaluated. Moreover, the effects of pH and initial BPA concentration on removal efficiency of BPA were also investigated. The results showed that MIP-TiO2/GR exhibited better adsorption capacity and adsorption selectivity towards the template molecule compared to NIP-TiO2/GR due to the imprinted cavities on the surface of MIP-TiO2/GR. Moreover, the photocatalytic activity of MIP-TiO2/GR toward the target molecules was stronger than that of NIP-TiO2/GR as a result of large adsorption capacity to target molecules and narrow band gap energy on MIP-TiO2/GR. Therefore, modifying the photocatalyst by the surface molecular imprinting is a promising method to improve the molecule recognition and photocatalytic efficiency of photocatalyst for target pollutant.

Conformation and activity alteration of horseradish peroxidase induced by the interaction with gene carrier polyethyleneimines

NASA Astrophysics Data System (ADS)

Huang, Aimin; Wei, Bangzhi; Mo, Junyong; Wang, Yajing; Ma, Lin

2018-01-01

Polyethyleneimine (PEI) has long been considered as "golden standard" for polymeric gene delivery carriers. However the molecular basis of the cytotoxicity of PEI is poorly understood. Little is known about the effects of PEI on the structure and functions of biomacromolecules. In this work, fluorescence, UV-vis absorption, circular dichroism spectroscopy were conducted to investigate the influence of PEI of average molecular weight 25, 10 and 1.8 kDa (denoted as PEI25k, PEI10k and PEI1.8k) on the conformation of horseradish peroxidase (HRP) and its catalytic efficiency. Zeta-potential measurement and isothermal titration calorimetry were used to reveal the mechanism of the interaction between PEIs and HRP. PEIs were found to bind onto the surface of HRP predominantly via hydrophobic interaction and hydrogen bond or van der Waals interaction. The complex formation between HRP and PEI induced a more compact conformation of the enzyme and an increased hydrophobicity of the microenvironment surrounding heme pocket. The conformational change of HRP had little impact on the affinity towards H2O2 and phenol. However, the increase in the non-planarity of porphyrin ring in the heme group led to an increase in the exposure degree of the active center and thus an enhancement of catalytic efficiency of HRP in the presence of high molecular weight PEIs (PEI25k and PEI10k). The polymer size played an important role in PEI-HRP interaction. PEI of low molecular weight (PEI1.8k) was less efficient to alter the conformation and catalytic activity of HRP in aqueous solutions.

Unrevealed part of myosin's powerstroke accounts for high efficiency of muscle contraction.

PubMed

Bibó, András; Károlyi, György; Kovács, Mihály

2017-09-01

Myosin II, the motor protein driving muscle contraction, uses energy of ATP hydrolysis to produce movement along actin. The key step of energy transduction is the powerstroke, involving rotation of myosin's lever while myosin is attached to actin. Macroscopic measurements indicated high thermodynamic efficiency for energy conversion. However, single-molecule experiments indicated lower efficiency, provoking a long-standing discrepancy. Based on the Fluctuation-Dissipation Theorem, we built a sufficiently detailed but low degree-of-freedom model reconstructing the entire mechanoenzymatic cycle. We show that a high axial stiffness of the lever during an initial, experimentally yet unrevealed part of the powerstroke results in a short-time, ratchet-like Kramers effect, and is responsible for the missing efficiency. The second part of the powerstroke is an Eyring-like relaxation that dominantly contributes to lever rotation, but produces only a minor part of the work. The model reveals the structural background of myosin's capability to function as a robust molecular engine and a very precise load sensor as well. Our model also suggests an explanation for the malfunction of myosins harboring mutations that lead to hypertrophic cardiomyopathies with most severe clinical prognosis. The model explains how a force-transmitting device within a biological motor can enable high energetic efficiency. Copyright © 2017 Elsevier B.V. All rights reserved.

Mitoregulin: A lncRNA-Encoded Microprotein that Supports Mitochondrial Supercomplexes and Respiratory Efficiency.

PubMed

Stein, Colleen S; Jadiya, Pooja; Zhang, Xiaoming; McLendon, Jared M; Abouassaly, Gabrielle M; Witmer, Nathan H; Anderson, Ethan J; Elrod, John W; Boudreau, Ryan L

2018-06-26

Mitochondria are composed of many small proteins that control protein synthesis, complex assembly, metabolism, and ion and reactive oxygen species (ROS) handling. We show that a skeletal muscle- and heart-enriched long non-coding RNA, LINC00116, encodes a highly conserved 56-amino-acid microprotein that we named mitoregulin (Mtln). Mtln localizes to the inner mitochondrial membrane, where it binds cardiolipin and influences protein complex assembly. In cultured cells, Mtln overexpression increases mitochondrial membrane potential, respiration rates, and Ca 2+ retention capacity while decreasing mitochondrial ROS and matrix-free Ca 2+ . Mtln-knockout mice display perturbations in mitochondrial respiratory (super)complex formation and activity, fatty acid oxidation, tricarboxylic acid (TCA) cycle enzymes, and Ca 2+ retention capacity. Blue-native gel electrophoresis revealed that Mtln co-migrates alongside several complexes, including the complex I assembly module, complex V, and supercomplexes. Under denaturing conditions, Mtln remains in high-molecular-weight complexes, supporting its role as a sticky molecular tether that enhances respiratory efficiency by bolstering protein complex assembly and/or stability. Copyright © 2018 The Authors. Published by Elsevier Inc. All rights reserved.

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

Trędak, Przemysław, E-mail: przemyslaw.tredak@fuw.edu.pl; Rudnicki, Witold R.; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, ul. Pawińskiego 5a, 02-106 Warsaw

The second generation Reactive Bond Order (REBO) empirical potential is commonly used to accurately model a wide range hydrocarbon materials. It is also extensible to other atom types and interactions. REBO potential assumes complex multi-body interaction model, that is difficult to represent efficiently in the SIMD or SIMT programming model. Hence, despite its importance, no efficient GPGPU implementation has been developed for this potential. Here we present a detailed description of a highly efficient GPGPU implementation of molecular dynamics algorithm using REBO potential. The presented algorithm takes advantage of rarely used properties of the SIMT architecture of a modern GPUmore » to solve difficult synchronizations issues that arise in computations of multi-body potential. Techniques developed for this problem may be also used to achieve efficient solutions of different problems. The performance of proposed algorithm is assessed using a range of model systems. It is compared to highly optimized CPU implementation (both single core and OpenMP) available in LAMMPS package. These experiments show up to 6x improvement in forces computation time using single processor of the NVIDIA Tesla K80 compared to high end 16-core Intel Xeon processor.« less

NGL Viewer: Web-based molecular graphics for large complexes.

PubMed

Rose, Alexander S; Bradley, Anthony R; Valasatava, Yana; Duarte, Jose M; Prlic, Andreas; Rose, Peter W

2018-05-29

The interactive visualization of very large macromolecular complexes on the web is becoming a challenging problem as experimental techniques advance at an unprecedented rate and deliver structures of increasing size. We have tackled this problem by developing highly memory-efficient and scalable extensions for the NGL WebGL-based molecular viewer and by using MMTF, a binary and compressed Macromolecular Transmission Format. These enable NGL to download and render molecular complexes with millions of atoms interactively on desktop computers and smartphones alike, making it a tool of choice for web-based molecular visualization in research and education. The source code is freely available under the MIT license at github.com/arose/ngl and distributed on NPM (npmjs.com/package/ngl). MMTF-JavaScript encoders and decoders are available at github.com/rcsb/mmtf-javascript. asr.moin@gmail.com.

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.

Emission behaviors of unsymmetrical 1,3-diaryl-β-diketones: A model perfectly disclosing the effect of molecular conformation on luminescence of organic solids

NASA Astrophysics Data System (ADS)

Cheng, Xiao; Li, Feng; Han, Shenghua; Zhang, Yufei; Jiao, Chuanjun; Wei, Jinbei; Ye, Kaiqi; Wang, Yue; Zhang, Hongyu

2015-03-01

A series of unsymmetrical 1,3-diaryl-β-diketones 1-6 displaying molecular conformation-dependent fluorescence quantum yields have been synthesized. Crystals with planar molecular conformation such as 1, 2, 3 and 4 are highly fluorescent (φf: 39-53%), and the one holding slightly twisted conformation (5) is moderately luminescent (φf = 17%), while crystal 6 possessing heavily bent structure is completely nonluminous (φf ~ 0). The distinct fluorescence efficiencies are ascribed to their different molecular conformations, since all the crystals hold the same crystal system, space group and crystal packing structures. Additionally, the fluorescent crystals 1-5 display low threshold amplified spontaneous emission (ASE) with small full widths at half-maximum (FWHM: 3-7 nm), indicating their potential as candidates for organic crystal lasing devices.

Detection of DNA damage by using hairpin molecular beacon probes and graphene oxide.

PubMed

Zhou, Jie; Lu, Qian; Tong, Ying; Wei, Wei; Liu, Songqin

2012-09-15

A hairpin molecular beacon tagged with carboxyfluorescein in combination with graphene oxide as a quencher reagent was used to detect the DNA damage by chemical reagents. The fluorescence of molecular beacon was quenched sharply by graphene oxide; while in the presence of its complementary DNA the quenching efficiency decreased because their hybridization prevented the strong adsorbability of molecular beacon on graphene oxide. If the complementary DNA was damaged by a chemical reagent and could not form intact duplex structure with molecular beacon, more molecular beacon would adsorb on graphene oxide increasing the quenching efficiency. Thus, damaged DNA could be detected based on different quenching efficiencies afforded by damaged and intact complementary DNA. The damage effects of chlorpyrifos-methyl and three metabolites of styrene such as mandelieaeids, phenylglyoxylieaeids and epoxystyrene on DNA were studied as models. The method for detection of DNA damage was reliable, rapid and simple compared to the biological methods. Copyright © 2012 Elsevier B.V. All rights reserved.

Influence of Molecular Shape on Molecular Orientation and Stability of Vapor-Deposited Organic Semiconductors

NASA Astrophysics Data System (ADS)

Walters, Diane M.; Johnson, Noah D.; Ediger, M. D.

Physical vapor deposition is commonly used to prepare active layers in organic electronics. Recently, it has been shown that molecular orientation and packing can be tuned by changing the substrate temperature during deposition, while still producing macroscopically homogeneous films. These amorphous materials can be highly anisotropic when prepared with low substrate temperatures, and they can exhibit exceptional kinetic stability; films retain their favorable packing when heated to high temperatures. Here, we study the influence of molecular shape on molecular orientation and stability. We investigate disc-shaped molecules, such as TCTA and m-MTDATA, nearly spherical molecules, such as Alq3, and linear molecules covering a broad range of aspect ratios, such as p-TTP and BSB-Cz. Disc-shaped molecules have preferential horizontal orientation when deposited at low substrate temperatures, and their orientation can be tuned by changing the substrate temperature. Alq3 forms stable, amorphous films that are optically isotropic when vapor deposited over a broad range of substrate temperatures. This work may guide the choice of material and deposition conditions for vapor-deposited films used in organic electronics and allow for more efficient devices to be fabricated.

Electric Field Tuning Molecular Packing and Electrical Properties of Solution-Shearing Coated Organic Semiconducting Thin Films

DOE PAGES

Molina-Lopez, Francisco; Yan, Hongping; Gu, Xiaodan; ...

2017-01-17

Recent improvements in solution-coated organic semiconductors (OSCs) evidence their high potential for cost-efficient organic electronics and sensors. Molecular packing structure determines the charge transport property of molecular solids. However, it remains challenging to control the molecular packing structure for a given OSC. Here, the application of alternating electric fields is reported to fine-tune the crystal packing of OSC solution-shearing coated at ambient conditions. First, a theoretical model based on dielectrophoresis is developed to guide the selection of the optimal conditions (frequency and amplitude) of the electric field applied through the solution-shearing blade during coating of OSC thin films. Next, electricmore » field-induced polymorphism is demonstrated for OSCs with both herringbone and 2D brick-wall packing motifs in 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene and 6,13-bis(triisopropylsilylethynyl) pentacene, respectively. Favorable molecular packing can be accessible in some cases, resulting in higher charge carrier mobilities. In conclusion, this work provides a new approach to tune the properties of solution-coated OSCs in functional devices for high-performance printed electronics.« less

Selective enrichment and separation of phosphotyrosine peptides by thermosensitive molecularly imprinted polymers.

PubMed

Yang, Xiaoqing; Xia, Yan

2016-01-01

Novel thermosensitive molecularly imprinted polymers were successfully prepared using the epitope imprinting approach in the presence of the mimic template phenylphosphonic acid, the functional monomer vinylphosphonic acid-Ti(4+) , the temperature-sensitive monomer N-isopropylacrylamide and the crosslinker N,N'-methylenebisacrylamide. The ratio of the template/thermosensitive monomers/crosslinker was optimized, and when the ratio was 2:2:1, the prepared thermosensitive molecularly imprinted polymers had the highest imprinting factor. The synthetic thermosensitive molecularly imprinted polymers were characterized by Fourier transform infrared spectroscopy to reveal the combination and elution processes of the template. Then, the adsorption capacity and thermosensitivity was measured. When the temperature was 28°C, the imprinting factor was the highest. The selectivity and adsorption capacity of the thermosensitive molecularly imprinted polymers for phosphotyrosine peptides from a mixture of three tailor-made peptides were measured by high-performance liquid chromatography. The results showed that the thermosensitive molecularly imprinted polymers have good selectivity for phosphotyrosine peptides. Finally, the imprinted hydrogels were applied to specifically adsorb phosphotyrosine peptides from a sample mixture containing phosphotyrosine and a tryptic digest of β-casein, which demonstrated high selectivity. After four rebinding cycles, 78.9% adsorption efficiency was still retained. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Rational molecular engineering of cyclopentadithiophene-bridged D-A-π-A sensitizers combining high photovoltaic efficiency with rapid dye adsorption

PubMed Central

Chai, Qipeng; Li, Wenqin; Liu, Jingchuan; Geng, Zhiyuan; Tian, He; Zhu, Wei-hong

2015-01-01

Dye-sensitized solar cell (DSSC) is considered as a feasible route to the clean and renewable energy conversion technique. The commercial application requires further enhancements on photovoltaic efficiency and simplification on the device fabrication. For avoiding the unpreferable trade-off between photocurrent (JSC) and photovoltage (VOC), here we report the molecular engineering and comprehensive photovoltaic characterization of three cyclopentadithiophene-bridged D-A-π-A motif sensitizers with a change in donor group. We make a careful choice on the donor and conjugation bridge for synergistically increasing JSC and VOC. Comparing with the reference dye WS-2, the photovoltaic efficiency with the single component dye of WS-51 increases by 18%, among one of the rare examples in pure metal-free organic dyes exceeding 10% in combination with traditional iodine redox couples. Moreover, WS-51 exhibits several prominent merits on potentially scale-up industrial application: i) facile synthetic route to target molecule, ii) simple dipping procedure without requirement of co-sensitization, and iii) rapid dye adsorption capability. PMID:26066974

Molecular mechanisms influencing efficiency of RNA interference in insects.

PubMed

Cooper, Anastasia M W; Silver, Kristopher; Jianzhen, Zhang; Park, Yoonseong; Zhu, Kun Yan

2018-06-21

RNA interference (RNAi) is an endogenous, sequence-specific gene silencing mechanism elicited by small RNA molecules. RNAi is a powerful reverse genetic tool, and is currently being utilized for managing insects and viruses. Widespread implementation of RNAi-based pest management strategies is currently hindered by inefficient and highly variable results when different insect species, strains, developmental stages, tissues, and genes are targeted. Mechanistic studies have shown that double-stranded ribonucleases (dsRNases), endosomal entrapment, deficient function of the core machinery, and inadequate immune stimulation contribute to limited RNAi efficiency. However, a comprehensive understanding of the molecular mechanisms limiting RNAi efficiency remains elusive. The recent advances in dsRNA stability in physiological tissues, dsRNA internalization into cells, the composition and function of the core RNAi machinery, as well as small-interfering RNA/double-stranded RNA amplification and spreading mechanisms are reviewed to establish a global understanding of the obstacles impeding wider understanding of RNAi mechanisms in insects. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

In-vitro engineering of novel bioactivity in the natural enzymes

NASA Astrophysics Data System (ADS)

Tiwari, Vishvanath

2016-10-01

Enzymes catalyze various biochemical functions with high efficiency and specificity. In-vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. Enzyme engineering technology involves directed evolution, rational designing, semi-rational designing and structure-based designing using chemical modifications. Similarly, combined computational and in-vitro evolution approaches together help in artificial designing of novel bioactivity in the natural enzyme. DNA shuffling, error prone PCR and staggered extension process are used to artificially redesign active site of enzyme, which can alter its efficiency and specificity. Modifications of the enzyme can lead to the discovery of new path of molecular evolution, designing of efficient enzymes, locating active sites and crucial residues, shift in substrate and cofactor specificity. The methods and thermodynamics of in-vitro designing of the enzyme are also discussed. Similarly, engineered thermophilic and psychrophilic enzymes attain substrate specificity and activity of mesophilic enzymes that may also be beneficial for industry and therapeutics.

Comparative Analysis of the Molecular Adjuvants and Their Binding Efficiency with CR1.

PubMed

Saranya, B; Saxena, Shweta; Saravanan, K M; Shakila, H

2016-03-01

There are so many obstacles in developing a vaccine or vaccine technology for diseases like cancer and human immunodeficiency virus infection. While developing vaccines that target specific infection, molecular adjuvants are indispensable. These molecular adjuvants act as a vaccine delivery vehicle to the immune system to increase the effectiveness of the specific antigens. In the present work, a computational study has been done on molecular adjuvants like IgGFc, GMCSF and C3d to find out how efficiently they are binding to CR1. Sequence, structure and mutational analysis are performed on the molecular adjuvants to understand the features important for their binding with the receptor. Results obtained from our study indicate that the adjuvant IgGFc complexed with the receptor CR1 has the best binding efficiency, which can be used further to develop better vaccine technologies.

Crack-free polydimethylsiloxane-bioactive glass-poly(ethylene glycol) hybrid monoliths with controlled biomineralization activity and mechanical property for bone tissue regeneration.

PubMed

Chen, Jing; Du, Yuzhang; Que, Wenxiu; Xing, Yonglei; Chen, Xiaofeng; Lei, Bo

2015-12-01

Crack-free organic-inorganic hybrid monoliths with controlled biomineralization activity and mechanical property have an important role for highly efficient bone tissue regeneration. Here, biomimetic and crack-free polydimethylsiloxane (PDMS)-modified bioactive glass (BG)-poly(ethylene glycol) (PEG) (PDMS-BG-PEG) hybrids monoliths were prepared by a facile sol-gel technique. Results indicate that under the assist of co-solvents, BG sol and PDMS and PEG could be hybridized at a molecular level, and effects of the PEG molecular weight on the structure, biomineralization activity, and mechanical property of the as-prepared hybrid monoliths were also investigated in detail. It is found that an addition of low molecular weight PEG can significantly prevent the formation of cracks and speed up the gelation of the hybrid monoliths, and the surface microstructure of the hybrid monoliths can be changed from the porous to the smooth as the PEG molecular weight increases. Additionally, the hybrid monoliths with low molecular weight PEG show the high formation of the biological apatite layer, while the hybrids with high molecular weight PEG exhibit negligible biomineralization ability in simulated body fluid (SBF). Furthermore, the PDMS-BG-PEG 600 hybrid monolith has significantly high compressive strength (32 ± 3 MPa) and modulus (153 ± 11 MPa), as well as good cell biocompatibility by supporting osteoblast (MC3T3-E1) attachment and proliferation. These results indicate that the as-prepared PDMS-BG-PEG hybrid monoliths may have promising applications for bone tissue regeneration. Copyright © 2015 Elsevier B.V. All rights reserved.

1,3,4-Oxadiazole containing silanes as novel hosts for blue phosphorescent organic light emitting diodes.

PubMed

Leung, Man-kit; Yang, Wan-Hsi; Chuang, Ching-Nan; Lee, Jiun-Haw; Lin, Chi-Feng; Wei, Mao-Kuo; Liu, Yu-Hao

2012-10-05

Five rigid oxadiazole (OXD) containing silanes, denoted 1-5, have been developed with high morphological stability. Disruption of the π-aromatic conjugation by introduction of Si atoms leads to a large band gap and high triplet energy. Among the OXDs we studied, 2,5-bis(triphenylsilylphenyl)-1,3,4-oxadiazole 5 is the best host for FIrpic, with a phosphorescent organic light emitting diode (PHOLED) turn-on voltage of 6.9 V, maximum luminance of 5124 cd/m(2), current efficiency of 39.9 cd/A, and external quantum efficiency of 13.1%. Special molecular stacking in the single crystal of 5 was discussed.

Surface engineering on mesoporous silica chips for enriching low molecular weight phosphorylated proteins

NASA Astrophysics Data System (ADS)

Hu, Ye; Peng, Yang; Lin, Kevin; Shen, Haifa; Brousseau, Louis C., III; Sakamoto, Jason; Sun, Tong; Ferrari, Mauro

2011-02-01

Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV = 18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications.Phosphorylated peptides and proteins play an important role in normal cellular activities, e.g., gene expression, mitosis, differentiation, proliferation, and apoptosis, as well as tumor initiation, progression and metastasis. However, technical hurdles hinder the use of common fractionation methods to capture phosphopeptides from complex biological fluids such as human sera. Herein, we present the development of a dual strategy material that offers enhanced capture of low molecular weight phosphoproteins: mesoporous silica thin films with precisely engineered pore sizes that sterically select for molecular size combined with chemically selective surface modifications (i.e. Ga3+, Ti4+ and Zr4+) that target phosphoroproteins. These materials provide high reproducibility (CV = 18%) and increase the stability of the captured proteins by excluding degrading enzymes, such as trypsin. The chemical and physical properties of the composite mesoporous thin films were characterized by X-ray diffraction, transmission electron microscopy, X-ray photoelectron spectroscopy, energy dispersive X-ray spectroscopy and ellipsometry. Using mass spectroscopy and biostatistics analysis, the enrichment efficiency of different metal ions immobilized on mesoporous silica chips was investigated. The novel technology reported provides a platform capable of efficiently profiling the serum proteome for biomarker discovery, forensic sampling, and routine diagnostic applications. Electronic supplementary information (ESI) available. See DOI: 10.1039/c0nr00720j

Charge Generation Dynamics in Efficient All-Polymer Solar Cells: Influence of Polymer Packing and Morphology.

PubMed

Gautam, Bhoj R; Lee, Changyeon; Younts, Robert; Lee, Wonho; Danilov, Evgeny; Kim, Bumjoon J; Gundogdu, Kenan

2015-12-23

All-polymer solar cells exhibit rapid progress in power conversion efficiency (PCE) from 2 to 7.7% over the past few years. While this improvement is primarily attributed to efficient charge transport and balanced mobility between the carriers, not much is known about the charge generation dynamics in these systems. Here we measured exciton relaxation and charge separation dynamics using ultrafast spectroscopy in polymer/polymer blends with different molecular packing and morphology. These measurements indicate that preferential face-on configuration with intermixed nanomorphology increases the charge generation efficiency. In fact, there is a direct quantitative correlation between the free charge population in the ultrafast time scales and the external quantum efficiency, suggesting not only the transport but also charge generation is key for the design of high performance all polymer solar cells.

Density-Functional Theory with Dispersion-Correcting Potentials for Methane: Bridging the Efficiency and Accuracy Gap between High-Level Wave Function and Classical Molecular Mechanics Methods.

PubMed

Torres, Edmanuel; DiLabio, Gino A

2013-08-13

Large clusters of noncovalently bonded molecules can only be efficiently modeled by classical mechanics simulations. One prominent challenge associated with this approach is obtaining force-field parameters that accurately describe noncovalent interactions. High-level correlated wave function methods, such as CCSD(T), are capable of correctly predicting noncovalent interactions, and are widely used to produce reference data. However, high-level correlated methods are generally too computationally costly to generate the critical reference data required for good force-field parameter development. In this work we present an approach to generate Lennard-Jones force-field parameters to accurately account for noncovalent interactions. We propose the use of a computational step that is intermediate to CCSD(T) and classical molecular mechanics, that can bridge the accuracy and computational efficiency gap between them, and demonstrate the efficacy of our approach with methane clusters. On the basis of CCSD(T)-level binding energy data for a small set of methane clusters, we develop methane-specific, atom-centered, dispersion-correcting potentials (DCPs) for use with the PBE0 density-functional and 6-31+G(d,p) basis sets. We then use the PBE0-DCP approach to compute a detailed map of the interaction forces associated with the removal of a single methane molecule from a cluster of eight methane molecules and use this map to optimize the Lennard-Jones parameters for methane. The quality of the binding energies obtained by the Lennard-Jones parameters we obtained is assessed on a set of methane clusters containing from 2 to 40 molecules. Our Lennard-Jones parameters, used in combination with the intramolecular parameters of the CHARMM force field, are found to closely reproduce the results of our dispersion-corrected density-functional calculations. The approach outlined can be used to develop Lennard-Jones parameters for any kind of molecular system.

In vivo endothelial siRNA delivery using polymeric nanoparticles with low molecular weight

NASA Astrophysics Data System (ADS)

Dahlman, James E.; Barnes, Carmen; Khan, Omar F.; Thiriot, Aude; Jhunjunwala, Siddharth; Shaw, Taylor E.; Xing, Yiping; Sager, Hendrik B.; Sahay, Gaurav; Speciner, Lauren; Bader, Andrew; Bogorad, Roman L.; Yin, Hao; Racie, Tim; Dong, Yizhou; Jiang, Shan; Seedorf, Danielle; Dave, Apeksha; Singh Sandhu, Kamaljeet; Webber, Matthew J.; Novobrantseva, Tatiana; Ruda, Vera M.; Lytton-Jean, Abigail K. R.; Levins, Christopher G.; Kalish, Brian; Mudge, Dayna K.; Perez, Mario; Abezgauz, Ludmila; Dutta, Partha; Smith, Lynelle; Charisse, Klaus; Kieran, Mark W.; Fitzgerald, Kevin; Nahrendorf, Matthias; Danino, Dganit; Tuder, Rubin M.; von Andrian, Ulrich H.; Akinc, Akin; Panigrahy, Dipak; Schroeder, Avi; Koteliansky, Victor; Langer, Robert; Anderson, Daniel G.

2014-08-01

Dysfunctional endothelium contributes to more diseases than any other tissue in the body. Small interfering RNAs (siRNAs) can help in the study and treatment of endothelial cells in vivo by durably silencing multiple genes simultaneously, but efficient siRNA delivery has so far remained challenging. Here, we show that polymeric nanoparticles made of low-molecular-weight polyamines and lipids can deliver siRNA to endothelial cells with high efficiency, thereby facilitating the simultaneous silencing of multiple endothelial genes in vivo. Unlike lipid or lipid-like nanoparticles, this formulation does not significantly reduce gene expression in hepatocytes or immune cells even at the dosage necessary for endothelial gene silencing. These nanoparticles mediate the most durable non-liver silencing reported so far and facilitate the delivery of siRNAs that modify endothelial function in mouse models of vascular permeability, emphysema, primary tumour growth and metastasis.

A Novel Sensitive Luminescence Probe Microspheres for Rapid and Efficient Detection of τ-Fluvalinate in Taihu Lake

PubMed Central

Wang, Jixiang; Wang, Yunyun; Qiu, Hao; Sun, Lin; Dai, Xiaohui; Pan, Jianming; Yan, Yongsheng

2017-01-01

Fluorescent molecularly imprinted polymers have shown great promise in biological or chemical separations and detection, due to their high stability, selectivity and sensitivity. In this work, fluorescent molecularly imprinted microsphere was synthesized via precipitation polymerization, which could separate efficiently and rapidly detect τ-fluvalinate (a toxic insecticide) in water samples, was reported. The fluorescent imprinted sensor showed excellent stability, outstanding selectivity and the limit of detection low to 12.14 nM, good regeneration ability which still kept good sensitivity after 8 cycling experiments and fluorescence quenching mechanism was illustrated in details. In addition, the fluorescent sensor was further used to detect τ-fluvalinate in real samples from Taihu Lake. Despite the relatively complex components of the environment water, the fluorescent imprinted microspheres sitll showed good recovery, clearly demonstrating the potental value of this smart sensor nanomaterial in environment monitoring. PMID:28485402

Efficient oxidation of alcohols to carbonyl compounds with molecular oxygen catalyzed by N-hydroxyphthalimide combined with a Co species

PubMed

Iwahama; Yoshino; Keitoku; Sakaguchi; Ishii

2000-10-06

Highly efficient catalytic oxidation of alcohols with molecular oxygen by N-hydroxyphthalimide (NHPI) combined with a Co species was developed. The oxidation of 2-octanol in the presence of catalytic amounts of NHPI and Co(OAc)2 under atmospheric dioxygen in AcOEt at 70 degrees C gave 2-octanone in 93% yield. The oxidation was significantly enhanced by adding a small amount of benzoic acid to proceed smoothly even at room temperature. Primary alcohols were oxidized by NHPI in the absence of any metal catalyst to form the corresponding carboxylic acids in good yields. In the oxidation of terminal vic-diols such as 1,2-butanediol, carbon-carbon bond cleavage was induced to give one carbon less carboxylic acids such as propionic acid, while internal vic-diols were selectively oxidized to 1,2-diketones.

High-efficiency V-band GaAs IMPATT diodes

NASA Technical Reports Server (NTRS)

Ma, Y. E.; Benko, E.; Trinh, T.; Erickson, L. P.; Mattord, T. J.

1984-01-01

Double-drift GaAs IMPATT diodes were designed for V-band frequency operations and fabricated using molecular-beam epitaxy. The diodes were fabricated in two configurations: (1) circular mesa diodes with silver-plated (integrated) heat sinks: (2) pill-type diodes bonded to diamond heat sinks. Both configurations utilized a miniature quartz-ring package. Output power greater than 1 W CW was achieved at V-band frequencies from diodes on diamond heat sinks. The best conversion efficiency was 13.3 percent at 55.5 GHz with 1 W output power.

Base-catalyzed efficient tandem [3 + 3] and [3 + 2 + 1] annulation-aerobic oxidative benzannulations.

PubMed

Diallo, Aboubacar; Zhao, Yu-Long; Wang, He; Li, Sha-Sha; Ren, Chuan-Qing; Liu, Qun

2012-11-16

An efficient synthesis of substituted benzenes via a base-catalyzed [3 + 3] aerobic oxidative aromatization of α,β-unsaturated carbonyl compounds with dimethyl glutaconate was reported. All the reactions were carried out under mild, metal-free conditions to afford the products in high to excellent yields with molecular oxygen as the sole oxidant and water as the sole byproduct. Furthermore, a more convenient tandem [3 + 2 + 1] aerobic oxidative aromatization reaction was developed through the in situ generation of the α,β-unsaturated carbonyl compounds from aldehydes and ketones.

Molecular Insights into the pH-Dependent Adsorption and Removal of Ionizable Antibiotic Oxytetracycline by Adsorbent Cyclodextrin Polymers

PubMed Central

Zhang, Yu; Cai, Xiyun; Xiong, Weina; Jiang, Hao; Zhao, Haitong; Yang, Xianhai; Li, Chao; Fu, Zhiqiang; Chen, Jingwen

2014-01-01

Effects of pH on adsorption and removal efficiency of ionizable organic compounds (IOCs) by environmental adsorbents are an area of debate, because of its dual mediation towards adsorbents and adsorbate. Here, we probe the pH-dependent adsorption of ionizable antibiotic oxytetracycline (comprising OTCH2 +, OTCH±, OTC−, and OTC2−) onto cyclodextrin polymers (CDPs) with the nature of molecular recognition and pH inertness. OTCH± commonly has high adsorption affinity, OTC− exhibits moderate affinity, and the other two species have negligible affinity. These species are evidenced to selectively interact with structural units (e.g., CD cavity, pore channel, and network) of the polymers and thus immobilized onto the adsorbents to different extents. The differences in adsorption affinity and mechanisms of the species account for the pH-dependent adsorption of OTC. The mathematical equations are derived from the multiple linear regression (MLR) analysis of quantitatively relating adsorption affinity of OTC at varying pH to adsorbent properties. A combination of the MLR analysis for OTC and molecular recognition of adsorption of the species illustrates the nature of the pH-dependent adsorption of OTC. Based on this finding, γ-HP-CDP is chosen to adsorb and remove OTC at pH 5.0 and 7.0, showing high removal efficiency and strong resistance to the interference of coexisting components. PMID:24465975

High-Speed High-Efficiency Large-Area Resonant Cavity Enhanced p-i-n Photodiodes for Multimode Fiber Communications

DTIC Science & Technology

2001-12-01

850 nm. The layers are grown by molecular beam epitaxy . The AlGaAs–GaAs inter- faces are alloy-graded for 30 nm to eliminate charge trapping that may... beam of the VCSELs allow for easy coupling of light into the MMF, it is also desirable to have photodetectors with large active windows compatible with... VCSEL )emitting at 850 nm [1] have become the preferred source for high-speed short-wavelength communication systems. These VCSELs are particularly

High-temperature LC-MS/MS of permethylated glycans derived from glycoproteins.

PubMed

Zhou, Shiyue; Hu, Yunli; Mechref, Yehia

2016-06-01

Various glycomic analysis methods have been developed due to the essential roles of glycans in biological processes as well as the potential application of glycomics in biomarker discovery in many diseases. Permethylation is currently considered to be one of the most common derivatization methods in MS-based glycomic analysis. Permethylation not only improves ionization efficiency and stability of sialylated glycans in positive mode but also allows for enhanced separation performance on reversed-phase liquid chromatography (RPLC). Recently, RPLC-MS analysis of permethylated glycans exhibited excellent performance in sensitivity and reproducibility and became a widely-applied comprehensive strategy in glycomics. However, separating permethylated glycans by RPLC always suffers from peak broadening for high-molecular-weight branched glycans, which probably due to the low exchange rate between the stationary phase and mobile phase limited by intermolecular interactions of the methyl groups associated with the branching of the glycan structures. In this study, we employed high separation temperature conditions for RPLC of permethylated glycans, thus achieving enhanced peak capacity, improving peak shape, and enhancing separation efficiency. Additionally, partial isomeric separation were observed in RPLC of permethylated glycans at high-temperature. Mathematical processing of the correlation between retention time and molecular weight also revealed the advantage of high-temperature LC method for both manual and automatic glycan identification. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A new concept of efficient therapeutic drug monitoring using the high-resolution continuum source absorption spectrometry and the surface enhanced Raman spectroscopy

NASA Astrophysics Data System (ADS)

Xing, Yanlong; Fuss, Harald; Lademann, Jürgen; Huang, Mao Dong; Becker-Ross, Helmut; Florek, Stefan; Patzelt, Alexa; Meinke, Martina C.; Jung, Sora; Esser, Norbert

2018-04-01

In this study, a new therapeutic drug monitoring approach has been tested based on the combination of CaF molecular absorption using high-resolution continuum source absorption spectrometry (HR-CSAS) and surface enhanced Raman spectroscopy (SERS). HR-CSAS with mini graphite tube was successfully tested for clinical therapeutic drug monitoring of the fluorine-containing drug capecitabine in sweat samples of cancer patients: It showed advantageous features of high selectivity (no interference from Cl), high sensitivity (characteristic mass of 0.1 ng at CaF 583.069 nm), low sample consumption (down to 30 nL) and fast measurement (no sample pretreatment and less than 1 min of responding time) in tracing the fluorine signal out of capecitabine. However, this technique has the disadvantage of the total loss of the drug's structure information after burning the sample at very high temperature. Therefore, a new concept of combining HR-CSAS with a non-destructive spectroscopic method (SERS) was proposed for the sensitive sensing and specific identification of capecitabine. We tested and succeed in obtaining the molecular characteristics of the metabolite of capecitabine (named 5-fluorouracil) by the non-destructive SERS technique. With the results shown in this work, it is demonstrated that the combined spectroscopic technique of HR-CSAS and SERS will be very useful in efficient therapeutic drug monitoring in the future.

Enrichment of low molecular weight serum proteins using acetonitrile precipitation for mass spectrometry based proteomic analysis.

PubMed

Kay, Richard; Barton, Chris; Ratcliffe, Lucy; Matharoo-Ball, Balwir; Brown, Pamela; Roberts, Jane; Teale, Phil; Creaser, Colin

2008-10-01

A rapid acetonitrile (ACN)-based extraction method has been developed that reproducibly depletes high abundance and high molecular weight proteins from serum prior to mass spectrometric analysis. A nanoflow liquid chromatography/tandem mass spectrometry (nano-LC/MS/MS) multiple reaction monitoring (MRM) method for 57 high to medium abundance serum proteins was used to characterise the ACN-depleted fraction after tryptic digestion. Of the 57 targeted proteins 29 were detected and albumin, the most abundant protein in serum and plasma, was identified as the 20th most abundant protein in the extract. The combination of ACN depletion and one-dimensional nano-LC/MS/MS enabled the detection of the low abundance serum protein, insulin-like growth factor-I (IGF-I), which has a serum concentration in the region of 100 ng/mL. One-dimensional sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) analysis of the depleted serum showed no bands corresponding to proteins of molecular mass over 75 kDa after extraction, demonstrating the efficiency of the method for the depletion of high molecular weight proteins. Total protein analysis of the ACN extracts showed that approximately 99.6% of all protein is removed from the serum. The ACN-depletion strategy offers a viable alternative to the immunochemistry-based protein-depletion techniques commonly used for removing high abundance proteins from serum prior to MS-based proteomic analyses.

DNA Duplex-Based Photodynamic Molecular Beacon for Targeted Killing of Retinoblastoma Cell.

PubMed

Wei, Yanchun; Lu, Cuixia; Chen, Qun; Xing, Da

2016-11-01

Retinoblastoma (RB) is the most common primary intraocular malignancy of infancy. An alternative RB treatment protocol is proposed and tested. It is based on a photodynamic therapy (PDT) with a designed molecular beacon that specifically targets the murine double minute x (MDMX) high-expressed RB cells. A MDMX mRNA triggered photodynamic molecular beacon is designed by binding a photosensitizer molecule (pyropheophorbide-a, or PPa) and a black hole quencher-3 (BHQ3) through a complementary oligonucleotide sequence. Cells with and without MDMX high-expression are incubated with the beacon and then irradiated with a laser. The fluorescence and reactive oxygen species are detected in solution to verify the specific activation of PPa by the perfectly matched DNA targets. The cell viabilities are evaluated with CCK-8 and flow cytometry assay. The fluorescence and photo-cytoxicity of PPa is recovered and significantly higher in the MDMX high-expressed Y79 and WERI-Rb1 cells, compared to that with the MDMX low-expressed cells. The synthesized beacon exhibits high PDT efficiency toward MDMX high-expressed RB cells. The data suggest that the designed beacon may provide a potential alternative for RB therapy and secures the ground for future investigation.

Fast and high-efficiency magnetic surface imprinting based on microwave-accelerated reversible addition fragmentation chain transfer polymerization for the selective extraction of estrogen residues in milk.

PubMed

Chen, Fangfang; Wang, Jiayu; Lu, Ruicong; Chen, Huiru; Xie, Xiaoyu

2018-08-10

A novel microwave-accelerated reversible addition fragmentation chain transfer (RAFT) polymerization strategy has been introduced to shorten reaction time and improved polymerization efficiency of the conventional molecularly imprinting technology based on RAFT. Magnetic molecular imprinted polymers (MMIPs) were successfully synthesized much more efficiently using 17β-estradiol (E2) as a template for the determination of estrogen residues. The resultant MMIPs had well-defined thin imprinted film, favoring the fast mass transfer. Moreover, the reaction time, which was just 1/24 of the time taken by conventional heating, was significantly decreased, improving the reaction efficiency and reducing the probability of side reactions. Meanwhile, the obtained polymers have good capacity of 6.67 mg g -1 and satisfactory selectivity to template molecule with the imprinting factor of 5.11. As a result, a method combination of the resultant MMIPs as solid phase extraction sorbents and high-performance liquid chromatography was successfully set up to determinate three estrogen residues in milk samples. For E2, estrone, and estriol, the limit of detections were calculated to be 0.03, 0.08, and 0.06 ng mL -1 , respectively, and the limit of quantifications were 0.11, 0.27, and 0.21 ng mL -1 , respectively. At the spiked level of 1, 5, and 10 ng mL -1 , the recoveries of the three estrogens were ranged from 69.1% to 91.9% and the intra-day relative standard deviation (RSD) was less than 5.7%. In addition, the resultant MMIPs exhibited good reproducibility and reusability with the inter-batch RSD of 5.3% and the intra-batch RSD of 6.2%, respectively. Overall, the realization of this strategy facilitates the preparation of MMIPs with good architecture and high reaction efficiencies for the analysis of complicated real samples. Copyright © 2018 Elsevier B.V. All rights reserved.

A high-efficiency regime for gas-phase terahertz lasers.

PubMed

Wang, Fan; Lee, Jeongwon; Phillips, Dane J; Holliday, Samuel G; Chua, Song-Liang; Bravo-Abad, Jorge; Joannopoulos, John D; Soljačić, Marin; Johnson, Steven G; Everitt, Henry O

2018-06-11

We present both an innovative theoretical model and an experimental validation of a molecular gas optically pumped far-infrared (OPFIR) laser at 0.25 THz that exhibits 10× greater efficiency (39% of the Manley-Rowe limit) and 1,000× smaller volume than comparable commercial lasers. Unlike previous OPFIR-laser models involving only a few energy levels that failed even qualitatively to match experiments at high pressures, our ab initio theory matches experiments quantitatively, within experimental uncertainties with no free parameters, by accurately capturing the interplay of millions of degrees of freedom in the laser. We show that previous OPFIR lasers were inefficient simply by being too large and that high powers favor high pressures and small cavities. We believe that these results will revive interest in OPFIR laser as a powerful and compact source of terahertz radiation.

Molecular approaches to solar energy conversion: the energetic cost of charge separation from molecular-excited states.

PubMed

Durrant, James R

2013-08-13

This review starts with a brief overview of the technological potential of molecular-based solar cell technologies. It then goes on to focus on the core scientific challenge associated with using molecular light-absorbing materials for solar energy conversion, namely the separation of short-lived, molecular-excited states into sufficiently long-lived, energetic, separated charges capable of generating an external photocurrent. Comparisons are made between different molecular-based solar cell technologies, with particular focus on the function of dye-sensitized photoelectrochemical solar cells as well as parallels with the function of photosynthetic reaction centres. The core theme of this review is that generating charge carriers with sufficient lifetime and a high quantum yield from molecular-excited states comes at a significant energetic cost-such that the energy stored in these charge-separated states is typically substantially less than the energy of the initially generated excited state. The role of this energetic loss in limiting the efficiency of solar energy conversion by such devices is emphasized, and strategies to minimize this energy loss are compared and contrasted.

The effect of conjugation to gold nanoparticles on the ability of low molecular weight chitosan to transfer DNA vaccine.

PubMed

Zhou, Xianfeng; Zhang, Xizhen; Yu, Xianghui; Zha, Xiao; Fu, Qiuan; Liu, Bin; Wang, Xueyun; Chen, Yan; Chen, Yue; Shan, Yaming; Jin, Yinghua; Wu, Yongge; Liu, Junqiu; Kong, Wei; Shen, Jiacong

2008-01-01

Nonviral gene delivery systems based on conventional high molecular weight chitosans are efficient as DNA vaccine delivery system, but have poor physical properties such as aggregated shapes, low solubility at neutral pH, high viscosity at concentrations used for in vivo delivery and a slow onset of action. Furthermore, Chitosan oligomers shorter than 14 monomers units were recently found to form only weak complexes with DNA, resulting in physically unstable polyplexes in vitro and in vivo. Here, low molecular weight chitosans with an average molecular mass of 6kDa (Chito6) have been covalently attached to gold nanoparticles (GNPs), and the potency of the resulting Chito6-GNPs conjugates as vectors for the delivery of plasmid DNA has been investigated in vitro and in vivo. After delivery by intramuscular immunization in BALB/c mice, the Chito6-GNPs conjugates induced an enhanced serum antibody response 10 times more potent than naked DNA vaccine. Additionally, in contrast to naked DNA, the Chito6-GNPs conjugates induced potent cytotoxic T lymphocyte responses at a low dose.

Bioinspired Electrocatalysis of Oxygen Reduction Reaction in Fuel Cells Using Molecular Catalysts.

PubMed

Zion, Noam; Friedman, Ariel; Levy, Naomi; Elbaz, Lior

2018-04-23

One of the most important chemical reactions for renewable energy technologies such as fuel cells and metal-air batteries today is oxygen reduction. Due to the relatively sluggish reaction kinetics, catalysts are necessary to generate high power output. The most common catalyst for this reaction is platinum, but its scarcity and derived high price have raised the search for abundant nonprecious metal catalysts. Inspired from enzymatic processes which are known to catalyze oxygen reduction reaction efficiently, employing transition metal complexes as their catalytic centers, many are working on the development of bioinspired and biomimetic catalysts of this class. This research news article gives a glimpse of the recent progress on the development of bioinspired molecular catalyst for oxygen reduction, highlighting the importance of the molecular structure of the catalysts, from advancements in porphyrins and phthalocyanines to the most recent work on corroles, and 3D networks such as metal-organic frameworks and polymeric networks, all with nonpyrolyzed, well-defined molecular catalysts for oxygen reduction reaction. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Dialkylthio Substitution: An Effective Method to Modulate the Molecular Energy Levels of 2D-BDT Photovoltaic Polymers.

PubMed

Yao, Huifeng; Zhang, Hao; Ye, Long; Zhao, Wenchao; Zhang, Shaoqing; Hou, Jianhui

2016-02-17

Dialkylthio-substituted thienyl-benzodithiophene (BDT-DST) was designed and synthesized as a building block to modulate the molecular levels of the conjugated polymers, and three copolymers named PDST-BDD, PDST-TT and PDST-DPP were prepared and applied in polymer solar cells (PSCs). Theoretical calculations and electrochemical cyclic voltammetry (CV) measurement suggested that the dialkylthio group could decrease the molecular energy levels of the resulting polymers distinctly. The open-circuit voltage (VOC) of PSC devices based on PDST-BDD, PDST-TT, and PDST-DPP are as high as 1.0, 0.98, and 0.88 V, respectively, which are ∼0.15 V higher than those of the corresponding alky-substituted analogues. Moreover, the influence of the dialkylthio group on the absorption spectra, crystalline properties, hole mobilities, and blend morphologies of the polymers was also investigated. The results indicate that the dialkythio substitution is an effective method to modulate the molecular energy levels and that the BDT-DST unit has potential for constructing high-efficiency photovoltaic polymers.

Pronounced Effects of a Triazine Core on Photovoltaic Performance-Efficient Organic Solar Cells Enabled by a PDI Trimer-Based Small Molecular Acceptor.

PubMed

Duan, Yuwei; Xu, Xiaopeng; Yan, He; Wu, Wenlin; Li, Zuojia; Peng, Qiang

2017-02-01

A novel-small molecular acceptor with electron-deficient 1,3,5-triazine as the core and perylene diimides as the arms is developed as the acceptor material for efficient bulk heterojunction organic solar cells with an efficiency of 9.15%. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Contorted Organic Semiconductors for Molecular Electronics

NASA Astrophysics Data System (ADS)

Zhong, Yu

This thesis focuses on the synthesis, properties and applications of two types of contorted organic molecules: contorted molecular ribbons and conjugated corrals. We utilized the power of reaction chemistry to writing information into conjugated molecules with contorted structures and studied "structure-property" relationships. The unique properties of the molecules were expressed in electronic and optoelectronic devices such as field-effect transistors, solar cells, photodetectors, etc. In Chapter 2, I describe the design and synthesis of a new graphene ribbon architecture that consists of perylenediimide (PDI) subunits fused together by ethylene bridges. We created a prototype series of oligomers consisting of the dimer, trimer, and tetramer. The steric congestion at the fusion point between the PDI units creates helical junctions, and longer oligomers form helical ribbons. Thin films of these oligomers form the active layer in n-type field effect transistors. UV-vis spectroscopy reveals the emergence of an intense long-wavelength transition in the tetramer. From DFT calculations, we find that the HOMO-2 to LUMO transition is isoenergetic with the HOMO to LUMO transition in the tetramer. We probe these transitions directly using femtosecond transient absorption spectroscopy. The HOMO-2 to LUMO transition electronically connects the PDI subunits with the ethylene bridges, and its energy depends on the length of the oligomer. In Chapter 3, I describe an efficiency of 6.1% for a solution processed non-fullerene solar cell using a helical PDI dimer as the electron acceptor. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces, indicating that charge carriers are created from photogenerated excitons in both the electron donor and acceptor phases. Light-intensity-dependent current?voltage measurements suggested different recombination rates under short-circuit and open-circuit conditions. In Chapter 4, I discuss helical molecular semiconductors as electron acceptors that are on par with fullerene derivatives in efficient solar cells. We achieved an 8.3% power conversion efficiency in a solar cell, which is a record high for non-fullerene bulk heterojunctions. Femtosecond transient absorption spectroscopy revealed both electron and hole transfer processes at the donor-acceptor interfaces. Atomic force microscopy reveals a mesh-like network of acceptors with pores that are tens of nanometers in diameter for efficient exciton separation and charge transport. This study describes a new motif for designing highly efficient acceptors for organic solar cells. In Chapter 5, I compare analogous cyclic and acyclic pi-conjugated molecules as n-type electronic materials and find that the cyclic molecules have numerous benefits in organic photovoltaics. We designed two conjugated cycles for this study. Each comprises four subunits; one combines four electron-accepting, redox-active, diphenyl-perylenediimide subunits, and the other alternates two electron-donating bithiophene units with two diphenyl-perylenediimide units. We compare the macrocycles to acyclic versions of these molecules and find that, relative to the acyclic analogs, the conjugated macrocycles have bathochromically shifted UV-vis absorbances and are more easily reduced. In blended films, macrocycle-based devices show higher electron mobility and good morphology. All of these factors contribute to the more than doubling of the power conversion efficiency observed in organic photovoltaic devices with these macrocycles as the n-type, electron transporting material. This study highlights the importance of geometric design in creating new molecular semiconductors. In Chapter 6, I describe a new molecular design that enables high performance organic photodetectors. We use a rigid, conjugated macrocycle as the electron acceptor in devices to obtain high photocurrent and low dark current. We directly compare the macrocyclic acceptor devices to an acyclic control device; we find that the superior performance of the macrocycle originates from its rigid, conjugated, and cyclic structure. The macrocycle's rigid structure reduces the number of charged defects originating from deformed sp 2 carbons and covalent defects from photo/thermo-activation. With this molecular design we are able to suppress dark current density while retaining high responsivity in an ultra-sensitive non-fullerene organic photodetector. Importantly, we achieve a detectivity of 1014 Jones at near zero bias voltage. This is without the need for extra carrier blocking layers commonly employed in fullerene-based devices. Our devices are comparable to the best fullerene-based photodetectors, and the sensitivity at low working voltages (< 0.1 V) is a record for non-fullerene OPDs.

Enhanced Electron Affinity and Exciton Confinement in Exciplex-Type Host: Power Efficient Solution-Processed Blue Phosphorescent OLEDs with Low Turn-on Voltage.

PubMed

Ban, Xinxin; Sun, Kaiyong; Sun, Yueming; Huang, Bin; Jiang, Wei

2016-01-27

A benzimidazole/phosphine oxide hybrid 1,3,5-tris(1-(4-(diphenylphosphoryl)phenyl)-1H-benzo[d]imidazol-2-yl)benzene (TPOB) was newly designed and synthesized as the electron-transporting component to form an exciplex-type host with the conventional hole-transporting material tris(4-carbazoyl-9-ylphenyl)amine (TCTA). Because of the enhanced triplet energy and electron affinity of TPOB, the energy leakage from exciplex-state to the constituting molecule was eliminated. Using energy transfer from exciplex-state, solution-processed blue phosphorescent organic light-emitting diodes (PHOLEDs) achieved an extremely low turn-on voltage of 2.8 V and impressively high power efficiency of 22 lm W(-1). In addition, the efficiency roll-off was very small even at luminance up to 10 000 cd m(-2), which suggested the balanced charge transfer in the emission layer. This study demonstrated that molecular modulation was an effective way to develop efficient exciplex-type host for high performanced PHOLEDs.

Rapid and efficient method to extract metagenomic DNA from estuarine sediments.

PubMed

Shamim, Kashif; Sharma, Jaya; Dubey, Santosh Kumar

2017-07-01

Metagenomic DNA from sediments of selective estuaries of Goa, India was extracted using a simple, fast, efficient and environment friendly method. The recovery of pure metagenomic DNA from our method was significantly high as compared to other well-known methods since the concentration of recovered metagenomic DNA ranged from 1185.1 to 4579.7 µg/g of sediment. The purity of metagenomic DNA was also considerably high as the ratio of absorbance at 260 and 280 nm ranged from 1.88 to 1.94. Therefore, the recovered metagenomic DNA was directly used to perform various molecular biology experiments viz. restriction digestion, PCR amplification, cloning and metagenomic library construction. This clearly proved that our protocol for metagenomic DNA extraction using silica gel efficiently removed the contaminants and prevented shearing of the metagenomic DNA. Thus, this modified method can be used to recover pure metagenomic DNA from various estuarine sediments in a rapid, efficient and eco-friendly manner.

A systems biology strategy to identify molecular mechanisms of action and protein indicators of traumatic brain injury.

PubMed

Yu, Chenggang; Boutté, Angela; Yu, Xueping; Dutta, Bhaskar; Feala, Jacob D; Schmid, Kara; Dave, Jitendra; Tawa, Gregory J; Wallqvist, Anders; Reifman, Jaques

2015-02-01

The multifactorial nature of traumatic brain injury (TBI), especially the complex secondary tissue injury involving intertwined networks of molecular pathways that mediate cellular behavior, has confounded attempts to elucidate the pathology underlying the progression of TBI. Here, systems biology strategies are exploited to identify novel molecular mechanisms and protein indicators of brain injury. To this end, we performed a meta-analysis of four distinct high-throughput gene expression studies involving different animal models of TBI. By using canonical pathways and a large human protein-interaction network as a scaffold, we separately overlaid the gene expression data from each study to identify molecular signatures that were conserved across the different studies. At 24 hr after injury, the significantly activated molecular signatures were nonspecific to TBI, whereas the significantly suppressed molecular signatures were specific to the nervous system. In particular, we identified a suppressed subnetwork consisting of 58 highly interacting, coregulated proteins associated with synaptic function. We selected three proteins from this subnetwork, postsynaptic density protein 95, nitric oxide synthase 1, and disrupted in schizophrenia 1, and hypothesized that their abundance would be significantly reduced after TBI. In a penetrating ballistic-like brain injury rat model of severe TBI, Western blot analysis confirmed our hypothesis. In addition, our analysis recovered 12 previously identified protein biomarkers of TBI. The results suggest that systems biology may provide an efficient, high-yield approach to generate testable hypotheses that can be experimentally validated to identify novel mechanisms of action and molecular indicators of TBI. © 2014 The Authors. Journal of Neuroscience Research Published by Wiley Periodicals, Inc.

Boron doped graphene wrapped silver nanowires as an efficient electrocatalyst for molecular oxygen reduction

PubMed Central

Nair, Anju K.; Thazhe veettil, Vineesh; Kalarikkal, Nandakumar; Thomas, Sabu; Kala, M. S.; Sahajwalla, Veena; Joshi, Rakesh K.; Alwarappan, Subbiah

2016-01-01

Metal nanowires exhibit unusually high catalytic activity towards oxygen reduction reaction (ORR) due to their inherent electronic structures. However, controllable synthesis of stable nanowires still remains as a daunting challenge. Herein, we report the in situ synthesis of silver nanowires (AgNWs) over boron doped graphene sheets (BG) and demonstrated its efficient electrocatalytic activity towards ORR for the first time. The electrocatalytic ORR efficacy of BG-AgNW is studied using various voltammetric techniques. The BG wrapped AgNWs shows excellent ORR activity, with very high onset potential and current density and it followed four electron transfer mechanism with high methanol tolerance and stability towards ORR. The results are comparable to the commercially available 20% Pt/C in terms of performance. PMID:27941954

The rate and efficiency of high-mass star formation along the Hubble sequence

NASA Technical Reports Server (NTRS)

Devereux, Nicholas A.; Young, Judith S.

1991-01-01

Data obtained with IRAS are used to compare and contrast the global star formation rates for a galactic sample which represents essentially all known noninteracting spiral and lenticular galaxies within 40 Mpc. The distribution of 60 micron luminosity is similar for spirals of types Sa-Scd inclusively, although the luminosities of the very early and very late types are, on average, one order of magnitude lower. High-mass star formation rates are similar for early, intermediate, and late type spirals, and the average high-mass star formation rate per unit molecular gas mass is independent of type for spiral galaxies. A remarkable homogeneity exists in the high-mass star-forming capabilities of spiral galaxies, particularly among the Sa-Scd types. The Hubble sequence is therefore not a sequence in the present-day rate or production efficiency of high-mass stars.

Degradation of polycyclic aromatic hydrocarbons (PAHs) in textile dyeing sludge with ultrasound and Fenton processes: Effect of system parameters and synergistic effect study.

PubMed

Lin, Meiqing; Ning, Xun-an; An, Taicheng; Zhang, Jianhao; Chen, Changmin; Ke, Yaowei; Wang, Yujie; Zhang, Yaping; Sun, Jian; Liu, Jingyong

2016-04-15

To establish an efficient oxidation process for the degradation of polycyclic aromatic hydrocarbons (PAHs) in textile dyeing sludge, the effects of various operating parameters were optimized during the ultrasound process, Fenton process and the combined ultrasound-Fenton process. The results showed that the ultrasonic density of 1.80w/cm(3), both H2O2 and Fe(2+) dosages of 140mmol/L and pH 3 were favorable conditions for the degradation of PAHs. The degradation efficiency of high molecular weight PAHs was close to or even higher than that of light molecular weight PAHs. The highest degradation efficiencies of Σ16 PAHs were obtained within 30min in the order of: Fenton (83.5%) >ultrasound-Fenton (75.5%) >ultrasound (45.5%), then the efficiencies were decreased in the other of: ultrasound-Fenton (73.0%) >Fenton (70.3%) >ultrasound (41.4%) in 60min. The extra PAHs were released from the intracellular substances and the cavities of sludge due to the disruption of sludge during the oxidation process. Also, the degradation of PAHs could be inhibited by the other organic matter in the sludge. The combined ultrasound-Fenton process showed more efficient than both ultrasound process and Fenton process not only in the surface of sludge but also in the sludge interior. Copyright © 2015 Elsevier B.V. All rights reserved.

Reduced-droop green III-nitride light-emitting diodes utilizing GaN tunnel junction

NASA Astrophysics Data System (ADS)

Alhassan, Abdullah I.; Young, Erin C.; Alyamani, Ahmed Y.; Albadri, Abdulrahman; Nakamura, Shuji; DenBaars, Steven P.; Speck, James S.

2018-04-01

We report the fabrication of low-droop high-efficiency green c-plane light-emitting diodes (LEDs) utilizing GaN tunnel junction (TJ) contacts. The LED epitaxial layers with a top p-GaN layer were grown by metal organic chemical vapor deposition and an n++-GaN layer was deposited by molecular beam epitaxy to form a TJ. The TJ LEDs were then compared with equivalent LEDs having a tin-doped indium oxide (ITO) contact. The TJ LEDs exhibited a higher performance and a lower efficiency droop than did the ITO LEDs. At 35 A/cm2, the external quantum efficiencies for the TJ and ITO LEDs were 31.2 and 27%, respectively.

Silicon oxycarbide glass-graphene composite paper electrode for long-cycle lithium-ion batteries.

PubMed

David, Lamuel; Bhandavat, Romil; Barrera, Uriel; Singh, Gurpreet

2016-03-30

Silicon and graphene are promising anode materials for lithium-ion batteries because of their high theoretical capacity; however, low volumetric energy density, poor efficiency and instability in high loading electrodes limit their practical application. Here we report a large area (approximately 15 cm × 2.5 cm) self-standing anode material consisting of molecular precursor-derived silicon oxycarbide glass particles embedded in a chemically-modified reduced graphene oxide matrix. The porous reduced graphene oxide matrix serves as an effective electron conductor and current collector with a stable mechanical structure, and the amorphous silicon oxycarbide particles cycle lithium-ions with high Coulombic efficiency. The paper electrode (mass loading of 2 mg cm(-2)) delivers a charge capacity of ∼588 mAh g(-1)electrode (∼393 mAh cm(-3)electrode) at 1,020th cycle and shows no evidence of mechanical failure. Elimination of inactive ingredients such as metal current collector and polymeric binder reduces the total electrode weight and may provide the means to produce efficient lightweight batteries.

High efficiency and low cost preparation of size controlled starch nanoparticles through ultrasonic treatment and precipitation.

PubMed

Chang, Yanjiao; Yan, Xiaoxia; Wang, Qian; Ren, Lili; Tong, Jin; Zhou, Jiang

2017-07-15

The purpose of this work was to develop an approach to produce size controlled starch nanoparticles (SNPs), via precipitation with high efficiency and low cost. High concentration starch aqueous pastes (up to 5wt.%) were treated by ultrasound. Viscosity measurements and size exclusion chromatography characterization revealed that, after 30min ultrasonic treatment, viscosity of the starch pastes decreased two orders of magnitude and the weight average molecular weight of the starch decreased from 8.4×10 7 to 2.7×10 6 g/mol. Dynamic light scattering measurements and scanning electron microscopy observations showed that the SNPs prepared from the starch pastes with ultrasonic treatments were smaller (∼75nm) and more uniform. Moreover, SNPs could be obtained using less non-solvents. X-ray diffraction results indicated that effect of the ultrasonic treatment on crystalline structure of the SNPs was negligible. Ultrasound can be utilized to prepare smaller SNPs through nanoprecipitation with higher efficiency and lower cost. Copyright © 2017 Elsevier Ltd. All rights reserved.

Molecular characterization of a thermophilic endo-polygalacturonase from Thielavia arenaria XZ7 with high catalytic efficiency and application potential in the food and feed industries.

PubMed

Tu, Tao; Meng, Kun; Huang, Huoqing; Luo, Huiying; Bai, Yingguo; Ma, Rui; Su, Xiaoyun; Shi, Pengjun; Yang, Peilong; Wang, Yaru; Yao, Bin

2014-12-31

Thermophilic endo-polygalacturonases with high catalytic efficiency are of great interest in the food and feed industries. This study identified an endo-polygalacturonase gene (pg7fn) of glycoside hydrolase family 28 in the thermophilic fungus Thielavia arenaria XZ7. Recombinant PG7fn produced in Pichia pastoris is distinguished from other enzyme counterparts by its high functional temperature (60 °C) and specific activity (34382 ± 351 U/mg toward polygalacturonic acid). The enzyme exhibited good pH stability (pH 3.0-8.0) and resistance to pepsin and trypsin digestion and had a significant effect on disaggregation of soybean meal. Addition of 1 U/g PG7fn increased the pectin bioavailability by 19.33%. The excellent properties described above make PG7fn valuable for applications in the food and feed industries. Furthermore, a comparative study showed that N-glycosylation improved the thermostability and catalytic efficiency of PG7fn.

High Photoelectric Conversion Efficiency of Metal Phthalocyanine/Fullerene Heterojunction Photovoltaic Device

PubMed Central

Lin, Chi-Feng; Zhang, Mi; Liu, Shun-Wei; Chiu, Tien-Lung; Lee, Jiun-Haw

2011-01-01

This paper introduces the fundamental physical characteristics of organic photovoltaic (OPV) devices. Photoelectric conversion efficiency is crucial to the evaluation of quality in OPV devices, and enhancing efficiency has been spurring on researchers to seek alternatives to this problem. In this paper, we focus on organic photovoltaic (OPV) devices and review several approaches to enhance the energy conversion efficiency of small molecular heterojunction OPV devices based on an optimal metal-phthalocyanine/fullerene (C60) planar heterojunction thin film structure. For the sake of discussion, these mechanisms have been divided into electrical and optical sections: (1) Electrical: Modification on electrodes or active regions to benefit carrier injection, charge transport and exciton dissociation; (2) Optical: Optional architectures or infilling to promote photon confinement and enhance absorption. PMID:21339999

On-surface formation of one-dimensional polyphenylene through Bergman cyclization.

PubMed

Sun, Qiang; Zhang, Chi; Li, Zhiwen; Kong, Huihui; Tan, Qinggang; Hu, Aiguo; Xu, Wei

2013-06-12

On-surface fabrication of covalently interlinked conjugated nanostructures has attracted significant attention, mainly because of the high stability and efficient electron transport ability of these structures. Here, from the interplay of scanning tunneling microscopy imaging and density functional theory calculations, we report for the first time on-surface formation of one-dimensional polyphenylene chains through Bergman cyclization followed by radical polymerization on Cu(110). The formed surface nanostructures were further corroborated by the results for the ex situ-synthesized molecular product after Bergman cyclization. These findings are of particular interest and importance for the construction of molecular electronic nanodevices on surfaces.

High molecular gas fractions in normal massive star-forming galaxies in the young Universe.

PubMed

Tacconi, L J; Genzel, R; Neri, R; Cox, P; Cooper, M C; Shapiro, K; Bolatto, A; Bouché, N; Bournaud, F; Burkert, A; Combes, F; Comerford, J; Davis, M; Schreiber, N M Förster; Garcia-Burillo, S; Gracia-Carpio, J; Lutz, D; Naab, T; Omont, A; Shapley, A; Sternberg, A; Weiner, B

2010-02-11

Stars form from cold molecular interstellar gas. As this is relatively rare in the local Universe, galaxies like the Milky Way form only a few new stars per year. Typical massive galaxies in the distant Universe formed stars an order of magnitude more rapidly. Unless star formation was significantly more efficient, this difference suggests that young galaxies were much more molecular-gas rich. Molecular gas observations in the distant Universe have so far largely been restricted to very luminous, rare objects, including mergers and quasars, and accordingly we do not yet have a clear idea about the gas content of more normal (albeit massive) galaxies. Here we report the results of a survey of molecular gas in samples of typical massive-star-forming galaxies at mean redshifts of about 1.2 and 2.3, when the Universe was respectively 40% and 24% of its current age. Our measurements reveal that distant star forming galaxies were indeed gas rich, and that the star formation efficiency is not strongly dependent on cosmic epoch. The average fraction of cold gas relative to total galaxy baryonic mass at z = 2.3 and z = 1.2 is respectively about 44% and 34%, three to ten times higher than in today's massive spiral galaxies. The slow decrease between z approximately 2 and z approximately 1 probably requires a mechanism of semi-continuous replenishment of fresh gas to the young galaxies.

Molecular cancer classification using a meta-sample-based regularized robust coding method.

PubMed

Wang, Shu-Lin; Sun, Liuchao; Fang, Jianwen

2014-01-01

Previous studies have demonstrated that machine learning based molecular cancer classification using gene expression profiling (GEP) data is promising for the clinic diagnosis and treatment of cancer. Novel classification methods with high efficiency and prediction accuracy are still needed to deal with high dimensionality and small sample size of typical GEP data. Recently the sparse representation (SR) method has been successfully applied to the cancer classification. Nevertheless, its efficiency needs to be improved when analyzing large-scale GEP data. In this paper we present the meta-sample-based regularized robust coding classification (MRRCC), a novel effective cancer classification technique that combines the idea of meta-sample-based cluster method with regularized robust coding (RRC) method. It assumes that the coding residual and the coding coefficient are respectively independent and identically distributed. Similar to meta-sample-based SR classification (MSRC), MRRCC extracts a set of meta-samples from the training samples, and then encodes a testing sample as the sparse linear combination of these meta-samples. The representation fidelity is measured by the l2-norm or l1-norm of the coding residual. Extensive experiments on publicly available GEP datasets demonstrate that the proposed method is more efficient while its prediction accuracy is equivalent to existing MSRC-based methods and better than other state-of-the-art dimension reduction based methods.

Air filtration in the free molecular flow regime: a review of high-efficiency particulate air filters based on carbon nanotubes.

PubMed

Li, Peng; Wang, Chunya; Zhang, Yingying; Wei, Fei

2014-11-01

Air filtration in the free molecular flow (FMF) regime is important and challenging because a higher filtration efficiency and lower pressure drop are obtained when the fiber diameter is smaller than the gas mean free path in the FMF regime. In previous studies, FMF conditions have been obtained by increasing the gas mean free path through reducing the pressure and increasing the temperature. In the case of carbon nanotubes (CNTs) with nanoscale diameters, it is possible to filtrate in the FMF regime under normal conditions. This paper reviews recent progress in theoretical and experimental studies of air filtration in the FMF regime. Typical structure models of high-efficiency particulate (HEPA) air filters based on CNTs are introduced. The pressure drop in air filters operated in the FMF regime is less than that predicted by the conventional air filtration theory. The thinnest HEPA filters fabricated from single-walled CNT films have an extremely low pressure drop. CNT air filters with a gradient nanostructure are shown to give a much better filtration performance in dynamic filtration. CNT air filters with a hierarchical structure and an agglomerated CNT fluidized bed air filter are also introduced. Finally, the challenges and opportunities for the application of CNTs in air filtration are discussed. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Complementing in vitro screening assays with in silico molecular chemistry tools to examine potential in vivo metabolite-mediated effects

EPA Science Inventory

High-throughput in vitro assays offer a rapid, cost-efficient means to screen thousands of chemicals across hundreds of pathway-based toxicity endpoints. However, one main concern involved with the use of in vitro assays is the erroneous omission of chemicals that are inactive un...

QTL mapping for grain yield, flowering time, and stay-green traits in sorghum with genotyping-by-sequencing markers

USDA-ARS?s Scientific Manuscript database

Molecular breeding can complement traditional breeding approaches to achieve genetic gains in a more efficient way. In the present study, genetic mapping was conducted in a sorghum recombinant inbred line (RIL) population developed from Tx436 (a non-stay-green high food quality inbred) × 00MN7645 (a...

The use of adverse outcome pathway-based toxicity predictions: A case study evaluating the effects of imazalil on fathead minnow reproduction

EPA Science Inventory

Product Description: As a means to increase the efficiency of chemical safety assessment, there is an interest in using data from molecular and cellular bioassays, conducted in a highly automated fashion using modern robotics, to predict toxicity in humans and wildlife. The prese...

High-throughput genotyping-by-sequencing facilitates molecular tagging of a novel rust resistance gene, R15, in sunflower (Helianthus annuus L.)

USDA-ARS?s Scientific Manuscript database

The rust virulence gene is co-evolving with the resistance gene in sunflower, leading to the emergence of new physiologic pathotypes. This presents a continuous threat to the sunflower crop necessitating the development of resistant sunflower hybrids providing a more efficient, durable, and environm...

High Bandwidth-Efficiency Resonant Cavity Enhanced Schottky Photodiodes for 800-850 nm Wavelength Operation

DTIC Science & Technology

1998-05-25

at least 50 nm wide centered around 830 nm wavelength. The layers are grown by molecular beam epitaxy on a semi- insulating GaAs substrate. The...limited by the material properties. With the advent of GaAs vertical-cavity surface-emitting lasers ~ VCSEL !,2 the 800–850 nm wavelength range has recently

Improvement of efficiency in graphene/gallium nitride nanowire on Silicon photoelectrode for overall water splitting

NASA Astrophysics Data System (ADS)

Bae, Hyojung; Rho, Hokyun; Min, Jung-Wook; Lee, Yong-Tak; Lee, Sang Hyun; Fujii, Katsushi; Lee, Hyo-Jong; Ha, Jun-Seok

2017-11-01

Gallium nitride (GaN) nanowires are one of the most promising photoelectrode materials due to their high stability in acidic and basic electrolytes, and tunable band edge potentials. In this study, GaN nanowire arrays (GaN NWs) were prepared by molecular beam epitaxy (MBE); their large surface area enhanced the solar to hydrogen conversion efficiency. More significantly, graphene was grown by chemical vapor deposition (CVD), which enhanced the electron transfer between NWs for water splitting and protected the GaN NW surface. Structural characterizations of the prepared composite were performed using scanning electron microscopy (SEM) and transmission electron microscopy (TEM). The photocurrent density of Gr/GaN NWs exhibited a two-fold increase over pristine GaN NWs and sustained water splitting up to 70 min. These improvements may accelerate possible applications for hydrogen generation with high solar to hydrogen conversion efficiency.

YAMAT-seq: an efficient method for high-throughput sequencing of mature transfer RNAs

PubMed Central

Shigematsu, Megumi; Honda, Shozo; Loher, Phillipe; Telonis, Aristeidis G.; Rigoutsos, Isidore

2017-01-01

Abstract Besides translation, transfer RNAs (tRNAs) play many non-canonical roles in various biological pathways and exhibit highly variable expression profiles. To unravel the emerging complexities of tRNA biology and molecular mechanisms underlying them, an efficient tRNA sequencing method is required. However, the rigid structure of tRNA has been presenting a challenge to the development of such methods. We report the development of Y-shaped Adapter-ligated MAture TRNA sequencing (YAMAT-seq), an efficient and convenient method for high-throughput sequencing of mature tRNAs. YAMAT-seq circumvents the issue of inefficient adapter ligation, a characteristic of conventional RNA sequencing methods for mature tRNAs, by employing the efficient and specific ligation of Y-shaped adapter to mature tRNAs using T4 RNA Ligase 2. Subsequent cDNA amplification and next-generation sequencing successfully yield numerous mature tRNA sequences. YAMAT-seq has high specificity for mature tRNAs and high sensitivity to detect most isoacceptors from minute amount of total RNA. Moreover, YAMAT-seq shows quantitative capability to estimate expression levels of mature tRNAs, and has high reproducibility and broad applicability for various cell lines. YAMAT-seq thus provides high-throughput technique for identifying tRNA profiles and their regulations in various transcriptomes, which could play important regulatory roles in translation and other biological processes. PMID:28108659

Controllable Spatial Configuration on Cathode Interface for Enhanced Photovoltaic Performance and Device Stability.

PubMed

Li, Jiangsheng; Duan, Chenghao; Wang, Ning; Zhao, Chengjie; Han, Wei; Jiang, Li; Wang, Jizheng; Zhao, Yingjie; Huang, Changshui; Jiu, Tonggang

2018-05-08

The molecular structure of cathode interface modification materials can affect the surface morphology of the active layer and key electron transfer processes occurring at the interface of polymer solar cells in inverted structures mostly due to the change of molecular configuration. To investigate the effects of spatial configuration of the cathode interfacial modification layer on polymer solar cells device performances, we introduced two novel organic ionic salts (linear NS2 and three-dimensional (3D) NS4) combined with the ZnO film to fabricate highly efficient inverted solar cells. Both organic ionic salts successfully decreased the surface traps of the ZnO film and made its work function more compatible. Especially NS4 in three-dimensional configuration increased the electron mobility and extraction efficiency of the interfacial film, leading to a significant improvement of device performance. Power conversion efficiency (PCE) of 10.09% based on NS4 was achieved. Moreover, 3D interfacial modification could retain about 92% of its initial PCE over 160 days. It is proposed that 3D interfacial modification retards the element penetration-induced degradation without impeding the electron transfer from the active layer to the ZnO film, which significantly improves device stability. This indicates that inserting three-dimensional organic ionic salt is an efficient strategy to enhance device performance.

Extraction of inhibitor-free metagenomic DNA from polluted sediments, compatible with molecular diversity analysis using adsorption and ion-exchange treatments.

PubMed

Desai, Chirayu; Madamwar, Datta

2007-03-01

PCR inhibitor-free metagenomic DNA of high quality and high yield was extracted from highly polluted sediments using a simple remediation strategy of adsorption and ion-exchange chromatography. Extraction procedure was optimized with series of steps, which involved gentle mechanical lysis, treatment with powdered activated charcoal (PAC) and ion-exchange chromatography with amberlite resin. Quality of the extracted DNA for molecular diversity analysis was tested by amplifying bacterial 16S rDNA (16S rRNA gene) with eubacterial specific universal primers (8f and 1492r), cloning of the amplified 16S rDNA and ARDRA (amplified rDNA restriction analysis) of the 16S rDNA clones. The presence of discrete differences in ARDRA banding profiles provided evidence for expediency of the DNA extraction protocol in molecular diversity studies. A comparison of the optimized protocol with commercial Ultraclean Soil DNA isolation kit suggested that method described in this report would be more efficient in removing metallic and organic inhibitors, from polluted sediment samples.

In-situ preparation of functionalized molecular sieve material and a methodology to remove template

NASA Astrophysics Data System (ADS)

Yadav, Rekha; Ahmed, Maqsood; Singh, Arvind Kumar; Sakthivel, Ayyamperumal

2016-03-01

A series of diaminosilane-functionalized silicoaluminophosphate molecular sieve (SAPO-37) was prepared by in-situ synthesis, and a novel method was developed for the selective removal of structure directing agent (SDA)/template from the functionalized SAPO-37.The complete removal of the SDA was evident according to FT-IR, TGA, 13C MAS-NMR and elemental analysis. The developed method was found to be efficient for removal of template from microporous molecular sieve viz., SAPO-37 and can be applied for other microporous molecular sieves such as SAPO-5, SAPO-40, etc. The powder XRD pattern of the template-removed samples showed a highly crystalline SAPO-37 phase. Argentometric titration revealed that more than 90% of diamine functionality exposed on the surface was accessible for catalytic applications. The resultant materials showed promising activity for ring opening of epoxide with aniline to yield β-amino-alcohol.

Combining configurational energies and forces for molecular force field optimization

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

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Combining configurational energies and forces for molecular force field optimization

DOE PAGES

Vlcek, Lukas; Sun, Weiwei; Kent, Paul R. C.

2017-07-21

While quantum chemical simulations have been increasingly used as an invaluable source of information for atomistic model development, the high computational expenses typically associated with these techniques often limit thorough sampling of the systems of interest. It is therefore of great practical importance to use all available information as efficiently as possible, and in a way that allows for consistent addition of constraints that may be provided by macroscopic experiments. We propose a simple approach that combines information from configurational energies and forces generated in a molecular dynamics simulation to increase the effective number of samples. Subsequently, this information ismore » used to optimize a molecular force field by minimizing the statistical distance similarity metric. We also illustrate the methodology on an example of a trajectory of configurations generated in equilibrium molecular dynamics simulations of argon and water and compare the results with those based on the force matching method.« less

Recognition-driven chemical labeling of endogenous proteins in multi-molecular crowding in live cells.

PubMed

Amaike, Kazuma; Tamura, Tomonori; Hamachi, Itaru

2017-11-14

Endogenous protein labeling is one of the most invaluable methods for studying the bona fide functions of proteins in live cells. However, multi-molecular crowding conditions, such as those that occur in live cells, hamper the highly selective chemical labeling of a protein of interest (POI). We herein describe how the efficient coupling of molecular recognition with a chemical reaction is crucial for selective protein labeling. Recognition-driven protein labeling is carried out by a synthetic labeling reagent containing a protein (recognition) ligand, a reporter tag, and a reactive moiety. The molecular recognition of a POI can be used to greatly enhance the reaction kinetics and protein selectivity, even under live cell conditions. In this review, we also briefly discuss how such selective chemical labeling of an endogenous protein can have a variety of applications at the interface of chemistry and biology.

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

Reaching multi-nanosecond timescales in combined QM/MM molecular dynamics simulations through parallel horsetail sampling.

PubMed

Martins-Costa, Marilia T C; Ruiz-López, Manuel F

2017-04-15

We report an enhanced sampling technique that allows to reach the multi-nanosecond timescale in quantum mechanics/molecular mechanics molecular dynamics simulations. The proposed technique, called horsetail sampling, is a specific type of multiple molecular dynamics approach exhibiting high parallel efficiency. It couples a main simulation with a large number of shorter trajectories launched on independent processors at periodic time intervals. The technique is applied to study hydrogen peroxide at the water liquid-vapor interface, a system of considerable atmospheric relevance. A total simulation time of a little more than 6 ns has been attained for a total CPU time of 5.1 years representing only about 20 days of wall-clock time. The discussion of the results highlights the strong influence of the solvation effects at the interface on the structure and the electronic properties of the solute. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

Cavity-enhanced Raman microscopy of individual carbon nanotubes

PubMed Central

Hümmer, Thomas; Noe, Jonathan; Hofmann, Matthias S.; Hänsch, Theodor W.; Högele, Alexander; Hunger, David

2016-01-01

Raman spectroscopy reveals chemically specific information and provides label-free insight into the molecular world. However, the signals are intrinsically weak and call for enhancement techniques. Here, we demonstrate Purcell enhancement of Raman scattering in a tunable high-finesse microcavity, and utilize it for molecular diagnostics by combined Raman and absorption imaging. Studying individual single-wall carbon nanotubes, we identify crucial structural parameters such as nanotube radius, electronic structure and extinction cross-section. We observe a 320-times enhanced Raman scattering spectral density and an effective Purcell factor of 6.2, together with a collection efficiency of 60%. Potential for significantly higher enhancement, quantitative signals, inherent spectral filtering and absence of intrinsic background in cavity-vacuum stimulated Raman scattering render the technique a promising tool for molecular imaging. Furthermore, cavity-enhanced Raman transitions involving localized excitons could potentially be used for gaining quantum control over nanomechanical motion and open a route for molecular cavity optomechanics. PMID:27402165

In-situ preparation of functionalized molecular sieve material and a methodology to remove template.

PubMed

Yadav, Rekha; Ahmed, Maqsood; Singh, Arvind Kumar; Sakthivel, Ayyamperumal

2016-03-10

A series of diaminosilane-functionalized silicoaluminophosphate molecular sieve (SAPO-37) was prepared by in-situ synthesis, and a novel method was developed for the selective removal of structure directing agent (SDA)/template from the functionalized SAPO-37.The complete removal of the SDA was evident according to FT-IR, TGA, (13)C MAS-NMR and elemental analysis. The developed method was found to be efficient for removal of template from microporous molecular sieve viz., SAPO-37 and can be applied for other microporous molecular sieves such as SAPO-5, SAPO-40, etc. The powder XRD pattern of the template-removed samples showed a highly crystalline SAPO-37 phase. Argentometric titration revealed that more than 90% of diamine functionality exposed on the surface was accessible for catalytic applications. The resultant materials showed promising activity for ring opening of epoxide with aniline to yield β-amino-alcohol.

High-performance multilayer composite membranes with mussel-inspired polydopamine as a versatile molecular bridge for CO2 separation.

PubMed

Li, Panyuan; Wang, Zhi; Li, Wen; Liu, Yanni; Wang, Jixiao; Wang, Shichang

2015-07-22

It is desirable to develop high-performance composite membranes for efficient CO2 separation in CO2 capture process. Introduction of a highly permeable polydimethylsiloxane (PDMS) intermediate layer between a selective layer and a porous support has been considered as a simple but efficient way to enhance gas permeance while maintaining high gas selectivity, because the introduced intermediate layer could benefit the formation of an ultrathin defect-free selective layer owing to the circumvention of pore penetration phenomenon. However, the selection of selective layer materials is unfavorably restricted because of the low surface energy of PDMS. Various highly hydrophilic membrane materials such as amino group-rich polyvinylamine (PVAm), a representative facilitated transport membrane material for CO2 separation, could not be facilely coated over the surface of the hydrophobic PDMS intermediate layer uniformly. Inspired by the hydrophilic nature and strong adhesive ability of polydopamine (PDA), PDA was therefore selected as a versatile molecular bridge between hydrophobic PDMS and hydrophilic PVAm. The PDA coating endows a highly compatible interface between both components with a large surface energy difference via multiple-site cooperative interactions. The resulting multilayer composite membrane with a thin facilitated transport PVAm selective layer exhibits a notably enhanced CO2 permeance (1887 GPU) combined with a slightly improved CO2/N2 selectivity (83), as well as superior structural stability. Similarly, the multilayer composite membrane with a hydrophilic CO2-philic Pebax 1657 selective layer was also developed for enhanced CO2 separation performance.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein-Zernike self-consistent field approach

NASA Astrophysics Data System (ADS)

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-01

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl- + CH3Cl → ClCH3 + Cl-) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: multi-center molecular Ornstein-Zernike self-consistent field approach.

PubMed

Kido, Kentaro; Kasahara, Kento; Yokogawa, Daisuke; Sato, Hirofumi

2015-07-07

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein-Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple SN2 reaction (Cl(-) + CH3Cl → ClCH3 + Cl(-)) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

Clinical Trials of Precision Medicine through Molecular Profiling: Focus on Breast Cancer.

PubMed

Zardavas, Dimitrios; Piccart-Gebhart, Martine

2015-01-01

High-throughput technologies of molecular profiling in cancer, such as gene-expression profiling and next-generation sequencing, are expanding our knowledge of the molecular landscapes of several cancer types. This increasing knowledge coupled with the development of several molecularly targeted agents hold the promise for personalized cancer medicine to be fully realized. Moreover, an expanding armamentarium of targeted agents has been approved for the treatment of specific molecular cancer subgroups in different diagnoses. According to this paradigm, treatment selection should be dictated by the specific molecular aberrations found in each patient's tumor. The classical clinical trials paradigm of patients' eligibility being based on clinicopathologic parameters is being abandoned, with current clinical trials enrolling patients on the basis of specific molecular aberrations. New, innovative trial designs have been generated to better tackle the multiple challenges induced by the increasing molecular fragmentation of cancer, namely: (1) longitudinal cohort studies with or without downstream trials, (2) studies assessing the clinical utility of molecular profiling, (3) master or umbrella trials, (4) basket trials, (5) N-of-1 trials, and (6) adaptive design trials. This article provides an overview of the challenges for clinical trials in the era of molecular profiling of cancer. Subsequently, innovative trial designs with respective examples and their potential to expedite efficient clinical development of targeted anticancer agents is discussed.

High efficiency low threshold current 1.3 μm InAs quantum dot lasers on on-axis (001) GaP/Si

NASA Astrophysics Data System (ADS)

Jung, Daehwan; Norman, Justin; Kennedy, M. J.; Shang, Chen; Shin, Bongki; Wan, Yating; Gossard, Arthur C.; Bowers, John E.

2017-09-01

We demonstrate highly efficient, low threshold InAs quantum dot lasers epitaxially grown on on-axis (001) GaP/Si substrates using molecular beam epitaxy. Electron channeling contrast imaging measurements show a threading dislocation density of 7.3 × 106 cm-2 from an optimized GaAs template grown on GaP/Si. The high-quality GaAs templates enable as-cleaved quantum dot lasers to achieve a room-temperature continuous-wave (CW) threshold current of 9.5 mA, a threshold current density as low as 132 A/cm2, a single-side output power of 175 mW, and a wall-plug-efficiency of 38.4% at room temperature. As-cleaved QD lasers show ground-state CW lasing up to 80 °C. The application of a 95% high-reflectivity coating on one laser facet results in a CW threshold current of 6.7 mA, which is a record-low value for any kind of Fabry-Perot laser grown on Si.

High Performance Parallel Computational Nanotechnology

NASA Technical Reports Server (NTRS)

Saini, Subhash; Craw, James M. (Technical Monitor)

1995-01-01

At a recent press conference, NASA Administrator Dan Goldin encouraged NASA Ames Research Center to take a lead role in promoting research and development of advanced, high-performance computer technology, including nanotechnology. Manufacturers of leading-edge microprocessors currently perform large-scale simulations in the design and verification of semiconductor devices and microprocessors. Recently, the need for this intensive simulation and modeling analysis has greatly increased, due in part to the ever-increasing complexity of these devices, as well as the lessons of experiences such as the Pentium fiasco. Simulation, modeling, testing, and validation will be even more important for designing molecular computers because of the complex specification of millions of atoms, thousands of assembly steps, as well as the simulation and modeling needed to ensure reliable, robust and efficient fabrication of the molecular devices. The software for this capacity does not exist today, but it can be extrapolated from the software currently used in molecular modeling for other applications: semi-empirical methods, ab initio methods, self-consistent field methods, Hartree-Fock methods, molecular mechanics; and simulation methods for diamondoid structures. In as much as it seems clear that the application of such methods in nanotechnology will require powerful, highly powerful systems, this talk will discuss techniques and issues for performing these types of computations on parallel systems. We will describe system design issues (memory, I/O, mass storage, operating system requirements, special user interface issues, interconnects, bandwidths, and programming languages) involved in parallel methods for scalable classical, semiclassical, quantum, molecular mechanics, and continuum models; molecular nanotechnology computer-aided designs (NanoCAD) techniques; visualization using virtual reality techniques of structural models and assembly sequences; software required to control mini robotic manipulators for positional control; scalable numerical algorithms for reliability, verifications and testability. There appears no fundamental obstacle to simulating molecular compilers and molecular computers on high performance parallel computers, just as the Boeing 777 was simulated on a computer before manufacturing it.

A Targeted "Capture" and "Removal" Scavenger toward Multiple Pollutants for Water Remediation based on Molecular Recognition.

PubMed

Wang, Jie; Shen, Haijing; Hu, Xiaoxia; Li, Yan; Li, Zhihao; Xu, Jinfan; Song, Xiufeng; Zeng, Haibo; Yuan, Quan

2016-03-01

For the water remediation techniques based on adsorption, the long-standing contradictories between selectivity and multiple adsorbability, as well as between affinity and recyclability, have put it on weak defense amid more and more severe environment crisis. Here, a pollutant-targeting hydrogel scavenger is reported for water remediation with both high selectivity and multiple adsorbability for several pollutants, and with strong affinity and good recyclability through rationally integrating the advantages of multiple functional materials. In the scavenger, aptamers fold into binding pockets to accommodate the molecular structure of pollutants to afford perfect selectivity, and Janus nanoparticles with antibacterial function as well as anisotropic surfaces to immobilize multiple aptamers allow for simultaneously handling different kinds of pollutants. The scavenger exhibits high efficiencies in removing pollutants from water and it can be easily recycled for many times without significant loss of loading capacities. Moreover, the residual concentrations of each contaminant are well below the drinking water standards. Thermodynamic behavior of the adsorption process is investigated and the rate-controlling process is determined. Furthermore, a point of use device is constructed and it displays high efficiency in removing pollutants from environmental water. The scavenger exhibits great promise to be applied in the next generation of water purification systems.

Biochemical characterization of Aspergillus oryzae recombinant α-l-rhamnosidase expressed in Pichia pastoris.

PubMed

Ishikawa, Mai; Shiono, Yoshihito; Koseki, Takuya

2017-12-01

An α-l-rhamnosidase-encoding gene from Aspergillus oryzae, which belongs to the glycoside hydrolase family 78, was cloned and expressed in Pichia pastoris. SDS-PAGE of the purified recombinant α-l-rhamnosidase protein revealed smeared bands with apparent molecular mass of 90-130 kDa. After N-deglycosylation, the recombinant enzyme showed a molecular mass of 70 kDa. The enzyme exhibited optimal activity at a pH of 5.0 and a temperature of 70 °C. Specific activity of the enzyme was higher toward hesperidin than toward naringin, which consist of α-1,6 and α-1,2 linkages, respectively. The activity was also higher toward hesperidin than toward rutin, which consist of 7-O- and 3-O-glycosyl linkages of flavonoids, respectively. Kinetic analysis of the enzyme showed that the Michaelis constant (K m ) was lowest toward rutin, moderate toward naringin, and higher toward p-nitrophenyl-α-l-rhamnopyranoside and hesperidin. Its high catalytic efficiency (k cat /K m ) toward rutin was results of its low K m value while its high catalytic efficiency toward hesperidin was results of a considerably high k cat value. Copyright © 2017 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Nitrated carbon nanoblisters for high-performance glucose dehydrogenase bioanodes.

PubMed

de Souza, João C P; Iost, Rodrigo M; Crespilho, Frank N

2016-03-15

Recently, many strategies are being explored for efficiently wiring glucose dehydrogenase (GDh) enzymes capable of glucose (fuel) oxidation. For instance, the use of GDh NAD(+)-dependent for glucose oxidation is of great interest in biofuel cell technology because the enzyme are unaffected by the presence of molecular oxygen commonly present in electrolyte. Here we present the fabrication of flexible carbon fibers modified with nitrated carbon nanoblisters and their application as high-performance GDh bioanodes. These bioelectrodes could electro-oxidize glucose at -360 mV (vs. Ag/AgClsat) in the presence of a molecular oxygen saturated electrolyte with current densities higher than 1.0 mAcm(-2) at 0.0 V. It is corroborated by open circuit potential, where a potential stabilization occurs at -150 mV in a long term stability current-transient experiment. This value is in agreement with the quasi-steady current obtained at very low scan rate (0.1 mVs(-1)), where the onset potential for glucose oxidation is -180 mV. X-ray photoelectron spectroscopy and scanning electron microscopy revealed that the nitrated blisters and edge-like carbon structures, enabling highly efficient enzyme immobilization and low overpotential for electron transfer, allowing for glucose oxidation with potential values close to the thermodynamic cofactor. Copyright © 2015 Elsevier B.V. All rights reserved.

Ultrahigh mobility and efficient charge injection in monolayer organic thin-film transistors on boron nitride.

PubMed

He, Daowei; Qiao, Jingsi; Zhang, Linglong; Wang, Junya; Lan, Tu; Qian, Jun; Li, Yun; Shi, Yi; Chai, Yang; Lan, Wei; Ono, Luis K; Qi, Yabing; Xu, Jian-Bin; Ji, Wei; Wang, Xinran

2017-09-01

Organic thin-film transistors (OTFTs) with high mobility and low contact resistance have been actively pursued as building blocks for low-cost organic electronics. In conventional solution-processed or vacuum-deposited OTFTs, due to interfacial defects and traps, the organic film has to reach a certain thickness for efficient charge transport. Using an ultimate monolayer of 2,7-dioctyl[1]benzothieno[3,2- b ][1]benzothiophene (C 8 -BTBT) molecules as an OTFT channel, we demonstrate remarkable electrical characteristics, including intrinsic hole mobility over 30 cm 2 /Vs, Ohmic contact with 100 Ω · cm resistance, and band-like transport down to 150 K. Compared to conventional OTFTs, the main advantage of a monolayer channel is the direct, nondisruptive contact between the charge transport layer and metal leads, a feature that is vital for achieving low contact resistance and current saturation voltage. On the other hand, bilayer and thicker C 8 -BTBT OTFTs exhibit strong Schottky contact and much higher contact resistance but can be improved by inserting a doped graphene buffer layer. Our results suggest that highly crystalline molecular monolayers are promising form factors to build high-performance OTFTs and investigate device physics. They also allow us to precisely model how the molecular packing changes the transport and contact properties.

Ultrahigh mobility and efficient charge injection in monolayer organic thin-film transistors on boron nitride

PubMed Central

He, Daowei; Qiao, Jingsi; Zhang, Linglong; Wang, Junya; Lan, Tu; Qian, Jun; Li, Yun; Shi, Yi; Chai, Yang; Lan, Wei; Ono, Luis K.; Qi, Yabing; Xu, Jian-Bin; Ji, Wei; Wang, Xinran

2017-01-01

Organic thin-film transistors (OTFTs) with high mobility and low contact resistance have been actively pursued as building blocks for low-cost organic electronics. In conventional solution-processed or vacuum-deposited OTFTs, due to interfacial defects and traps, the organic film has to reach a certain thickness for efficient charge transport. Using an ultimate monolayer of 2,7-dioctyl[1]benzothieno[3,2-b][1]benzothiophene (C8-BTBT) molecules as an OTFT channel, we demonstrate remarkable electrical characteristics, including intrinsic hole mobility over 30 cm2/Vs, Ohmic contact with 100 Ω · cm resistance, and band-like transport down to 150 K. Compared to conventional OTFTs, the main advantage of a monolayer channel is the direct, nondisruptive contact between the charge transport layer and metal leads, a feature that is vital for achieving low contact resistance and current saturation voltage. On the other hand, bilayer and thicker C8-BTBT OTFTs exhibit strong Schottky contact and much higher contact resistance but can be improved by inserting a doped graphene buffer layer. Our results suggest that highly crystalline molecular monolayers are promising form factors to build high-performance OTFTs and investigate device physics. They also allow us to precisely model how the molecular packing changes the transport and contact properties. PMID:28913429

Atomic-like high-harmonic generation from two-dimensional materials.

PubMed

Tancogne-Dejean, Nicolas; Rubio, Angel

2018-02-01

The generation of high-order harmonics from atomic and molecular gases enables the production of high-energy photons and ultrashort isolated pulses. Obtaining efficiently similar photon energy from solid-state systems could lead, for instance, to more compact extreme ultraviolet and soft x-ray sources. We demonstrate from ab initio simulations that it is possible to generate high-order harmonics from free-standing monolayer materials, with an energy cutoff similar to that of atomic and molecular gases. In the limit in which electrons are driven by the pump laser perpendicularly to the monolayer, they behave qualitatively the same as the electrons responsible for high-harmonic generation (HHG) in atoms, where their trajectories are described by the widely used semiclassical model, and exhibit real-space trajectories similar to those of the atomic case. Despite the similarities, the first and last steps of the well-established three-step model for atomic HHG are remarkably different in the two-dimensional materials from gases. Moreover, we show that the electron-electron interaction plays an important role in harmonic generation from monolayer materials because of strong local-field effects, which modify how the material is ionized. The recombination of the accelerated electron wave packet is also found to be modified because of the infinite extension of the material in the monolayer plane, thus leading to a more favorable wavelength scaling of the harmonic yield than in atomic HHG. Our results establish a novel and efficient way of generating high-order harmonics based on a solid-state device, with an energy cutoff and a more favorable wavelength scaling of the harmonic yield similar to those of atomic and molecular gases. Two-dimensional materials offer a unique platform where both bulk and atomic HHG can be investigated, depending on the angle of incidence. Devices based on two-dimensional materials can extend the limit of existing sources.

Double-cladding-fiber-based detection system for intravascular mapping of fluorescent molecular probes

NASA Astrophysics Data System (ADS)

Razansky, R. Nika; Rozental, Amir; Mueller, Mathias S.; Deliolanis, Nikolaos; Jaffer, Farouc A.; Koch, Alexander W.; Ntziachristos, Vasilis

2011-03-01

Early detection of high-risk coronary atherosclerosis remains an unmet clinical challenge. We have previously demonstrated a near-infrared fluorescence catheter system for two-dimensional intravascular detection of fluorescence molecular probes [1]. In this work we improve the system performance by introducing a novel high resolution sensor. The main challenge of the intravascular sensor is to provide a highly focused spot at an application relevant distance on one hand and a highly efficient collection of emitted light on the other. We suggest employing a double cladding optical fiber (DCF) in combination with focusing optics to provide a sensor with both highly focused excitation light and highly efficient fluorescent light collection. The excitation laser is coupled into the single mode core of DCF and guided through a focusing element and a right angle prism. The resulting side-fired beam exhibits a small spot diameter (50 μm) throughout a distance of up to 2 mm from the sensor. This is the distance of interest for intravascular coronary imaging application, determined by an average human coronary artery diameter. At the blood vessel wall, an activatable fluorescence molecular probe is excited in the diseased lesions. Next light of slightly shifted wavelength emits only in the places of the inflammations, associated with dangerous plaques [2]. The emitted light is collected by the cladding of the DCF, with a large collection angle (NA=0.4). The doublecladding acts as multimodal fiber and guides the collected light to the photo detection elements. The sensor automatically rotates and pulled-back, while each scanned point is mapped according to the amount of detected fluorescent emission. The resulting map of fluorescence activity helps to associate the atherosclerotic plaques with the inflammation process. The presented detection system is a valuable tool in the intravascular plaque detection and can help to differentiate the atherosclerotic plaques based on their biological activity, identify the ones that prone to rupture and therefore require more medical attention.

Leveraging Gibbs Ensemble Molecular Dynamics and Hybrid Monte Carlo/Molecular Dynamics for Efficient Study of Phase Equilibria.

PubMed

Gartner, Thomas E; Epps, Thomas H; Jayaraman, Arthi

2016-11-08

We describe an extension of the Gibbs ensemble molecular dynamics (GEMD) method for studying phase equilibria. Our modifications to GEMD allow for direct control over particle transfer between phases and improve the method's numerical stability. Additionally, we found that the modified GEMD approach had advantages in computational efficiency in comparison to a hybrid Monte Carlo (MC)/MD Gibbs ensemble scheme in the context of the single component Lennard-Jones fluid. We note that this increase in computational efficiency does not compromise the close agreement of phase equilibrium results between the two methods. However, numerical instabilities in the GEMD scheme hamper GEMD's use near the critical point. We propose that the computationally efficient GEMD simulations can be used to map out the majority of the phase window, with hybrid MC/MD used as a follow up for conditions under which GEMD may be unstable (e.g., near-critical behavior). In this manner, we can capitalize on the contrasting strengths of these two methods to enable the efficient study of phase equilibria for systems that present challenges for a purely stochastic GEMC method, such as dense or low temperature systems, and/or those with complex molecular topologies.

Conformational Control of Ultrafast Molecular Rotor Property: Tuning Viscosity Sensing Efficiency by Twist Angle Variation.

PubMed

Ghosh, Rajib; Kushwaha, Archana; Das, Dipanwita

2017-09-21

Fluorescent molecular rotors find widespread application in sensing and imaging of microscopic viscosity in complex chemical and biological media. Development of viscosity-sensitive ultrafast molecular rotor (UMR) relies upon the understanding of the excited-state dynamics and their implications for viscosity-dependent fluorescence signaling. Unraveling the structure-property relationship of UMR behavior is of significance toward development of an ultrasensitive fluorescence microviscosity sensor. Herein we show that the ground-state equilibrium conformation has an important role in the ultrafast twisting dynamics of UMRs and consequent viscosity sensing efficiency. Synthesis, photophysics, and ultrafast spectroscopic experiments in conjunction with quantum chemical calculation of a series of UMRs based on dimethylaniline donor and benzimidazolium acceptor with predefined ground-state torsion angle led us to unravel that the ultrafast torsional dynamics around the bond connecting donor and acceptor groups profoundly influences the molecular rotor efficiency. This is the first experimental demonstration of conformational control of small-molecule-based UMR efficiencies which can have wider implication toward development of fluorescence sensors based on the UMR principle. Conformation-controlled UMR efficiency has been shown to exhibit commensurate fluorescence enhancement upon DNA binding.

Controlling carbon-nanotube-phospholipid solubility by curvature-dependent self-assembly.

PubMed

Määttä, Jukka; Vierros, Sampsa; Sammalkorpi, Maria

2015-03-12

Control of aqueous dispersion is central in the processing and usage of nanoscale hydrophobic objects. However, selecting dispersive agents based on the size and form of the hydrophobic object and the role of coating morphology in dispersion efficiency remain important open questions. Here, the effect of the substrate and the dispersing molecule curvature, as well as, the influence of dispersant concentration on the adsorption morphology are examined by molecular simulations of graphene and carbon nanotube (CNT) substrates with phospholipids of varying curvature as the dispersing agents. Lipid spontaneous curvature is increased from close to zero (effectively cylindrical lipid) to highly positive (effectively conical lipid) by studying double tailed dipalmitoylphosphadidylcholine (DPPC) and single tailed lysophosphadidylcholine (LPC) which differ in the number of acyl chains but have identical headgroup. We find that lipids are good dispersion agents for both planar and curved nanoparticles and induce a dispersive barrier nonsize selectively. Differences in dispersion efficiency arise from lipid headgroup density and their extension from the hydrophobic substrate in the adsorption morphology. We map the packing morphology contributing factors and report that the aggregate morphologies depend on the competition of interactions rising from (1) hydrophobicity driven maximization of lipid-substrate contacts and lipid self-adhesion, (2) tail bending energy cost, (3) preferential alignment along the graphitic substrate principal axes, and (4) lipid headgroup preferential packing. Curved substrates adjust the morphology by changing the balance between the interaction strengths. Jointly, the findings show substrate curvature and dimensions are a way to tune lipid adsorption to desired, self-assembling patterns. Besides engineering dispersion efficiency, the findings could bear significance in designing materials with defined molecular scale, molecular coatings for orientation specific CNT assembly or lipid-based molecular masks and patterning on graphene.

Multiscale Quantum Mechanics/Molecular Mechanics Simulations with Neural Networks.

PubMed

Shen, Lin; Wu, Jingheng; Yang, Weitao

2016-10-11

Molecular dynamics simulation with multiscale quantum mechanics/molecular mechanics (QM/MM) methods is a very powerful tool for understanding the mechanism of chemical and biological processes in solution or enzymes. However, its computational cost can be too high for many biochemical systems because of the large number of ab initio QM calculations. Semiempirical QM/MM simulations have much higher efficiency. Its accuracy can be improved with a correction to reach the ab initio QM/MM level. The computational cost on the ab initio calculation for the correction determines the efficiency. In this paper we developed a neural network method for QM/MM calculation as an extension of the neural-network representation reported by Behler and Parrinello. With this approach, the potential energy of any configuration along the reaction path for a given QM/MM system can be predicted at the ab initio QM/MM level based on the semiempirical QM/MM simulations. We further applied this method to three reactions in water to calculate the free energy changes. The free-energy profile obtained from the semiempirical QM/MM simulation is corrected to the ab initio QM/MM level with the potential energies predicted with the constructed neural network. The results are in excellent accordance with the reference data that are obtained from the ab initio QM/MM molecular dynamics simulation or corrected with direct ab initio QM/MM potential energies. Compared with the correction using direct ab initio QM/MM potential energies, our method shows a speed-up of 1 or 2 orders of magnitude. It demonstrates that the neural network method combined with the semiempirical QM/MM calculation can be an efficient and reliable strategy for chemical reaction simulations.

MSM/RD: Coupling Markov state models of molecular kinetics with reaction-diffusion simulations

NASA Astrophysics Data System (ADS)

Dibak, Manuel; del Razo, Mauricio J.; De Sancho, David; Schütte, Christof; Noé, Frank

2018-06-01

Molecular dynamics (MD) simulations can model the interactions between macromolecules with high spatiotemporal resolution but at a high computational cost. By combining high-throughput MD with Markov state models (MSMs), it is now possible to obtain long time-scale behavior of small to intermediate biomolecules and complexes. To model the interactions of many molecules at large length scales, particle-based reaction-diffusion (RD) simulations are more suitable but lack molecular detail. Thus, coupling MSMs and RD simulations (MSM/RD) would be highly desirable, as they could efficiently produce simulations at large time and length scales, while still conserving the characteristic features of the interactions observed at atomic detail. While such a coupling seems straightforward, fundamental questions are still open: Which definition of MSM states is suitable? Which protocol to merge and split RD particles in an association/dissociation reaction will conserve the correct bimolecular kinetics and thermodynamics? In this paper, we make the first step toward MSM/RD by laying out a general theory of coupling and proposing a first implementation for association/dissociation of a protein with a small ligand (A + B ⇌ C). Applications on a toy model and CO diffusion into the heme cavity of myoglobin are reported.

Highly efficient and robust molecular ruthenium catalysts for water oxidation.

PubMed

Duan, Lele; Araujo, Carlos Moyses; Ahlquist, Mårten S G; Sun, Licheng

2012-09-25

Water oxidation catalysts are essential components of light-driven water splitting systems, which could convert water to H(2) driven by solar radiation (H(2)O + hν → 1/2O(2) + H(2)). The oxidation of water (H(2)O → 1/2O(2) + 2H(+) + 2e(-)) provides protons and electrons for the production of dihydrogen (2H(+) + 2e(-) → H(2)), a clean-burning and high-capacity energy carrier. One of the obstacles now is the lack of effective and robust water oxidation catalysts. Aiming at developing robust molecular Ru-bda (H(2)bda = 2,2'-bipyridine-6,6'-dicarboxylic acid) water oxidation catalysts, we carried out density functional theory studies, correlated the robustness of catalysts against hydration with the highest occupied molecular orbital levels of a set of ligands, and successfully directed the synthesis of robust Ru-bda water oxidation catalysts. A series of mononuclear ruthenium complexes [Ru(bda)L(2)] (L = pyridazine, pyrimidine, and phthalazine) were subsequently synthesized and shown to effectively catalyze Ce(IV)-driven [Ce(IV) = Ce(NH(4))(2)(NO(3))(6)] water oxidation with high oxygen production rates up to 286 s(-1) and high turnover numbers up to 55,400.

Utilizing Benzotriazole and Indacenodithiophene Units to Construct both Polymeric Donor and Small Molecular Acceptors to Realize Organic Solar Cells with High Open-Circuit Voltages beyond 1.2 V

NASA Astrophysics Data System (ADS)

Tang, Ailing; Chen, Fan; Xiao, Bo; Yang, Jing; Li, Jianfeng; Wang, Xiaochen; Zhou, Erjun

2018-05-01

Devolopment of organic solar cells with high open-circuit voltage (VOC) and power conversion efficiency (PCE) simutaniously plays a significant role, but there is no guideline how to choose the suitable photovoltaic material combinations. In this study, we adopted a simple and feasible strategy by utilizing the same electron-donating unit and electron-accepting segment to construct both polymeric donor and small molecular acceptors. The p-type polymer of PIDT-DTffBTA is designed by inserting conjugated bridge between indacenodithiophene (IDT) and fluorinated benzotriazole (BTA), while the n-type small molecules of BTAx (x = 1, 2, 3) are obtained by introducing different end-capped groups to BTA-IDT-BTA backbone. PIDT-DTffBTA: BTAx (x = 1-3) based photovolatic devices can realize high VOC of 1.21-1.37 V with the very small voltage loss (0.55-0.60 V), while only the PIDT-DTffBTA: BTA3 based device possesses the enough driving force for efficient hole and electron transfer and yields the optimal PCE of 5.67%, which is among the highest value for organic solar cells with a VOC beyond 1.20 V reported so far. Our results provide a simple and effective method to obtain fullerene-free organic solar cells with a high VOC and PCE.

Molecular design for recombinant adeno-associated virus (rAAV) vector production.

PubMed

Aponte-Ubillus, Juan Jose; Barajas, Daniel; Peltier, Joseph; Bardliving, Cameron; Shamlou, Parviz; Gold, Daniel

2018-02-01

Recombinant adeno-associated virus (rAAV) vectors are increasingly popular tools for gene therapy applications. Their non-pathogenic status, low inflammatory potential, availability of viral serotypes with different tissue tropisms, and prospective long-lasting gene expression are important attributes that make rAAVs safe and efficient therapeutic options. Over the last three decades, several groups have engineered recombinant AAV-producing platforms, yielding high titers of transducing vector particles. Current specific productivity yields from different platforms range from 10 3 to 10 5 vector genomes (vg) per cell, and there is an ongoing effort to improve vector yields in order to satisfy high product demands required for clinical trials and future commercialization.Crucial aspects of vector production include the molecular design of the rAAV-producing host cell line along with the design of AAV genes, promoters, and regulatory elements. Appropriately, configuring and balancing the expression of these elements not only contributes toward high productivity, it also improves process robustness and product quality. In this mini-review, the rational design of rAAV-producing expression systems is discussed, with special attention to molecular strategies that contribute to high-yielding, biomanufacturing-amenable rAAV production processes. Details on molecular optimization from four rAAV expression systems are covered: adenovirus, herpesvirus, and baculovirus complementation systems, as well as a recently explored yeast expression system.

AN EFFICIENT HIGHER-ORDER FAST MULTIPOLE BOUNDARY ELEMENT SOLUTION FOR POISSON-BOLTZMANN BASED MOLECULAR ELECTROSTATICS

PubMed Central

Bajaj, Chandrajit; Chen, Shun-Chuan; Rand, Alexander

2011-01-01

In order to compute polarization energy of biomolecules, we describe a boundary element approach to solving the linearized Poisson-Boltzmann equation. Our approach combines several important features including the derivative boundary formulation of the problem and a smooth approximation of the molecular surface based on the algebraic spline molecular surface. State of the art software for numerical linear algebra and the kernel independent fast multipole method is used for both simplicity and efficiency of our implementation. We perform a variety of computational experiments, testing our method on a number of actual proteins involved in molecular docking and demonstrating the effectiveness of our solver for computing molecular polarization energy. PMID:21660123

Conformations of low-molecular-weight lignin polymers in water

DOE PAGES

Petridis, Loukas; Smith, Jeremy C.

2016-01-13

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a criticalmore » degree of polymerization, N c=15, the polymer adopts less spherical conformations than above N c. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. As a result, an implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures.« less

Conformations of Low-Molecular-Weight Lignin Polymers in Water.

PubMed

Petridis, Loukas; Smith, Jeremy C

2016-02-08

Low-molecular-weight lignin binds to cellulose during the thermochemical pretreatment of biomass for biofuel production, which prevents the efficient hydrolysis of the cellulose to sugars. The binding properties of lignin are influenced strongly by the conformations it adopts. Here, we use molecular dynamics simulations in aqueous solution to investigate the dependence of the shape of lignin polymers on chain length and temperature. Lignin is found to adopt collapsed conformations in water at 300 and 500 K. However, at 300 K, a discontinuous transition is found in the shape of the polymer as a function of the chain length. Below a critical degree of polymerization, Nc =15, the polymer adopts less spherical conformations than above Nc. The transition disappears at high temperatures (500 K) at which only spherical shapes are adopted. An implication relevant to cellulosic biofuel production is that lignin will self-aggregate even at high pretreatment temperatures. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Effect of Chemical and Physical Properties on the In Vitro Degradation of 3D Printed High Resolution Poly(propylene fumarate) Scaffolds.

PubMed

Walker, Jason M; Bodamer, Emily; Krebs, Olivia; Luo, Yuanyuan; Kleinfehn, Alex; Becker, Matthew L; Dean, David

2017-04-10

Two distinct molecular masses of poly(propylene fumarate) (PPF) are combined with an additive manufacturing process to fabricate highly complex scaffolds possessing controlled chemical properties and porous architecture. Scaffolds were manufactured with two polymer molecular masses and two architecture styles. Degradation was assessed in an accelerated in vitro environment. The purpose of the degradation study is not to model or mimic in vivo degradation, but to efficiently compare the effect of modulating scaffold properties. This is the first study addressing degradation of chain-growth synthesized PPF, a process that allows for considerably more control over molecular mass distribution. It demonstrates that, with greater process control, not only is scaffold fabrication reproducible, but the mechanical properties and degradation kinetics can be tailored by altering the physical properties of the scaffold. This is a clear step forward in using PPF to address unmet medical needs while meeting regulatory demands and ultimately obtaining clinical relevancy.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Integrated electrocoagulation-electrooxidation process for the treatment of soluble coffee effluent: Optimization of COD degradation and operation time analysis.

PubMed

Ibarra-Taquez, Harold N; GilPavas, Edison; Blatchley, Ernest R; Gómez-García, Miguel-Ángel; Dobrosz-Gómez, Izabela

2017-09-15

Soluble coffee production generates wastewater containing complex mixtures of organic macromolecules. In this work, a sequential Electrocoagulation-Electrooxidation (EC-EO) process, using aluminum and graphite electrodes, was proposed as an alternative way for the treatment of soluble coffee effluent. Process operational parameters were optimized, achieving total decolorization, as well as 74% and 63.5% of COD and TOC removal, respectively. The integrated EC-EO process yielded a highly oxidized (AOS = 1.629) and biocompatible (BOD 5 /COD ≈ 0.6) effluent. The Molecular Weight Distribution (MWD) analysis showed that during the EC-EO process, EC effectively decomposed contaminants with molecular weight in the range of 10-30 kDa. In contrast, EO was quite efficient in mineralization of contaminants with molecular weight higher than 30 kDa. A kinetic analysis allowed determination of the time required to meet Colombian permissible discharge limits. Finally, a comprehensive operational cost analysis was performed. The integrated EC-EO process was demonstrated as an efficient alternative for the treatment of industrial effluents resulting from soluble coffee production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Driving and controlling molecular surface rotors with a terahertz electric field.

PubMed

Neumann, Jan; Gottschalk, Kay E; Astumian, R Dean

2012-06-26

Great progress has been made in the design and synthesis of molecular motors and rotors. Loosely inspired by biomolecular machines such as kinesin and the FoF1 ATPsynthase, these molecules are hoped to provide elements for construction of more elaborate structures that can carry out tasks at the nanoscale corresponding to the tasks accomplished by elementary machines in the macroscopic world. Most of the molecular motors synthesized to date suffer from the drawback that they operate relatively slowly (less than kHz). Here we show by molecular dynamics studies of a diethyl sulfide rotor on a gold(111) surface that a high-frequency oscillating electric field normal to the surface can drive directed rotation at GHz frequencies. The maximum directed rotation rate is 10(10) rotations per second, significantly faster than the rotation of previously reported directional molecular rotors. Understanding the fundamental basis of directed motion of surface rotors is essential for the further development of efficient externally driven artificial rotors. Our results represent a step toward the design of a surface-bound molecular rotary motor with a tunable rotation frequency and direction.

A diversity-oriented synthesis strategy enabling the combinatorial-type variation of macrocyclic peptidomimetic scaffolds† †Electronic supplementary information (ESI) available: Experimental procedures, characterization data and details of the computational analyses. See DOI: 10.1039/c5ob00371g Click here for additional data file.

PubMed Central

Isidro-Llobet, Albert; Hadje Georgiou, Kathy; Galloway, Warren R. J. D.; Giacomini, Elisa; Hansen, Mette R.; Méndez-Abt, Gabriela; Tan, Yaw Sing; Carro, Laura; Sore, Hannah F.

2015-01-01

Macrocyclic peptidomimetics are associated with a broad range of biological activities. However, despite such potentially valuable properties, the macrocyclic peptidomimetic structural class is generally considered as being poorly explored within drug discovery. This has been attributed to the lack of general methods for producing collections of macrocyclic peptidomimetics with high levels of structural, and thus shape, diversity. In particular, there is a lack of scaffold diversity in current macrocyclic peptidomimetic libraries; indeed, the efficient construction of diverse molecular scaffolds presents a formidable general challenge to the synthetic chemist. Herein we describe a new, advanced strategy for the diversity-oriented synthesis (DOS) of macrocyclic peptidomimetics that enables the combinatorial variation of molecular scaffolds (core macrocyclic ring architectures). The generality and robustness of this DOS strategy is demonstrated by the step-efficient synthesis of a structurally diverse library of over 200 macrocyclic peptidomimetic compounds, each based around a distinct molecular scaffold and isolated in milligram quantities, from readily available building-blocks. To the best of our knowledge this represents an unprecedented level of scaffold diversity in a synthetically derived library of macrocyclic peptidomimetics. Cheminformatic analysis indicated that the library compounds access regions of chemical space that are distinct from those addressed by top-selling brand-name drugs and macrocyclic natural products, illustrating the value of our DOS approach to sample regions of chemical space underexploited in current drug discovery efforts. An analysis of three-dimensional molecular shapes illustrated that the DOS library has a relatively high level of shape diversity. PMID:25778821

Increased expressions of genes and proteins involved in mitochondrial oxidation and antioxidant pathway in adipose tissue of pigs selected for a low residual feed intake.

PubMed

Louveau, I; Vincent, A; Tacher, S; Gilbert, H; Gondret, F

2016-12-01

Adipose tissue is a primary sensor for nutrient availability and regulates many functions including feed intake and energy homeostasis. This study was undertaken to determine the molecular responses of adipose tissue to differences in feed intake and feed efficiency. Subcutaneous adipose tissue was collected from two lines of pigs divergently selected for residual feed intake (RFI), a measure of feed efficiency defined as the difference between actual and expected feed intake, and from a subset of high-RFI pigs that were feed-restricted at the level of the voluntary feed intake of low-RFI pigs during the growing-finishing period. Transcriptomics analyses indicated that the number of genes that were differentially expressed ( < 0.01) between low- and high-RFI pigs ( = 8 per group at each stage) in adipose tissue was much lower when pigs were considered at 19 kg (postweaning) than at 115 kg BW (market weight). Extended investigations were performed at 115 kg BW to compare low-RFI ( = 8), high-RFI ( = 8), and feed-restricted high-RFI ( = 8) pigs. They included in silico pathway analyses of the differentially expressed (DE) genes ( < 0.01) and a complementary proteomic investigation to list adipose proteins with a differential abundance ( < 0.10). Only 23% of the DE genes were affected by both RFI and feed restriction. This indicates that the responses of adipose tissue to RFI difference shared only some common mechanisms with feed intake modulation, notably the regulation of cell cycle (including ) and transferase activity pathway. Two carboxylesterase genes (, ) involved in lipolysis, were among the most overexpressed genes in the low-RFI pigs; they were also affected by feed restriction within the high-RFI line. About 60% of the molecular changes between low- and high-RFI pigs were specific to genetic divergence in feed efficiency, independently of feed intake. Different genes and proteins known to be associated with mitochondrial oxidative metabolism were overexpressed in adipose tissue of low-RFI pigs compared with high-RFI pigs; other proteins participating in the generation of energy were also affected by feed restriction within the high-RFI line. Finally, mitochondrial antioxidant genes were upregulated in low-RFI pigs vs. high-RFI pigs. Altogether, increased oxidative and antioxidant processes in adipose tissue might be associated with improved feed efficiency.

Cyndi: a multi-objective evolution algorithm based method for bioactive molecular conformational generation.

PubMed

Liu, Xiaofeng; Bai, Fang; Ouyang, Sisheng; Wang, Xicheng; Li, Honglin; Jiang, Hualiang

2009-03-31

Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Numerous in silico methods have been proposed in an attempt to resolve the problem, ranging from deterministic to non-deterministic and systemic to stochastic ones. In this work, we described an efficient conformation sampling method named Cyndi, which is based on multi-objective evolution algorithm. The conformational perturbation is subjected to evolutionary operation on the genome encoded with dihedral torsions. Various objectives are designated to render the generated Pareto optimal conformers to be energy-favoured as well as evenly scattered across the conformational space. An optional objective concerning the degree of molecular extension is added to achieve geometrically extended or compact conformations which have been observed to impact the molecular bioactivity (J Comput -Aided Mol Des 2002, 16: 105-112). Testing the performance of Cyndi against a test set consisting of 329 small molecules reveals an average minimum RMSD of 0.864 A to corresponding bioactive conformations, indicating Cyndi is highly competitive against other conformation generation methods. Meanwhile, the high-speed performance (0.49 +/- 0.18 seconds per molecule) renders Cyndi to be a practical toolkit for conformational database preparation and facilitates subsequent pharmacophore mapping or rigid docking. The copy of precompiled executable of Cyndi and the test set molecules in mol2 format are accessible in Additional file 1. On the basis of MOEA algorithm, we present a new, highly efficient conformation generation method, Cyndi, and report the results of validation and performance studies comparing with other four methods. The results reveal that Cyndi is capable of generating geometrically diverse conformers and outperforms other four multiple conformer generators in the case of reproducing the bioactive conformations against 329 structures. The speed advantage indicates Cyndi is a powerful alternative method for extensive conformational sampling and large-scale conformer database preparation.

Molecular design of donor-acceptor dyes for efficient dye-sensitized solar cells I: a DFT study.

PubMed

El-Shishtawy, Reda M; Asiri, Abdullah M; Aziz, Saadullah G; Elroby, Shaaban A K

2014-06-01

Dye-sensitized solar cells (DSSCs) have drawn great attention as low cost and high performance alternatives to conventional photovoltaic devices. The molecular design presented in this work is based on the use of pyran type dyes as donor based on frontier molecular orbitals (FMO) and theoretical UV-visible spectra in combination with squaraine type dyes as an acceptor. Density functional theory has been used to investigate several derivatives of pyran type dyes for a better dye design based on optimization of absorption, regeneration, and recombination processes in gas phase. The frontier molecular orbital (FMO) of the HOMO and LUMO energy levels plays an important role in the efficiency of DSSCs. These energies contribute to the generation of exciton, charge transfer, dissociation and exciton recombination. The computations of the geometries and electronic structures for the predicted dyes were performed using the B3LYP/6-31+G** level of theory. The FMO energies (EHOMO, ELUMO) of the studied dyes are calculated and analyzed in the terms of the UV-visible absorption spectra, which have been examined using time-dependent density functional theory (TD-DFT) techniques. This study examined absorption properties of pyran based on theoretical UV-visible absorption spectra, with comparisons between TD-DFT using B3LYP, PBE, and TPSSH functionals with 6-31+G (d) and 6-311++G** basis sets. The results provide a valuable guide for the design of donor-acceptor (D-A) dyes with high molar absorptivity and current conversion in DSSCs. The theoretical results indicated 4-(dicyanomethylene)-2-methyl-6-(p-dimethylaminostyryl)-4H-pyran dye (D2-Me) can be effectively used as a donor dye for DSSCs. This dye has a low energy gap by itself and a high energy gap with squaraine acceptor type dye, the design that reduces the recombination and improves the photocurrent generation in solar cell.

Parallel high-performance grid computing: capabilities and opportunities of a novel demanding service and business class allowing highest resource efficiency.

PubMed

Kepper, Nick; Ettig, Ramona; Dickmann, Frank; Stehr, Rene; Grosveld, Frank G; Wedemann, Gero; Knoch, Tobias A

2010-01-01

Especially in the life-science and the health-care sectors the huge IT requirements are imminent due to the large and complex systems to be analysed and simulated. Grid infrastructures play here a rapidly increasing role for research, diagnostics, and treatment, since they provide the necessary large-scale resources efficiently. Whereas grids were first used for huge number crunching of trivially parallelizable problems, increasingly parallel high-performance computing is required. Here, we show for the prime example of molecular dynamic simulations how the presence of large grid clusters including very fast network interconnects within grid infrastructures allows now parallel high-performance grid computing efficiently and thus combines the benefits of dedicated super-computing centres and grid infrastructures. The demands for this service class are the highest since the user group has very heterogeneous requirements: i) two to many thousands of CPUs, ii) different memory architectures, iii) huge storage capabilities, and iv) fast communication via network interconnects, are all needed in different combinations and must be considered in a highly dedicated manner to reach highest performance efficiency. Beyond, advanced and dedicated i) interaction with users, ii) the management of jobs, iii) accounting, and iv) billing, not only combines classic with parallel high-performance grid usage, but more importantly is also able to increase the efficiency of IT resource providers. Consequently, the mere "yes-we-can" becomes a huge opportunity like e.g. the life-science and health-care sectors as well as grid infrastructures by reaching higher level of resource efficiency.

A molecular nematic liquid crystalline material for high-performance organic photovoltaics

PubMed Central

Sun, Kuan; Xiao, Zeyun; Lu, Shirong; Zajaczkowski, Wojciech; Pisula, Wojciech; Hanssen, Eric; White, Jonathan M.; Williamson, Rachel M.; Subbiah, Jegadesan; Ouyang, Jianyong; Holmes, Andrew B.; Wong, Wallace W.H.; Jones, David J.

2015-01-01

Solution-processed organic photovoltaic cells (OPVs) hold great promise to enable roll-to-roll printing of environmentally friendly, mechanically flexible and cost-effective photovoltaic devices. Nevertheless, many high-performing systems show best power conversion efficiencies (PCEs) with a thin active layer (thickness is ~100 nm) that is difficult to translate to roll-to-roll processing with high reproducibility. Here we report a new molecular donor, benzodithiophene terthiophene rhodanine (BTR), which exhibits good processability, nematic liquid crystalline behaviour and excellent optoelectronic properties. A maximum PCE of 9.3% is achieved under AM 1.5G solar irradiation, with fill factor reaching 77%, rarely achieved in solution-processed OPVs. Particularly promising is the fact that BTR-based devices with active layer thicknesses up to 400 nm can still afford high fill factor of ~70% and high PCE of ~8%. Together, the results suggest, with better device architectures for longer device lifetime, BTR is an ideal candidate for mass production of OPVs. PMID:25586307

Separation of three phenolic high-molecular-weight compounds from the crude extract of Terminalia Chebula Retz. by ultrasound-assisted extraction and high-speed counter-current chromatography.

PubMed

Zou, Deng-lang; Chen, Tao; Li, Hong-mei; Chen, Chen; Zhao, Jing-yang; Li, Yu-lin

2016-04-01

This study presents an efficient strategy for separation of three phenolic compounds with high molecular weight from the crude extract of Terminalia chebula Retz. by ultrasound-assisted extraction and high-speed counter-current chromatography. The ultrasound-assisted extraction conditions were optimized by response surface methodology and the results showed the target compounds could be well enriched under the optimized extraction conditions. Then the crude extract was directly separated by high-speed counter-current chromatography without any pretreatment using n-hexane/ethyl acetate/methanol/water (1:7:0.5:3, v/v/v/v) as the solvent system. In 180 min, 13 mg of A, 18 mg of B, and 9 mg of C were obtained from 200 mg of crude sample. Their structures were identified as Chebulagic acid (A, 954 Da), Chebulinic acid (B, 956 Da), and Ellagic acid (C) by (1) H NMR spectroscopy. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Hydrogen Recombination and Dimer Formation on Graphite from Ab Initio Molecular Dynamics Simulations.

PubMed

Casolo, S; Tantardini, G F; Martinazzo, R

2016-07-14

We studied Eley-Rideal molecular hydrogen formation on graphite using ab initio molecular dynamics, in the energy range relevant for the chemistry of the interstellar medium and for terrestrial experiments employing cold plasma (0.02-1 eV). We found substantial projectile steering effects that prevent dimer formation at low energies, thereby ruling out any catalytic synthetic pathways that form hydrogen molecules. Ortho and para dimers do form efficiently thanks to preferential sticking, but only at energies that are too high to be relevant for the chemistry of the interstellar medium. Computed reaction cross sections and ro-vibrational product populations are in good agreement with available experimental data and capable of generating adsorbate configurations similar to those observed with scanning tunneling microscopy techniques.

Ni-O4 species anchored on N-doped graphene-based materials as molecular entities and electrocatalytic performances for oxygen reduction reaction

NASA Astrophysics Data System (ADS)

Jang, Dawoon; Lee, Seungjun; Shin, Yunseok; Ohn, Saerom; Park, Sunghee; Lim, Donggyu; Park, Gilsoo; Park, Sungjin

2017-12-01

The generation of molecular active species on the surface of nano-materials has become promising routes to produce efficient electrocatalysts. Development of cost-effective catalysts with high performances for oxygen reduction reaction (ORR) is an important challenge for fuel cell and metal-air battery applications. In this work, we report a novel hybrid produced by room-temperature solution processes using Ni-based organometallic molecules and N-doped graphene-based materials. Chemical and structural characterizations reveal that Ni-containing species are well-dispersed on the surface of graphene network as molecular entity. The hybrid shows excellent electrocatalytic performances for ORR in basic medium with an onset potential of 0.87 V (vs. RHE), superior durability and good methanol tolerance.

Improving the efficiency of molecular replacement by utilizing a new iterative transform phasing algorithm

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

He, Hongxing; Fang, Hengrui; Miller, Mitchell D.

2016-07-15

An iterative transform algorithm is proposed to improve the conventional molecular-replacement method for solving the phase problem in X-ray crystallography. Several examples of successful trial calculations carried out with real diffraction data are presented. An iterative transform method proposed previously for direct phasing of high-solvent-content protein crystals is employed for enhancing the molecular-replacement (MR) algorithm in protein crystallography. Target structures that are resistant to conventional MR due to insufficient similarity between the template and target structures might be tractable with this modified phasing method. Trial calculations involving three different structures are described to test and illustrate the methodology. The relationshipmore » of the approach to PHENIX Phaser-MR and MR-Rosetta is discussed.« less

Photoionization studies with molecular beams

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

Ng, C.Y.

1976-09-01

A molecular beam photoionization apparatus which combines the advantages of both the molecular beam method with photoionization mass spectrometry has been designed and constructed for carrying out some unique photoionization experiments. Rotational cooling during the supersonic expansion has resulted in high resolution photoionization efficiency curves for NO, ICl, C/sub 2/H/sub 2/ and CH/sub 3/I. The analysis of these spectra has yielded ionization potentials for these molecules to an accuracy of +- 3 MeV. Detailed autoionization structures were also resolved. This allows the investigation of the selection rules for autoionization, and the identification of the Rydberg series which converge to themore » excited states of the molecular ions. The degree of relaxation for thermally populated excited states has been examined using NO and ICl as examples. As a result of adiabatic cooling, a small percentage of dimers is also formed during the expansion. The photoionization efficiency curves for (NO)/sub 2/, ArICl, Ar/sub 2/, Kr/sub 2/ and Xe/sub 2/ have been obtained near the thresholds. Using the known dissociation energies of the (NO)/sub 2/, Ar/sub 2/, Kr/sub 2/ and Xe/sub 2/ van der Waals molecules, the corresponding dissociation energies for NO-NO/sup +/, Ar/sub 2//sup +/, Kr/sub 2//sup +/, and Xe/sub 2//sup +/ have been determined. The ionization mechanisms for this class of molecules are examined and discussed.« less

Molecular pathway activation - new type of biomarkers for tumor morphology and personalized selection of target drugs.

PubMed

Buzdin, Anton; Sorokin, Maxim; Garazha, Andrew; Sekacheva, Marina; Kim, Ella; Zhukov, Nikolay; Wang, Ye; Li, Xinmin; Kar, Souvik; Hartmann, Christian; Samii, Amir; Giese, Alf; Borisov, Nicolas

2018-06-20

Anticancer target drugs (ATDs) specifically bind and inhibit molecular targets that play important roles in cancer development and progression, being deeply implicated in intracellular signaling pathways. To date, hundreds of different ATDs were approved for clinical use in the different countries. Compared to previous chemotherapy treatments, ATDs often demonstrate reduced side effects and increased efficiency, but also have higher costs. However, the efficiency of ATDs for the advanced stage tumors is still insufficient. Different ATDs have different mechanisms of action and are effective in different cohorts of patients. Personalized approaches are therefore needed to select the best ATD candidates for the individual patients. In this review, we focus on a new generation of biomarkers - molecular pathway activation - and on their applications for predicting individual tumor response to ATDs. The success in high throughput gene expression profiling and emergence of novel bioinformatic tools reinforced quick development of pathway related field of molecular biomedicine. The ability to quantitatively measure degree of a pathway activation using gene expression data has revolutionized this field and made the corresponding analysis quick, robust and inexpensive. This success was further enhanced by using machine learning algorithms for selection of the best biomarkers. We review here the current progress in translating these studies to clinical oncology and patient-oriented adjustment of cancer therapy. Copyright © 2018. Published by Elsevier Ltd.

Development of the Next Generation of Biogeochemistry Simulations Using EMSL's NWChem Molecular Modeling Software

NASA Astrophysics Data System (ADS)

Bylaska, E. J.; Kowalski, K.; Apra, E.; Govind, N.; Valiev, M.

2017-12-01

Methods of directly simulating the behavior of complex strongly interacting atomic systems (molecular dynamics, Monte Carlo) have provided important insight into the behavior of nanoparticles, biogeochemical systems, mineral/fluid systems, nanoparticles, actinide systems and geofluids. The limitation of these methods to even wider applications is the difficulty of developing accurate potential interactions in these systems at the molecular level that capture their complex chemistry. The well-developed tools of quantum chemistry and physics have been shown to approach the accuracy required. However, despite the continuous effort being put into improving their accuracy and efficiency, these tools will be of little value to condensed matter problems without continued improvements in techniques to traverse and sample the high-dimensional phase space needed to span the ˜10^12 time scale differences between molecular simulation and chemical events. In recent years, we have made considerable progress in developing electronic structure and AIMD methods tailored to treat biochemical and geochemical problems, including very efficient implementations of many-body methods, fast exact exchange methods, electron-transfer methods, excited state methods, QM/MM, and new parallel algorithms that scale to +100,000 cores. The poster will focus on the fundamentals of these methods and the realities in terms of system size, computational requirements and simulation times that are required for their application to complex biogeochemical systems.

Confinement of Aggregation-Induced Emission Molecular Rotors in Ultrathin Two-Dimensional Porous Organic Nanosheets for Enhanced Molecular Recognition.

PubMed

Dong, Jinqiao; Li, Xu; Zhang, Kang; Di Yuan, Yi; Wang, Yuxiang; Zhai, Linzhi; Liu, Guoliang; Yuan, Daqiang; Jiang, Jianwen; Zhao, Dan

2018-03-21

Despite the rapid development of molecular rotors over the past decade, it still remains a huge challenge to understand their confined behavior in ultrathin two-dimensional (2D) nanomaterials for molecular recognition. Here, we report an all-carbon, 2D π-conjugated aromatic polymer, named NUS-25, containing flexible tetraphenylethylene (TPE) units as aggregation-induced emission (AIE) molecular rotors. NUS-25 bulk powder can be easily exfoliated into micrometer-sized lamellar freestanding nanosheets with a thickness of 2-5 nm. The dynamic behavior of the TPE rotors is partially restricted through noncovalent interactions in the ultrathin 2D nanosheets, which is proved by comparative experimental studies including AIE characteristics, size-selective molecular recognition, and theoretical calculations of rotary energy barrier. Because of the partially restricted TPE rotors, NUS-25 nanosheets are highly fluorescent. This property allows NUS-25 nanosheets to be used as a chemical sensor for the specific detection of acenaphthylene among a series of polycyclic aromatic hydrocarbons (PAHs) via fluorescent quenching mechanism. Further investigations show that NUS-25 nanosheets have much higher sensitivity and selectivity than their stacked bulk powder and other similar polymers containing dynamic TPE rotors. The highly efficient molecular recognition can be attributed to the photoinduced electron transfer (PET) from NUS-25 nanosheets to acenaphthylene, which is investigated by time-resolved photoluminescence measurements (TRPL), excitation and emission spectra, and density functional theory (DFT) calculations. Our findings demonstrate that confinement of AIE molecular rotors in 2D nanomaterials can enhance the molecular recognition. We anticipate that the material design strategy demonstrated in this study will inspire the development of other ultrathin 2D nanomaterials equipped with smart molecular machines for various applications.

Molecular profiling of single circulating tumor cells from lung cancer patients.

PubMed

Park, Seung-Min; Wong, Dawson J; Ooi, Chin Chun; Kurtz, David M; Vermesh, Ophir; Aalipour, Amin; Suh, Susie; Pian, Kelsey L; Chabon, Jacob J; Lee, Sang Hun; Jamali, Mehran; Say, Carmen; Carter, Justin N; Lee, Luke P; Kuschner, Ware G; Schwartz, Erich J; Shrager, Joseph B; Neal, Joel W; Wakelee, Heather A; Diehn, Maximilian; Nair, Viswam S; Wang, Shan X; Gambhir, Sanjiv S

2016-12-27

Circulating tumor cells (CTCs) are established cancer biomarkers for the "liquid biopsy" of tumors. Molecular analysis of single CTCs, which recapitulate primary and metastatic tumor biology, remains challenging because current platforms have limited throughput, are expensive, and are not easily translatable to the clinic. Here, we report a massively parallel, multigene-profiling nanoplatform to compartmentalize and analyze hundreds of single CTCs. After high-efficiency magnetic collection of CTC from blood, a single-cell nanowell array performs CTC mutation profiling using modular gene panels. Using this approach, we demonstrated multigene expression profiling of individual CTCs from non-small-cell lung cancer (NSCLC) patients with remarkable sensitivity. Thus, we report a high-throughput, multiplexed strategy for single-cell mutation profiling of individual lung cancer CTCs toward minimally invasive cancer therapy prediction and disease monitoring.

Dual-junction GaAs solar cells and their application to smart stacked III–V//Si multijunction solar cells

NASA Astrophysics Data System (ADS)

Sugaya, Takeyoshi; Tayagaki, Takeshi; Aihara, Taketo; Makita, Kikuo; Oshima, Ryuji; Mizuno, Hidenori; Nagato, Yuki; Nakamoto, Takashi; Okano, Yoshinobu

2018-05-01

We report high-quality dual-junction GaAs solar cells grown using solid-source molecular beam epitaxy and their application to smart stacked III–V//Si quadruple-junction solar cells with a two-terminal configuration for the first time. A high open-circuit voltage of 2.94 eV was obtained in an InGaP/GaAs/GaAs triple-junction top cell that was stacked to a Si bottom cell. The short-circuit current density of a smart stacked InGaP/GaAs/GaAs//Si solar cell was in good agreement with that estimated from external quantum efficiency measurements. An efficiency of 18.5% with a high open-circuit voltage of 3.3 V was obtained in InGaP/GaAs/GaAs//Si two-terminal solar cells.

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

PubMed Central

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-01-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health. PMID:26213417

Geometric analysis characterizes molecular rigidity in generic and non-generic protein configurations

NASA Astrophysics Data System (ADS)

Budday, Dominik; Leyendecker, Sigrid; van den Bedem, Henry

2015-10-01

Proteins operate and interact with partners by dynamically exchanging between functional substates of a conformational ensemble on a rugged free energy landscape. Understanding how these substates are linked by coordinated, collective motions requires exploring a high-dimensional space, which remains a tremendous challenge. While molecular dynamics simulations can provide atomically detailed insight into the dynamics, computational demands to adequately sample conformational ensembles of large biomolecules and their complexes often require tremendous resources. Kinematic models can provide high-level insights into conformational ensembles and molecular rigidity beyond the reach of molecular dynamics by reducing the dimensionality of the search space. Here, we model a protein as a kinematic linkage and present a new geometric method to characterize molecular rigidity from the constraint manifold Q and its tangent space Tq Q at the current configuration q. In contrast to methods based on combinatorial constraint counting, our method is valid for both generic and non-generic, e.g., singular configurations. Importantly, our geometric approach provides an explicit basis for collective motions along floppy modes, resulting in an efficient procedure to probe conformational space. An atomically detailed structural characterization of coordinated, collective motions would allow us to engineer or allosterically modulate biomolecules by selectively stabilizing conformations that enhance or inhibit function with broad implications for human health.

Heavy metal accumulation and signal transduction in herbaceous and woody plants: Paving the way for enhancing phytoremediation efficiency.

PubMed

Luo, Zhi-Bin; He, Jiali; Polle, Andrea; Rennenberg, Heinz

2016-11-01

Heavy metal (HM)-accumulating herbaceous and woody plants are employed for phytoremediation. To develop improved strategies for enhancing phytoremediation efficiency, knowledge of the microstructural, physiological and molecular responses underlying HM-accumulation is required. Here we review the progress in understanding the structural, physiological and molecular mechanisms underlying HM uptake, transport, sequestration and detoxification, as well as the regulation of these processes by signal transduction in response to HM exposure. The significance of genetic engineering for enhancing phytoremediation efficiency is also discussed. In herbaceous plants, HMs are taken up by roots and transported into the root cells via transmembrane carriers for nutritional ions. The HMs absorbed by root cells can be further translocated to the xylem vessels and unloaded into the xylem sap, thereby reaching the aerial parts of plants. HMs can be sequestered in the cell walls, vacuoles and the Golgi apparatuses. Plant roots initially perceive HM stress and trigger the signal transduction, thereby mediating changes at the molecular, physiological, and microstructural level. Signaling molecules such as phytohormones, reactive oxygen species (ROS) and nitric oxide (NO), modulate plant responses to HMs via differentially expressed genes, activation of the antioxidative system and coordinated cross talk among different signaling molecules. A number of genes participated in HM uptake, transport, sequestration and detoxification have been functionally characterized and transformed to target plants for enhancing phytoremediation efficiency. Fast growing woody plants hold an advantage over herbaceous plants for phytoremediation in terms of accumulation of high HM-amounts in their large biomass. Presumably, woody plants accumulate HMs using similar mechanisms as herbaceous counterparts, but the processes of HM accumulation and signal transduction can be more complex in woody plants. Copyright © 2016 Elsevier Inc. All rights reserved.

Theoretical characterisation of highly efficient dye-sensitised solar cells

NASA Astrophysics Data System (ADS)

Shalabi, A. S.; El Mahdy, A. M.; Assem, M. M.; Taha, H. O.; Abdel Halim, W. S.

2014-01-01

Molecular electronic structure calculations, employing density functional theory (DFT) and time-dependent density functional theory (TD-DFT) methodologies, have been carried out to improve the performance of the synthesised dye YD2-o-C8 which is characterised by 11.9%-12.7% efficiencies. We aimed to narrow the band gap of YD2-o-C8 to extend the light-harvesting region to near-infrared (NIR). This was done by incorporating Cd instead of Zn onto the porphyrin ring and elongating the length of π-conjugation by adding ethynylene link and anthracene unit, so that the performances of the suggested cells could be expected to exceed the 11.9%-12.7% efficiencies with TiO2, ZnO2, and WO3 oxide electrodes. The effects of modifying the central metal and elongating the length of π-conjugation on cell performance are confirmed in terms of frontier molecular orbital (FMO) energy gaps, density of states (DOS), molecular electrostatic potentials (MEPs), non-linear optical (NLO) properties, ultraviolet-visible (UV-vis) electronic absorption, and 1H nuclear magnetic resonance chemical shifts. Increasing the length of π-conjugation of the D-π-A dyes leads to increasing the DOS near Fermi levels, more active NLO performance, strong response to the external electric field, delocalisation of the negative charges near the anchoring groups, deep electron injection, suppressing macrocycle aggregation, active dye regeneration, and inhibited dye recombination. The calculated band gap/eV of the present DMP-Zn is correlated with the experimental (E1/2(oxidation)-E1/2(reduction)/V) potentials of the identical YD2-o-C8. A co-sensitiser is suggested for NIR sensitisation (550-950 nm) to increase the power-to-conversion efficiency beyond 14%.

High-order fractional partial differential equation transform for molecular surface construction.

PubMed

Hu, Langhua; Chen, Duan; Wei, Guo-Wei

2013-01-01

Fractional derivative or fractional calculus plays a significant role in theoretical modeling of scientific and engineering problems. However, only relatively low order fractional derivatives are used at present. In general, it is not obvious what role a high fractional derivative can play and how to make use of arbitrarily high-order fractional derivatives. This work introduces arbitrarily high-order fractional partial differential equations (PDEs) to describe fractional hyperdiffusions. The fractional PDEs are constructed via fractional variational principle. A fast fractional Fourier transform (FFFT) is proposed to numerically integrate the high-order fractional PDEs so as to avoid stringent stability constraints in solving high-order evolution PDEs. The proposed high-order fractional PDEs are applied to the surface generation of proteins. We first validate the proposed method with a variety of test examples in two and three-dimensional settings. The impact of high-order fractional derivatives to surface analysis is examined. We also construct fractional PDE transform based on arbitrarily high-order fractional PDEs. We demonstrate that the use of arbitrarily high-order derivatives gives rise to time-frequency localization, the control of the spectral distribution, and the regulation of the spatial resolution in the fractional PDE transform. Consequently, the fractional PDE transform enables the mode decomposition of images, signals, and surfaces. The effect of the propagation time on the quality of resulting molecular surfaces is also studied. Computational efficiency of the present surface generation method is compared with the MSMS approach in Cartesian representation. We further validate the present method by examining some benchmark indicators of macromolecular surfaces, i.e., surface area, surface enclosed volume, surface electrostatic potential and solvation free energy. Extensive numerical experiments and comparison with an established surface model indicate that the proposed high-order fractional PDEs are robust, stable and efficient for biomolecular surface generation.

Fe-porphyrin-based metal–organic framework films as high-surface concentration, heterogeneous catalysts for electrochemical reduction of CO 2

DOE PAGES

Hod, Idan; Sampson, Matthew D.; Deria, Pravas; ...

2015-09-18

Realization of heterogeneous electrochemical CO 2-to-fuel conversion via molecular catalysis under high-flux conditions requires the assembly of large quantities of reactant-accessible catalysts on conductive surfaces. As a proof of principle, we demonstrate that electrophoretic deposition of thin films of an appropriately chosen metal–organic framework (MOF) material is an effective method for immobilizing the needed quantity of catalyst. For electrocatalytic CO 2 reduction, we used a material that contains functionalized Fe-porphyrins as catalytically competent, redox-conductive linkers. The approach yields a high effective surface coverage of electrochemically addressable catalytic sites (~10 15 sites/cm 2). The chemical products of the reduction, obtained withmore » ~100% Faradaic efficiency, are mixtures of CO and H 2. The results validate the strategy of using MOF chemistry to obtain porous, electrode-immobilized, networks of molecular catalysts having competency for energy-relevant electrochemical reactions.« less

Development and cytotoxicity of Schiff base derivative as a fluorescence probe for the detection of L-Arginine

NASA Astrophysics Data System (ADS)

Shang, Xuefang; Li, Jie; Guo, Kerong; Ti, Tongyu; Wang, Tianyun; Zhang, Jinlian

2017-04-01

Inspired from biological counter parts, chemical modification of Schiff base derivatives with function groups may provide a highly efficient method to detect amino acids. Therefore, a fluorescent probe involving Schiff base and hydroxyl group has been designed and prepared, which showed high response and specificity for Arginine (Arg) among normal eighteen standard kinds of amino acids (Alanine, Valine, Leucine, Isoleucine, Methionine, Asparticacid, Glutamicacid, Arginine, Glycine, Serine, Threonine, Asparagine, Phenylalanine, Histidine, Tryptophan, Proline, Lysine, Glutamine, Tyrosine and Cysteine). Furthermore, theoretical investigation further illustrated the possible binding mode in the host-guest interaction and the roles of molecular frontier orbitals in molecular interplay. In addition, the synthesized fluorescent probe exhibited high binding ability for Arg and low cytotoxicity to MCF-7 cells over a concentration range of 0-200 μg mL-1 which can be also used as a biosensor for the Arg detection in vivo.

Bulk and integrated acousto-optic spectrometers for molecular astronomy with heterodyne spectrometers

NASA Technical Reports Server (NTRS)

Chin, G.; Buhl, D.; Florez, J. M.

1981-01-01

A survey of acousto-optic spectrometers for molecular astronomy is presented, noting a technique of combining the acoustic bending of a collimated coherent light beam with a Bragg cell followed by an array of sensitive photodetectors. This acousto-optic spectrometer has a large bandwidth, a large number of channels, high resolution, and is energy efficient. Receiver development has concentrated on high-frequency heterodyne systems for the study of the chemical composition of the interstellar medium. RF spectrometers employing acousto-optic diffraction cells are described. Acousto-optic techniques have been suggested for applications to electronic warfare, electronic countermeasures and electronic support systems. Plans to use integrated optics for the further miniaturization of acousto-optic spectrometers are described. Bulk acousto-optic spectrometers with 300 MHz and 1 GHz bandwidths are being developed for use in the back-end of high-frequency heterodyne receivers for astronomical research.

High-resolution internal state control of ultracold 23Na87Rb molecules

NASA Astrophysics Data System (ADS)

Guo, Mingyang; Ye, Xin; He, Junyu; Quéméner, Goulven; Wang, Dajun

2018-02-01

We report the full internal state control of ultracold 23Na87Rb molecules, including vibrational, rotational, and hyperfine degrees of freedom. Starting from a sample of weakly bound Feshbach molecules, we realize the creation of molecules in single hyperfine levels of both the rovibrational ground and excited states with a high-efficiency and high-resolution stimulated Raman adiabatic passage. This capability brings broad possibilities for investigating ultracold polar molecules with different chemical reactivities and interactions with a single molecular species. Moreover, starting from the rovibrational and hyperfine ground state, we achieve rotational and hyperfine control with one- and two-photon microwave spectroscopy to reach levels not accessible by the stimulated Raman transfer. The combination of these two techniques results in complete control over the internal state of ultracold polar molecules, which paves the way to study state-dependent molecular collisions and state-controlled chemical reactions.

Peptidylation for the determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.

PubMed

Tang, Feng; Cen, Si-Ying; He, Huan; Liu, Yi; Yuan, Bi-Feng; Feng, Yu-Qi

2016-05-23

Determination of low-molecular-weight compounds by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) has been a great challenge in the analytical research field. Here we developed a universal peptide-based derivatization (peptidylation) strategy for the sensitive analysis of low-molecular-weight compounds by MALDI-TOF-MS. Upon peptidylation, the molecular weights of target analytes increase, thus avoiding serious matrix ion interference in the low-molecular-weight region in MALDI-TOF-MS. Since peptides typically exhibit good signal response during MALDI-TOF-MS analysis, peptidylation endows high detection sensitivities of low-molecular-weight analytes. As a proof-of-concept, we analyzed low-molecular-weight compounds of aldehydes and thiols by the developed peptidylation strategy. Our results showed that aldehydes and thiols can be readily determined upon peptidylation, thus realizing the sensitive and efficient determination of low-molecular-weight compounds by MALDI-TOF-MS. Moreover, target analytes also can be unambiguously detected in biological samples using the peptidylation strategy. The established peptidylation strategy is a universal strategy and can be extended to the sensitive analysis of various low-molecular-weight compounds by MALDI-TOF-MS, which may be potentially used in areas such as metabolomics.

Electrochemical remediation produces a new high-nitrogen compound from NTO wastewaters.

PubMed

Cronin, Michael P; Day, Anthony I; Wallace, Lynne

2007-10-22

A new high-nitrogen molecule, identified as azoxytriazolone (AZTO), has been generated in high yield by electroreduction of acidic aqueous solutions of nitrotriazolone (NTO). The near-quantitative conversion appears to be driven by the low solubility of the product. AZTO precipitates readily, leaving the solution virtually free of organic material, and the process may therefore present an efficient and productive remediation method for wastewater from NTO manufacture. The chemical formula and molecular structure of AZTO indicate that it may be effective as an insensitive explosive.

Cleavage of the main carbon chain backbone of high molecular weight polyacrylamide by aerobic and anaerobic biological treatment.

PubMed

Song, Wenzhe; Zhang, Yu; Gao, Yingxin; Chen, Dong; Yang, Min

2017-12-01

High molecular weight partially hydrolyzed polyacrylamide (PAM) can be bio-hydrolyzed on the amide side group, however, solid evidence regarding the biological cleavage of its main carbon chain backbone is limited. In this study, viscometry, flow field-flow fractionation multi-angle light scattering (FFF-MALS), and attenuated total reflectance-Fourier transform infrared (ATR-FTIR) analysis were used to investigate the biodegradability of PAM with a nominal molecular weight of 2 × 10 7  Da (Da) in two suspended aerobic (25 and 40 °C) and two upflow anaerobic blanket reactors (35 and 55 °C) operated for 470 d under a hydraulic residence time (HRT) of 2 d. Both anaerobic and aerobic biological treatment reduced the viscosity from 2.02 cp in the influent to 1.45-1.60 cp, and reduced the molecular weight of PAM using FFF-MALS from 2.17 × 10 7  Da to less than one-third its original size. The removals of both the amide group and carbon chain backbone in the PAM molecule were further supported by the FTIR analysis. In comparison with the other conditions, thermophilic anaerobic treatment exhibited higher efficiency for PAM biodegradation. Batch test excluded the influence of temperature on the molecular weight of PAM over the range 25-55 °C, suggesting that cleavage of the main carbon chain backbone was attributed to biological degradation. Our results suggested that high molecular weight PAM was biodegradable, but mineralization did not occur. Copyright © 2017 Elsevier Ltd. All rights reserved.

Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs

NASA Astrophysics Data System (ADS)

Fu, Liangliang; Xu, Yueyuan; Hou, Ye; Qi, Xiaolong; Zhou, Lian; Liu, Huiying; Luan, Yu; Jing, Lu; Miao, Yuanxin; Zhao, Shuhong; Liu, Huazhen; Li, Xinyun

2017-03-01

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs.

Proteomic analysis indicates that mitochondrial energy metabolism in skeletal muscle tissue is negatively correlated with feed efficiency in pigs

PubMed Central

Fu, Liangliang; Xu, Yueyuan; Hou, Ye; Qi, Xiaolong; Zhou, Lian; Liu, Huiying; Luan, Yu; Jing, Lu; Miao, Yuanxin; Zhao, Shuhong; Liu, Huazhen; Li, Xinyun

2017-01-01

Feed efficiency (FE) is a highly important economic trait in pig production. Investigating the molecular mechanisms of FE is essential for trait improvement. In this study, the skeletal muscle proteome of high-FE and low-FE pigs were investigated by the iTRAQ approach. A total of 1780 proteins were identified, among which 124 proteins were differentially expressed between the high- and low-FE pigs, with 74 up-regulated and 50 down-regulated in the high-FE pigs. Ten randomly selected differentially expressed proteins (DEPs) were validated by Western blotting and quantitative PCR (qPCR). Gene ontology (GO) analysis showed that all the 25 DEPs located in mitochondria were down-regulated in the high-FE pigs. Furthermore, the glucose-pyruvate-tricarboxylic acid (TCA)-oxidative phosphorylation energy metabolism signaling pathway was found to differ between high- and low-FE pigs. The key enzymes involved in the conversion of glucose to pyruvate were up-regulated in the high-FE pigs. Thus, our results suggested mitochondrial energy metabolism in the skeletal muscle tissue was negatively correlated with FE in pigs, and glucose utilization to generate ATP was more efficient in the skeletal muscle tissue of high-FE pigs. This study offered new targets and pathways for improvement of FE in pigs. PMID:28345649

Molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin.

PubMed

Wang, Xiaoyan; Yu, Jialuo; Kang, Qi; Shen, Dazhong; Li, Jinhua; Chen, Lingxin

2016-03-15

A facile strategy was developed to prepare molecular imprinting ratiometric fluorescence sensor for highly selective and sensitive detection of phycocyanin (PC) based on fluorescence resonance energy transfer (FRET), via a sol-gel polymerization process using nitrobenzoxadiazole (NBD) as fluorescent signal source. The ratio of two fluorescence peak emission intensities of NBD and PC was utilized to determine the concentration of PC, which could effectively reduce the background interference and fluctuation of diverse conditions. As a result, this sensor obtained high sensitivity with a low detection limit of 0.14 nM within 6 min, and excellent recognition specificity for PC over its analogues with a high imprinting factor of 9.1. Furthermore, the sensor attained high recoveries in the range of 93.8-110.2% at three spiking levels of PC, with precisions below 4.7% in seawater and lake water samples. The developed sensor strategy demonstrated simplicity, reliability, rapidity, high selectivity and high sensitivity, proving to be a feasible way to develop high efficient fluorescence sensors and thus potentially applicable for ultratrace analysis of complicated matrices. Copyright © 2015 Elsevier B.V. All rights reserved.

Sex chromosomal abnormalities associated with equine infertility: validation of a simple molecular screening tool in the Purebred Spanish Horse.

PubMed

Anaya, G; Molina, A; Valera, M; Moreno-Millán, M; Azor, P; Peral-García, P; Demyda-Peyrás, S

2017-08-01

Chromosomal abnormalities in the sex chromosome pair (ECAX and ECAY) are widely associated with reproductive problems in horses. However, a large proportion of these abnormalities remains undiagnosed due to the lack of an affordable diagnostic tool that allows for avoiding karyotyping tests. Hereby, we developed an STR (single-tandem-repeat)-based molecular method to determine the presence of the main sex chromosomal abnormalities in horses in a fast, cheap and reliable way. The frequency of five ECAX-linked (LEX026, LEX003, TKY38, TKY270 and UCDEQ502) and two ECAY-linked (EcaYH12 and SRY) markers was characterized in 261 Purebred Spanish Horses to determine the efficiency of the methodology developed to be used as a chromosomal diagnostic tool. All the microsatellites analyzed were highly polymorphic, with a sizeable number of alleles (polymorphic information content > 0.5). Based on this variability, the methodology showed 100% sensitivity and 99.82% specificity to detect the most important sex chromosomal abnormalities reported in horses (chimerism, Turner's syndrome and sex reversal syndromes). The method was also validated with 100% efficiency in 10 individuals previously diagnosed as chromosomally aberrant. This STR screening panel is an efficient and reliable molecular-cytogenetic tool for the early detection of sex chromosomal abnormalities in equines that could be included in breeding programs to save money, effort and time of veterinary practitioners and breeders. © 2017 Stichting International Foundation for Animal Genetics.

Polycyclic aromatic hydrocarbons in the leaves of twelve plant species along an urbanization gradient in Shanghai, China.

PubMed

Liang, Jing; Fang, Hailan; Zhang, Taolin; Wang, Xingxiang

2017-04-01

Plants, particularly their leaves, play an important role in filtering both gas-phase and particle-phase polycyclic aromatic hydrocarbons (PAHs). However, many studies have focused on the accumulation and adsorption functions of plant leaves, possibly underestimating the effects that plants have on air quality. Therefore, eight tree species from different locations in Shanghai were selected to assess PAH filtering (via adsorption and capture) using washed and unwashed plant leaves. The differences in the total PAH contents in the washed leaves were constant for the different species across the different sampling sites. The PAH levels decreased in the following order: industrial areas > traffic areas > urban areas > background area. The PAH compositions in the different plant leaves were dominated by fluorene (Fle), phenanthrene (Phe), anthracene (Ant), chrysene (Chr), fluoranthene (Flu), and pyrene (Pyr); notably, Phe accounted for 49.4-76.7% of the total PAHs. By comparing the PAH contents in the washed leaves with the PAH contents in the unwashed leaves, Pittosporum tobira (P. tobira), Ginkgo biloba (G. biloba), and Platanus acerifolia (P. acerifolia) were found to be efficient species for adsorbing PAHs, while Osmanthus fragrans (O. fragrans), Magnolia grandiflora (M. grandiflora), and Prunus cerasifera Ehrh. (P. cerasifera Ehrh.) were efficient species for capturing PAHs. The efficiencies of the plant leaves for the removal of PAHs from air occurred in the order of low molecular weight > medium molecular weight > high molecular weight PAHs.

Efficient Red-Emitting Platinum Complex with Long Operational Stability.

PubMed

Fleetham, Tyler; Li, Guijie; Li, Jian

2015-08-05

A tetradentate cyclometalated Pt(II) complex, PtN3N-ptb, was developed as an emissive dopant for stable and efficient red phosphorescent OLEDs. Devices employing PtN3N-ptb in electrochemically stable device architectures achieved long operational lifetimes with estimated LT97, of over 600 h at luminances of 1000 cd/m(2). Such long operational lifetimes were achieved utilizing only literature reported host, transporting and blocking materials with known molecular structures. Additionally, a thorough study of the effects of various host and transport materials on the efficiency, turn on voltage, and stability of the devices was carried out. Ultimately, maximum forward viewing EQEs as high as 21.5% were achieved, demonstrating that Pt(II) complexes can act as stable and efficient dopants with operational lifetimes comparable or superior to those of the best literature-reported Ir(III) complexes.

Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors.

PubMed

Martinez-Rosell, Gerard; Harvey, Matt J; De Fabritiis, Gianni

2018-03-26

Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein-ligand efficiency interactions that can later be grown into drug-like leads. In this work, we leverage high-throughput molecular dynamics (MD) simulations to screen a library of 129 fragments for a total of 5.85 ms against the CXCL12 monomer, a chemokine involved in inflammation and diseases such as cancer. Our in silico binding assay was able to recover binding poses, affinities, and kinetics for the selected library and was able to predict 8 mM-affinity fragments with ligand efficiencies higher than 0.3. All of the fragment hits present a similar chemical structure, with a hydrophobic core and a positively charged group, and bind to either sY7 or H1S68 pockets, where they share pharmacophoric properties with experimentally resolved natural binders. This work presents a large-scale screening assay using an exclusive combination of thousands of short MD adaptive simulations analyzed with a Markov state model (MSM) framework.

High pressure chemistry of red phosphorus by photoactivated simple molecules

NASA Astrophysics Data System (ADS)

Ceppatelli, Matteo; Bini, Roberto; Fanetti, Samuele; Caporali, Maria; Peruzzini, Maurizio

2013-06-01

High pressure (HP) is very effective in reducing intermolecular distances and inducing unexpected chemical reactions. In particular the photoactivation of the reactants in HP conditions can lead to very efficient and selective processes. The chemistry of phosphorus is currently based on the white molecular form. The red polymeric allotrope, despite more stable and much less toxic, has not attracted much attention so far. However, switching from the white to the red form would benefit any industrial procedure, especially from an environmental point of view. On the other side, water and ethanol are renewable, environmental friendly and largely available molecules, usable as reactants and photoactivators in HP conditions. Here we report a study on the HP photoinduced reactivity of red phosphorus with water and ethanol, showing the possibility of very efficient and selective processes, leading to molecular hydrogen and valuable phosphorus compounds. The reactions have been studied by means of FTIR and Raman spectroscopy and pressure has been generated using DAC and SAC. HP reactivity has been activated by the two-photon absorption of near-UV wavelengths and occured in total absence of solvents, catalysts and radical initiators, at room T and mild pressure conditions (0.2-1.5 GPa).

Covalent Attachment of the Water-insoluble Ni(P Cy 2 N Phe 2 ) 2 Electrocatalyst to Electrodes Showing Reversible Catalysis in Aqueous Solution

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

Rodríguez-Maciá, Patricia; Priyadarshani, Nilusha; Dutta, Arnab

Hydrogenases are a diverse group of metalloenzymes which catalyze the reversible conversion between molecular hydrogen and protons at high rates. The catalytic activity of these enzymes does not require overpotential because their active site has been evolutionarily optimized to operate fast and efficiently. These enzymes have inspired the development of molecular catalysts, which have dramatically improved in efficiency in recent years, to the point that some synthetic catalysts even outperform hydrogenases under certain conditions. In this work, we use a reversible noble-metal-free homogeneous catalyst, the [Ni(PCy2NPhe2)2]2+ complex, and we covalently immobilize it on a functionalized highly oriented pyrolytic graphite “edge”more » (HOPGe) electrode surface. This catalyst is not water soluble, but once it is surface-confined on the electrode, it maintains its catalytic properties in aqueous solutions, showing reversibility for H2 oxidation/reduction. Immobilization of the [Ni(PCy2NPhe2)2]2+ complex onto a multi-walled carbon nanotubes coated electrode leads to even higher catalytic current densities and enhanced stability.« less

Efficient compression of molecular dynamics trajectory files.

PubMed

Marais, Patrick; Kenwood, Julian; Smith, Keegan Carruthers; Kuttel, Michelle M; Gain, James

2012-10-15

We investigate whether specific properties of molecular dynamics trajectory files can be exploited to achieve effective file compression. We explore two classes of lossy, quantized compression scheme: "interframe" predictors, which exploit temporal coherence between successive frames in a simulation, and more complex "intraframe" schemes, which compress each frame independently. Our interframe predictors are fast, memory-efficient and well suited to on-the-fly compression of massive simulation data sets, and significantly outperform the benchmark BZip2 application. Our schemes are configurable: atomic positional accuracy can be sacrificed to achieve greater compression. For high fidelity compression, our linear interframe predictor gives the best results at very little computational cost: at moderate levels of approximation (12-bit quantization, maximum error ≈ 10(-2) Å), we can compress a 1-2 fs trajectory file to 5-8% of its original size. For 200 fs time steps-typically used in fine grained water diffusion experiments-we can compress files to ~25% of their input size, still substantially better than BZip2. While compression performance degrades with high levels of quantization, the simulation error is typically much greater than the associated approximation error in such cases. Copyright © 2012 Wiley Periodicals, Inc.

Molecular Markers and Cotton Genetic Improvement: Current Status and Future Prospects

PubMed Central

Malik, Waqas; Iqbal, Muhammad Zaffar; Ali Khan, Asif; Qayyum, Abdul; Ali Abid, Muhammad; Noor, Etrat; Qadir Ahmad, Muhammad; Hasan Abbasi, Ghulam

2014-01-01

Narrow genetic base and complex allotetraploid genome of cotton (Gossypium hirsutum L.) is stimulating efforts to avail required polymorphism for marker based breeding. The availability of draft genome sequence of G. raimondii and G. arboreum and next generation sequencing (NGS) technologies facilitated the development of high-throughput marker technologies in cotton. The concepts of genetic diversity, QTL mapping, and marker assisted selection (MAS) are evolving into more efficient concepts of linkage disequilibrium, association mapping, and genomic selection, respectively. The objective of the current review is to analyze the pace of evolution in the molecular marker technologies in cotton during the last ten years into the following four areas: (i) comparative analysis of low- and high-throughput marker technologies available in cotton, (ii) genetic diversity in the available wild and improved gene pools of cotton, (iii) identification of the genomic regions within cotton genome underlying economic traits, and (iv) marker based selection methodologies. Moreover, the applications of marker technologies to enhance the breeding efficiency in cotton are also summarized. Aforementioned genomic technologies and the integration of several other omics resources are expected to enhance the cotton productivity and meet the global fiber quantity and quality demands. PMID:25401149

Selective Fenton-like oxidation of methylene blue on modified Fe-zeolites prepared via molecular imprinting technique.

PubMed

Zhang, Yuanyuan; Shang, Jiaobo; Song, Yanqun; Rong, Chuan; Wang, Yinghui; Huang, Wenyu; Yu, Kefu

2017-02-01

A facile strategy to increase the selectivity of heterogeneous Fenton oxidation is investigated. The increase was reached by increasing selective adsorption of heterogeneous Fenton catalyst to a target pollutant. The heterogeneous Fenton catalyst was prepared by a two-step process. First, zeolite particles were imprinted by the target pollutant, methylene blue (MB), in their aggregations, and second, iron ions were loaded on the zeolite aggregations to form the molecule imprinted Fe-zeolites (MI-FZ) Fenton catalyst. Its adsorption amount for MB reached as high as 44.6 mg g -1 while the adsorption amount of un-imprinted Fe-zeolites (FZ) is only 15.6 mg g -1 . Fenton removal efficiency of MI-FZ for MB was 87.7%, being 33.9% higher than that of FZ. The selective Fenton oxidation of MI-FZ for MB was further confirmed by its removal performance for the mixed MB and bisphenol A (BPA) in solution. The removal efficiency of MB was 44.7% while that of BPA was only 14.9%. This fact shows that molecular imprinting is suitable to prepare the Fe-zeolites (FZ)-based Fenton catalyst with high selectivity for removal of target pollutants, at least MB.

The role of COD/N ratio on the start-up performance and microbial mechanism of an upflow microaerobic reactor treating piggery wastewater.

PubMed

Meng, Jia; Li, Jiuling; Li, Jianzheng; Astals, Sergi; Nan, Jun; Deng, Kaiwen; Antwi, Philip; Xu, Pianpian

2018-07-01

This study investigated the role of COD/N ratio on the start-up and performance of an upflow microaerobic sludge reactor (UMSR) treating piggery wastewater at 0.5 mgO 2 /L. At high COD/N ratio (6.24 and 4.52), results showed that the competition for oxygen between ammonia-oxidizing bacteria, nitrite-oxidizing bacteria and heterotrophic bacteria limited the removal of nitrogen. Nitrogen removal efficiency was below 40% in both scenarios. Decreasing the influent COD/N ratio to 0.88 allowed achieving high removal efficiencies for COD (∼75%) and nitrogen (∼85%) due to the lower oxygen consumption for COD mineralization. Molecular biology techniques showed that nitrogen conversion at a COD/N ratio 0.88 was dominated by the anammox pathway and that Candidatus Brocadia sp. was the most important anammox bacteria in the reactor with a relative abundance of 58.5% among the anammox bacteria. Molecular techniques also showed that Nitrosomonas spp. was the major ammonia-oxidiser bacteria (relative abundance of 86.3%) and that denitrification via NO 3 - and NO 2 - also contributed to remove nitrogen from the system. Copyright © 2018 Elsevier Ltd. All rights reserved.

Discovery of CREBBP Bromodomain Inhibitors by High-Throughput Docking and Hit Optimization Guided by Molecular Dynamics.

PubMed

Xu, Min; Unzue, Andrea; Dong, Jing; Spiliotopoulos, Dimitrios; Nevado, Cristina; Caflisch, Amedeo

2016-02-25

We have identified two chemotypes of CREBBP bromodomain ligands by fragment-based high-throughput docking. Only 17 molecules from the original library of two-million compounds were tested in vitro. Optimization of the two low-micromolar hits, the 4-acylpyrrole 1 and acylbenzene 9, was driven by molecular dynamics results which suggested improvement of the polar interactions with the Arg1173 side chain at the rim of the binding site. The synthesis of only two derivatives of 1 yielded the 4-acylpyrrole 6 which shows a single-digit micromolar affinity for the CREBBP bromodomain and a ligand efficiency of 0.34 kcal/mol per non-hydrogen atom. Optimization of the acylbenzene hit 9 resulted in a series of derivatives with nanomolar potencies, good ligand efficiency and selectivity (see Unzue, A.; Xu, M.; Dong, J.; Wiedmer, L.; Spiliotopoulos, D.; Caflisch, A.; Nevado, C.Fragment-Based Design of Selective Nanomolar Ligands of the CREBBP Bromodomain. J. Med. Chem. 2015, DOI: 10.1021/acs.jmedchem.5b00172). The in silico predicted binding mode of the acylbenzene derivative 10 was validated by solving the structure of the complex with the CREBBP bromodomain.

Poly(ethylene glycol) analogs grafted with low molecular weight poly(ethylene imine) as non-viral gene vectors.

PubMed

Zhang, Zhenfang; Yang, Cuihong; Duan, Yajun; Wang, Yanming; Liu, Jianfeng; Wang, Lianyong; Kong, Deling

2010-07-01

A novel class of non-viral gene vectors consisting of low molecular weight poly(ethylene imine) (PEI) (molecular weight 800 Da) grafted onto degradable linear poly(ethylene glycol) (PEG) analogs was synthesized. First, a Michael addition reaction between poly(ethylene glycol) diacrylates (PEGDA) (molecular weight 258 Da) and d,l-dithiothreitol (DTT) was carried out to generate a linear polymer (PEG-DTT) having a terminal thiol, methacrylate and pendant hydroxyl functional groups. Five PEG-DTT analogs were synthesized by varying the molar ratio of diacrylates to thiols from 1.2:1 to 1:1.2. Then PEI (800 Da) was grafted onto the main chain of the PEG-DTTs using 1,1'-carbonyldiimidazole as the linker. The above reaction gave rise to a new class of non-viral gene vectors, (PEG-DTT)-g-PEI copolymers, which can effectively complex DNA to form nanoparticles. The molecular weights and structures of the copolymers were characterized by gel permeation chromatography, (1)H nuclear magnetic resonance and Fourier transform infrared spectroscopy. The size of the nanoparticles was<200 nm and the surface charge of the nanoparticles, expressed as the zeta potential, was between+20 and+40 mV. Cytotoxicity assays showed that the copolymers exhibited much lower cytotoxicities than high molecular weight PEI (25 kDa). Transfection was performed in cultured HeLa, HepG2, MCF-7 and COS-7 cells. The copolymers showed higher transfection efficiencies than PEI (25 kDa) tested in four cell lines. The presence of serum (up to 30%) had no inhibitory effect on the transfection efficiency. These results indicate that this new class of non-viral gene vectors may be a promising gene carrier that is worth further investigation. Copyright 2010 Acta Materialia Inc. Published by Elsevier Ltd. All rights reserved.

A simple and rapid technique for the authentication of the ginseng cultivar, Yunpoong, using an SNP marker in a large sample of ginseng leaves.

PubMed

Sun, Hua; Wang, Hong-Tao; Kwon, Woo-Saeng; Kim, Yeon-Ju; In, Jun-Gyo; Yang, Deok-Chun

2011-11-01

Yunpoong is an important Korean ginseng (Panax ginseng C. A. Meyer) cultivar, but no molecular marker has been available to identify Yunpoong from other cultivars. In this study, we developed a single nucleotide polymorphism (SNP) marker for Yunpoong based on analysis of expressed sequence tags (ESTs) in an exon region of the glyceraldehyde 3-phosphate dehydrogenase (GAPDH) gene. This SNP marker had high specificity to authenticate Yunpoong in twelve different main ginseng cultivars. For application of the molecular marker, a rapid identification method was established based on the NaOH-Tris method and real-time polymerase chain reaction (PCR) in order to ensure more efficiency in the cultivar selection. The biggest feature of the NaOH-Tris method was that it made the extraction of DNA very simple and rapid in young leaf tissues. We only spent 1 min to extract DNA and directly used it to do PCR. In this report, the conventional DNA extraction method was used to develop molecular marker process, and the NaOH-Tris method was applied in screening large numbers of cultivars. Moreover, the greatest advantage of the real-time PCR compared with traditional PCR, is time saving and high efficiency. Thus, this strategy provides a rapid and reliable method for the specific identification of Yunpoong in a large number of samples. Copyright © 2011 Elsevier B.V. All rights reserved.

Self-assembly of core-polyethylene glycol-lipid shell (CPLS) nanoparticles and their potential as drug delivery vehicles

NASA Astrophysics Data System (ADS)

Shen, Zhiqiang; Loe, David T.; Awino, Joseph K.; Kröger, Martin; Rouge, Jessica L.; Li, Ying

2016-08-01

Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms.Herein a new multifunctional formulation, referred to as a core-polyethylene glycol-lipid shell (CPLS) nanoparticle, has been proposed and studied in silico via large scale coarse-grained molecular dynamics simulations. A PEGylated core with surface tethered polyethylene glycol (PEG) chains is used as the starting configuration, where the free ends of the PEG chains are covalently bonded with lipid molecules (lipid heads). A complete lipid bilayer is formed at the surface of the PEGylated particle core upon addition of free lipids, driven by the hydrophobic properties of the lipid tails, leading to the formation of a CPLS nanoparticle. The self-assembly process is found to be sensitive to the grafting density and molecular weight of the tethered PEG chains, as well as the amount of free lipids added. At low grafting densities the assembly of CPLS nanoparticles cannot be accomplished. As demonstrated by simulations, a lipid bud/vesicle can be formed on the surface when an excess amount of free lipids is added at high grafting density. Therefore, the CPLS nanoparticles can only be formed under appropriate conditions of both PEG and free lipids. The CPLS nanoparticle has been recognized to be able to store a large quantity of water molecules, particularly with high molecular weight of PEG chains, indicating its capacity for carrying hydrophilic molecules such as therapeutic biomolecules or imaging agents. Under identical size and surface chemistry conditions of a liposome, it has been observed that the CPLS particle can be more efficiently wrapped by the lipid membrane, indicating its potential for a greater efficiency in delivering its hydrophilic cargo. As a proof-of-concept, the experimental realization of CPLS nanoparticles is explicitly demonstrated in this study. To test the capacity of the CPLS to store small molecule cargo a hydrophilic dye was successfully encapsulated in the particles' water soluble layer. The results of this study show the power and potential of simulation-driven approaches for guiding the design of more efficient nanomaterial delivery platforms. Electronic supplementary information (ESI) available: Simulation protocol, simulation results for the self-assembly of CPLS nanoparticles, membrane wrapping and free energy change of grafted PEG polymers. See DOI: 10.1039/C6NR04134E

Modeling Complex Workflow in Molecular Diagnostics

PubMed Central

Gomah, Mohamed E.; Turley, James P.; Lu, Huimin; Jones, Dan

2010-01-01

One of the hurdles to achieving personalized medicine has been implementing the laboratory processes for performing and reporting complex molecular tests. The rapidly changing test rosters and complex analysis platforms in molecular diagnostics have meant that many clinical laboratories still use labor-intensive manual processing and testing without the level of automation seen in high-volume chemistry and hematology testing. We provide here a discussion of design requirements and the results of implementation of a suite of lab management tools that incorporate the many elements required for use of molecular diagnostics in personalized medicine, particularly in cancer. These applications provide the functionality required for sample accessioning and tracking, material generation, and testing that are particular to the evolving needs of individualized molecular diagnostics. On implementation, the applications described here resulted in improvements in the turn-around time for reporting of more complex molecular test sets, and significant changes in the workflow. Therefore, careful mapping of workflow can permit design of software applications that simplify even the complex demands of specialized molecular testing. By incorporating design features for order review, software tools can permit a more personalized approach to sample handling and test selection without compromising efficiency. PMID:20007844

Water oxidation by a nickel-glycine catalyst.

PubMed

Wang, Dong; Ghirlanda, Giovanna; Allen, James P

2014-07-23

The utilization of solar energy requires an efficient means for its storage as chemical energy. In bioinspired artificial photosynthesis, light energy can be used to drive water oxidation, but catalysts that produce molecular oxygen from water are needed to avoid excessive driving potentials. In this paper, we demonstrate the utility of a novel complex utilizing earth-abundant Ni in combination with glycine as an efficient catalyst with a modest overpotential of 0.475 ± 0.005 V at a current density of 1 mA/cm(2) at pH 11. Catalysis requires the presence of the amine moiety with the glycine most likely coordinating the Ni in a 4:1 molar ratio. The production of molecular oxygen at a high potential is verified by measurement of the change in oxygen concentration, yielding a Faradaic efficiency of 60 ± 5%. The catalytic species is most likely a heterogeneous Ni-hydroxide formed by electrochemical oxidation. This Ni species can achieve a current density of 4 mA/cm(2) that persists for at least 10 h. Based upon the observed pH dependence of the current amplitude and oxidation/reduction peaks, the catalytic mechanism is an electron-proton coupled process.

Molecular Self-Assembly Fabrication and Carrier Dynamics of Stable and Efficient CH3 NH3 Pb(1-x) Snx I3 Perovskite Solar Cells.

PubMed

Fan, Jiandong; Liu, Chong; Li, Hongliang; Zhang, Cuiling; Li, Wenzhe; Mai, Yaohua

2017-10-09

The Sn-based perovskite solar cells (PSCs) provide the possibility of swapping the Pb element toward developing toxic-free PSCs. Here, we innovatively employed a molecular self-assembly approach to obtain a series CH 3 NH 3 Pb (1-x) Sn x I 3 (0≤x≤1) perovskite thin films with full coverage. The optimized planar CH 3 NH 3 Pb 0.75 Sn 0.25 I 3 PSC with inverted structure was consequently realized with a maximum power conversion efficiency (PCE) over 14 %, which displayed a stabilized power output (SPO) over 12 % within 200 s at 0.6 V forward bias. Afterward, we investigated the factors that limited the efficiency improvement of hybrid Sn-Pb PSCs, and analyzed the possible reason of the hysteresis effect occurred even in the inverted structure cell. Particularly, the oxidation of hybrid Sn-Pb perovskite thin film was demonstrated to be the main reason that limited its further efficiency improvement. The imbalance of charge transport was intensified, which was associated with the increased hole defect-state density and decreased electron defect-state density after Sn was introduced. This study helps tackle the intractable issue regarding the toxic Pb in perovskite devices and is a step forward toward realizing lead-free PSCs with high stability and efficiency. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.