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Sample records for investigating molecular interactions

  1. Investigating Molecular Interactions

    DEFF Research Database (Denmark)

    Clausen, Henrik Fanø

    2010-01-01

    ···π interactions are accommodated by electrostatic complementarity. The crystal structure of both the α- and the β-polymorph of hydroquinone is presented in Chapter 6 with focus on close intermolecular contacts between the molecules via Hirshfeld surface analysis. The charge density distribution of the empty β....... The last chapter of this dissertation presents the analysis of intermolecular interaction using both the Hirshfeld surface and charge density distribution of the acetonitrile β-hydroquinone clathrate. The local packing and related close contacts are examined by breakdown of the fingerprint plots revealing......, are also introduced, as a goal of the analysis of charge density distributions is to obtain further understanding of these macroscopic properties. Neutron diffraction will be used as a complementary tool to the X-ray diffraction experiment, as positional and thermal parameters of hydrogen atoms can...

  2. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    OpenAIRE

    Celebioglu, Hilal Yilmaz; Chronakis, Ioannis S.; Lee, Seunghwan; Guðjónsdóttir, María

    2017-01-01

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their f...

  3. Investigation of the molecular level interactions between mucins and food proteins: Spectroscopic, tribological and rheological studies

    DEFF Research Database (Denmark)

    Celebioglu, Hilal Yilmaz

    The thesis investigated the structure and molecular-level interaction of β-lactoglobulin (BLG) and mucins, representing major components of the dairy products and saliva/digestion systems, respectively. Mucins are long glycoprotein molecules responsible for the gel nature of the mucous layer covers...... epithelial surfaces throughout the body. A literature review of the interactions of different mucin types and saliva mucins with several food proteins and food protein emulsions, as well as their functional properties related to the food oral processing is presented at the first chapter of the thesis (Paper...... V). Most of the studies suggest an electrostatic attraction between positively charged food proteins with negatively charged moieties of mucins (mainly on glycosylated region of mucins). The structural changes occurring during the interaction between BLG, the major whey protein, and bovine...

  4. Investigation of Interactions between Thrombin and Ten Phenolic Compounds by Affinity Capillary Electrophoresis and Molecular Docking

    Directory of Open Access Journals (Sweden)

    Qiao-Qiao Li

    2018-01-01

    Full Text Available Thrombin plays a vital role in blood coagulation, which is a key process involved in thrombosis by promoting platelet aggregation and converting fibrinogen to form the fibrin clot. In the receptor concept, drugs produce their therapeutic effects via interactions with the targets. Therefore, investigation of interaction between thrombin and small molecules is important to find out the potential thrombin inhibitor. In this study, affinity capillary electrophoresis (ACE and in silico molecular docking methods were developed to study the interaction between thrombin and ten phenolic compounds (p-hydroxybenzoic acid, protocatechuic acid, vanillic acid, gallic acid, catechin, epicatechin, dihydroquercetin, naringenin, apigenin, and baicalein. The ACE results showed that gallic acids and six flavonoid compounds had relative strong interactions with thrombin. In addition, the docking results indicated that all of optimal conformations of the six flavonoid compounds were positioned into the thrombin activity centre and had interaction with the HIS57 or SER195 which was the key residue to bind thrombin inhibitors such as argatroban. Herein, these six flavonoid compounds might have the potential of thrombin inhibition activity. In addition, the developed method in this study can be further applied to study the interactions of other molecules with thrombin.

  5. The interaction between 4-aminoantipyrine and bovine serum albumin: Multiple spectroscopic and molecular docking investigations

    International Nuclear Information System (INIS)

    Teng Yue; Liu Rutao; Li Chao; Xia Qing; Zhang Pengjun

    2011-01-01

    4-Aminoantipyrine (AAP) is widely used in the pharmaceutical industry, in biochemical experiments and in environmental monitoring. AAP as an aromatic pollutant in the environment poses a great threat to human health. To evaluate the toxicity of AAP at the protein level, the effects of AAP on bovine serum albumin (BSA) were investigated by multiple spectroscopic techniques and molecular modeling. After the inner filter effect was eliminated, the experimental results showed that AAP effectively quenched the intrinsic fluorescence of BSA via static quenching. The number of binding sites, the binding constant, the thermodynamic parameters and binding subdomain were measured, and indicated that AAP could spontaneously bind with BSA on subdomain IIIA through electrostatic forces. Molecular docking results revealed that AAP interacted with the Glu 488 and Glu 502 residues of BSA. Furthermore, the conformation of BSA was demonstrably changed in the presence of AAP. The skeletal structure of BSA loosened, exposing internal hydrophobic aromatic ring amino acids and peptide strands to the solution.

  6. Polyphilic Interactions as Structural Driving Force Investigated by Molecular Dynamics Simulation (Project 7

    Directory of Open Access Journals (Sweden)

    Christopher Peschel

    2017-09-01

    Full Text Available We investigated the effect of fluorinated molecules on dipalmitoylphosphatidylcholine (DPPC bilayers by force-field molecular dynamics simulations. In the first step, we developed all-atom force-field parameters for additive molecules in membranes to enable an accurate description of those systems. On the basis of this force field, we performed extensive simulations of various bilayer systems containing different additives. The additive molecules were chosen to be of different size and shape, and they included small molecules such as perfluorinated alcohols, but also more complex molecules. From these simulations, we investigated the structural and dynamic effects of the additives on the membrane properties, as well as the behavior of the additive molecules themselves. Our results are in good agreement with other theoretical and experimental studies, and they contribute to a microscopic understanding of interactions, which might be used to specifically tune membrane properties by additives in the future.

  7. Molecular dynamics investigation of nanoscale substrate topography and its interaction with liquids

    Science.gov (United States)

    Cordeiro Rodrigues, Jhonatam

    Nanotechnology has been presenting successful applications in several areas. However, experimentation with nanoscale materials is costly and limited in analysis capability. This research investigates the use of molecular dynamics (MD) simulations to model and study nanomaterials and manufacturing processes. MD simulations are employed to reduce cost, optimize design, increase productivity and allow for the investigation of material interactions not yet observable through experimentation. This work investigates the interaction of water with substrates at the nanoscale. The effect of temperature, droplet impingement velocities and size, as well as substrate material, are investigated at the nanoscale. Several substrate topography designs were modeled to reveal their influence on the wettability of the substrate. Nanoscale gold and silicon substrates are more hydrophilic at higher temperatures than at room temperature. The reduction in droplet diameter increases its wettability. High impingement velocity of droplets does not influence final wettability of substrates but induces higher diffusion rates of droplets in a heated environment. Droplets deposited over a gradient of surface exposure presents spontaneous movement. The Leidenfrost effect was investigated at the nanoscale. Droplets of 4 and 10nm in diameter presented behaviors pertinent to the Leidenfrost effect at 373K, significantly lower than at micro scale and of potential impact to the field. Topographical features were manipulated using superhydrophobic coating resulting in micro whiskers. Nanoimprint lithography (NIL) was used to manufacture substrate topographies at the nanoscale. Water droplets were deposited on the substrates and their wettability was measured using droplet contact angles. Lower surface area exposure resulted in higher contact angles. The experimental relationships between surface topography and substrate wettability were used to validate the insights gained from MD simulations for

  8. Molecular Dynamics Simulation to Investigate the Interaction of Asphaltene and Oxide in Aggregate

    Directory of Open Access Journals (Sweden)

    Rui Li

    2016-01-01

    Full Text Available The asphalt-aggregate interface interaction (AAI plays a significant role in the overall performances of asphalt mixture, which is caused due to the complicated physicochemical processes and is influenced by various factors, including the acid-base property of aggregates. In order to analyze the effects of the chemical constitution of aggregate on the AAI, the average structure C65H74N2S2 is selected to represent the asphaltene in asphalt and magnesium oxide (MgO, calcium oxide (CaO, aluminium sesquioxide (Al2O3, and silicon dioxide (SiO2 are selected to represent the major oxides in aggregate. The molecular models are established for asphaltene and the four oxides, respectively, and the molecular dynamics (MD simulation was conducted for the four kinds of asphaltene-oxide system at different temperatures. The interfacial energy in MD simulation is calculated to evaluate the AAI, and higher value means better interaction. The results show that interfacial energy between asphaltene and oxide reaches the maximum value at 25°C and 80°C and the minimum value at 40°C. In addition, the interfacial energy between asphaltene and MgO was found to be the greatest, followed by CaO, Al2O3, and SiO2, which demonstrates that the AAI between asphalt and alkaline aggregates is better than acidic aggregates.

  9. Molecular Modeling of Myrosinase from Brassica oleracea: A Structural Investigation of Sinigrin Interaction

    Directory of Open Access Journals (Sweden)

    Sathishkumar Natarajan

    2015-12-01

    Full Text Available Myrosinase, which is present in cruciferous plant species, plays an important role in the hydrolysis of glycosides such as glucosinolates and is involved in plant defense. Brassicaceae myrosinases are diverse although they share common ancestry, and structural knowledge about myrosinases from cabbage (Brassica oleracea was needed. To address this, we constructed a three-dimensional model structure of myrosinase based on Sinapis alba structures using Iterative Threading ASSEmbly Refinement server (I-TASSER webserver, and refined model coordinates were evaluated with ProQ and Verify3D. The resulting model was predicted with β/α fold, ten conserved N-glycosylation sites, and three disulfide bridges. In addition, this model shared features with the known Sinapis alba myrosinase structure. To obtain a better understanding of myrosinase–sinigrin interaction, the refined model was docked using Autodock Vina with crucial key amino acids. The key nucleophile residues GLN207 and GLU427 were found to interact with sinigrin to form a hydrogen bond. Further, 20-ns molecular dynamics simulation was performed to examine myrosinase–sinigrin complex stability, revealing that residue GLU207 maintained its hydrogen bond stability throughout the entire simulation and structural orientation was similar to that of the docked state. This conceptual model should be useful for understanding the structural features of myrosinase and their binding orientation with sinigrin.

  10. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Ruiyong, E-mail: wangry@zzu.edu.cn; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun, E-mail: chjsong@zzu.edu.cn; Chang, Junbiao, E-mail: changjunbiao@zzu.edu.cn

    2014-10-15

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking.

  11. Investigation of the interaction between isomeric derivatives and human serum albumin by fluorescence spectroscopy and molecular modeling

    International Nuclear Information System (INIS)

    Wang, Ruiyong; Dou, Huanjing; Yin, Yujing; Xie, Yuanzhe; Sun, Li; Liu, Chunmei; Dong, Jingjing; Huang, Gang; Zhu, Yanyan; Song, Chuanjun; Chang, Junbiao

    2014-01-01

    In this paper, we have synthesized 9H-pyrrolo[1,2-a]indol-9-ones and the isomeric indeno[2,1-b]pyrrol-8-ones. The interactions of human serum albumin with series of isomeric derivatives have been studied by spectrophotometric methods. Results show the intrinsic fluorescence is quenched by the derivatives with a static quenching procedure. The thermodynamics parameters indicate that van der Waals forces and hydrogen bonds play a major role in the interactions. The results of synchronous fluorescence spectra demonstrate that the microenvironments of Trp residue of human serum albumin are disturbed by most derivatives. Thermodynamic results showed that the 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers and bind to human serum albumin with the higher affinity than isomeric indeno[2,1-b]pyrrol-8-ones. The influence of molecular structure on the binding aspects has been investigated. - Highlights: • The interactions between isomeric derivatives and HSA have been investigated. • Results reveal that 9H-pyrrolo[1,2-a]indol-9-ones are stronger quenchers for HSA. • Hydrogen bonds and van der Waals forces play major role in the binding process. • The influence of molecular structure on the binding aspects has been investigated. • The binding study was also modeled by molecular docking

  12. MDM2-MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance.

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2-MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2-MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD ) in the micromolar range for the MDM2-MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2-MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2-MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation.

  13. Investigating the Interaction of Fe Nanoparticles with Lysozyme by Biophysical and Molecular Docking Studies.

    Directory of Open Access Journals (Sweden)

    Zahra Aghili

    Full Text Available Herein, the interaction of hen egg white lysozyme (HEWL with iron nanoparticle (Fe NP was investigated by spectroscopic and docking studies. The zeta potential analysis revealed that addition of Fe NP (6.45±1.03 mV to HEWL (8.57±0.54 mV can cause to greater charge distribution of nanoparticle-protein system (17.33±1.84 mV. In addition, dynamic light scattering (DLS study revealed that addition of Fe NP (92.95±6.11 nm to HEWL (2.68±0.37 nm increases suspension potential of protein/nanoparticle system (51.17±3.19 nm. Fluorescence quenching studies reveled that both static and dynamic quenching mechanism occur and hydrogen bond and van der Waals interaction give rise to protein-NP system. Synchronous fluorescence spectroscopy of HEWL in the presence of Fe NP showed that the emission maximum wavelength of tryptophan (Trp residues undergoes a red-shift. ANS fluorescence data indicated a dramatic exposure of hydrophobic residues to the solvent. The considerable reduction in melting temperature (T(m of HEWL after addition of Fe NP determines an unfavorable interaction system. Furthermore circular dichoroism (CD experiments demonstrated that, the secondary structure of HEWL has not changed with increasing Fe NP concentrations; however, some conformational changes occur in tertiary structure of HEWL. Moreover, protein-ligand docking study confirmed that the Fe NP forms hydrogen bond contacts with HEWL.

  14. Investigation of the Interaction between Patulin and Human Serum Albumin by a Spectroscopic Method, Atomic Force Microscopy, and Molecular Modeling

    Directory of Open Access Journals (Sweden)

    Li Yuqin

    2014-01-01

    Full Text Available The interaction of patulin with human serum albumin (HSA was studied in vitro under normal physiological conditions. The study was performed using fluorescence, ultraviolet-visible spectroscopy (UV-Vis, circular dichroism (CD, atomic force microscopy (AFM, and molecular modeling techniques. The quenching mechanism was investigated using the association constants, the number of binding sites, and basic thermodynamic parameters. A dynamic quenching mechanism occurred between HSA and patulin, and the binding constants (K were 2.60 × 104, 4.59 × 104, and 7.01 × 104 M−1 at 288, 300, and 310 K, respectively. Based on fluorescence resonance energy transfer, the distance between the HSA and patulin was determined to be 2.847 nm. The ΔG0, ΔH0, and ΔS0 values across various temperatures indicated that hydrophobic interaction was the predominant binding force. The UV-Vis and CD results confirmed that the secondary structure of HSA was altered in the presence of patulin. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with patulin. In addition, molecular modeling showed that the patulin-HSA complex was stabilized by hydrophobic and hydrogen bond forces. The study results suggested that a weak intermolecular interaction occurred between patulin and HSA. Overall, the results are potentially useful for elucidating the toxigenicity of patulin when it is combined with the biomolecular function effect, transmembrane transport, toxicological, testing and other experiments.

  15. Atomic and Molecular Interactions

    International Nuclear Information System (INIS)

    2002-01-01

    The Gordon Research Conference (GRC) on Atomic and Molecular Interactions was held at Roger Williams University, Bristol, RI. Emphasis was placed on current unpublished research and discussion of the future target areas in this field

  16. Theoretical investigation of interaction of sorbitol molecules with alcohol dehydrogenase in aqueous solution using molecular dynamics simulation.

    Science.gov (United States)

    Bahrami, Homayoon; Zahedi, Mansour; Moosavi-Movahedi, Ali Akbar; Azizian, Homa; Amanlou, Massoud

    2011-03-01

    The nature of protein-sorbitol-water interaction in solution at the molecular level, has been investigated using molecular dynamics simulations. In order to do this task, two molecular dynamics simulations of the protein ADH in solution at room temperature have been carried out, one in the presence (about 0.9 M) and another in the absence of sorbitol. The results show that the sorbitol molecules cluster and move toward the protein, and form hydrogen bonds with protein. Also, coating by sorbitol reduces the conformational fluctuations of the protein compared to the sorbitol-free system. Thus, it is concluded that at moderate concentration of sorbitol solution, sorbitol molecules interact with ADH via many H-bonds that prevent the protein folding. In fact, at more concentrated sorbitol solution, water and sorbitol molecules accumulate around the protein surface and form a continuous space-filling network to reduce the protein flexibility. Namely, in such solution, sorbitol molecules can stabilize a misfolded state of ADH, and prevent the protein from folding to its native structure.

  17. Molecular Interactions at Membranes

    DEFF Research Database (Denmark)

    Jagalski, Vivien

    . Today, we know more than ever before about the properties of biological membranes. Advanced biophysical techniques and sophisticated membrane models allow us to answer specific questions about the structure of the components within membranes and their interactions. However, many detailed structural...... the surface-immobilization of LeuT by exchanging the detergent with natural phosphatidylcholine (PC) lipids. Various surface sensitive techniques, including neutron reflectometry (NR), are employed and finally enabled us to confirm the gross structure of LeuT in a lipid environment as predicted by molecular...... dynamic simulations. In a second study, the co-localization of three toxic plant-derived diterpene resin acids (RAs) within DPPC membranes was investigated. These compounds are reported to disrupt the membrane and increase its fluidity. The RAs used in this study vary in their toxicity while...

  18. Molecular interaction of 2,4-diacetylphloroglucinol (DAPG) with human serum albumin (HSA): The spectroscopic, calorimetric and computational investigation

    Science.gov (United States)

    Pragna Lakshmi, T.; Mondal, Moumita; Ramadas, Krishna; Natarajan, Sakthivel

    2017-08-01

    Drug molecule interaction with human serum albumin (HSA) affects the distribution and elimination of the drug. The compound, 2,4-diacetylphloroglucinol (DAPG) has been known for its antimicrobial, antiviral, antihelminthic and anticancer properties. However, its interaction with HSA is not yet reported. In this study, the interaction between HSA and DAPG was investigated through steady-state fluorescence, time-resolved fluorescence (TRF), circular dichroism (CD), Fourier transform infrared (FT-IR) spectroscopy, isothermal titration calorimetry (ITC), molecular docking and molecular dynamics simulation (MDS). Fluorescence spectroscopy results showed the strong quenching of intrinsic fluorescence of HSA due to interaction with DAPG, through dynamic quenching mechanism. The compound bound to HSA with reversible and moderate affinity which explained its easy diffusion from circulatory system to target tissue. The thermodynamic parameters from fluorescence spectroscopic data clearly revealed the contribution of hydrophobic forces but, the role of hydrogen bonds was not negligible according to the ITC studies. The interaction was exothermic and spontaneous in nature. Binding with DAPG reduced the helical content of protein suggesting the unfolding of HSA. Site marker fluorescence experiments revealed the change in binding constant of DAPG in the presence of site I (warfarin) but not site II marker (ibuprofen) which confirmed that the DAPG bound to site I. ITC experiments also supported this as site I marker could not bind to HSA-DAPG complex while site II marker was accommodated in the complex. In silico studies further showed the lowest binding affinity and more stability of DAPG in site I than in site II. Thus the data presented in this study confirms the binding of DAPG to the site I of HSA which may help in further understanding of pharmacokinetic properties of DAPG.

  19. Investigation on molecular interactions of antibiotics in alcohols using volumetric and acoustic studies at different temperatures

    International Nuclear Information System (INIS)

    Naseem, Bushra; Iftikhar, Madeeha

    2017-01-01

    Highlights: • Antibiotics in different alcohols are used to study their interactions in solutions. • Density and sound velocity for antibiotic solutions are measured at different temperatures. • Apparent molar volume and isentropic compressibility are used to calculate partial molar quantities. • Acoustical parameters are calculated and discussed in terms of solute–solute and solute–solvent interactions. - Abstract: The density and sound velocity for pure alcohols (methanol, ethanol, iso-propanol and n-butanol) and molal solutions of nitroimidazoles (metronidazole (MNZ) and dimetridazole (DMZ) have been measured at different temperatures (293.15–313.15 K). Different volumetric and acoustical parameters like apparent molar volume (V ϕ ), partial molar volume (VЛљ ϕ ), apparent molar isentropic compressibility (K ϕ ), partial molar isentropic compressibility (KЛљ ϕ ), hydration number (n H ), acoustic impedance (Z) and intermolecular free length (L f ) of antibiotic solutions were calculated from the experimental values of density and sound velocity. The derived values have been used to explore the solute–solute and solute–solvent interactions. The V ϕ values are positive and K ϕ values are negative in both antibiotics, indicative of strong solute–solvent interactions and closely packed structure of antibiotics in alcohols. The decreasing trend of L f with increasing antibiotic concentration shows the presence of strong intermolecular interactions in solutions.

  20. DSC and EPR investigations on effects of cholesterol component on molecular interactions between paclitaxel and phospholipid within lipid bilayer membrane.

    Science.gov (United States)

    Zhao, Lingyun; Feng, Si-Shen; Kocherginsky, Nikolai; Kostetski, Iouri

    2007-06-29

    Differential scanning calorimetry (DSC) and electron paramagnetic resonance spectroscopy (EPR) were applied to investigate effects of cholesterol component on molecular interactions between paclitaxel, which is one of the best antineoplastic agents found from nature, and dipalmitoylphosphatidylcholine (DPPC) within lipid bilayer vesicles (liposomes), which could also be used as a model cell membrane. DSC analysis showed that incorporation of paclitaxel into the DPPC bilayer causes a reduction in the cooperativity of bilayer phase transition, leading to a looser and more flexible bilayer structure. Including cholesterol component in the DPPC/paclitaxel mixed bilayer can facilitate the molecular interaction between paclitaxel and lipid and make the tertiary system more stable. EPR analysis demonstrated that both of paclitaxel and cholesterol have fluidization effect on the DPPC bilayer membranes although cholesterol has more significant effect than paclitaxel does. The reduction kinetics of nitroxides by ascorbic acid showed that paclitaxel can inhibit the reaction by blocking the diffusion of either the ascorbic acid or nitroxide molecules since the reaction is tested to be a first order one. Cholesterol can remarkably increase the reduction reaction speed. This research may provide useful information for optimizing liposomal formulation of the drug as well as for understanding the pharmacology of paclitaxel.

  1. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhou, Meng [Business School, University of Bedfordshire, Luton LU1 3JU (United Kingdom); Zhou, Zhiqiang [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China); Zhu, Wentao, E-mail: wentaozhu@cau.edu.cn [Department of Applied Chemistry, China Agricultural University, Beijing 100193 (China)

    2014-11-15

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA.

  2. Multispectroscopic and molecular modeling approach to investigate the interaction of diclofop-methyl enantiomers with human serum albumin

    International Nuclear Information System (INIS)

    Zhang, Ping; Liu, Donghui; Li, Zhe; Shen, Zhigang; Wang, Peng; Zhou, Meng; Zhou, Zhiqiang; Zhu, Wentao

    2014-01-01

    Pesticides and related environmental contaminants have always been threated to human health due to their intrinsic toxicity. In the context of this contribution, the interaction between diclofop-methyl (DM) enantiomers and human serum albumin (HSA) has been characterized by steady state and three-dimensional fluorescence, molecular modeling, circular dichroism (CD) and ultraviolet–visible (UV–vis) spectroscopy. The binding constants significantly showed the binding was enantioselective and HSA had higher affinity for S-DM. The thermodynamic parameters of the binding reaction (ΔG, ΔH and ΔS) clearly signified that hydrophobic effects and H-bonds contribute to the formation of DM-HSA complex. The alterations of protein secondary structure in the presence of DM enantiomers were confirmed by CD spectroscopy, UV–vis and three-dimensional fluorescence spectroscopy. In addition, both fluorescence probe study and molecular modeling simulation evidenced the binding of DM enantiomers to HSA primarily took place in subdomain IIIA (Sudlow's site II). This investigation highlights the binding mechanism, specific binding sites and binding region of DM enantiomers on human serum albumin at the first time. Besides, such task can provide important insight to the interaction of the physiological protein HSA with chiral aryloxyphenoxypropionate herbicides and give support to the human health risk assessment. - Highlights: • The binding of DM enantiomers to HSA was enantioselective. • HSA had higher affinity for S-DM than R-DM. • Hydrophobic effects and hydrogen bonds were involved in the DM-HSA interaction. • The binding of DM enantiomers to HSA primarily took place in Sudlow's site II. • DM enantiomers could alter the second structure of HSA

  3. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Yang Qing; Zhou Ximin [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Xingguo, E-mail: chenxg@lzu.edu.c [National Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000 (China); Department of Chemistry, Lanzhou University, Lanzhou 730000 (China)

    2011-04-15

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  4. Combined molecular docking and multi-spectroscopic investigation on the interaction between Eosin B and human serum albumin

    International Nuclear Information System (INIS)

    Yang Qing; Zhou Ximin; Chen Xingguo

    2011-01-01

    The binding of Eosin B to human serum albumin (HSA) was studied using molecular docking, fluorescence, UV-vis, circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy. The mechanism of interaction between Eosin B and HSA in terms of the binding parameters, the thermodynamic functions and the effect of Eosin B on the conformation of HSA were investigated. Protein-ligand docking study indicated that Eosin B bound to residues located in the subdomain IIA of HSA and Eosin B-HSA complex was stabilized by hydrophobic force and hydrogen bonding. In addition, fluorescence data revealed that Eosin B strongly quenched the intrinsic fluorescence of HSA through a static quenching procedure. Furthermore, alteration of the secondary structure of HSA in the presence of the dye was conformed by UV-vis, FT-IR and CD spectroscopy.

  5. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Energy Technology Data Exchange (ETDEWEB)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo [Department of Chemistry and Center of Excellence for Innovation in Chemistry, Faculty of Science, Mahidol University, Rama VI Road, Bangkok 10400 (Thailand); Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong [National Nanotechnology Center, National Science and Technology Development Agency, 111 Thailand Science Park, Paholyothin Road, Klong 1, Klong Luang, Pathumthani 12120 (Thailand); Pratontep, Sirapat [College of KMITL Nanotechnology, King Mongkut' s Institute of Technology Ladkrabang, Bangkok (Thailand); Puttipipatkhachorn, Satit, E-mail: uracha@nanotec.or.th [Department of Manufacturing Pharmacy, Faculty of Pharmacy, Mahidol University, Bangkok 10400 (Thailand)

    2010-03-26

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of {gamma}-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the {gamma}-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ({sup 1}H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the {sup 1}H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of {gamma}-oryzanol inside the lipid nanoparticles, the {sup 1}H-NMR revealed that the chemical shifts of the liquid lipid in {gamma}-oryzanol loaded systems were found at rather higher field than those in {gamma}-oryzanol free systems, suggesting incorporation of {gamma}-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of {gamma}-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models

  6. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    Science.gov (United States)

    Anantachaisilp, Suranan; Meejoo Smith, Siwaporn; Treetong, Alongkot; Pratontep, Sirapat; Puttipipatkhachorn, Satit; Rungsardthong Ruktanonchai, Uracha

    2010-03-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812® as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance (1H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  7. Chemical and structural investigation of lipid nanoparticles: drug-lipid interaction and molecular distribution

    International Nuclear Information System (INIS)

    Anantachaisilp, Suranan; Smith, Siwaporn Meejoo; Treetong, Alongkot; Ruktanonchai, Uracha Rungsardthong; Pratontep, Sirapat; Puttipipatkhachorn, Satit

    2010-01-01

    Lipid nanoparticles are a promising alternative to existing carriers in chemical or drug delivery systems. A key challenge is to determine how chemicals are incorporated and distributed inside nanoparticles, which assists in controlling chemical retention and release characteristics. This study reports the chemical and structural investigation of γ-oryzanol loading inside a model lipid nanoparticle drug delivery system composed of cetyl palmitate as solid lipid and Miglyol 812 as liquid lipid. The lipid nanoparticles were prepared by high pressure homogenization at varying liquid lipid content, in comparison with the γ-oryzanol free systems. The size of the lipid nanoparticles, as measured by the photon correlation spectroscopy, was found to decrease with increased liquid lipid content from 200 to 160 nm. High-resolution proton nuclear magnetic resonance ( 1 H-NMR) measurements of the medium chain triglyceride of the liquid lipid has confirmed successful incorporation of the liquid lipid in the lipid nanoparticles. Differential scanning calorimetric and powder x-ray diffraction measurements provide complementary results to the 1 H-NMR, whereby the crystallinity of the lipid nanoparticles diminishes with an increase in the liquid lipid content. For the distribution of γ-oryzanol inside the lipid nanoparticles, the 1 H-NMR revealed that the chemical shifts of the liquid lipid in γ-oryzanol loaded systems were found at rather higher field than those in γ-oryzanol free systems, suggesting incorporation of γ-oryzanol in the liquid lipid. In addition, the phase-separated structure was observed by atomic force microscopy for lipid nanoparticles with 0% liquid lipid, but not for lipid nanoparticles with 5 and 10% liquid lipid. Raman spectroscopic and mapping measurements further revealed preferential incorporation of γ-oryzanol in the liquid part rather than the solid part of in the lipid nanoparticles. Simple models representing the distribution of γ-oryzanol and

  8. Spectroscopic and molecular modeling approaches to investigate the interaction of bisphenol A, bisphenol F and their diglycidyl ethers with PPARα.

    Science.gov (United States)

    Zhang, Jie; Zhang, Tiehua; Guan, Tianzhu; Ruan, Ping; Ren, Dayong; Dai, Weichang; Yu, Hansong; Li, Tiezhu

    2017-08-01

    A fluorescence polarization (FP) assay for the simultaneous determination of bisphenol A (BPA), bisphenol F (BPF), bisphenol A diglycidyl ether (BADGE) and bisphenol F diglycidyl ether (BFDGE) was developed. The method was based on the competition between bisphenols (BPs) and fluorescein-labeled dexamethasone derivative (Dex-fl) for mouse peroxisome proliferator-activated receptor α ligand binding domain (mPPARα-LBD). A recombinant soluble protein derivative mPPARα-LBD* was prepared, then in vitro binding of 4 BPs to mPPARα-LBD* was investigated. Fluorescence polarization assay showed that these compounds exhibited different binding potencies with mPPARα-LBD*. Additionally, molecular dynamics simulations were performed to further understand the mechanism of BPs binding affinity for mPPARα-LBD*. Docking results elucidated that the driving forces for the binding of BPs to mPPARα-LBD* were predominantly dependent on hydrophobic and hydrogen-bonding interactions. Comparison of the calculated binding energies vs. experimental binding affinities yielded a good correlation (R 2  = 0.7258). The proposed method has potential for multi-residue detection of BPA, BPF, BADGE, and BFDGE. Copyright © 2017 Elsevier Ltd. All rights reserved.

  9. Investigations on the interactions of diclofenac sodium with HSA and ctDNA using molecular modeling and multispectroscopic methods

    Science.gov (United States)

    Cui, Yanrui; Hao, Erjun; Hui, Guangquan; Guo, Wei; Cui, Fengling

    2013-06-01

    A tentative study on interaction of diclofenac sodium (DF-Na) with human serum albumin (HSA) and calf thymus DNA (ctDNA) was conducted by using multi-spectroscopic and molecular modeling techniques under simulative physiological conditions. The results of spectroscopic measurements suggested that the quenching mechanisms were static quenching. Three-dimensional fluorescence spectroscopy clearly demonstrated the occurrence of conformational changes of HSA with addition of DF-Na. In addition, competitive studies with ethidium bromide (EB) have shown that DF-Na can bind to ctDNA relatively strong via groove binding. Based on the values of thermodynamic parameters and the results of molecular modeling, it was confirmed that hydrophobic forces and hydrogen bond were the mainly binding forces in DF-Na-HSA and DF-Na-DNA systems. The binding distance between DF-Na and HSA was also determined using the theory of the Förster energy transference.

  10. Probing the interaction of a therapeutic flavonoid, pinostrobin with human serum albumin: multiple spectroscopic and molecular modeling investigations.

    Directory of Open Access Journals (Sweden)

    Shevin R Feroz

    Full Text Available Interaction of a pharmacologically important flavonoid, pinostrobin (PS with the major transport protein of human blood circulation, human serum albumin (HSA has been examined using a multitude of spectroscopic techniques and molecular docking studies. Analysis of the fluorescence quenching data showed a moderate binding affinity (1.03 × 10(5 M(-1 at 25°C between PS and HSA with a 1∶1 stoichiometry. Thermodynamic analysis of the binding data (ΔS = +44.06 J mol(-1 K(-1 and ΔH = -15.48 kJ mol(-1 and molecular simulation results suggested the involvement of hydrophobic and van der Waals forces, as well as hydrogen bonding in the complex formation. Both secondary and tertiary structural perturbations in HSA were observed upon PS binding, as revealed by intrinsic, synchronous, and three-dimensional fluorescence results. Far-UV circular dichroism data revealed increased thermal stability of the protein upon complexation with PS. Competitive drug displacement results suggested the binding site of PS on HSA as Sudlow's site I, located at subdomain IIA, and was well supported by the molecular modelling data.

  11. A multispectroscopic and molecular docking investigation of the binding interaction between serum albumins and acid orange dye

    Science.gov (United States)

    Naveenraj, Selvaraj; Solomon, Rajadurai Vijay; Mangalaraja, Ramalinga Viswanathan; Venuvanalingam, Ponnambalam; Asiri, Abdullah M.; Anandan, Sambandam

    2018-03-01

    The interaction of Acid Orange 10 (AO10) with bovine serum albumin (BSA) was investigated comparatively with that of human serum albumin (HSA) using multispectroscopic techniques for understanding their toxic mechanism. Further, density functional theory calculations and docking studies have been carried out to gain more insights into the nature of interactions existing between AO10 and serum albumins. The fluorescence results suggest that AO10 quenched the fluorescence of BSA through the combination of static and dynamic quenching mechanism. The same trend was followed in the interaction of AO10 with HSA. In addition to the type of quenching mechanism, the fluorescence spectroscopic results suggest that the binding occurs near the tryptophan moiety of serum albumins and the binding. AO10 has more binding affinity towards BSA than HSA. An AO10-Trp model has been created to explicitly understand the Csbnd Htbnd π interactions from Bader's quantum theory of atoms in molecules analysis which confirmed that AO10 bind more strongly with BSA than that of HSA due to the formation of three hydrogen bonds with BSA whereas it forms two hydrogen bonds in the case of HSA. These obtained results provide an in-depth understanding of the interaction of the acid azo dye AO10 with serum albumins. This interaction study provides insights into the underlying reasons for toxicity of AO10 relevant to understand its effect on bovids and humans during the blood transportation process.

  12. Investigation on molecular interaction of amino acids in aqueous disodium hydrogen phosphate solutions with reference to volumetric and compressibility measurements

    International Nuclear Information System (INIS)

    Kumar, Harsh; Singla, Meenu; Jindal, Rajeev

    2014-01-01

    Highlights: • Densities and speeds of sound of amino acids in aqueous disodium hydrogen phosphate. • Partial molar volumes and compressibility of transfer. • Positive values of transfer volume indicates interactions between ions of amino acids and TSC. • Ion–hydrophilic and hydrophilic–hydrophilic interactions are present. • Pair-wise interactions are dominant in the mixtures. -- Abstract: The interactions of amino acids glycine (Gly), L-alanine (Ala), and L-valine (Val) with disodium hydrogen phosphate (DSHP) as a function of temperature have been investigated by combination of volumetric and acoustic measurements. Densities (ρ) and speeds of sound (u) of amino acids in aqueous solutions of disodium hydrogen phosphate have been measured at T = (288.15, 293.15, 298.15, 303.15 and 308.15) K and atmospheric pressure. The apparent molar volume (V ϕ ), the partial molar volume (V ϕ 0 ) and standard partial molar volumes of transfer (ΔV ϕ 0 ) for amino acids from water to aqueous disodium hydrogen phosphate solutions have been calculated from density data. Partial molar adiabatic compressibility (κ ϕ,s ) and partial molar adiabatic compressibility of transfer (Δκ ϕ,S 0 ) have been calculated from speed of sound data. The pair (V AB , κ AB ) and triplet (V ABB , κ ABB ) interaction coefficient have been calculated from both the properties. The results have been explained based on competing patterns of interactions of co-solvents and the solute

  13. Intramolecular interactions stabilizing compact conformations of the intrinsically disordered kinase-inhibitor domain of Sic1: a molecular dynamics investigation.

    Directory of Open Access Journals (Sweden)

    Matteo eLambrughi

    2012-11-01

    Full Text Available Cyclin-dependent kinase inhibitors (CKIs are key regulatory proteins of the eukaryotic cell cycle, which modulate cyclin-dependent kinase (Cdk activity. CKIs perform their inhibitory effect by the formation of ternary complexes with a target kinase and its cognate cyclin. These regulators generally belong to the class of intrinsically disordered proteins (IDPs, which lack a well-defined and organized three-dimensional structure in their free state, undergoing folding upon binding to specific partners. Unbound IDPs are not merely random-coil structures, but can present intrinsically folded structural units (IFSUs and collapsed conformations. These structural features can be relevant to protein function in vivo.The yeast CKI Sic1 is a 284-amino acid IDP that binds to Cdk1 in complex with the Clb5,6 cyclins, preventing phosphorylation of G1 substrates and, therefore, entrance to the S phase. Sic1 degradation, triggered by multiple phosphorylation events, promotes cell-cycle progression. Previous experimental studies pointed out a propensity of Sic1 and its isolated domains to populate both extended and compact conformations. The present contribution provides models of the compact conformations of the Sic1 kinase-inhibitory domain (KID by all-atom molecular-dynamics simulations in explicit solvent and in the absence of interactors. The results are integrated by spectroscopic and spectrometric data. Helical IFSUs are identified, along with networks of intramolecular interactions. The results identify a group of hub residues and electrostatic interactions which are likely to be involved in the stabilization of globular states.

  14. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Science.gov (United States)

    Moscetti, Ilaria; Teveroni, Emanuela; Moretti, Fabiola; Bizzarri, Anna Rita; Cannistraro, Salvatore

    2016-01-01

    Murine double minute 2 (MDM2) and 4 (MDM4) are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD) in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. PMID:27621617

  15. MDM2–MDM4 molecular interaction investigated by atomic force spectroscopy and surface plasmon resonance

    Directory of Open Access Journals (Sweden)

    Moscetti I

    2016-08-01

    Full Text Available Ilaria Moscetti,1 Emanuela Teveroni,2,3 Fabiola Moretti,3 Anna Rita Bizzarri,1 Salvatore Cannistraro1 1Biophysics and Nanoscience Centre, Department DEB, Università della Tuscia, Viterbo, Italy; 2Department of Endocrinology and Metabolism, Università Cattolica di Roma, Roma, Italy; 3Institute of Cell Biology and Neurobiology, Consiglio Nazionale delle Ricerche (CNR, Roma, Italy Abstract: Murine double minute 2 (MDM2 and 4 (MDM4 are known as the main negative regulators of p53, a tumor suppressor. They are able to form heterodimers that are much more effective in the downregulation of p53. Therefore, the MDM2–MDM4 complex could be a target for promising therapeutic restoration of p53 function. To this aim, a deeper understanding of the molecular mechanisms underlining the heterodimerization is needed. The kinetic and thermodynamic characterization of the MDM2–MDM4 complex was performed with two complementary approaches: atomic force spectroscopy and surface plasmon resonance. Both techniques revealed an equilibrium dissociation constant (KD in the micromolar range for the MDM2–MDM4 heterodimer, similar to related complexes involved in the p53 network. Furthermore, the MDM2–MDM4 complex is characterized by a relatively high free energy, through a single energy barrier, and by a lifetime in the order of tens of seconds. New insights into the MDM2–MDM4 interaction could be highly important for developing innovative anticancer drugs focused on p53 reactivation. Keywords: MDM2, MDM4, atomic force spectroscopy, surface plasmon resonance

  16. Interaction between molecular complexes in dispersive media

    International Nuclear Information System (INIS)

    Banagas, E.A.; Manykin, E.A.

    1987-01-01

    The interaction between molecular complexes in different dispersive media with local and nonlocal screening is investigated theoretically. On the basis of results of numerical analysis on a computer, the dependence of the coupled-system spectrum and the interaction energy of the polarized modes on the characteristic parameters of the dispersive media is considered

  17. Steered Molecular Dynamics for Investigating the Interactions Between Insulin Receptor Tyrosine Kinase (IRK) and Variants of Protein Tyrosine Phosphatase 1B (PTP1B).

    Science.gov (United States)

    Nguyen, Hung; Do, Nhat; Phan, Tuyn; Pham, Tri

    2018-02-01

    The aim of this study is to use steered molecular dynamics to investigate the dissociation process between IRK and PTP1Bs for wild type and five mutants (consisting of p.D181E, p.D181A, p.Q262A, p.D181A-Y46F, and p.D181A-Q262A). The gained results are observed not only the unbinding mechanism of IRK-PTP1B complexes came from pulling force profile, number of hydrogen bonds, and interaction energy between IRK and PTP1Bs but also described PTP1B's point mutations could variably change its binding affinity towards IRK. Additionally, the binding free energy calculated by Molecular Mechanics/Poisson-Boltzmann Surface Area (MM-PBSA) is also revealed that electrostatic energy and polar solvation energy mainly made up the binding free energy of PTP1B-IRK complexes.

  18. Molecular properties of metal difluorides and their interactions with CO2 and H2O molecules: a DFT investigation.

    Science.gov (United States)

    Arokiyanathan, Agnes Lincy; Lakshmipathi, Senthilkumar

    2017-11-18

    A computational study of metal difluorides (MF 2 ; M = Ca to Zn) and their interactions with carbon dioxide and water molecules was performed. The structural parameter values obtained and the results of AIM analysis and energy decomposition analysis indicated that the Ca-F bond is weaker and less ionic than the bonds in the transition metal difluorides. A deformation density plot revealed the stablizing influence of the Jahn-Teller effect in nonlinear MF 2 molecules (e.g., where M= Sc, Ti, Cr). An anaysis of the metal K-edge peaks of the difluorides showed that shifts in the edge energy were due to the combined effects of the ionicity, effective nuclear charge, and the spin state of the metal. The interactions of CO 2 with ScF 2 (Scc3 geometry) and TiF 2 (Tic2 geometry) caused CO 2 to shift from its usual linear geometry to a bent geometry (η 2 (C=O) binding mode), while it retained its linear geometry (η 1 (O) binding mode) when it interacted with the other metal difluorides. Energy decomposition analysis showed that, among the various geometries considered, the Scc3 and Tic2 geometries possessed the highest interaction energies and orbital interaction energies. Heavier transition metal difluorides showed stronger affinities for H 2 O, whereas the lighter transition metal (Sc and Ti) difluorides preferred CO 2 . Overall, the results of this study suggest that fluorides of lighter transition metals with partially filled d orbitals (e.g., Sc and Ti) could be used for CO 2 capture under moist conditions. Graphical abstract Interaction of metal difluorides with carbon dioxide and water.

  19. Topology of molecular interaction networks

    NARCIS (Netherlands)

    Winterbach, W.; Van Mieghem, P.; Reinders, M.; Wang, H.; De Ridder, D.

    2013-01-01

    Molecular interactions are often represented as network models which have become the common language of many areas of biology. Graphs serve as convenient mathematical representations of network models and have themselves become objects of study. Their topology has been intensively researched over

  20. Investigating the molecular pathway through which L-Lactate interacts with synaptic NMDAR to modulate neuronal plasticity

    KAUST Repository

    Ibrahim, Engy

    2016-12-01

    In the brain, glycogen, the storage form of glucose, is exclusively localized in astrocytes (Magistretti and Allaman, 2015). Glycogenolysis leads to the production of L-lactate, which is shuttled to neurons for ATP production. Interestingly, L-lactate was recently shown to be not only a source of energy, but also a signaling molecule to neurons. This was demonstrated through the inhibition of L-lactate production or transport in an inhibitory avoidance paradigm, where the rodents developed amnesia. This inhibition of memory consolidation was rescued by L-lactate and not by equicaloric glucose emphasizing that L-lactate acts as a signaling molecule as well (Suzuki et al., 2011). A recent study in our laboratory suggests that the action of L-lactate takes place through a cascade of molecular events via the modulation of N-methyl-D-aspartate receptor (NMDAR) activity (Yang et al., 2014). Since NADH produced similar results to those seen with L-lactate, it was hypothesized that the action of the latter is based on altering the redox state of the cell, in particular in view of the fact that redox-sensitive sites are present on the NMDAR. However, the precise molecular mechanism underlying the apparent change in the NMDAR activity is not fully elucidated. The objective of this study is to explore those mechanisms.

  1. Using Affinity Chromatography to Investigate Novel Protein-Protein Interactions in an Undergraduate Cell and Molecular Biology Lab Course

    Science.gov (United States)

    Belanger, Kenneth D.

    2009-01-01

    Inquiry-driven lab exercises require students to think carefully about a question, carry out an investigation of that question, and critically analyze the results of their investigation. Here, we describe the implementation and assessment of an inquiry-based laboratory exercise in which students obtain and analyze novel data that contribute to our…

  2. Techniques for Investigating Molecular Toxicology of Nanomaterials.

    Science.gov (United States)

    Wang, Yanli; Li, Chenchen; Yao, Chenjie; Ding, Lin; Lei, Zhendong; Wu, Minghong

    2016-06-01

    Nanotechnology has been a rapidly developing field in the past few decades, resulting in the more and more exposure of nanomaterials to human. The increased applications of nanomaterials for industrial, commercial and life purposes, such as fillers, catalysts, semiconductors, paints, cosmetic additives and drug carriers, have caused both obvious and potential impacts on human health and environment. Nanotoxicology is used to study the safety of nanomaterials and has grown at the historic moment. Molecular toxicology is a new subdiscipline to study the interactions and impacts of materials at the molecular level. To better understand the relationship between the molecular toxicology and nanomaterials, this review summarizes the typical techniques and methods in molecular toxicology which are applied when investigating the toxicology of nanomaterials and include six categories: namely; genetic mutation detection, gene expression analysis, DNA damage detection, chromosomal aberration analysis, proteomics, and metabolomics. Each category involves several experimental techniques and methods.

  3. Atomic-scale investigation of the interactions between tetrabromobisphenol A, tetrabromobisphenol S and bovine trypsin by spectroscopies and molecular dynamics simulations

    International Nuclear Information System (INIS)

    Ding, Keke; Zhang, Huanxin; Wang, Haifei; Lv, Xuan; Pan, Liumeng; Zhang, Wenjing; Zhuang, Shulin

    2015-01-01

    Highlights: • The interaction of TBBPA/TBBPS with bovine trypsin was deciphered for the first time. • The fluorescence of bovine trypsin was quenched in a concentration-dependent mode. • TBBPA and TBBPS bind at the ANS binding site with distinct binding modes. • TBBPS has a higher binding affinity toward bovine trypsin than TBBPA. • Our in vitro and in silico approach is helpful to assess risk of TBBPA-related BFRs. - Abstract: Tetrabromobisphenol A (TBBPA) and its replacement alternative tetrabromobisphenol S (TBBPS) are used widely as brominated flame retardants (BFRs). However, the potential risk of their effects on bovine trypsin remains largely unknown. We investigated the effects of TBBPA and TBBPS to bovine trypsin by the fluorescence spectroscopy, circular dichroism and molecular dynamics (MD) simulations. They statically quenched the intrinsic fluorescence of bovine trypsin in a concentration-dependent mode and caused slight red-shifted fluorescence. The short and long fluorescence lifetime decay components of bovine trypsin were both affected, partly due to the disturbed microenvironmental changes of Trp215. The β-sheet content of bovine trypsin was significantly reduced from 82.4% to 75.7% and 76.6% by TBBPA and TBBPS, respectively, possibly impairing the physiological function of bovine trypsin. TBBPA and TBBPS bind at the 8-anilinonaphthalene-1-sulfonate (ANS) binding site with an association constant of 1.09 × 10 4 M −1 and 2.41 × 10 4 M −1 at 298 K, respectively. MD simulations revealed that van der Waals interactions and hydrogen bond interactions are dominant for TBBPA, whereas electrostatic interactions are critical for TBBPS. Our in vitro and in silico studies are beneficial to the understanding of risk assessment and future design of environmental benign BFRs.

  4. Molecular interactions in nanocellulose assembly

    Science.gov (United States)

    Nishiyama, Yoshiharu

    2017-12-01

    The contribution of hydrogen bonds and the London dispersion force in the cohesion of cellulose is discussed in the light of the structure, spectroscopic data, empirical molecular-modelling parameters and thermodynamics data of analogue molecules. The hydrogen bond of cellulose is mainly electrostatic, and the stabilization energy in cellulose for each hydrogen bond is estimated to be between 17 and 30 kJ mol-1. On average, hydroxyl groups of cellulose form hydrogen bonds comparable to those of other simple alcohols. The London dispersion interaction may be estimated from empirical attraction terms in molecular modelling by simple integration over all components. Although this interaction extends to relatively large distances in colloidal systems, the short-range interaction is dominant for the cohesion of cellulose and is equivalent to a compression of 3 GPa. Trends of heat of vaporization of alkyl alcohols and alkanes suggests a stabilization by such hydroxyl group hydrogen bonding to be of the order of 24 kJ mol-1, whereas the London dispersion force contributes about 0.41 kJ mol-1 Da-1. The simple arithmetic sum of the energy is consistent with the experimental enthalpy of sublimation of small sugars, where the main part of the cohesive energy comes from hydrogen bonds. For cellulose, because of the reduced number of hydroxyl groups, the London dispersion force provides the main contribution to intermolecular cohesion. This article is part of a discussion meeting issue `New horizons for cellulose nanotechnology'.

  5. NMR investigations of molecular dynamics

    Science.gov (United States)

    Palmer, Arthur

    2011-03-01

    NMR spectroscopy is a powerful experimental approach for characterizing protein conformational dynamics on multiple time scales. The insights obtained from NMR studies are complemented and by molecular dynamics (MD) simulations, which provide full atomistic details of protein dynamics. Homologous mesophilic (E. coli) and thermophilic (T. thermophilus) ribonuclease H (RNase H) enzymes serve to illustrate how changes in protein sequence and structure that affect conformational dynamic processes can be monitored and characterized by joint analysis of NMR spectroscopy and MD simulations. A Gly residue inserted within a putative hinge between helices B and C is conserved among thermophilic RNases H, but absent in mesophilic RNases H. Experimental spin relaxation measurements show that the dynamic properties of T. thermophilus RNase H are recapitulated in E. coli RNase H by insertion of a Gly residue between helices B and C. Additional specific intramolecular interactions that modulate backbone and sidechain dynamical properties of the Gly-rich loop and of the conserved Trp residue flanking the Gly insertion site have been identified using MD simulations and subsequently confirmed by NMR spin relaxation measurements. These results emphasize the importance of hydrogen bonds and local steric interactions in restricting conformational fluctuations, and the absence of such interactions in allowing conformational adaptation to substrate binding.

  6. Spectroscopic and structural investigation of interaction of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt with molecular iodine

    Science.gov (United States)

    Ivolgina, Victoria A.; Chernov'yants, Margarita S.

    2018-06-01

    The interest in the study of heteroaromatic thioamides which are known to exhibit antithyroid activity is stimulated by the variety and an unusual structure their complexes with molecular iodine. The directions of dithiones investigation are diversity enough, however a few works are devoted to the study them as the potential thyreostatics. The ability of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thion potassium salt to form the outer-sphere charge-transfer complex in dilute chloroform solution, coordinating 2 iodine molecules has been studied by UV-vis spectroscopy (lgβ = 7.91). The compound of the 5,5‧-disulfanediylbis(3-phenyl-1,3,4-thiadiazole-2(3H)-thione) - product of irreversible oxidation of 5-mercapto-3-phenyl-1,3,4-thiadiazole-2-thione potassium salt has been isolated and characterized by X-ray diffraction. Intermolecular interactions between sulfur atoms are observed with very short interatomic distance, shorter than sum of van der Waals radii. The contact between heterocyclic sulfur and heterocyclic nitrogen is also slightly short - 3.169 Å (0.053 Å less than vdW radii sum). This investigation constitutes a starting point for study of novel antithyroid drugs in future.

  7. Targeting the cell wall of Mycobacterium tuberculosis: a molecular modeling investigation of the interaction of imipenem and meropenem with L,D-transpeptidase 2.

    Science.gov (United States)

    Silva, José Rogério A; Bishai, William R; Govender, Thavendran; Lamichhane, Gyanu; Maguire, Glenn E M; Kruger, Hendrik G; Lameira, Jeronimo; Alves, Cláudio N

    2016-01-01

    The single crystal X-ray structure of the extracellular portion of the L,D-transpeptidase (ex-LdtMt2 - residues 120-408) enzyme was recently reported. It was observed that imipenem and meropenem inhibit activity of this enzyme, responsible for generating L,D-transpeptide linkages in the peptidoglycan layer of Mycobacterium tuberculosis. Imipenem is more active and isothermal titration calorimetry experiments revealed that meropenem is subjected to an entropy penalty upon binding to the enzyme. Herein, we report a molecular modeling approach to obtain a molecular view of the inhibitor/enzyme interactions. The average binding free energies for nine commercially available inhibitors were calculated using MM/GBSA and Solvation Interaction Energy (SIE) approaches and the calculated energies corresponded well with the available experimentally observed results. The method reproduces the same order of binding energies as experimentally observed for imipenem and meropenem. We have also demonstrated that SIE is a reasonably accurate and cost-effective free energy method, which can be used to predict carbapenem affinities for this enzyme. A theoretical explanation was offered for the experimental entropy penalty observed for meropenem, creating optimism that this computational model can serve as a potential computational model for other researchers in the field.

  8. Theoretical studies of molecular interactions

    Energy Technology Data Exchange (ETDEWEB)

    Lester, W.A. Jr. [Univ. of California, Berkeley (United States)

    1993-12-01

    This research program is directed at extending fundamental knowledge of atoms and molecules including their electronic structure, mutual interaction, collision dynamics, and interaction with radiation. The approach combines the use of ab initio methods--Hartree-Fock (HF) multiconfiguration HF, configuration interaction, and the recently developed quantum Monte Carlo (MC)--to describe electronic structure, intermolecular interactions, and other properties, with various methods of characterizing inelastic and reaction collision processes, and photodissociation dynamics. Present activity is focused on the development and application of the QMC method, surface catalyzed reactions, and reorientation cross sections.

  9. Modeling of ultrafast THz interactions in molecular crystals

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    In this paper we present a numerical study of terahertz pulses interacting with crystals of cesium iodide. We model the molecular dynamics of the cesium iodide crystals with the Density Functional Theory software CASTEP, where ultrafast terahertz pulses are implemented to the CASTEP software...... to interact with molecular crystals. We investigate the molecular dynamics of cesium iodide crystals when interacting with realistic terahertz pulses of field strengths from 0 to 50 MV/cm. We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  10. A Spectroscopic Approach to Investigate the Molecular Interactions between the Newly Approved Irreversible ErbB blocker "Afatinib" and Bovine Serum Albumin.

    Directory of Open Access Journals (Sweden)

    Amer M Alanazi

    Full Text Available The interaction of afatinib (AFB with bovine serum albumin (BSA was examined via fluorescence and UV-Vis spectroscopy. Spectrofluorimetric measurements revealed that AFB can strongly quench the BSA intrinsic fluorescence through producing a non-fluorescent complex. This quenching mechanism was thoroughly investigated with regard to the type of quenching, binding constant, number of binding locations and the fundamental thermodynamic parameters. Subsequently, the association constant of AFB with BSA was computed at three different temperatures and was found to range from 7.34 to 13.19 x10(5 L mol(-1. Thermodynamic parameters calculations demonstrated a positive ΔSƟ value with both negative ΔHϴ and ΔGϴ values for AFB-BSA complex, which in turn infers that a spontaneous binding is taking place with both electrostatic bonding and hydrophobic interactions participating in the binding of AFB and BSA. Similarly, the UV absorption spectra of AFB-BSA system were studied and confirmed the interaction. Conformational alteration of the protein upon binding to AFB was elaborated with the aid of three dimensional fluorescence measurements as well as synchronous fluorescence spectra.

  11. Interactive association between biopolymers and biofunctions in carinata seeds as energy feedstock and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation: current advanced molecular spectroscopic investigations.

    Science.gov (United States)

    Yu, Peiqiang; Xin, Hangshu; Ban, Yajing; Zhang, Xuewei

    2014-05-07

    Recent advances in biofuel and bio-oil processing technology require huge supplies of energy feedstocks for processing. Very recently, new carinata seeds have been developed as energy feedstocks for biofuel and bio-oil production. The processing results in a large amount of coproducts, which are carinata meal. To date, there is no systematic study on interactive association between biopolymers and biofunctions in carinata seed as energy feedstocks for biofuel and bioethanol processing and their processing coproducts (carinata meal). Molecular spectroscopy with synchrotron and globar sources is a rapid and noninvasive analytical technique and is able to investigate molecular structure conformation in relation to biopolymer functions and bioavailability. However, to date, these techniques are seldom used in biofuel and bioethanol processing in other research laboratories. This paper aims to provide research progress and updates with molecular spectroscopy on the energy feedstock (carinata seed) and coproducts (carinata meal) from biofuel and bioethanol processing and show how to use these molecular techniques to study the interactive association between biopolymers and biofunctions in the energy feedstocks and their coproducts (carinata meal) from biofuel and bio-oil processing before and after biodegradation.

  12. Determination of morphological features and molecular interactions ...

    African Journals Online (AJOL)

    This research focused on identifying the morphological features and molecular interactions of the Nigerian Bentonitic clays using Scanning Electron Microscope (SEM) characterisation technique. The SEM microstructure images indicated that the bentonite samples are generally moderately dispersive to dispersive with ...

  13. Atomic and Molecular Manipulation of Chemical Interactions

    National Research Council Canada - National Science Library

    Ho, Wilson

    2007-01-01

    .... In effect, the goal is to carry out chemical changes by manipulating individual atoms and molecules to induce different bonding geometry and to create new interactions with their environment. These studies provide the scientific basis for the advancement of technology in catalysis, molecular electronics, optics, chemical and biological sensing, and magnetic storage.

  14. Microbial interactions: ecology in a molecular perspective.

    Science.gov (United States)

    Braga, Raíssa Mesquita; Dourado, Manuella Nóbrega; Araújo, Welington Luiz

    2016-12-01

    The microorganism-microorganism or microorganism-host interactions are the key strategy to colonize and establish in a variety of different environments. These interactions involve all ecological aspects, including physiochemical changes, metabolite exchange, metabolite conversion, signaling, chemotaxis and genetic exchange resulting in genotype selection. In addition, the establishment in the environment depends on the species diversity, since high functional redundancy in the microbial community increases the competitive ability of the community, decreasing the possibility of an invader to establish in this environment. Therefore, these associations are the result of a co-evolution process that leads to the adaptation and specialization, allowing the occupation of different niches, by reducing biotic and abiotic stress or exchanging growth factors and signaling. Microbial interactions occur by the transference of molecular and genetic information, and many mechanisms can be involved in this exchange, such as secondary metabolites, siderophores, quorum sensing system, biofilm formation, and cellular transduction signaling, among others. The ultimate unit of interaction is the gene expression of each organism in response to an environmental (biotic or abiotic) stimulus, which is responsible for the production of molecules involved in these interactions. Therefore, in the present review, we focused on some molecular mechanisms involved in the microbial interaction, not only in microbial-host interaction, which has been exploited by other reviews, but also in the molecular strategy used by different microorganisms in the environment that can modulate the establishment and structuration of the microbial community. Copyright © 2016 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

  15. Nanotribology investigations with classical molecular dynamics

    NARCIS (Netherlands)

    Solhjoo, Soheil

    2017-01-01

    This thesis presents a number of nanotribological problems investigated by means of classical molecular dynamics (MD) simulations, within the context of the applicability of continuum mechanics contact theories at the atomic scale. Along these lines, three different themes can be recognized herein:

  16. Investigating Ebola virus pathogenicity using molecular dynamics.

    Science.gov (United States)

    Pappalardo, Morena; Collu, Francesca; Macpherson, James; Michaelis, Martin; Fraternali, Franca; Wass, Mark N

    2017-08-11

    Ebolaviruses have been known to cause deadly disease in humans for 40 years and have recently been demonstrated in West Africa to be able to cause large outbreaks. Four Ebolavirus species cause severe disease associated with high mortality in humans. Reston viruses are the only Ebolaviruses that do not cause disease in humans. Conserved amino acid changes in the Reston virus protein VP24 compared to VP24 of other Ebolaviruses have been suggested to alter VP24 binding to host cell karyopherins resulting in impaired inhibition of interferon signalling, which may explain the difference in human pathogenicity. Here we used protein structural analysis and molecular dynamics to further elucidate the interaction between VP24 and KPNA5. As a control experiment, we compared the interaction of wild-type and R137A-mutant (known to affect KPNA5 binding) Ebola virus VP24 with KPNA5. Results confirmed that the R137A mutation weakens direct VP24-KPNA5 binding and enables water molecules to penetrate at the interface. Similarly, Reston virus VP24 displayed a weaker interaction with KPNA5 than Ebola virus VP24, which is likely to reduce the ability of Reston virus VP24 to prevent host cell interferon signalling. Our results provide novel molecular detail on the interaction of Reston virus VP24 and Ebola virus VP24 with human KPNA5. The results indicate a weaker interaction of Reston virus VP24 with KPNA5 than Ebola virus VP24, which is probably associated with a decreased ability to interfere with the host cell interferon response. Hence, our study provides further evidence that VP24 is a key player in determining Ebolavirus pathogenicity.

  17. Maximum power operation of interacting molecular motors

    DEFF Research Database (Denmark)

    Golubeva, Natalia; Imparato, Alberto

    2013-01-01

    , as compared to the non-interacting system, in a wide range of biologically compatible scenarios. We furthermore consider the case where the motor-motor interaction directly affects the internal chemical cycle and investigate the effect on the system dynamics and thermodynamics.......We study the mechanical and thermodynamic properties of different traffic models for kinesin which are relevant in biological and experimental contexts. We find that motor-motor interactions play a fundamental role by enhancing the thermodynamic efficiency at maximum power of the motors...

  18. Interactive investigations into planetary interiors

    Science.gov (United States)

    Rose, I.

    2015-12-01

    Many processes in Earth science are difficult to observe or visualize due to the large timescales and lengthscales over which they operate. The dynamics of planetary mantles are particularly challenging as we cannot even look at the rocks involved. As a result, much teaching material on mantle dynamics relies on static images and cartoons, many of which are decades old. Recent improvements in computing power and technology (largely driven by game and web development) have allowed for advances in real-time physics simulations and visualizations, but these have been slow to affect Earth science education.Here I demonstrate a teaching tool for mantle convection and seismology which solves the equations for conservation of mass, momentum, and energy in real time, allowing users make changes to the simulation and immediately see the effects. The user can ask and answer questions about what happens when they add heat in one place, or take it away from another place, or increase the temperature at the base of the mantle. They can also pause the simulation, and while it is paused, create and visualize seismic waves traveling through the mantle. These allow for investigations into and discussions about plate tectonics, earthquakes, hot spot volcanism, and planetary cooling.The simulation is rendered to the screen using OpenGL, and is cross-platform. It can be run as a native application for maximum performance, but it can also be embedded in a web browser for easy deployment and portability.

  19. Investigating the interactions of the enantiomers of phenylglycine ...

    Indian Academy of Sciences (India)

    In this study, molecular dynamics simulation has been used to investigate the interactions of both chiral forms of ... about two orders of magnitude less than that in free water. Keywords. ... acids, peptides, drugs, and proteins with the surfaces of inorganic .... and energy parameters, qi and qj are the atomic point charges ...

  20. Controlling single-molecule junction conductance by molecular interactions

    Science.gov (United States)

    Kitaguchi, Y.; Habuka, S.; Okuyama, H.; Hatta, S.; Aruga, T.; Frederiksen, T.; Paulsson, M.; Ueba, H.

    2015-01-01

    For the rational design of single-molecular electronic devices, it is essential to understand environmental effects on the electronic properties of a working molecule. Here we investigate the impact of molecular interactions on the single-molecule conductance by accurately positioning individual molecules on the electrode. To achieve reproducible and precise conductivity measurements, we utilize relatively weak π-bonding between a phenoxy molecule and a STM-tip to form and cleave one contact to the molecule. The anchoring to the other electrode is kept stable using a chalcogen atom with strong bonding to a Cu(110) substrate. These non-destructive measurements permit us to investigate the variation in single-molecule conductance under different but controlled environmental conditions. Combined with density functional theory calculations, we clarify the role of the electrostatic field in the environmental effect that influences the molecular level alignment. PMID:26135251

  1. 2010 Atomic & Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Todd Martinez

    2010-07-23

    The Atomic and Molecular Interactions Gordon Conferences is justifiably recognized for its broad scope, touching on areas ranging from fundamental gas phase and gas-condensed matter collision dynamics, to laser-molecule interactions, photophysics, and unimolecular decay processes. The meeting has traditionally involved scientists engaged in fundamental research in gas and condensed phases and those who apply these concepts to systems of practical chemical and physical interest. A key tradition in this meeting is the strong mixing of theory and experiment throughout. The program for 2010 conference continues these traditions. At the 2010 AMI GRC, there will be talks in 5 broadly defined and partially overlapping areas of intermolecular interactions and chemical dynamics: (1) Photoionization and Photoelectron Dynamics; (2) Quantum Control and Molecules in Strong Fields; (3) Photochemical Dynamics; (4) Complex Molecules and Condensed Phases; and (5) Clusters and Reaction Dynamics. These areas encompass many of the most productive and exciting areas of chemical physics, including both reactive and nonreactive processes, intermolecular and intramolecular energy transfer, and photodissociation and unimolecular processes. Gas phase dynamics, van der Waals and cluster studies, laser-matter interactions and multiple potential energy surface phenomena will all be discussed.

  2. Fanconi Anemia Proteins and Their Interacting Partners: A Molecular Puzzle

    Science.gov (United States)

    Kaddar, Tagrid; Carreau, Madeleine

    2012-01-01

    In recent years, Fanconi anemia (FA) has been the subject of intense investigations, primarily in the DNA repair research field. Many discoveries have led to the notion of a canonical pathway, termed the FA pathway, where all FA proteins function sequentially in different protein complexes to repair DNA cross-link damages. Although a detailed architecture of this DNA cross-link repair pathway is emerging, the question of how a defective DNA cross-link repair process translates into the disease phenotype is unresolved. Other areas of research including oxidative metabolism, cell cycle progression, apoptosis, and transcriptional regulation have been studied in the context of FA, and some of these areas were investigated before the fervent enthusiasm in the DNA repair field. These other molecular mechanisms may also play an important role in the pathogenesis of this disease. In addition, several FA-interacting proteins have been identified with roles in these “other” nonrepair molecular functions. Thus, the goal of this paper is to revisit old ideas and to discuss protein-protein interactions related to other FA-related molecular functions to try to give the reader a wider perspective of the FA molecular puzzle. PMID:22737580

  3. Nanoscale swimmers: hydrodynamic interactions and propulsion of molecular machines

    Science.gov (United States)

    Sakaue, T.; Kapral, R.; Mikhailov, A. S.

    2010-06-01

    Molecular machines execute nearly regular cyclic conformational changes as a result of ligand binding and product release. This cyclic conformational dynamics is generally non-reciprocal so that under time reversal a different sequence of machine conformations is visited. Since such changes occur in a solvent, coupling to solvent hydrodynamic modes will generally result in self-propulsion of the molecular machine. These effects are investigated for a class of coarse grained models of protein machines consisting of a set of beads interacting through pair-wise additive potentials. Hydrodynamic effects are incorporated through a configuration-dependent mobility tensor, and expressions for the propulsion linear and angular velocities, as well as the stall force, are obtained. In the limit where conformational changes are small so that linear response theory is applicable, it is shown that propulsion is exponentially small; thus, propulsion is nonlinear phenomenon. The results are illustrated by computations on a simple model molecular machine.

  4. Atom-scale molecular interactions in lipid raft mixtures

    DEFF Research Database (Denmark)

    Niemelä, Perttu S; Hyvönen, Marja T; Vattulainen, Ilpo

    2009-01-01

    We review the relationship between molecular interactions and the properties of lipid environments. A specific focus is given on bilayers which contain sphingomyelin (SM) and sterols due to their essential role for the formation of lipid rafts. The discussion is based on recent atom-scale molecular...... dynamics simulations, complemented by extensive comparison to experimental data. The discussion is divided into four sections. The first part investigates the properties of one-component SM bilayers and compares them to bilayers with phosphatidylcholine (PC), the focus being on a detailed analysis...... examples of this issue. The third part concentrates on the specificity of intermolecular interactions in three-component mixtures of SM, PC and cholesterol (CHOL) under conditions where the concentrations of SM and CHOL are dilute with respect to that of PC. The results show how SM and CHOL favor one...

  5. Investigation of Galactosylated Low Molecular Weight Chitosan ...

    African Journals Online (AJOL)

    was coupled with low molecular weight chitosan (LMWC) using carbodiimide chemistry. .... High molecular weight chitosan (minimum 85% ..... membrane permeability of drug and mutual repulsion ... coating thickness and the lower solubility of.

  6. Interacting With Robots to Investigate the Bases of Social Interaction.

    Science.gov (United States)

    Sciutti, Alessandra; Sandini, Giulio

    2017-12-01

    Humans show a great natural ability at interacting with each other. Such efficiency in joint actions depends on a synergy between planned collaboration and emergent coordination, a subconscious mechanism based on a tight link between action execution and perception. This link supports phenomena as mutual adaptation, synchronization, and anticipation, which cut drastically the delays in the interaction and the need of complex verbal instructions and result in the establishment of joint intentions, the backbone of social interaction. From a neurophysiological perspective, this is possible, because the same neural system supporting action execution is responsible of the understanding and the anticipation of the observed action of others. Defining which human motion features allow for such emergent coordination with another agent would be crucial to establish more natural and efficient interaction paradigms with artificial devices, ranging from assistive and rehabilitative technology to companion robots. However, investigating the behavioral and neural mechanisms supporting natural interaction poses substantial problems. In particular, the unconscious processes at the basis of emergent coordination (e.g., unintentional movements or gazing) are very difficult-if not impossible-to restrain or control in a quantitative way for a human agent. Moreover, during an interaction, participants influence each other continuously in a complex way, resulting in behaviors that go beyond experimental control. In this paper, we propose robotics technology as a potential solution to this methodological problem. Robots indeed can establish an interaction with a human partner, contingently reacting to his actions without losing the controllability of the experiment or the naturalness of the interactive scenario. A robot could represent an "interactive probe" to assess the sensory and motor mechanisms underlying human-human interaction. We discuss this proposal with examples from our

  7. Molecular interactions with ice: Molecular embedding, adsorption, detection, and release

    Energy Technology Data Exchange (ETDEWEB)

    Gibson, K. D.; Langlois, Grant G.; Li, Wenxin; Sibener, S. J., E-mail: s-sibener@uchicago.edu [The James Franck Institute and Department of Chemistry, The University of Chicago, 929 E. 57th Street, Chicago, Illinois 60637 (United States); Killelea, Daniel R. [Department of Chemistry and Biochemistry, Loyola University Chicago, 1068 W. Sheridan Ave., Chicago, Illinois 60660 (United States)

    2014-11-14

    The interaction of atomic and molecular species with water and ice is of fundamental importance for chemistry. In a previous series of publications, we demonstrated that translational energy activates the embedding of Xe and Kr atoms in the near surface region of ice surfaces. In this paper, we show that inert molecular species may be absorbed in a similar fashion. We also revisit Xe embedding, and further probe the nature of the absorption into the selvedge. CF{sub 4} molecules with high translational energies (≥3 eV) were observed to embed in amorphous solid water. Just as with Xe, the initial adsorption rate is strongly activated by translational energy, but the CF{sub 4} embedding probability is much less than for Xe. In addition, a larger molecule, SF{sub 6}, did not embed at the same translational energies that both CF{sub 4} and Xe embedded. The embedding rate for a given energy thus goes in the order Xe > CF{sub 4} > SF{sub 6}. We do not have as much data for Kr, but it appears to have a rate that is between that of Xe and CF{sub 4}. Tentatively, this order suggests that for Xe and CF{sub 4}, which have similar van der Waals radii, the momentum is the key factor in determining whether the incident atom or molecule can penetrate deeply enough below the surface to embed. The more massive SF{sub 6} molecule also has a larger van der Waals radius, which appears to prevent it from stably embedding in the selvedge. We also determined that the maximum depth of embedding is less than the equivalent of four layers of hexagonal ice, while some of the atoms just below the ice surface can escape before ice desorption begins. These results show that energetic ballistic embedding in ice is a general phenomenon, and represents a significant new channel by which incident species can be trapped under conditions where they would otherwise not be bound stably as surface adsorbates. These findings have implications for many fields including environmental science, trace gas

  8. Molecular effects: interactions with chemicals and viruses

    International Nuclear Information System (INIS)

    Hanawalt, P.C.

    1980-01-01

    Research focused upon an understanding of the cellular responses to the molecular effects of ionizing radiation should be an essential program component in the Federal Strategy for Research into the Biological Effects of Ionizing Radiation. Although we know that DNA is a principal target molecule for some highly significant biological effects of ionizing radiation, we need to learn which other target substances such as membrane components may also be important. Most of the emphasis should continue to be on DNA effects and highest priority should be assigned to the identification of the complete spectrum of products produced in DNA. Once the lesions are known we can proceed to determine how these behave as blocks to replication and transcription or as modulators on the fidelity of these crucial processes. Considerable work should be done on the repair of these lesions. High priority should be given to the search for mutants in mammalian cell systems with evident defects in the processing of specific lesions. Viruses should provide important tools for the research in this area, as probes for host cell repair responses and also for the isolation of mutants. Furthermore, it is important to consider the interaction of viruses and ionizing radiation with regard to possible modulating effects on repair processes and tumorigenesis. Finally we must consider the important problem of the modification of repair responses by environmental factors

  9. Probing molecular interactions in bone biomaterials: Through molecular dynamics and Fourier transform infrared spectroscopy

    International Nuclear Information System (INIS)

    Bhowmik, Rahul; Katti, Kalpana S.; Verma, Devendra; Katti, Dinesh R.

    2007-01-01

    Polymer-hydroxyapatite (HAP) composites are widely investigated for their potential use as bone replacement materials. The molecular interactions at mineral polymer interface are known to have significant role of mechanical response of the composite system. Modeling interactions between such dissimilar molecules using molecular dynamics (MD) is an area of current interest. Molecular dynamics studies require potential function or force field parameters. Some force fields are described in literature that represents the structure of hydroxyapatite reasonably well. Yet, the applicability of these force fields for studying the interaction between dissimilar materials (such as mineral and polymer) is limited, as there is no accurate representation of polymer in these force fields. We have obtained the parameters of consistent valence force field (CVFF) for monoclinic hydroxyapatite. Validation of parameters was done by comparing the computationally obtained unit cell parameters, vibrational spectra and atomic distances with XRD and FTIR experiments. Using the obtained parameters of HAP, and available parameters of polymer (polyacrylic acid), interaction study was performed with MD simulations. The MD simulations showed that several hydrogen bonds may form between HAP and polyacrylic acid depending upon the exposed surface of HAP. Also there are some favourable planes of HAP where polyacrylic acid is most likely to attach. We have also simulated the mineralization of HAP using a 'synthetic biomineralization'. These modeling studies are supported by photoacoustic spectroscopy experiments on both porous and non porous composite samples for potential joint replacement and bone tissue engineering applications

  10. Specificity of molecular interactions in transient protein-protein interaction interfaces.

    Science.gov (United States)

    Cho, Kyu-il; Lee, KiYoung; Lee, Kwang H; Kim, Dongsup; Lee, Doheon

    2006-11-15

    In this study, we investigate what types of interactions are specific to their biological function, and what types of interactions are persistent regardless of their functional category in transient protein-protein heterocomplexes. This is the first approach to analyze protein-protein interfaces systematically at the molecular interaction level in the context of protein functions. We perform systematic analysis at the molecular interaction level using classification and feature subset selection technique prevalent in the field of pattern recognition. To represent the physicochemical properties of protein-protein interfaces, we design 18 molecular interaction types using canonical and noncanonical interactions. Then, we construct input vector using the frequency of each interaction type in protein-protein interface. We analyze the 131 interfaces of transient protein-protein heterocomplexes in PDB: 33 protease-inhibitors, 52 antibody-antigens, 46 signaling proteins including 4 cyclin dependent kinase and 26 G-protein. Using kNN classification and feature subset selection technique, we show that there are specific interaction types based on their functional category, and such interaction types are conserved through the common binding mechanism, rather than through the sequence or structure conservation. The extracted interaction types are C(alpha)-- H...O==C interaction, cation...anion interaction, amine...amine interaction, and amine...cation interaction. With these four interaction types, we achieve the classification success rate up to 83.2% with leave-one-out cross-validation at k = 15. Of these four interaction types, C(alpha)--H...O==C shows binding specificity for protease-inhibitor complexes, while cation-anion interaction is predominant in signaling complexes. The amine ... amine and amine...cation interaction give a minor contribution to the classification accuracy. When combined with these two interactions, they increase the accuracy by 3.8%. In the case of

  11. Molecular interaction of pinic acid with sulfuric acid

    DEFF Research Database (Denmark)

    Elm, Jonas; Kurtén, Theo; Bilde, Merete

    2014-01-01

    We investigate the molecular interactions between the semivolatile α-pinene oxidation product pinic acid and sulfuric acid using computational methods. The stepwise Gibbs free energies of formation have been calculated utilizing the M06-2X functional, and the stability of the clusters is evaluated...... cluster. The involvement of more than one pinic acid molecule in a single cluster is observed to lead to the formation of favorable (pinic acid)2(H2SO4) and (pinic acid)2(H2SO4)2 clusters. The identified most favorable growth paths starting from a single pinic acid molecule lead to closed structures...

  12. The independent molecular interaction sites model. Pt. 1

    International Nuclear Information System (INIS)

    Naumann, K.H.; Lippert, E.

    1981-01-01

    A new reference system for the treatment of molecular fluids within the framework of thermodynamic perturbation theory is presented. The basic ingredient of our approach is a potential transformation which allows us to view molecular liquids and gases as mixtures of formally independent molecular interaction sites (IMIS model). Some relations between out method and the RAM theory are discussed. (orig.)

  13. Molecular interactions with reference to manifestation of solvation ...

    African Journals Online (AJOL)

    The density and viscosity data were analyzed by some semi-empirical viscosity models, and the results have been discussed in terms of molecular interactions and structural effects. The excess properties were found to be either negative or positive depending on the molecular interactions and the nature of liquid mixtures.

  14. Conformation, orientation and interaction in molecular monolayers

    International Nuclear Information System (INIS)

    Superfine, R.; Huang, J.Y.; Shen, Y.R.

    1989-01-01

    Knowledge of the conformation and ordering of molecular monolayers is essential for a detailed understanding of a wide variety of surface and interfacial phenomena. Over the past several years, surface second harmonic generation (SHG) has proven to be a valuable and versatile probe of monolayer systems. Our group has recently extended the technique to infrared-visible sum frequency generation (SFG) which has unique capabilities for surface vibrational spectroscopy. Like second harmonic generation, SFG is highly surface specific with submonolayer sensitivity at all interfaces accessible by light. The orientation of individual groups within an adsorbate molecule can be deduced by a polarization analysis of the SFG signal from the vibrational modes of the groups. The authors have used SHG and SFG to study orientations and conformations of surfactant and liquid crystal (LC) monolayers and their interaction on a substrate. The interfacial properties of LC are of great interest to many researchers for both basic science understanding and practical application to LC devices. It is well known that the bulk alignment of a liquid crystal in a cell is strongly affected by the surface treatment of the cell walls. The reason behind it is not yet clear. The theoretical background and experimental arrangement of SHG and SFG have been described elsewhere. In the setup, a 30 psec. Nd:YAG mode-locked laser system together with nonlinear accessories generates a visible beam at .532μm and an infrared beam tunable about 3.4μm. Both beams are focused to a common spot of 300μm dia. The typical signal off the surface from a compact ordered alkyl chain monolayer is ∼500 photons per pulse, easily detected with a photomultiplier tube

  15. Experimental investigation on particle-wall interactions

    International Nuclear Information System (INIS)

    Zeisel, H.; Dorfner, V.

    1988-01-01

    There is still a lack in the knowledge about many physical processes in two-phase flows and therefore their mathematical description for the modelling of two-phase flows by computer simulations still needs some improvement. One required information is the physical procedure of the momentum transfer between the phases themselves, such as particle-particle or particle-fluid interactions, and between the phases and the flow boundaries, such as particle-wall or fluid-wall interactions. The interaction between the two phases can be either a 'long-range' interference or a direct contact between both. For the particle-fluid two-phase flow system the interaction can be devided in particle-fluid, particle-particle and particle-boundary interactions. In this investigation the attention is drawn to the special case of a particle-wall interaction and its 'long-range' interference effect between the wall and a small particle which approaches the wall in normal direction. (orig./GL)

  16. Molecular Contamination Investigation Facility (MCIF) Capabilities

    Science.gov (United States)

    Soules, David M.

    2013-01-01

    This facility was used to guide the development of ASTM E 1559 center dot Multiple Quartz Crystal Microbalances (QCMs), large sample and spectral effects capability center dot Several instrumented, high vacuum chamber systems are used to evaluate the molecular outgassing characteristics of materials, flight components and other sensitive surfaces. Test materials for spacecraft/instrument selection center.Test flight components for acceptable molecular outgas levels center dot Determine time/temperature vacuum bake-out requirements center. Data used to set limits for use of materials and specific components center. Provide Input Data to Contamination Transport Models -Applied to numerous flight projects over the past 20 years.

  17. Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy

    Science.gov (United States)

    2015-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy PRINCIPAL INVESTIGATOR: John F...Include area code) October 2015 Annual Report 30 Sep 2014 - 29 Sep 2015 Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy John... encephalopathy (CTE), but the underlying molecular changes remain unclear. Here, biochemical and genetic studies that deepen our understanding of the

  18. Investigation of Dendrimer-Membrane Interactions

    Science.gov (United States)

    Mecke, Almut; Hessler, Jessica; Lee, Inhan; Banaszak Holl, Mark; Orr, Bradford; Patri, Anil K.; Baker, J. R.

    2003-03-01

    Modified Polyamidoamine (PAMAM) dendrimers show great promise as targeted drug transport agents. Current research efforts point to the possibility of dramatic improvements to conventional chemotherapy by selectively delivering a therapeutic to antigen bearing tumor cells. In order to better understand the uptake mechanism of such devices into cells we are investigating dendrimer-surface adsorption and dendrimer-membrane interactions using atomic force microscopy, light scattering and computer simulations. Model systems consisting of supported DMPC lipid bilayers have shown interesting results suggesting the shape and architecture of nano-devices play an important role for their biologic activity. We are also investigating the effect of targeted drug vehicles on cells in vitro.

  19. Investigation of migrant-polymer interaction in pharmaceutical packaging material using the linear interaction energy algorithm.

    Science.gov (United States)

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2014-10-01

    The interaction between drug products and polymeric packaging materials is an important topic in the pharmaceutical industry and often associated with high costs because of the required elaborative interaction studies. Therefore, a theoretical prediction of such interactions would be beneficial. Often, material parameters such as the octanol water partition coefficient are used to predict the partitioning of migrant molecules between a solvent and a polymeric packaging material. Here, we present the investigation of the partitioning of various migrant molecules between polymers and solvents using molecular dynamics simulations for the calculation of interaction energies. Our results show that the use of a model for the interaction between the migrant and the polymer at atomistic detail can yield significantly better results when predicting the polymer solvent partitioning than a model based on the octanol water partition coefficient. © 2014 Wiley Periodicals, Inc. and the American Pharmacists Association.

  20. Molecular infection biology : interactions between microorganisms and cells

    National Research Council Canada - National Science Library

    Hacker, Jörg (Jörg Hinrich); Heesemann, Jurgen

    2002-01-01

    ... and epidemiology of infectious diseases. Investigators, specialists, clinicians, and graduate students in biology, pharmacy, and medicine will find Molecular Infection Biology an invaluable addition to their professional libraries...

  1. Molecular microenvironments: Solvent interactions with nucleic acid bases and ions

    Science.gov (United States)

    Macelroy, R. D.; Pohorille, A.

    1986-01-01

    The possibility of reconstructing plausible sequences of events in prebiotic molecular evolution is limited by the lack of fossil remains. However, with hindsight, one goal of molecular evolution was obvious: the development of molecular systems that became constituents of living systems. By understanding the interactions among molecules that are likely to have been present in the prebiotic environment, and that could have served as components in protobiotic molecular systems, plausible evolutionary sequences can be suggested. When stable aggregations of molecules form, a net decrease in free energy is observed in the system. Such changes occur when solvent molecules interact among themselves, as well as when they interact with organic species. A significant decrease in free energy, in systems of solvent and organic molecules, is due to entropy changes in the solvent. Entropy-driven interactioins played a major role in the organization of prebiotic systems, and understanding the energetics of them is essential to understanding molecular evolution.

  2. Molecular and biological interactions in colorectal cancer

    NARCIS (Netherlands)

    Heer, Pieter de

    2007-01-01

    The current thesis discusses the use of molecular and biological tumor markers to predict clinical outcome. By studying several key processes in the develepment of cancer as regulation of cell motility (non-receptor protein tyrosin adesion kinases, FAK, Src and paxillin, Apoptosis (caspase-3

  3. Molecular dynamics investigation of tracer diffusion in a simple liquid

    International Nuclear Information System (INIS)

    Ould-Kaddour, F.; Barrat, J.L.

    1991-05-01

    Extensive Molecular-Dynamics (MD) simulations have been carried out for a model trace-solvent system made up of 100 solvent molecules and 8 tracer molecules interacting through truncated Lennard-Jones potentials. The influence of the size ratio between solute and solvent, of their mass ratio and of the solvent viscosity on the diffusivity of a small tracer were investigated. Positive deviations from a Stokes-Einstein behaviour are observed, in qualitative agreement with experimental observations. It was also observed that as tracer and solvent become increasingly dissimilar, their respective dynamics becomes decoupled. We suggest that such decouplings can be interpreted by writing their mobility of the tracer as the sum of two terms, the first one arising from a coupling between tracer dynamics and hydrodynamics modes of the solvent, and the second one describing jump motion in a locally nearly frozen environment. (author). 17 refs, 4 figs, 6 tabs

  4. Probing gas-surface interactions with a molecular beam

    International Nuclear Information System (INIS)

    Spruit, M.E.M.

    1988-01-01

    The dynamics of direct scattering, trapping and sticking in molecular beam scattering is probed. The O 2 /Ag interaction was chosen, using the close-packed (111) plane of Ag as target surface. 170 refs.; 22 figs.; 3 tabs

  5. Tick-Pathogen Ensembles: Do Molecular Interactions Lead Ecological Innovation?

    Czech Academy of Sciences Publication Activity Database

    Cabezas Cruz, Alejandro; Estrada-Peňa, A.; Rego, Ryan O. M.; de la Fuente, J.

    2017-01-01

    Roč. 7, 13 March (2017), č. článku 74. ISSN 2235-2988 Institutional support: RVO:60077344 Keywords : tick-pathogen interactions * transcriptional reprogramming * epigenetics * ecological adaptation * Anaplasma phagocytophilum Subject RIV: EB - Genetics ; Molecular Biology OBOR OECD: Biochemistry and molecular biology Impact factor: 4.300, year: 2016

  6. On the strong influence of molecular interactions over large distances

    Science.gov (United States)

    Pfennig, Andreas

    2018-03-01

    Molecular-dynamics simulations of liquid water show deterministic chaos, i.e. an intentionally introduced molecular position shift of an individual molecule increases exponentially by a factor of 10 in 0.23 ps. This is a Lyaponov instability. As soon as it reaches molecular scale, the direction of the resulting shift in molecular motions is unpredictable. The influence of any individual distant particle on an observed molecule will be minute, but the effect will quickly increase to molecular scale and beyond due to this exponential growth. Consequently, any individual particle in the universe will affect the behavior of any molecule within at most 33 ps after the interaction reaches it. A larger distance of the faraway particle does not decrease the influence on an observed molecule, but the effect reaches molecular scale only some ps later. Thus in evaluating the interactions, nearby and faraway molecules have to be equally accounted for. The consequences of this quickly reacting network of interactions on universal scale are fundamental. Even in a strictly deterministic view, molecular behavior is principally unpredictable, and thus has to be regarded random. Corresponding statements apply for any particles interacting. This result leads to a fundamental rethinking of the structure of interactions of molecules and particles as well as the behavior of reality.

  7. Molecular Characterization of Macrophage-Biomaterial Interactions.

    Science.gov (United States)

    Moore, Laura Beth; Kyriakides, Themis R

    2015-01-01

    Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulation. In this review, we discuss the molecular events that contribute to macrophage activation and fusion with a focus on the role of the inflammasome, signaling pathways such as JAK/STAT and NF-κB, and the putative involvement of micro RNAs in the regulation of these processes.

  8. Interactive analysis of systems biology molecular expression data

    Directory of Open Access Journals (Sweden)

    Prabhakar Sunil

    2008-02-01

    Full Text Available Abstract Background Systems biology aims to understand biological systems on a comprehensive scale, such that the components that make up the whole are connected to one another and work through dependent interactions. Molecular correlations and comparative studies of molecular expression are crucial to establishing interdependent connections in systems biology. The existing software packages provide limited data mining capability. The user must first generate visualization data with a preferred data mining algorithm and then upload the resulting data into the visualization package for graphic visualization of molecular relations. Results Presented is a novel interactive visual data mining application, SysNet that provides an interactive environment for the analysis of high data volume molecular expression information of most any type from biological systems. It integrates interactive graphic visualization and statistical data mining into a single package. SysNet interactively presents intermolecular correlation information with circular and heatmap layouts. It is also applicable to comparative analysis of molecular expression data, such as time course data. Conclusion The SysNet program has been utilized to analyze elemental profile changes in response to an increasing concentration of iron (Fe in growth media (an ionomics dataset. This study case demonstrates that the SysNet software is an effective platform for interactive analysis of molecular expression information in systems biology.

  9. Molecular Characterization of Macrophage-Biomaterial Interactions

    OpenAIRE

    Moore, Laura Beth; Kyriakides, Themis R.

    2015-01-01

    Implantation of biomaterials in vascularized tissues elicits the sequential engagement of molecular and cellular elements that constitute the foreign body response. Initial events include the non-specific adsorption of proteins to the biomaterial surface that render it adhesive for cells such as neutrophils and macrophages. The latter undergo unique activation and in some cases undergo cell-cell fusion to form foreign body giant cells that contribute to implant damage and fibrotic encapsulati...

  10. Interaction of methotrexate with trypsin analyzed by spectroscopic and molecular modeling methods

    Science.gov (United States)

    Wang, Yanqing; Zhang, Hongmei; Cao, Jian; Zhou, Qiuhua

    2013-11-01

    Trypsin is one of important digestive enzymes that have intimate correlation with human health and illness. In this work, the interaction of trypsin with methotrexate was investigated by spectroscopic and molecular modeling methods. The results revealed that methotrexate could interact with trypsin with about one binding site. Methotrexate molecule could enter into the primary substrate-binding pocket, resulting in inhibition of trypsin activity. Furthermore, the thermodynamic analysis implied that electrostatic force, hydrogen bonding, van der Waals and hydrophobic interactions were the main interactions for stabilizing the trypsin-methotrexate system, which agreed well with the results from the molecular modeling study.

  11. DockingShop: A Tool for Interactive Molecular Docking

    Energy Technology Data Exchange (ETDEWEB)

    Lu, Ting-Cheng; Max, Nelson L.; Ding, Jinhui; Bethel, E. Wes; Crivelli, Silvia N.

    2005-04-24

    Given two independently determined molecular structures, the molecular docking problem predicts the bound association, or best fit between them, while allowing for conformational changes of the individual molecules during construction of a molecular complex. Docking Shop is an integrated environment that permits interactive molecular docking by navigating a ligand or protein to an estimated binding site of a receptor with real-time graphical feedback of scoring factors as visual guides. Our program can be used to create initial configurations for a protein docking prediction process. Its output--the structure of aprotein-ligand or protein-protein complex--may serve as an input for aprotein docking algorithm, or an optimization process. This tool provides molecular graphics interfaces for structure modeling, interactive manipulation, navigation, optimization, and dynamic visualization to aid users steer the prediction process using their biological knowledge.

  12. Molecular basis and regulation of OTULIN-LUBAC interaction

    DEFF Research Database (Denmark)

    Elliott, Paul R.; Al-Saoudi, Sofie Vincents; Marco-Casanova, Paola

    2014-01-01

    Ub. Now, we show that OTULIN binds via a conserved PUB-interacting motif (PIM) to the PUB domain of the LUBAC component HOIP. Crystal structures and nuclear magnetic resonance experiments reveal the molecular basis for the high-affinity interaction and explain why OTULIN binds the HOIP PUB domain...

  13. Cellular and molecular interaction in HIV infection: A review | Timbo ...

    African Journals Online (AJOL)

    Objective: To review the cellular and molecular interactions between HIV and the host immune system that lead to full-blown AIDS. Data Sources: Published reports on HIV/host interaction during a fifteen year period beginning from 1987. Study selection: Only those studies involving humans and non-human primates were ...

  14. Soft matter interactions at the molecular scale: interaction forces and energies between single hydrophobic model peptides.

    Science.gov (United States)

    Stock, Philipp; Utzig, Thomas; Valtiner, Markus

    2017-02-08

    In all realms of soft matter research a fundamental understanding of the structure/property relationships based on molecular interactions is crucial for developing a framework for the targeted design of soft materials. However, a molecular picture is often difficult to ascertain and yet essential for understanding the many different competing interactions at play, including entropies and cooperativities, hydration effects, and the enormous design space of soft matter. Here, we characterized for the first time the interaction between single hydrophobic molecules quantitatively using atomic force microscopy, and demonstrated that single molecular hydrophobic interaction free energies are dominated by the area of the smallest interacting hydrophobe. The interaction free energy amounts to 3-4 kT per hydrophobic unit. Also, we find that the transition state of the hydrophobic interactions is located at 3 Å with respect to the ground state, based on Bell-Evans theory. Our results provide a new path for understanding the nature of hydrophobic interactions at the single molecular scale. Our approach enables us to systematically vary hydrophobic and any other interaction type by utilizing peptide chemistry providing a strategic advancement to unravel molecular surface and soft matter interactions at the single molecular scale.

  15. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    International Nuclear Information System (INIS)

    Matsushita, Y.; Murakawa, T.; Shimamura, K.; Oishi, M.; Ohyama, T.; Kurita, N.

    2015-01-01

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA

  16. Specific interactions between DNA and regulatory protein controlled by ligand-binding: Ab initio molecular simulation

    Energy Technology Data Exchange (ETDEWEB)

    Matsushita, Y., E-mail: kurita@cs.tut.ac.jp; Murakawa, T., E-mail: kurita@cs.tut.ac.jp; Shimamura, K., E-mail: kurita@cs.tut.ac.jp; Oishi, M., E-mail: kurita@cs.tut.ac.jp; Ohyama, T., E-mail: kurita@cs.tut.ac.jp; Kurita, N., E-mail: kurita@cs.tut.ac.jp [Department of Computer Science and Engineering, Toyohashi University of Technology, Tempaku-cho, Toyohashi, Aichi, 441-8580 (Japan)

    2015-02-27

    The catabolite activator protein (CAP) is one of the regulatory proteins controlling the transcription mechanism of gene. Biochemical experiments elucidated that the complex of CAP with cyclic AMP (cAMP) is indispensable for controlling the mechanism, while previous molecular simulations for the monomer of CAP+cAMP complex revealed the specific interactions between CAP and cAMP. However, the effect of cAMP-binding to CAP on the specific interactions between CAP and DNA is not elucidated at atomic and electronic levels. We here considered the ternary complex of CAP, cAMP and DNA in solvating water molecules and investigated the specific interactions between them at atomic and electronic levels using ab initio molecular simulations based on classical molecular dynamics and ab initio fragment molecular orbital methods. The results highlight the important amino acid residues of CAP for the interactions between CAP and cAMP and between CAP and DNA.

  17. Chemical protection and sensitization to ionizing radiation:molecular investigations

    International Nuclear Information System (INIS)

    Badiello, R.

    1980-01-01

    Chemical radioprotection and radiosensitization are induced by the presence of certain chemical compounds, which reduce or enhance the effect of ionizing radiation on living organisms. Such substances are either naturally present or may be artificially introduced in the living cells. Chemical radioprotectors are interesting for possible application in the health protection of both professionally exposed workers and patients treated by radiation for diagnostic and thereapeutic purposes. Interest in chemical radiosensitization has increased recently because of its potential application in the radiotherapy of tumours. Both radioprotection and radiosensitization occur by means of complicated mechanisms, which at first correspond to very fast reactions. The mechanism of the interaction between such substances and radiation-induced biological radicals has been investigated by means of pulse radiolysis and rapid mixing techniques. Examples of the application of these techniques are given to illustrate how information has been obtained on the molecular basis of radiation chemical modi-fication at the cellular level. In particular some interactions between model systems of biological interest (DNA, DNA components, enzymes, amino acids, etc.) and sulphur-containing radioprotectors (glutathione, cysteine, etc.) and/or electroaffinic radiosensitizers, are described. (H.K.)

  18. Detailed Investigations of Interactions between Ionizing Radiation and Neutral Gases

    Energy Technology Data Exchange (ETDEWEB)

    Landers, Allen L

    2014-03-31

    We are investigating phenomena that stem from the many body dynamics associated with ionization of an atom or molecule by photon or charged particle. Our program is funded through the Department of Energy EPSCoR Laboratory Partnership Award in collaboration with Lawrence Berkeley National Laboratory. We are using variations on the well established COLTRIMS technique to measure ions and electrons ejected during these interactions. Photoionization measurements take place at the Advanced Light Source at LBNL as part of the ALS-COLTRIMS collaboration with the groups of Reinhard Dörner at Frankfurt and Ali Belkacem at LBNL. Additional experiments on charged particle impact are conducted locally at Auburn University where we are studying the dissociative molecular dynamics following interactions with either ions or electrons over a velocity range of 1 to 12 atomic units.

  19. Interaction Between New Anti-cancer Drug Syndros and CNT(6,6-6) Nanotube for Medical Applications: Geometry Optimization, Molecular Structure, Spectroscopic (NMR, UV/Vis, Excited state), FMO, MEP and HOMO-LUMO Investigation

    Science.gov (United States)

    Sheikhi, Masoome; Shahab, Siyamak; Khaleghian, Mehrnoosh; Kumar, Rakesh

    2018-03-01

    In the present work, Density Functional Theory (DFT) was first time employed to investigate the interaction between new drug (6aR,10aR)-6,6,9-trimethyl-3-pentyl-6a,7,8,10a-tetrahydrobenzo[c]chromen-1-ol (Syndros) and the CNT(6,6-6) Nanotube in the gaseous phase. The interaction effects of compounds Syndros and CNT (6,6-6) nanotube on the electronic properties, chemical shift tensors and natural charge was also determined and discussed. The electronic spectra of the Syndros and the complex CNT(6,6-6)/Syndros in the gas phase were calculated by Time Dependent Density Functional Theory (TD-DFT) for the formation of adsorption effect on maximum wavelength of the Syndros. Nucleus-Independent Chemical Shifts (NICS) calculations have also been carried out for the compound Syndors and the complex CNT(6,6-6)/Syndros and the aromaticity of the compound Syndors before and after interaction with the CNT(6,6-6) Nanotube was investigated.

  20. Developing a molecular roadmap of drug-food interactions.

    Directory of Open Access Journals (Sweden)

    Kasper Jensen

    2015-02-01

    Full Text Available Recent research has demonstrated that consumption of food -especially fruits and vegetables- can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes. Despite the recognition of such drug-food associations as an important element for successful therapeutic interventions, a systematic approach for identifying, predicting and preventing potential interactions between food and marketed or novel drugs is not yet available. The overall objective of this work was to sketch a comprehensive picture of the interference of ∼ 4,000 dietary components present in ∼1800 plant-based foods with the pharmacokinetics and pharmacodynamics processes of medicine, with the purpose of elucidating the molecular mechanisms involved. By employing a systems chemical biology approach that integrates data from the scientific literature and online databases, we gained a global view of the associations between diet and dietary molecules with drug targets, metabolic enzymes, drug transporters and carriers currently deposited in DrugBank. Moreover, we identified disease areas and drug targets that are most prone to the negative effects of drug-food interactions, showcasing a platform for making recommendations in relation to foods that should be avoided under certain medications. Lastly, by investigating the correlation of gene expression signatures of foods and drugs we were able to generate a completely novel drug-diet interactome map.

  1. Shaping distinct magnetic interactions in molecular compounds

    International Nuclear Information System (INIS)

    Filoti, George; Bartolome, Juan; Palade, Petru; Prisecaru, Ion; Valsangiacom, Cristina; Kuncser, Victor; Mindru, Ioana; Patron, Luminita

    2011-01-01

    Oxalates containing various 3d transitional elements and positive NH 4 or negative OH groups were newly synthesized. Each above-mentioned component has directly influenced the structure, the electronic or interaction properties, while some unexpected behaviors were revealed by various magnetic and Moessbauer measurements. The main magnetic parameters, the long-range anti-ferromagnetic couplings observed at very low temperature and, particularly the uncompensated moment are discussed in detail. The induced lower spin states for bivalent ions and especially the anti-parallel arrangement of the spins belonging to trivalent and bivalent iron inside the molecule are also emphasized. - Research highlights: → Nine new oxalates, with 3d elements, showing interesting characteristics were synthesized. →The oxalate units and the positive or negative groups have induced various magnetic properties. → The Moessbauer data revealed two different positions for each valence state of iron in molecule. → There is a competition of anti-ferromagnetic couplings inside the magnetic units and between them. → An overall ferri-magnetic long range ordering was demonstrated unambiguously.

  2. Investigation of nanodiamonds interactions in canine blood

    Science.gov (United States)

    WÄ sowicz, Michał; Marek, Kulka; Cićkiewicz, Maciej; Cymerman, Magdalena

    2017-02-01

    The whole blood contains red cells, white cells, and platelets suspended in plasma. In the following study we investigated an impact of nanodiamond particles on blood elements over various periods of time.The material used in the study consisted of samples taken from ten healthy canines (Canis lupus f. domestica) of various age, different blood types and both sexes. The markings were conducted by adding to the blood unmodified diamonds (SND), modified O2 (SO2) suspended in 0,9% NaCl. The blood was put under an impact of two diamond concentrations: 20μl and 100μl. The amount of abnormal cells increased with time. The percentage of echinocytes as a result of interaction with nanodiamonds in various time periods for individual specimens was scarce. In the examined microscopic image a summary was made for 100 white blood cells. Following cells were included in said group: band neutrophils, segmented neutrophils, eosinophils, basophils, lymphocytes, monocytes, lymphocytes with granulates, stimulated lymphocytes, lymphocytes with vacuoles, metamielocytes and smudge cells. The impact of the three diamond types had no clinical importance on red blood cells. After the diamonds mixed with white blood cells, atypical cells came into being, in the range of agranulocytes in stimulated form or with granulates and/or vacuoles. It is supposed that as a result of longlasting exposure a stimulation and vacuolisation takes place, because of the function of the cells.

  3. Plant-aphid interactions: molecular and ecological perspectives.

    Science.gov (United States)

    Goggin, Fiona L

    2007-08-01

    Many aphids are major agricultural pests because of their unparalleled reproductive capacity and their ability to manipulate host plant physiology. Aphid population growth and its impact on plant fitness are strongly influenced by interactions with other organisms, including plant pathogens, endophytes, aphid endosymbionts, predators, parasitoids, ants, and other herbivores. Numerous molecular and genomic resources have recently been developed to identify sources of aphid resistance in plants, as well as potentially novel targets for control in aphids. Moreover, the same model systems that are used to explore direct molecular interactions between plants and aphids can be utilized to study the ecological context in which they occur.

  4. 2004 Atomic and Molecular Interactions Gordon Research Conference

    International Nuclear Information System (INIS)

    Dr. Paul J. Dagdigian

    2004-01-01

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference

  5. 2004 Atomic and Molecular Interactions Gordon Research Conference

    Energy Technology Data Exchange (ETDEWEB)

    Dr. Paul J. Dagdigian

    2004-10-25

    The 2004 Gordon Research Conference on Atomic and Molecular Interactions was held July 11-16 at Colby-Sawyer College, New London, New Hampshire. This latest edition in a long-standing conference series featured invited talks and contributed poster papers on dynamics and intermolecular interactions in a variety of environments, ranging from the gas phase through surfaces and condensed media. A total of 90 conferees participated in the conference.

  6. Experimental investigation of shock wave - bubble interaction

    Energy Technology Data Exchange (ETDEWEB)

    Alizadeh, Mohsen

    2010-04-09

    In this work, the dynamics of laser-generated single cavitation bubbles exposed to lithotripter shock waves has been investigated experimentally. The energy of the impinging shock wave is varied in several steps. High-speed photography and pressure field measurements simultaneously with image acquisition provide the possibility of capturing the fast bubble dynamics under the effect of the shock wave impact. The pressure measurement is performed using a fiber optic probe hydrophone (FOPH) which operates based on optical diagnostics of the shock wave propagating medium. After a short introduction in chapter 1 an overview of the previous studies in chapter 2 is presented. The reported literatures include theoretical and experimental investigations of several configurations of physical problems in the field of bubble dynamics. In chapter 3 a theoretical description of propagation of a shock wave in a liquid like water has been discussed. Different kinds of reflection of a shock wave at an interface are taken into account. Undisturbed bubble dynamics as well as interaction between a planar shock wave and an initially spherical bubble are explored theoretically. Some physical parameters which are important in this issue such as the velocity of the shock-induced liquid jet, Kelvin impulse and kinetic energy are explained. The shock waves are generated in a water filled container by a focusing piezoelectric generator. The shock wave profile has a positive part with pulse duration of ∼1 μs followed by a longer tension tail (i.e. ∼3 μs). In chapter 4 high-speed images depict the propagation of a shock wave in the water filled tank. The maximum pressure is also derived for different intensity levels of the shock wave generator. The measurement is performed in the free field (i.e. in the absence of laser-generated single bubbles). In chapter 5 the interaction between lithotripter shock waves and laserinduced single cavitation bubbles is investigated experimentally. An

  7. Density functional study of molecular interactions in secondary structures of proteins.

    Science.gov (United States)

    Takano, Yu; Kusaka, Ayumi; Nakamura, Haruki

    2016-01-01

    Proteins play diverse and vital roles in biology, which are dominated by their three-dimensional structures. The three-dimensional structure of a protein determines its functions and chemical properties. Protein secondary structures, including α-helices and β-sheets, are key components of the protein architecture. Molecular interactions, in particular hydrogen bonds, play significant roles in the formation of protein secondary structures. Precise and quantitative estimations of these interactions are required to understand the principles underlying the formation of three-dimensional protein structures. In the present study, we have investigated the molecular interactions in α-helices and β-sheets, using ab initio wave function-based methods, the Hartree-Fock method (HF) and the second-order Møller-Plesset perturbation theory (MP2), density functional theory, and molecular mechanics. The characteristic interactions essential for forming the secondary structures are discussed quantitatively.

  8. JAMI: a Java library for molecular interactions and data interoperability.

    Science.gov (United States)

    Sivade Dumousseau, M; Koch, M; Shrivastava, A; Alonso-López, D; De Las Rivas, J; Del-Toro, N; Combe, C W; Meldal, B H M; Heimbach, J; Rappsilber, J; Sullivan, J; Yehudi, Y; Orchard, S

    2018-04-11

    A number of different molecular interactions data download formats now exist, designed to allow access to these valuable data by diverse user groups. These formats include the PSI-XML and MITAB standard interchange formats developed by Molecular Interaction workgroup of the HUPO-PSI in addition to other, use-specific downloads produced by other resources. The onus is currently on the user to ensure that a piece of software is capable of read/writing all necessary versions of each format. This problem may increase, as data providers strive to meet ever more sophisticated user demands and data types. A collaboration between EMBL-EBI and the University of Cambridge has produced JAMI, a single library to unify standard molecular interaction data formats such as PSI-MI XML and PSI-MITAB. The JAMI free, open-source library enables the development of molecular interaction computational tools and pipelines without the need to produce different versions of software to read different versions of the data formats. Software and tools developed on top of the JAMI framework are able to integrate and support both PSI-MI XML and PSI-MITAB. The use of JAMI avoids the requirement to chain conversions between formats in order to reach a desired output format and prevents code and unit test duplication as the code becomes more modular. JAMI's model interfaces are abstracted from the underlying format, hiding the complexity and requirements of each data format from developers using JAMI as a library.

  9. Molecular dynamics study of the silica-water-SDA interactions

    NARCIS (Netherlands)

    Szyja, B.M.; Jansen, A.P.J.; Verstraelen, T.; Santen, van R.A.

    2009-01-01

    In this paper we have applied the molecular dynamics simulations in order to analyse the role of the structure directing tetrapropylammonium ions in the aggregation process that leads to silicalite formation. We address the specific question of how the interactions between silica precursor species

  10. Modeling molecular boiling points using computed interaction energies.

    Science.gov (United States)

    Peterangelo, Stephen C; Seybold, Paul G

    2017-12-20

    The noncovalent van der Waals interactions between molecules in liquids are typically described in textbooks as occurring between the total molecular dipoles (permanent, induced, or transient) of the molecules. This notion was tested by examining the boiling points of 67 halogenated hydrocarbon liquids using quantum chemically calculated molecular dipole moments, ionization potentials, and polarizabilities obtained from semi-empirical (AM1 and PM3) and ab initio Hartree-Fock [HF 6-31G(d), HF 6-311G(d,p)], and density functional theory [B3LYP/6-311G(d,p)] methods. The calculated interaction energies and an empirical measure of hydrogen bonding were employed to model the boiling points of the halocarbons. It was found that only terms related to London dispersion energies and hydrogen bonding proved significant in the regression analyses, and the performances of the models generally improved at higher levels of quantum chemical computation. An empirical estimate for the molecular polarizabilities was also tested, and the best models for the boiling points were obtained using either this empirical polarizability itself or the polarizabilities calculated at the B3LYP/6-311G(d,p) level, along with the hydrogen-bonding parameter. The results suggest that the cohesive forces are more appropriately described as resulting from highly localized interactions rather than interactions between the global molecular dipoles.

  11. Gesture Interaction Browser-Based 3D Molecular Viewer.

    Science.gov (United States)

    Virag, Ioan; Stoicu-Tivadar, Lăcrămioara; Crişan-Vida, Mihaela

    2016-01-01

    The paper presents an open source system that allows the user to interact with a 3D molecular viewer using associated hand gestures for rotating, scaling and panning the rendered model. The novelty of this approach is that the entire application is browser-based and doesn't require installation of third party plug-ins or additional software components in order to visualize the supported chemical file formats. This kind of solution is suitable for instruction of users in less IT oriented environments, like medicine or chemistry. For rendering various molecular geometries our team used GLmol (a molecular viewer written in JavaScript). The interaction with the 3D models is made with Leap Motion controller that allows real-time tracking of the user's hand gestures. The first results confirmed that the resulting application leads to a better way of understanding various types of translational bioinformatics related problems in both biomedical research and education.

  12. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    Energy Technology Data Exchange (ETDEWEB)

    Uppulury, Karthik, E-mail: karthik.uppulury@gmail.com [Department of Chemistry, Texas Tech University, Lubbock, TX 79409 (United States); Kolomeisky, Anatoly B. [Department of Chemistry, Department of Chemical and Biomolecular Engineering, Center for Theoretical Biological Physics, Rice University, Houston, TX 77005 (United States)

    2016-12-20

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  13. Channel-facilitated molecular transport: The role of strength and spatial distribution of interactions

    International Nuclear Information System (INIS)

    Uppulury, Karthik; Kolomeisky, Anatoly B.

    2016-01-01

    Highlights: • Molecular flux strongly depends on the strength of the molecule-pore interactions. • There exists an optimal molecule-pore interaction potential for maximal flux. • Volume of interactions depends inversely on the strength for maximal flux. • Stronger interactions need more number of attractive sites for maximal flux. • Channels with few special sites need more attractive sites for higher flux. - Abstract: Molecular transport across channels and pores is critically important for multiple natural and industrial processes. Recent advances in single-molecule techniques have allowed researchers to probe translocation through nanopores with unprecedented spatial and temporal resolution. However, our understanding of the mechanisms of channel-facilitated molecular transport is still not complete. We present a theoretical approach that investigates the role of molecular interactions in the transport through channels. It is based on the discrete-state stochastic analysis that provides a fully analytical description of this complex process. It is found that a spatial distribution of the interactions strongly influences the translocation dynamics. We predict that there is the optimal distribution that leads to the maximal flux through the channel. It is also argued that the channel transport depends on the strength of the molecule-pore interactions, on the shape of interaction potentials and on the relative contributions of entrance and diffusion processes in the system. These observations are discussed using simple physical-chemical arguments.

  14. Investigation on particle-solid interactions

    International Nuclear Information System (INIS)

    Yano, Syukuro

    1988-08-01

    Basic processes in plasma-material interactions have been surveyed and reviewed. Problems concerned with carbon materials, which have been progressively used for the first wall and limiters in Tokamaks, are mainly discussed. Recent usage of carbon materials, basic properties and characteristics of carbon/graphite materials, desorption of gasses are described. As to the interactions of incident hydrogen isotope particles with graphite surface, data of trapping, depth profile, reemission, isotope exchange, and diffusion are reviewed and discussed. (author)

  15. NGLview-interactive molecular graphics for Jupyter notebooks.

    Science.gov (United States)

    Nguyen, Hai; Case, David A; Rose, Alexander S

    2018-04-01

    NGLview is a Jupyter/IPython widget to interactively view molecular structures as well as trajectories from molecular dynamics simulations. Fast and scalable molecular graphics are provided through the NGL Viewer. The widget supports showing data from the file-system, online data bases and from objects of many popular analysis libraries including mdanalysis, mdtraj, pytraj, rdkit and more. The source code is freely available under the MIT license at https://github.com/arose/nglview. Python packages are available from PyPI and bioconda. NGLview uses Python on the server-side and JavaScript on the client. The integration with Jupyter is done through the ipywidgets package. The NGL Viewer is embedded client-side to provide WebGL accelerated molecular graphics. asr.moin@gmail.com.

  16. Thermal conductivity of ZnTe investigated by molecular dynamics

    International Nuclear Information System (INIS)

    Wang Hanfu; Chu Weiguo

    2009-01-01

    The thermal conductivity of ZnTe with zinc-blende structure has been computed by equilibrium molecular dynamics method based on Green-Kubo formalism. A Tersoff's potential is adopted in the simulation to model the atomic interactions. The calculations are performed as a function of temperature up to 800 K. The calculated thermal conductivities are in agreement with the experimental values between 150 K and 300 K, while the results above the room temperature are comparable with the Slack's equation.

  17. Molecular interactions of Leucoagaricus naucinus with uranium(VI) and europium(III)

    Energy Technology Data Exchange (ETDEWEB)

    Wollenberg, Anne; Raff, Johannes [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biogeochemistry; Guenther, A. [Helmholtz Institute Freiberg for Resource Technology, Freiberg (Germany)

    2017-06-01

    With regard to a molecular understanding of the interaction of fungal mycelium with radionuclides and its possible application for precautionary radiation protection and bio-remediation, the binding mechanism of the radionuclide uranium and the metal europium, as surrogate for trivalent actinides, where investigated with different starting conditions by the living fungal cells of Leucoagaricus naucinus.

  18. Comparison of molecular dynamics and kinetic modeling of gas-surface interactions

    NARCIS (Netherlands)

    Frezzotti, A.; Gaastra - Nedea, S.V.; Markvoort, A.J.; Spijker, P.; Gibelli, L.

    2008-01-01

    The interaction of a dilute monatomic gas with a solid surface is studied byMolecular Dynamics (MD) simulations and by numerical solutions of a recently proposed kinetic model. Following previous investigations, the heat transport between parallel walls and Couette flow have been adopted as test

  19. Molecular interactions of Leucoagaricus naucinus with uranium(VI) and europium(III)

    International Nuclear Information System (INIS)

    Wollenberg, Anne; Raff, Johannes

    2017-01-01

    With regard to a molecular understanding of the interaction of fungal mycelium with radionuclides and its possible application for precautionary radiation protection and bio-remediation, the binding mechanism of the radionuclide uranium and the metal europium, as surrogate for trivalent actinides, where investigated with different starting conditions by the living fungal cells of Leucoagaricus naucinus.

  20. Lysozyme-magnesium aluminum silicate microparticles: Molecular interaction, bioactivity and release studies

    DEFF Research Database (Denmark)

    Kanjanakawinkul, Watchara; Medlicott, Natalie J.; Rades, Thomas

    2015-01-01

    The objectives of this study were to investigate the adsorption behavior of lysozyme (LSZ) onto magnesium aluminum silicate (MAS) at various pHs and to characterize the LSZ–MAS microparticles obtained from the molecular interaction between LSZ and MAS. The results showed that LSZ could be bound...

  1. Hadronic molecular states from the K anti K* interaction

    Energy Technology Data Exchange (ETDEWEB)

    Lue, Pei-Liang; He, Jun [Chinese Academy of Sciences, Theoretical Physics Division, Institute of Modern Physics, Lanzhou (China); Institute of Modern Physics of CAS and Lanzhou University, Research Center for Hadron and CSR Physics, Lanzhou (China)

    2016-12-15

    In this work, the K anti K* interaction is studied in a quasipotential Bethe-Salpeter equation approach combined with the one-boson-exchange model. With the help of the hidden-gauge Lagrangian, the exchanges of pseudoscalar mesons (π and η) and vector mesons (ρ, ω and φ) are considered to describe the K anti K* interaction. Besides the direct vector-meson exchange which can be related to the Weinberg-Tomozawa term, pseudoscalar-meson exchanges also play important roles in the mechanism of the K anti K* interaction. The poles of scattering amplitude are searched to find the molecular states produced from the K anti K* interaction. In the case of quantum number I{sup G}(J{sup PC}) = 0{sup +}(1{sup ++}), a pole is found with a reasonable cutoff, which can be related to the f{sub 1}(1285) in experiment. Another bound state with 0{sup -}(1{sup +-}) is also produced from the K anti K* interaction, which can be related to the h{sub 1}(1380). In the isovector sector, the interaction is much weaker and a bound state with 1{sup +}(1{sup +}) relevant to the b{sub 1}(1235) is produced but at a larger cutoff. Our results suggest that in the hadronic molecular state picture the f{sub 1}(1285) and b{sub 1}(1235) are the strange partners of the X(3872) and Z{sub c}(3900), respectively. (orig.)

  2. Effect of molecular interactions on retention and selectivity in reversed-phase liquid chromatography.

    Science.gov (United States)

    Szepesy, László

    2002-06-25

    The linear solvation energy relationships (LSERs) have been applied in the last years for description and prediction of retention and selectivity in reversed-phase liquid chromatography with good results. Widely different stationary phases have been compared and characterized by LSERs. In recent publications the influence of the type of the organic moderator and the composition of the mobile phase have also been described. However, the influence of the molecular properties of the solutes to be separated has never been discussed. According to the LSER model variation in retention factors (log k) with solute structure can be related to their potential for various intermolecular interactions. The retention factor is given as the sum of the terms of the LSER equation representing various types of molecular interactions. For this reason the influence of the structure and molecular properties of the solutes to be separated can also be investigated using the LSER equation. In this study we shall demonstrate how the specific molecular interactions influence chromatographic retention and selectivity. We intend to show that retention and selectivity depend on all participants of the system. In addition to the structure and properties of the stationary phase and the type and composition of the mobile phase the molecular properties of the solutes, characterized by the solvation parameters, will also influence the type and extent of the various molecular interactions governing retention and selectivity.

  3. Free-solution, label-free molecular interactions studied by back-scattering interferometry

    DEFF Research Database (Denmark)

    Bornhop, D.J.; Latham, J.C.; Kussrow, A.

    2007-01-01

    Free-solution, label-free molecular interactions were investigated with back-scattering interferometry in a simple optical train composed of a helium-neon laser, a microfluidic channel, and a position sensor. Molecular binding interactions between proteins, ions and protein, and small molecules...... and protein, were determined with high dynamic range dissociation constants (K-d spanning six decades) and unmatched sensitivity (picomolar K-d's and detection limits of 10,000s of molecules). With this technique, equilibrium dissociation constants were quantified for protein A and immunoglobulin G...

  4. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Grain yield under post anthesis high temperature stress is largely influenced by grain filling rate (GFR). To investigate molecular basis of this trait, a set of 111 recombinant inbred lines (RILs) derived from Raj 4014, a heat sensitive genotype and WH 730, heat tolerant cultivar was phenotyped during 2009-2010 and ...

  5. Immobilized enzymes: understanding enzyme - surface interactions at the molecular level.

    Science.gov (United States)

    Hoarau, Marie; Badieyan, Somayesadat; Marsh, E Neil G

    2017-11-22

    Enzymes immobilized on solid supports have important and industrial and medical applications. However, their uses are limited by the significant reductions in activity and stability that often accompany the immobilization process. Here we review recent advances in our understanding of the molecular level interactions between proteins and supporting surfaces that contribute to changes in stability and activity. This understanding has been facilitated by the application of various surface-sensitive spectroscopic techniques that allow the structure and orientation of enzymes at the solid/liquid interface to be probed, often with monolayer sensitivity. An appreciation of the molecular interactions between enzyme and surface support has allowed the surface chemistry and method of enzyme attachement to be fine-tuned such that activity and stability can be greatly enhanced. These advances suggest that a much wider variety of enzymes may eventually be amenable to immobilization as green catalysts.

  6. Fluid-structure interaction investigations for pipelines

    International Nuclear Information System (INIS)

    Altstadt, E.; Carl, H.; Weiss, R.

    2003-12-01

    In existing Nuclear Power Plants water hammers can occur in case of an inflow of sub-cooled water into pipes or other parts of the equipment, which are filled with steam or steam-water mixture. They also may appear as the consequence of fast valve closing or opening actions or of breaks in pipelines, with single phase or two-phase flow. In the latter case, shock waves in two-phase flow must be expected. In all cases, strong dynamic stresses are induced in the wall of the equipment. Further, the change of the momentum of the liquid motion and the deformation of the component due to the dynamic stresses generate high loads on the support structures of the component, in which the water hammer respectively the shock wave occurs. The influence of the fluid-structure interaction on the magnitude of the loads on pipe walls and support structures is not yet completely understood. In case of a dynamic load caused by a pressure wave, the stresses in pipe walls, especially in bends, are different from the static case. The propagating pressure wave may cause additional non-symmetric deformations which increase the equivalent stresses in comparison to the symmetric load created by a static inner pressure. On the other hand, fluid-structure interaction causes the structure to deform, which leads to a decrease of the resulting stresses. The lack of experimental data obtained at well defined geometric boundary conditions is a significant obstacle for the validation of codes which consider fluid-structure interaction. Furthermore, up to now the feedback from structural deformations to the fluid mechanics has not been fully implemented in existing calculation software codes. Therefore, at FZR a cold water hammer test facility (CWHTF) was designed and built up. (orig.)

  7. Weak Molecular Interactions in Clathrin-Mediated Endocytosis

    Directory of Open Access Journals (Sweden)

    Sarah M. Smith

    2017-11-01

    Full Text Available Clathrin-mediated endocytosis is a process by which specific molecules are internalized from the cell periphery for delivery to early endosomes. The key stages in this step-wise process, from the starting point of cargo recognition, to the later stage of assembly of the clathrin coat, are dependent on weak interactions between a large network of proteins. This review discusses the structural and functional data that have improved our knowledge and understanding of the main weak molecular interactions implicated in clathrin-mediated endocytosis, with a particular focus on the two key proteins: AP2 and clathrin.

  8. Investigations of interactions mediated by neutral currents

    International Nuclear Information System (INIS)

    Witek, M.

    2007-03-01

    The report is devoted to four-fermion interactions mediated by the neutral currents. The results from the second phase of LEP are presented, when the production of two massive bosons was possible with the increased energy of the e + e - collisions. It enabled for a direct test of nonabelian structure of the electroweak theory. The results concern the four-fermion production of the pairs of the ZZ bosons, single Z and Zγ * production as well as search for anomalous gauge bosons couplings. The large part of the report is devoted to experimental techniques, physics analyses and discussion of results. (author)

  9. Numerical Investigation of Ultrafast interaction between THz Fields and Crystalline Materials

    DEFF Research Database (Denmark)

    Pedersen, Pernille Klarskov; Clark, Stewart J.; Jepsen, Peter Uhd

    2014-01-01

    We present a quantum - mechanical molecular dynamics investigation of the interaction between strong single - cyc le THz pulses and ionic crystals . We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm.......We present a quantum - mechanical molecular dynamics investigation of the interaction between strong single - cyc le THz pulses and ionic crystals . We find nonlinearities in the response of the CsI crystals at field strengths higher than 10 MV/cm....

  10. Molecular Analysis of AFP and HSA Interactions with PTEN Protein

    Directory of Open Access Journals (Sweden)

    Mingyue Zhu

    2015-01-01

    Full Text Available Human cytoplasmic alpha-fetoprotein (AFP has been classified as a member of the albuminoid gene family. The protein sequence of AFP has significant homology to that of human serum albumin (HSA, but its biological characteristics are vastly different from HSA. The AFP functions as a regulator in the phosphatidylinositol 3-kinase (PI3K/protein kinase B (AKT pathway, but HSA plays a key role as a transport protein. To probe their molecular mechanisms, we have applied colocalization, coimmunoprecipitation (co-IP, and molecular docking approaches to analyze the differences between AFP and HSA. The data from colocalization and co-IP displayed a strong interaction between AFP and PTEN (phosphatase and tensin homolog, demonstrating that AFP did bind to PTEN, but HSA did not. The molecular docking study further showed that the AFP domains I and III could contact with PTEN. In silicon substitutions of AFP binding site residues at position 490M/K and 105L/R corresponding to residues K490 and R105 in HSA resulted in steric clashes with PTEN residues R150 and K46, respectively. These steric clashes may explain the reason why HSA cannot bind to PTEN. Ultimately, the experimental results and the molecular modeling data from the interactions of AFP and HSA with PTEN will help us to identify targets for designing drugs and vaccines against human hepatocellular carcinoma.

  11. Investigation of pollutant gases with molecular absorption spectroscopy

    International Nuclear Information System (INIS)

    Izairi, N; Ajredini, F.; Shehabi, M.

    2011-01-01

    This paper contains the molecular absorption spectroscopic investigation on environmental pollution by many pollutants. For this purpose a laser absorption spectroscopy at 630 nm wavelength has been applied to excite the molecular spectra in order to identify the presence of main gas pollutants. The following was the experimental procedure. Preliminary the presence of pollutants was identified. The gas champions were taken in live environment, in Tetovo streets where cars moved, and in some points in Tetovo suburbia, during different periods of the day. A special civet, part of the apparatus, has been filled by environmental air, and latter, put into the apparatus. A laser beam pulse passes throughout absorbing gas medium in the civet to excite the gas, and the absorbing spectra were automatically registered. The molecular band spectra registration has been performed by an FT-IR Spectrometer (Spectrum BX FT-IR Perkin Elmer). For this purpose the measurements were focused in spectral region of 2075 cm -1 to 2384 cm -1 for CO 2 and CO bands investigation. The importance of such measurements is to investigate the spectral properties of absorption spectra and molecular structure, and for monitoring the environmental pollution. (Author)

  12. Probing Molecular Insights into Zika Virus–Host Interactions

    Directory of Open Access Journals (Sweden)

    Ina Lee

    2018-05-01

    Full Text Available The recent Zika virus (ZIKV outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain–Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1 what virologic factors are involved in the ZIKV-associated human diseases; (2 which ZIKV protein(s contributes to the enhanced viral pathogenicity; and (3 how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV–host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV–host Interactions.

  13. Probing Molecular Insights into Zika Virus–Host Interactions

    Science.gov (United States)

    Lee, Ina; Li, Ge; Wang, Shusheng; Desprès, Philippe; Zhao, Richard Y.

    2018-01-01

    The recent Zika virus (ZIKV) outbreak in the Americas surprised all of us because of its rapid spread and association with neurologic disorders including fetal microcephaly, brain and ocular anomalies, and Guillain–Barré syndrome. In response to this global health crisis, unprecedented and world-wide efforts are taking place to study the ZIKV-related human diseases. Much has been learned about this virus in the areas of epidemiology, genetic diversity, protein structures, and clinical manifestations, such as consequences of ZIKV infection on fetal brain development. However, progress on understanding the molecular mechanism underlying ZIKV-associated neurologic disorders remains elusive. To date, we still lack a good understanding of; (1) what virologic factors are involved in the ZIKV-associated human diseases; (2) which ZIKV protein(s) contributes to the enhanced viral pathogenicity; and (3) how do the newly adapted and pandemic ZIKV strains alter their interactions with the host cells leading to neurologic defects? The goal of this review is to explore the molecular insights into the ZIKV–host interactions with an emphasis on host cell receptor usage for viral entry, cell innate immunity to ZIKV, and the ability of ZIKV to subvert antiviral responses and to cause cytopathic effects. We hope this literature review will inspire additional molecular studies focusing on ZIKV–host Interactions. PMID:29724036

  14. Investigation of beryllium/steam interaction

    Energy Technology Data Exchange (ETDEWEB)

    Chekhonadskikh, A.M.; Vurim, A.D.; Vasilyev, Yu.S.; Pivovarov, O.S. [Inst. of Atomic Energy National Nuclear Center of the Republic of Kazakstan Semipalatinsk (Kazakhstan); Shestakov, V.P.; Tazhibayeva, I.L.

    1998-01-01

    In this report program on investigations of beryllium emissivity and transient processes on overheated beryllium surface attacked by water steam to be carried out in IAE NNC RK within Task S81 TT 2096-07-16 FR. The experimental facility design is elaborated in this Report. (author)

  15. Investigation of molybdenum pentachloride interaction with chlorine

    International Nuclear Information System (INIS)

    Salyulev, A.B.; Vovkotrub, Eh.G.; Strekalovskij, V.N.

    1993-01-01

    In Raman spectra of molybdenum pentachloride solutions in liquid chlorine lines were recorded in case of 397, 312, 410, 217 and 180 cm - 1 vibrations of ν 1 (A 1 '), ν 2 (A 1 '), ν 5 (E'), ν 6 (E') and ν 8 (E'') monomer (symmetry D 3h ) molecules of MoCl 5 . Interaction of molten molybdenum pentachloride with chlorine at increased (up to 6 MPa) pressures of Cl 2 was studied. In Raman spectra of its vapour distillation in liquid chlorine alongside with MoCl 5 lines appearance of new lines at 363 and 272 cm -1 , similar in their frequency to the ones calculated for the vibrations ν 1 (A 1g ) and ν 2 (E g ) of MoCl 6 molecules (symmetry O h ), was observed

  16. Proceedings of 4 conference on hyperfine interaction spectroscopic investigations

    International Nuclear Information System (INIS)

    Shpinel', V.S.

    1992-01-01

    Results of theoretical and experimental investigations on nuclear-spectroscopy of hyperfine interactions are presented. Possibility of the data use for technological and materials sceince problems is demonstrated

  17. Comparison of biomolecules on the basis of Molecular Interaction Potentials

    Directory of Open Access Journals (Sweden)

    Rodrigo Jordi

    2002-01-01

    Full Text Available Molecular Interaction Potentials (MIP are frequently used for the comparison of series of compounds displaying related biological behaviors. These potentials are interaction energies between the considered compounds and relevant probes. The interaction energies are computed in the nodes of grids defined around the compounds. There is a need of detailed and objective comparative analyses of MIP distributions in the framework of structure-activity studies. On the other hand, MIP-based studies do not have to be restricted to series of small ligands, since such studies present also interesting possibilities for the analysis and comparison of biological macromolecules. Such analyses can benefit from the application of new methods and computational approaches. The new software MIPSim (Molecular Interaction Potentials Similarity analysis has recently been introduced with the purpose of analyzing and comparing MIP distributions of series of biomolecules. This program is transparently integrated with other programs, like GAMESS or GRID, which can be used for the computation of the potentials to be analyzed or compared. MIPSim incorporates several definitions of similarity coefficients, and is capable of combining several similarity measures into a single one. On the other hand, MIPSim can perform automatic explorations of the maximum similarity alignments between pairs of molecules.

  18. Molecular electrostatics for probing lone pair-π interactions.

    Science.gov (United States)

    Mohan, Neetha; Suresh, Cherumuttathu H; Kumar, Anmol; Gadre, Shridhar R

    2013-11-14

    An electrostatics-based approach has been proposed for probing the weak interactions between lone pair containing molecules and π deficient molecular systems. For electron-rich molecules, the negative minima in molecular electrostatic potential (MESP) topography give the location of electron localization and the MESP value at the minimum (Vmin) quantifies the electron-rich character of that region. Interactive behavior of a lone pair bearing molecule with electron deficient π-systems, such as hexafluorobenzene, 1,3,5-trinitrobenzene, 2,4,6-trifluoro-1,3,5-triazine and 1,2,4,5-tetracyanobenzene explored within DFT brings out good correlation of the lone pair-π interaction energy (E(int)) with the Vmin value of the electron-rich system. Such interaction is found to be portrayed well with the Electrostatic Potential for Intermolecular Complexation (EPIC) model. On the basis of the precise location of MESP minimum, a prediction for the orientation of a lone pair bearing molecule with an electron deficient π-system is possible in the majority of the cases studied.

  19. Molecular interaction of PCB153 to human serum albumin: Insights from spectroscopic and molecular modeling studies

    Energy Technology Data Exchange (ETDEWEB)

    Han, Chao; Fang, Senbiao; Cao, Huiming; Lu, Yan; Ma, Yaqiong [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Wei, Dongfeng [Institute of Basic Research in Clinical Medicine, China Academy of Chinese Medical Sciences, Beijing 100700 (China); Xie, Xiaoyun [College of Earth and Environmental Science, Lanzhou University, Lanzhou 730000 (China); Liu, Xiaohua [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Li, Xin [College of Food and Bioengineering, Henan University of Science and Technology, Luoyang 471003 (China); Fei, Dongqing [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China); Zhao, Chunyan, E-mail: zhaochy07@lzu.edu.cn [School of Pharmacy, Lanzhou University, Lanzhou 730000 (China)

    2013-03-15

    Highlights: ► We identify the binding mode of PCB153 to human serum albumin (HSA). ► Spectroscopic and molecular modeling results reveal that PCB153 binds at the site II. ► The interaction is mainly governed by hydrophobic and hydrogen bond forces. ► The work helps to probe transporting, distribution and toxicity effect of PCBs. -- Abstract: Polychlorinated biphenyls (PCBs) possessed much potential hazard to environment because of its chemical stability and biological toxicity. Here, we identified the binding mode of a representative compound, PCB153, to human serum albumin (HSA) using fluorescence and molecular dynamics simulation methods. The fluorescence study showed that the intrinsic fluorescence of HSA was quenched by addition of PCB153 through a static quenching mechanism. The thermodynamic analysis proved the binding behavior was mainly governed by hydrophobic force. Furthermore, as evidenced by site marker displacement experiments using two probe compounds, it revealed that PCB153 acted exactly on subdomain IIIA (site II) of HSA. On the other hand, the molecular dynamics studies as well as free energy calculations made another important contribution to understand the conformational changes of HSA and the stability of HSA-PCB153 system. Molecular docking revealed PCB153 can bind in a large hydrophobic activity of subdomain IIIA by the hydrophobic interaction and hydrogen bond interactions between chlorine atoms and residue ASN391. The present work provided reasonable models helping us further understand the transporting, distribution and toxicity effect of PCBs when it spread into human blood serum.

  20. Application of proteomics to investigate barley-Fusarium graminearum interaction

    OpenAIRE

    Yang, Fen; Finnie, Christine; Jacobsen, Susanne

    2011-01-01

    Due to the great loss of barley grain yield and quality in addition to mycotoxins contamination caused by Fusarium head blight (FHB), it is essential to understand the molecular interaction between barley and Fusarium graminearum, one of the primary Fusarium species causing FHB, in order to control the disease. Due to the advantages of gel-based proteomics that differentially expressed proteins involved in the interaction can be directly detected by comparing protein profiles displayed on 2-D...

  1. Investigation of the ion beryllium surface interaction

    International Nuclear Information System (INIS)

    Guseva, M.I.; Birukov, A.Yu.; Gureev, V.M.

    1995-01-01

    The self -sputtering yield of the Be was measured. The energy dependence of the Be self-sputtering yield agrees well with that calculated by W. Eckstein et. al. Below 770 K the self-sputtering yield is temperature independent; at T irr .> 870 K it increases sharply. Hot-pressed samples at 370 K were implanted with monoenergetic 5 keV hydrogen ions and with a stationary plasma (flux power ∼ 5 MW/m 2 ). The investigation of hydrogen behavior in beryllium shows that at low doses hydrogen is solved, but at doses ≥ 5x10 22 m -2 the bubbles and channels are formed. It results in hydrogen profile shift to the surface and decrease of its concentration. The sputtering results in further concentration decrease at doses > 10 25 m -2

  2. Investigation of uranium molecular species using laser ablation

    Energy Technology Data Exchange (ETDEWEB)

    Curreli, Davide [Univ. of Illinois, Urbana, IL (United States). Dept. of Nuclear, Plasma, and Radiological Engineering

    2017-07-12

    The goal of this project is to investigate the dynamic evolution of uranium oxide (UOx) molecular species in a rapidly cooling low-temperature plasma using a coupled experimental and modeling approach. Our purpose is to develop quantitative constraints on the UOx phase chemistry under physical conditions similar to that of a nuclear fireball at the time of debris condensation. This work is motivated by a need to better understand the factors controlling uranium chemical fractionation in post-detonation nuclear debris.

  3. Comprehensive characterization of molecular interactions based on nanomechanics.

    Directory of Open Access Journals (Sweden)

    Murali Krishna Ghatkesar

    Full Text Available Molecular interaction is a key concept in our understanding of the biological mechanisms of life. Two physical properties change when one molecular partner binds to another. Firstly, the masses combine and secondly, the structure of at least one binding partner is altered, mechanically transducing the binding into subsequent biological reactions. Here we present a nanomechanical micro-array technique for bio-medical research, which not only monitors the binding of effector molecules to their target but also the subsequent effect on a biological system in vitro. This label-free and real-time method directly and simultaneously tracks mass and nanomechanical changes at the sensor interface using micro-cantilever technology. To prove the concept we measured lipid vesicle (approximately 748*10(6 Da adsorption on the sensor interface followed by subsequent binding of the bee venom peptide melittin (2840 Da to the vesicles. The results show the high dynamic range of the instrument and that measuring the mass and structural changes simultaneously allow a comprehensive discussion of molecular interactions.

  4. Depletion interactions in two-dimensional colloid-polymer mixtures: molecular dynamics simulations

    International Nuclear Information System (INIS)

    Kim, Soon-Chul; Seong, Baek-Seok; Suh, Soong-Hyuck

    2009-01-01

    The depletion interactions acting between two hard colloids immersed in a bath of polymers, in which the interaction potentials include the soft repulsion/attraction, are extensively studied by using the molecular dynamics simulations. The collision frequencies and collision angle distributions for both incidental and reflection conditions are computed to study the dynamic properties of the colloidal mixtures. The depletion effect induced by the polymer-polymer and colloid-polymer interactions are investigated as well as the size ratio of the colloid and polymer. The simulated results show that the strong depletion interaction between two hard colloids appears for the highly asymmetric hard-disc mixtures. The attractive depletion force at contact becomes deeper and the repulsive barrier becomes wider as the asymmetry in size ratio increases. The strong polymer-polymer attraction leads to the purely attractive depletion interaction between two hard colloids, whereas the purely repulsive depletion interaction is induced by the strong colloid-polymer attraction.

  5. Probing Interactions in Complex Molecular Systems through Ordered Assembly

    International Nuclear Information System (INIS)

    De Yoreo, J.J.; Bartelt, M.C.; Orme, C.A.; Villacampa, A.; Weeks, B.L.; Miller, A.E.

    2002-01-01

    Emerging from the machinery of epitaxial science and chemical synthesis, is a growing emphasis on development of self-organized systems of complex molecular species. The nature of self-organization in these systems spans the continuum from simple crystallization of large molecules such as dendrimers and proteins, to assembly into large organized networks of nanometer-scale structures such as quantum dots or nanoparticles. In truth, self-organization in complex molecular systems has always been a central feature of many scientific disciplines including fields as diverse as structural biology, polymer science and geochemistry. But over the past decade, changes in those fields have often been marked by the degree to which researchers are using molecular-scale approaches to understand the hierarchy of structures and processes driven by this ordered assembly. At the same time, physical scientists have begun to use their knowledge of simple atomic and molecular systems to fabricate synthetic self-organized systems. This increasing activity in the field of self-organization is testament to the success of the physical and chemical sciences in building a detailed understanding of crystallization and epitaxy in simple atomic and molecular systems, one that is soundly rooted in thermodynamics and chemical kinetics. One of the fundamental challenges of chemistry and materials science in the coming decades is to develop a similarly well-founded physical understanding of assembly processes in complex molecular systems. Over the past five years, we have successfully used in situ atomic force microscopy (AFM) to investigate the physical controls on single crystal epitaxy from solutions for a wide range of molecular species. More recently, we have combined this method with grazing incidence X-ray diffraction and kinetic Monte Carlo modeling in order to relate morphology to surface atomic structure and processes. The purpose of this proposal was to extend this approach to assemblies

  6. Ultrasonic Studies of Molecular Interactions in Organic Binary Liquid Mixtures

    Directory of Open Access Journals (Sweden)

    S. Thirumaran

    2010-01-01

    Full Text Available The ultrasonic velocity, density and viscosity have been measured for the mixtures of 1-alkanols such as 1-propanol and 1-butanol with N-N dimethylformamide (DMF at 303 K. The experimental data have been used to calculate the acoustical parameters namely adiabatic compressibility (β, free length (Lf, free volume (Vf and internal pressure (πi. The excess values of the above parameters are also evaluated and discussed in the light of molecular interaction existing in the mixtures. It is obvious that there is a formation of hydrogen bonding between DMF and 1-alkanols. Further, the addition of DMF causes dissociation of hydrogen bonded structure of 1-alkanols. The evaluated excess values confirm that the molecular association is more pronounced in system-II comparing to the system-I.

  7. VPAC receptors: structure, molecular pharmacology and interaction with accessory proteins.

    Science.gov (United States)

    Couvineau, Alain; Laburthe, Marc

    2012-05-01

    The vasoactive intestinal peptide (VIP) is a neuropeptide with wide distribution in both central and peripheral nervous systems, where it plays important regulatory role in many physiological processes. VIP displays a large biological functions including regulation of exocrine secretions, hormone release, fetal development, immune responses, etc. VIP appears to exert beneficial effect in neuro-degenerative and inflammatory diseases. The mechanism of action of VIP implicates two subtypes of receptors (VPAC1 and VPAC2), which are members of class B receptors belonging to the super-family of GPCR. This article reviews the current knowledge regarding the structure and molecular pharmacology of VPAC receptors. The structure-function relationship of VPAC1 receptor has been extensively studied, allowing to understand the molecular basis for receptor affinity, specificity, desensitization and coupling to adenylyl cyclase. Those studies have clearly demonstrated the crucial role of the N-terminal ectodomain (N-ted) of VPAC1 receptor in VIP recognition. By using different approaches including directed mutagenesis, photoaffinity labelling, NMR, molecular modelling and molecular dynamic simulation, it has been shown that the VIP molecule interacts with the N-ted of VPAC1 receptor, which is itself structured as a 'Sushi' domain. VPAC1 receptor also interacts with a few accessory proteins that play a role in cell signalling of receptors. Recent advances in the structural characterization of VPAC receptor and more generally of class B GPCRs will lead to the design of new molecules, which could have considerable interest for the treatment of inflammatory and neuro-degenerative diseases. © 2011 The Authors. British Journal of Pharmacology © 2011 The British Pharmacological Society.

  8. Coulomb interactions via local dynamics: a molecular-dynamics algorithm

    International Nuclear Information System (INIS)

    Pasichnyk, Igor; Duenweg, Burkhard

    2004-01-01

    We derive and describe in detail a recently proposed method for obtaining Coulomb interactions as the potential of mean force between charges which are dynamically coupled to a local electromagnetic field. We focus on the molecular dynamics version of the method and show that it is intimately related to the Car-Parrinello approach, while being equivalent to solving Maxwell's equations with a freely adjustable speed of light. Unphysical self-energies arise as a result of the lattice interpolation of charges, and are corrected by a subtraction scheme based on the exact lattice Green function. The method can be straightforwardly parallelized using standard domain decomposition. Some preliminary benchmark results are presented

  9. Molecular analysis of interactions between dendrimers and asymmetric membranes at different transport stages.

    Science.gov (United States)

    He, XiaoCong; Qu, ZhiGuo; Xu, Feng; Lin, Min; Wang, JiuLing; Shi, XingHua; Lu, TianJian

    2014-01-07

    Studying dendrimer-biomembrane interactions is important for understanding drug and gene delivery. In this study, coarse-grained molecular dynamics simulations were performed to investigate the behaviors of polyamidoamine (PAMAM) dendrimers (G4 and G5) as they interacted with asymmetric membranes from different sides of the bilayer, thus mimicking different dendrimer transport stages. The G4 dendrimer could insert into the membrane during an equilibrated state, and the G5 dendrimer could induce pore formation in the membrane when the dendrimers interacted with the outer side (outer interactions) of an asymmetric membrane [with 10% dipalmitoyl phosphatidylserine (DPPS) in the inner leaflet of the membrane]. During the interaction with the inner side of the asymmetric membrane (inner interactions), the G4 and G5 dendrimers only adsorbed onto the membrane. As the membrane asymmetry increased (e.g., increased DPPS percentage in the inner leaflet of the membrane), the G4 and G5 dendrimers penetrated deeper into the membrane during the outer interactions and the G4 and G5 dendrimers were adsorbed more tightly onto the membrane for the inner interactions. When the DPPS content reached 50%, the G4 dendrimer could completely penetrate through the membrane from the outer side to the inner side. Our study provides molecular understanding and reference information about different dendrimer transport stages during drug and gene delivery.

  10. Experimental investigation of interactions between proteins and carbon nanomaterials

    Science.gov (United States)

    Sengupta, Bishwambhar

    The global market for nanomaterials based products is forecasted to reach $1 trillion per annum per annum for 2015. Engineered nanomaterials (ENMs) exhibit unique physicochemical properties with potential to impact diverse aspects of society through applications in electronics, renewable energy, and medicine. While the research and proposed applications of ENMs continue to grow rapidly, the health and safety of ENMs still remains a major concern to the public as well as to policy makers and funding agencies. It is now widely accepted that focused efforts are needed for identifying the list of physicochemical descriptors of ENM before they can be evaluated for nanotoxicity and biological response. This task is surprisingly challenging, as many physicochemical properties of ENMs are closely inter related and cannot be varied independently (e.g. increasing the size of an ENM can introduce additional defects). For example, varying toxic response may ensue due to different methods of nanomaterial preparation, dissimilar impurities and defects. Furthermore, the inadvertent coating of proteins on ENM surface in any biological milieu results in the formation of the so-called "protein/bio-corona" which can in turn alter the fate of ENMs and their biological response. Carbon nanomaterials (CNMs) such as carbon nanotubes, graphene, and graphene oxide are widely used ENMs. It is now known that defects in CNMs play an important role not only in materials properties but also in the determination of how materials interact at the nano-bio interface. In this regard, this work investigates the influence of defect-induced hydrophilicity on the bio-corona formation using micro Raman, photoluminescence, infrared spectroscopy, electrochemistry, and molecular dynamics simulations. Our results show that the interaction of proteins (albumin and fibrinogen) with CNMs is strongly influenced by charge transfer between them, inducing protein unfolding which enhances conformational entropy and

  11. Characterization of the Interaction between Eupatorin and Bovine Serum Albumin by Spectroscopic and Molecular Modeling Methods

    Science.gov (United States)

    Xu, Hongliang; Yao, Nannan; Xu, Haoran; Wang, Tianshi; Li, Guiying; Li, Zhengqiang

    2013-01-01

    This study investigated the interaction between eupatorin and bovine serum albumin (BSA) using ultraviolet-visible (UV-vis) absorption, fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular modeling at pH 7.4. Results of UV-vis and fluorescence spectroscopies illustrated that BSA fluorescence was quenched by eupatorin via a static quenching mechanism. Thermodynamic parameters revealed that hydrophobic and electrostatic interactions played major roles in the interaction. Moreover, the efficiency of energy transfer, and the distance between BSA and acceptor eupatorin, were calculated. The effects of eupatorin on the BSA conformation were analyzed using UV-vis, CD, and synchronous fluorescence. Finally, the binding of eupatorin to BSA was modeled using the molecular docking method. PMID:23839090

  12. DP 71 AND BETA DYSTROGLYCAN INTERACTION: A MOLECULAR MODELING APPROACH TO UNDERSTAND DUCHENNE MUSCULAR DYSTROPHY

    Directory of Open Access Journals (Sweden)

    Simanti Bhattacharya,

    2013-12-01

    Full Text Available Dp 71 is the most prevalent and widely expressed non muscle isoform of dystrophin (Dp and its mutations are associated with Duchenne muscular dystrophy, a severe form of muscular disorder. Dp 71 deviates from the canonical Dp by means of its truncated N terminal which also has abolished certain amino acids that comprise WW domain in the canonical form. This WW domain is very crucial for Dp’s interaction with partner proteins to establish a bridge between extra cellular matrices and cellular cytoskeleton. In our current study we have employed molecular modeling technique to understand the structural architecture of the N terminal region of Dp 71 and its deviation from the canonical form. We have further extended our studies to analyze the interaction probabilities between Dp 71 and β-DG applying molecular docking. Our studies for the first time have revealed that in spite of the underlying differences in terms of amino acids and structural organization, Dp 71 can interact with β-DG with its N terminal region which shares the similar molecular surface with the canonical form of Dp. These findings have opened up a platform to investigate the molecular interactions, spatio temporal orientations of the amino acids of Dp 71 and β-DG to understand the onset of DMD in much more greater detail

  13. Molecular Insights into the Potential Toxicological Interaction of 2-Mercaptothiazoline with the Antioxidant Enzyme—Catalase

    Science.gov (United States)

    Huang, Zhenxing; Huang, Ming; Mi, Chenyu; Wang, Tao; Chen, Dong; Teng, Yue

    2016-01-01

    2-mercaptothiazoline (2-MT) is widely used in many industrial fields, but its residue is potentially harmful to the environment. In this study, to evaluate the biological toxicity of 2-MT at protein level, the interaction between 2-MT and the pivotal antioxidant enzyme—catalase (CAT) was investigated using multiple spectroscopic techniques and molecular modeling. The results indicated that the CAT fluorescence quenching caused by 2-MT should be dominated by a static quenching mechanism through formation of a 2-MT/CAT complex. Furthermore, the identifications of the binding constant, binding forces, and the number of binding sites demonstrated that 2-MT could spontaneously interact with CAT at one binding site mainly via Van der Waals’ forces and hydrogen bonding. Based on the molecular docking simulation and conformation dynamic characterization, it was found that 2-MT could bind into the junctional region of CAT subdomains and that the binding site was close to enzyme active sites, which induced secondary structural and micro-environmental changes in CAT. The experiments on 2-MT toxicity verified that 2-MT significantly inhibited CAT activity via its molecular interaction, where 2-MT concentration and exposure time both affected the inhibitory action. Therefore, the present investigation provides useful information for understanding the toxicological mechanism of 2-MT at the molecular level. PMID:27537873

  14. Magnetic effects on the solvent properties investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Moosavi, Fatemeh, E-mail: moosavibaigi@um.ac.ir; Gholizadeh, Mostafa

    2014-03-15

    This paper investigates how an external constant magnetic field in the Z-direction affects the performance of a solvent. The molecular dynamics simulation comprised common inorganic and organic solvents including water, acetone, acetonitrile, toluene, and n-hexane at the ambient temperature and pressure. A static magnetic field applied in the simulation process is able to reduce the solvent mobility in the solution in order to enhance the solvent–solute reaction. Simulation results show that the diffusivity decreases because of increasing the effective interactions. Besides, magnetic field reduces the volume of the solvent and increases the strength of the hydrogen bonds by maximizing attractive electrostatic and vdW interactions caused by changes in the radial distribution function of the solvents. Hydrogen-bonding characteristics of solvents investigated by molecular dynamics simulations were evidence for the hydrogen bonding strength of O···H that is a more efficient intermolecular hydrogen-bonding in comparison with N···H. - Highlights: • Molecular dynamics simulation technique investigates the effect of magnetic field on transport dynamics inside the solvent bulk. • External constant magnetic field influences on intermolecular interactions, thermophysics, and transport properties of the solvents. • Applying magnetic field strengthened hydrogen bond maximizes attractive electrostatic interactions, charge distribution becomes stronger, and the molecule mobility is demoted. • The low diffusivity of the solvents in the solutions increases the performance of the interactions and promotes the interactions. • On introducing a magnetic field of flux density parallel to the Z-direction, solvent acts as an obstacle to diffusion of solutes.

  15. An Investigation of Molecular Docking and Molecular Dynamic Simulation on Imidazopyridines as B-Raf Kinase Inhibitors

    Directory of Open Access Journals (Sweden)

    Huiding Xie

    2015-11-01

    Full Text Available In the recent cancer treatment, B-Raf kinase is one of key targets. Nowadays, a group of imidazopyridines as B-Raf kinase inhibitors have been reported. In order to investigate the interaction between this group of inhibitors and B-Raf kinase, molecular docking, molecular dynamic (MD simulation and binding free energy (ΔGbind calculation were performed in this work. Molecular docking was carried out to identify the key residues in the binding site, and MD simulations were performed to determine the detail binding mode. The results obtained from MD simulation reveal that the binding site is stable during the MD simulations, and some hydrogen bonds (H-bonds in MD simulations are different from H-bonds in the docking mode. Based on the obtained MD trajectories, ΔGbind was computed by using Molecular Mechanics Generalized Born Surface Area (MM-GBSA, and the obtained energies are consistent with the activities. An energetic analysis reveals that both electrostatic and van der Waals contributions are important to ΔGbind, and the unfavorable polar solvation contribution results in the instability of the inhibitor with the lowest activity. These results are expected to understand the binding between B-Raf and imidazopyridines and provide some useful information to design potential B-Raf inhibitors.

  16. Spectroscopic analysis and molecular docking of imidazole derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Thomas, Renjith; Hossain, Mossaraf; Mary, Y. Sheena; Resmi, K. S.; Armaković, Stevan; Armaković, Sanja J.; Nanda, Ashis Kumar; Ranjan, Vivek Kumar; Vijayakumar, G.; Van Alsenoy, C.

    2018-04-01

    Solvent-free synthesis pathway for obtaining two imidazole derivatives (2-chloro-1-(4-methoxyphenyl)-4,5-dimethyl-1H-imidazole (CLMPDI) and 1-(4-bromophenyl)-2-chloro-4,5-dimethyl-1H-imidazole (BPCLDI) has been reported in this work, followed by detailed experimental and computational spectroscopic characterization and reactivity study. Spectroscopic methods encompassed IR, FT-Raman and NMR techniques, with the mutual comparison of experimentally and computationally obtained results at DFT/B3LYP level of theory. Reactivity study based on DFT calculations encompassed molecular orbitals analysis, followed by calculations of molecular electrostatic potential (MEP) and average local ionization energy (ALIE) values, Fukui functions and bond dissociation energies (BDE). Additionally, the stability of title molecules in water has been investigated via molecular dynamics (MD) simulations, while interactivity with aspulvinonedimethylallyl transferase protein has been evaluated by molecular docking procedure. CLMPDI compound showed antimicrobial activity against all four bacterial strain in both gram positive and gram negative bacteria while, BPCLDI showed only in gram positive bacteria, Staphylococcus Aureus (MTCC1144). The first order hyperpolarizability of CLMPDI and BPCLDI are 20.15 and 6.10 times that of the standard NLO material urea.

  17. Molecular interactions in particular Van der Waals nanoclusters

    Energy Technology Data Exchange (ETDEWEB)

    Jungclas, Hartmut; Schmidt, Lothar [Marburg Univ. (Germany). Chemistry Dept.; Komarov, Viacheslav V.; Popova, Anna M. [Marburg Univ. (Germany). Chemistry Dept.; Lomonosov Moscow State Univ. (Russian Federation). Skobeltzin Inst. of Nuclear Physics

    2017-04-01

    A method is presented to analyse the interaction energies in a nanocluster, which is consisting of three neutral molecules bound by non-covalent long range Van der Waals forces. One of the molecules (M{sub 0}) in the nanocluster has a permanent dipole moment, whereas the two other molecules (M{sub 1} and M{sub 2}) are non-polar. Analytical expressions are obtained for the numerical calculation of the dispersion and induction energies of the molecules in the considered nanocluster. The repulsive forces at short intermolecular distances are taken into account by introduction of damping functions. Dispersion and induction energies are calculated for a nanocluster with a definite geometry, in which the polar molecule M{sub 0} is a linear hydrocarbon molecule C{sub 5}H{sub 10} and M{sub 1} and M{sub 2} are pyrene molecules. The calculations are done for fixed distances between the two pyrene molecules. The results show that the induction energies in the considered three-molecular nanocluster are comparable with the dispersion energies. Furthermore, the sum of induction energies in the substructure (M{sub 0}, M{sub 1}) of the considered nanocluster is much higher than the sum of induction energies in a two-molecular nanocluster with similar molecules (M{sub 0}, M{sub 1}) because of the absence of an electrostatic field in the latter case. This effect can be explained by the essential intermolecular induction in the three-molecular nanocluster.

  18. Molecular interactions in a surfactant-water-polyacrylamide system, according to densimetry, viscometry, conductometry, and spectroscopy data

    Science.gov (United States)

    Harutyunyan, R. S.

    2013-08-01

    Molecular interactions in a surfactant-polyacrylamide-water system are investigated. It is established that the interactions affect such physicochemical parameters of the system as viscosity, density, surface tension, conductivity, and critical micelle concentration. It is shown that in a polyacrylamide-water system, raising the polyacrylamide concentration to 0.02% causes conformational changes in its macromolecule.

  19. Characterization of Hydrophobic Interactions of Polymers with Water and Phospholipid Membranes Using Molecular Dynamics Simulations

    Science.gov (United States)

    Drenscko, Mihaela

    Polymers and lipid membranes are both essential soft materials. The structure and hydrophobicity/hydrophilicity of polymers, as well as the solvent they are embedded in, ultimately determines their size and shape. Understating the variation of shape of the polymer as well as its interactions with model biological membranes can assist in understanding the biocompatibility of the polymer itself. Computer simulations, in particular molecular dynamics, can aid in characterization of the interaction of polymers with solvent, as well as polymers with model membranes. In this thesis, molecular dynamics serve to describe polymer interactions with a solvent (water) and with a lipid membrane. To begin with, we characterize the hydrophobic collapse of single polystyrene chains in water using molecular dynamics simulations. Specifically, we calculate the potential of mean force for the collapse of a single polystyrene chain in water using metadynamics, comparing the results between all atomistic with coarse-grained molecular simulation. We next explore the scaling behavior of the collapsed globular shape at the minimum energy configuration, characterized by the radius of gyration, as a function of chain length. The exponent is close to one third, consistent with that predicted for a polymer chain in bad solvent. We also explore the scaling behavior of the Solvent Accessible Surface Area (SASA) as a function of chain length, finding a similar exponent for both all-atomistic and coarse-grained simulations. Furthermore, calculation of the local water density as a function of chain length near the minimum energy configuration suggests that intermediate chain lengths are more likely to form dewetted states, as compared to shorter or longer chain lengths. Next, in order to investigate the molecular interactions between single hydrophobic polymer chains and lipids in biological membranes and at lipid membrane/solvent interface, we perform a series of molecular dynamics simulations of

  20. Molecular dynamics simulations of interfacial interactions between small nanoparticles during diffusion-limited aggregation

    International Nuclear Information System (INIS)

    Lu, Jing; Liu, Dongmei; Yang, Xiaonan; Zhao, Ying; Liu, Haixing; Tang, Huan; Cui, Fuyi

    2015-01-01

    Graphical abstract: - Highlights: • Diffusion-limited aggregation is analyzed using molecular dynamic simulations. • The aggregation processand aggregate structure vary with particle size. • Particle-particle interaction and surface diffusion result in direct bonding. • Water-mediated interaction is responsible for the separation betweennanoparticles. - Abstract: Due to the limitations of experimental methods at the atomic level, research on the aggregation of small nanoparticles (D < 5 nm) in aqueous solutions is quite rare. The aggregation of small nanoparticles in aqueous solutions is very different than that of normal sized nanoparticles. The interfacial interactions play a dominant role in the aggregation of small nanoparticles. In this paper, molecular dynamics simulations, which can explore the microscopic behavior of nanoparticles during the diffusion-limited aggregation at an atomic level, were employed to reveal the aggregation mechanism of small nanoparticles in aqueous solutions. First, the aggregation processes and aggregate structure were depicted. Second, the particle–particle interaction and surface diffusion of nanoparticles during aggregation were investigated. Third, the water-mediated interactions during aggregation were ascertained. The results indicate that the aggregation of nanoparticle in aqueous solutions is affected by particle size. The strong particle–particle interaction and high surface diffusion result in the formation of particle–particle bonds of 2 nm TiO 2 nanoparticles, and the water-mediated interaction plays an important role in the aggregation process of 3 and 4 nm TiO 2 nanoparticles.

  1. Dynamics of relaxation to a stationary state for interacting molecular motors

    Science.gov (United States)

    Gomes, Luiza V. F.; Kolomeisky, Anatoly B.

    2018-01-01

    Motor proteins are active enzymatic molecules that drive a variety of biological processes, including transfer of genetic information, cellular transport, cell motility and muscle contraction. It is known that these biological molecular motors usually perform their cellular tasks by acting collectively, and there are interactions between individual motors that specify the overall collective behavior. One of the fundamental issues related to the collective dynamics of motor proteins is the question if they function at stationary-state conditions. To investigate this problem, we analyze a relaxation to the stationary state for the system of interacting molecular motors. Our approach utilizes a recently developed theoretical framework, which views the collective dynamics of motor proteins as a totally asymmetric simple exclusion process of interacting particles, where interactions are taken into account via a thermodynamically consistent approach. The dynamics of relaxation to the stationary state is analyzed using a domain-wall method that relies on a mean-field description, which takes into account some correlations. It is found that the system quickly relaxes for repulsive interactions, while attractive interactions always slow down reaching the stationary state. It is also predicted that for some range of parameters the fastest relaxation might be achieved for a weak repulsive interaction. Our theoretical predictions are tested with Monte Carlo computer simulations. The implications of our findings for biological systems are briefly discussed.

  2. Echinococcus-Host Interactions at Cellular and Molecular Levels.

    Science.gov (United States)

    Brehm, K; Koziol, U

    2017-01-01

    The potentially lethal zoonotic diseases alveolar and cystic echinococcosis are caused by the metacestode larval stages of the tapeworms Echinococcus multilocularis and Echinococcus granulosus, respectively. In both cases, metacestode growth and proliferation occurs within the inner organs of mammalian hosts, which is associated with complex molecular host-parasite interactions that regulate nutrient uptake by the parasite as well as metacestode persistence and development. Using in vitro cultivation systems for parasite larvae, and informed by recently released, comprehensive genome and transcriptome data for both parasites, these molecular host-parasite interactions have been subject to significant research during recent years. In this review, we discuss progress in this field, with emphasis on parasite development and proliferation. We review host-parasite interaction mechanisms that occur early during an infection, when the invading oncosphere stage undergoes a metamorphosis towards the metacestode, and outline the decisive role of parasite stem cells during this process. We also discuss special features of metacestode morphology, and how this parasite stage takes up nutrients from the host, utilizing newly evolved or expanded gene families. We comprehensively review mechanisms of host-parasite cross-communication via evolutionarily conserved signalling systems and how the parasite signalling systems might be exploited for the development of novel chemotherapeutics. Finally, we point to an urgent need for the development of functional genomic techniques in this parasite, which will be imperative for hypothesis-driven analyses into Echinococcus stem cell biology, developmental mechanisms and immunomodulatory activities, which are all highly relevant for the development of anti-infective measures. Copyright © 2017 Elsevier Ltd. All rights reserved.

  3. Molecular basis of Bcl-X(L-p53 interaction: insights from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Nagakumar Bharatham

    Full Text Available Bcl-X(L, an antiapoptotic Bcl-2 family protein, plays a central role in the regulation of the apoptotic pathway. Heterodimerization of the antiapoptotic Bcl-2 family proteins with the proapoptotic family members such as Bad, Bak, Bim and Bid is a crucial step in the apoptotic regulation. In addition to these conventional binding partners, recent evidences reveal that the Bcl-2 family proteins also interact with noncanonical binding partners such as p53. Our previous NMR studies showed that Bcl-X(L: BH3 peptide and Bcl-X(L: SN15 peptide (a peptide derived from residues S15-N29 of p53 complex structures share similar modes of bindings. To further elucidate the molecular basis of the interactions, here we have employed molecular dynamics simulations coupled with MM/PBSA approach. Bcl-X(L and other Bcl-2 family proteins have 4 hydrophobic pockets (p1-p4, which are occupied by four systematically spaced hydrophobic residues (h1-h4 of the proapoptotic Bad and Bak BH3 peptides. We observed that three conserved hydrophobic residues (F19, W23 and L26 of p53 (SN15 peptide anchor into three hydrophobic pockets (p2-p4 of Bcl-X(L in a similar manner as BH3 peptide. Our results provide insights into the novel molecular recognition by Bcl-X(L with p53.

  4. Intra-membrane molecular interactions of K+ channel proteins :

    Energy Technology Data Exchange (ETDEWEB)

    Moczydlowski, Edward G.

    2013-07-01

    Ion channel proteins regulate complex patterns of cellular electrical activity and ionic signaling. Certain K+ channels play an important role in immunological biodefense mechanisms of adaptive and innate immunity. Most ion channel proteins are oligomeric complexes with the conductive pore located at the central subunit interface. The long-term activity of many K+ channel proteins is dependent on the concentration of extracellular K+; however, the mechanism is unclear. Thus, this project focused on mechanisms underlying structural stability of tetrameric K+ channels. Using KcsA of Streptomyces lividans as a model K+ channel of known structure, the molecular basis of tetramer stability was investigated by: 1. Bioinformatic analysis of the tetramer interface. 2. Effect of two local anesthetics (lidocaine, tetracaine) on tetramer stability. 3. Molecular simulation of drug docking to the ion conduction pore. The results provide new insights regarding the structural stability of K+ channels and its possible role in cell physiology.

  5. Molecular recognition of malachite green by hemoglobin and their specific interactions: insights from in silico docking and molecular spectroscopy.

    Science.gov (United States)

    Peng, Wei; Ding, Fei; Peng, Yu-Kui; Sun, Ying

    2014-01-01

    Malachite green is an organic compound that can be widely used as a dyestuff for various materials; it has also emerged as a controversial agent in aquaculture. Since malachite green is proven to be carcinogenic and mutagenic, it may become a hazard to public health. For this reason, it is urgently required to analyze this controversial dye in more detail. In our current research, the interaction between malachite green and hemoglobin under physiological conditions was investigated by the methods of molecular modeling, fluorescence spectroscopy, circular dichroism (CD) as well as hydrophobic ANS displacement experiments. From the molecular docking, the central cavity of hemoglobin was assigned to possess high-affinity for malachite green, this result was corroborated by time-resolved fluorescence and hydrophobic ANS probe results. The recognition mechanism was found to be of static type, or rather the hemoglobin-malachite green complex formation occurred via noncovalent interactions such as π-π interactions, hydrogen bonds and hydrophobic interactions with an association constant of 10(4) M(-1). Moreover, the results also show that the spatial structure of the biopolymer was changed in the presence of malachite green with a decrease of the α-helix and increase of the β-sheet, turn and random coil suggesting protein damage, as derived from far-UV CD and three-dimensional fluorescence. Results of this work will help to further comprehend the molecular recognition of malachite green by the receptor protein and the possible toxicological profiles of other compounds, which are the metabolites and ramifications of malachite green.

  6. Investigation on the interaction of catalase with sodium lauryl sulfonate and the underlying mechanisms.

    Science.gov (United States)

    Wang, Jing; Jia, Rui; Wang, Jiaxi; Sun, Zhiqiang; Wu, Zitao; Liu, Rutao; Zong, Wansong

    2018-02-01

    As a classic type of anionic surfactants, sodium lauryl sulfonate (SLS) might change the structure and function of antioxidant enzyme catalase (CAT) through their direct interactions. However, the underlying molecular mechanism is still unknown. This study investigated the direct interaction of SLS with CAT molecule and the underlying mechanisms using multi-spectroscopic methods, isothermal titration calorimetry, and molecular docking studies. No obvious effects were observed on CAT structure and activity under low SLS concentration exposure. The particle size of CAT molecule decreased and CAT activity was slightly inhibited under high SLS concentration exposure. SLS prefers to bind to the interface of CAT mainly via van der Waals' forces and hydrogen bonds. Subsequently, SLS interacts with the amino acid residues around the heme groups of CAT via hydrophobic interactions and might inhibit CAT activity. © 2017 Wiley Periodicals, Inc.

  7. Calsyntenin-3 molecular architecture and interaction with neurexin 1α.

    Science.gov (United States)

    Lu, Zhuoyang; Wang, Yun; Chen, Fang; Tong, Huimin; Reddy, M V V V Sekhar; Luo, Lin; Seshadrinathan, Suchithra; Zhang, Lei; Holthauzen, Luis Marcelo F; Craig, Ann Marie; Ren, Gang; Rudenko, Gabby

    2014-12-12

    Calsyntenin 3 (Cstn3 or Clstn3), a recently identified synaptic organizer, promotes the development of synapses. Cstn3 localizes to the postsynaptic membrane and triggers presynaptic differentiation. Calsyntenin members play an evolutionarily conserved role in memory and learning. Cstn3 was recently shown in cell-based assays to interact with neurexin 1α (n1α), a synaptic organizer that is implicated in neuropsychiatric disease. Interaction would permit Cstn3 and n1α to form a trans-synaptic complex and promote synaptic differentiation. However, it is contentious whether Cstn3 binds n1α directly. To understand the structure and function of Cstn3, we determined its architecture by electron microscopy and delineated the interaction between Cstn3 and n1α biochemically and biophysically. We show that Cstn3 ectodomains form monomers as well as tetramers that are stabilized by disulfide bonds and Ca(2+), and both are probably flexible in solution. We show further that the extracellular domains of Cstn3 and n1α interact directly and that both Cstn3 monomers and tetramers bind n1α with nanomolar affinity. The interaction is promoted by Ca(2+) and requires minimally the LNS domain of Cstn3. Furthermore, Cstn3 uses a fundamentally different mechanism to bind n1α compared with other neurexin partners, such as the synaptic organizer neuroligin 2, because Cstn3 does not strictly require the sixth LNS domain of n1α. Our structural data suggest how Cstn3 as a synaptic organizer on the postsynaptic membrane, particularly in tetrameric form, may assemble radially symmetric trans-synaptic bridges with the presynaptic synaptic organizer n1α to recruit and spatially organize proteins into networks essential for synaptic function. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  8. Molecular dynamics investigation on adsorption layer of alcohols at the air/brine interface.

    Science.gov (United States)

    Nguyen, Cuong V; Phan, Chi M; Ang, Ha M; Nakahara, Hiromichi; Shibata, Osamu; Moroi, Yoshikiyo

    2015-01-01

    Alcohols are a significant group of surfactants which have been employed extensively in industry to improve the interfacial effects. Recently, the change in surface potential (ΔV) of two isomeric hexanols, methyl isobutyl carbinol (MIBC) and 1-hexanol, was investigated by using an ionizing (241)Am electrode. It clearly showed the opposite effects between MIBC and 1-hexanol in the interfacial zone: one enhanced the presence of cations, whereas the other enhanced the presence of anions. This study employs molecular dynamics simulation to provide new insights into the interactions between alcohol molecules and ions as well as water at the molecular level. The results qualitatively agreed with the experimental data and verified the significance of MIBC branching structure on the molecular arrangement within the interfacial zone. The results also highlighted the role of the second water layer on the interfacial properties.

  9. Molecular investigations of β-thalassemic children in Erbil governorate

    Science.gov (United States)

    Hasan, Ahmad N.; Al-Attar, Mustafa S.

    2017-09-01

    The present work studies the molecular investigation of 40 thalassemic carriers using polymerase chain reaction. Forty thalassemic carriers who were registered and treated at Erbil thalassemic center and twenty apparently healthy children have been included in the present study. Ages of both groups ranged between 1-18 years. Four primers used to detect four different beta thalassemia mutations they were codon 8/9, codon 8, codon 41/42 and IVS-1-5. The two most common mutations detected among thalassemia group were Cd8/9 with 8 cases (20%) and Cd-8 with 6 cases (15%) followed by codon 41/42 with 4 cases (10%) which investigated and detected for the first time in Erbil governorate through the present study and finally IVS-1-5 with 3 cases (7.5%), while no any cases detected among control group.

  10. Investigation on molecular interactions of binary mixtures of isobutanol with 1-alkanols (C1 - C6) at different temperatures. Application of the Peng-Robinson-Stryjek-Vera (PSRV) equation of state (EOS)

    Science.gov (United States)

    Khanlarzadeh, K.; Iloukhani, H.; Soleimani, M.

    2017-07-01

    Densities were measured for binary mixtures of isobutanol with 1-alkanols, namely: methanol, ethanol, 1-propanol, 1-butanol, 1-pentanol and 1-hexanol at the temperatures of (288.15, 298.15 and 308.15) K and ambient pressure. Excess molar volumes, VmE , thermal expansion coefficients α, excess thermal expansion coefficients αE, and isothermal coefficients of pressure excess molar enthalpy, (∂HmE / ∂ P) T , x , were derived from the experimental data and the computed results were fitted to the Redlich-Kister equation. The Peng-Robinson-Stryjek-Vera (PRSV) equation of state was applied, in combination with simple mixing rules to predict the excess molar volume. The VmE results were positive for the mixtures of isobutanol with methanol, ethanol, 1-propanol, 1-butanol, and negative for isobutanol with 1-pentanol and 1-hexanol over the whole composition range. The results showed very small deviations from the behavior of ideal solutions in these mixtures and were analyzed to discuss the nature and strength of intermolecular interactions.

  11. Molecular interactions in gelatin/chitosan composite films.

    Science.gov (United States)

    Qiao, Congde; Ma, Xianguang; Zhang, Jianlong; Yao, Jinshui

    2017-11-15

    Gelatin and chitosan were mixed at different mass ratios in solution forms, and the rheological properties of these film-forming solutions, upon cooling, were studied. The results indicate that the significant interactions between gelatin and chitosan promote the formation of multiple complexes, reflected by an increase in the storage modulus of gelatin solution. Furthermore, these molecular interactions hinder the formation of gelatin networks, consequently decreasing the storage modulus of polymer gels. Both hydrogen bonds and electrostatic interactions are formed between gelatin and chitosan, as evidenced by the shift of the amide-II bands of polymers. X-ray patterns of composite films indicate that the contents of triple helices decrease with increasing chitosan content. Only one glass transition temperature (T g ) was observed in composite films with different composition ratios, and it decreases gradually with an increase in chitosan proportion, indicating that gelatin and chitosan have good miscibility and form a wide range of blends. Copyright © 2017 Elsevier Ltd. All rights reserved.

  12. Interactive Multimodal Molecular Set – Designing Ludic Engaging Science Learning Content

    DEFF Research Database (Denmark)

    Thorsen, Tine Pinholt; Christiansen, Kasper Holm Bonde; Jakobsen Sillesen, Kristian

    2014-01-01

    This paper reports on an exploratory study investigating 10 primary school students’ interaction with an interactive multimodal molecular set fostering ludic engaging science learning content in primary schools (8th and 9th grade). The concept of the prototype design was to bridge the physical...... and virtual worlds with electronic tags and, through this, blend the familiarity of the computer and toys, to create a tool that provided a ludic approach to learning about atoms and molecules. The study was inspired by the participatory design and informant design methodologies and included design...

  13. Structural Refinement of Proteins by Restrained Molecular Dynamics Simulations with Non-interacting Molecular Fragments.

    Directory of Open Access Journals (Sweden)

    Rong Shen

    2015-10-01

    Full Text Available The knowledge of multiple conformational states is a prerequisite to understand the function of membrane transport proteins. Unfortunately, the determination of detailed atomic structures for all these functionally important conformational states with conventional high-resolution approaches is often difficult and unsuccessful. In some cases, biophysical and biochemical approaches can provide important complementary structural information that can be exploited with the help of advanced computational methods to derive structural models of specific conformational states. In particular, functional and spectroscopic measurements in combination with site-directed mutations constitute one important source of information to obtain these mixed-resolution structural models. A very common problem with this strategy, however, is the difficulty to simultaneously integrate all the information from multiple independent experiments involving different mutations or chemical labels to derive a unique structural model consistent with the data. To resolve this issue, a novel restrained molecular dynamics structural refinement method is developed to simultaneously incorporate multiple experimentally determined constraints (e.g., engineered metal bridges or spin-labels, each treated as an individual molecular fragment with all atomic details. The internal structure of each of the molecular fragments is treated realistically, while there is no interaction between different molecular fragments to avoid unphysical steric clashes. The information from all the molecular fragments is exploited simultaneously to constrain the backbone to refine a three-dimensional model of the conformational state of the protein. The method is illustrated by refining the structure of the voltage-sensing domain (VSD of the Kv1.2 potassium channel in the resting state and by exploring the distance histograms between spin-labels attached to T4 lysozyme. The resulting VSD structures are in good

  14. Interactive display of molecular models using a microcomputer system

    Science.gov (United States)

    Egan, J. T.; Macelroy, R. D.

    1980-01-01

    A simple, microcomputer-based, interactive graphics display system has been developed for the presentation of perspective views of wire frame molecular models. The display system is based on a TERAK 8510a graphics computer system with a display unit consisting of microprocessor, television display and keyboard subsystems. The operating system includes a screen editor, file manager, PASCAL and BASIC compilers and command options for linking and executing programs. The graphics program, written in USCD PASCAL, involves the centering of the coordinate system, the transformation of centered model coordinates into homogeneous coordinates, the construction of a viewing transformation matrix to operate on the coordinates, clipping invisible points, perspective transformation and scaling to screen coordinates; commands available include ZOOM, ROTATE, RESET, and CHANGEVIEW. Data file structure was chosen to minimize the amount of disk storage space. Despite the inherent slowness of the system, its low cost and flexibility suggests general applicability.

  15. Phase equilibria and molecular interaction studies on (naphthols + vanillin) systems

    International Nuclear Information System (INIS)

    Gupta, Preeti; Agrawal, Tanvi; Das, Shiva Saran; Singh, Nakshatra Bahadur

    2012-01-01

    Highlights: ► Phase equilibria of (naphthol + vanillin) systems have been studied for the first time. ► Eutectic type phase diagrams are obtained. ► Eutectic mixtures show nonideal behaviour. ► There is a weak molecular interaction between the components in the eutectic mixtures. ► α-Naphthol–vanillin eutectic is more stable as compared to β-naphthol–vanillin. - Abstract: Phase equilibria between (α-naphthol + vanillin) and (β-naphthol + vanillin) systems have been studied by thaw-melt method and the results show the formation of simple eutectic mixtures. Crystallization velocities of components and eutectic mixtures were determined at different stages under cooling. With the help of differential scanning calorimeter (DSC), the enthalpy of fusion of components and eutectic mixtures was determined and from the values excess thermodynamic functions viz., excess Gibbs free energy (G E ), excess entropy (S E ), excess enthalpy (H E ) of hypo-, hyper- and eutectic mixtures were calculated. Flexural strength measurements were made in order to understand the non-ideal nature of eutectics. FT-IR spectral studies indicate the formation of hydrogen bond in the eutectic mixture. Anisotropic and isotropic microstructural studies of components, hypo-, hyper- and eutectic mixtures were made. Jackson’s roughness parameter was calculated and found to be greater than 2 suggesting the faceted morphology with irregular structures. The overall results have shown that there is a weak molecular interaction between the components in the eutectic mixtures and the (α-naphthol + vanillin) eutectic is more stable as compared to the (β-naphthol + vanillin) eutectic system.

  16. Determination and Quantification of Molecular Interactions in Protein Films: A Review

    Directory of Open Access Journals (Sweden)

    Felicia Hammann

    2014-12-01

    Full Text Available Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography and analysis of solid films (spectroscopy techniques, X-ray scattering methods. To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

  17. Determination and Quantification of Molecular Interactions in Protein Films: A Review.

    Science.gov (United States)

    Hammann, Felicia; Schmid, Markus

    2014-12-10

    Protein based films are nowadays also prepared with the aim of replacing expensive, crude oil-based polymers as environmentally friendly and renewable alternatives. The protein structure determines the ability of protein chains to form intra- and intermolecular bonds, whereas the degree of cross-linking depends on the amino acid composition and molecular weight of the protein, besides the conditions used in film preparation and processing. The functionality varies significantly depending on the type of protein and affects the resulting film quality and properties. This paper reviews the methods used in examination of molecular interactions in protein films and discusses how these intermolecular interactions can be quantified. The qualitative determination methods can be distinguished by structural analysis of solutions (electrophoretic analysis, size exclusion chromatography) and analysis of solid films (spectroscopy techniques, X-ray scattering methods). To quantify molecular interactions involved, two methods were found to be the most suitable: protein film swelling and solubility. The importance of non-covalent and covalent interactions in protein films can be investigated using different solvents. The research was focused on whey protein, whereas soy protein and wheat gluten were included as further examples of proteins.

  18. Molecular interaction of 2-mercaptobenzimidazole with catalase reveals a potentially toxic mechanism of the inhibitor.

    Science.gov (United States)

    Teng, Yue; Zou, Luyi; Huang, Ming; Zong, Wansong

    2014-12-01

    2-Mercaptobenzimidazole (MBI) is widely utilized as a corrosion inhibitor, copper-plating brightener and rubber accelerator. The residue of MBI in the environment possesses a potential risk to human health. In this work, the toxic interaction of MBI with the important antioxidant enzyme catalase (CAT) was investigated using spectroscopic and molecular docking methods under physiological conditions. MBI can spontaneously bind with CAT with one binding site through hydrogen bonds and van der Waals forces to form MBI-CAT complex. The molecular docking study revealed that MBI bound into the CAT interface of chains B and C, which led to some conformational and microenvironmental changes of CAT and further resulted in the inhibition of CAT activity. This present study provides direct evidence at a molecular level to show that exposure to MBI could induce changes in the structure and function of the enzyme CAT. Copyright © 2014 Elsevier B.V. All rights reserved.

  19. Molecular Investigation of Pediatric Portuguese Patients with Sensorineural Hearing Loss

    Directory of Open Access Journals (Sweden)

    Célia Nogueira

    2011-01-01

    Full Text Available The understanding of the molecular genetics in sensorineural hearing loss (SNHL has advanced rapidly during the last decade, but the molecular etiology of hearing impairment in the Portuguese population has not been investigated thoroughly. To provide appropriate genetic testing and counseling to families, we analyzed the whole mitochondrial genome in 95 unrelated children with SNHL (53 nonsyndromic and 42 syndromic and searched for variations in two frequent genes, GJB2 and GJB6, in the non-syndromic patients. Mutations in mtDNA were detected in 4.2% of the cases, including a hitherto undescribed change in the mtDNA-tRNATrp gene (namely, m.5558A>G. We also identified mono- or biallelic GJB2 mutations in 20 of 53 non-syndromic cases and also detected two novel mutations (p.P70R and p.R127QfsX84. Our data further reinforce the notion that genetic heterogeneity is paramount in children with SNHL.

  20. Thermal and molecular investigation of laser tissue welding

    Energy Technology Data Exchange (ETDEWEB)

    Small, W., IV

    1998-06-01

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack oil both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub-surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of tile probability of long-term success. Molecular effects induced In the tissue by laser irradiation were investigated by measuring tile concentrations of specific collagen covalent crosslinks and characterizing the Fourier-Transform infrared (FTIR) spectra before and after the laser exposure.

  1. Interaction of Chelerythrine with Keyhole Limpet Hemocyanin: a Fluorescence Spectroscopy and Molecular Docking Study

    Science.gov (United States)

    Zhong, M.; Long, R. Q.; Wang, Y. H.; Chen, C. L.

    2018-05-01

    The quenching mechanism between chelerythrine (CHE) and keyhole limpet hemocyanin (KLH) was investigated using fluorescence spectroscopy and molecular docking. The experiments were conducted at three different temperatures (293, 298, and 303 K). The results revealed that the intrinsic fluorescence of KLH was strongly quenched by CHE through a static quenching mechanism. The thermodynamic parameters (ΔG, ΔH, and ΔS) of the interaction were calculated, indicating that the interaction between CHE and KLH was spontaneous and that van der Waals forces and hydrogen bond formation played major roles in the binding process. The intrinsic fluorescence of the tyrosine and tryptophan residues in KLH was studied by synchronous fluorescence, which suggested that CHE changed the conformation of KLH. Finally, molecular docking was used to obtain detailed information on the binding sites and binding affinities between CHE and KLH.

  2. Interaction of lysozyme with a tear film lipid layer model: A molecular dynamics simulation study.

    Science.gov (United States)

    Wizert, Alicja; Iskander, D Robert; Cwiklik, Lukasz

    2017-12-01

    The tear film is a thin multilayered structure covering the cornea. Its outermost layer is a lipid film underneath of which resides on an aqueous layer. This tear film lipid layer (TFLL) is itself a complex structure, formed by both polar and nonpolar lipids. It was recently suggested that due to tear film dynamics, TFLL contains inhomogeneities in the form of polar lipid aggregates. The aqueous phase of tear film contains lachrymal-origin proteins, whereby lysozyme is the most abundant. These proteins can alter TFLL properties, mainly by reducing its surface tension. However, a detailed nature of protein-lipid interactions in tear film is not known. We investigate the interactions of lysozyme with TFLL in molecular details by employing coarse-grained molecular dynamics simulations. We demonstrate that lysozyme, due to lateral restructuring of TFLL, is able to penetrate the tear lipid film embedded in inverse micellar aggregates. Copyright © 2017 Elsevier B.V. All rights reserved.

  3. Collapse and coexistence for a molecular braid with an attractive interaction component subject to mechanical forces.

    Science.gov (United States)

    Lee, Dominic J O'

    2015-04-15

    Dual mechanical braiding experiments provide a useful tool with which to investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an appearance of a local minimum in the interaction potential between the two molecules. We investigate this situation, introducing an attractive component into the interaction potential, using a model developed for describing such experiments. We consider both attractive interactions that do not depend on molecular structure and those which depend on a DNA-like helix structure. In braiding experiments, an attractive term may lead to certain effects. A local minimum may cause molecules to collapse from a loosely braided configuration into a tight one, occurring at a critical value of the moment applied about the axis of the braid. For a fixed number of braid pitches, this may lead to coexistence between the two braiding states, tight and loose. Coexistence implies certain proportions of the braid are in each state, their relative size depending on the number of braid pitches. This manifests itself as a linear dependence in numerically calculated quantities as functions of the number of braid pitches. Also, in the collapsed state, the braid radius stays roughly constant. Furthermore, if the attractive interaction is helix dependent, the left-right handed braid symmetry is broken. For a DNA like charge distribution, using the Kornyshev-Leikin interaction model, our results suggest that significant braid collapse and coexistence only occurs for left handed braids. Regardless of the interaction model, the study highlights the possible qualitative physics of braid collapse and coexistence; and the role helix specific forces might play, if important. The model could be used to connect other microscopic theories of interaction with braiding experiments.

  4. Collapse and coexistence for a molecular braid with an attractive interaction component subject to mechanical forces

    International Nuclear Information System (INIS)

    Lee, Dominic J

    2015-01-01

    Dual mechanical braiding experiments provide a useful tool with which to investigate the nature of interactions between rod-like molecules, for instance actin and DNA. In conditions close to molecular condensation, one would expect an appearance of a local minimum in the interaction potential between the two molecules. We investigate this situation, introducing an attractive component into the interaction potential, using a model developed for describing such experiments. We consider both attractive interactions that do not depend on molecular structure and those which depend on a DNA-like helix structure. In braiding experiments, an attractive term may lead to certain effects. A local minimum may cause molecules to collapse from a loosely braided configuration into a tight one, occurring at a critical value of the moment applied about the axis of the braid. For a fixed number of braid pitches, this may lead to coexistence between the two braiding states, tight and loose. Coexistence implies certain proportions of the braid are in each state, their relative size depending on the number of braid pitches. This manifests itself as a linear dependence in numerically calculated quantities as functions of the number of braid pitches. Also, in the collapsed state, the braid radius stays roughly constant. Furthermore, if the attractive interaction is helix dependent, the left-right handed braid symmetry is broken. For a DNA like charge distribution, using the Kornyshev–Leikin interaction model, our results suggest that significant braid collapse and coexistence only occurs for left handed braids. Regardless of the interaction model, the study highlights the possible qualitative physics of braid collapse and coexistence; and the role helix specific forces might play, if important. The model could be used to connect other microscopic theories of interaction with braiding experiments. (paper)

  5. Stability investigations of relaxing molecular gas flows. Results and perspectives

    Science.gov (United States)

    Grigor'ev, Yurii N.; Ershov, Igor V.

    2017-10-01

    This article presents results of systematic investigations of a dissipative effect which manifests itself as the growth of hydrodynamic stability and suppression of turbulence in relaxing molecular gas flows. The effect can be a new way for control stability and laminar turbulent transition in aerodynamic flows. The consideration of suppression of inviscid acoustic waves in 2D shear flows is presented. Nonlinear evolution of large-scale vortices and Kelvin — Helmholtz waves in relaxing shear flows are studied. Critical Reynolds numbers in supersonic Couette flows are calculated analytically and numerically within the framework of both classical linear and nonlinear energy hydrodynamic stability theories. The calculations clearly show that the relaxation process can appreciably delay the laminar-turbulent transition. The aim of this article is to show the new dissipative effect, which can be used for flow control and laminarization.

  6. PathSys: integrating molecular interaction graphs for systems biology

    Directory of Open Access Journals (Sweden)

    Raval Alpan

    2006-02-01

    Full Text Available Abstract Background The goal of information integration in systems biology is to combine information from a number of databases and data sets, which are obtained from both high and low throughput experiments, under one data management scheme such that the cumulative information provides greater biological insight than is possible with individual information sources considered separately. Results Here we present PathSys, a graph-based system for creating a combined database of networks of interaction for generating integrated view of biological mechanisms. We used PathSys to integrate over 14 curated and publicly contributed data sources for the budding yeast (S. cerevisiae and Gene Ontology. A number of exploratory questions were formulated as a combination of relational and graph-based queries to the integrated database. Thus, PathSys is a general-purpose, scalable, graph-data warehouse of biological information, complete with a graph manipulation and a query language, a storage mechanism and a generic data-importing mechanism through schema-mapping. Conclusion Results from several test studies demonstrate the effectiveness of the approach in retrieving biologically interesting relations between genes and proteins, the networks connecting them, and of the utility of PathSys as a scalable graph-based warehouse for interaction-network integration and a hypothesis generator system. The PathSys's client software, named BiologicalNetworks, developed for navigation and analyses of molecular networks, is available as a Java Web Start application at http://brak.sdsc.edu/pub/BiologicalNetworks.

  7. Diagnosis for the interaction of supersonic molecular beam with plasma

    International Nuclear Information System (INIS)

    Yao Lianghua; Feng Beibing; Feng Zhen; Luo Junlin; Dong Jiafu; Yan Longwen; Hong Wenyu

    2001-01-01

    Supersonic Molecular Beam Injection (SMBI) is a new fuelling method for Tokamaks and has recently been improved to enhance the flux of the beam and to make a survey of the cluster effect within the beam. There are a series of new phenomena, which implicate the interaction of the beam (including clusters) with the toroidal plasma of HL-1M Tokamak. The H α signals from the edge show a regular variation around the torus. Around the injection port, the edge H α signals are positive rectangular wave, which is consistent with that of the injection beam pulses. The edge electron temperature, measured with movable Langmuir probes, decreases by an order of magnitude and the density increases by an order of magnitude. H α emission at the beam injection port, measured with CCD camera at an angle of 13.4 degrees to the SMBI line, shows many separate peaks within the contour plot. These peaks may show the strong emission produced by the interaction of the hydrogen clusters with the plasma. Hydrogen clusters may be produced in the beam according to the empirical scaling (Hagena) law of clustering onset, Γ* = kd 0.85 P 0 /T 0 2.29 , here d is the nozzle diameter in μm, P 0 the stagnation pressure in mbar, T 0 the source temperature in K, and k is a constant related to the gas species. If Γ* > 100, clusters will be formed. In present experiment Γ* is about 127

  8. Molecular interactions between (--epigallocatechin gallate analogs and pancreatic lipase.

    Directory of Open Access Journals (Sweden)

    Shihui Wang

    Full Text Available The molecular interactions between pancreatic lipase (PL and four tea polyphenols (EGCG analogs, like (--epigallocatechin gallate (EGCG, (--gallocatechin gallate (GCG, (--epicatechin gallate (ECG, and (--epigallocatechin (EC, were studied from PL activity, conformation, kinetics and thermodynamics. It was observed that EGCG analogs inhibited PL activity, and their inhibitory rates decreased by the order of EGCG>GCG>ECG>EC. PL activity at first decreased rapidly and then slowly with the increase of EGCG analogs concentrations. α-Helix content of PL secondary structure decreased dependent on EGCG analogs concentration by the order of EGCG>GCG>ECG>EC. EGCG, ECG, and EC could quench PL fluorescence both dynamically and statically, while GCG only quenched statically. EGCG analogs would induce PL self-assembly into complexes and the hydrodynamic radii of the complexes possessed a close relationship with the inhibitory rates. Kinetics analysis showed that EGCG analogs non-competitively inhibited PL activity and did not bind to PL catalytic site. DSC measurement revealed that EGCG analogs decreased the transition midpoint temperature of PL enzyme, suggesting that these compounds reduced PL enzyme thermostability. In vitro renaturation through urea solution indicated that interactions between PL and EGCG analogs were weak and non-covalent.

  9. Thermal and molecular investigation of laser tissue welding

    Science.gov (United States)

    Small, Ward, IV

    Despite the growing number of successful animal and human trials, the exact mechanisms of laser tissue welding remain unknown. Furthermore, the effects of laser heating on tissue on the molecular scale are not fully understood. To address these issues, a multi-front attack on both extrinsic (solder/patch mediated) and intrinsic (laser only) tissue welding was launched using two-color infrared thermometry, computer modeling, weld strength assessment, biochemical assays, and vibrational spectroscopy. The coupling of experimentally measured surface temperatures with the predictive numerical simulations provided insight into the sub surface dynamics of the laser tissue welding process. Quantification of the acute strength of the welds following the welding procedure enabled comparison among trials during an experiment, with previous experiments, and with other studies in the literature. The acute weld integrity also provided an indication of the probability of long-term success. Molecular effects induced in the tissue by laser irradiation were investigated by measuring the concentrations of specific collagen covalent crosslinks and measuring the infrared absorption spectra before and after the laser exposure. This investigation yielded results pertaining to both the methods and mechanisms of laser tissue welding. The combination of two-color infrared thermometry to obtain accurate surface temperatures free from emissivity bias and computer modeling illustrated the importance of including evaporation in the simulations, which effectively serves as an inherent cooling mechanism during laser irradiation. Moreover, the hydration state predicted by the model was useful in assessing the role of electrostatic versus covalent bonding in the fusion. These tools also helped elicit differences between dye- enhanced liquid solders and solid-matrix patches in laser-assisted tissue welding, demonstrating the significance of repeatable energy delivery. Surprisingly, covalent bonds

  10. Exploration of molecular interactions in cholesterol superlattices: effect of multibody interactions.

    Science.gov (United States)

    Huang, Juyang

    2002-08-01

    Experimental evidences have indicated that cholesterol may adapt highly regular lateral distributions (i.e., superlattices) in a phospholipid bilayer. We investigated the formations of superlattices at cholesterol mole fraction of 0.154, 0.25, 0.40, and 0.5 using Monte Carlo simulation. We found that in general, conventional pairwise-additive interactions cannot produce superlattices. Instead, a multibody (nonpairwise) interaction is required. Cholesterol superlattice formation reveals that although the overall interaction between cholesterol and phospholipids is favorable, it contains two large opposing components: an interaction favoring cholesterol-phospholipid mixing and an unfavorable acyl chain multibody interaction that increases nonlinearly with the number of cholesterol contacts. The magnitudes of interactions are in the order of kT. The physical origins of these interactions can be explained by our umbrella model. They most likely come from the requirement for polar phospholipid headgroups to cover the nonpolar cholesterol to avoid the exposure of cholesterol to water and from the sharp decreasing of acyl chain conformation entropy due to cholesterol contact. This study together with our previous work demonstrate that the driving force of cholesterol-phospholipid mixing is a hydrophobic interaction, and multibody interactions dominate others over a wide range of cholesterol concentration.

  11. Reverse engineering of an affinity-switchable molecular interaction characterized by atomic force microscopy single-molecule force spectroscopy.

    Science.gov (United States)

    Anselmetti, Dario; Bartels, Frank Wilco; Becker, Anke; Decker, Björn; Eckel, Rainer; McIntosh, Matthew; Mattay, Jochen; Plattner, Patrik; Ros, Robert; Schäfer, Christian; Sewald, Norbert

    2008-02-19

    Tunable and switchable interaction between molecules is a key for regulation and control of cellular processes. The translation of the underlying physicochemical principles to synthetic and switchable functional entities and molecules that can mimic the corresponding molecular functions is called reverse molecular engineering. We quantitatively investigated autoinducer-regulated DNA-protein interaction in bacterial gene regulation processes with single atomic force microscopy (AFM) molecule force spectroscopy in vitro, and developed an artificial bistable molecular host-guest system that can be controlled and regulated by external signals (UV light exposure and thermal energy). The intermolecular binding functionality (affinity) and its reproducible and reversible switching has been proven by AFM force spectroscopy at the single-molecule level. This affinity-tunable optomechanical switch will allow novel applications with respect to molecular manipulation, nanoscale rewritable molecular memories, and/or artificial ion channels, which will serve for the controlled transport and release of ions and neutral compounds in the future.

  12. Molecular modeling studies of interactions between sodium polyacrylate polymer and calcite surface

    Energy Technology Data Exchange (ETDEWEB)

    Ylikantola, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Linnanto, J., E-mail: juha.m.linnanto@gmail.com [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); University of Tartu, Institute of Physics, Riia 142, EE-51014 Tartu (Estonia); Knuutinen, J.; Oravilahti, A. [University of Jyväskylä, Department of Chemistry, P.O. Box 35, University of Jyväskylä, FI-40014 (Finland); Toivakka, M. [Åbo Akademi University, Laboratory of Paper Coating and Converting and Center for Functional Materials, FI-20500 Turku/Åbo (Finland)

    2013-07-01

    The interactions between calcite pigment and sodium polyacrylate dispersing agent, widely used in papermaking as paper coating components, were investigated using classical force field and quantum chemical approaches. The objective was to understand interactions between the calcite surface and sodium polyacrylate polymer at 300 K using molecular dynamics simulations. A quantum mechanical ab initio Hartree–Fock method was also used to obtain detailed information about the sodium polyacrylate polymer structure. The effect of water molecules (moisture) on the interactions was also examined. Calculations showed that molecular weight, branching and the orientation of sodium polyacrylate polymers influence the interactions between the calcite surface and the polymer. The force field applied, and also water molecules, were found to have an impact on all systems studied. Ab initio Hartree–Fock calculations indicated that there are two types of coordination between sodium atoms and carboxylate groups of the sodium polyacrylate polymer, inter- and intra-carboxylate group coordination. In addition, ab initio Hartree–Fock calculations of the structure of the sodium polyacrylate polymer produced important information regarding interactions between the polymers and carboxylated styrene-butadiene latex particles.

  13. Investigation of the Physical and Molecular Properties of Asphalt Binders Processed with Used Motor Oils

    Directory of Open Access Journals (Sweden)

    Mohyeldin Ragab

    2015-01-01

    Full Text Available In this work we investigated the performance aspects of addition of used motor oils (UMO to neat and crumb rubber modified asphalts (CRMA and related that to the change of molecular size distribution of modified asphalt’s fractions; asphaltenes, saturates, naphthene aromatics, and polar aromatics. Based on the results of temperature sweep viscoelastic tests, addition of crumb rubber modifier (CRM alone or with UMO results in the formation of internal network within the modified asphalt. Based on the results of short and long term aged asphalts, the utilization of combination of UMO and CRM enhanced the aging behavior of asphalt. Bending beam rheometer was utilized to investigate the low temperature behavior of UMO modified asphalts. Based on those tests, the utilization of the UMO and CRM enhanced the low temperature properties of asphalts. Based on the results of the asphalt separation tests and the Gel Permeation Chromatography (GPC analysis, it was found that saturates and naphthene aromatics are the two asphalt fractions that have similar molecular size fractions as those of UMO. However, UMO only shifts the molecular sizes of saturates after interaction with asphalt. Results also show that polar aromatics pose higher molecular size structures than UMO.

  14. Post-foil interaction in foil-induced molecular dissociation

    International Nuclear Information System (INIS)

    Faibis, A.; Kanter, E.P.; Koenig, W.; Plesser, I.; Vager, Z.

    1985-01-01

    The authors have investigated the foil-induced dissociation of 175- 250- keV/amu CH + , NH + , and OH + , FH + and NeH + ions by coincident detection of the fragment atoms. The dissociation energies corresponding to in-foil and post-foil interactions were deduced from the measured relative flight times of the fragment pairs to a set of detectors downstream from the target. The authors considered final states consisting of a) a proton and a heavy-ion and, b) a hydrogen atom and a heavy-ion. Surprisingly, in both cases the energy released in the post-target interaction shows a similar linear increase with the charge state of the heavy partner

  15. A probe to study the toxic interaction of tartrazine with bovine hemoglobin at the molecular level.

    Science.gov (United States)

    Li, Yating; Wei, Haoran; Liu, Rutao

    2014-03-01

    Tartrazine is an artificial azo dye commonly used in food products, but tartrazine in the environment is potentially harmful. The toxic interaction between tartrazine and bovine hemoglobin (BHb) was investigated using fluorescence, synchronous fluorescence, UV-vis absorption, circular dichroism (CD) and molecular modeling techniques under simulated physiological conditions. The fluorescence data showed that tartrazine can bind with BHb to form a complex. The binding process was a spontaneous molecular interaction, in which van der Waals' forces and hydrogen bonds played major roles. Molecular docking results showed that the hydrogen bonds exist between the oxygen atoms at position 31 of tartrazine and the nitrogen atom NZ7 on Lys99, and also between the oxygen atoms at position 15 of tartrazine and the nitrogen atom NZ7 on Lys104, Lys105. The results of UV-vis and CD spectra revealed that tartrazine led to conformational changes in BHb, including loosening of the skeleton structure and decreasing α helix in the secondary structure. The synchronous fluorescence experiment revealed that tartrazine binds into the hemoglobin central cavity, and this was verified using a molecular modeling study. Copyright © 2013 John Wiley & Sons, Ltd.

  16. Investigating physics learning with layered student interaction networks

    DEFF Research Database (Denmark)

    Bruun, Jesper; Traxler, Adrienne

    Centrality in student interaction networks (SINs) can be linked to variables like grades [1], persistence [2], and participation [3]. Recent efforts in the field of network science have been done to investigate layered - or multiplex - networks as mathematical objects [4]. These networks can be e......, this study investigates how target entropy [5,1] and pagerank [6,7] are affected when we take time and modes of interaction into account. We present our preliminary models and results and outline our future work in this area....

  17. Application of proteomics to investigate barley-Fusarium graminearum interaction

    DEFF Research Database (Denmark)

    Yang, Fen

    in plants under low N and iv) proteomes of uninfected plants were similar under two N levels. Correlation of level of proteolysis induced by the fungus with measurement of Fusarium-damaged kernels, fungal biomass and mycotoxin levels indicated that FHB was more severe in barley with low N. In Chapter 3......, the molecular mechanisms of barley defense to Fusarium graminearum at the early infection stage were studied. Antibodies against barley β-amylases were shown to be the markers for infection at proteome level and for selection of the time for proteome analysis before extensive degradation caused by the fungus...... the disease. Due to the advantages of gel-based proteomics that differentially expressed proteins involved in the interaction can be directly detected by comparing protein profiles displayed on 2-D gels, it is used as a tool for studying the barley- Fusarium graminearum interaction form three different...

  18. Stable Molecular Diodes Based on π-π Interactions of the Molecular Frontier Orbitals with Graphene Electrodes.

    Science.gov (United States)

    Song, Peng; Guerin, Sarah; Tan, Sherman Jun Rong; Annadata, Harshini Venkata; Yu, Xiaojiang; Scully, Micheál; Han, Ying Mei; Roemer, Max; Loh, Kian Ping; Thompson, Damien; Nijhuis, Christian A

    2018-03-01

    In molecular electronics, it is important to control the strength of the molecule-electrode interaction to balance the trade-off between electronic coupling strength and broadening of the molecular frontier orbitals: too strong coupling results in severe broadening of the molecular orbitals while the molecular orbitals cannot follow the changes in the Fermi levels under applied bias when the coupling is too weak. Here, a platform based on graphene bottom electrodes to which molecules can bind via π-π interactions is reported. These interactions are strong enough to induce electronic function (rectification) while minimizing broadening of the molecular frontier orbitals. Molecular tunnel junctions are fabricated based on self-assembled monolayers (SAMs) of Fc(CH 2 ) 11 X (Fc = ferrocenyl, X = NH 2 , Br, or H) on graphene bottom electrodes contacted to eutectic alloy of gallium and indium top electrodes. The Fc units interact more strongly with graphene than the X units resulting in SAMs with the Fc at the bottom of the SAM. The molecular diodes perform well with rectification ratios of 30-40, and they are stable against bias stressing under ambient conditions. Thus, tunnel junctions based on graphene with π-π molecule-electrode coupling are promising platforms to fabricate stable and well-performing molecular diodes. © 2018 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  19. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    Science.gov (United States)

    Miller, Matthew J; Esser, Helen J; Loaiza, Jose R; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna). Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology and the dynamics of

  20. Molecular Ecological Insights into Neotropical Bird-Tick Interactions.

    Directory of Open Access Journals (Sweden)

    Matthew J Miller

    Full Text Available In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In contrast, immature Neotropical ticks are often found on wild birds, yet difficulties in identifying immatures hinder studies of birds' role in tropical tick ecology and tick-borne disease transmission. In Panama, we found immature ticks on 227 out of 3,498 individually-sampled birds representing 93 host species (24% of the bird species sampled, and 13% of the Panamanian land bird fauna. Tick parasitism rates did not vary with rainfall or temperature, but did vary significantly with several host ecological traits. Likewise, Neotropical-Nearctic migratory birds were significantly less likely to be infested than resident species. Using a molecular library developed from morphologically-identified adult ticks specifically for this study, we identified eleven tick species parasitizing birds, indicating that a substantial portion of the Panamanian avian species pool is parasitized by a diversity of tick species. Tick species that most commonly parasitized birds had the widest diversity of avian hosts, suggesting that immature tick species are opportunistic bird parasites. Although certain avian ecological traits are positively associated with parasitism, we found no evidence that individual tick species show specificity to particular avian host ecological traits. Finally, our data suggest that the four principal vectors of Rocky Mountain Spotted Fever in the Neotropics rarely, if ever, parasitize Panamanian birds. However, other tick species that harbor newly-discovered rickettsial parasites of unknown pathogenicity are frequently found on these birds. Given our discovery of broad interaction between Panamanian tick and avian biodiversity, future work on tick ecology

  1. Molecular modeling of human neutral sphingomyelinase provides insight into its molecular interactions.

    Science.gov (United States)

    Dinesh; Goswami, Angshumala; Suresh, Panneer Selvam; Thirunavukkarasu, Chinnasamy; Weiergräber, Oliver H; Kumar, Muthuvel Suresh

    2011-01-01

    The neutral sphingomyelinase (N-SMase) is considered a major candidate for mediating the stress-induced production of ceramide, and it plays an important role in cell-cycle arrest, apoptosis, inflammation, and eukaryotic stress responses. Recent studies have identified a small region at the very N-terminus of the 55 kDa tumour necrosis factor receptor (TNF-R55), designated the neutral sphingomyelinase activating domain (NSD) that is responsible for the TNF-induced activation of N-SMase. There is no direct association between TNF-R55 NSD and N-SMase; instead, a protein named factor associated with N-SMase activation (FAN) has been reported to couple the TNF-R55 NSD to N-SMase. Since the three-dimensional fold of N-SMase is still unknown, we have modeled the structure using the protein fold recognition and threading method. Moreover, we propose models for the TNF-R55 NSD as well as the FAN protein in order to study the structural basis of N-SMase activation and regulation. Protein-protein interaction studies suggest that FAN is crucially involved in mediating TNF-induced activation of the N-SMase pathway, which in turn regulates mitogenic and proinflammatory responses. Inhibition of N-SMase may lead to reduction of ceramide levels and hence may provide a novel therapeutic strategy for inflammation and autoimmune diseases. Molecular dynamics (MD) simulations were performed to check the stability of the predicted model and protein-protein complex; indeed, stable RMS deviations were obtained throughout the simulation. Furthermore, in silico docking of low molecular mass ligands into the active site of N-SMase suggests that His135, Glu48, Asp177, and Asn179 residues play crucial roles in this interaction. Based on our results, these ligands are proposed to be potent and selective N-SMase inhibitors, which may ultimately prove useful as lead compounds for drug development.

  2. Molecular dynamics simulations of lipid bilayers : major artifacts due to truncating electrostatic interactions

    NARCIS (Netherlands)

    Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Lindqvist, P.; Vattulainen, I.

    2003-01-01

    We study the influence of truncating the electrostatic interactions in a fully hydrated pure dipalmitoylphosphatidylcholine (DPPC) bilayer through 20 ns molecular dynamics simulations. The computations in which the electrostatic interactions were truncated are compared to similar simulations using

  3. Diffraction stress analysis of thin films; investigating elastic grain interaction

    International Nuclear Information System (INIS)

    Kumar, A.

    2005-12-01

    This work is dedicated to the investigation of specimens exhibiting anisotropic microstructures (and thus macroscopic elastic anisotropy) and/or inhomogeneous microstructures, as met near surfaces and in textured materials. The following aspects are covered: (i) Analysis of specimens with direction-dependent (anisotropic) elastic grain-interaction. Elastic grain-interaction determines the distribution of stresses and strains over the (crystallographically) differently oriented grains of a mechanically stressed polycrystal and the mechanical and diffraction (X-ray) elastic constants (relating (diffraction) lattice strains to mechanical stresses). Grain interaction models that allow for anisotropic, direction-dependent grain interaction have been developed very recently. The notion 'direction-dependent' grain-interaction signifies that different grain-interaction constraints prevail along different directions in a specimen. Practical examples of direction-dependent grain interaction are the occurrence of surface anisotropy in thin films and the surface regions of bulk polycrystals and the occurrence of grain-shape (morphological) texture. In this work, for the first time, stress analyses of thin films have been performed on the basis of these newly developed grain-interaction models. It has also been demonstrated that the identification of the (dominant) source of direction-dependent grain interaction is possible. The results for the grain interaction have been discussed in the light of microstructural investigations of the specimens by microscopic techniques. (ii) Analysis of specimens with depth gradients: Diffraction stress analysis can be hindered if gradients of the stress state, the composition or the microstructure occur in the specimen under investigation, as the so-called information depth varies in the course of a traditional stress measurement: Ambiguous results are thus generally obtained. In this work, a strategy for stress measurements at fixed

  4. Molecular docking and spectroscopic investigations aided by density functional theory of Parkinson's drug 2-(3,4-dihydroxyphenyl)ethylamine

    Science.gov (United States)

    Sherlin, Y. Sheeba; Vijayakumar, T.; Roy, S. D. D.; Jayakumar, V. S.

    2018-05-01

    Molecular geometry of Parkinson's drug 2-(3,4-Dihydroxyphenyl)ethylamine hydrochloride (Dopamine, DA) has been evaluated and compared with experimental XRD data. Molecular docking and vibrational spectral analysis of DA have been carried out using FT-Raman and FT-IR spectra aided by Density Functional Theory at B3LYP/6-311++G(d,p). The present investigation deals with the analysis of structural and spectral features responsible for drug activities, nature of hydrogen bonding interactions of the molecule and the correlation of Parkinson's nature with its molecular structural features.

  5. Interaction of diuron to human serum albumin: Insights from spectroscopic and molecular docking studies.

    Science.gov (United States)

    Chen, Huilun; Rao, Honghao; Yang, Jian; Qiao, Yongxiang; Wang, Fei; Yao, Jun

    2016-01-01

    This investigation was undertaken to determine the interaction of diuron with human serum albumin (HSA) was studied by monitoring the spectral behavior of diuron-HSA system. The fluorescence of HSA at 340 nm excited at 230 nm was obviously quenched by diuron due to dynamic collision and the quenching constant was of the order of 10(4) L mol(-1) at 310 K. However, no fluorescence quenching was observed when excited at 280 nm. Thermodynamic investigations revealed that the combination between diuron and HSA was entropy driven by predominantly hydrophobic interactions. The binding of diuron induced the drastic reduction in α-helix conformation and the significant enhancement in β-turn conformation of HSA. In addition, both sites marker competition study and molecular modeling simulation evidenced the binding of diuron to HSA primarily took place in subdomain IIIA (Sudlow's site II).

  6. Prediction of drug-packaging interactions via molecular dynamics (MD) simulations.

    Science.gov (United States)

    Feenstra, Peter; Brunsteiner, Michael; Khinast, Johannes

    2012-07-15

    The interaction between packaging materials and drug products is an important issue for the pharmaceutical industry, since during manufacturing, processing and storage a drug product is continuously exposed to various packaging materials. The experimental investigation of a great variety of different packaging material-drug product combinations in terms of efficacy and safety can be a costly and time-consuming task. In our work we used molecular dynamics (MD) simulations in order to evaluate the applicability of such methods to pre-screening of the packaging material-solute compatibility. The solvation free energy and the free energy of adsorption of diverse solute/solvent/solid systems were estimated. The results of our simulations agree with experimental values previously published in the literature, which indicates that the methods in question can be used to semi-quantitatively reproduce the solid-liquid interactions of the investigated systems. Copyright © 2012 Elsevier B.V. All rights reserved.

  7. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    The purpose of the study was to investigate a possible genotype by environment interaction in first calf South African Holstein cows for both production and reproduction traits. Data from 100 975 cows on a total mixed ration (TMR) and 22 083 pasture based cows were used. These cows were the progeny of 4 391 sires and ...

  8. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations. Copyright © 2014 Elsevier Ltd. All rights reserved.

  9. Investigation on the toxic interaction of typical plasticizers with calf thymus DNA

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Xiaojing [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Zong, Wansong, E-mail: gaocz@sdu.edu.cn [College of Population, Resources and Environment, Shandong Normal University, 88# East Wenhua Road, Jinan 250014 (China); Liu, Chunguang; Liu, Yang [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Gao, Canzhu, E-mail: rutaoliu@sdu.edu.cn [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China); Liu, Rutao [School of Environmental Science and Engineering, China–America CRC for Environment & Health, Shandong University, 27# Shanda South Road, Jinan 250100, Shandong Province (China)

    2015-05-15

    The interactions of typical plasticizers dimethyl phthalate (DMP), diethyl phthalate (DEP) and dibutyl phthalate (DBP) with calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopic techniques and molecular modeling. Experimental results indicated that the characteristic fluorescence intensity of phthalic acid rose with the increase of DNA concentration; while the characteristic fluorescence intensities of plasticizers decreased with the increase of DNA concentration. Experiments on native and denatured DNA determined that plasticizers interacted with DNA both in groove and electrostatic binding mode. The molecular modeling results further illustrated that there is groove binding between them; hydrogen bonding and Van der Waals interactions were the main forces. With the extension of branched-chains, the binding effects between plasticizers and DNA were weakened, which could be related to the increased steric hindrance. - Highlights: • This work established the binding mode of plasticizers with DNA on molecular level. • The mechanism was explored by fluorescence spectroscopic and molecular docking methods. • There are two kinds of binding mode between DMP, DEP, DBP and DNA, electrostatic and groove. • With the branched chain extension, the binding effect of plasticizers and DNA has been weakened.

  10. Molecular interactions of alcohols with zeolite BEA and MOR frameworks.

    Science.gov (United States)

    Stückenschneider, Kai; Merz, Juliane; Schembecker, Gerhard

    2013-12-01

    Zeolites can adsorb small organic molecules such as alcohols from a fermentation broth. Also in the zeolite-catalyzed conversion of alcohols to biofuels, biochemicals, or gasoline, adsorption is the first step. Several studies have investigated the adsorption of alcohols in different zeolites experimentally, but computational investigations in this field have mostly been restricted to zeolite MFI. In this study, the adsorption of C1-C4 alcohols in BEA and MOR was investigated using density functional theory (DFT). Calculated adsorption geometries and the corresponding energies of the designed cluster models were comparable to periodic calculations, and the adsorption energies were in the same range as the corresponding computational and experimental values reported in the literature for zeolite MFI. Thus, BEA and MOR may be good adsorption materials for alcohols in the field of downstream processing and catalysis. Aside from the DFT calculations, adsorption isotherms were determined experimentally in this study from aqueous solutions. For BEA, the adsorption of significant amounts of alcohol from aqueous solution was observed experimentally. In contrast, MOR was loaded with only a very small amount of alcohol. Although differences were found between the affinities obtained from gas-phase DFT calculations and those observed experimentally in aqueous solution, the computational data presented here represent molecular level information on the geometries and energies of C1-C4 alcohols adsorbed in zeolites BEA and MOR. This knowledge should prove very useful in the design of zeolite materials intended for use in adsorption and catalytic processes, as it allows adsorption behavior to be predicted via judiciously designed computational models.

  11. Electron, ion and atomic beams interaction with solid high-molecular dielectrics

    Energy Technology Data Exchange (ETDEWEB)

    Milyavskij, V V; Skvortsov, V A [Russian Academy of Sciences, Moscow (Russian Federation). High Energy Density Research Center

    1997-12-31

    A mathematical model was constructed and numerical investigation performed of the interaction between intense electron, ion and atomic beams and solid high-molecular dielectrics under various boundary conditions. The model is based on equations of the mechanics of continuum, electrodynamics and kinetics, describing the accumulation and relaxation of space charge and shock-wave processes, as well as the evolution of electric field in the sample. A semi-empirical procedure is proposed for the calculation of energy deposition by electron beam in a target in the presence of a non-uniform electric field. (author). 4 figs., 2 refs.

  12. Scanning probe and optical tweezer investigations of biomolecular interactions

    International Nuclear Information System (INIS)

    Rigby-Singleton, Shellie

    2002-01-01

    A complex array of intermolecular forces controls the interactions between and within biological molecules. The desire to empirically explore the fundamental forces has led to the development of several biophysical techniques. Of these, the atomic force microscope (AFM) and the optical tweezers have been employed throughout this thesis to monitor the intermolecular forces involved in biomolecular interactions. The AFM is a well-established force sensing technique capable of measuring biomolecular interactions at a single molecule level. However, its versatility has not been extrapolated to the investigation of a drug-enzyme complex. The energy landscape for the force induced dissociation of the DHFR-methotrexate complex was studied. Revealing an energy barrier to dissociation located ∼0.3 nm from the bound state. Unfortunately, the AFM has a limited range of accessible loading rates and in order to profile the complete energy landscape alternative force sensing instrumentation should be considered, for example the BFP and optical tweezers. Thus, this thesis outlines the development and construction an optical trap capable of measuring intermolecular forces between biomolecules at the single molecule level. To demonstrate the force sensing abilities of the optical set up, proof of principle measurements were performed which investigate the interactions between proteins and polymer surfaces subjected to varying degrees of argon plasma treatment. Complementary data was gained from measurements performed independently by the AFM. Changes in polymer resistance to proteins as a response to changes in polymer surface chemistry were detected utilising both AFM and optical tweezers measurements. Finally, the AFM and optical tweezers were employed as ultrasensitive biosensors. Single molecule investigations of the antibody-antigen interaction between the cardiac troponin I marker and its complementary antibody, reveals the impact therapeutic concentrations of heparin have

  13. Investigation on human serum albumin and Gum Tragacanth interactions using experimental and computational methods.

    Science.gov (United States)

    Moradi, Sajad; Taran, Mojtaba; Shahlaei, Mohsen

    2018-02-01

    The study on the interaction of human serum albumin and Gum Tragacanth, a biodegradable bio-polymer, has been undertaken. For this purpose, several experimental and computational methods were used. Investigation of thermodynamic parameters and mode of interactions were carried out using Fluorescence spectroscopy in 300 and 310K. Also, a Fourier transformed infrared spectra and synchronous fluorescence spectroscopy was performed. To give detailed insight of possible interactions, docking and molecular dynamic simulations were also applied. Results show that the interaction is based on hydrogen bonding and van der Waals forces. Structural analysis implies on no adverse change in protein conformation during binding of GT. Furthermore, computational methods confirm some evidence on secondary structure enhancement of protein as a presence of combining with Gum Tragacanth. Copyright © 2017 Elsevier B.V. All rights reserved.

  14. Application of the RISM theory to Lennard-Jones interaction site molecular fluids

    International Nuclear Information System (INIS)

    Johnson, E.; Hazoume, R.P.

    1979-01-01

    It seems that reference interaction site model (RISM) theory atom--atom distribution functions have been obtained directly from the RISM equations only for fused hard sphere molecular fluids. RISM distribution functions for Lennard-Jones interaction site fluids are presented. Results presented suggest that these distribution functions are as accurate as RISM distribution functions for fused hard sphere molecular fluids

  15. Interaction of molecular oxygen with single wall nanotubes: Role of surfactant contamination

    International Nuclear Information System (INIS)

    Larciprete, R.; Goldoni, A.; Lizzit, S.

    2003-01-01

    The interaction of molecular oxygen with single wall nanotubes in the form of a commercial bucky paper was investigated by high resolution photoemission spectroscopy. Sodium contamination was found in the sample, which was completely removed only after prolonged heating at 1250 K. The C 1s core level spectrum measured on the sample annealed to 1020 K dramatically changed upon exposure to molecular oxygen. On the contrary, when exposing the Na-free SWNTs to several KL of O 2 , the sample remained oxygen free and no modification in the C 1s core level was observed. Therefore the observed sensitivity of the sample to O 2 was due to a Na mediated oxidation, determining a charge transfer from the C tubes to the Na-O complex

  16. Nanoparticle decoration with surfactants: Molecular interactions, assembly, and applications

    Science.gov (United States)

    Heinz, Hendrik; Pramanik, Chandrani; Heinz, Ozge; Ding, Yifu; Mishra, Ratan K.; Marchon, Delphine; Flatt, Robert J.; Estrela-Lopis, Irina; Llop, Jordi; Moya, Sergio; Ziolo, Ronald F.

    2017-02-01

    Nanostructures of diverse chemical nature are used as biomarkers, therapeutics, catalysts, and structural reinforcements. The decoration with surfactants has a long history and is essential to introduce specific functions. The definition of surfactants in this review is very broad, following its lexical meaning ;surface active agents;, and therefore includes traditional alkyl modifiers, biological ligands, polymers, and other surface active molecules. The review systematically covers covalent and non-covalent interactions of such surfactants with various types of nanomaterials, including metals, oxides, layered materials, and polymers as well as their applications. The major themes are (i) molecular recognition and noncovalent assembly mechanisms of surfactants on the nanoparticle and nanocrystal surfaces, (ii) covalent grafting techniques and multi-step surface modification, (iii) dispersion properties and surface reactions, (iv) the use of surfactants to influence crystal growth, as well as (v) the incorporation of biorecognition and other material-targeting functionality. For the diverse materials classes, similarities and differences in surfactant assembly, function, as well as materials performance in specific applications are described in a comparative way. Major factors that lead to differentiation are the surface energy, surface chemistry and pH sensitivity, as well as the degree of surface regularity and defects in the nanoparticle cores and in the surfactant shell. The review covers a broad range of surface modifications and applications in biological recognition and therapeutics, sensors, nanomaterials for catalysis, energy conversion and storage, the dispersion properties of nanoparticles in structural composites and cement, as well as purification systems and classical detergents. Design principles for surfactants to optimize the performance of specific nanostructures are discussed. The review concludes with challenges and opportunities.

  17. Understanding Molecular Interactions within Chemically Selective Layered Polymer Assemblies

    Energy Technology Data Exchange (ETDEWEB)

    Gary J. Blanchard

    2009-06-30

    This work focuses on two broad issues. These are (1) the molecular origin of the chemical selectivity achieved with ultrathin polymer multilayers, and (2) how the viscoelastic properties of the polymer layers are affected by exposure to solvent and analytes. These issues are inter-related, and to understand them we need to design experiments that probe both the energetic and kinetic aspects of interfacial adsorption processes. This project focuses on controling the chemical structure, thickness, morphology and sequential ordering of polymer layers bound to interfaces using maleimide-vinyl ether and closely related alternating copolymerization chemistry and efficient covalent cross-linking reactions that allow for layer-by-layer polymer deposition. This chemistry has been developed during the funding cycle of this Grant. We have measure the equilibrium constants for interactions between specific layers within the polymer interfaces and size-controlled, surface-functionalized gold nanoparticles. The ability to control both size and functionality of gold nanoparticle model analytes allows us to evaluate the average “pore size” that characterizes our polymer films. We have measured the “bulk” viscosity and shear modulus of the ultrathin polymer films as a function of solvent overlayer identity using quartz crystal microbalance complex impedance measurements. We have measured microscopic viscosity at specific locations within the layered polymer interfaces with time-resolved fluorescence lifetime and depolarization techniques. We combine polymer, cross-linking and nanoparticle synthetic expertise with a host of characterization techniques, including QCM gravimetry and complex impedance analysis, steady state and time-resolved spectroscopies.

  18. Contributions to advances in blend pellet products (BPP) research on molecular structure and molecular nutrition interaction by advanced synchrotron and globar molecular (Micro)spectroscopy.

    Science.gov (United States)

    Guevara-Oquendo, Víctor H; Zhang, Huihua; Yu, Peiqiang

    2018-04-13

    To date, advanced synchrotron-based and globar-sourced techniques are almost unknown to food and feed scientists. There has been little application of these advanced techniques to study blend pellet products at a molecular level. This article aims to provide recent research on advanced synchrotron and globar vibrational molecular spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction. How processing induced molecular structure changes in relation to nutrient availability and utilization of the blend pellet products. The study reviews Utilization of co-product components for blend pellet product in North America; Utilization and benefits of inclusion of pulse screenings; Utilization of additives in blend pellet products; Application of pellet processing in blend pellet products; Conventional evaluation techniques and methods for blend pellet products. The study focus on recent applications of cutting-edge vibrational molecular spectroscopy for molecular structure and molecular structure association with nutrient utilization in blend pellet products. The information described in this article gives better insight on how advanced molecular (micro)spectroscopy contributions to advances in blend pellet products research on molecular structure and molecular nutrition interaction.

  19. Measuring pair-wise molecular interactions in a complex mixture

    Science.gov (United States)

    Chakraborty, Krishnendu; Varma, Manoj M.; Venkatapathi, Murugesan

    2016-03-01

    Complex biological samples such as serum contain thousands of proteins and other molecules spanning up to 13 orders of magnitude in concentration. Present measurement techniques do not permit the analysis of all pair-wise interactions between the components of such a complex mixture to a given target molecule. In this work we explore the use of nanoparticle tags which encode the identity of the molecule to obtain the statistical distribution of pair-wise interactions using their Localized Surface Plasmon Resonance (LSPR) signals. The nanoparticle tags are chosen such that the binding between two molecules conjugated to the respective nanoparticle tags can be recognized by the coupling of their LSPR signals. This numerical simulation is done by DDA to investigate this approach using a reduced system consisting of three nanoparticles (a gold ellipsoid with aspect ratio 2.5 and short axis 16 nm, and two silver ellipsoids with aspect ratios 3 and 2 and short axes 8 nm and 10 nm respectively) and the set of all possible dimers formed between them. Incident light was circularly polarized and all possible particle and dimer orientations were considered. We observed that minimum peak separation between two spectra is 5 nm while maximum is 184nm.

  20. Investigation of impurity defects in α-iron by molecular dynamics method

    International Nuclear Information System (INIS)

    Kevorkyan, Yu.R.

    1986-01-01

    Investigation of the configuration of impurity defects in α-iron by the molecular dynamics method is presented. The Jhonson model potential has been used to calculate the interaction of matrix atoms. The impurity-matrix atom interaction is described by the same form of the potential shifted along the axis of interatomic distances for a definite value. The correspondence between the shift value and change in the radius of the impurity defect is established on the basis of calculation of the relaxation volume. Possible configurations of the impurity - interstitial matrix atom complexes are obtained for the given model of the impurity defect, dimensional boundaries of possible transitions between different configurations are determined. Formation and bound energies, relaxation volumes of impurity defects are calculated

  1. New Diethyl Ammonium Salt of Thiobarbituric Acid Derivative: Synthesis, Molecular Structure Investigations and Docking Studies

    Directory of Open Access Journals (Sweden)

    Assem Barakat

    2015-11-01

    Full Text Available The synthesis of the new diethyl ammonium salt of diethylammonium(E-5-(1,5-bis(4-fluorophenyl-3-oxopent-4-en-1-yl-1,3-diethyl-4,6-dioxo-2-thioxohexaydropyrimidin-5-ide 3 via a regioselective Michael addition of N,N-diethylthiobarbituric acid 1 to dienone 2 is described. In 3, the carboanion of the thiobarbituric moiety is stabilized by the strong intramolecular electron delocalization with the adjacent carbonyl groups and so the reaction proceeds without any cyclization. The molecular structure investigations of 3 were determined by single-crystal X-ray diffraction as well as DFT computations. The theoretically calculated (DFT/B3LYP geometry agrees well with the crystallographic data. The effect of fluorine replacement by chlorine atoms on the molecular structure aspects were investigated using DFT methods. Calculated electronic spectra showed a bathochromic shift of the π-π* transition when fluorine is replaced by chlorine. Charge decomposition analyses were performed to study possible interaction between the different fragments in the studied systems. Molecular docking simulations examining the inhibitory nature of the compound show an anti-diabetic activity with Pa (probability of activity value of 0.229.

  2. Molecular modeling of polymer composite-analyte interactions in electronic nose sensors

    Science.gov (United States)

    Shevade, A. V.; Ryan, M. A.; Homer, M. L.; Manfreda, A. M.; Zhou, H.; Manatt, K. S.

    2003-01-01

    We report a molecular modeling study to investigate the polymer-carbon black (CB) composite-analyte interactions in resistive sensors. These sensors comprise the JPL electronic nose (ENose) sensing array developed for monitoring breathing air in human habitats. The polymer in the composite is modeled based on its stereoisomerism and sequence isomerism, while the CB is modeled as uncharged naphthalene rings with no hydrogens. The Dreiding 2.21 force field is used for the polymer, solvent molecules and graphite parameters are assigned to the carbon black atoms. A combination of molecular mechanics (MM) and molecular dynamics (NPT-MD and NVT-MD) techniques are used to obtain the equilibrium composite structure by inserting naphthalene rings in the polymer matrix. Polymers considered for this work include poly(4-vinylphenol), polyethylene oxide, and ethyl cellulose. Analytes studied are representative of both inorganic and organic compounds. The results are analyzed for the composite microstructure by calculating the radial distribution profiles as well as for the sensor response by predicting the interaction energies of the analytes with the composites. c2003 Elsevier Science B.V. All rights reserved.

  3. Molecular models of alginic acid: Interactions with calcium ions and calcite surfaces

    Science.gov (United States)

    Perry, Thomas D.; Cygan, Randall T.; Mitchell, Ralph

    2006-07-01

    Cation binding by polysaccharides is observed in many environments and is important for predictive environmental modeling, and numerous industrial and food technology applications. The complexities of these cation-organic interactions are well suited for predictive molecular modeling and the analysis of conformation and configuration of polysaccharides and their influence on cation binding. In this study, alginic acid was chosen as a model polymer system and representative disaccharide and polysaccharide subunits were developed. Molecular dynamics simulation of the torsion angles of the ether linkage between various monomeric subunits identified local and global energy minima for selected disaccharides. The simulations indicate stable disaccharide configurations and a common global energy minimum for all disaccharide models at Φ = 274 ± 7°, Ψ = 227 ± 5°, where Φ and Ψ are the torsion angles about the ether linkage. The ability of disaccharide subunits to bind calcium ions and to associate with the (101¯4) surface of calcite was also investigated. Molecular models of disaccharide interactions with calcite provide binding energy differences for conformations that are related to the proximity and residence densities of the electron-donating moieties with calcium ions on the calcite surface, which are controlled, in part, by the torsion of the ether linkage between monosaccharide units. Dynamically optimized configurations for polymer alginate models with calcium ions were also derived.

  4. Investigation of hybrid molecular material prepared by ionic liquid ...

    Indian Academy of Sciences (India)

    Wintec

    Near IR spectral region (1000–2500 nm) shows the elimination of water in the compound which ... 1-Butyl 3-methyl imidazolium bromide; molecular material; phosphotungstic acid; near IR. ..... attributable to the first overtone of hydroxyl groups,.

  5. Molecular structure and DFT investigations on new cobalt(II ...

    Indian Academy of Sciences (India)

    tion process was demonstrated.9 Late-transition metals, especially Ni, Pd ..... in table S2 (Supplementary Information). Most of the ... to molecular system because of atomic charges affect ... structure, acidity–basicity behavior and other proper-.

  6. Monitoring peptide-surface interaction by means of molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Nonella, Marco, E-mail: mnonella@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland); Seeger, Stefan, E-mail: sseeger@pci.uzh.ch [Physikalisch-Chemisches Institut, Universitaet Zuerich, Winterthurerstrasse 190, CH-8057 Zuerich (Switzerland)

    2010-12-09

    Graphical abstract: Protein-surface interactions play a crucial role in a wide field of research areas like biology, biotechnology, or pharmacology. Only recently, it has been shown that not only peptide adsorption represents an important process but also spreading and clustering of adsorbed proteins. By means of classical molecular dynamics, peptide adsorption as well as the dynamics of adsorbed peptides have been investigated in order to gain deeper insight into such processes. The picture shows a snapshot of an adsorbed peptide on a silica surface showing strong direct hydrogen bonding. Research highlights: {yields} Simulation of peptide surface interaction. {yields} Dynamics of hydrogen bond formation and destruction. {yields} Internal flexibility of adsorbed peptides. - Abstract: Protein adsorption and protein surface interactions have become an important research topic in recent years. Very recently, for example, it has been shown that protein clusters can undergo a surface-induced spreading after adsorption. Such phenomena emphasize the need of a more detailed insight into protein-silica interaction at an atomic level. Therefore, we have studied a model system consisting of a short peptide, a silica slab, and water molecules by means of classical molecular dynamics simulations. The study reveals that, besides of electrostatic interactions caused by the chosen charge distribution, the peptide interacts with the silica surface through formation of direct peptide-surface hydrogen bonds as well as indirect peptide-water-surface hydrogen bonds. The number of created hydrogen bonds varies considerably among the simulated structures. The strength of hydrogen bonding determines the mobility of the peptide on the surface and the internal flexibility of the adsorbed peptide.

  7. Synthesis, spectroscopic investigations, DFT studies, molecular docking and antimicrobial potential of certain new indole-isatin molecular hybrids: Experimental and theoretical approaches

    Science.gov (United States)

    Almutairi, Maha S.; Zakaria, Azza S.; Ignasius, P. Primsa; Al-Wabli, Reem I.; Joe, Isaac Hubert; Attia, Mohamed I.

    2018-02-01

    Indole-isatin molecular hybrids 5a-i have been synthesized and characterized by different spectroscopic methods to be evaluated as new antimicrobial agents against a panel of Gram positive bacteria, Gram negative bacteria, and moulds. Compound 5h was selected as a representative example of the prepared compounds 5a-i to perform computational investigations. Its vibrational properties have been studied using FT-IR and FT-Raman with the aid of density functional theory approach. The natural bond orbital analysis as well as HOMO and LUMO molecular orbitals investigations of compound 5h were carried out to explore its possible intermolecular delocalization or hyperconjugation and its possible interactions with the target protein. Molecular docking of compound 5h predicted its binding mode with the fungal target protein.

  8. Experimental investigations and modelling of sodium-concrete interaction

    International Nuclear Information System (INIS)

    Schultheiss, G.F.; Deeg, H.J.

    1990-01-01

    The use of sodium as a coolant in liquid metal fast breeder reactors, fusion reactors, and solar plants requires special consideration of its chemical reactivity and related safety problems in the case of sodium leckage. On contact between hot sodium and concrete an interaction takes place resulting in energy release and hydrogen generation, which may contribute to containment loading by pressurization in a hypothetical accident situation. For this reason, sodium-concrete interactions were investigated experimentally and theoretically. The experiments revealed important effects of quartzitic material within the concrete and of the sodium temperature on the interaction mechanisms, the energy release and the consequent hydrogen production. The numerical model shows good agreement with the experimental results. (orig.) [de

  9. A Bone-Implant Interaction Mouse Model for Evaluating Molecular Mechanism of Biomaterials/Bone Interaction.

    Science.gov (United States)

    Liu, Wenlong; Dan, Xiuli; Wang, Ting; Lu, William W; Pan, Haobo

    2016-11-01

    The development of an optimal animal model that could provide fast assessments of the interaction between bone and orthopedic implants is essential for both preclinical and theoretical researches in the design of novel biomaterials. Compared with other animal models, mice have superiority in accessing the well-developed transgenic modification techniques (e.g., cell tracing, knockoff, knockin, and so on), which serve as powerful tools in studying molecular mechanisms. In this study, we introduced the establishment of a mouse model, which was specifically tailored for the assessment of bone-implant interaction in a load-bearing bone marrow microenvironment and could potentially allow the molecular mechanism study of biomaterials by using transgenic technologies. The detailed microsurgery procedures for developing a bone defect (Φ = 0.8 mm) at the metaphysis region of the mouse femur were recorded. According to our results, the osteoconductive and osseointegrative properties of a well-studied 45S5 bioactive glass were confirmed by utilizing our mouse model, verifying the reliability of this model. The feasibility and reliability of the present model were further checked by using other materials as objects of study. Furthermore, our results indicated that this animal model provided a more homogeneous tissue-implant interacting surface than the rat at the early stage of implantation and this is quite meaningful for conducting quantitative analysis. The availability of transgenic techniques to mechanism study of biomaterials was further testified by establishing our model on Nestin-GFP transgenic mice. Intriguingly, the distribution of Nestin + cells was demonstrated to be recruited to the surface of 45S5 glass as early as 3 days postsurgery, indicating that Nestin + lineage stem cells may participate in the subsequent regeneration process. In summary, the bone-implant interaction mouse model could serve as a potential candidate to evaluate the early stage tissue

  10. Investigating the association between social interactions and personality states dynamics.

    Science.gov (United States)

    Gundogdu, Didem; Finnerty, Ailbhe N; Staiano, Jacopo; Teso, Stefano; Passerini, Andrea; Pianesi, Fabio; Lepri, Bruno

    2017-09-01

    The recent personality psychology literature has coined the name of personality states to refer to states having the same behavioural, affective and cognitive content (described by adjectives) as the corresponding trait, but for a shorter duration. The variability in personality states may be the reaction to specific characteristics of situations. The aim of our study is to investigate whether specific situational factors, that is, different configurations of face-to-face interactions, are predictors of variability of personality states in a work environment. The obtained results provide evidence that within-person variability in personality is associated with variation in face-to-face interactions. Interestingly, the effects differ by type and level of the personality states: adaptation effects for Agreeableness and Emotional Stability, whereby the personality states of an individual trigger similar states in other people interacting with them and complementarity effects for Openness to Experience, whereby the personality states of an individual trigger opposite states in other people interacting with them. Overall, these findings encourage further research to characterize face-to-face and social interactions in terms of their relevance to personality states.

  11. Investigating the amplitude of interactive footstep sounds and soundscape reproduction

    DEFF Research Database (Denmark)

    Turchet, Luca; Serafin, Stefania

    2013-01-01

    In this paper, we study the perception of amplitude of soundscapes and interactively generated footstep sounds provided both through headphones and a surround sound system. In particular, we investigate whether there exists a value for the amplitude of soundscapes and footstep sounds which...... of soundscapes does not significantly affect the selected amplitude of footstep sounds. Similarly, the perception of the soundscapes amplitude is not significantly affected by the selected amplitude of footstep sounds....

  12. The selective interaction between silica nanoparticles and enzymes from molecular dynamics simulations.

    Directory of Open Access Journals (Sweden)

    Xiaotian Sun

    Full Text Available Nanoscale particles have become promising materials in many fields, such as cancer therapeutics, diagnosis, imaging, drug delivery, catalysis, as well as biosensors. In order to stimulate and facilitate these applications, there is an urgent need for the understanding of the interaction mode between the nano-particles and proteins. In this study, we investigate the orientation and adsorption between several enzymes (cytochrome c, RNase A, lysozyme and 4 nm/11 nm silica nanoparticles (SNPs by using molecular dynamics (MD simulation. Our results show that three enzymes are adsorbed onto the surfaces of both 4 nm and 11 nm SNPs during our MD simulations and the small SNPs induce greater structural stabilization. The active site of cytochrome c is far away from the surface of 4 nm SNPs, while it is adsorbed onto the surface of 11 nm SNPs. We also explore the influences of different groups (-OH, -COOH, -NH2 and CH3 coated onto silica nanoparticles, which show significantly different impacts. Our molecular dynamics results indicate the selective interaction between silicon nanoparticles and enzymes, which is consistent with experimental results. Our study provides useful guides for designing/modifying nanomaterials to interact with proteins for their bio-applications.

  13. Characterization of the Interaction between Gallic Acid and Lysozyme by Molecular Dynamics Simulation and Optical Spectroscopy

    Directory of Open Access Journals (Sweden)

    Minzhong Zhan

    2015-07-01

    Full Text Available The binding interaction between gallic acid (GA and lysozyme (LYS was investigated and compared by molecular dynamics (MD simulation and spectral techniques. The results from spectroscopy indicate that GA binds to LYS to generate a static complex. The binding constants and thermodynamic parameters were calculated. MD simulation revealed that the main driving forces for GA binding to LYS are hydrogen bonding and hydrophobic interactions. The root-mean-square deviation verified that GA and LYS bind to form a stable complex, while the root-mean-square fluctuation results showed that the stability of the GA-LYS complex at 298 K was higher than that at 310 K. The calculated free binding energies from the molecular mechanics/Poisson-Boltzmann surface area method showed that van der Waals forces and electrostatic interactions are the predominant intermolecular forces. The MD simulation was consistent with the spectral experiments. This study provides a reference for future study of the pharmacological mechanism of GA.

  14. Study on the interaction of catalase with pesticides by flow injection chemiluminescence and molecular docking.

    Science.gov (United States)

    Tan, Xijuan; Wang, Zhuming; Chen, Donghua; Luo, Kai; Xiong, Xunyu; Song, Zhenghua

    2014-08-01

    The interaction mechanisms of catalase (CAT) with pesticides (including organophosphates: disulfoton, isofenphos-methyl, malathion, isocarbophos, dimethoate, dipterex, methamidophos and acephate; carbamates: carbaryl and methomyl; pyrethroids: fenvalerate and deltamethrin) were first investigated by flow injection (FI) chemiluminescence (CL) analysis and molecular docking. By homemade FI-CL model of lg[(I0-I)/I]=lgK+nlg[D], it was found that the binding processes of pesticides to CAT were spontaneous with the apparent binding constants K of 10(3)-10(5) L mol(-1) and the numbers of binding sites about 1.0. The binding abilities of pesticides to CAT followed the order: fenvalerate>deltamethrin>disulfoton>isofenphos-methyl>carbaryl>malathion>isocarbophos>dimethoate>dipterex>acephate>methomyl>methamidophos, which was generally similar to the order of determination sensitivity of pesticides. The thermodynamic parameters revealed that CAT bound with hydrophobic pesticides by hydrophobic interaction force, and with hydrophilic pesticides by hydrogen bond and van der Waals force. The pesticides to CAT molecular docking study showed that pesticides could enter into the cavity locating among the four subdomains of CAT, giving the specific amino acid residues and hydrogen bonds involved in CAT-pesticides interaction. It was also found that the lgK values of pesticides to CAT increased regularly with increasing lgP, Mr, MR and MV, suggesting that the hydrophobicity and steric property of pesticide played essential roles in its binding to CAT. Copyright © 2014 Elsevier Ltd. All rights reserved.

  15. Investigating Atmospheric Oxidation with Molecular Dynamics Imaging and Spectroscopy

    Science.gov (United States)

    Merrill, W. G.; Case, A. S.; Keutsch, F. N.

    2013-06-01

    Volatile organic compounds (VOCs) in the Earth's atmosphere constitute trace gas species emitted primarily from the biosphere, and are the subject of inquiry for a variety of air quality and climate studies. Reactions intiated (primarily) by the hydroxyl radical (OH) lead to a myriad of oxygenated species (OVOCs), which in turn are prone to further oxidation. Investigations of the role that VOC oxidation plays in tropospheric chemistry have brought to light two troubling scenarios: (1) VOCs are responsible in part for the production of two EPA-regulated pollutants---tropospheric ozone and organic aerosol---and (2) the mechanistic details of VOC oxidation remain convoluted and poorly understood. The latter issue hampers the implementation of near-explicit atmospheric simulations, and large discrepancies in OH reactivity exist between measurements and models at present. Such discrepancies underscore the need for a more thorough description of VOC oxidation. Time-of-flight measurements and ion-imaging techniques are viable options for resolving some of the mechanistic and energetic details of VOC oxidation. Molecular beam studies have the advantage of foregoing unwanted bimolecular reactions, allowing for the characterization of specific processes which must typically compete with the complex manifold of VOC oxidation pathways. The focus of this work is on the unimolecular channels of organic peroxy radical intermediates, which are necessarily generated during VOC oxidation. Such intermediates may isomerize and decompose into distinct chemical channels, enabling the unambiguous detection of each pathway. For instance, a (1 + 1') resonance enhanced multiphoton ionization (REMPI) scheme may be employed to detect carbon monoxide generated from a particular unimolecular process. A number of more subtle mechanistic details may be explored as well. By varying the mean free path of the peroxy radicals in a flow tube, the role of collisional quenching in these unimolecular

  16. A molecular investigation of adsorption onto mineral pigments

    Science.gov (United States)

    Ninness, Brian J.

    Pigment suspensions are important in several processes such as ceramics, paints, inks, and coatings. In the wet state, pigments are combined with a variety of chemical species such as polymers, surfactants, and polyelectrolytes which produce a complex colloidal system. The adsorption, desorption, and redistribution of these species at the pigment-aqueous solution interface can have an impact on the behavior in both the wet state or its final dried state. The goal of this work is to establish a molecular picture of the adsorption properties of these pigmented systems. A novel in situ infrared technique has been developed which allows the detection of adsorbed surface species on pigment particles in an aqueous environment. The technique involves the use of a polymeric binder to anchor the colloidal pigment particles to the surface of an internal reflection element (IRE). The binder only weakly perturbs about 25% of the reactive surface sites (hydroxyl groups) on silica. The reaction of succinic anhydride with an aminosilanized silica surface has been quantified using this technique. The adsorption dynamics of the cationic surfactant cetyltrimethylammonium bromide (C16TAB) at the TiO2-aqueous solution interface has been investigated using Fourier transform infrared-attenuated total reflection spectroscopy (FTIR-ATR) and electrokinetic analysis. At low bulk concentrations, C16TAB is shown to adsorb as isolated islands with a "defective" bilayer structure. Anionic probe molecules are shown to effectively "tune" the adsorbed surfactant microstructure. The results indicate that the structure of the adsorbed surfactant layer, and not the amount of adsorbed surfactant, dictates the subsequent adsorption behavior of the system. Atomic Layer Deposition is used to deposit a TiO2 layer onto the surfaces of silica and kaolin pigments. The process involves the cyclic reaction sequence of the vapors of TiCl4 and H2O. Three complete deposition cycles are needed before the surfaces

  17. Isolate extended state in the DNA molecular transistor with surface interaction

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Le, E-mail: wang_le917@gs.zzu.edu.cn; Qin, Zhi-Jie

    2016-02-01

    The field effect characteristic of a DNA molecular device is investigated in a tight binding model with binary disorder and side site correlation. Using the transfer-matrix method and Landauer–Büttiker theory, we find that the system has isolated extended state that is irrespective of the DNA sequence and can be modulated by the gate voltage. When the gate voltage reaches some proper value, the isolated extended state appears at the Fermi level of the system and the long range charge transport is greatly enhanced. We attribute this phenomenon to the combination of the external field, the surface interaction, and the intrinsic disorder of DNA. The result is a generic feature of the nanowire with binary disorder and surface interaction.

  18. Translational-rotational interaction in dynamics and thermodynamics of 2D atomic crystal with molecular impurity

    International Nuclear Information System (INIS)

    Antsygina, T.N.; Poltavskaya, M.I.; Chishko, K.A.

    2003-01-01

    The interaction between the rotational degrees of freedom of a diatomic molecular impurity and the phonon excitations of a two-dimensional atomic matrix commensurate with a substrate is investigated theoretically. It is shown, that the translational-rotational interaction changes the form of the rotational kinetic energy operator as compared to the corresponding expression for a free rotator, and also renormalized the parameters of the crystal field without change in its initial form. The contribution of the impurity rotational degrees of freedom to the low-temperature heat capacity for a dilute solution of diatomic molecules in an atomic two-dimensional matrix is calculated. The possibility of experimental observation of the effects obtained is discussed

  19. Advanced Characterization of Molecular Interactions in TALSPEAK-like Separations Systems

    Energy Technology Data Exchange (ETDEWEB)

    Nash, Kenneth [Washington State Univ., Pullman, WA (United States); Guelis, Artem [Argonne National Lab. (ANL), Argonne, IL (United States); Lumetta, Gregg J. [Pacific Northwest National Lab. (PNNL), Richland, WA (United States); Sinkov, Sergey [Pacific Northwest National Lab. (PNNL), Richland, WA (United States)

    2015-10-21

    Combining unit operations in advanced aqueous reprocessing schemes brings obvious process compactness advantages, but at the same time greater complexity in process design and operation. Unraveling these interactions requires increasingly sophisticated analytical tools and unique approaches for adequate analysis and characterization that probe molecular scale interactions. Conventional slope analysis methods of solvent extraction are too indirect to provide much insight into such interactions. This project proposed the development and verification of several analytical tools based on studies of TALSPEAK-like aqueous processes. As such, the chemistry of trivalent fission product lanthanides, americium, curium, plutonium, neptunium and uranium figure prominently in these studies. As the project was executed, the primary focus fell upon the chemistry or trivalent lanthanides and actinides. The intent of the investigation was to compare and contrast the results from these various complementary techniques/studies to provide a stronger basis for predicting the performance of extractant/diluent mixtures as media for metal ion separations. As many/most of these techniques require the presence of metal ions at elevated concentrations, it was expected that these studies would take this investigation into the realm of patterns of supramolecular organization of metal complexes and extractants in concentrated aqueous/organic media. We expected to advance knowledge of the processes that enable and limit solvent extraction reactions as a result of the application of fundamental chemical principles to explaining interactions in complex media.

  20. Atomistic interactions of clusters on surfaces using molecular dynamics and hyper molecular dynamics

    International Nuclear Information System (INIS)

    Sanz-Navarro, Carlos F.

    2002-01-01

    The work presented in this thesis describes the results of Molecular Dynamics (MD) simulations applied to the interaction of silver clusters with graphite surfaces and some numerical and theoretical methods concerning the extension of MD simulations to longer time scales (hyper-MD). The first part of this thesis studies the implantation of clusters at normal incidence onto a graphite surface in order to determine the scaling of the penetration depth (PD) against the impact energy. A comparison with experimental results is made with good agreement. The main physical observations of the impact process are described and analysed. It is shown that there is a threshold impact velocity above which the linear dependence on PD on impact energy changes to a linear dependence on velocity. Implantation of silver clusters at oblique incidence is also considered. The second part of this work analyses the validity and feasibility of the three minimisation methods for the hyper-MD simulation method whereby time scales of an MD simulation can be extended. A correct mathematical basis for the iterative method is derived. It is found that one of the iterative methods, upon which hyper-lD is based, is very likely to fail in high-dimensional situations because it requires a too expensive convergence. Two new approximations to the hyper-MD approach are proposed, which reduce the computational effort considerably. Both approaches, although not exact, can help to search for some of the most likely transitions in the system. Some examples are given to illustrate this. (author)

  1. Spectroscopic and molecular modeling investigation on the binding of a synthesized steroidal amide to protein

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Hua-xin, E-mail: h.x.zhang@yeah.net; Liu, E.

    2014-09-15

    Owing to the various valuable biological activities, steroidal amides have become a hot topic in steroidal pharmaceutical chemistry. In this paper, an anti-tumor steroid derivate (DAAO) was synthesized and identified. The interaction between DAAO and human serum albumin (HSA) was studied by fluorescence spectra, circular dichroism (CD) spectra, molecular modeling and molecular probe techniques. The results suggested that DAAO had reacted with HSA through hydrogen bonds and van der Waals power. The formation of DAAO–HSA complex at ground state led to static quenching of HSA's fluorescence. The number of binding sites, binding constants, enthalpy change (ΔH{sup θ}), Gibbs free energy change (ΔG{sup θ}) and entropy change (ΔS{sup θ}) were calculated at different temperatures based on fluorescence quenching theory and classic equation. Molecular modeling investigation indicated that DAAO was more inclined to absorb on Sudlow's site I in subdomain IIA of HSA molecule on grounds of the lowest energy principle and steric hindrance effect. The binding location was further confirmed by fluorescence probe experiment using warfarin (site I probe) for displacement. Furthermore, the conformational changes of HSA in presence of DAAO were investigated by CD spectra. The results could provide new evidence explaining the relationship between the chemical structure and biological activity and may be useful for understanding the anti-cancer mechanism of steroidal drug. - Highlights: • A designed steroidal amide compound (DAAO) was synthesized by introducing amido bonds into a steroid nucleus. • DAAO binds to Sudlow's site I in HSA through hydrogen bonds and van der Waals power. • The interaction was a spontaneous and exothermic process with modest degree of reversibility. • The secondary structure of HSA and the microenvironment of TRP214 altered. • Amido bond in steroid nucleus (–NH–CO–) plays important role in stabling the structure of

  2. Molecular fundamentals of drug interactions in the therapy of colorectal cancer

    Directory of Open Access Journals (Sweden)

    Katarzyna Regulska

    2014-03-01

    Full Text Available Rapid advances in the field of chemotherapy have resulted in the introduction of numerous antineoplastic drugs into clinical practice, which increased the efficiency of patient management. Also the prevalent use of combination treatment based on drug action synergy contributed to the improved clinical effect associated with cytotoxic drug administration. It seems, however, obvious that the multidirectional pharmacotherapy in oncology requires a thorough knowledge of drugs’ pharmaceutical behavior in order to maximize their collective action and prevent the occurrence of unintended drug interactions that could potentially impair treatment effectiveness. In fact, drug interactions constitute a serious problem for current oncology primarily resulting from a narrow therapeutic index specific for the majority of anticancer drugs. This, in turn, indicates that even slight deviations of their pharmacokinetics could cause significant clinical consequences, manifested by alteration of the toxicological profile or reduction of therapeutic efficiency. Hence, the investigation of molecular aspects underlying the mechanisms of various drug interactions seems to be essential for proper and safe patient management. The present article is devoted to the extensive subject of drug interactions occurring in the therapy of colorectal cancer. It presents the available literature data on both positive and negative effects of interactions and it discusses their mechanisms complying with their classification into pharmacokinetic and pharmacodynamic ones.

  3. [Molecular fundamentals of drug interactions in the therapy of colorectal cancer].

    Science.gov (United States)

    Regulska, Katarzyna; Stanisz, Beata; Regulski, Miłosz; Gieremek, Paulina

    2014-03-04

    Rapid advances in the field of chemotherapy have resulted in the introduction of numerous antineoplastic drugs into clinical practice, which increased the efficiency of patient management. Also the prevalent use of combination treatment based on drug action synergy contributed to the improved clinical effect associated with cytotoxic drug administration. It seems, however, obvious that the multidirectional pharmacotherapy in oncology requires a thorough knowledge of drugs' pharmaceutical behavior in order to maximize their collective action and prevent the occurrence of unintended drug interactions that could potentially impair treatment effectiveness. In fact, drug interactions constitute a serious problem for current oncology primarily resulting from a narrow therapeutic index specific for the majority of anticancer drugs. This, in turn, indicates that even slight deviations of their pharmacokinetics could cause significant clinical consequences, manifested by alteration of the toxicological profile or reduction of therapeutic efficiency. Hence, the investigation of molecular aspects underlying the mechanisms of various drug interactions seems to be essential for proper and safe patient management. The present article is devoted to the extensive subject of drug interactions occurring in the therapy of colorectal cancer. It presents the available literature data on both positive and negative effects of interactions and it discusses their mechanisms complying with their classification into pharmacokinetic and pharmacodynamic ones.

  4. Experimental investigation of electron beam wave interactions utilising short pulses

    International Nuclear Information System (INIS)

    Wiggins, Samuel Mark

    2000-01-01

    Experiments have investigated the production of ultra-short electromagnetic pulses and their interaction with electrons in various resonant structures. Diagnostic systems used in the measurements included large bandwidth detection systems for capturing the short pulses. Deconvolution techniques have been applied to account for bandwidth limitation of the detection systems and to extract the actual pulse amplitudes and durations from the data. A Martin-Puplett interferometer has been constructed for use as a Fourier transform spectrometer. The growth of superradiant electromagnetic spikes from short duration (0.5-1.0 ns), high current (0.6-2.0 kA) electron pulses has been investigated in a Ka-band Cherenkov maser and Ka- and W-band backward wave oscillators (BWO). In the Cherenkov maser, radiation spikes were produced with a peak power ≤ 3 MW, a duration ≥ 70 ps and a bandwidth ≤ 19 %. It is shown that coherent spontaneous emission from the leading edge of the electron pulse drives these interactions, giving rise to self-amplified coherent spontaneous emission (SACSE). BWO spikes were produced with a peak power ≤ 63 MW and a pulse duration ∼ 250 ps in the Ka-band and ≤ 12 MW and ∼ 170 ps in the W-band. Evidence of superradiant evolution has been observed in the measurements of scaling laws such as power scaling with the current squared and duration scaling inversely with the fourth root of the power. An X-band free-electron maser amplifier, in which a short (1.0ns) injected radiation pulse interacts with a long (∼ 140 ns) electron beam, has been investigated. The interaction is shown to evolve in the linear regime. The peak output power was 320 kW, which corresponded to a gain, approximately constant across the band, of 42 dB. Changes to the spectrum, that occur when the input radiation pulse is injected into electrons with an energy gradient, have been analysed. (author)

  5. Investigations of the D-multi-ρ interactions

    Energy Technology Data Exchange (ETDEWEB)

    Xiao, C.W. [Institut fuer Kernphysik (Theorie), Institute for Advanced Simulation, and Juelich Center for Hadron Physics, Forschungszentrum Juelich (Germany); Central South University, School of Physics and Electronics, Changsha (China)

    2017-09-15

    In the present work, which aims at searching for bound states, the interactions of the D-multi-ρ systems are investigated by means of the formalism of the fixed-center approximation to Faddeev equations. Reproducing the states of f{sub 2}(1270) and D{sub 1}(2420) dynamically in the two-body ρρ and ρD interactions, respectively, as the clusters of the fixed-center approximation, the state of D(3000){sup 0} is found as a molecule of D - f{sub 2} or ρ - D{sub 1} structures in the three-body interactions, where we determine its quantum number J{sup P} = 2{sup -} and find another possible state of D{sub 2}(3100) with isospin I = 3/2. In our results, there are some other predictions with uncertainties, a D{sub 3}(3160) state with I(J{sup P}) = (1)/(2)(3{sup +}) in the four-body interactions, a narrow D{sub 4}(3730) state with I(J{sup P}) = (1)/(2)(4{sup -}), a wide D{sub 4}(3410) state of I(J{sup P}) = (1)/(2)(4{sup -}), and another wide D{sub 4}(3770) state but with I(J{sup P}) = (3)/(2)(4{sup -}) in the five-body interactions, and a D{sub 5}(3570) state with I(J{sup P}) = (1)/(2)(5{sup +}) in the six-body interactions. (orig.)

  6. In vitro and in silico investigations of the binding interactions between chlorophenols and trypsin

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Yan-Qing, E-mail: wyqing76@126.com [Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province (China); Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Tan, Chun-Yun [Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Zhuang, Shu-Lin [Institute of Environmental Science, College of Environmental and Resource Science, Zhejiang University, Hangzhou 310058 (China); Zhai, Peng-Zhan; Cui, Yun; Zhou, Qiu-Hua; Zhang, Hong-Mei [Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China); Fei, Zhenghao [Jiangsu Provincial Key Laboratory of Coastal Wetland Bioresources and Environmental Protection, Yancheng City 224002, Jiangsu Province (China); Institute of Applied Chemistry and Environmental Engineering, Yancheng Teachers University, Yancheng City 224002, Jiangsu Province (China)

    2014-08-15

    Graphical abstract: - Highlights: • Binding interactions of five chlorophenols with trypsin were investigated. • The number of chlorine atoms of chlorophenols partly affected the binding ability of them to trypsin. • Noncovalent interactions stabilized the trypsin–chlorophenols complexes. • There was the one main binding site of trypsin for chlorophenols. - Abstract: Being the first-degree toxic pollutants, chlorophenols (CP) have potential carcinogenic and mutagenic activity and toxicity. Since there still lacks studies on molecular interactions of chlorophenols with trypsin, one major binding target of many exogenous environmental pollutants, the binding interactions between five chlorophenols, 2-CP, 2,6-DCP, 2,4,6-TCP, 2,4,6-TCP, 2,3,4,6-TCP and PCP and trypsin were characterized by the combination of multispectroscopic techniques and molecular modeling. The chlorophenols bind at the one main site of trypsin and the binding induces the changes of microenvironment and global conformations of trypsin. Different number of chloride atoms significantly affects the binding and the binding constants K{sub A} ranks as K{sub A} (2-CP) < K{sub A} (2,6-DCP) ≈ K{sub A} (2,4,6-TCP) < K{sub A} (2,3,4,6-TCP) < K{sub A} (PCP). These chlorophenols interacts with trypsin mainly through hydrophobic interactions and via hydrogen bonding interactions and aromatic–aromatic π–π stacking interaction. Our results offer insights into the binding mechanism of chlorophenols with trypsin and provide important information for possible toxicity risk of chlorophenols to human health.

  7. Molecular Interactions and Reaction Dynamics in Supercritical Water Oxidation

    National Research Council Canada - National Science Library

    Johnston, K

    1998-01-01

    .... From UV-vis spectroscopic measurements and molecular dynamics simulation of chemical equilibria, we have shown that density effects on broad classes of reactions may be explained in terms of changes...

  8. Molecular Dynamics Investigation of Efficient SO₂ Absorption by ...

    Indian Academy of Sciences (India)

    Ionic liquids are appropriate candidates for the absorption of acid gases such as SO₂. Six anion functionalized ionic liquids with different basicities have been studied for SO₂ absorption capacity by employing quantum chemical calculations and molecular dynamics (MD) simulations. Gas phase quantum calculations ...

  9. Interactive Molecular Graphics for Augmented Reality Using HoloLens.

    Science.gov (United States)

    Müller, Christoph; Krone, Michael; Huber, Markus; Biener, Verena; Herr, Dominik; Koch, Steffen; Reina, Guido; Weiskopf, Daniel; Ertl, Thomas

    2018-06-13

    Immersive technologies like stereo rendering, virtual reality, or augmented reality (AR) are often used in the field of molecular visualisation. Modern, comparably lightweight and affordable AR headsets like Microsoft's HoloLens open up new possibilities for immersive analytics in molecular visualisation. A crucial factor for a comprehensive analysis of molecular data in AR is the rendering speed. HoloLens, however, has limited hardware capabilities due to requirements like battery life, fanless cooling and weight. Consequently, insights from best practises for powerful desktop hardware may not be transferable. Therefore, we evaluate the capabilities of the HoloLens hardware for modern, GPU-enabled, high-quality rendering methods for the space-filling model commonly used in molecular visualisation. We also assess the scalability for large molecular data sets. Based on the results, we discuss ideas and possibilities for immersive molecular analytics. Besides more obvious benefits like the stereoscopic rendering offered by the device, this specifically includes natural user interfaces that use physical navigation instead of the traditional virtual one. Furthermore, we consider different scenarios for such an immersive system, ranging from educational use to collaborative scenarios.

  10. Experimental investigation of the piano hammer-string interaction.

    Science.gov (United States)

    Birkett, Stephen

    2013-04-01

    Experimental techniques for investigating the piano hammer-string interaction are described. It is argued that the accuracy, consistency, and scope of conclusions of previous studies can be compromised by limitations of the conventional methods relating to key inputs; physical distortion; numerical distortion, particularly when differentiation or integration of measured signals is used to derive primary response variables; contact identification; and synchronization issues. These problems are discussed, and experimental methods that have been devised to avoid them are described and illustrated by detailed results from a study of the hammer-string interaction in a vertical piano. High resolution displacements are obtained directly by non-contact high-speed imaging and quantitative motion tracking. The attention focused on achieving very accurate and consistent temporal and spatial alignment, including the objective procedure used for contact identification, allows meaningful comparisons of responses from separate tests. String motion at the strike point and on each side of it, as well as hammer motion, is obtained for eight dynamic levels from 1.06 to 2.98 m/s impact velocity. Detailed observations of the force-compression behavior of the hammer interacting with real strings are presented. The direct effects of hammer shank deflection and agraffe string pulses on the interaction are also highlighted.

  11. Low energy Cu clusters slow deposition on a Fe (001) surface investigated by molecular dynamics simulation

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Shixu [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China); Gong, Hengfeng [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Division of Nuclear Materials Science and Engineering, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800 (China); Chen, Xuanzhi [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Li, Gongping, E-mail: ligp@lzu.edu.cn [School of Nuclear Science and Technology, Lanzhou University, Lanzhou 730000 (China); Wang, Zhiguang, E-mail: zhgwang@impcas.ac.cn [Laboratory of Advanced Nuclear Materials, Institute of Modern Physics, Chinese Academy of Sciences, Lanzhou 730000 (China)

    2014-09-30

    Highlights: • We study the deposition of low energy Cu clusters on Fe (001) surface by molecular dynamics. • The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. • The phenomenon of contact epitaxy of cluster occurred. • The thermal diffusion of cluster atoms was analyzed. - Abstract: The slow deposition of low energy Cu clusters on a Fe (001) surface was investigated by molecular dynamics simulation. A many-body potential based on Finnis–Sinclair model was used to describe the interactions among atoms. Three clusters comprising of 13, 55 and 147 atoms, respectively, were deposited with incident energies ranging from 0.0 to 1.0 eV/atom at various substrate temperatures (0, 300 and 800 K). The rearrangement and the diffusion of cluster can occur, only when the cluster atoms are activated and obtained enough migration energy. The interaction between low energy cluster and substrate can be divided to the landing and the thermal diffusion phases. In the former, the migration energy originates from the latent heat of binding energy for the soft deposition regime and primarily comes from the incident energy of cluster for the energetic cluster deposition regime. In the latter, the thermal vibration would result in some cluster atoms activated again at medium and high substrate temperatures. Also, the effects of incident energy, cluster size and substrate temperature on the interaction potential energy between cluster and substrate, the final deposition morphology of cluster, the spreading index and the structure parameter of cluster are analyzed.

  12. Optoelectronic investigation of nanodiamond interactions with human blood

    Science.gov (United States)

    Ficek, M.; Wróbel, M. S.; Wasowicz, M.; Jedrzejewska-Szczerska, M.

    2016-03-01

    We present optoelectronic investigation of in vitro interactions of whole human blood with different nanodiamond biomarkers. Plasmo-chemical modifications of detonation nanodiamond particles gives the possibility for controlling their surface for biological applications. Optical investigations reveal the biological activity of nanodiamonds in blood dependent on its surface termination. We compare different types of nanodiamonds: commercial non-modified detonation nanodiamonds, and nanodiamonds modified by MW PACVD method with H2-termination, and chemically modified nanodiamond with O2-termination. The absorption spectra, and optical microscope investigations were conducted. The results indicate haemocompatibility of non-modified detonation nanodiamond as well as modified nanodiamonds, which enables their application for drug delivery, as well as sensing applications.

  13. Experimental and molecular docking studies on DNA binding interaction of adefovir dipivoxil: Advances toward treatment of hepatitis B virus infections

    Science.gov (United States)

    Shahabadi, Nahid; Falsafi, Monireh

    The toxic interaction of adefovir dipivoxil with calf thymus DNA (CT-DNA) was investigated in vitro under simulated physiological conditions by multi-spectroscopic techniques and molecular modeling study. The fluorescence spectroscopy and UV absorption spectroscopy indicated drug interacted with CT-DNA in a groove binding mode. The binding constant of UV-visible and the number of binding sites were 3.33 ± 0.2 × 104 L mol-1and 0.99, respectively. The fluorimetric studies showed that the reaction between the drug and CT-DNA is exothermic (ΔH = 34.4 kJ mol-1; ΔS = 184.32 J mol-1 K-1). Circular dichroism spectroscopy (CD) was employed to measure the conformational change of CT-DNA in the presence of adefovir dipivoxil, which verified the groove binding mode. Furthermore, the drug induces detectable changes in its viscosity. The molecular modeling results illustrated that adefovir strongly binds to groove of DNA by relative binding energy of docked structure -16.83 kJ mol-1. This combination of multiple spectroscopic techniques and molecular modeling methods can be widely used in the investigation on the toxic interaction of small molecular pollutants and drugs with bio macromolecules, which contributes to clarify the molecular mechanism of toxicity or side effect in vivo.

  14. Reconstruction and validation of RefRec: a global model for the yeast molecular interaction network.

    Directory of Open Access Journals (Sweden)

    Tommi Aho

    2010-05-01

    Full Text Available Molecular interaction networks establish all cell biological processes. The networks are under intensive research that is facilitated by new high-throughput measurement techniques for the detection, quantification, and characterization of molecules and their physical interactions. For the common model organism yeast Saccharomyces cerevisiae, public databases store a significant part of the accumulated information and, on the way to better understanding of the cellular processes, there is a need to integrate this information into a consistent reconstruction of the molecular interaction network. This work presents and validates RefRec, the most comprehensive molecular interaction network reconstruction currently available for yeast. The reconstruction integrates protein synthesis pathways, a metabolic network, and a protein-protein interaction network from major biological databases. The core of the reconstruction is based on a reference object approach in which genes, transcripts, and proteins are identified using their primary sequences. This enables their unambiguous identification and non-redundant integration. The obtained total number of different molecular species and their connecting interactions is approximately 67,000. In order to demonstrate the capacity of RefRec for functional predictions, it was used for simulating the gene knockout damage propagation in the molecular interaction network in approximately 590,000 experimentally validated mutant strains. Based on the simulation results, a statistical classifier was subsequently able to correctly predict the viability of most of the strains. The results also showed that the usage of different types of molecular species in the reconstruction is important for accurate phenotype prediction. In general, the findings demonstrate the benefits of global reconstructions of molecular interaction networks. With all the molecular species and their physical interactions explicitly modeled, our

  15. Investigation of nuclear multifragmentation using molecular dynamics and restructured aggregation

    International Nuclear Information System (INIS)

    Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Leray, S.; Ngo, C.; Souza, S.R.; Yu-Ming, Zheng; Paula, L. de; Nemeth, J.; Ben-Hao, Sa.; Yu-Ming, Zheng; Ngo, H.

    1991-01-01

    We study the stability of excited 197 Au nuclei with respect to multifragmentation. For that we use a dynamical simulation based on molecular dynamics and restructured aggregation. A particular attention is paid to check the stability of the ground state nuclei generated by the simulation. Four kinds of excitations are considered: heat, compression, rotation and a geometrical instability created when a projectile drills a hole in a 197 Au nucleus

  16. Experimental investigation of molecular beam injection in HL-1 tokamak

    International Nuclear Information System (INIS)

    Yao Lianghua; Diao Guangyao; Wang Zhanhe; Deng Huichen; Luo Junlin; Duan Xuru; Cui Zhengying

    1993-07-01

    A new method of gas puffing is presented. The molecular beam, formed by high pressure deuterium gas through Larval nozzle and skimmer slit, is injected into the HL-1 vacuum vessel. The deuterium molecular current from the nozzle passing through the skimmer is about 3 x 10 20 /s. At the line average electron density of 5.2 x 10 19 m -3 , the beam velocity is about 100 m/s. As the plasma density and temperature increasing, the influxes of deuterium particles attenuate quickly. When the molecular beam injection (MBI) just returned to normal gas puffing, the D α emission rapidly decreases, meanwhile, the particles move toward plasma center, the electron density is continuously peaking. The line average electron density rising lasts 45 ms. The thermal energy of plasma and confinement time for particles and energy are also increasing. the MBI is a direct and efficient gas fuelling mode, and the injected particles can reach to inside about 8 cm of plasma and q ≅ 2 confinement region. Its efficiency of injection is about 50%. After the MBI, the particle recycling coefficient R on the wall is 0.6 which is 10% lower than that of normal gas puffing

  17. Interactive house investigation and radon diagnostics computer program

    International Nuclear Information System (INIS)

    Gillette, L.M.

    1990-01-01

    This paper reports on the interactive computer program called Dungeons and Radon which was developed as part of the Environmental Protection Agency's (EPA's) Radon Contractor Proficiency (RCP) Program's Radon Technology for Mitigators (RTM) course which is currently being offered in the Regional Radon Training Centers (RRTCs). The program was designed by Terry Brennan to be used in training radon mitigation contractors. The Macintosh based program consists of a series of animated, sound and voice enhanced house scenes. The participants choose where and what to investigate and where to perform diagnostic tests in order to gather enough information to design a successful mitigation system

  18. Intermolecular interaction of fosinopril with bovine serum albumin (BSA): The multi-spectroscopic and computational investigation.

    Science.gov (United States)

    Zhou, Kai-Li; Pan, Dong-Qi; Lou, Yan-Yue; Shi, Jie-Hua

    2018-04-16

    The intermolecular interaction of fosinopril, an angiotensin converting enzyme inhibitor with bovine serum albumin (BSA), has been investigated in physiological buffer (pH 7.4) by multi-spectroscopic methods and molecular docking technique. The results obtained from fluorescence and UV absorption spectroscopy revealed that the fluorescence quenching mechanism of BSA induced by fosinopril was mediated by the combined dynamic and static quenching, and the static quenching was dominant in this system. The binding constant, K b , value was found to lie between 2.69 × 10 3 and 9.55 × 10 3  M -1 at experimental temperatures (293, 298, 303, and 308 K), implying the low or intermediate binding affinity between fosinopril and BSA. Competitive binding experiments with site markers (phenylbutazone and diazepam) suggested that fosinopril preferentially bound to the site I in sub-domain IIA on BSA, as evidenced by molecular docking analysis. The negative sign for enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) indicated that van der Waals force and hydrogen bonds played important roles in the fosinopril-BSA interaction, and 8-anilino-1-naphthalenesulfonate binding assay experiments offered evidence of the involvements of hydrophobic interactions. Moreover, spectroscopic results (synchronous fluorescence, 3-dimensional fluorescence, and Fourier transform infrared spectroscopy) indicated a slight conformational change in BSA upon fosinopril interaction. Copyright © 2018 John Wiley & Sons, Ltd.

  19. Theoretical investigations of molecular wires: Electronic spectra and electron transport

    Science.gov (United States)

    Palma, Julio Leopoldo

    The results of theoretical and computational research are presented for two promising molecular wires, the Nanostar dendrimer, and a series of substituted azobenzene derivatives connected to aluminum electrodes. The electronic absorption spectra of the Nanostar (a phenylene-ethynylene dendrimer attached to an ethynylperylene chromophore) were calculated using a sequential Molecular Dynamics/Quantum Mechanics (MD/QM) method to perform an analysis of the temperature dependence of the electronic absorption process. We modeled the Nanostar as a series of connected units, and performed MD simulations for each chromophore at 10 K and 300 K to study how the temperature affected the structures and, consequently, the spectra. The absorption spectra of the Nanostar were computed using an ensemble of 8000 structures for each chromophore. Quantum Mechanical (QM) ZINDO/S calculations were performed for each conformation in the ensemble, including 16 excited states, for a total of 128,000 excitation energies. The spectral intensity was then scaled linearly with the number of conjugated units. Our calculations for both the individual chromophores and the Nanostar, are in good agreement with experiments. We explain in detail the effects of temperature and the consequences for the absorption process. The second part of this thesis presents a study of the effects of chemical substituents on the electron transport properties of the azobenzene molecule, which has been proposed recently as a component of a light-driven molecular switch. This molecule has two stable conformations (cis and trans) in its electronic ground state, with considerable differences in their conductance. The electron transport properties were calculated using first-principles methods combining non-equilibrium Green's function (NEGF) techniques with density functional theory (DFT). For the azobenzene studies, we included electron-donating groups and electron-withdrawing groups in meta- and ortho-positions with

  20. Investigation of polarization effects in the gramicidin A channel from ab initio molecular dynamics simulations.

    Science.gov (United States)

    Timko, Jeff; Kuyucak, Serdar

    2012-11-28

    Polarization is an important component of molecular interactions and is expected to play a particularly significant role in inhomogeneous environments such as pores and interfaces. Here we investigate the effects of polarization in the gramicidin A ion channel by performing quantum mechanics/molecular mechanics molecular dynamics (MD) simulations and comparing the results with those obtained from classical MD simulations with non-polarizable force fields. We consider the dipole moments of backbone carbonyl groups and channel water molecules as well as a number of structural quantities of interest. The ab initio results show that the dipole moments of the carbonyl groups and water molecules are highly sensitive to the hydrogen bonds (H-bonds) they participate in. In the absence of a K(+) ion, water molecules in the channel are quite mobile, making the H-bond network highly dynamic. A central K(+) ion acts as an anchor for the channel waters, stabilizing the H-bond network and thereby increasing their average dipole moments. In contrast, the K(+) ion has little effect on the dipole moments of the neighboring carbonyl groups. The weakness of the ion-peptide interactions helps to explain the near diffusion-rate conductance of K(+) ions through the channel. We also address the sampling issue in relatively short ab initio MD simulations. Results obtained from a continuous 20 ps ab initio MD simulation are compared with those generated by sampling ten windows from a much longer classical MD simulation and running each window for 2 ps with ab initio MD. Both methods yield similar results for a number of quantities of interest, indicating that fluctuations are fast enough to justify the short ab initio MD simulations.

  1. Insight into molecular interactions between two PB1 domains

    NARCIS (Netherlands)

    van Drogen-Petit, A.; Zwahlen, C.; Peter, M.; Bonvin, A.M.J.J.

    2004-01-01

    Specific protein–protein interactions play crucial roles in the regulation of any biological process. Recently, a new protein–protein interaction domain termed PB1 (Phox and Bem1) was identified, which is conserved throughout evolution and present in diverse proteins functioning in signal

  2. Characterization of wise protein and its molecular mechanism to interact with both Wnt and BMP signals.

    Science.gov (United States)

    Lintern, Katherine B; Guidato, Sonia; Rowe, Alison; Saldanha, José W; Itasaki, Nobue

    2009-08-21

    Cross-talk of BMP and Wnt signaling pathways has been implicated in many aspects of biological events during embryogenesis and in adulthood. A secreted protein Wise and its orthologs (Sostdc1, USAG-1, and Ectodin) have been shown to modulate Wnt signaling and also inhibit BMP signals. Modulation of Wnt signaling activity by Wise is brought about by an interaction with the Wnt co-receptor LRP6, whereas BMP inhibition is by binding to BMP ligands. Here we have investigated the mode of action of Wise on Wnt and BMP signals. It was found that Wise binds LRP6 through one of three loops formed by the cystine knot. The Wise deletion construct lacking the LRP6-interacting loop domain nevertheless binds BMP4 and inhibits BMP signals. Moreover, BMP4 does not interfere with Wise-LRP6 binding, suggesting separate domains for the physical interaction. Functional assays also show that the ability of Wise to block Wnt1 activity through LRP6 is not impeded by BMP4. In contrast, the ability of Wise to inhibit BMP4 is prevented by additional LRP6, implying a preference of Wise in binding LRP6 over BMP4. In addition to the interaction of Wise with BMP4 and LRP6, the molecular characteristics of Wise, such as glycosylation and association with heparan sulfate proteoglycans on the cell surface, are suggested. This study helps to understand the multiple functions of Wise at the molecular level and suggests a possible role for Wise in balancing Wnt and BMP signals.

  3. Study of DNA interactions with bifenthrin by spectroscopic techniques and molecular modeling

    Science.gov (United States)

    Zhu, Pan; Zhang, Guowen; Ma, Yadi; Zhang, Yepeng; Miao, Hong; Wu, Yongning

    2013-08-01

    The interaction between bifenthrin (BF) and calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by UV-vis absorption, fluorescence, circular dichroism (CD), and Fourier transform infrared (FT-IR) spectroscopy, coupled with viscosity measurements and molecular docking techniques. It was found that BF molecular could intercalate into the base pairs of ctDNA as evidenced by significant increases in absorption intensity, fluorescence polarization and relative viscosity of ctDNA, decrease in iodide quenching effect, and induced CD spectral changes. The association constant of BF with ctDNA was evaluated to be in the order of 104 L mol-1. Thermodynamic analysis of the binding data obtained at different temperatures suggested that the binding process was primarily driven by hydrogen bonds and van der Waals forces, as the values of the enthalpy change (ΔH) and the entropy change (ΔS) were calculated to be -31.13 ± 1.89 kJ mol-1 and -22.79 ± 1.21 J mol-1 K-1, respectively. The results of FT-IR spectra and molecular docking showed that a specific binding mainly existed between BF and adenine and guanine bases.

  4. Interaction of Lysozyme with Rhodamine B: A combined analysis of spectroscopic & molecular docking.

    Science.gov (United States)

    Millan, Sabera; Satish, Lakkoji; Kesh, Sandeep; Chaudhary, Yatendra S; Sahoo, Harekrushna

    2016-09-01

    The interaction of Rhodamine B (RB) with Lysozyme (Lys) was investigated by different optical spectroscopic techniques such as absorption, fluorescence, and circular-dichroism (CD), along with molecular docking studies. The fluorescence results (including steady-state and time-resolved mode) revealed that the addition of RB effectively causes strong quenching of intrinsic fluorescence in Lysozyme and mostly, by the static quenching mechanism. Different binding and thermodynamic parameters were calculated at different temperatures and the binding constant value was found to be 2963.54Lmol(-1) at 25°C. The average distance (r0) was found to be 3.31nm according to Förster's theory of non-radiative energy transfer between Lysozyme and RB. The conformational change in Lysozyme during interaction with RB was confirmed from absorbance, synchronous fluorescence, and circular dichroism measurements. Finally, molecular docking studies were done to confirm that the dye binds with Lysozyme. Copyright © 2016 Elsevier B.V. All rights reserved.

  5. Effect of electron-vibration interactions on the thermoelectric efficiency of molecular junctions.

    Science.gov (United States)

    Hsu, Bailey C; Chiang, Chi-Wei; Chen, Yu-Chang

    2012-07-11

    From first-principles approaches, we investigate the thermoelectric efficiency of a molecular junction where a benzene molecule is connected directly to the platinum electrodes. We calculate the thermoelectric figure of merit ZT in the presence of electron-vibration interactions with and without local heating under two scenarios: linear response and finite bias regimes. In the linear response regime, ZT saturates around the electrode temperature T(e) = 25 K in the elastic case, while in the inelastic case we observe a non-saturated and a much larger ZT beyond T(e) = 25 K attributed to the tail of the Fermi-Dirac distribution. In the finite bias regime, the inelastic effects reveal the signatures of the molecular vibrations in the low-temperature regime. The normal modes exhibiting structures in the inelastic profile are characterized by large components of atomic vibrations along the current density direction on top of each individual atom. In all cases, the inclusion of local heating leads to a higher wire temperature T(w) and thus magnifies further the influence of the electron-vibration interactions due to the increased number of local phonons.

  6. An interactive data management and analysis system for clinical investigators.

    Science.gov (United States)

    Groner, G F; Hopwood, M D; Palley, N A; Sibley, W L; Baker, W R; Christopher, T G; Thompson, H K

    1978-09-01

    An interactive minicomputer-based system has been developed that enables the clinical research investigator to personally explore and analyze his research data and, as a consequence of these explorations, to acquire more information. This system, which does not require extensive training or computer programming, enables the investigator to describe his data interactively in his own terms, enter data values while having them checked for validity, store time-oriented patient data in a carefully controlled on-line data base, retrieve data by patient, variable, and time, create subsets of patients with common characteristics, perform statistical analyses, and produce tables and graphs. It also permits data to be transferred to and from other computers. The system is well accepted and is being used by a variety of medical specialists at the three clinical research centers where it is operational. Reported benefits include less elapsed and nonproductive time, more thorough analysis of more data, greater and earlier insight into the meaning of research data, and increased publishable results.

  7. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Science.gov (United States)

    Mathiazhagan, S.; Anup, S.

    2016-08-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models.

  8. Molecular investigations on grain filling rate under terminal heat ...

    African Journals Online (AJOL)

    Ezedom Theresa

    2013-07-10

    Jul 10, 2013 ... under terminal heat stress in bread wheat. (Triticum aestivum L.) Girish Chandra Pandey1, Jagadish ... ficantly in all the bread and durum wheat genotypes, because of significant interaction of each ..... wheat varieties and registered genetic stocks (Triticum L.). Technical. Bulletin No.13, Directorate of Wheat ...

  9. Identifying gene-environment interactions in schizophrenia: contemporary challenges for integrated, large-scale investigations.

    Science.gov (United States)

    van Os, Jim; Rutten, Bart P; Myin-Germeys, Inez; Delespaul, Philippe; Viechtbauer, Wolfgang; van Zelst, Catherine; Bruggeman, Richard; Reininghaus, Ulrich; Morgan, Craig; Murray, Robin M; Di Forti, Marta; McGuire, Philip; Valmaggia, Lucia R; Kempton, Matthew J; Gayer-Anderson, Charlotte; Hubbard, Kathryn; Beards, Stephanie; Stilo, Simona A; Onyejiaka, Adanna; Bourque, Francois; Modinos, Gemma; Tognin, Stefania; Calem, Maria; O'Donovan, Michael C; Owen, Michael J; Holmans, Peter; Williams, Nigel; Craddock, Nicholas; Richards, Alexander; Humphreys, Isla; Meyer-Lindenberg, Andreas; Leweke, F Markus; Tost, Heike; Akdeniz, Ceren; Rohleder, Cathrin; Bumb, J Malte; Schwarz, Emanuel; Alptekin, Köksal; Üçok, Alp; Saka, Meram Can; Atbaşoğlu, E Cem; Gülöksüz, Sinan; Gumus-Akay, Guvem; Cihan, Burçin; Karadağ, Hasan; Soygür, Haldan; Cankurtaran, Eylem Şahin; Ulusoy, Semra; Akdede, Berna; Binbay, Tolga; Ayer, Ahmet; Noyan, Handan; Karadayı, Gülşah; Akturan, Elçin; Ulaş, Halis; Arango, Celso; Parellada, Mara; Bernardo, Miguel; Sanjuán, Julio; Bobes, Julio; Arrojo, Manuel; Santos, Jose Luis; Cuadrado, Pedro; Rodríguez Solano, José Juan; Carracedo, Angel; García Bernardo, Enrique; Roldán, Laura; López, Gonzalo; Cabrera, Bibiana; Cruz, Sabrina; Díaz Mesa, Eva Ma; Pouso, María; Jiménez, Estela; Sánchez, Teresa; Rapado, Marta; González, Emiliano; Martínez, Covadonga; Sánchez, Emilio; Olmeda, Ma Soledad; de Haan, Lieuwe; Velthorst, Eva; van der Gaag, Mark; Selten, Jean-Paul; van Dam, Daniella; van der Ven, Elsje; van der Meer, Floor; Messchaert, Elles; Kraan, Tamar; Burger, Nadine; Leboyer, Marion; Szoke, Andrei; Schürhoff, Franck; Llorca, Pierre-Michel; Jamain, Stéphane; Tortelli, Andrea; Frijda, Flora; Vilain, Jeanne; Galliot, Anne-Marie; Baudin, Grégoire; Ferchiou, Aziz; Richard, Jean-Romain; Bulzacka, Ewa; Charpeaud, Thomas; Tronche, Anne-Marie; De Hert, Marc; van Winkel, Ruud; Decoster, Jeroen; Derom, Catherine; Thiery, Evert; Stefanis, Nikos C; Sachs, Gabriele; Aschauer, Harald; Lasser, Iris; Winklbaur, Bernadette; Schlögelhofer, Monika; Riecher-Rössler, Anita; Borgwardt, Stefan; Walter, Anna; Harrisberger, Fabienne; Smieskova, Renata; Rapp, Charlotte; Ittig, Sarah; Soguel-dit-Piquard, Fabienne; Studerus, Erich; Klosterkötter, Joachim; Ruhrmann, Stephan; Paruch, Julia; Julkowski, Dominika; Hilboll, Desiree; Sham, Pak C; Cherny, Stacey S; Chen, Eric Y H; Campbell, Desmond D; Li, Miaoxin; Romeo-Casabona, Carlos María; Emaldi Cirión, Aitziber; Urruela Mora, Asier; Jones, Peter; Kirkbride, James; Cannon, Mary; Rujescu, Dan; Tarricone, Ilaria; Berardi, Domenico; Bonora, Elena; Seri, Marco; Marcacci, Thomas; Chiri, Luigi; Chierzi, Federico; Storbini, Viviana; Braca, Mauro; Minenna, Maria Gabriella; Donegani, Ivonne; Fioritti, Angelo; La Barbera, Daniele; La Cascia, Caterina Erika; Mulè, Alice; Sideli, Lucia; Sartorio, Rachele; Ferraro, Laura; Tripoli, Giada; Seminerio, Fabio; Marinaro, Anna Maria; McGorry, Patrick; Nelson, Barnaby; Amminger, G Paul; Pantelis, Christos; Menezes, Paulo R; Del-Ben, Cristina M; Gallo Tenan, Silvia H; Shuhama, Rosana; Ruggeri, Mirella; Tosato, Sarah; Lasalvia, Antonio; Bonetto, Chiara; Ira, Elisa; Nordentoft, Merete; Krebs, Marie-Odile; Barrantes-Vidal, Neus; Cristóbal, Paula; Kwapil, Thomas R; Brietzke, Elisa; Bressan, Rodrigo A; Gadelha, Ary; Maric, Nadja P; Andric, Sanja; Mihaljevic, Marina; Mirjanic, Tijana

    2014-07-01

    Recent years have seen considerable progress in epidemiological and molecular genetic research into environmental and genetic factors in schizophrenia, but methodological uncertainties remain with regard to validating environmental exposures, and the population risk conferred by individual molecular genetic variants is small. There are now also a limited number of studies that have investigated molecular genetic candidate gene-environment interactions (G × E), however, so far, thorough replication of findings is rare and G × E research still faces several conceptual and methodological challenges. In this article, we aim to review these recent developments and illustrate how integrated, large-scale investigations may overcome contemporary challenges in G × E research, drawing on the example of a large, international, multi-center study into the identification and translational application of G × E in schizophrenia. While such investigations are now well underway, new challenges emerge for G × E research from late-breaking evidence that genetic variation and environmental exposures are, to a significant degree, shared across a range of psychiatric disorders, with potential overlap in phenotype. © The Author 2014. Published by Oxford University Press on behalf of the Maryland Psychiatric Research Center. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  10. Molecular dynamics simulations revealed structural differences among WRKY domain-DNA interaction in barley (Hordeum vulgare).

    Science.gov (United States)

    Pandey, Bharati; Grover, Abhinav; Sharma, Pradeep

    2018-02-12

    The WRKY transcription factors are a class of DNA-binding proteins involved in diverse plant processes play critical roles in response to abiotic and biotic stresses. Genome-wide divergence analysis of WRKY gene family in Hordeum vulgare provided a framework for molecular evolution and functional roles. So far, the crystal structure of WRKY from barley has not been resolved; moreover, knowledge of the three-dimensional structure of WRKY domain is pre-requisites for exploring the protein-DNA recognition mechanisms. Homology modelling based approach was used to generate structures for WRKY DNA binding domain (DBD) and its variants using AtWRKY1 as a template. Finally, the stability and conformational changes of the generated model in unbound and bound form was examined through atomistic molecular dynamics (MD) simulations for 100 ns time period. In this study, we investigated the comparative binding pattern of WRKY domain and its variants with W-box cis-regulatory element using molecular docking and dynamics (MD) simulations assays. The atomic insight into WRKY domain exhibited significant variation in the intermolecular hydrogen bonding pattern, leading to the structural anomalies in the variant type and differences in the DNA-binding specificities. Based on the MD analysis, residual contribution and interaction contour, wild-type WRKY (HvWRKY46) were found to interact with DNA through highly conserved heptapeptide in the pre- and post-MD simulated complexes, whereas heptapeptide interaction with DNA was missing in variants (I and II) in post-MD complexes. Consequently, through principal component analysis, wild-type WRKY was also found to be more stable by obscuring a reduced conformational space than the variant I (HvWRKY34). Lastly, high binding free energy for wild-type and variant II allowed us to conclude that wild-type WRKY-DNA complex was more stable relative to variants I. The results of our study revealed complete dynamic and structural information

  11. Investigations of transport properties of molten sodium fluoride using molecular dynamics simulations

    International Nuclear Information System (INIS)

    Chattaraj, D.; Dash, Smruti

    2013-01-01

    The thermal conductivity and coefficient of shear viscosity of molten sodium fluoride were calculated using Green-Kubo equilibrium molecular dynamics (EMD) simulation. The Green-Kubo method is an equilibrium technique based on the fluctuation-dissipation theorem of statistical thermodynamics. The canonical ensemble (N, V, T) was used in the MD simulation to obtain the transport properties of molten NaF. In this simulation, several state points were investigated using the Born-Meyer-Huggins-Tosi-Fumi interionic potential model. The electrostatic interactions present in this ionic fluid were calculated through the Ewald method. The results obtained in this study were found to be in good agreement with the reported experimental data. (author)

  12. Fragment molecular orbital method for studying lanthanide interactions with proteins

    Energy Technology Data Exchange (ETDEWEB)

    Tsushima, Satoru [Helmholtz-Zentrum Dresden-Rossendorf e.V., Dresden (Germany). Biophysics; Komeiji, Y. [National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba (Japan); Mochizuki, Y. [Rikkyo Univ., Tokyo (Japan)

    2017-06-01

    The binding affinity of the calcium-binding protein calmodulin towards Eu{sup 3+} was studied as a model for lanthanide protein interactions in the large family of ''EF-hand'' calcium-binding proteins.

  13. Interactive domains in the molecular chaperone human alphaB crystallin modulate microtubule assembly and disassembly.

    Directory of Open Access Journals (Sweden)

    Joy G Ghosh

    2007-06-01

    Full Text Available Small heat shock proteins regulate microtubule assembly during cell proliferation and in response to stress through interactions that are poorly understood.Novel functions for five interactive sequences in the small heat shock protein and molecular chaperone, human alphaB crystallin, were investigated in the assembly/disassembly of microtubules and aggregation of tubulin using synthetic peptides and mutants of human alphaB crystallin.The interactive sequence (113FISREFHR(120 exposed on the surface of alphaB crystallin decreased microtubule assembly by approximately 45%. In contrast, the interactive sequences, (131LTITSSLSSDGV(142 and (156ERTIPITRE(164, corresponding to the beta8 strand and the C-terminal extension respectively, which are involved in complex formation, increased microtubule assembly by approximately 34-45%. The alphaB crystallin peptides, (113FISREFHR(120 and (156ERTIPITRE(164, inhibited microtubule disassembly by approximately 26-36%, and the peptides (113FISREFHR(120 and (131LTITSSLSSDGV(142 decreased the thermal aggregation of tubulin by approximately 42-44%. The (131LTITSSLSSDGV(142 and (156ERTIPITRE(164 peptides were more effective than the widely used anti-cancer drug, Paclitaxel, in modulating tubulinmicrotubule dynamics. Mutagenesis of these interactive sequences in wt human alphaB crystallin confirmed the effects of the alphaB crystallin peptides on microtubule assembly/disassembly and tubulin aggregation. The regulation of microtubule assembly by alphaB crystallin varied over a narrow range of concentrations. The assembly of microtubules was maximal at alphaB crystallin to tubulin molar ratios between 1:4 and 2:1, while molar ratios >2:1 inhibited microtubule assembly.Interactive sequences on the surface of human alphaB crystallin collectively modulate microtubule assembly through a dynamic subunit exchange mechanism that depends on the concentration and ratio of alphaB crystallin to tubulin. These are the first

  14. Simulation of aerosol flow interaction with a solid body on molecular level

    Science.gov (United States)

    Amelyushkin, Ivan A.; Stasenko, Albert L.

    2018-05-01

    Physico-mathematical models and numerical algorithm of two-phase flow interaction with a solid body are developed. Results of droplet motion and its impingement upon a rough surface in real gas boundary layer simulation on the molecular level obtained via molecular dynamics technique are presented.

  15. Modeling of nanotoxicity molecular interactions of nanomaterials with bionanomachines

    CERN Document Server

    Zhou, Ruhong

    2015-01-01

    This book provides a comprehensive overview of the fundamentals of nanotoxicity modeling and its implications for the development of novel nanomedicines. It lays out the fundamentals of nanotoxicity modeling for an array of nanomaterial systems, ranging from carbon-based nanoparticles to noble metals, metal oxides, and quantum dots. The author illustrates how molecular (classical mechanics) and atomic (quantum mechanics) modeling approaches can be applied to bolster our understanding of many important aspects of this critical nanotoxicity issue. Each chapter is organized by types of nanomaterials for practicality, making this an ideal book for senior undergraduate students, graduate students, and researchers in nanotechnology, chemistry, physics, molecular biology, and computer science. It is also of interest to academic and industry professionals who work on nanodrug delivery and related biomedical applications, and aids readers in their biocompatibility assessment efforts in the coming age of nanotechnology...

  16. Molecular interactions between the olive and the fruit fly Bactrocera oleae

    Directory of Open Access Journals (Sweden)

    Corrado Giandomenico

    2012-06-01

    Full Text Available Abstract Background The fruit fly Bactrocera oleae is the primary biotic stressor of cultivated olives, causing direct and indirect damages that significantly reduce both the yield and the quality of olive oil. To study the olive-B. oleae interaction, we conducted transcriptomic and proteomic investigations of the molecular response of the drupe. The identifications of genes and proteins involved in the fruit response were performed using a Suppression Subtractive Hybridisation technique and a combined bi-dimensional electrophoresis/nanoLC-ESI-LIT-MS/MS approach, respectively. Results We identified 196 ESTs and 26 protein spots as differentially expressed in olives with larval feeding tunnels. A bioinformatic analysis of the identified non-redundant EST and protein collection indicated that different molecular processes were affected, such as stress response, phytohormone signalling, transcriptional control and primary metabolism, and that a considerable proportion of the ESTs could not be classified. The altered expression of 20 transcripts was also analysed by real-time PCR, and the most striking differences were further confirmed in the fruit of a different olive variety. We also cloned the full-length coding sequences of two genes, Oe-chitinase I and Oe-PR27, and showed that these are wound-inducible genes and activated by B. oleae punctures. Conclusions This study represents the first report that reveals the molecular players and signalling pathways involved in the interaction between the olive fruit and its most damaging biotic stressor. Drupe response is complex, involving genes and proteins involved in photosynthesis as well as in the production of ROS, the activation of different stress response pathways and the production of compounds involved in direct defence against phytophagous larvae. Among the latter, trypsin inhibitors should play a major role in drupe resistance reaction.

  17. Conserved molecular interactions in centriole-to-centrosome conversion.

    Science.gov (United States)

    Fu, Jingyan; Lipinszki, Zoltan; Rangone, Hélène; Min, Mingwei; Mykura, Charlotte; Chao-Chu, Jennifer; Schneider, Sandra; Dzhindzhev, Nikola S; Gottardo, Marco; Riparbelli, Maria Giovanna; Callaini, Giuliano; Glover, David M

    2016-01-01

    Centrioles are required to assemble centrosomes for cell division and cilia for motility and signalling. New centrioles assemble perpendicularly to pre-existing ones in G1-S and elongate throughout S and G2. Fully elongated daughter centrioles are converted into centrosomes during mitosis to be able to duplicate and organize pericentriolar material in the next cell cycle. Here we show that centriole-to-centrosome conversion requires sequential loading of Cep135, Ana1 (Cep295) and Asterless (Cep152) onto daughter centrioles during mitotic progression in both Drosophila melanogaster and human. This generates a molecular network spanning from the inner- to outermost parts of the centriole. Ana1 forms a molecular strut within the network, and its essential role can be substituted by an engineered fragment providing an alternative linkage between Asterless and Cep135. This conserved architectural framework is essential for loading Asterless or Cep152, the partner of the master regulator of centriole duplication, Plk4. Our study thus uncovers the molecular basis for centriole-to-centrosome conversion that renders daughter centrioles competent for motherhood.

  18. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Mathiazhagan, S., E-mail: smathi.research@gmail.com; Anup, S., E-mail: anupiist@gmail.com

    2016-08-19

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  19. Investigation of deformation mechanisms of staggered nanocomposites using molecular dynamics

    International Nuclear Information System (INIS)

    Mathiazhagan, S.; Anup, S.

    2016-01-01

    Biological materials with nanostructure of regularly or stair-wise staggered arrangements of hard platelets reinforced in a soft protein matrix have superior mechanical properties. Applications of these nanostructures to ceramic matrix composites could enhance their toughness. Using molecular dynamics simulations, mechanical behaviour of the bio-inspired nanocomposites is studied. Regularly staggered model shows better flow behaviour compared to stair-wise staggered model due to the symmetrical crack propagation along the interface. Though higher stiffness and strength are obtained for stair-wise staggered models, rapid crack propagation reduces the toughness. Arresting this crack propagation could lead to superior mechanical properties in stair-wise staggered models. - Highlights: • The deformation behaviour of staggered nanocomposites is studied. • Stair-wise staggered model has high stiffness and strength, but low toughness. • Rapid crack growth in overlap region causes this low toughness. • Toughness could be enhanced by arresting interfacial crack in the overlap.

  20. Investigating Viruses during the Transformation of Molecular Biology.

    Science.gov (United States)

    Moss, Bernard

    2017-03-10

    This Reflections article describes my early work on viral enzymes and the discovery of mRNA capping, how my training in medicine and biochemistry merged as I evolved into a virologist, the development of viruses as vaccine vectors, and how scientific and technological developments during the 1970s and beyond set the stage for the interrogation of nearly every step in the reproductive cycle of vaccinia virus (VACV), a large DNA virus with about 200 genes. The reader may view this article as a work in progress, because I remain actively engaged in research at the National Institutes of Health (NIH) notwithstanding 50 memorable years there. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.

  1. Study on the interaction between tabersonine and human serum albumin by optical spectroscopy and molecular modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Jiang Hua; Chen, Rongrong [Department of Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632 (China); Pu Hanlin, E-mail: tphl@jnu.edu.cn [Department of Biology, College of Life Science and Technology, Jinan University, Guangzhou 510632 (China)

    2012-03-15

    The mechanism of interaction between tabersonine (TAB) and human serum albumin (HSA) was investigated by the methods of fluorescence spectroscopy, UV-vis absorption spectroscopy and molecular modeling under simulative physiological conditions. Results obtained from analysis of fluorescence spectrum and fluorescence intensity indicated that TAB has a strong ability to quench the intrinsic fluorescence of HSA through a static quenching procedure. The binding site number n and apparent binding constant K{sub a}, corresponding thermodynamic parameters {Delta}G, {Delta}H and {Delta}S at different temperatures were calculated. The distance r between donor (human serum albumin) and acceptor (tabersonine) was obtained according to the Foerster theory of non-radiation energy transfer. The effect of common ions on binding constant was also investigated. The synchronous fluorescence and three-dimensional fluorescence spectra were used to investigate the structural change of HSA molecules with addition of TAB. Furthermore, the study of molecular modeling indicated that TAB could bind to the site I of HSA and hydrophobic interaction was the major acting force, which was in agreement with the binding mode study. - Highlights: Black-Right-Pointing-Pointer Fluorescence study of the mechanism of interaction between tabersonine and HSA. Black-Right-Pointing-Pointer The binding parameters and thermodynamic parameters were calculated. Black-Right-Pointing-Pointer The distance r was obtained and common ions effects was investigated. Black-Right-Pointing-Pointer Conformation of HSA and its molecular modeling was analyzed.

  2. Vitamin E-drug interactions: molecular basis and clinical relevance.

    Science.gov (United States)

    Podszun, Maren; Frank, Jan

    2014-12-01

    Vitamin E (α-, β-, γ- and δ-tocopherol and -tocotrienol) is an essential factor in the human diet and regularly taken as a dietary supplement by many people, who act under the assumption that it may be good for their health and can do no harm. With the publication of meta-analyses reporting increased mortality in persons taking vitamin E supplements, the safety of the micronutrient was questioned and interactions with prescription drugs were suggested as one potentially underlying mechanism. Here, we review the evidence in the scientific literature for adverse vitamin E-drug interactions and discuss the potential of each of the eight vitamin E congeners to alter the activity of drugs. In summary, there is no evidence from animal models or randomised controlled human trials to suggest that the intake of tocopherols and tocotrienols at nutritionally relevant doses may cause adverse nutrient-drug interactions. Consumption of high-dose vitamin E supplements ( ≥  300 mg/d), however, may lead to interactions with the drugs aspirin, warfarin, tamoxifen and cyclosporine A that may alter their activities. For the majority of drugs, however, interactions with vitamin E, even at high doses, have not been observed and are thus unlikely.

  3. MIiSR: Molecular Interactions in Super-Resolution Imaging Enables the Analysis of Protein Interactions, Dynamics and Formation of Multi-protein Structures.

    Directory of Open Access Journals (Sweden)

    Fabiana A Caetano

    2015-12-01

    Full Text Available Our current understanding of the molecular mechanisms which regulate cellular processes such as vesicular trafficking has been enabled by conventional biochemical and microscopy techniques. However, these methods often obscure the heterogeneity of the cellular environment, thus precluding a quantitative assessment of the molecular interactions regulating these processes. Herein, we present Molecular Interactions in Super Resolution (MIiSR software which provides quantitative analysis tools for use with super-resolution images. MIiSR combines multiple tools for analyzing intermolecular interactions, molecular clustering and image segmentation. These tools enable quantification, in the native environment of the cell, of molecular interactions and the formation of higher-order molecular complexes. The capabilities and limitations of these analytical tools are demonstrated using both modeled data and examples derived from the vesicular trafficking system, thereby providing an established and validated experimental workflow capable of quantitatively assessing molecular interactions and molecular complex formation within the heterogeneous environment of the cell.

  4. Alternative Radioligands for Investigating the Molecular Pharmacology of Melatonin Receptors.

    Science.gov (United States)

    Legros, Céline; Brasseur, Chantal; Delagrange, Philippe; Ducrot, Pierre; Nosjean, Olivier; Boutin, Jean A

    2016-03-01

    Melatonin exerts a variety of physiologic activities that are mainly relayed through the melatonin receptors MT1 and MT2 Low expressions of these receptors in tissues have led to widespread experimental use of the agonist 2-[(125)I]-iodomelatonin as a substitute for melatonin. We describe three iodinated ligands: 2-(2-[(2-iodo-4,5-dimethoxyphenyl)methyl]-4,5-dimethoxy phenyl) (DIV880) and (2-iodo-N-2-[5-methoxy-2-(naphthalen-1-yl)-1H-pyrrolo[3,2-b]pyridine-3-yl])acetamide (S70254), which are specific ligands at MT2 receptors, and N-[2-(5-methoxy-1H-indol-3-yl)ethyl]iodoacetamide (SD6), an analog of 2-[(125)I]-iodomelatonin with slightly different characteristics. Here, we further characterized these new ligands with regards to their molecular pharmacology. We performed binding experiments, saturation assays, association/dissociation rate measurements, and autoradiography using sheep and rat tissues and recombinant cell lines. Our results showed that [(125)I]-S70254 is receptor, and can be used with both cells and tissue. This radioligand can be used in autoradiography. Similarly, DIV880, a partial agonist [43% of melatonin on guanosine 5'-3-O-(thio)triphosphate binding assay], selective for MT2, can be used as a tool to selectively describe the pharmacology of this receptor in tissue samples. The molecular pharmacology of both human melatonin receptors MT1 and MT2, using a series of 24 ligands at these receptors and the new radioligands, did not lead to noticeable variations in the profiles. For the first time, we described radiolabeled tools that are specific for one of the melatonin receptors (MT2). These tools are amenable to binding experiments and to autoradiography using sheep or rat tissues. These specific tools will permit better understanding of the role and implication in physiopathologic processes of the melatonin receptors. Copyright © 2016 by The American Society for Pharmacology and Experimental Therapeutics.

  5. Nuclear magnetic resonance studies of conformations and molecular interactions in lyotropic mesophases - Applications to solubilization problems

    International Nuclear Information System (INIS)

    Caniparoli, Jean-Philippe

    1988-01-01

    After having determined the structural properties of smectic liquid crystals made from double chain surfactants/water binary systems, residual anisotropic interactions and relaxation times measurements were used to investigate the molecular ordering. Phosphorus, deuterium and nitrogen NMR of the surfactant molecules evidenced their high degree of order and the strong anisotropy of their motions. Quantitative results depended on the surfactant polar head -phosphate or ammonium-, while they displayed little variations with the hydrocarbon tail size. The marked dependence of the order and dynamics of small solutes in a lamellar phase on their hydrophilic or hydrophobic behaviour was shown using the same methods. By means of para-magnetically induced relaxation, it was proved that the non-polar solute benzene is located in the organic domain of the liquid crystalline matrix. (author) [fr

  6. Ultrasonic study of molecular interaction in binary liquid mixtures at ...

    Indian Academy of Sciences (India)

    The variation of these parameters with composition of the mixture helps us in understanding the nature and extent of interaction between unlike molecules in the mixtures. Further, theoretical values of ultrasonic speed were evaluated using theories and empirical relations. The relative merits of these theories and relations ...

  7. Interacting with molecular structures : user performance versus system complexity

    NARCIS (Netherlands)

    Liere, van R.; Martens, J.B.; Kok, A.J.F.; van Tienen, M.H.A.; Blach, R.; Kjems, E.

    2005-01-01

    Effective interaction in a virtual environment requires that the user can adequately judge the spatial relationships between the objects in a 3D scene. In order to accomplish adequate depth perception, existing virtual environments create useful perceptual cues through stereoscopy, motion parallax

  8. Studies on Molecular Interaction in Ternary Liquid Mixtures

    Directory of Open Access Journals (Sweden)

    R. Uvarani

    2010-01-01

    Full Text Available Ultrasonic velocity, density and viscosity for the ternary liquid mixtures of cyclohexanone with 1-propanol and 1-butanol in carbon tetrachloride were measured at 303 K. The acoustical parameters and their excess values were calculated. The trends in the variation of these excess parameters were used to discuss the nature and strength of the interactions present between the component molecules.

  9. Long-range interactions and parallel scalability in molecular simulations

    NARCIS (Netherlands)

    Patra, M.; Hyvönen, M.T.; Falck, E.; Sabouri-Ghomi, M.; Vattulainen, I.; Karttunen, M.E.J.

    2007-01-01

    Typical biomolecular systems such as cellular membranes, DNA, and protein complexes are highly charged. Thus, efficient and accurate treatment of electrostatic interactions is of great importance in computational modeling of such systems. We have employed the GROMACS simulation package to perform

  10. Molecular ecological insights into neotropical bird-tick interactions

    NARCIS (Netherlands)

    Miller, Matthew J.; Esser, Helen J.; Loaiza, Jose R.; Herre, Edward Allen; Aguilar, Celestino; Quintero, Diomedes; Alvarez, Eric; Bermingham, Eldredge

    2016-01-01

    In the tropics, ticks parasitize many classes of vertebrate hosts. However, because many tropical tick species are only identifiable in the adult stage, and these adults usually parasitize mammals, most attention on the ecology of tick-host interactions has focused on mammalian hosts. In

  11. Molecular simulations of lipid-mediated protein-protein interactions

    NARCIS (Netherlands)

    de Meyer, F.J.M.; Venturoli, M.; Smit, B.

    2008-01-01

    Recent experimental results revealed that lipid-mediated interactions due to hydrophobic forces may be important in determining the protein topology after insertion in the membrane, in regulating the protein activity, in protein aggregation and in signal transduction. To gain insight into the

  12. Binding interaction of atorvastatin with bovine serum albumin: Spectroscopic methods and molecular docking

    Science.gov (United States)

    Wang, Qi; Huang, Chuan-ren; Jiang, Min; Zhu, Ying-yao; Wang, Jing; Chen, Jun; Shi, Jie-hua

    2016-03-01

    The interaction of atorvastatin with bovine serum albumin (BSA) was investigated using multi-spectroscopic methods and molecular docking technique for providing important insight into further elucidating the store and transport process of atorvastatin in the body and the mechanism of action and pharmacokinetics. The experimental results revealed that the fluorescence quenching mechanism of BSA induced atorvastatin was a combined dynamic and static quenching. The binding constant and number of binding site of atorvastatin with BSA under simulated physiological conditions (pH = 7.4) were 1.41 × 105 M- 1 and about 1 at 310 K, respectively. The values of the enthalpic change (ΔH0), entropic change (ΔS0) and Gibbs free energy (ΔG0) in the binding process of atorvastatin with BSA at 310 K were negative, suggesting that the binding process of atorvastatin and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen bonding interaction. Moreover, atorvastatin was bound into the subdomain IIA (site I) of BSA, resulting in a slight change of the conformation of BSA.

  13. Chitosan nanoparticles-trypsin interactions: Bio-physicochemical and molecular dynamics simulation studies.

    Science.gov (United States)

    Salar, Safoura; Mehrnejad, Faramarz; Sajedi, Reza H; Arough, Javad Mohammadnejad

    2017-10-01

    Herein, we investigated the effect of the chitosan nanoparticles (CsNP) on the structure, dynamics, and activity of trypsin. The enzyme activity in complex with the nanoparticles slightly increased, which represents the interactions between the nanoparticles and the enzyme. The kinetic parameters of the enzyme, K m and k cat , increased after adding the nanoparticles, resulting in a slight increase in the catalytic efficiency (k cat /K m ). However, the effect of the nanoparticles on the kinetic stability of trypsin has not exhibited significant variations. Fluorescence spectroscopy did not show remarkable changes in the trypsin conformation in the presence of the nanoparticles. The circular dichroism (CD) spectroscopy results also revealed the secondary structure of trypsin attached to the nanoparticles slightly changed. Furthermore, we used molecular dynamics (MD) simulation to find more information about the interaction mechanisms between the nanoparticles and trypsin. The root mean square deviation (RMSD) of Cα atoms results have shown that in the presence of the nanoparticles, trypsin was stable. The simulation and the calculation of the binding free energy demonstrate that the nonpolar interactions are the most important forces for the formation of stable nanoparticle-trypsin complex. This study has explicitly elucidated that the nanoparticles have not considerable effect on the trypsin. Copyright © 2017. Published by Elsevier B.V.

  14. Molecular Investigation of the Stem Snap Point in Textile Hemp

    Directory of Open Access Journals (Sweden)

    Marc Behr

    2017-12-01

    Full Text Available Fibre crops are important natural resources, as they sustainably provide bast fibres, an economically-valuable raw material used in the textile and biocomposite sectors. Among fibre crops, textile hemp (Cannabis sativa L. is appreciated for its long and strong gelatinous bast fibres. The stem of fibre crops is a useful system for cell wall-oriented studies, because it shows a strong tissue polarity with a lignified inner core and a cellulosic hypolignified cortex, as well as a basipetal lignification gradient. Along the stem axis of fibre crops, a specific region, denoted snap point, marks the transition from elongation (above it to fibre thickening (below it. After empirically determining the snap point by tilting the plant, we divided the stem segment containing it into three non-overlapping consecutive regions measuring 1 cm each, and carried out targeted RT-qPCR on cell wall-related genes separately, in outer and inner tissues. Different gene clusters can be observed, two of which are the major gene groups, i.e., one group with members expressed at higher levels in the inner tissues, and one group whose genes are more expressed in the cortex. The present results provide a molecular validation that the snap point is characterised by a gradient of events associated with the shift from fibre elongation to thickening.

  15. Molecular-orbital and structural descriptors in theoretical investigation of electroreduction of nitrodiazoles

    Directory of Open Access Journals (Sweden)

    BRANKO KOLARIC

    2005-07-01

    Full Text Available It is shown how a simple theoretical approach can be used for the investigation of electro-organic reactions.Mononitroimidazoles and mononitropyrazoles were studied by the semiempirical MNDO-PM3 molecular orbital method. The electrochemical reduction potentials of diazoles have been correlated with the energy of the lowest unoccupied molecular orbital (LUMO. It was found that an admirable correlation could be obtained by the introduction of simple structural descriptors as a correction to the energy of the LUMO. The interaction of a molecule with its surrounding depends on electrostatic potential and on steric hindrance. Most of these steric effects are taken into account using two parameters having a very limited set of integer values. The first (b is the position of a ring substituent regarding ring nitrogens, which accounts for the different orientations of dipole moments and for the different shape of the electrostatic potential. The second (structural parameter (t is the type of the ring, which accounts mostly for different modes of electrode approach, and for different charge polarization patterns in two diazole rings. The extended correlation with ELUMO, b and t, is very good, having a regression coefficient r = 0.991. The intrinsic importance of b and t is exemplified by their high statistical weight.

  16. Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Zeynab Mohammad Hosseini Naveh

    Full Text Available Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP, a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD and Temperature Accelerated Molecular Dynamics (TAMD simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both conformations of the native protein are stable, while the agonist-bound structure evolves toward the apo one if the orientation of few key sidechains in the orthosteric cavity is modified. Conversely, TAMD simulations initiated from the native conformations are able to produce the spontaneous transition. With respect to the modified conformations, TAMD accelerates the transition by at least a factor 10. The analysis of some specific residue-residue interactions points out that the transition mechanism is based on the disruption/formation of few key hydrogen bonds. Finally, while early events of ligand dissociation are observed already in standard MD, TAMD accelerates the ligand detachment and, at the highest TAMD effective temperature, it is able to produce a complete dissociation path in one AChBP subunit.

  17. Conformations and molecular interactions of poly-γ-glutamic acid as a soluble microbial product in aqueous solutions

    OpenAIRE

    Wang, Ling-Ling; Chen, Jian-Tao; Wang, Long-Fei; Wu, Sha; Zhang, Guang-zhao; Yu, Han-Qing; Ye, Xiao-dong; Shi, Qing-Shan

    2017-01-01

    Soluble microbial products (SMPs) are of significant concern in the natural environment and in engineered systems. In this work, poly-γ-glutamic acid (γ-PGA), which is predominantly produced by Bacillus sp., was investigated in terms of pH-induced conformational changes and molecular interactions in aqueous solutions; accordingly, its sedimentation coefficient distribution and viscosity were also elucidated. Experimental results indicate that pH has a significant impact on the structure and m...

  18. Challenges for automatically extracting molecular interactions from full-text articles.

    Science.gov (United States)

    McIntosh, Tara; Curran, James R

    2009-09-24

    The increasing availability of full-text biomedical articles will allow more biomedical knowledge to be extracted automatically with greater reliability. However, most Information Retrieval (IR) and Extraction (IE) tools currently process only abstracts. The lack of corpora has limited the development of tools that are capable of exploiting the knowledge in full-text articles. As a result, there has been little investigation into the advantages of full-text document structure, and the challenges developers will face in processing full-text articles. We manually annotated passages from full-text articles that describe interactions summarised in a Molecular Interaction Map (MIM). Our corpus tracks the process of identifying facts to form the MIM summaries and captures any factual dependencies that must be resolved to extract the fact completely. For example, a fact in the results section may require a synonym defined in the introduction. The passages are also annotated with negated and coreference expressions that must be resolved.We describe the guidelines for identifying relevant passages and possible dependencies. The corpus includes 2162 sentences from 78 full-text articles. Our corpus analysis demonstrates the necessity of full-text processing; identifies the article sections where interactions are most commonly stated; and quantifies the proportion of interaction statements requiring coherent dependencies. Further, it allows us to report on the relative importance of identifying synonyms and resolving negated expressions. We also experiment with an oracle sentence retrieval system using the corpus as a gold-standard evaluation set. We introduce the MIM corpus, a unique resource that maps interaction facts in a MIM to annotated passages within full-text articles. It is an invaluable case study providing guidance to developers of biomedical IR and IE systems, and can be used as a gold-standard evaluation set for full-text IR tasks.

  19. A MOLECULAR DYNAMICS STUDY ON SLOW ION INTERACTIONS WITH THE POLYCYCLIC AROMATIC HYDROCARBON MOLECULE ANTHRACENE

    NARCIS (Netherlands)

    Postma, J.; Hoekstra, Ronnie; Tielens, A. G. G. M.; Schlathölter, Thomas

    2014-01-01

    Atomic collisions with polycyclic aromatic hydrocarbon (PAH) molecules are astrophysically particularly relevant for collision energies of less than 1 keV. In this regime, the interaction dynamics are dominated by elastic interactions. We have employed a molecular dynamics simulation based on

  20. Molecular interactions in the betaine monohydrate-polyol deep eutectic solvents: Experimental and computational studies

    Science.gov (United States)

    Zahrina, Ida; Mulia, Kamarza; Yanuar, Arry; Nasikin, Mohammad

    2018-04-01

    DES (deep eutectic solvents) are a new class of ionic liquids that have excellent properties. The strength of interaction between molecules in the DES affects their properties and applications. In this work, the strength of molecular interactions between components in the betaine monohydrate salt and polyol (glycerol or/and propylene glycol) eutectic mixtures was studied by experimental and computational studies. The melting point and fusion enthalpy of the mixtures were measured using STA (Simultaneous Thermal Analyzer). The nature and strength of intermolecular interactions were observed by FT-IR and NMR spectroscopy. The molecular dynamics simulation was used to determine the number of H-bonds, percent occupancy, and radial distribution functions in the eutectic mixtures. The interaction between betaine monohydrate and polyol is following order: betaine monohydrate-glycerol-propylene glycol > betaine monohydrate-glycerol > betaine monohydrate-propylene glycol, where the latter is the eutectic mixture with the lowest stability, strength and extent of the hydrogen bonding interactions between component molecules. The presence of intra-molecular hydrogen bonding interactions, the inter-molecular hydrogen bonding interactions between betaine molecule and polyol, and also interactions between polyol and H2O of betaine monohydrate in the eutectic mixtures.

  1. Interaction of albumins and heparinoids investigated by affinity capillary electrophoresis and free flow electrophoresis.

    Science.gov (United States)

    Mozafari, Mona; El Deeb, Sami; Krull, Friederike; Wildgruber, Robert; Weber, Gerhard; Reiter, Christian G; Wätzig, Hermann

    2018-02-01

    A fast and precise affinity capillary electrophoresis (ACE) method has been applied to investigate the interactions between two serum albumins (HSA and BSA) and heparinoids. Furthermore, different free flow electrophoresis methods were developed to separate the species which appears owing to interaction of albumins with pentosan polysulfate sodium (PPS) under different experimental conditions. For ACE experiments, the normalized mobility ratios (∆R/R f ), which provided information about the binding strength and the overall charge of the protein-ligand complex, were used to evaluate the binding affinities. ACE experiments were performed at two different temperatures (23 and 37°C). Both BSA and HSA interact more strongly with PPS than with unfractionated and low molecular weight heparins. For PPS, the interactions can already be observed at low mg/L concentrations (3 mg/L), and saturation is already obtained at approximately 20 mg/L. Unfractionated heparin showed almost no interactions with BSA at 23°C, but weak interactions at 37°C at higher heparin concentrations. The additional signals also appeared at higher concentrations at 37°C. Nevertheless, in most cases the binding data were similar at both temperatures. Furthermore, HSA showed a characteristic splitting in two peaks especially after interacting with PPS, which is probably attributable to the formation of two species or conformational change of HSA after interacting with PPS. The free flow electrophoresis methods have confirmed and completed the ACE experiments. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  2. Molecular Dynamics Investigation of Efficient SO2 Absorption by ...

    Indian Academy of Sciences (India)

    ANIRBAN MONDAL

    J. Chem. Sci. Vol. 129, No. 7, July 2017, pp. 859–872. c Indian Academy of Sciences. ... Ionic liquids are appropriate candidates for the absorption of acid gases such as SO2. Six anion- ... nificant number of task-specific ILs were designed and used to ...... investigation of a pilot-scale jet bubbling reactor for wet flue gas ...

  3. Analytic nuclear forces and molecular properties from full configuration interaction quantum Monte Carlo

    International Nuclear Information System (INIS)

    Thomas, Robert E.; Overy, Catherine; Opalka, Daniel; Alavi, Ali; Knowles, Peter J.; Booth, George H.

    2015-01-01

    Unbiased stochastic sampling of the one- and two-body reduced density matrices is achieved in full configuration interaction quantum Monte Carlo with the introduction of a second, “replica” ensemble of walkers, whose population evolves in imaginary time independently from the first and which entails only modest additional computational overheads. The matrices obtained from this approach are shown to be representative of full configuration-interaction quality and hence provide a realistic opportunity to achieve high-quality results for a range of properties whose operators do not necessarily commute with the Hamiltonian. A density-matrix formulated quasi-variational energy estimator having been already proposed and investigated, the present work extends the scope of the theory to take in studies of analytic nuclear forces, molecular dipole moments, and polarisabilities, with extensive comparison to exact results where possible. These new results confirm the suitability of the sampling technique and, where sufficiently large basis sets are available, achieve close agreement with experimental values, expanding the scope of the method to new areas of investigation

  4. Investigation of Ion-Solvent Interactions in Nonaqueous Electrolytes Using in Situ Liquid SIMS

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Yanyan; Su, Mao; Yu, Xiaofei; Zhou, Yufan; Wang, Jungang; Cao, Ruiguo; Xu, Wu; Wang, Chongmin; Baer, Donald R.; Borodin, Oleg; Xu, Kang; Wang, Yanting; Wang, Xue-Lin; Xu, Zhijie; Wang, Fuyi; Zhu, Zihua

    2018-02-06

    Ion-solvent interactions in non-aqueous electrolytes are of fundamental interest and practical importance, yet debates regarding ion preferential solvation and coordination numbers persist. In this work, in situ liquid SIMS was used to examine ion-solvent interactions in three representative electrolytes, i.e., lithium hexafluorophosphate (LiPF6) at 1.0 M in ethylene carbonate (EC)-dimethyl carbonate (DMC), and lithium bis(fluorosulfonyl)imide (LiFSI) at both low (1.0 M) and high (4.0 M) concentrations in 1,2-dimethoxyethane (DME). In the positive ion mode, solid molecular evidence strongly supports the preferential solvation of Li+ by EC. Besides, from the negative spectra, we also found that PF6- forms association with EC, which has been neglected by previous studies due to the relatively weak interaction. While in both LiFSI in DME electrolytes, no evidence shows that FSI- is associated with DME. Furthermore, strong salt ion cluster signals were observed in the 1.0 M LiPF6 in EC-DMC electrolyte, suggesting that a significant amount of Li+ ions stay in vicinity of anions. In sharp comparison, weak ion cluster signals were detected in dilute LiFSI in DME electrolyte, suggesting most ions are well separated, in agreement with our molecular dynamics (MD) simulation results. These findings indicate that with virtues of little bias on detecting positive and negative ions and the capability of directly analyzing concentrated electrolytes, in situ liquid SIMS is a powerful tool that can provide key evidence for improved understanding on the ion-solvent interactions in non-aqueous electrolytes. Therefore, we anticipate wide applications of in situ liquid SIMS on investigations of various ion-solvent interactions in the near future.

  5. Copromicroscopic and molecular investigations on intestinal parasites in kenneled dogs.

    Science.gov (United States)

    Simonato, Giulia; Frangipane di Regalbono, Antonio; Cassini, Rudi; Traversa, Donato; Beraldo, Paola; Tessarin, Cinzia; Pietrobelli, Mario

    2015-05-01

    Intestinal parasites are common in dogs worldwide, and their importance has recently increased for a renewed awareness on the public health relevance that some of them have. In this study, the prevalence of helminths and protozoa was evaluated by microscopy in 318 canine faecal samples collected from eight rescue shelters in the North-eastern Italy; 285 of them were also submitted to the molecular characterization of Giardia duodenalis and Cryptosporidium spp. isolates. An analysis was performed to evaluate the prevalence rates in relation to canine individual data, shelter provenance and anthelmintic treatments. Overall, 52.5% (167/318) of faecal samples were positive for at least one parasite. Trichuris vulpis showed the highest overall prevalence rate (29.2%), followed by G. duodenalis (15.1%), Toxocara canis (9.7%), ancylostomatids (8.2%) and Cystoisospora (5.7%). The prevalence of G. duodenalis, evaluated by real-time PCR, was 57.9% (165/285), and 79 isolates were characterized by nested PCR on the β-giardin gene. The assemblages found were mainly the host-specific genotypes C and D, while only one assemblage was identified as the human-specific genotype B1. Isolates of Cryptosporidium spp., recorded in 3/285 (1.1%) stool samples, were Cryptosporidium parvum based on the characterization of the Cryptosporidium oocyst wall protein (COWP) gene. Although the results describe a relatively limited risk of dog-originating zoonoses, there is the need to improve the quality of shelter practices towards better health managements for safe pet-adoption campaigns and a minimization of the environmental faecal pollution with canine intestinal parasites.

  6. Developing a Molecular Roadmap of Drug-Food Interactions

    DEFF Research Database (Denmark)

    Jensen, Kasper; Ni, Yueqiong; Panagiotou, Gianni

    2015-01-01

    therapeutic interventions, a systematic approach for identifying, predicting and preventing potential interactions between food and marketed or novel drugs is not yet available. The overall objective of this work was to sketch a comprehensive picture of the interference of ∼ 4,000 dietary components present...... view of the associations between diet and dietary molecules with drug targets, metabolic enzymes, drug transporters and carriers currently deposited in Drug-Bank. Moreover, we identified disease areas and drug targets that are most prone to the negative effects of drug-food interactions, showcasing......Recent research has demonstrated that consumption of food -especially fruits and vegetables-can alter the effects of drugs by interfering either with their pharmacokinetic or pharmacodynamic processes. Despite the recognition of such drug-food associations as an important element for successful...

  7. Molecular Interaction of Bone Marrow Adipose Tissue with Energy Metabolism.

    Science.gov (United States)

    Suchacki, Karla J; Cawthorn, William P

    2018-01-01

    The last decade has seen a resurgence in the study of bone marrow adipose tissue (BMAT) across diverse fields such as metabolism, haematopoiesis, skeletal biology and cancer. Herein, we review the most recent developments of BMAT research in both humans and rodents, including the distinct nature of BMAT; the autocrine, paracrine and endocrine interactions between BMAT and various tissues, both in physiological and pathological scenarios; how these interactions might impact energy metabolism; and the most recent technological advances to quantify BMAT. Though still dwarfed by research into white and brown adipose tissues, BMAT is now recognised as endocrine organ and is attracting increasing attention from biomedical researchers around the globe. We are beginning to learn the importance of BMAT both within and beyond the bone, allowing us to better appreciate the role of BMAT in normal physiology and disease.

  8. Interaction of Caffeine Molecular Associates with Water: Theory and Experiment

    OpenAIRE

    Shestopalova, Anna V.

    1990-01-01

    Results of a Monte Carlo simulation of the association process of caffeine (1,3,7-trimethyl-2,6-dioxipurine) in water are presented. Simulation was performed in a cluster approximation ; the system contained 200 water molecules. The nature of the stabilization of caffeine stacking associates in water was considered. Hydrophobic behaviour of methyl group s during association of caffeine molecules in water is shown. The peculiarity of interaction of caffeine associates with wa...

  9. Molecular simulation of polar molecules interaction with MOFs family materials

    International Nuclear Information System (INIS)

    De Toni, M.

    2012-01-01

    The topic of this thesis is the adsorption of simple molecular fluids in nano-porous materials. Many industrial processes are based on this phenomenon, including ionic exchange, selective separation and heterogeneous catalysis. I used molecular simulation to study the adsorption properties of polar molecules of industrial interest (CO 2 and H 2 O) in a new class of crystalline microporous hybrid organic-inorganic materials called Metal-Organic Frameworks (MOFs). They have exceptional adsorption properties due to their topological variety and their versatility, allowed by the large range of possibilities offered by organic and coordination chemistry and functionalizations. I first studied the adsorption of CO 2 in a family of materials called IRMOFs, which share the same topology but have different porous volume, in order to characterize the effect of confinement on their adsorption performance. In particular, a general behavior has been highlighted: the critical temperature decreases when the confinement increases. Then, I looked at a recently synthesized cationic MOF called Zn2(CBTACN). After having localized the extra-framework halogen anions in the unit cell of the material, something which was not possible experimentally, I characterized CO 2 adsorption in this system first as a pure gas and then as a component of different mixtures. Finally, I was interested in the hydrothermal stability of MOFs, a crucial issue for their use in industrial applications. I observed the hydration mechanism of system that is analogous to the MOF-5 (IRMOF-0h) and shed light on some collaborative effects of the attack of water that were unknown to in the literature. (author)

  10. Molecular-scale hydrophobic interactions between hard-sphere reference solutes are attractive and endothermic.

    Science.gov (United States)

    Chaudhari, Mangesh I; Holleran, Sinead A; Ashbaugh, Henry S; Pratt, Lawrence R

    2013-12-17

    The osmotic second virial coefficients, B2, for atomic-sized hard spheres in water are attractive (B2 attractive with increasing temperature (ΔB2/ΔT attractive and endothermic at moderate temperatures. Hydrophobic interactions between atomic-sized hard spheres in water are more attractive than predicted by the available statistical mechanical theory. These results constitute an initial step toward detailed molecular theory of additional intermolecular interaction features, specifically, attractive interactions associated with hydrophobic solutes.

  11. [Binding interaction of harpagoside and bovine serum albumin: spectroscopic methodologies and molecular docking].

    Science.gov (United States)

    Cao, Tuan-Wu; Huang, Wen-Bing; Shi, Jian-Wei; He, Wei

    2018-03-01

    Scrophularia ningpoensis has exhibited a variety of biological activities and been used as a pharmaceutical product for the treatment of inflammatory ailment, rheumatoid arthritis, osteoarthritis and so on. Harpagoside (HAR) is considerer as a main bioactive compound in this plant. Serum albumin has important physiological roles in transportation, distribution and metabolism of many endogenous and exogenous substances in body. It is of great significance to study the interaction mechanism between HAR and bovine serum albumin (BSA). The mechanism of interaction between HAR and BSA was investigated using 2D and 3D fluorescence, synchronous florescence, ultraviolet spectroscopy and molecular docking. According to the analysis of fluorescence spectra, HAR could strongly quench the fluorescence of BSA, and the static quenching process indicated that the decrease in the quenching constant was observed with the increase in temperature. The magnitude of binding constants (KA) was more than 1×10⁵ L·mol⁻¹, and the number of binding sites(n) was approximate to 1. The thermodynamic parameters were calculated through analysis of fluorescence data with Stern-Volmer and Van't Hoff equation. The calculated enthalpy change (ΔH) and entropy change (ΔS) implied that the main interaction forces of HAR with BSA were the bonding interaction between van der Waals forces and hydrogen. The negative values of energy (ΔG) demonstrated that the binding of HAR with BSA was a spontaneous and exothermic process. The binding distance(r) between HAR and BSA was calculated to be about 2.80 nm based on the theory of Frster's non-radiation energy transfer, which indicated that energy is likely to be transfer from BSA to HAR. Both synchronous and 3D florescence spectroscopy clearly revealed that the microenvironment and conformation of BSA changed during the binding interaction between HAR and BSA. The molecular docking analysis revealed HAR is more inclined to BSA and human serum albumin

  12. A preliminary investigation into genotype x environment interaction ...

    African Journals Online (AJOL)

    uvp

    2014-08-24

    Aug 24, 2014 ... Genotype x environment interaction (G x E) in dairy cattle is a contentious ... environments, if it exists, with a negative impact on genetic response ..... interaction for Holstein milk yield in Colombia, Mexico and Puerto Rico.

  13. Single NdPc{sub 2} molecules on surfaces. Adsorption, interaction, and molecular magnetism

    Energy Technology Data Exchange (ETDEWEB)

    Fahrendorf, Sarah

    2013-01-24

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc{sub 2}) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc{sub 2}) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc{sub 2} molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the

  14. Single NdPc2 molecules on surfaces. Adsorption, interaction, and molecular magnetism

    International Nuclear Information System (INIS)

    Fahrendorf, Sarah

    2013-01-01

    They have huge potential for application in molecular-spin-transistors, molecular-spinvalves, and molecular quantum computing. SMMs are characterized by high spin ground states with zero-field splitting leading to high relaxation barriers and long relaxation times. A relevant class of molecules are the lanthanide double-decker phthalocyanines (LaPc 2 ) with only one metal atom sandwiched between two organic phthalocyanine (Pc) ligands. For envisaged spintronic applications it is important to understand the interaction between the molecules and the substrate and its influence on the electronic and magnetic properties. The subject of this thesis is the investigation of the adsorbed neodymium double-decker phthalocyanine (NdPc 2 ) by means of low temperature scanning tunneling microscopy and spectroscopy (STM and STS). The molecules are deposited by sublimation onto different substrates. It is observed that a large fraction of the double-decker molecules decomposes during deposition. The decomposition probability strongly depends on the chosen substrate. Therefore it is concluded that the substrate modifies the electronic structure of the molecule leading to a stabilization or destabilization of the molecular entity. Charge transfer from the surface to the molecule is identified as a potential stabilizing mechanism. The electronic and magnetic properties are investigated in detail for adsorbed NdPc 2 molecules on Cu(100). The results of the experimental study are compared to state-of-the-art density functional theory calculations performed by our colleagues from the Peter Gruenberg Institute (PGI-1) at the Forschungszentrum Juelich. Interestingly, the lower Pc ring of the molecule hybridizes intensely with the substrate leading to strong chemisorption of the molecule, while the upper Pc ring keeps its molecular type electronic states, which can be energetically shifted by an external electric field. Importantly, it is possible to get direct access to the spin

  15. Correlations and symmetry of interactions influence collective dynamics of molecular motors

    International Nuclear Information System (INIS)

    Celis-Garza, Daniel; Teimouri, Hamid; Kolomeisky, Anatoly B

    2015-01-01

    Enzymatic molecules that actively support many cellular processes, including transport, cell division and cell motility, are known as motor proteins or molecular motors. Experimental studies indicate that they interact with each other and they frequently work together in large groups. To understand the mechanisms of collective behavior of motor proteins we study the effect of interactions in the transport of molecular motors along linear filaments. It is done by analyzing a recently introduced class of totally asymmetric exclusion processes that takes into account the intermolecular interactions via thermodynamically consistent approach. We develop a new theoretical method that allows us to compute analytically all dynamic properties of the system. Our analysis shows that correlations play important role in dynamics of interacting molecular motors. Surprisingly, we find that the correlations for repulsive interactions are weaker and more short-range than the correlations for the attractive interactions. In addition, it is shown that symmetry of interactions affect dynamic properties of molecular motors. The implications of these findings for motor proteins transport are discussed. Our theoretical predictions are tested by extensive Monte Carlo computer simulations. (paper)

  16. Cloning Yeast Actin cDNA Leads to an Investigative Approach for the Molecular Biology Laboratory

    Science.gov (United States)

    Black, Michael W.; Tuan, Alice; Jonasson, Erin

    2008-01-01

    The emergence of molecular tools in multiple disciplines has elevated the importance of undergraduate laboratory courses that train students in molecular biology techniques. Although it would also be desirable to provide students with opportunities to apply these techniques in an investigative manner, this is generally not possible in the…

  17. Molecular interaction and energy transfer between human serum albumin and bioactive component Aloe dihydrocoumarin

    Science.gov (United States)

    Zhang, Xiu-Feng; Xie, Ling; Liu, Yang; Xiang, Jun-Feng; Li, Lin; Tang, Ya-Lin

    2008-10-01

    Aloe dihydrocoumarin is an antioxidant and a candidate of immunomodulatory drug on the immune system and can balance physiological reactive oxygen species (ROS) levels which may be useful to maintain homeostasis. In order to explore the mechanism of drug action at a molecular level, the binding of Aloe dihydrocoumarin with human serum albumin (HSA) has been investigated by fluorescence, ultraviolet (UV), circular dichroism (CD) and Fourier transform infrared (FT-IR) spectroscopy, fluorescence dynamics, and molecular dynamic docking for the first time. We observed a quenching of fluorescence of HSA in the presence of Aloe dihydrocoumarin and also analyzed the quenching results using the Stern-Volmer equation and obtained high affinity binding to HSA. A Förster type fluorescence resonance energy transfer mechanism is involved in this quenching of Trp fluorescence by Aloe dihydrocoumarin. From the CD and FT-IR results, it is apparent that the interaction of Aloe dihydrocoumarin with HSA causes a conformational change of the protein, with the loss of α-helix stability and the gain of β-sheet and β-turn content. Data obtained by fluorescence spectroscopy, fluorescence dynamics, CD, and FT-IR experiments along with the docking studies suggest that Aloe dihydrocoumarin binds to residues located in subdomain IIA of HSA.

  18. Circadian Rhythms in Fear Conditioning: An Overview of Behavioral, Brain System, and Molecular Interactions

    Directory of Open Access Journals (Sweden)

    Anne Albrecht

    2017-01-01

    Full Text Available The formation of fear memories is a powerful and highly evolutionary conserved mechanism that serves the behavioral adaptation to environmental threats. Accordingly, classical fear conditioning paradigms have been employed to investigate fundamental molecular processes of memory formation. Evidence suggests that a circadian regulation mechanism allows for a timestamping of such fear memories and controlling memory salience during both their acquisition and their modification after retrieval. These mechanisms include an expression of molecular clocks in neurons of the amygdala, hippocampus, and medial prefrontal cortex and their tight interaction with the intracellular signaling pathways that mediate neural plasticity and information storage. The cellular activities are coordinated across different brain regions and neural circuits through the release of glucocorticoids and neuromodulators such as acetylcholine, which integrate circadian and memory-related activation. Disturbance of this interplay by circadian phase shifts or traumatic experience appears to be an important factor in the development of stress-related psychopathology, considering these circadian components are of critical importance for optimizing therapeutic approaches to these disorders.

  19. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    Energy Technology Data Exchange (ETDEWEB)

    Mehranfar, Fahimeh [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Bordbar, Abdol-Khalegh, E-mail: bordbar@chem.ui.ac.ir [Department of Chemistry, University of Isfahan, Isfahan 81746-73441 (Iran, Islamic Republic of); Keyhanfar, Mehrnaz; Behbahani, Mandana [Faculty of Advanced Sciences and Technologies, Department of Biotechnology, University of Isfahan, Isfahan, 81746-73441 (Iran, Islamic Republic of)

    2013-11-15

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles.

  20. Clavibacter michiganensis ssp. michiganensis: bacterial canker of tomato, molecular interactions and disease management.

    Science.gov (United States)

    Nandi, Munmun; Macdonald, Jacqueline; Liu, Peng; Weselowski, Brian; Yuan, Ze-Chun

    2018-03-12

    Bacterial canker disease is considered to be one of the most destructive diseases of tomato (Solanum lycopersicum), and is caused by the seed-borne Gram-positive bacterium Clavibacter michiganensis ssp. michiganensis (Cmm). This vascular pathogen generally invades and proliferates in the xylem through natural openings or wounds, causing wilt and canker symptoms. The incidence of symptomless latent infections and the invasion of tomato seeds by Cmm are widespread. Pathogenicity is mediated by virulence factors and transcriptional regulators encoded by the chromosome and two natural plasmids. The virulence factors include serine proteases, cell wall-degrading enzymes (cellulases, xylanases, pectinases) and others. Mutational analyses of these genes and gene expression profiling (via quantitative reverse transcription-polymerase chain reaction, transcriptomics and proteomics) have begun to shed light on their roles in colonization and virulence, whereas the expression of tomato genes in response to Cmm infection suggests plant factors involved in the defence response. These findings may aid in the generation of target-specific bactericides or new resistant varieties of tomato. Meanwhile, various chemical and biological controls have been researched to control Cmm. This review presents a detailed investigation regarding the pathogen Cmm, bacterial canker infection, molecular interactions between Cmm and tomato, and current perspectives on improved disease management. © 2018 AGRICULTURE AND AGRI-FOOD CANADA. MOLECULAR PLANT PATHOLOGY © 2018 JOHN WILEY & SONS LTD.

  1. Spectrofluoremetric and molecular docking study on the interaction of bisdemethoxycurcumin with bovine β-casein nanoparticles

    International Nuclear Information System (INIS)

    Mehranfar, Fahimeh; Bordbar, Abdol-Khalegh; Keyhanfar, Mehrnaz; Behbahani, Mandana

    2013-01-01

    The interaction of bisdemethoxycurcumin (BDMC), as one of the main active component of turmeric (Curcuma longa L.), with bovine β-casein nanoparticle, as an efficient drug carrier system, was investigated using steady-state fluorescence spectroscopy and molecular docking calculations. Results of fluorescence quenching experiments, Forster energy transfer measurements and molecular docking calculations suggested that BDMC bind to the hydrophobic core of β-casein via formation of 3 hydrogen bonds and several vander Waals contacts that represented the encapsulation of BDMC in β-casein micelle nanoparticles. The binding parameters including number of substantive binding sites and the binding constants were evaluated by fluorescence quenching method. Additionally, the cytotoxicity of free BDMC and BDMC-β-casein complex in human breast cancer cell line MCF7 was evaluated in vitro. The study revealed the higher cytotoxic effects of encapsulated BDMC on MCF7 cells compared to equal dose of free BDMC. -- Highlights: • BDMC binds to the hydrophobic core of β-casein. • The effective encapsulation of BDMC in β-casein micelle nanoparticles was shown. • Enhanced cytotoxicity was observed for encapsulated BDMC in β-casein nanoparticles

  2. Thermal characterization of static and dynamical properties of the confined molecular systems interacting through dispersion force.

    Science.gov (United States)

    Ramos, Sergio Luis L M; Ogino, Michihiko; Oguni, Masaharu

    2015-01-28

    We investigated the thermal properties of liquid methylcyclohexane and racemic sec-butylcyclohexane, as representatives of a molecular system with only dispersion-force intermolecular interactions, confined in the pores (thickness/diameter d = 12, 6, 1.1 nm) of silica gels by adiabatic calorimetry. The results imply a heterogeneous picture for molecular aggregate under confinement consisting of an interfacial region and an inner pore one. In the vicinity of a glass-transition temperature T(g,bulk) of bulk liquid, two distinguishable relaxation phenomena were observed for the confined systems and their origins were attributed to the devitrification, namely glass transition, processes of (1) a layer of interfacial molecules adjacent to the pore walls and (2) the molecules located in the middle of the pore. A third glass-transition phenomenon was observed at lower temperatures and ascribed to a secondary relaxation process. The glass transition of the interfacial-layer molecules was found to proceed at temperatures rather above T(g,bulk), whereas that of the molecules located in the inner pore region occurred at temperatures below T(g,bulk). We discuss the reason why the molecules located in different places in the pores reveal the respectively different dynamical properties.

  3. Study of interaction of butyl p-hydroxybenzoate with human serum albumin by molecular modeling and multi-spectroscopic method

    Energy Technology Data Exchange (ETDEWEB)

    Wang Qin, E-mail: wqing07@lzu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Zhang Yaheng, E-mail: zhangyah04@lzu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Sun Huijun, E-mail: sun.hui.jun-04@163.co [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Hongli, E-mail: hlchen@lzu.edu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China); Chen Xingguo, E-mail: chenxg@lzu.edu.c [Department of Chemistry, Lanzhou University, Lanzhou 730000 (China)

    2011-02-15

    Study of the interaction between butyl p-hydroxybenzoate (butoben) and human serum albumin (HSA) has been performed by molecular modeling and multi-spectroscopic method. The interaction mechanism was predicted through molecular modeling first, then the binding parameters were confirmed using a series of spectroscopic methods, including fluorescence spectroscopy, UV-visible absorbance spectroscopy, circular dichroism (CD) spectroscopy and Fourier transform infrared (FT-IR) spectroscopy. The thermodynamic parameters of the reaction, standard enthalpy {Delta}H{sup 0} and entropy {Delta}S{sup 0}, have been calculated to be -29.52 kJ mol{sup -1} and -24.23 J mol{sup -1} K{sup -1}, respectively, according to the Van't Hoff equation, which suggests the van der Waals force and hydrogen bonds are the predominant intermolecular forces in stabilizing the butoben-HSA complex. Results obtained by spectroscopic methods are consistent with that of the molecular modeling study. In addition, alteration of secondary structure of HSA in the presence of butoben was evaluated using the data obtained from UV-visible absorbance, CD and FT-IR spectroscopies. - Research highlights: The interaction between butyl p-hydroxybenzoate with HSA has been investigated for the first time. Molecular modeling study can provide theoretical direction for experimental design. Multi-spectroscopic method can provide the binding parameters and thermodynamic parameters. These results are important for food safety and human health when using parabens as a preservative.

  4. Pathogenic Leptospira spp. in bats: Molecular investigation in Southern Brazil.

    Science.gov (United States)

    Mayer, Fabiana Quoos; Dos Reis, Emily Marques; Bezerra, André Vinícius Andrade; Cerva, Cristine; Rosa, Júlio; Cibulski, Samuel Paulo; Lima, Francisco Esmaile Sales; Pacheco, Susi Missel; Rodrigues, Rogério Oliveira

    2017-06-01

    The present study aimed to investigate the frequency of pathogenic Leptospira spp. in Brazilian bats and to determine possible risk factors associated to it. Ninety two bats of 12 species were evaluated. Whole genomic DNA from kidneys was extracted and real-time PCR specific to pathogenic Leptospira spp. was applied. Association between the frequency of specimens positive for Leptospira spp. and sex, age, bat species or family, season of collection, geographic localization and feeding habits was evaluated. The results showed that 39.13% of analyzed bats were found positive for Leptospira spp. Nine bat species had at least one positive result. There was no association among the evaluated variables and frequency of pathogenic Leptospira spp. Although the limitations due to lack of Leptospira spp. isolation, leptospiral carriage was demonstrated in bats of different species from southern Brazil, which reinforces the need for surveillance of infectious agents in wild animals. Copyright © 2017 Elsevier Ltd. All rights reserved.

  5. Effects of molecular interactions and the existence of different molecular forms of sodium fluoresceinate in solutions

    International Nuclear Information System (INIS)

    Golubeva, N.G.

    1989-01-01

    The results of measurement of fluorescence and absorption spectra of sodium fluoresceinate (FLNa) in different solutions and blood plasma are presented. The influence of solvent nature, its polarity, medium concentration and acidity on frequency, intensity and shape of fluorescence and absorption lines was analyzed. A general medium effect on fluorescence line spectral absorption was calculated from Lippert's equation. The influence of specific interactions has been analyzed on the example of acid-base interactions and hydrogen bonds in two- and multicomponent solutions. Computer processing of the spectra obtained allows to separate some forms of existing fluorophor molecules and to get data on the dynamics of their changes in different solutions. A special attention was given to the analysis of absorption and fluorescence bands of FLNa at its interaction with different proteins and lipids in solutions. From the analysis of data obtained a number of conclusions was drawn on the state of fluophor at its interactions with biological media. (author)

  6. Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.

    Science.gov (United States)

    Miryala, Sravan Kumar; Anbarasu, Anand; Ramaiah, Sudha

    2018-02-05

    Computational analysis of biomolecular interaction networks is now gaining a lot of importance to understand the functions of novel genes/proteins. Gene interaction (GI) network analysis and protein-protein interaction (PPI) network analysis play a major role in predicting the functionality of interacting genes or proteins and gives an insight into the functional relationships and evolutionary conservation of interactions among the genes. An interaction network is a graphical representation of gene/protein interactome, where each gene/protein is a node, and interaction between gene/protein is an edge. In this review, we discuss the popular open source databases that serve as data repositories to search and collect protein/gene interaction data, and also tools available for the generation of interaction network, visualization and network analysis. Also, various network analysis approaches like topological approach and clustering approach to study the network properties and functional enrichment server which illustrates the functions and pathway of the genes and proteins has been discussed. Hence the distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks. Copyright © 2017 Elsevier B.V. All rights reserved.

  7. Molecular analysis of the interaction between the hematopoietic master transcription factors GATA-1 and PU.1

    DEFF Research Database (Denmark)

    Liew, Chu Wai; Rand, Kasper Dyrberg; Simpson, Raina J Y

    2006-01-01

    GATA-1 and PU.1 are transcription factors that control erythroid and myeloid development, respectively. The two proteins have been shown to function in an antagonistic fashion, with GATA-1 repressing PU.1 activity during erythropoiesis and PU.1 repressing GATA-1 function during myelopoiesis. It has...... also become clear that this functional antagonism involves direct interactions between the two proteins. However, the molecular basis for these interactions is not known, and a number of inconsistencies exist in the literature. We have used a range of biophysical methods to define the molecular details...... of the GATA-1-PU.1 interaction. A combination of NMR titration data and extensive mutagenesis revealed that the PU.1-Ets domain and the GATA-1 C-terminal zinc finger (CF) form a low affinity interaction in which specific regions of each protein are implicated. Surprisingly, the interaction cannot be disrupted...

  8. Investigation of processes of interaction relativistic electrons with the solutions of organic dyes

    International Nuclear Information System (INIS)

    Buki, A.Yu.; Gokov, S.P.; Kazarinov, Yu.G.; Kalenik, S.A.; Kasilov, V.I.; Kochetov, S.S.; Makhnenko, P.L.; Mel'nitskiy, I.V.; Tverdohvalov, A.V.; Tsyatsko, V.V.; Shopen, O.A.

    2014-01-01

    Investigation of the processes of interaction of ionizing radiation with complex organic objects can solve a number of fundamental and applied problems in radiation physics, chemistry and biology. In this work we investigated the dose dependence (dose range 1...5MRad) optical density relative concentrations of water, alcohol and glycerine solution following organic dyes: methylene blue - C 16 H 18 N 3 SCl and methyl orange - C 14 H 14 N 3 O 3 SNa, irradiated with an electron beam with an energy of 16MeV. In the analysis of absorption spectra, it was found that water solutions of dyes have less resistance to radiation as compared with the alcohol and glycerol. Also, all solutions of methyl orange less radiation resistant than the methylene blue solution. Analysis of the spectra showed that these relationships are close to linear in the range of doses. To understand the physical and chemical processes occurring in the interaction of relativistic electrons with the studied organic objects were performed the computer simulations of the energy spectra of ions formed due to breaking the chemical bonds of molecules of dye solutions using the program SRIM-2010. The analysis showed that radiation - stimulated chemical processes play a major role in the destruction of the source of organic dye molecules. The remaining processes (interaction of electrons and nuclei, the cascade processes) accounts for about 10% of all molecular breaks.

  9. Nanopore wall-liquid interaction under scope of molecular dynamics study: Review

    Science.gov (United States)

    Tsukanov, A. A.; Psakhie, S. G.

    2017-12-01

    The present review is devoted to the analysis of recent molecular dynamics based on the numerical studies of molecular aspects of solid-fluid interaction in nanoscale channels. Nanopore wall-liquid interaction plays the crucial role in such processes as gas separation, water desalination, liquids decontamination, hydrocarbons and water transport in nano-fractured geological formations. Molecular dynamics simulation is one of the most suitable tools to study molecular level effects occurred in such multicomponent systems. The nanopores are classified by their geometry to four groups: nanopore in nanosheet, nanotube-like pore, slit-shaped nanopore and soft-matter nanopore. The review is focused on the functionalized nanopores in boron nitride nanosheets as novel selective membranes and on the slit-shaped nanopores formed by minerals.

  10. A network-based biomarker approach for molecular investigation and diagnosis of lung cancer

    Directory of Open Access Journals (Sweden)

    Chen Bor-Sen

    2011-01-01

    Full Text Available Abstract Background Lung cancer is the leading cause of cancer deaths worldwide. Many studies have investigated the carcinogenic process and identified the biomarkers for signature classification. However, based on the research dedicated to this field, there is no highly sensitive network-based method for carcinogenesis characterization and diagnosis from the systems perspective. Methods In this study, a systems biology approach integrating microarray gene expression profiles and protein-protein interaction information was proposed to develop a network-based biomarker for molecular investigation into the network mechanism of lung carcinogenesis and diagnosis of lung cancer. The network-based biomarker consists of two protein association networks constructed for cancer samples and non-cancer samples. Results Based on the network-based biomarker, a total of 40 significant proteins in lung carcinogenesis were identified with carcinogenesis relevance values (CRVs. In addition, the network-based biomarker, acting as the screening test, proved to be effective in diagnosing smokers with signs of lung cancer. Conclusions A network-based biomarker using constructed protein association networks is a useful tool to highlight the pathways and mechanisms of the lung carcinogenic process and, more importantly, provides potential therapeutic targets to combat cancer.

  11. Intermolecular interactions between σ- and π-holes of bromopentafluorobenzene and pyridine: computational and experimental investigations.

    Science.gov (United States)

    Yang, Fang-Ling; Yang, Xing; Wu, Rui-Zhi; Yan, Chao-Xian; Yang, Fan; Ye, Weichun; Zhang, Liang-Wei; Zhou, Pan-Pan

    2018-04-25

    The characters of σ- and π-holes of bromopentafluorobenzene (C6F5Br) enable it to interact with an electron-rich atom or group like pyridine which possesses an electron lone-pair N atom and a π ring. Theoretical studies of intermolecular interactions between C6F5Br and C5H5N have been carried out at the M06-2X/aug-cc-pVDZ level without and with the counterpoise method, together with single point calculations at M06-2X/TZVP, wB97-XD/aug-cc-pVDZ and CCSD(T)/aug-cc-pVDZ levels. The σ- and π-holes of C6F5Br exhibiting positive electrostatic potentials make these sites favorably interact with the N atom and the π ring of C5H5N with negative electrostatic potentials, leading to five different dimers connected by a σ-holen bond, a σ-holeπ bond or a π-holeπ bond. Their geometrical structures, characteristics, nature and spectroscopy behaviors were systematically investigated. EDA analyses reveal that the driving forces in these dimers are different. NCI, QTAIM and NBO analyses confirm the existence of intermolecular interactions formed via σ- and π-holes of C6F5Br and the N atom and the π ring of C5H5N. The experimental IR and Raman spectra gave us important information about the formation of molecular complexes between C6F5Br and C5H5N. We expect that the results could provide valuable insights into the investigation of intermolecular interactions involving σ- and π-holes.

  12. Molecular Model of a Quantum Dot Beyond the Constant Interaction Approximation

    Science.gov (United States)

    Temirov, Ruslan; Green, Matthew F. B.; Friedrich, Niklas; Leinen, Philipp; Esat, Taner; Chmielniak, Pawel; Sarwar, Sidra; Rawson, Jeff; Kögerler, Paul; Wagner, Christian; Rohlfing, Michael; Tautz, F. Stefan

    2018-05-01

    We present a physically intuitive model of molecular quantum dots beyond the constant interaction approximation. It accurately describes their charging behavior and allows the extraction of important molecular properties that are otherwise experimentally inaccessible. The model is applied to data recorded with a noncontact atomic force microscope on three different molecules that act as a quantum dot when attached to the microscope tip. The results are in excellent agreement with first-principles simulations.

  13. An autosampling differential scanning calorimeter instrument for studying molecular interactions.

    Science.gov (United States)

    Plotnikov, Valerian; Rochalski, Andrew; Brandts, Michael; Brandts, John F; Williston, Samuel; Frasca, Verna; Lin, Lung-Nan

    2002-11-01

    A new ultrasensitive differential scanning calorimeter (DSC) instrument is described, which utilizes autosampling for continuous operation. High scanning rates to 250 deg/h with rapid cooling and equilibration between scans facilitates higher sample throughput up to 50 samples during each 24 h of unattended operation. The instrument is suited for those pharmaceutical applications where higher throughput is important, such as screening drug candidates for binding constant or screening solution conditions for stability of liquid protein formulations. Results are presented on the binding of five different anionic inhibitors to ribonuclease A, which included cytidine 2'-monophosphate (2'CMP), 3'CMP, uridine 3'-monophosphate, pyrophosphate, and phosphate. Binding constants K(B) (or dissociation constants K(d)) are obtained from the shift in the transition temperature T(M) for ribonuclease thermal unfolding in the presence of ligand relative to the transition temperature in the absence of ligand. Measured binding constants ranged from 155 M(-1) (K(d) = 6.45 mM) for the weak-binding phosphate anion to 13100 M(-1) (K(d) = 76.3 microM) for the strongest binding ligand, 2'CMP. The DSC method for measuring binding constants can also be extended to ultratight interactions involving either ligand-protein or protein-protein binding.

  14. Quantum chemical investigation of attractive non-covalent interactions between halomethanes and rare gases.

    Science.gov (United States)

    McAllister, Linda J; Bruce, Duncan W; Karadakov, Peter B

    2012-11-01

    The interaction between rare gas atoms and trifluoromethylhalides and iodomethane is investigated using ab initio and density functional theory (DFT) methods: MP2, CCSD, B3LYP, M06, M06-L, M06-2X, M06-HF, X3LYP, PBE, B97-D, B3LYP-D3, and M06-L-D3, in combination with the aug-cc-pVTZ and aug-cc-pVTZ-PP basis sets. A weakly attractive interaction is observed for all complexes, whose strength increases as the rare gas and halogen bond donor become more polarizable, and as the group bound to the halogen bond donor becomes more electron-withdrawing. The separation between iodine and krypton in the complex CF(3)I···Kr, calculated at the MP2 and B3LYP-D3 levels of theory, agrees very well with recent experimental results (Stephens, S. L.; Walker, N. R.; Legon, A. C. J. Chem. Phys. 2011, 135, 224309). Analysis of the ability of theoretical methods to account for the dispersion interaction present in these complexes leads to the conclusion that MP2 and B3LYP-D3, which produce very similar results, are the better performing methods, followed by B97-D and the M06 suite of functionals; the popular B3LYP as well as X3LYP perform poorly and significantly underestimate the interaction strength. The orbitals responsible for the interaction are identified through Edmiston-Ruedenberg localization; it is shown that, by combining the key orbitals, it is possible to observe a molecular orbital picture of a σ-hole interaction.

  15. π-Cation Interactions in Molecular Recognition: Perspectives on Pharmaceuticals and Pesticides.

    Science.gov (United States)

    Liang, Zhibin; Li, Qing X

    2018-04-04

    The π-cation interaction that differs from the cation-π interaction is a valuable concept in molecular design of pharmaceuticals and pesticides. In this Perspective we present an up-to-date review (from 1995 to 2017) on bioactive molecules involving π-cation interactions with the recognition site, and categorize into systems of inhibitor-enzyme, ligand-receptor, ligand-transporter, and hapten-antibody. The concept of π-cation interactions offers use of π systems in a small molecule to enhance the binding affinity, specificity, selectivity, lipophilicity, bioavailability, and metabolic stability, which are physiochemical features desired for drugs and pesticides.

  16. Investigation of physical structures and interactions at high energy

    International Nuclear Information System (INIS)

    Anderson, E.W.

    1991-01-01

    Contract AC02-85ER40193 supports the investigation of fundamental structures and interactions at high energy by the Iowa State University Alpha HEP Group. Three major activities constitute the present focus of our research. Experiment E-735, performed at the Fermilab Tevatron Collider, is a search for a deconfined quark-gluon plasma phase of hadronic matter predicted to occur when temperatures of 240 MeV are achieved. The primary data were obtained in 1988--1989, from these data the collaboration is analyzing the charged particle multiplicity and transverse momentum distributions of the produced secondaries. These measurements are regarded on theoretical grounds to be sensitive indicators of the formation of a high-temperature plasma. The TPC detector, installed in the PEP ring at SLAC, has accumulated about 60,000 hadronic events at 29 GeV center-of-mass energy. Several thousand events have high-precision vertex chamber measurements. Physics analysis of charmed quark events, in addition to a measurement of the QCD strong coupling, are in progress. Our identification and reconstruction of D o , D*, and D s , charmed mesons will be useful for subsequent B meson studies in the TPC detector. The SSC liquid argon major subsystem tests at BNL and studies of gauge boson identification and reconstruction for large SSC detectors are in progress. Several crucial problems related to calorimeter geometries, coil geometries, and discrimination methods in full SSC events have been solved, and work is in progress on a one million event test of WW scattering capability up to 2 TeV. Our participation in the subsystem proposal involves construction of the module, data-taking at the AGS, and data analysis

  17. Interaction of pathology and molecular characterization of thyroid cancers

    International Nuclear Information System (INIS)

    Williams, E.D.; Cherstvoy, E.; Egloff, B.; Hoefler, H.; Vecchio, G.; Bogdanova, T.; Bragarnik, M.; Tronko, N.D.

    1996-01-01

    This paper presents the results of joint studies of thyroid cancer in children under 15 years of age between departments in Cambridge, Brussels, Naples and Munich in the European Union, and departments in Minsk, Kiev and Obninsk in the newly independent states of Eastern Europe. The pathology of 264 cases of childhood thyroid cancer out of 430 that have occurred since 1990 in the 3 countries in which high levels of fallout from the Chernobyl accident occurred has been restudied by NIS and EU pathologists. The overall level of agreement reached was about 97%. The diagnosis was supported by immunocytochemistry and ISH for the differentiation markers, thyroglobulin and calcitonin, and the tumors were classified according to the WHO, with papillary carcinomas being further subclassified. 99% of the 134 Belarussian cases were papillary carcinomas, as were 94% of the 114 Ukrainian tumors. All 9 of the Russian cases available for study were papillary in type. 76 of 154 cases of childhood thyroid cancer reviewed over a 30 year period in England and Wales and were also studied, 68% of these were papillary carcinoma. Histological study showed that a subtype of papillary carcinoma, rarely found in adults, with a solid/follicular architecture occurred in children. It was found in 72% of the Belarussian papillary carcinomas, 76% of the Ukrainian cases, but only 40% of the England and Wales cases. Molecular biological studies showed that the proportion of cases of papillary carcinoma expressing the ret gene was not significantly different in the exposed and the unexposed tumors, studies of the type of translocation leading to ret gene expression are not yet conclusive. Ras gene mutations were found as expected in follicular carcinoma, but were absent from any papillary carcinoma, whether from exposed or unexposed cases. TSH receptor mutations, normally found in follicular tumors were not found in any papillary carcinomas, nor were any p53 mutations identified. All these results

  18. Exploring the mechanism of interaction between sulindac and human serum albumin: Spectroscopic and molecular modeling methods

    Energy Technology Data Exchange (ETDEWEB)

    Zhang, Xiao-Ping; Hou, Ya-He [Department of Material Engineering, Xuzhou College of Industrial Technology, Xuzhou, Jiangsu 221140 (China); Wang, Li [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); Zhang, Ye-Zhong, E-mail: zhangfluorescence@126.com [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); Liu, Yi, E-mail: prof.liuyi@263.net [Department of Chemistry, College of Chemistry and Environmental Engineering, Yangtze University, Jingzhou, Hubei 434023 (China); College of Chemistry and Molecular Sciences and State Key Laboratory of Virology, Wuhan University, Wuhan 430072 (China)

    2013-06-15

    In the present study, a combination of fluorescence, molecular modeling and circular dichroism (CD) approaches had been employed to investigate the interaction between sulindac and human serum albumin (HSA). Results of mechanism discussion demonstrated that the fluorescence quenching of HSA by sulindac was a static quenching procedure. Binding parameters calculated from the modified Stern–Volmer equation showed that sulindac bound to HSA with the binding affinities in the order of 10{sup 5} L mol{sup −1}. The thermodynamic parameters (ΔH=−18.58 kJ mol{sup −1}; ΔS=37.26 J mol{sup −1} K{sup −1}) obtained by the van′t Hoff equation revealed that hydrophobic forces played a leading role in the formation of sulindac–HSA complex, but hydrogen bonds could not be omitted. Site marker competitive experiments revealed a displacement of warfarin by sulindac, which indicated that the binding site of sulindac to HSA located in the sub-domain IIA (Sudlow′s site I). The molecular docking study confirmed the specific binding mode and binding site obtained by fluorescence and site marker competitive experiments. CD and three-dimensional fluorescence spectroscopy were used to investigate the changes of HSA secondary structure and microenvironment in the presence of sulindac. Alterations of HSA conformation were observed with the reduction of α-helix from 60.1% (free HSA) to 57.3%, manifesting a slight unfolding of the polypeptides of protein. -- Highlights: ► The quenching mechanism between sulindac and HSA is a static process. ► The binding of sulindac to HSA takes place in sub-domain IIA (Sudlow′s site I). ► The binding is spontaneous and hydrophobic force plays major role in stabilizing the complex. ► CD and 3-D fluorescence spectra prove the change of the microenvironment and conformation of HSA.

  19. Lipid bilayers driven to a wrong lane in molecular dynamics simulations by subtle changes in long-range electrostatic interactions

    NARCIS (Netherlands)

    Patra, M.; Karttunen, M.E.J.; Hyvönen, M.T.; Falck, E.; Vattulainen, I.

    2004-01-01

    We provide compelling evidence that different treatments of electrostatic interactions in molecular dynamics simulations may dramatically affect dynamic properties of lipid bilayers. To this end, we consider a fully hydrated pure dipalmitoylphosphatidylcholine bilayer through 50-ns molecular

  20. Optical spectroscopy and system–bath interactions in molecular aggregates with full configuration interaction Frenkel exciton model

    Energy Technology Data Exchange (ETDEWEB)

    Seibt, Joachim; Sláma, Vladislav; Mančal, Tomáš, E-mail: mancal@karlov.mff.cuni.cz

    2016-12-20

    Highlights: • Standard Frenkel exciton model is extended to include inter-band coupling. • It is formally linked with configuration interaction method of quantum chemistry. • Spectral shifts due to inter-band coupling are found in molecular aggregates. • Effects of peak amplitude redistribution in two-dimensional spectra are found. - Abstract: Standard application of the Frenkel exciton model neglects resonance coupling between collective molecular aggregate states with different number of excitations. These inter-band coupling terms are, however, of the same magnitude as the intra-band coupling between singly excited states. We systematically derive the Frenkel exciton model from quantum chemical considerations, and identify it as a variant of the configuration interaction method. We discuss all non-negligible couplings between collective aggregate states, and provide compact formulae for their calculation. We calculate absorption spectra of molecular aggregate of carotenoids and identify significant band shifts as a result of inter-band coupling. The presence of inter-band coupling terms requires renormalization of the system–bath coupling with respect to standard formulation, but renormalization effects are found to be weak. We present detailed discussion of molecular dimer and calculate its time-resolved two-dimensional Fourier transformed spectra to find weak but noticeable effects of peak amplitude redistribution due to inter-band coupling.

  1. Ab initio calculation of molecular energies including parity violating interactions

    International Nuclear Information System (INIS)

    Bakasov, A.; Ha Taekyu; Quack, M.

    1995-01-01

    A new approach, RHF-CIS, based on the perturbation of the ground state RHF wave function by the CIS excitations, has been implemented for evaluation of energy of parity violating interaction in molecules, E pv . The earlier approach, RHF-SDE, was based on the perturbation of the RHF ground states by the single-determinant ''excitations'' (SDE). The results obtained show the dramatic difference between E pv values in the RHF-CIS framework and those in the RHF-SDE framework: the E pv values of the RHF-CIS formalism are more than one order of magnitude greater compared to the RHF-SDE formalism as well as the corresponding tensor components. The maximal total value obtained for hydrogen peroxide in the RHF-CIS framework is 3.661 X 10 -19 E H (DZ ** basis set) while the maximal E pv value for the RHF-SDE formalism is just 3.635 X 10 -20 E H (TZ basis set). It is remarkable that both in the RFH-CIS and in the RHF-SDE approaches the diagonal tensor components of E pv strictly follow the geometry of a molecule and are always different from zero at chiral conformations. The zeros of the total E pv at chiral geometries are now found to be the results of the interplay between the diagonal tensor components values. We have carried out exhaustive analysis of the RHF-SDE formalism and found that it is not sufficiently accurate for studies of E pv . To this end, we have completely reproduced the previous work, which has been done in the RHF-SDE frame-work, and developed it further, studying how the RHF-SDE results vary when changing size and quality of basis sets. This last resource does not save the RHF-SDE formalism for evaluations of E pv from the general failure. Packages of FORTRAN routines called ENWEAK/RHFSDE-93 and ENWEAK/RHFCIS-94 have been developed which run on top of an ab initio MO package. We used 6-31G and 6-31G**, DZ and DZ**, TZ and TZ**, and (10s, 6p,**) basis sets. We will discuss the importance of the present results for possible measurement of the parity

  2. Large Scale Molecular Simulation of Nanoparticle-Biomolecule Interactions and their Implications in Nanomedicine

    Science.gov (United States)

    Zhou, Ruhong

    Nanoscale particles have become promising materials in various biomedical applications, however, in order to stimulate and facilitate these applications, there is an urgent need for a better understanding of their biological effects and related molecular mechanism/physics as well. In this talk, I will discuss some of our recent works, mostly molecular modelling, on nanotoxicity and their implications in de novo design of nanomedicine. We show that carbon-based nanoparticles (carbon nanotubes, graphene nanosheets, and fullerenes) can interact and disrupt the structures and functions of many important proteins. The hydrophobic interactions between the carbon nanotubes and hydrophobic residues, particularly aromatic residues through the so-called π- π stacking interactions, are found to play key roles. Meanwhile, metallofullerenol Gd@C82(OH)22 is found to inhibit tumour growth and metastases with both experimental and theoretical approaches. Graphene and graphene oxide (GO) nanosheets show strong destructive interactions to E. coli cell membranes (antibacterial activity) and A β amyloid fibrils (anti-AD, Alzheimer's disease, capability) with unique molecular mechanisms, while on the other hand, they also show a strong supportive role in enzyme immobilisation such as lipases through lid opening. In particular, the lid opening is assisted by lipase's sophisticated interaction with GO, which allows the adsorbed lipase to enhance its enzyme activity. The lipase enzymatic activity can be further optimized through fine tuning of the GO surface hydrophobicity. These findings might provide a better understanding of ``nanotoxicity'' at the molecular level with implications in de novo nanomedicine design.

  3. Prediction and Dissection of Protein-RNA Interactions by Molecular Descriptors.

    Science.gov (United States)

    Liu, Zhi-Ping; Chen, Luonan

    2016-01-01

    Protein-RNA interactions play crucial roles in numerous biological processes. However, detecting the interactions and binding sites between protein and RNA by traditional experiments is still time consuming and labor costing. Thus, it is of importance to develop bioinformatics methods for predicting protein-RNA interactions and binding sites. Accurate prediction of protein-RNA interactions and recognitions will highly benefit to decipher the interaction mechanisms between protein and RNA, as well as to improve the RNA-related protein engineering and drug design. In this work, we summarize the current bioinformatics strategies of predicting protein-RNA interactions and dissecting protein-RNA interaction mechanisms from local structure binding motifs. In particular, we focus on the feature-based machine learning methods, in which the molecular descriptors of protein and RNA are extracted and integrated as feature vectors of representing the interaction events and recognition residues. In addition, the available methods are classified and compared comprehensively. The molecular descriptors are expected to elucidate the binding mechanisms of protein-RNA interaction and reveal the functional implications from structural complementary perspective.

  4. Molecular dynamics investigations of BioH protein substrate specificity for biotin synthesis.

    Science.gov (United States)

    Xue, Qiao; Cui, Ying-Lu; Zheng, Qing-Chuan; Zhang, Hong-Xing

    2016-05-01

    BioH, an enzyme of biotin synthesis, plays an important role in fatty acid synthesis which assembles the pimelate moiety. Pimeloyl-acyl carrier protein (ACP) methyl ester, which is long known to be a biotin precursor, is the physiological substrate of BioH. Azelayl methyl ester, which has a longer chain than pimeloyl methyl ester, conjugated to ACP is also indeed accepted by BioH with very low rate of hydrolysis. To date, the substrate specificity for BioH and the molecular origin for the experimentally observed rate changes of hydrolysis by the chain elongation have remained elusive. To this end, we have investigated chain elongation effects on the structures by using the fully atomistic molecular dynamics simulations combined with binding free energy calculations. The results indicate that the substrate specificity is determined by BioH together with ACP. The added two methylenes would increase the structural flexibility by protein motions at the interface of ACP and BioH, instead of making steric clashes with the side chains of the BioH hydrophobic cavity. On the other hand, the slower hydrolysis of azelayl substrate is suggested to be associated with the loose of contacts between BioH and ACP, and with the lost electrostatic interactions of two ionic/hydrogen bonding networks at the interface of the two proteins. The present study provides important insights into the structure-function relationships of the complex of BioH with pimeloyl-ACP methyl ester, which could contribute to further understanding about the mechanism of the biotin synthetic pathway, including the catalytic role of BioH.

  5. [From Purkinje's pharmacologic observations to molecular drug interactions].

    Science.gov (United States)

    Kvĕtina, J

    1998-11-01

    The 650th anniversary of the foundation of Charles University (7 April 1348) in Prague has initiated a number of historical surveys of the subjects which has been taught at the University for a longer period of time. The disciplines connected with pharmacotherapy were being developed in an empirical conception at the University from the second half of the 14th century but the beginnings of experimental drug research date as late as the mid-19th century. The present survey of the history of "the sciences of medicaments" therefore attempts to outline in short entries the developmental stages of pharmaceutical and pharmacological investigations in the territory of Bohemia and Moravia in about recent 150 years. The arrangement of data is chronological; in the part covering the second half of the 20th century the research of a predominantly exploratory character (universities and academic institutions and their representatives) and research aimed primarily to innovate medicaments (research institutions of pharmaceutical industry and clinical pharmacology and some of their representatives) are treated separately.

  6. DyNet: visualization and analysis of dynamic molecular interaction networks.

    Science.gov (United States)

    Goenawan, Ivan H; Bryan, Kenneth; Lynn, David J

    2016-09-01

    : The ability to experimentally determine molecular interactions on an almost proteome-wide scale under different conditions is enabling researchers to move from static to dynamic network analysis, uncovering new insights into how interaction networks are physically rewired in response to different stimuli and in disease. Dynamic interaction data presents a special challenge in network biology. Here, we present DyNet, a Cytoscape application that provides a range of functionalities for the visualization, real-time synchronization and analysis of large multi-state dynamic molecular interaction networks enabling users to quickly identify and analyze the most 'rewired' nodes across many network states. DyNet is available at the Cytoscape (3.2+) App Store (http://apps.cytoscape.org/apps/dynet). david.lynn@sahmri.com Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

  7. Molecular interactions of mussel protective coating protein, mcfp-1, from Mytilus californianus.

    Science.gov (United States)

    Lu, Qingye; Hwang, Dong Soo; Liu, Yang; Zeng, Hongbo

    2012-02-01

    Protective coating of the byssus of mussels (Mytilus sp.) has been suggested as a new paradigm of medical coating due to its high extensibility and hardness co-existence without their mutual detriment. The only known biomacromolecule in the extensible and tough coating on the byssus is mussel foot protein-1 (mfp-1), which is made up with positively charged residues (~20 mol%) and lack of negatively charged residues. Here, adhesion and molecular interaction mechanisms of Mytilus californianus foot protein-1 (mcfp-1) from California blue mussel were investigated using a surface forces apparatus (SFA) in buffer solutions of different ionic concentrations (0.2-0.7 M) and pHs (3.0-5.5). Strong and reversible cohesion between opposed positively charged mcfp-1 films was measured in 0.1 M sodium acetate buffer with 0.1 M KNO(3). Cohesion of mcfp-1 was gradually reduced with increasing the ionic strength, but was not changed with pH variations. Oxidation of 3,4-dihydroxyphenylalanine (DOPA) residues of mcfp-1, a key residue for adhesive and coating proteins of mussel, didn't change the cohesion strength of mcfp-1 films, but the addition of chemicals with aromatic groups (i.e., aspirin and 4-methylcatechol) increased the cohesion. These results suggest that the cohesion of mcfp-1 films is mainly mediated by cation-π interactions between the positively charged residues and benzene rings of DOPA and other aromatic amino acids (~20 mol% of total amino acids of mcfp-1), and π-π interactions between the phenyl groups in mcfp-1. The adhesion mechanism obtained for the mcfp-1 proteins provides important insight into the design and development of functional biomaterials and coatings mimicking the extensible and robust mussel cuticle coating. Copyright © 2011 Elsevier Ltd. All rights reserved.

  8. Experimental Investigation of Turbulence-Chemistry Interaction in High-Reynolds-Number Turbulent Partially Premixed Flames

    Science.gov (United States)

    2016-06-23

    AFRL-AFOSR-VA-TR-2016-0277 Experimental Investigation of Turbulence-Chemistry Interaction in High- Reynolds -Number Turbulent Partially Premixed...4. TITLE AND SUBTITLE [U] Experimental investigation of turbulence-chemistry interaction in high- Reynolds -number 5a. CONTRACT NUMBER turbulent...for public release Final Report: Experimental investigation of turbulence-chemistry interaction in high- Reynolds -number turbulent partially premixed

  9. A molecular dynamics study on the interaction between epoxy and functionalized graphene sheets

    DEFF Research Database (Denmark)

    Melro, Liliana Sofia S. F. P.; Pyrz, Ryszard; Jensen, Lars Rosgaard

    2016-01-01

    The interaction between graphene and epoxy resin was studied using molecular dynamics simulations. The interfacial shear strength and pull out force were calculated for functionalised graphene layers (carboxyl, carbonyl, and hydroxyl) and epoxy composites interfaces. The influence of functional...... groups, as well as their distribution and coverage density on the graphene sheets were also analysed through the determination of the Young's modulus. Functionalisation proved to be detrimental to the mechanical properties, nonetheless according to interfacial studies the interaction between graphene...

  10. The impact of long-range electron-hole interaction on the charge separation yield of molecular photocells

    Science.gov (United States)

    Nemati Aram, Tahereh; Ernzerhof, Matthias; Asgari, Asghar; Mayou, Didier

    2017-01-01

    We discuss the effects of charge carrier interaction and recombination on the operation of molecular photocells. Molecular photocells are devices where the energy conversion process takes place in a single molecular donor-acceptor complex attached to electrodes. Our investigation is based on the quantum scattering theory, in particular on the Lippmann-Schwinger equation; this minimizes the complexity of the problem while providing useful and non-trivial insight into the mechanism governing photocell operation. In this study, both exciton pair creation and dissociation are treated in the energy domain, and therefore there is access to detailed spectral information, which can be used as a framework to interpret the charge separation yield. We demonstrate that the charge carrier separation is a complex process that is affected by different parameters, such as the strength of the electron-hole interaction and the non-radiative recombination rate. Our analysis helps to optimize the charge separation process and the energy transfer in organic solar cells and in molecular photocells.

  11. Investigating Near Space Interaction Regions: Developing a Remote Observatory

    Science.gov (United States)

    Gallant, M.; Mierkiewicz, E. J.; Oliversen, R. J.; Jaehnig, K.; Percival, J.; Harlander, J.; Englert, C. R.; Kallio, R.; Roesler, F. L.; Nossal, S. M.; Gardner, D.; Rosborough, S.

    2016-12-01

    The Investigating Near Space Interaction Regions (INSpIRe) effort will (1) establish an adaptable research station capable of contributing to terrestrial and planetary aeronomy; (2) integrate two state-of-the-art second generation Fabry-Perot (FP) and Spatial Heteorodyne Spectrometers (SHS) into a remotely operable configuration; (3) deploy this instrumentation to a clear-air site, establishing a stable, well-calibrated observatory; (4) embark on a series of observations designed to contribute to three major areas of geocoronal research: geocoronal physics, structure/coupling, and variability. This poster describes the development of the INSpIRe remote observatory. Based at Embry-Riddle Aeronautical University (ERAU), initiative INSpIRe provides a platform to encourage the next generation of researchers to apply knowledge gained in the classroom to real-world science and engineering. Students at ERAU contribute to the INSpIRe effort's hardware and software needs. Mechanical/optical systems are in design to bring light to any of four instruments. Control software is in development to allow remote users to control everything from dome and optical system operations to calibration and data collection. In April 2016, we also installed and tested our first science instrument in the INSpIRe trailer, the Redline DASH Demonstration Instrument (REDDI). REDDI uses Doppler Asymmetric Spatial Heterodyne (DASH) spectroscopy, and its deployment as part of INSpIRe is a collaborative research effort between the Naval Research Lab, St Cloud State University, and ERAU. Similar to a stepped Michelson device, REDDI measures oxygen (630.0 nm) winds from the thermosphere. REDDI is currently mounted in a temporary location under INSpIRe's main siderostat until its entrance optical system can be modified. First light tests produced good signal-to-noise fringes in ten minute integrations, indicating that we will soon be able to measure thermospheric winds from our Daytona Beach testing site

  12. Fluorescence spectroscopic investigation of the interaction of citrinin with native and chemically modified cyclodextrins

    Energy Technology Data Exchange (ETDEWEB)

    Poór, Miklós, E-mail: poor.miklos@pte.hu [Department of Pharmacology and Pharmacotherapy, Toxicology Section, University of Pécs, Szigeti út 12, Pécs H-7624 (Hungary); Matisz, Gergely; Kunsági-Máté, Sándor [Department of General and Physical Chemistry, University of Pécs, Ifjúság útja 6, Pécs H-7624 (Hungary); János Szentágothai Research Center, Ifjúság útja 20, Pécs H-7624 (Hungary); Derdák, Diána [Department of General and Physical Chemistry, University of Pécs, Ifjúság útja 6, Pécs H-7624 (Hungary); Szente, Lajos [CycloLab Cyclodextrin Research & Development Laboratory Ltd., Illatos út 7, Budapest H-1097 (Hungary); and others

    2016-04-15

    Citrinin (CIT) is a nephrotoxic mycotoxin produced by several Aspergillus, Penicillium and Monascus species. CIT is unavoidable contaminant of different foods and drinks due to its wide occurrence and high thermal stability. For this reason, development of new, more sensitive analytical methods and decontamination strategies has high importance. In our study, the complex formation of CIT with native and chemically modified cyclodextrins was investigated using fluorescence spectroscopy. Furthermore, thermodynamic and molecular modeling studies were also performed for the deeper understanding of these host-guest interactions. Our results show that among the tested compounds methylated β-cyclodextrins form the most stable complexes with CIT and these derivatives cause the highest fluorescence enhancement of CIT as well. These observations recommend that some of the chemically modified derivatives show more favourable properties than the native cyclodextrin, and suggesting more promising analytical applicability and higher affinity as potential toxin binders.

  13. Spectroscopic investigation on the interaction of titanate nanotubes with bovine serum albumin

    International Nuclear Information System (INIS)

    Zhao, L.Z.; Zhao, Y.S.; Teng, H.H.; Shi, S.Y.; Ren, B.X.

    2014-01-01

    In order to understand the transport mechanism and evaluate the biological safety of titanate nanotubes, the interactions of titanate nanotubes (TNTs) with bovine serum albumin (BSA) were investigated by applying spectroscopic methods under simulated physiological conditions. After taking into account the inner filter effect, the fluorescence intensity of BSA was found to be significantly enhanced by the presence of TNTs, indicating that the microenvironment of tryptophan and tyrosine residues in BSA became more hydrophobic. In addition, the absorption spectra of BSA showed a hyperchromic effect around 280 nm as the concentration of TNTs increased, suggesting that TNTs changed the microenvironment of the tryptophan and tyrosine residues. This is consistent with the results from fluorescence spectroscopy studies. However, circular dichroism spectroscopy revealed that no significant conformational change in BSA occurred during the interaction. We believe that Trp-213 was buried more compactly in the internal hydrophobic region, and hydrophobicity increased around Trp-134 with increasing TNTs concentration. From a spectroscopic point of view, this work elucidates the interaction mechanism of titanate nanotubes with BSA, and the methods used in this paper can also be applied to explore the molecular mechanism underlying toxicity of other nanomaterials. (authors)

  14. A versatile tunable microcavity for investigation of light-matter interaction

    Science.gov (United States)

    Mochalov, Konstantin E.; Vaskan, Ivan S.; Dovzhenko, Dmitriy S.; Rakovich, Yury P.; Nabiev, Igor

    2018-05-01

    Light-matter interaction between a molecular ensemble and a confined electromagnetic field is a promising area of research, as it allows light-control of the properties of coupled matter. The common way to achieve coupling is to place an ensemble of molecules or quantum emitters into a cavity. In this approach, light-matter coupling is evidenced by modification of the spectral response of the emitter, which depends on the strength of interaction between emitter and cavity modes. However, there is not yet a user-friendly approach that allows the study of a large number of different and replaceable samples in a wide optical range using the same resonator. Here, we present the design of such a device that can speed up and facilitate investigation of light-matter interaction ranging from weak to strong coupling regimes in ultraviolet-visible and infrared (IR) spectral regions. The device is based on a tunable unstable λ/2 Fabry-Pérot microcavity consisting of plane and convex mirrors that satisfy the plane-parallelism condition at least at one point of the curved mirror and minimize the mode volume. Fine tuning of the microcavity length is provided by a Z-piezopositioner in a range up to 10 μm with a step of several nm. This design makes a device a versatile instrument that ensures easy finding of optimal conditions for light-matter interaction for almost any sample in both visible and IR areas, enabling observation of both electronic and vibrational couplings with microcavity modes thus paving the way to investigation of various coupling effects including Raman scattering enhancement, modification of chemical reactivity rate, lasing, and long-distance nonradiative energy transfer.

  15. Detailed investigation on the effect of wall spring stiffness on velocity profile in molecular dynamics simulation

    International Nuclear Information System (INIS)

    Namvar, S; Karimian, S M H

    2012-01-01

    In this paper, motion of 576 monatomic argon molecules is studied in a channel with two 2-layered wall molecules. The effect of wall spring stiffness (K) on maximum value of velocity profile is investigated in the channel. It was observed that for K −2 , there is a decrease in the maximum value of velocity profile with an increase in K. This observation has been already reported by Sofos et al. To investigate a wider range of spring stiffness, in this paper the value of K was increased to more than 500εσ −2 . In this range of wall spring stiffness the behavior of maximum value of velocity profile changed; it increased with an increase in K. In a separate simulation the external force applied to the molecules was also increased and the same non-monotonic behavior of maximum value of velocity was observed. To clarify the reason of this behavior, the concepts of original and effective wall are introduced and through several test it is inferred that the mentioned concepts are not successful to demonstrate the reason of such behavior. It is suggested to obtain non-dimensional parameters governing the simulation in order to investigate the effect of every involved parameter on such a behavior. It is finally concluded that while wall spring stiffness affects the maximum velocity magnitude within the flow, the interaction of the two has not been clearly shown yet. The behavior of the maximum velocity is non-monotonic with the change of K. This is why no specific criterion has been reported for suitable value of wall spring stiffness in molecular dynamics simulation.

  16. Molecular investigation of evaporation of biodroplets containing single-strand DNA on graphene surface.

    Science.gov (United States)

    Akbari, Fahimeh; Foroutan, Masumeh

    2018-02-14

    In this study, the water droplet behaviour of four different types of single-strand DNA with homogeneous base sequence on a graphene substrate during evaporation of the droplet was investigated using molecular dynamics (MD) simulation. The simulation results indicated that the evaporation depended on the DNA sequence. The observed changes can be divided into four parts: (i) vaporization mode, (ii) evaporation flux, (iii) mechanism of single-strand placement on the surface, and (iv) consideration of remaining single strands after evaporation. Our simulation observations indicated different evaporation modes for thymine biodroplets as compared to those for other biodroplets. The evaporation of the thymine biodroplets occurred with an increase in the contact angle, while that of the other biodroplets occur in a constant contact angle mode. Moreover, thymine biodroplets generate the lowest contact line compared to other single strands, and it is always placed far away from the centre of the droplets during evaporation. Investigating variations in the evaporation flux shows that thymine has the highest evaporation flux and guanine has the lowest. Moreover, during initial evaporation, the flux of evaporation increases at the triple point of the biodroplets containing thymine single strands, while it decreases in the other biodroplets. The following observation was obtained from the study of the placement of single strands on the substrate: guanine and thymine interacted slower than other single strands during evaporation with graphene, adenine single strand had a higher folding during evaporation, and guanine single strand showed the lowest end-to-end distance. The investigation of single-strand DNA after evaporation shows that adenine produces the most stable structure at the end of evaporation. In addition, cytosine is the most stretched single-strand DNA due to its lack of internal π-π stacking and hydrogen bonding. Therefore, cytosine single strand is more

  17. Molecular modeling and multispectroscopic studies of the interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin

    International Nuclear Information System (INIS)

    Shahabadi, Nahid; Falsafi, Monireh; Hadidi, Saba

    2015-01-01

    The interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin (HSA) was studied by using UV–vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that the binding of the drug to HSA caused fluorescence quenching through static quenching mechanism with binding constant of 1.3×103 M −1 . The thermodynamic parameters indicated that the hydrophobic force contacts are the major forces in the stability of protein-drug complex (ΔH>0 and ΔS>0). The displacement experiments using the site probes viz., warfarin and ibuprofen showed that adefovir dipivoxil could bind to the site III of HSA. The results of CD and UV–vis spectroscopy indicated that the binding of the drug induced some conformational changes in HSA. Furthermore, the study of molecular docking also confirmed binding of adefovir dipivoxil to the site III of HSA by hydrophobic interaction. - Highlights: • The interaction of adefovir dipivoxil, drug for the treatment of HIV and HBV with human serum albumin (HSA) is investigated. • The drug bound to HSA by hydrophobic force and induced some conformational changes in HSA. • The study of molecular docking showed that adefovir dipivoxil could bind to the site III of HSA mainly

  18. Molecular modeling and multispectroscopic studies of the interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Shahabadi, Nahid, E-mail: nahidshahabadi@yahoo.com [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of); Falsafi, Monireh [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Hadidi, Saba [Department of Chemistry, Faculty of Science, Razi University, Kermanshah (Iran, Islamic Republic of); Medical Biology Research Center (MBRC) Kermanshah University of Medical Sciences, Kermanshah (Iran, Islamic Republic of)

    2015-11-15

    The interaction of hepatitis B drug, adefovir dipivoxil with human serum albumin (HSA) was studied by using UV–vis, fluorometric, circular dichroism (CD) and molecular docking techniques. The results indicated that the binding of the drug to HSA caused fluorescence quenching through static quenching mechanism with binding constant of 1.3×103 M{sup −1}. The thermodynamic parameters indicated that the hydrophobic force contacts are the major forces in the stability of protein-drug complex (ΔH>0 and ΔS>0). The displacement experiments using the site probes viz., warfarin and ibuprofen showed that adefovir dipivoxil could bind to the site III of HSA. The results of CD and UV–vis spectroscopy indicated that the binding of the drug induced some conformational changes in HSA. Furthermore, the study of molecular docking also confirmed binding of adefovir dipivoxil to the site III of HSA by hydrophobic interaction. - Highlights: • The interaction of adefovir dipivoxil, drug for the treatment of HIV and HBV with human serum albumin (HSA) is investigated. • The drug bound to HSA by hydrophobic force and induced some conformational changes in HSA. • The study of molecular docking showed that adefovir dipivoxil could bind to the site III of HSA mainly.

  19. Multi-spectroscopic and molecular docking studies on the interaction of darunavir, a HIV protease inhibitor with calf thymus DNA.

    Science.gov (United States)

    Shi, Jie-Hua; Zhou, Kai-Li; Lou, Yan-Yue; Pan, Dong-Qi

    2018-03-15

    Molecular interaction of darunavir (DRV), a HIV protease inhibitor with calf thymus deoxyribonucleic acid (ct-DNA) was studied in physiological buffer (pH7.4) by multi-spectroscopic approaches hand in hand with viscosity measurements and molecular docking technique. The UV absorption and fluorescence results together revealed the formation of a DRV-ct-DNA complex having binding affinities of the order of 10 3 M -1 , which was more in keeping with the groove binding. The results that DRV bound to ct-DNA via groove binding mode was further evidenced by KI quenching studies, viscosity measurements, competitive binding investigations with EB and Rhodamine B and CD spectral analysis. The effect of ionic strength indicated the negligible involvement of electrostatic interaction between DRV and ct-DNA. The thermodynamic parameters regarding the binding interaction of DRV with ct-DNA in terms of enthalpy change (ΔH 0 ) and entropy change (ΔS 0 ) were -63.19kJ mol -1 and -141.92J mol -1 K -1 , indicating that hydrogen bonds and van der Waals forces played a predominant role in the binding process. Furthermore, molecular simulation studies suggested that DRV molecule was prone to bind in the A-T rich region of the minor groove of DNA. Copyright © 2017 Elsevier B.V. All rights reserved.

  20. Interaction of monomeric Ebola VP40 protein with a plasma membrane: A coarse-grained molecular dynamics (CGMD) simulation study.

    Science.gov (United States)

    Mohamad Yusoff, Mohamad Ariff; Abdul Hamid, Azzmer Azzar; Mohammad Bunori, Noraslinda; Abd Halim, Khairul Bariyyah

    2018-06-01

    Ebola virus is a lipid-enveloped filamentous virus that affects human and non-human primates and consists of several types of protein: nucleoprotein, VP30, VP35, L protein, VP40, VP24, and transmembrane glycoprotein. Among the Ebola virus proteins, its matrix protein VP40 is abundantly expressed during infection and plays a number of critical roles in oligomerization, budding and egress from the host cell. VP40 exists predominantly as a monomer at the inner leaflet of the plasma membrane, and has been suggested to interact with negatively charged lipids such as phosphatidylinositol 4,5-bisphosphate (PIP 2 ) and phosphatidylserine (PS) via its cationic patch. The hydrophobic loop at the C-terminal domain has also been shown to be important in the interaction between the VP40 and the membrane. However, details of the molecular mechanisms underpinning their interactions are not fully understood. This study aimed at investigating the effects of mutation in the cationic patch and hydrophobic loop on the interaction between the VP40 monomer and the plasma membrane using coarse-grained molecular dynamics simulation (CGMD). Our simulations revealed that the interaction between VP40 and the plasma membrane is mediated by the cationic patch residues. This led to the clustering of PIP 2 around the protein in the inner leaflet as a result of interactions between some cationic residues including R52, K127, K221, K224, K225, K256, K270, K274, K275 and K279 and PIP 2 lipids via electrostatic interactions. Mutation of the cationic patch or hydrophobic loop amino acids caused the protein to bind at the inner leaflet of the plasma membrane in a different orientation, where no significant clustering of PIP 2 was observed around the mutated protein. This study provides basic understanding of the interaction of the VP40 monomer and its mutants with the plasma membrane. Copyright © 2018 Elsevier Inc. All rights reserved.

  1. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    International Nuclear Information System (INIS)

    Sun, Hui-Yong; Ji, Feng-Qin

    2012-01-01

    Highlights: ► The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. ► C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. ► The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  2. A molecular dynamics investigation on the crizotinib resistance mechanism of C1156Y mutation in ALK

    Energy Technology Data Exchange (ETDEWEB)

    Sun, Hui-Yong [Shandong University of Technology, Zibo 255049 (China); Ji, Feng-Qin, E-mail: fengqinji@mail.hzau.edu.cn [National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070 (China); Center for Bioinformatics, Huazhong Agricultural University, Wuhan 430070 (China)

    2012-06-29

    Highlights: Black-Right-Pointing-Pointer The study revealed the detailed resistance mechanism of the non-active mutation C1156Y in ALK. Black-Right-Pointing-Pointer C1156Y leads to crizotinib displacement and conformational changes in the binding cavity. Black-Right-Pointing-Pointer The conformations cause a decline in the vdW and electrostatic energy between crizotinib and ALK. -- Abstract: Crizotinib is an anaplastic lymphoma kinase (ALK) inhibitor that has recently been approved in the US for the treatment of non-small cell lung carcinoma (NSCLC). Despite its outstanding safety and efficacy, several resistant mutations against crizotinib have been detected in the treatment of NSCLC. However, in contrast to the widely accepted mechanism of steric hindrance by mutations at the active site, the mechanism by which the C1156Y non-active site mutation confers resistance against crizotinib remains unclear. In the present study, the resistance mechanism of C1156Y in ALK was investigated using molecular dynamics simulations. The results suggest that despite the non-active site mutation, C1156Y causes the dislocation of crizotinib as well as the indirect conformational changes in the binding cavity, which results in a marked decrease in the van der Waals and electrostatic interactions between crizotinib and ALK. The obtained results provide a detailed explanation of the resistance caused by C1156Y and may give a vital clue for the design of drugs to combat crizotinib resistance.

  3. Spectroscopic Parameter and Molecular Constant Investigations on Low-Lying States of BeF Radical

    Directory of Open Access Journals (Sweden)

    Jin Feng Sun

    2012-02-01

    Full Text Available The potential energy curves (PECs of X2Σ+, A2Πr and B2Σ+ states of BeF radical have been investigated using the complete active space self-consistent-field (CASSCF method, followed by the highly accurate valence internally contracted multireference configuration interaction (MRCI approach at the correlation-consistent basis sets, cc-pV5Z for Be and aug-cc-pV6Z for F. Based on the PECs of X2Σ+, A2Πr and B2Σ+ states, the spectroscopic parameters (De, Re, ωe, ωeχe, αe and Be have also been determined in the present work. With the PECs determined at the present level of theory, vibrational states have been predicted for each state when the rotational quantum number J equals zero (J = 0. The vibrational levels, inertial rotation and centrifugal distortion constants are determined for the three states, and the classical turning points are also calculated for the X2Σ+ state. Compared with the available experiments and other theories, it can be seen that the present spectroscopic parameter and molecular constant results are more fully in agreement with the experimental findings.

  4. Investigation and molecular docking studies of Bassianolide from Lecanicillium lecanii against Plutella xylostella (Lepidoptera: Plutellidae).

    Science.gov (United States)

    Ravindran, Keppanan; Sivaramakrishnan, Sivaperumal; Hussain, Mubasher; Dash, Chandra Kanta; Bamisile, Bamisope Steve; Qasim, Muhammad; Liande, Wang

    2018-04-01

    Entomopathogenic fungi are rich sources of bioactive secondary metabolites that possess insecticidal properties. The present study reported a novel approach for the identification of insecticidal compounds produced by Lecanicillium lecanii 09 and to assess their toxicity against the diamondback moth Plutella xylostella L. The cyclic peptides groups of toxic substances were separated from L. lecanii 09 through submerged liquid state fermentation. The most abundant toxic metabolite, Bassianolide was purified by high-performance liquid chromatography (HPLC) and its molecular weight and purity were determined by Liquid chromatography - mass spectroscopy (LC-MS), Fourier transformed infrared spectroscopy (FT-IR), and H 1 nuclear magnetic resonance (NMR) respectively. Subsequently, the toxicity of bassianolide was tested against third instar larvae of P. xylostella at three different concentrations (0.01, 0.1, 0.5 mg/ml). The results showed that higher concentration of 0.5 mg/ml had significant maximum mortality at 120 hour post inoculation. Furthermore, we investigated the ligand-target interaction of secondary metabolite binding with target insect immune receptor proteins and predicted the role of toxicity against insect host. This is the first study to report the infection process and the interaction of fungal mediated cyclicdepsipeptide compound (bassianolide) from L. lecanii 09 against the insect host P. xylostella. This novel approach provides a potential impact on biological control using natural toxic compound which acts as good inhibitor on pest insect and prevents toxicity hazards, pollution as well as ecocidal effects killing several beneficial insects. Copyright © 2018 Elsevier Inc. All rights reserved.

  5. Getting the ion-protein interactions right in molecular dynamics simulations

    Czech Academy of Sciences Publication Activity Database

    Duboué-Dijon, Elise; Mason, Philip E.; Jungwirth, Pavel

    2017-01-01

    Roč. 46, Suppl 1 (2017), S66 ISSN 0175-7571. [IUPAB congress /19./ and EBSA congress /11./. 16.07.2017-20.07.2017, Edinburgh] Institutional support: RVO:61388963 Keywords : ion-protein interaction * molecular dynamics simulations * neutron scattering * insulin Subject RIV: BO - Biophysics

  6. Dzyaloshinskii-Moriya interactions and adiabatic magnetization dynamics in molecular magnets

    NARCIS (Netherlands)

    De Raedt, H; Miyashita, S; Michielsen, K; Machida, M

    A microscopic model of the molecular magnet V-15 is used to study mechanisms for the adiabatic change of the magnetization in time-dependent magnetic fields. The effects of the Dzyaloshinskii-Moriya interaction, the most plausible source for the energy-level repulsions that lead to adiabatic changes

  7. Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

    KAUST Repository

    Joya, Khurram

    2015-07-15

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

  8. PREDICTION OF THE MIXING ENTHALPIES OF BINARY LIQUID ALLOYS BY MOLECULAR INTERACTION VOLUME MODEL

    Institute of Scientific and Technical Information of China (English)

    H.W.Yang; D.P.Tao; Z.H.Zhou

    2008-01-01

    The mixing enthalpies of 23 binary liquid alloys are calculated by molecular interaction volume model (MIVM), which is a two-parameter model with the partial molar infinite dilute mixing enthalpies. The predicted values are in agreement with the experimental data and then indicate that the model is reliable and convenient.

  9. Immobilization of molecular cobalt electrocatalyst by hydrophobic interaction with hematite photoanode for highly stable oxygen evolution

    KAUST Repository

    Joya, Khurram; Morlanes, Natalia; Maloney, Edward; Rodionov, Valentin; Takanabe, Kazuhiro

    2015-01-01

    A unique modification of a hematite photoanode with perfluorinated Co-phthalocyanine (CoFPc) by strong binding associated with hydrophobic interaction is demonstrated. The resultant molecular electrocatalyst – hematite photoanode hybrid material showed significant onset shift and high stability for photoelectrochemical oxidation evolution reaction (OER).

  10. Crowding of Interacting Fluid Particles in Porous Media through Molecular Dynamics: Breakdown of Universality for Soft Interactions

    Science.gov (United States)

    Schnyder, Simon K.; Horbach, Jürgen

    2018-02-01

    Molecular dynamics simulations of interacting soft disks confined in a heterogeneous quenched matrix of soft obstacles show dynamics which is fundamentally different from that of hard disks. The interactions between the disks can enhance transport when their density is increased, as disks cooperatively help each other over the finite energy barriers in the matrix. The system exhibits a transition from a diffusive to a localized state, but the transition is strongly rounded. Effective exponents in the mean-squared displacement can be observed over three decades in time but depend on the density of the disks and do not correspond to asymptotic behavior in the vicinity of a critical point, thus, showing that it is incorrect to relate them to the critical exponents in the Lorentz model scenario. The soft interactions are, therefore, responsible for a breakdown of the universality of the dynamics.

  11. Cyrus Levinthal, the Kluge and the origins of interactive molecular graphics.

    Science.gov (United States)

    Francoeur, Eric

    2002-12-01

    In the mid-1960s, a group of scientists at Massachusetts Institute of Technology, led by Cyrus Levinthal, took hold of one of the early interactive graphics terminals and used it to visualize, study and model the structure of proteins and nucleic acids. From this encounter between cutting-edge computer technology and molecular biology emerged the crucial elements for the development of a research-technology field known today as interactive molecular graphics. The following account is not only about how computer graphics technology has literally changed the way scientists view the molecular realm, but also a look at how an epistemic and institutional space was created to integrate this technology into scientific research.

  12. Investigating EFL Classroom Interaction Process in Iraqi Intermediate Schools

    Directory of Open Access Journals (Sweden)

    Muna Mohammed Abbas Alkhateeb

    2017-09-01

    Full Text Available In recent times, the traditional interaction structures of English both language classrooms and roles of teachers and students are gradually changing. This marks the shift from the teacher-centered classrooms to student-centered classrooms; moving towards ‘student-centered learning’ and‘collaborative working modes’. The contemporary educational world views teachers and students as communicators. In such situations students get more opportunity to ‘participate’, ‘observe’, ‘reflect on’ and ‘practice social ways’. These opportunities expose the students to a more ‘meaning-making’ and ‘knowledge construction processes’. The shift from traditional teaching and learning process to the contemporary one has posed great challenges for teachers, who are always working under pressure to complete the syllabus designed for the academic year. In such a situation it is very important to ascertain if this idea of student-centered classroom is present in the recent classroom. Educationally oriented research into classroom interaction makes it essential for further studies into the classroom interaction in the modern classroom. Hence, this study aims to observe the interaction process that takes place in English classrooms of four government schools in Hilla (Centre of Babylon Governorate. This paper also suggests measures to improve classroom interaction and language learning in the English classes. The main findings from the study are as follows: (a the classroom interaction is teacher-centered, (b teachers partially facilitate learning, the classrooms are controlled by teachers (c the ratio of the teacher-talk is more than student-talk."

  13. Computational study of the human dystrophin repeats: interaction properties and molecular dynamics.

    Directory of Open Access Journals (Sweden)

    Baptiste Legrand

    Full Text Available Dystrophin is a large protein involved in the rare genetic disease Duchenne muscular dystrophy (DMD. It functions as a mechanical linker between the cytoskeleton and the sarcolemma, and is able to resist shear stresses during muscle activity. In all, 75% of the dystrophin molecule consists of a large central rod domain made up of 24 repeat units that share high structural homology with spectrin-like repeats. However, in the absence of any high-resolution structure of these repeats, the molecular basis of dystrophin central domain's functions has not yet been deciphered. In this context, we have performed a computational study of the whole dystrophin central rod domain based on the rational homology modeling of successive and overlapping tandem repeats and the analysis of their surface properties. Each tandem repeat has very specific surface properties that make it unique. However, the repeats share enough electrostatic-surface similarities to be grouped into four separate clusters. Molecular dynamics simulations of four representative tandem repeats reveal specific flexibility or bending properties depending on the repeat sequence. We thus suggest that the dystrophin central rod domain is constituted of seven biologically relevant sub-domains. Our results provide evidence for the role of the dystrophin central rod domain as a scaffold platform with a wide range of surface features and biophysical properties allowing it to interact with its various known partners such as proteins and membrane lipids. This new integrative view is strongly supported by the previous experimental works that investigated the isolated domains and the observed heterogeneity of the severity of dystrophin related pathologies, especially Becker muscular dystrophy.

  14. Investigation into the use of molecular hydrogen on the growth of gallium nitride via metal-organic molecular beam epitaxy

    Energy Technology Data Exchange (ETDEWEB)

    Billingsley, Daniel; Pritchett, David; Henderson, Walter; Carver, Alexander G.; Burnham, Shawn D.; Doolittle, W.A. [Georgia Institute of Technology, School of Electrical and Computer Engineering, 777 Atlantic Dr., Atlanta, GA 30332 (United States)

    2008-07-01

    Molecular hydrogen (H{sub 2}) has been investigated as a means to improve ammonia nitridation efficiency and attempts to reduce carbon contamination in ammonia-based metal-organic molecular beam epitaxy (MOMBE). A 30% improvement in crystalline quality, inferred from XRD, as well as an increase in subsequent GaN bulk growth rate was observed when bare sapphire was subject to H{sub 2} annealing before nitridation. However, the use of H{sub 2} during GaN homoepitaxy on GaN templates resulted in increased carbon contamination and decreased growth rate of GaN. The results demonstrate promise and proper uses of H{sub 2} during GaN growth under certain conditions. (copyright 2008 WILEY-VCH Verlag GmbH and Co. KGaA, Weinheim) (orig.)

  15. SIMULATION AND INVESTIGATION OF TIRE TREAD BLOCKS INTERACTION WITH ICE

    Directory of Open Access Journals (Sweden)

    Andrius Ružinskas

    2017-12-01

    Full Text Available The car tire is an essential subject analysing its interaction with the road. From tire’s tread condition, geometry and rubber compound depends grip and vehicle stability. This is especially relevant in winter time, when roads are covered with the layer of snow or ice. Generally, new tires are tested in real traffic conditions using vehicles. However, ensuring these conditions requires many resources and sometimes it could be a big challenge. For this reason, simulation of the tire interaction with the road becomes more important in nowadays tire researches. Since the tire is a complex engineering subject, the tire tread blocks could be separated for individual analysis. The interaction between the dry ice and the tread block with sipes was analysed using finite element analysis. The tread block was described using hyperelastic Mooney­Rivlin material model. The deformations, distribution of the contact pressure and shear stresses were obtained for the soft and hard rubber compounds with different vertical load conditions. Also a solid tread block interaction was analysed and it was found that values of contact pressure and shear stresses are much lower comparing to siped tread block.

  16. Electrochemical Investigation of the Interaction between Catecholamines and ATP.

    Science.gov (United States)

    Taleat, Zahra; Estévez-Herrera, Judith; Machado, José D; Dunevall, Johan; Ewing, Andrew G; Borges, Ricardo

    2018-02-06

    The study of the colligative properties of adenosine 5'-triphosphate (ATP) and catecholamines has received the attention of scientists for decades, as they could explain the capabilities of secretory vesicles (SVs) to accumulate neurotransmitters. In this Article, we have applied electrochemical methods to detect such interactions in vitro, at the acidic pH of SVs (pH 5.5) and examined the effect of compounds having structural similarities that correlate with functional groups of ATP (adenosine, phosphoric acid and sodium phosphate salts) and catecholamines (catechol). Chronoamperometry and fast scan cyclic voltammetry (FSCV) provide evidence compatible with an interaction of the catechol and adenine rings. This interaction is also reinforced by an electrostatic interaction between the phosphate group of ATP and the protonated ammonium group of catecholamines. Furthermore, chronoamperometry data suggest that the presence of ATP subtlety reduces the apparent diffusion coefficient of epinephrine in aqueous media that adds an additional factor leading to a slower rate of catecholamine exocytosis. This adds another plausible mechanism to regulate individual exocytosis events to alter communication.

  17. Structural aspects of the solvation shell of lysine and acetylated lysine: A Car-Parrinello and classical molecular dynamics investigation

    International Nuclear Information System (INIS)

    Carnevale, V.; Raugei, S.

    2009-01-01

    Lysine acetylation is a post-translational modification, which modulates the affinity of protein-protein and/or protein-DNA complexes. Its crucial role as a switch in signaling pathways highlights the relevance of charged chemical groups in determining the interactions between water and biomolecules. A great effort has been recently devoted to assess the reliability of classical molecular dynamics simulations in describing the solvation properties of charged moieties. In the spirit of these investigations, we performed classical and Car-Parrinello molecular dynamics simulations on lysine and acetylated-lysine in aqueous solution. A comparative analysis between the two computational schemes is presented with a focus on the first solvation shell of the charged groups. An accurate structural analysis unveils subtle, yet statistically significant, differences which are discussed in connection to the significant electronic density charge transfer occurring between the solute and the surrounding water molecules.

  18. Molecular dynamics simulations of matrix assisted laser desorption ionization: Matrix-analyte interactions

    International Nuclear Information System (INIS)

    Nangia, Shivangi; Garrison, Barbara J.

    2011-01-01

    There is synergy between matrix assisted laser desorption ionization (MALDI) experiments and molecular dynamics (MD) simulations. To understand analyte ejection from the matrix, MD simulations have been employed. Prior calculations show that the ejected analyte molecules remain solvated by the matrix molecules in the ablated plume. In contrast, the experimental data show free analyte ions. The main idea of this work is that analyte molecule ejection may depend on the microscopic details of analyte interaction with the matrix. Intermolecular matrix-analyte interactions have been studied by focusing on 2,5-dihydroxybenzoic acid (DHB; matrix) and amino acids (AA; analyte) using Chemistry at HARvard Molecular Mechanics (CHARMM) force field. A series of AA molecules have been studied to analyze the DHB-AA interaction. A relative scale of AA molecule affinity towards DHB has been developed.

  19. Interaction of an antiepileptic drug, lamotrigine with human serum albumin (HSA): Application of spectroscopic techniques and molecular modeling methods.

    Science.gov (United States)

    Poureshghi, Fatemeh; Ghandforoushan, Parisa; Safarnejad, Azam; Soltani, Somaieh

    2017-01-01

    Lamotrigine (an epileptic drug) interaction with human serum albumin (HSA) was investigated by fluorescence, UV-Vis, FTIR, CD spectroscopic techniques, and molecular modeling methods. Binding constant (K b ) of 5.74×10 3 and number of binding site of 0.97 showed that there is a slight interaction between lamotrigine and HSA. Thermodynamic studies was constructed using the flourimetric titrations in three different temperatures and the resulted data used to calculate the parameters using Vant Hoff equation. Decreased Stern Volmer quenching constant by enhanced temperature revealed the static quenching mechanism. Negative standard enthalpy (ΔH) and standard entropy (ΔS) changes indicated that van der Waals interactions and hydrogen bonds were dominant forces which facilitate the binding of Lamotrigine to HSA, the results were confirmed by molecular docking studies which showed no hydrogen binding. The FRET studies showed that there is a possibility of energy transfer between Trp214 and lamotrigine. Also the binding of lamotrigine to HSA in the studied concentrations was not as much as many other drugs, but the secondary structure of the HSA was significantly changed following the interaction in a way that α-helix percentage was reduced from 67% to 57% after the addition of lamotrigine in the molar ratio of 4:1 to HSA. According to the docking studies, lamotrigine binds to IB site preferably. Copyright © 2016. Published by Elsevier B.V.

  20. Finding the best density functional approximation to describe interaction energies and structures of ionic liquids in molecular dynamics studies

    Science.gov (United States)

    Perlt, Eva; Ray, Promit; Hansen, Andreas; Malberg, Friedrich; Grimme, Stefan; Kirchner, Barbara

    2018-05-01

    Ionic liquids raise interesting but complicated questions for theoretical investigations due to the fact that a number of different inter-molecular interactions, e.g., hydrogen bonding, long-range Coulomb interactions, and dispersion interactions, need to be described properly. Here, we present a detailed study on the ionic liquids ethylammonium nitrate and 1-ethyl-3-methylimidazolium acetate, in which we compare different dispersion corrected density functional approximations to accurate local coupled cluster data in static calculations on ionic liquid clusters. The efficient new composite method B97-3c is tested and has been implemented in CP2K for future studies. Furthermore, tight-binding based approaches which may be used in large scale simulations are assessed. Subsequently, ab initio as well as classical molecular dynamics simulations are conducted and structural analyses are presented in order to shed light on the different short- and long-range structural patterns depending on the method and the system size considered in the simulation. Our results indicate the presence of strong hydrogen bonds in ionic liquids as well as the aggregation of alkyl side chains due to dispersion interactions.

  1. Combined spectroscopies and molecular docking approach to characterizing the binding interaction of enalapril with bovine serum albumin.

    Science.gov (United States)

    Pan, Dong-Qi; Jiang, Min; Liu, Ting-Ting; Wang, Qi; Shi, Jie-Hua

    2017-06-01

    The binding interaction between bovine serum albumin (BSA) and enalapril (ENPL) at the imitated physiological conditions (pH = 7.4) was investigated using UV-vis absorption spectroscopy (UV-vis), fluorescence emission spectroscopy (FES), synchronous fluorescence spectroscopy (SFS), Fourier transform infrared spectroscopy (FT-IR), circular dichroism (CD) and molecular docking methods. It can be deduced from the experimental results from the steady-state fluorescence spectroscopic titration that the intrinsic BSA fluorescence quenching mechanism induced by ENPL is static quenching, based on the decrease in the BSA quenching constants in the presence of ENPL with increase in temperature and BSA quenching rates >10 10  L mol -1  sec -1 . This result indicates that the ENPL-BSA complex is formed through an intermolecular interaction of ENPL with BSA. The main bonding forces for interaction of BSA and ENPL are van der Waal's forces and hydrogen bonding interaction based on negative values of Gibbs free energy change (ΔG 0 ), enthalpic change (ΔH 0 ) and entropic change (ΔS 0 ). The binding of ENPL with BSA is an enthalpy-driven process due to |ΔH°| > |TΔS°| in the binding process. The results of competitive binding experiments and molecular docking confirm that ENPL binds in BSA sub-domain IIA (site I) and results in a slight change in BSA conformation, but BSA still retains its α-helical secondary structure. Copyright © 2016 John Wiley & Sons, Ltd.

  2. The interaction of 2-mercaptobenzimidazole with human serum albumin as determined by spectroscopy, atomic force microscopy and molecular modeling.

    Science.gov (United States)

    Li, Yuqin; Jia, Baoxiu; Wang, Hao; Li, Nana; Chen, Gaopan; Lin, Yuejuan; Gao, Wenhua

    2013-04-01

    The interaction of 2-mercaptobenzimidazole (MBI) with human serum albumin (HSA) was studied in vitro by equilibrium dialysis under normal physiological conditions. This study used fluorescence, ultraviolet-visible spectroscopy (UV-vis), Fourier transform infrared (FT-IR), circular dichroism (CD) and Raman spectroscopy, atomic force microscopy (AFM) and molecular modeling techniques. Association constants, the number of binding sites and basic thermodynamic parameters were used to investigate the quenching mechanism. Based on the fluorescence resonance energy transfer, the distance between the HSA and MBI was 2.495 nm. The ΔG(0), ΔH(0), and ΔS(0) values across temperature indicated that the hydrophobic interaction was the predominant binding Force. The UV, FT-IR, CD and Raman spectra confirmed that the HSA secondary structure was altered in the presence of MBI. In addition, the molecular modeling showed that the MBI-HSA complex was stabilized by hydrophobic forces, which resulted from amino acid residues. The AFM results revealed that the individual HSA molecule dimensions were larger after interaction with MBI. Overall, this study suggested a method for characterizing the weak intermolecular interaction. In addition, this method is potentially useful for elucidating the toxigenicity of MBI when it is combined with the biomolecular function effect, transmembrane transport, toxicological testing and other experiments. Copyright © 2012 Elsevier B.V. All rights reserved.

  3. A theoretical and experimental investigation of the interaction between gas molecules and cryogenic surfaces

    International Nuclear Information System (INIS)

    Varlam, M.; Steflea, D.; Chiriloaie, N.

    1992-01-01

    The cryo-pumping performance of a cryo-surface subjected to the impingement of low-pressure, thermal-velocity air flow is experimentally and theoretically investigated. Our purpose is to determine the angular dependence of capture coefficients for gas molecules incident on a cryogenic surface under conditions closely approximating those prevailing in cryo-pumped high vacuum chambers. The classical model for the interaction of gas atoms and the solid surface - the 'soft-tube' model - is developed and the basic assumption are examined. Starting from this theory we have calculated the capture coefficient of the Ag - N system and these values are discussed in terms of principal parameters considered. Despite the many simplifying assumptions, this model has the important attribute that it yields closed-form expressions for the capture coefficient of gas molecules. The molecular beam technique offers a direct experimental method for determining the capture coefficient for molecules with given angles of incidence by measuring the incident and reflected molecular fluxes. An experimental setup is also designed and the method for determining these coefficients is proposed. (Author)

  4. Density functional theory investigation of oxygen interaction with boron-doped graphite

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Juan; Wang, Chen [State Key Lab of New Ceramic and Fine Processing, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Liang, Tongxiang, E-mail: txliang@tsinghua.edu.cn [State Key Lab of New Ceramic and Fine Processing, Institute of Nuclear and New Energy Technology, Tsinghua University, Beijing 100084 (China); Lai, Wensheng [Advanced Material Laboratory, School of Materials Science & Engineering, Tsinghua University, Beijing, 100084 (China)

    2016-12-30

    Highlights: • Density-functional approach is applied to study the interaction of oxygen with boron-doped graphite. • Adsorption and diffusion of oxygen atoms on boron doped graphite surfaces are studied. • Recombination of oxygen is investigated by ER and LH mechanisms. • Low boron concentration facilitates O{sub 2} formation while high boron loading inhibits the recombination. • The presence of B−B bonds due to boron accumulation makes it impossible for oxygen recombination. - Abstract: Boron inserted as impurity by substitution of carbon atoms in graphite is known to change (improve or deteriorate) oxidation resistance of nuclear graphite, but the reason for both catalytic and inhibiting oxidation is still uncertain. As a first step, this work is more specially devoted to the adsorption and diffusion of oxygen atoms on the surface and related to the problem of oxygen retention on the pure and boron-containing graphite surfaces. Adsorption energies and energy barriers associated to the diffusion for molecular oxygen recombination are calculated in the density functional theory framework. The existence of boron modifies the electronic structure of the surface, which results in an increase of the adsorption energy for O. However, low boron loading makes it easier for the recombination into molecular oxygen. For high boron concentration, it induces a better O retention capability in graphite because the presence of B-B bonds decreases recombination of the adsorbed oxygen atoms. A possible explanation for both catalytic and inhibiting effects of boron in graphite is proposed.

  5. Molecular interactions in biomineralized hydroxyapatite amino acid modified nanoclay: In silico design of bone biomaterials

    International Nuclear Information System (INIS)

    Katti, Dinesh R.; Sharma, Anurag; Ambre, Avinash H.; Katti, Kalpana S.

    2015-01-01

    A simulations driven approach to design of a novel biomaterial nanocomposite system is described in this study. Nanoclays modified with amino acids (OMMT) were used to mineralize hydroxyapatite (HAP), mimicking biomineralization. Representative models of organically modified montmorillonite clay (OMMT) and OMMT-hydroxyapatite (OMMT-HAP) were constructed using molecular dynamics and validated using X-ray Diffraction (XRD), Fourier Transforms Infrared (FTIR) spectroscopy and Transmission Electron Microscopy (TEM). Attractive interactions exist between Ca atoms of HAP and C=O group of aminovaleric acid, indicating chelate formation in OMMT-HAP. Interaction energy maps describe molecular interactions among different constituents and their quantitative contributions in the OMMT and OMMT-HAP systems at both parallel and perpendicular orientations. High attractive and high repulsive interactions were found between PO 4 3− and MMT clay as well as aminovaleric molecules in OMMT-HAP perpendicular and parallel models. Large non-bonded interactions in OMMT-HAP indicate influence of neighboring environment on PO 4 3− in in situ HAPclay. Extensive hydrogen bonds were observed between functional hydrogen atoms of modifier and MMT clay in OMMT-HAP as compared to OMMT. Thus, HAP interacts with clay through the aminovaleric acid. This computational study provides a framework for materials design and selection for biomaterials used in tissue engineering and other areas of regenerative medicine. - Highlights: • Representative models of a hybrid nanoclay-hydroxyapatite biomaterial are built. • Interaction energy maps are constructed using a molecular dynamics. • Quantitative interactions between the three components of the biomaterial are found. • The modeling and experimental approach provides insight into the complex nanomaterial

  6. Quantifying the molecular origins of opposite solvent effects on protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Vincent Vagenende

    Full Text Available Although the nature of solvent-protein interactions is generally weak and non-specific, addition of cosolvents such as denaturants and osmolytes strengthens protein-protein interactions for some proteins, whereas it weakens protein-protein interactions for others. This is exemplified by the puzzling observation that addition of glycerol oppositely affects the association constants of two antibodies, D1.3 and D44.1, with lysozyme. To resolve this conundrum, we develop a methodology based on the thermodynamic principles of preferential interaction theory and the quantitative characterization of local protein solvation from molecular dynamics simulations. We find that changes of preferential solvent interactions at the protein-protein interface quantitatively account for the opposite effects of glycerol on the antibody-antigen association constants. Detailed characterization of local protein solvation in the free and associated protein states reveals how opposite solvent effects on protein-protein interactions depend on the extent of dewetting of the protein-protein contact region and on structural changes that alter cooperative solvent-protein interactions at the periphery of the protein-protein interface. These results demonstrate the direct relationship between macroscopic solvent effects on protein-protein interactions and atom-scale solvent-protein interactions, and establish a general methodology for predicting and understanding solvent effects on protein-protein interactions in diverse biological environments.

  7. Interaction of Flavonoids from Woodwardia unigemmata with Bovine Serum Albumin (BSA): Application of Spectroscopic Techniques and Molecular Modeling Methods.

    Science.gov (United States)

    Ma, Rui; Pan, Hong; Shen, Tao; Li, Peng; Chen, Yanan; Li, Zhenyu; Di, Xiaxia; Wang, Shuqi

    2017-08-09

    Phytochemical investigation on the methanol extract of Woodwardia unigemmata resulted in the isolation of seven flavonoids, including one new flavonol acylglycoside ( 1 ). The structures of these compounds were elucidated on the basis of extensive spectroscopic analysis and comparison of literature data. The multidrug resistance (MDR) reversing activity was evaluated for the isolated compounds using doxorubicin-resistant K562/A02 cells model. Compound 6 showed comparable MDR reversing effect to verapamil. Furthermore, the interaction between compounds and bovine serum albumin (BSA) was investigated by spectroscopic methods, including steady-state fluorescence, synchronous fluorescence, circular dichroism (CD) spectroscopies, and molecular docking approach. The experimental results indicated that the seven flavonoids bind to BSA by static quenching mechanisms. The negative ΔH and ΔS values indicated that van der Waals interactions and hydrogen bonds contributed in the binding of compounds 2 - 6 to BSA. In the case of compounds 1 and 7 systems, the hydrophobic interactions play a major role. The binding of compounds to BSA causes slight changes in the secondary structure of BSA. There are two binding sites of compound 6 on BSA and site I is the main site according to the molecular docking studies and the site marker competitive binding assay.

  8. Molecular equilibrium structures from experimental rotational constants and calculated vibration-rotation interaction constants

    DEFF Research Database (Denmark)

    Pawlowski, F; Jorgensen, P; Olsen, Jeppe

    2002-01-01

    A detailed study is carried out of the accuracy of molecular equilibrium geometries obtained from least-squares fits involving experimental rotational constants B(0) and sums of ab initio vibration-rotation interaction constants alpha(r)(B). The vibration-rotation interaction constants have been...... calculated for 18 single-configuration dominated molecules containing hydrogen and first-row atoms at various standard levels of ab initio theory. Comparisons with the experimental data and tests for the internal consistency of the calculations show that the equilibrium structures generated using Hartree......-Fock vibration-rotation interaction constants have an accuracy similar to that obtained by a direct minimization of the CCSD(T) energy. The most accurate vibration-rotation interaction constants are those calculated at the CCSD(T)/cc-pVQZ level. The equilibrium bond distances determined from these interaction...

  9. Molecular Understanding of Fullerene - Electron Donor Interactions in Organic Solar Cells

    KAUST Repository

    Ryno, Sean

    2016-09-13

    Organic solar cells hold promise of providing low-cost, renewable power generation, with current devices providing up to 13% power conversion efficiency. The rational design of more performant systems requires an in-depth understanding of the interactions between the electron donating and electron accepting materials within the active layers of these devices. Here, we explore works that give insight into the intermolecular interactions between electron donors and electron acceptors, and the impact of molecular orientations and environment on these interactions. We highlight, from a theoretical standpoint, the effects of intermolecular interactions on the stability of charge carriers at the donor/acceptor interface and in the bulk and how these interactions influence the nature of the charge transfer states as wells as the charge separation and charge transport processes. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  10. Molecular dynamics study of interstitial-solute interactions in irradiated alloys

    International Nuclear Information System (INIS)

    Lam, N.Q.; Doan, N.V.; Adda, Y.

    1980-01-01

    The molecular dynamics technique has been used, in conjunction with the interionic potentials of Dagens et al, to study the stability, configuration, binding, and induced migration of mixed dumbbells in an irradiated Al-Zn alloy. For the purpose of comparisons, self-interstitials in pure Al were also investigated. The Al-Al and Al-Zn interactions were described by pair potentials which extended to ninth-neighbour distances. Both the self-interstitial dumbbell and the mixed dumbbell were found to be stable in the configuration. The formation energy of the self-interstitial is 2.89 eV and the mixed-dumbbell binding energy is 0.38 eV. As a result of this strong binding, the threshold energy required to induce the migration of the mixed dumbbell is about 1.2 eV, which is significantly larger than the minimum energy of about 0.15 eV transferred to a self-interstitial to induce its jumps in pure Al. Caging motions of the mixed dumbbell were observed. The present computer-simulation results are compared with experimental measurements. (author)

  11. Understanding trophic interactions of Orius spp. (Hemiptera: Anthocoridae) in lettuce crops by molecular methods.

    Science.gov (United States)

    Gomez-Polo, Priscila; Alomar, Oscar; Castañé, Cristina; Aznar-Fernández, Thaïs; Lundgren, Jonathan G; Piñol, Josep; Agustí, Nuria

    2016-02-01

    The aphid Nasonovia ribisnigri (Mosley) (Hemiptera: Aphididae) and the thrips Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae) are common pests in Mediterranean lettuce crops, where Orius spp. are common generalist predators. Predation by Orius spp. was studied in a lettuce plot by conventional polymerase chain reaction (PCR) and real-time PCR analyses using specific primers of both main pests. Also, high-throughput sequencing was used to have a wider approach of the diet of these predators in natural field conditions. Molecular analyses indicated a higher predation on N. ribisnigri in spring and on F. occidentalis in summer. Predation on alternative prey, like Collembola, was also found in both seasons. Real-time PCR was more sensitive than conventional PCR in showing the target trophic links, whereas high-throughput sequencing revealed predation on other natural enemies - intraguild predation (IGP), showing other trophic interactions of Orius majusculus within the studied ecosystem. This study gives important information about the trophic relationships present in Mediterranean lettuce crops in different periods of the year. The detected predation by Orius spp. on alternative prey, as well as on other natural enemies, should be further investigated to clarify whether it adds or detracts to the biological control of N. ribisnigri and F. occidentalis. © 2015 Society of Chemical Industry.

  12. Modeling techniques and fluorescence imaging investigation of the interactions of an anthraquinone derivative with HSA and ctDNA

    Science.gov (United States)

    Fu, Zheng; Cui, Yanrui; Cui, Fengling; Zhang, Guisheng

    2016-01-01

    A new anthraquinone derivative (AORha) was synthesized. Its interactions with human serum albumin (HSA) and calf thymus DNA (ctDNA) were investigated by fluorescence spectroscopy, UV-visible absorption spectroscopy and molecular modeling. Cell viability assay and cell imaging experiment were performed using cervical cancer cells (HepG2 cells). The fluorescence results revealed that the quenching mechanism was static quenching. At different temperatures (290, 300, 310 K), the binding constants (K) and the number of binding sites (n) were determined, respectively. The positive ΔH and ΔS values showed that the binding of AORha with HSA was hydrophobic force, which was identical with the molecular docking result. Studying the fluorescence spectra, UV spectra and molecular modeling also verified that the binding mode of AORha and ctDNA might be intercalative. When HepG2 cells were treated with AORha, the fluorescence became brighter and turned green, which could be used for bioimaging.

  13. Investigation of sodium - carbon dioxide interactions with calorimetric studies

    International Nuclear Information System (INIS)

    Simon, N.; Latge, C.; Gicquel, L.

    2007-01-01

    The supercritical CO 2 Brayton cycle could be a promising option to enhance the competitiveness of future Sodium fast reactors but it is highly necessary to get thermodynamic and kinetics information on potential sodium-CO 2 chemical reactions and their consequences. We have studied the interaction between Na and CO 2 via calorimetric methods. These methods are able to point out exothermic/endothermic phenomena and to measure heat of chemical reactions. The main feature of the Na/CO 2 interaction seems to be its sharp dependence on temperature. At low temperature, below 500 C degrees, CO 2 and sodium react and exhibit an induction time which decreases when temperature increases. Above 500 C degrees, we observe a global phenomenon with a fast and instantaneous chemical reaction which may be understood as an auto-combustion of CO 2 in sodium. We clearly demonstrated that Na/CO 2 interaction does not proceed as an auto-catalytic process and is more satisfactorily explained by the occurring of an auto-combustion phenomenon

  14. Molecular modeling study for interaction between Bacillus subtilis Obg and Nucleotides.

    Directory of Open Access Journals (Sweden)

    Yuno Lee

    Full Text Available The bacterial Obg proteins (Spo0B-associated GTP-binding protein belong to the subfamily of P-loop GTPase proteins that contain two equally and highly conserved domains, a C-terminal GTP binding domain and an N-terminal glycine-rich domain which is referred as the "Obg fold" and now it is considered as one of the new targets for antibacterial drug. When the Obg protein is associated with GTP, it becomes activated, because conformation of Obg fold changes due to the structural changes of GTPase switch elements in GTP binding site. In order to investigate the effects and structural changes in GTP bound to Obg and GTPase switch elements for activation, four different molecular dynamics (MD simulations were performed with/without the three different nucleotides (GTP, GDP, and GDP + Pi using the Bacillus subtilis Obg (BsObg structure. The protein structures generated from the four different systems were compared using their representative structures. The pattern of C(alpha-C(alpha distance plot and angle between the two Obg fold domains of simulated apo form and each system (GTP, GDP, and GDP+Pi were significantly different in the GTP-bound system from the others. The switch 2 element was significantly changed in GTP-bound system. Also root-mean-square fluctuation (RMSF analysis revealed that the flexibility of the switch 2 element region was much higher than the others. This was caused by the characteristic binding mode of the nucleotides. When GTP was bound to Obg, its gamma-phosphate oxygen was found to interact with the key residue (D212 of the switch 2 element, on the contrary there was no such interaction found in other systems. Based on the results, we were able to predict the possible binding conformation of the activated form of Obg with L13, which is essential for the assembly with ribosome.

  15. Molecular interactions between selected sodium salts of bile acids and morphine hydrochloride.

    Science.gov (United States)

    Poša, Mihalj; Csanádi, János; Kövér, Katalin E; Guzsvány, Valéria; Batta, Gyula

    2012-06-01

    The objective of this study was to understand the prolonged analgesic action of morphine hydrochloride observed in the presence of sodium 12-oxochenodeoxycholanate. Based on literature, this phenomenon may be due to the formation of aggregates in the cell between the molecules of bile acids and morphine. In addition to the sodium 12-oxochenodeoxycholanate, the present investigation also included salts of cholic and 7-oxodeoxycholic acids. Saturation transfer difference NMR experiments showed that morphine binds to the bile acid molecule close to the aromatic protons H1 and H2 provided that the concentration of the bile acid salt approaches the critical micellar concentration (CMC). The spin-lattice relaxation times (T(1)) of the affected protons decrease significantly in the presence of micellar solutions of the bile acid salts, and the most pronounced change in T(1) was observed for sodium 7-oxodeoxycholate. Diffusion-ordered NMR experiments suggested that morphine hydrochloride can interact only with sodium 7-oxochenodeoxycholate. It can be supposed that the molecular ratio of sodium 7-oxodeoxycholate and morphine hydrochloride in the mixed micelle is 2:1. The CMC values of mixed micelles do not differ from the CMC values of the micelle constituents, which suggests that the binding of morphine hydrochloride does not perturb the hydrophobic domain of the bile acid molecule. In the presence of bile acids, the transfer rate constant (k(12)) of morphine hydrochloride from the buffered aqueous solution to chloroform (model of the cell membrane) shows a decrease. A significant decrease of the k(12) was also observed in the presence of micellar solutions. Kinetic measurements indicated that, in addition to micellar interaction between morphine hydrochloride and sodium salts of bile acids, a complex may also be formed in chloroform via hydrogen bonds formed between the drug and bile acid molecules. Copyright © 2012 Elsevier B.V. All rights reserved.

  16. Interaction of bovine serum albumin with a psychotropic drug alprazolam: Physicochemical, photophysical and molecular docking studies

    Energy Technology Data Exchange (ETDEWEB)

    Sarkar, Moumita; Paul, Shiv Shankar; Mukherjea, Kalyan K., E-mail: k_mukherjea@yahoo.com

    2013-10-15

    The interaction between alprazolam (Alp) and bovine serum albumin (BSA) has been investigated under physiological conditions by UV–vis, steady state as well as time-resolved fluorescence, circular dichroism (CD) spectroscopic and molecular docking studies. The binding constant K of Alp to BSA was found to be 1.8×10{sup 5} L mol{sup −1} from absorption data. Fluorometric studies suggested the formation of the Alp–BSA complex, while time-resolved fluorescence studies showed that the binding of Alp by BSA was mainly static and the effective rate constant is found to be 2.33×10{sup 13} L mol{sup −1} s{sup −1}. According to the modified Stern–Volmer equation, the Stern–Volmer quenching constants (K{sub SV}) between Alp and BSA at four different temperatures 295, 303, 308, 313 K were obtained to be 1.19×10{sup 5}, 1.05×10{sup 5}, 0.99×10{sup 5} and 0.90×10{sup 5} L mol{sup −1}, respectively. The change in enthalpy (ΔH) and entropy (ΔS) were calculated to be −11.66 and 57.64 J mol{sup −1} K{sup −1}, respectively, indicating that the interaction was hydrophobic in nature. Site marker competitive experiments suggested that the binding of Alp to BSA primarily took place in sub-domain IIA, whereas the binding distance (r) between Alp and the tryptophan residue of BSA was obtained to be 1.87 nm by Förster's theory of non-radiative energy transfer. The conformational studies by CD spectroscopy showed that the presence of Alp decreased the α-helical content of BSA and induced the unfolding of the polypeptide of the protein. The change in conformation was also supported by excitation–emission matrix spectroscopy (EEMS) studies. The molecular docking experiment supports the above results and effectively proves the binding of Alp to BSA. -- Highlights: • Alprazolam: a benzodiazepine drug with anxiolytic and anticonvulsant properties. • Alprazolam induces conformational change on the native as well as urea denatured BSA. • Alprazolam may

  17. Study on the molecular interaction of graphene quantum dots with human serum albumin: Combined spectroscopic and electrochemical approaches

    Energy Technology Data Exchange (ETDEWEB)

    Huang, Shan; Qiu, Hangna; Lu, Shuangyan; Zhu, Fawei [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); Xiao, Qi, E-mail: qi.xiao@whu.edu.cn [College of Chemistry and Material Science, Guangxi Teachers Education University, Nanning 530001 (China); State Key Laboratory of Virology, College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072 (China)

    2015-03-21

    Highlights: • The interactions between GQDs and HSA were systematically investigated. • GQDs could quench the intrinsic fluorescence of HSA via static mode. • The binding site of GQDs was mainly located in site I of HSA. • The potential toxicity of GQDs resulted in the structural damage of HSA. - Abstract: Graphene quantum dots (GQDs) have attracted great attention in biological and biomedical applications due to their super properties, but their potential toxicity investigations are rarely involved. Since few studies have addressed whether GQDs could bind and alter the structure and function of human serum albumin (HSA), the molecular interaction between GQDs and HSA was systematically characterized by the combination of multispectroscopic and electrochemical approaches. GQDs could quench the intrinsic fluorescence of HSA via static mode. The competitive binding fluorescence assay revealed that the binding site of GQDs was site I of HSA. Some thermodynamic parameters suggested that GQDs interacted with HSA mainly through van der Waals interactions and hydrogen bonding interactions, and protonation might also participate in the process. As further revealed by FT-IR spectroscopy and circular dichroism technique, GQDs could cause the global and local conformational change of HSA, which illustrated the potential toxicity of GQDs that resulted in the structural damage of HSA. Electrochemical techniques demonstrated the complex formation between GQDs and HSA. Our results offered insights into the binding mechanism of GQDs with HSA and provided important information for possible toxicity risk of GQDs to human health.

  18. Interaction of Classical Platinum Agents with the Monomeric and Dimeric Atox1 Proteins: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Xiaolei Wang

    2013-12-01

    Full Text Available We carried out molecular dynamics simulations and free energy calculations for a series of binary and ternary models of the cisplatin, transplatin and oxaliplatin agents binding to a monomeric Atox1 protein and a dimeric Atox1 protein to investigate their interaction mechanisms. All three platinum agents could respectively combine with the monomeric Atox1 protein and the dimeric Atox1 protein to form a stable binary and ternary complex due to the covalent interaction of the platinum center with the Atox1 protein. The results suggested that the extra interaction from the oxaliplatin ligand–Atox1 protein interface increases its affinity only for the OxaliPt + Atox1 model. The binding of the oxaliplatin agent to the Atox1 protein might cause larger deformation of the protein than those of the cisplatin and transplatin agents due to the larger size of the oxaliplatin ligand. However, the extra interactions to facilitate the stabilities of the ternary CisPt + 2Atox1 and OxaliPt + 2Atox1 models come from the α1 helices and α2-β4 loops of the Atox1 protein–Atox1 protein interface due to the cis conformation of the platinum agents. The combinations of two Atox1 proteins in an asymmetric way in the three ternary models were analyzed. These investigations might provide detailed information for understanding the interaction mechanism of the platinum agents binding to the Atox1 protein in the cytoplasm.

  19. Spectroscopic investigations of novel pharmaceuticals: Stability and resonant interaction with laser beam

    Science.gov (United States)

    Smarandache, Adriana; Boni, Mihai; Andrei, Ionut Relu; Handzlik, Jadwiga; Kiec-Kononowicz, Katarzyna; Staicu, Angela; Pascu, Mihail-Lucian

    2017-09-01

    This paper presents data about photophysics of two novel thio-hydantoins that exhibit promising pharmaceutical properties in multidrug resistance control. Time stability studies are necessary to establish the proper use of these compounds in different applications. As for their administration as drugs, it is imperative to know their shelf life, as well as storage conditions. At the same time, laser induced modified properties of the two new compounds are valuable to further investigate their specific interactions with other materials, including biological targets. The two new thio-hydantoins under generic names SZ-2 and SZ-7 were prepared as solutions in dimethyl sulfoxide at different concentrations, as well as in deionised water. For the stability assay they were kept in various light/temperature conditions up to 60 days. The stability was estimates based on UV-vis absorption measurements. The samples in bulk shape were exposed different time intervals to laser radiation emitted at 266 nm as the fourth harmonic of a Nd:YAG laser. The resonant interaction of the studied compounds with laser beams was analysed through spectroscopic methods UV-vis and FTIR absorption, as well as laser induced fluorescence spectroscopy. As for stability assay, only solutions kept in dark at 4 °C have preserved the absorption characteristics, considering the cumulated measuring errors, less than one week. The vibrational changes that occur in their FTIR and modified fluorescence spectra upon laser beam exposure are also discussed. A result of the experimental analysis is that modifications are induced in molecular structures of the investigated compounds by resonant interaction with laser radiation. This fact evidences that the molecules are photoreactive and their characteristics might be shaped through controlled laser radiation exposure using appropriate protocols. This conclusion opens many opportunities both in the biomedical field, but also in other industrial activities

  20. Investigation on the toxic interaction of superparamagnetic iron oxide nanoparticles with catalase

    Energy Technology Data Exchange (ETDEWEB)

    Yu, Zehua [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Liu, Hongwei [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085 (China); Hu, Xinxin; Song, Wei [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China); Liu, Rutao, E-mail: rutaoliu@sdu.edu.cn [Shandong Key Laboratory of Water Pollution Control and Resource Reuse, School of Environmental Science and Engineering, China–America CRC for Environment and Health, Shandong Province, Shandong University, 27# Shanda South Road, Jinan 250100 (China)

    2015-03-15

    Superparamagnetic iron oxide nanoparticles (SPIONs) have been investigated for various applications in targeted drug delivery and magnetic resonance imaging. Given their clinical relevance, there is a need to understand these particles' potential cytotoxic effects and possible mechanisms of cytotoxicity. Using a variety of spectroscopic techniques, we investigated the interaction of SPIONs with catalase (CAT) in an aqueous environment. Catalase is an important enzyme that protects cells and tissues from oxidative damage by reactive oxygen species (ROS). Therefore, in this work, CAT served as a model protein for examining the physiological effects of SPIONs due to is function in eliminating H{sub 2}O{sub 2}. Synchronous fluorescence spectroscopy results showed that SPIONs have little effect on tryptophan residues in CAT. Data from circular dichroism (CD) and UV–vis spectroscopies showed that CAT α-helical content decreased from 32.4% to 29.1% in the presence of SPIONs. Moreover, a ca. 10% decrease in CAT activity was observed in the presence of SPIONs at a 20:1 particle:protein ratio. These results show that SPIONs can interact with proteins to alter both their structure and function. Further studies with CAT or other toxicologically relevant enzymes may be used for elucidating the mechanisms of SPION cytotoxicity. - Highlights: • This work established the binding mode of SPIONs with CAT on molecular level. • The interaction mechanism was explored by multiple spectroscopic techniques. • SPIONs can loosen the skeleton of protein and increase the exposure of amide moieties in the hydrophobic pocket. • SPIONs can inhibit CAT activity and trigger conformational changes in CAT.

  1. Investigation on the toxic interaction of superparamagnetic iron oxide nanoparticles with catalase

    International Nuclear Information System (INIS)

    Yu, Zehua; Liu, Hongwei; Hu, Xinxin; Song, Wei; Liu, Rutao

    2015-01-01

    Superparamagnetic iron oxide nanoparticles (SPIONs) have been investigated for various applications in targeted drug delivery and magnetic resonance imaging. Given their clinical relevance, there is a need to understand these particles' potential cytotoxic effects and possible mechanisms of cytotoxicity. Using a variety of spectroscopic techniques, we investigated the interaction of SPIONs with catalase (CAT) in an aqueous environment. Catalase is an important enzyme that protects cells and tissues from oxidative damage by reactive oxygen species (ROS). Therefore, in this work, CAT served as a model protein for examining the physiological effects of SPIONs due to is function in eliminating H 2 O 2 . Synchronous fluorescence spectroscopy results showed that SPIONs have little effect on tryptophan residues in CAT. Data from circular dichroism (CD) and UV–vis spectroscopies showed that CAT α-helical content decreased from 32.4% to 29.1% in the presence of SPIONs. Moreover, a ca. 10% decrease in CAT activity was observed in the presence of SPIONs at a 20:1 particle:protein ratio. These results show that SPIONs can interact with proteins to alter both their structure and function. Further studies with CAT or other toxicologically relevant enzymes may be used for elucidating the mechanisms of SPION cytotoxicity. - Highlights: • This work established the binding mode of SPIONs with CAT on molecular level. • The interaction mechanism was explored by multiple spectroscopic techniques. • SPIONs can loosen the skeleton of protein and increase the exposure of amide moieties in the hydrophobic pocket. • SPIONs can inhibit CAT activity and trigger conformational changes in CAT

  2. Multilevel summation with B-spline interpolation for pairwise interactions in molecular dynamics simulations

    International Nuclear Information System (INIS)

    Hardy, David J.; Schulten, Klaus; Wolff, Matthew A.; Skeel, Robert D.; Xia, Jianlin

    2016-01-01

    The multilevel summation method for calculating electrostatic interactions in molecular dynamics simulations constructs an approximation to a pairwise interaction kernel and its gradient, which can be evaluated at a cost that scales linearly with the number of atoms. The method smoothly splits the kernel into a sum of partial kernels of increasing range and decreasing variability with the longer-range parts interpolated from grids of increasing coarseness. Multilevel summation is especially appropriate in the context of dynamics and minimization, because it can produce continuous gradients. This article explores the use of B-splines to increase the accuracy of the multilevel summation method (for nonperiodic boundaries) without incurring additional computation other than a preprocessing step (whose cost also scales linearly). To obtain accurate results efficiently involves technical difficulties, which are overcome by a novel preprocessing algorithm. Numerical experiments demonstrate that the resulting method offers substantial improvements in accuracy and that its performance is competitive with an implementation of the fast multipole method in general and markedly better for Hamiltonian formulations of molecular dynamics. The improvement is great enough to establish multilevel summation as a serious contender for calculating pairwise interactions in molecular dynamics simulations. In particular, the method appears to be uniquely capable for molecular dynamics in two situations, nonperiodic boundary conditions and massively parallel computation, where the fast Fourier transform employed in the particle–mesh Ewald method falls short.

  3. Molecular dynamics simulations of the interaction between 60 deg. dislocation and self-interstitial cluster in silicon

    International Nuclear Information System (INIS)

    Jing Yuhang; Meng Qingyuan; Zhao Wei

    2009-01-01

    Molecular dynamics simulations are performed to investigate the interaction between 60 deg. shuffle dislocation and tetrainterstitial (I 4 ) cluster in silicon, using Stillinger-Weber (SW) potential to calculate the interatomic forces. Based on Parrinello-Rahman method, shear stress is exerted on the model to move the dislocation. Simulation results show that the I 4 cluster can bend the dislocation line and delay the dislocation movement. During the course of intersection the dislocation line sections relatively far away from the I 4 cluster accelerate first, and then decelerate. The critical shear stress unpinning the 60 deg. dislocation from the I 4 cluster decreases as the temperature increases in the models.

  4. Interaction of norfloxacin with bovine serum albumin studied by different spectrometric methods; displacement studies, molecular modeling and chemometrics approaches

    Energy Technology Data Exchange (ETDEWEB)

    Naseri, Abdolhossein, E-mail: a_naseri@tabrizu.ac.ir [Departments of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Hosseini, Soheila [Departments of Analytical Chemistry, Faculty of Chemistry, University of Tabriz, Tabriz 51666-16471 (Iran, Islamic Republic of); Rasoulzadeh, Farzaneh [Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Rashidi, Mohammad-Reza [Research Center for Pharmaceutical Nanotechnology, Tabriz University of Medical Sciences, Tabriz 51644-14766 (Iran, Islamic Republic of); Zakery, Maryam; Khayamian, Taghi [Department of Chemistry, College of Chemistry, Isfahan University of Technology, Isfahan 84154 (Iran, Islamic Republic of)

    2015-01-15

    Serum albumins as major target proteins can bind to other ligands leading to alteration of their pharmacological properties. The mechanism of interaction between norfloxacin (NFLX) with bovine serum albumin (BSA) was investigated. Fuorescence quenching of serum albumin by this drug was found to be a static quenching process. The binding sites number, n, apparent binding constant, K, and thermodynamic parameters were calculated at different temperatures. The distance, r, between donor, BSA, and acceptor, NFLX, was calculated according to the Forster theory of non-radiation energy transfer. Also binding characteristics of NFLX with BSA together with its displacement from its binding site by kanamycin and effect of common metal ions on binding constant were investigated by the spectroscopic methods. The conformational change in the secondary structure of BSA upon interaction with NFLX was investigated qualitatively from synchronous fluorescence spectra, Fourier Transform Infrared (FTIR) and circular dichroism (CD) spectrometric methods. Molecular docking studies were performed to obtain information on the possible residues involved in the interaction process and changes in accessible surface area of the interacting residues. The results showed that the conformation of BSA changed in the presence of NFLX. For the first time, displacement studies were used for this interaction; displacement studies showed that NFLX was displaced by phenylbutazon and ketoprofen but was not displaced by ibuprofen indicating that the binding site of NFLX on albumin was site I. In addition a powerful chemometrics method, multivariate curve resolution-alternating least square, was used for resolution of spectroscopic augmented data obtained in two different titration modes in order to extract spectral information regardless of spectral overlapping of components. - Highlights: • Interaction between norfloxacin and BSA is studied by spectral methods. • Chemometrics methods are used to

  5. Molecular mechanics and microcalorimetric investigations of the effects of molecular water on the aggregation of asphaltenes in solutions

    DEFF Research Database (Denmark)

    Murgich, J.; Lira-Galeana, C.; Garcia, Daniel Merino

    2002-01-01

    The interaction of two model asphaltene molecules from the Athabasca sand oil with a water molecule in a toluene solution was studied by means of molecular mechanics calculations. It was found that water forms bridging H bonds between the heteroatoms of asphaltenes with a considerable span...... in energies. The stronger H bond found has energies higher than those corresponding to the stacking of the aromatic areas of the same asphaltene molecules. This shows that the water molecule may generate additional mechanisms of aggregation of asphaltenes in toluene solution, as found experimentally. The H...... by titration calorimetry. A simple dimer dissociation model was used to derive the information about the heat and the constant of dissociation from asphaltenes of Mexico and Alaska obtained from the calorimetric data. The association enthalpies calculated were found to be in excellent agreement with those...

  6. Investigation on the protein-binding properties of icotinib by spectroscopic and molecular modeling method

    Science.gov (United States)

    Zhang, Hua-xin; Xiong, Hang-xing; Li, Li-wei

    2016-05-01

    Icotinib is a highly-selective epidermal growth factor receptor tyrosine kinase inhibitor with preclinical and clinical activity in non-small cell lung cancer, which has been developed as a new targeted anti-tumor drug in China. In this work, the interaction of icotinib and human serum albumin (HSA) were studied by three-dimensional fluorescence spectra, ultraviolet spectra, circular dichroism (CD) spectra, molecular probe and molecular modeling methods. The results showed that icotinib binds to Sudlow's site I in subdomain IIA of HSA molecule, resulting in icotinib-HSA complexes formed at ground state. The number of binding sites, equilibrium constants, and thermodynamic parameters of the reaction were calculated at different temperatures. The negative enthalpy change (ΔHθ) and entropy change (ΔSθ) indicated that the structure of new complexes was stabilized by hydrogen bonds and van der Waals power. The distance between donor and acceptor was calculated according to Förster's non-radiation resonance energy transfer theory. The structural changes of HSA caused by icotinib binding were detected by synchronous spectra and circular dichroism (CD) spectra. Molecular modeling method was employed to unfold full details of the interaction at molecular level, most of which could be supported by experimental results. The study analyzed the probability that serum albumins act as carriers for this new anticarcinogen and provided fundamental information on the process of delivering icotinib to its target tissues, which might be helpful in understanding the mechanism of icotinib in cancer therapy.

  7. Compensation effects in molecular interactions and the quantum chemical le Chatelier principle.

    Science.gov (United States)

    Mezey, Paul G

    2015-05-28

    Components of molecular interactions and various changes in the components of total energy changes during molecular processes typically exhibit some degrees of compensation. This may be as prominent as the over 90% compensation of the electronic energy and nuclear repulsion energy components of the total energy in some conformational changes. Some of these compensations are enhanced by solvent effects. For various arrangements of ions in a solvent, however, not only compensation but also a formal, mutual enhancement between the electronic energy and nuclear repulsion energy components of the total energy may also occur, when the tools of nuclear charge variation are applied to establish quantum chemically rigorous energy inequalities.

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

    Science.gov (United States)

    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.

  9. Study of Molecular Interactions in Binary Liquid Mixtures by Acoustical Method at 303K

    Directory of Open Access Journals (Sweden)

    P. Paul Divakar

    2012-01-01

    Full Text Available Ultrasonic velocity and density measurements were made in two binary liquid mixtures Isopropyl acetate (IPA and Isobutyl acetate (IBA with cyclohexanone (CY as a common component at 303K, at fixed frequency of 2MHz using single crystal variable path interferometer and specific gravity bottle respectively. The experimental data have been used to calculate the acoustic impedance, adiabatic compressibility, inter molecular free length and molar volume. The excess thermodynamic parameters have been evaluated and discussed in the light of molecular interactions.

  10. Microscopic investigation of the 12C + 12C interaction

    International Nuclear Information System (INIS)

    Baye, D.; Pecher, N.; Brussels Univ.

    1982-01-01

    The 12 C + 12 C system is studied in the framework of the generator coordinate method. Each 12 C nucleus is described by a closed psub(3/2) subshell. Phase shifts and resonances are determined for several effective two-body interactions involving a spin-orbit term. The existence and properties of simple local equivalent potentials for the 12 C + 12 C collision are discussed. The 12 C + 12 C system is too light to be well described by potentials independent of the angular momentum or weakly dependent on it. (orig.)

  11. Further investigations of the NN interaction in the Skyrme model

    International Nuclear Information System (INIS)

    Kaelbermann, G.; Eisenberg, J.M.

    1989-01-01

    We examine the influence of the coupling to NΔ and ΔΔ degrees of freedom for the NN interaction as derived in the Skyrme model, carrying out an extensive search for parameters in the basic Lagrangian that will yield both reasonable single-baryon results and appreciable attraction. Separately the free one-body skyrmeon solution and an improved two-body solution are inserted in the product ansatz for the two-body system both with and without time-dependent dynamical terms. No appreciable central attraction between nucleons is found with either of these approaches. (author)

  12. Multiscale Molecular Dynamics Simulations of Beta-Amyloid Interactions with Neurons

    Science.gov (United States)

    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.

  13. Investigating Conversational Dynamics: Interactive Alignment, Interpersonal Synergy, and Collective Task Performance

    Science.gov (United States)

    Fusaroli, Riccardo; Tylén, Kristian

    2016-01-01

    This study investigates interpersonal processes underlying dialog by comparing two approaches, "interactive alignment" and "interpersonal synergy", and assesses how they predict collective performance in a joint task. While the interactive alignment approach highlights imitative patterns between interlocutors, the synergy…

  14. Interaction between the SNR Sagittarius A East and the 50-km s-1 Molecular Cloud

    International Nuclear Information System (INIS)

    Tsuboi, Masato; Okumura, Sachiko K; Miyazaki, Atsushi

    2006-01-01

    We performed high-resolution observations of the Galactic Center 50-km s -1 molecular cloud in the CS J = 1 - 0 line using the Nobeyama Millimeter Array. The 50-km s -1 molecular cloud corresponds to a break in the Sagittarius (Sgr) A east shell. A very broad and negative velocity wing feature is detected at an apparent contact spot between the molecular cloud and the Sgr A east shell. The velocity width of the wing feature is over 50-km s -1 . The width is three times wider than those of typical Galactic Center clouds. This strongly suggests that the shell is interacting physically with the molecular cloud. The asymmetric velocity profile of the wing feature indicates that the Sgr A east shell expands and crashes into the far side of the molecular cloud. About 50 clumps are identified in the cloud using CLUMPFIND. The velocity width-size relation and the mass spectrum of clumps in the cloud are similar to those in Central Molecular Zone (CMZ)

  15. Proof of concept for molecular velcro based on the attractive interaction between porphyrin and pyridine containing copolymers

    Directory of Open Access Journals (Sweden)

    M. Sievers

    2018-06-01

    Full Text Available In this short communication, we investigated the synthesis and mixing of porphyrin and pyridine functionalized copolymers as a proof of concept for a velcro-like interaction. A functionalized porphyrin monomer with one polymerizable side chain was synthesized following a rational synthetic pathway. Subsequent copolymerization and careful removal of residual free porphyrin led to poly(n-butyl acrylate-co-5,10,15-triphenyl-20-(3-vinylphenylporphyrin. The immobilized porphyrin was transformed into the corresponding zinc(II complex, which is capable of the coordinative binding of one pyridine moiety. Complete metallation was proven by absorption spectroscopy. 4-Vinylpyridine was immobilized by copolymerization with n-butyl acrylate, too. Via controlled radical polymerization conditions, the molecular weight of poly(n-butyl acrylate-co-4-vinylpyridine was limited to one tenth of the molecular weight of the porphyrin containing copolymer. This large difference in the molecular weight easily allowed identifying the polymers in the mixture of both. With the help of diffusion ordered nuclear magnetic resonance spectroscopy, the complete and temperature-stable precipitation of the porphyrin containing copolymer was observed, proving the expected attractive interaction and supramolecular network formation.

  16. Experimental Investigation of Hypersonic Flow and Plasma Aerodynamic Actuation Interaction

    International Nuclear Information System (INIS)

    Sun Quan; Cheng Bangqin; Li Yinghong; Cui Wei; Yu Yonggui; Jie Junhun

    2013-01-01

    For hypersonic flow, it was found that the most effective plasma actuator is derived from an electromagnetic perturbation. An experimental study was performed between hypersonic flow and plasma aerodynamic actuation interaction in a hypersonic shock tunnel, in which a Mach number of 7 was reached. The plasma discharging characteristic was acquired in static flows. In a hypersonic flow, the flow field can affect the plasma discharging characteristics. DC discharging without magnetic force is unstable, and the discharge channel cannot be maintained. When there is a magnetic field, the energy consumption of the plasma source is approximately three to four times larger than that without a magnetic field, and at the same time plasma discharge can also affect the hypersonic flow field. Through schlieren pictures and pressure measurement, it was found that plasma discharging could induce shockwaves and change the total pressure and wall pressure of the flow field

  17. Investigating the role of aesthetics for interaction design

    DEFF Research Database (Denmark)

    Stavrakos, Stavros-Konstantinos; Ahmed-Kristensen, Saeema

    2013-01-01

    Two important aspects when designing products is to focus on comfort and to define the aesthetic and emotional value of the product. The main purpose of this research is to answer the question of how attractiveness perceived through the sensory inputs affects the assessment of comfort as well...... when the levels of attractiveness increase and vice versa. The findings further indicate that there are strong, significant correlations between scores of comfort and product adjectives commonly used to describe product attributes such as size, weight and surface material. Hence, there is an emotional...... dimension of comfort which is initiated by the visual input during a human – product interaction and is affected by the attractiveness towards the product. In their endeavor to develop successful and comfortable products designers should focus more on attractiveness....

  18. Quantitative image analysis for investigating cell-matrix interactions

    Science.gov (United States)

    Burkel, Brian; Notbohm, Jacob

    2017-07-01

    The extracellular matrix provides both chemical and physical cues that control cellular processes such as migration, division, differentiation, and cancer progression. Cells can mechanically alter the matrix by applying forces that result in matrix displacements, which in turn may localize to form dense bands along which cells may migrate. To quantify the displacements, we use confocal microscopy and fluorescent labeling to acquire high-contrast images of the fibrous material. Using a technique for quantitative image analysis called digital volume correlation, we then compute the matrix displacements. Our experimental technology offers a means to quantify matrix mechanics and cell-matrix interactions. We are now using these experimental tools to modulate mechanical properties of the matrix to study cell contraction and migration.

  19. Study of the interaction of multiply charged ions and complex systems of biological interest: effects of the molecular environment

    International Nuclear Information System (INIS)

    Capron, Michael

    2011-01-01

    This PhD thesis describes the experimental study of the interaction between slow multiply charged ions (tens of keV) and molecular systems of biological interest (amino acids and nucleobases). It is the aim to identify and to better understand the effect of a molecular environment on different collision induced phenomena. To do so, the time of flight spectra of cationic products emerging from collisions with isolated molecules as well as clusters are compared. It is shown that the molecular environment protects the molecule as it allows to distribute the transferred energies and charges over the whole system (global decrease of the fragmentation and quenching of some fragmentation channels). Furthermore, in the case of adenine clusters, the molecular environment weakens some intramolecular bonds. Moreover, products of chemical reactions are observed concerning proton transfer processes in hydrated cluster of adenine and the formation of peptides bonds between beta-alanine molecules in a cluster. The latter finding is studied as a function of the cluster size and type of the projectile. Some criteria for peptide bond formation, such as flexibility and geometry of the molecule, are investigated for different amino acids. (author)

  20. Molecular structure and interactions of nucleic acid components in nanoparticles: ab initio calculations

    International Nuclear Information System (INIS)

    Rubin, Yu.V.; Belous, L.F.

    2012-01-01

    Self-associates of nucleic acid components (stacking trimers and tetramers of the base pairs of nucleic acids) and short fragments of nucleic acids are nanoparticles (linear sizes of these particles are more than 10 A). Modern quantum-mechanical methods and softwares allow one to perform ab initio calculations of the systems consisting of 150-200 atoms with enough large basis sets (for example, 6-31G * ). The aim of this work is to reveal the peculiarities of molecular and electronic structures, as well as the energy features of nanoparticles of nucleic acid components. We had carried out ab initio calculations of the molecular structure and interactions in the stacking dimer, trimer, and tetramer of nucleic base pairs and in the stacking (TpG)(ApC) dimer and (TpGpC) (ApCpG) trimer of nucleotides, which are small DNA fragments. The performed calculations of molecular structures of dimers and trimers of nucleotide pairs showed that the interplanar distance in the structures studied is equal to 3.2 A on average, and the helical angle in a trimer is approximately equal to 30 o : The distance between phosphor atoms in neighboring chains is 13.1 A. For dimers and trimers under study, we calculated the horizontal interaction energies. The analysis of interplanar distances and angles between nucleic bases and their pairs in the calculated short oligomers of nucleic acid base pairs (stacking dimer, trimer, and tetramer) has been carried out. Studies of interactions in the calculated short oligomers showed a considerable role of the cross interaction in the stabilization of the structures. The contribution of cross interactions to the horizontal interactions grows with the length of an oligomer. Nanoparticle components get electric charges in nanoparticles. Longwave low-intensity bands can appear in the electron spectra of nanoparticles.

  1. Dislocation-cavity interaction in Fe: a comparison between molecular dynamics and dislocation dynamics

    International Nuclear Information System (INIS)

    Hafez Haghighat, S.M.; Schaeublin, R.; Fivel, M.C.

    2007-01-01

    Full text of publication follows: multi-scale modeling, including molecular dynamics (MD) and discrete dislocation dynamics (DDD) methods, appears as a significant tool for the description of plasticity and mechanical properties of materials. This research is on the investigation of the subsequence effects of irradiation on the plasticity of pure Fe and focuses on the interaction of a single dislocation and a spherical cavity, as void or He bubble. Extensive MD simulations of the interaction under imposed strain rate [1, 2] have shown that various temperatures and cavity sizes result in different release stresses depending on dislocation bow out. It appears that a temperature increase and cavity size decrease reduce the cavity strength. MD simulation shows that the elastic field around the cavity is largely anisotropic. This anisotropy may influence the way the dislocation unpins from the cavity. Following the MD simulations, the interaction of a single dislocation and a spherical cavity is now simulated using a DDD discrete dislocation dynamics model. The simulation accounts for the non-Schmidt effect induced by the bcc structure of Fe through local rules derived from MD simulations [3]. The cavity is introduced in the simulation by computing the image forces using a finite element technique. The effective stress applied on the dislocation is then obtained as the superimposition of the applied stress field, the image stress field and the internal stresses. Note that such a model only uses elasticity theory and no core effect of dislocations is taken into account. One of the objectives of this work is to check whether elasticity is responsible of the behaviour observed by MD. Several cases are tested. First an edge dislocation in a (110) plane is pushed against the cavity under a pure shear loading. The local reaction of the dislocations and the cavity are compared to the MD simulations. Then, the case of a screw dislocation is studied. Finally, other loading

  2. REVIEW - Advances on molecular studies of the interaction soybean - Asian rust

    Directory of Open Access Journals (Sweden)

    Aguida Maria Alves Pereira Morales

    2012-01-01

    Full Text Available Effective management practices are essential for controlling rust outbreaks. The main control methodused is the application of fungicides, which increases substantially the cost of production and is harmful to theenvironment. Prevention is still the best way to avoid more significant losses in soybean yields. Alternatives,such as planting resistant varieties to the fungus, are also important. The use of resistant or tolerant varietiesis the most promising method for controlling Asian soybean rust. Recently, five dominant genes resistant to soybean rust were described: Rpp1, Rpp2, Rpp3, Rpp4 and Rpp5. However, little is known about the molecular interaction among soybean plant and soybean rust and on the molecular pathway triggered by pathogen recognition. Understanding the molecular mechanisms involved in defense responses is of primary importance for planning strategies to control stress and, consequently, to increase plant adaptation to limiting conditions

  3. Mutation analysis and molecular modeling for the investigation of ligand-binding modes of GPR84.

    Science.gov (United States)

    Nikaido, Yoshiaki; Koyama, Yuuta; Yoshikawa, Yasushi; Furuya, Toshio; Takeda, Shigeki

    2015-05-01

    GPR84 is a G protein-coupled receptor for medium-chain fatty acids. Capric acid and 3,3'-diindolylmethane are specific agonists for GPR84. We built a homology model of a GPR84-capric acid complex to investigate the ligand-binding mode using the crystal structure of human active-state β2-adrenergic receptor. We performed site-directed mutagenesis to subject ligand-binding sites to our model using GPR84-Giα fusion proteins and a [(35)S]GTPγS-binding assay. We compared the activity of the wild type and mutated forms of GPR84 by [(35)S]GTPγS binding to capric acid and diindolylmethane. The mutations L100D `Ballesteros-Weinstein numbering: 3.32), F101Y (3.33) and N104Q (3.36) in the transmembrane helix III and N357D (7.39) in the transmembrane helix VII resulted in reduced capric acid activity but maintained the diindolylmethane responses. Y186F (5.46) and Y186H (5.46) mutations had no characteristic effect on capric acid but with diindolylmethane they significantly affected the G protein activation efficiency. The L100D (3.32) mutant responded to decylamine, a fatty amine, instead of a natural agonist, the fatty acid capric acid, suggesting that we have identified a mutated G protein-coupled receptor-artificial ligand pairing. Our molecular model provides an explanation for these results and interactions between GPR84 and capric acid. Further, from the results of a double stimulation assay, we concluded that diindolylmethane was a positive allosteric modulator for GPR84. © The Authors 2014. Published by Oxford University Press on behalf of the Japanese Biochemical Society. All rights reserved.

  4. Molecular and biopharmaceutical investigation of alginate-inulin synbiotic coencapsulation of probiotic to target the colon.

    Science.gov (United States)

    Atia, Abdelbasset; Gomma, Ahmed I; Fliss, Ismail; Beyssac, Eric; Garrait, Ghislain; Subirade, Muriel

    2017-03-01

    Colon targeting, as a site-specific delivery for oral formulation, remains a major challenge, especially for sensitive bioactive components such as therapeutic forms of phages, live attenuated virus and prebiotics-probiotics association. Synbiotics could be used to protect encapsulated probiotics during the gastrointestinal tract and control their release in the colon. To achieve these goals, effective prebiotics, such as inulin, could be combined with alginate - the most exploited polymer used for probiotic encapsulation - in the form of beads. This work aimed to study the biopharmaceutical behaviour of alginate beads (A) and inulin-alginate beads of different inulin concentrations (5 or 20%) in 2% alginate (AI5, AI20). Beads were loaded with three probiotic strains (Pediococcus acidilactici Ul5, Lactobacillus reuteri and Lactobacillus salivarius). Dissolution of beads was studied by USP4 under conditions simulating the gastrointestinal condition. The survival rates of the bacterial strains were measured by a specific qPCR bacterial count. Mucoadhesiveness of beads was studied by an ex vivo method using intestinal mucosa. To understand the behaviour of each formulation, the ultrastructure of the polymeric network was studied using scanning electron microscopy (SEM). Molecular interactions between alginate and inulin were studied by Fourier transform infra-red spectroscopy (FTIR). Dissolution results suggested that the presence of inulin in beads provided more protection for the tested bacterial strains against the acidic pH. AI5 was the most effective formulation to deliver probiotics to the colon simulation conditions. FTIR and SEM investigations explained the differences in behaviour of each formula. The developed symbiotic form provided a promising matrix for the development of colonic controlled release systems.

  5. Investigation of the Behavior of Ethylene Molecular Films Using High Resolution Adsorption Isotherms and Neutron Scattering

    International Nuclear Information System (INIS)

    Barbour, Andi M.; Telling, Mark T.; Larese, John Z.

    2010-01-01

    The wetting behavior of ethylene adsorbed on MgO(100) was investigated from 83-135 K using high resolution volumetric adsorption isotherms. The results are compared to ethylene adsorption on graphite, a prototype adsorption system, in an effort to gain further insight into the forces that drive the observed film growth. Layering transitions for ethylene on MgO(100) are observed below the bulk triple point of ethylene (T = 104.0 K). The formation of three discrete adlayers is observed on the MgO(100) surface; onset of the second and third layers occurs at 79.2 ± 1.3 K and 98.3 ± 0.9 K, respectively. Thermodynamic quantities such as differential enthalpy and entropy, heat of adsorption, and isosteric heat of adsorption are determined and compared to the previously published values for ethylene on graphite. The average area occupied by a ethylene molecule on MgO(100) is 22.6 ± 1.1 (angstrom) 2 molecule -1 . The locations of two phase transitions are identified (i.e., layer critical temperatures at T c2 (n=1) at 108.6 ± 1.7 K and T c2 (n=2) at 116.5 ± 1.2 K) and a phase diagram is proposed. Preliminary neutron diffraction measurements reveal evidence of a monolayer solid with a lattice constant of ∼4.2 (angstrom). High resolution INS measurements show that the onset to dynamical motion and monolayer melting take place at 35 K and 65 K, respectively. The data reported here exhibit a striking similarity to ethylene on graphite which suggests that molecule-molecule interactions play an important role in determining the physical properties and growth of molecularly thin ethylene films.

  6. 2D IR spectra of cyanide in water investigated by molecular dynamics simulations

    Science.gov (United States)

    Lee, Myung Won; Carr, Joshua K.; Göllner, Michael; Hamm, Peter; Meuwly, Markus

    2013-01-01

    Using classical molecular dynamics simulations, the 2D infrared (IR) spectroscopy of CN− solvated in D2O is investigated. Depending on the force field parametrizations, most of which are based on multipolar interactions for the CN− molecule, the frequency-frequency correlation function and observables computed from it differ. Most notably, models based on multipoles for CN− and TIP3P for water yield quantitatively correct results when compared with experiments. Furthermore, the recent finding that T 1 times are sensitive to the van der Waals ranges on the CN− is confirmed in the present study. For the linear IR spectrum, the best model reproduces the full widths at half maximum almost quantitatively (13.0 cm−1 vs. 14.9 cm−1) if the rotational contribution to the linewidth is included. Without the rotational contribution, the lines are too narrow by about a factor of two, which agrees with Raman and IR experiments. The computed and experimental tilt angles (or nodal slopes) α as a function of the 2D IR waiting time compare favorably with the measured ones and the frequency fluctuation correlation function is invariably found to contain three time scales: a sub-ps, 1 ps, and one on the 10-ps time scale. These time scales are discussed in terms of the structural dynamics of the surrounding solvent and it is found that the longest time scale (≈10 ps) most likely corresponds to solvent exchange between the first and second solvation shell, in agreement with interpretations from nuclear magnetic resonance measurements.

  7. Interaction of sucralose with whey protein: Experimental and molecular modeling studies

    Science.gov (United States)

    Zhang, Hongmei; Sun, Shixin; Wang, Yanqing; Cao, Jian

    2017-12-01

    The objective of this research was to study the interactions of sucralose with whey protein isolate (WPI) by using the three-dimensional fluorescence spectroscopy, circular dichroism spectroscopy and molecular modeling. The results showed that the peptide strands structure of WPI had been changed by sucralose. Sucralose binding induced the secondary structural changes and increased content of aperiodic structure of WPI. Sucralose decreased the thermal stability of WPI and acted as a structure destabilizer during the thermal unfolding process of protein. In addition, the existence of sucralose decreased the reversibility of the unfolding of WPI. Nonetheless, sucralose-WPI complex was less stable than protein alone. The molecular modeling result showed that van der Waals and hydrogen bonding interactions contribute to the complexation free binding energy. There are more than one possible binding sites of WPI with sucralose by surface binding mode.

  8. Architecture of transcriptional regulatory circuits is knitted over the topology of bio-molecular interaction networks

    DEFF Research Database (Denmark)

    Soberano de Oliveira, Ana Paula; Patil, Kiran Raosaheb; Nielsen, Jens

    2008-01-01

    is to use the topology of bio-molecular interaction networks in order to constrain the solution space. Such approaches systematically integrate the existing biological knowledge with the 'omics' data. Results: Here we introduce a hypothesis-driven method that integrates bio-molecular network topology......Background: Uncovering the operating principles underlying cellular processes by using 'omics' data is often a difficult task due to the high-dimensionality of the solution space that spans all interactions among the bio-molecules under consideration. A rational way to overcome this problem...... with transcriptome data, thereby allowing the identification of key biological features (Reporter Features) around which transcriptional changes are significantly concentrated. We have combined transcriptome data with different biological networks in order to identify Reporter Gene Ontologies, Reporter Transcription...

  9. Investigation of uranyl phosphite interaction with some amides

    International Nuclear Information System (INIS)

    Avduevskaya, K.A.; Ragulina, N.B.; Rozanov, I.A.; Mukhajlov, Yu.N.; Kanishcheva, A.S.; Grevtseva, T.G.

    1981-01-01

    Uranyl (amide) phosphitocomplexes of [UO 2 HPO 3 H 2 OAA]xH 2 O, [UO 2 HPO 3 (AA) 2 ], [UO 2 HPO 3 H 2 O DMC], [UO 2 HPO 3 H 2 ODMFA], [UO 2 HPO 3 DAMA] and UO 2 HPO 3 x2FAxH 2 O compositions, where AA-acetamide; DMC-N, N-dimetyl carbamide, DMFA-dimetyl formamide; DAMA-diamide of malonic acid; FA-formamide, are separated, identified and investigated. Derivatives of mono substituted uranyl phosphite of UO 2 (H 2 PO 3 ) 2 x2FA and [UO 2 (H 2 PO 3 ) 2 H 2 O]x2TMC composition (where TMC-tetramethyl carbamide), are synthesized. Structures of complexes with DAMA, TMC, DMFA and acid dimethyl-ammonium diphosphitouranylate-(CH 3 ] 2 NH 2 x[UO 2 (HPO 3 ) 3 (H 2 PO 3 )] are investigated [ru

  10. Interaction of Tenebrio Molitor Antifreeze Protein with Ice Crystal: Insights from Molecular Dynamics Simulations.

    Science.gov (United States)

    Ramya, L; Ramakrishnan, Vigneshwar

    2016-07-01

    Antifreeze proteins (AFP) observed in cold-adapting organisms bind to ice crystals and prevent further ice growth. However, the molecular mechanism of AFP-ice binding and AFP-inhibited ice growth remains unclear. Here we report the interaction of the insect antifreeze protein (Tenebrio molitor, TmAFP) with ice crystal by molecular dynamics simulation studies. Two sets of simulations were carried out at 263 K by placing the protein near the primary prism plane (PP) and basal plane (BL) of the ice crystal. To delineate the effect of temperatures, both the PP and BL simulations were carried out at 253 K as well. The analyses revealed that the protein interacts strongly with the ice crystal in BL simulation than in PP simulation both at 263 K and 253 K. Further, it was observed that the interactions are primarily mediated through the interface waters. We also observed that as the temperature decreases, the interaction between the protein and the ice increases which can be attributed to the decreased flexibility and the increased structuring of the protein at low temperature. In essence, our study has shed light on the interaction mechanism between the TmAFP antifreeze protein and the ice crystal. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  11. Modelling of water-rock interaction at TVO investigation sites

    International Nuclear Information System (INIS)

    Pitkaenen, P.; Leino-Forsman, H.

    1992-12-01

    The geochemistry of the groundwater at the Kivetty, Syyry and Olkiluoto site investigation areas in Finland for nuclear waste disposal is evaluated. The hydrogeological data is collected from boreholes drilled down to 100-m depth into crystalline bedrock. The interpretation is based on groundwater chemistry and isotope data, mineralogical data, and the structure and hydrology of the bedrock, using correlation diagrams and the thermodynamic calculations (PHREEQE,EQ3NR). The hydrogeochemistry and major processes controlling the groundwater chemistry are discussed

  12. The Importance of Interactions at the Molecular Level: A Spectroscopic Study of a New Composite Sorber Material.

    Science.gov (United States)

    Crocellà, Valentina; Groppo, Elena; Dani, Alessandro; Castellero, Alberto; Bordiga, Silvia; Zilio, Stefano; De Simone, Agnello; Vacca, Paolo

    2017-10-01

    The functional properties of a new composite material having water vapor getter properties have been investigated by a large arsenal of characterization techniques. The composite system is originated by combining two constituents having very different chemical natures, a magnesium perchlorate (Mg(ClO 4 ) 2 ) salt and a polymeric acrylic matrix. In particular, Fourier transform infrared (FT-IR) and Raman spectroscopy have been fundamental to understand the type of interactions between the salt and the matrix in different hydration conditions. It was found that in the anhydrous composite system the dispersed Mg(ClO 4 ) 2 salt retains its molecular structure, because Mg 2+ cations are still surrounded by their [ClO 4 ] - counter-anions; at the same time, the salt and the polymeric matrix chemically interact each other at the molecular level. These interactions gradually vanish in the presence of water, and disappear in the fully hydrated composite system, where the Mg 2+ cations are completely solvated by the water molecules.

  13. Mixtures of nonionic and anionic surfactants: interactions with low-molecular-mass homopeptides

    Czech Academy of Sciences Publication Activity Database

    Forgács, E.; Cserháti, T.; Deyl, Zdeněk; Mikšík, Ivan; Eckhardt, Adam

    2001-01-01

    Roč. 917, 1-2 (2001), s. 287-295 ISSN 0021-9673 R&D Projects: GA ČR GV203/96/K128; GA ČR GA203/99/0191; GA ČR GA203/00/D032 Institutional research plan: CEZ:AV0Z5011922 Keywords : molecular interactions * regression analysis * surfactants Subject RIV: BH - Optics, Masers, Lasers Impact factor: 2.793, year: 2001

  14. Interactions of cephalexin with bovine serum albumin: displacement reaction and molecular docking

    Directory of Open Access Journals (Sweden)

    Hamed Hamishehkar

    2016-09-01

    Conclusion: The outcomes of spectroscopic methods revealed that the conformation of BSA changed during drug-BSA interaction. The results of FRET propose that CPL quenches the fluorescence of BSA by static quenching and FRET. The displacement study showed that phenylbutazon and ketoprofen displaced CPL, indicating that its binding site on albumin is site I and Gentamicin cannot be displaced from the binding site of CPL. All results of molecular docking method agreed with the results of experimental data.

  15. SChiSM2: creating interactive web page annotations of molecular structure models using Jmol.

    Science.gov (United States)

    Cammer, Stephen

    2007-02-01

    SChiSM2 is a web server-based program for creating web pages that include interactive molecular graphics using the freely-available applet, Jmol, for illustration. The program works with Internet Explorer and Firefox on Windows, Safari and Firefox on Mac OSX and Firefox on Linux. The program can be accessed at the following address: http://ci.vbi.vt.edu/cammer/schism2.html.

  16. Quantum molecular modeling of the interaction between guanine and alkylating agents--2--nitrogen mustard.

    Science.gov (United States)

    Hamza, A; Broch, H; Vasilescu, D

    1996-06-01

    The alkylation mechanism of guanine by nitrogen mustard (HN2) was studied by using a supermolecular modeling at the ab initio 6-31G level. Our computations show that interaction of guanine with the aziridinium form of HN2 necessitates a transition state for the N7 alkylation route. The pathway of N7-guanine alkylation by nitrogen and sulfur mustards is discussed on the basis of the Molecular Electrostatic Potential and HOMO-LUMO properties of these molecules.

  17. Mechanism and kinetics of Fe, Cr, Mo and Mn atom interaction with molecular oxygen

    International Nuclear Information System (INIS)

    Akhmadov, U.S.; Zaslonko, I.S.; Smirnov, V.N.

    1988-01-01

    Rate constants of atomic interaction of some transition metals (Fe, Cr, Mo, Mn) with molecular oxygen are measured in shock waves using the resonance atomic-absorption method. A new method for determination of the parameter γ in the modified Lambert-Beer law D=ε(lN)γ is suggested and applied. Bond strength in CrO and MoO molecules is estimated

  18. Investigation of a metal-organic interface. Realization and understanding of a molecular switch

    Energy Technology Data Exchange (ETDEWEB)

    Neucheva, Olga [Forschungszentrum Juelich (DE). Institute of Bio- and Nanosystems (IBN), Functional Nanostructures at Surfaces (IBN-3)

    2010-07-01

    The field of molecular organic electronics is an emerging and very dynamic area. The continued trend to miniaturisation, combined with increasing complexity and cost of production in conventional semiconductor electronics, forces companies to turn their attention to alternatives that promise the next levels of scale at significantly lower cost. After consumer electronic devices based on organic transistors, such as TVs and book readers, have already been presented, molecular electronics is expected to offer the next breakthrough in feature size. Unfortunately, most of the organic/metal interfaces contain intrinsic defects that break the homogeneity of the interface properties. In this thesis, the electronic and structural properties of such defects were examined in order to understand the influence of the inhomogeneities on the quality of the interface layer. However, the main focus of this work was the investigation of the local properties of a single molecule. Taking advantage of the Scanning Tunnelling Microscope's (STM's) ability to act as a local probe, a single molecular switch was realized and studied. Moreover, in close collaboration with theory groups, the underlying mechanism driving the switching process was identified and described. Besides the investigation of the switching process, the ability of the STM to build nanostructures of different shapes from large organic molecules was shown. Knowing the parameters for realization and control of the switching process and for building the molecular corrals, the results of this investigation enable the reconstruction of the studied molecular ensemble and its deployment in electric molecular circuits, constituting a next step towards further miniaturization of electronic devices. (orig.)

  19. AESOP: A Python Library for Investigating Electrostatics in Protein Interactions.

    Science.gov (United States)

    Harrison, Reed E S; Mohan, Rohith R; Gorham, Ronald D; Kieslich, Chris A; Morikis, Dimitrios

    2017-05-09

    Electric fields often play a role in guiding the association of protein complexes. Such interactions can be further engineered to accelerate complex association, resulting in protein systems with increased productivity. This is especially true for enzymes where reaction rates are typically diffusion limited. To facilitate quantitative comparisons of electrostatics in protein families and to describe electrostatic contributions of individual amino acids, we previously developed a computational framework called AESOP. We now implement this computational tool in Python with increased usability and the capability of performing calculations in parallel. AESOP utilizes PDB2PQR and Adaptive Poisson-Boltzmann Solver to generate grid-based electrostatic potential files for protein structures provided by the end user. There are methods within AESOP for quantitatively comparing sets of grid-based electrostatic potentials in terms of similarity or generating ensembles of electrostatic potential files for a library of mutants to quantify the effects of perturbations in protein structure and protein-protein association. Copyright © 2017 Biophysical Society. Published by Elsevier Inc. All rights reserved.

  20. Investigation of nuclear interactions around 20 TeV

    Energy Technology Data Exchange (ETDEWEB)

    Sato, Y [Waseda Univ., Tokyo (Japan). Science and Engineering Research Lab.; Sugimoto, H; Saito, T

    1976-12-01

    Nuclear interactions at a mean energy of about 20 TeV are studied by means of a nuclear emulsion chamber with jet producer. In the present analysis, particular emphasis is placed on the experimental condition. The transverse momentum spectrum of secondary ..gamma.. rays is approximated by a single exponential in a range of 0.3

  1. ACCOUNTING OF MANY-PARTICLE INTERACTIONS IN MOLECULAR J-AGGREGATES AND NONLINEAR OPTICAL EFFECTS IN THESE SYSTEMS

    Directory of Open Access Journals (Sweden)

    N. A. Veretenov

    2014-09-01

    Full Text Available The paper deals with generalization of investigation materials performed by the authors in recent years and analysis of obtained results. The subject of the paper is accounting of many-particle interactions in molecular J-aggregates at their resonance excitation by laser radiation. In this case, not only twin interactions are taken into considerations, but also the interactions of a given particle with three and more particles simultaneously. Three basic directions can be denoted among carried out investigations. The first direction is connected with derivation (from the first principles of motion equations for molecular of J-aggregates in view of many-particle interactions, and also twin correlations between particles. The derivation of equations from the first principles leads in general to the system of coupled equations for the means of products of n operators relating to n different molecules. Since n increases in every following equation, the problems arise, connected with uncoupling of this system and also factorization of the means with the highest n. The most difficult and complicated problem in this process is correct calculation of relaxed terms, arising due to exciton-exciton annihilation. The first direction is connected concretely with solution of all above mentioned problems. Within the second direction the study of bistability has been carried out on the basis of obtained equations, in view of three-particle interactions. Meanwhile primary attention has been concentrated on analysis of homogeneous regimes in J-aggregates. It has been shown, in particular, that accounting of many-particle contributions leads to the shift of bistability boundary into region of smaller constants of exciton-exciton annihilation. And, at last, the third direction of investigations is connected with analysis of modulation instability for stationary states of J-aggregates considered earlier at bistability study. The study of stability region boundaries

  2. Molecular dynamics simulations of protein-tyrosine phosphatase 1B: II. Substrate-enzyme interactions and dynamics

    DEFF Research Database (Denmark)

    Peters, Günther H.j.; Frimurer, T. M.; Andersen, J. N.

    2000-01-01

    Molecular dynamics simulations of protein tyrosine phosphatase 1B (PTP1B) complexed with the phosphorylated peptide substrate DADEpYL and the free substrate have been conducted to investigate 1) the physical forces involved in substrate-protein interactions, 2) the importance of enzyme...... to substrate binding. Based on essential dynamics analysis of the PTP1B/DADEpYL trajectory, it is shown that internal motions in the binding pocket occur in a subspace of only a few degrees of freedom. in particular, relatively large flexibilities are observed along several eigenvectors in the segments: Arg(24...... for catalysis. Analysis of the individual enzyme-substrate interaction energies revealed that mainly electrostatic forces contribute to binding. Indeed, calculation of the electrostatic field of the enzyme reveals that only the field surrounding the binding pocket is positive, while the remaining protein...

  3. Molecular dynamics simulations of the DNA interaction with metallic nanoparticles and TiO2 surfaces

    International Nuclear Information System (INIS)

    Kholmurodov, Kh.T.; Krasavin, E.A.; Dushanov, E.B.; Hassan, H.K.; Galal, A.; ElHabashy, H.A.; Sweilam, N.H.; Yasuoka, K.

    2013-01-01

    The understanding of the mechanism of DNA interactions and binding with metallic nanoparticles (NPs) and surfaces represents a great interest in today's medicine applications due to diagnostic and treatment of oncology diseases. Recent experimental and simulation studies involve the DNA interaction with highly localized proton beams or metallic NPs (such as Ag, Au, etc.), aimed at targeted cancer therapy through the injection of metal micro- or nanoparticles into the tumor tissue with consequent local microwave or laser heating. The effects of mutational structure changes in DNA and protein structures could result in destroying of native chemical (hydrogen) bonds or, on the contrary, creating of new bonds that do not normally exist there. The cause of such changes might be the alteration of one or several nucleotides (in DNA) or the substitution of specific amino acid residues (in proteins) that can lead to the essential structural destabilization or unfolding. At the atomic or molecular level, the replacement of one nucleotide by another (in DNA double helices) or replacement of one amino acid residue by another (in proteins) cause essential modifications of the molecular force fields of the environment that break locally important hydrogen bonds underlying the structural stability of the biological molecules. In this work, the molecular dynamics(MD) simulations were performed for four DNA models and the flexibilities of the purine and pyrimidine nucleotides during the interaction process with the metallic NPs and TiO 2 surface were clarified

  4. Murine transgenic embryonic stem cell lines for the investigation of sinoatrial node-related molecular pathways

    Directory of Open Access Journals (Sweden)

    Stefanie Schmitteckert

    2017-12-01

    Full Text Available The elucidation of molecular mechanisms that restrict the potential of pluripotent stem cells and promote cardiac lineage differentiation is of crucial relevance, since embryonic stem cells (ESCs hold great potential for cell based heart therapies. The homeodomain transcription factor Shox2 is essential for the development and proper function of the native cardiac pacemaker, the sinoatrial node. This prompted us to develop a cardiac differentiation model using ESC lines isolated from blastocysts of Shox2-deficient mice. The established cell model provides a fundamental basis for the investigation of molecular pathways under physiological and pathophysiological conditions for evaluating novel therapeutic approaches.

  5. Investigation of heavy quark and multiple interactions at HERA

    International Nuclear Information System (INIS)

    Magro, L.M.

    2005-09-01

    This thesis is oriented to the study of heavy quark photoproduction and multiple interactions, MI. For this reason we search for D* Mesons, in order to tag the charm quark, and we restrict ourselves in the region: Q 2 2 . For the theoretical calculations we use two Monte Carlo event generators: RAPGAP 3.1 and PYTHIA 6.2. Heavy quark production provides a large hard scale and therefore a small α s , which allows to test the perturbative QCD theory. On the other hand, MI has been proven to be important in hadron-hadron collisions. In this thesis, using MC event generators, we search for possible signals of MI in heavy quark production in electron-proton, ep, collisions. The thesis begins with a Theoretical Overview, with an introduction to ep collisions physics and the heavy quark photoproduction. We also give an introduction to the MI model included in PYTHIA. The next chapter introduces the concept of jet and presents some methods for the Heavy Quark Identification. After these two theoretical chapters there is a study of the direct and photon resolved processes, as well as the parton showering with RAPGAP. Since this thesis is oriented to the study of MI, PYTHIA plays a very important role because it includes a MI model also for ep collisions. Therefore, the fourth chapter is oriented to study the different steps in the event generation in PYTHIA. Chapter 7 is a D* Meson photoproduction study, where we include a comparison between the data, taken from the PhD Thesis of Gero Flucke. Finally, chapter 8 is a search for possible signals on MI. In hadron-hadron collisions it is clear that MI play a role. In ep collisions it is not so clear although MI could play a role in resolved photon events. The aim of this chapter is to find signals where HERA measurements could be sensitive to MI. (orig.)

  6. Fundamental properties of molecules on surfaces. Molecular switching and interaction of magnetic molecules with superconductors

    Energy Technology Data Exchange (ETDEWEB)

    Hatter, Nino

    2016-12-14

    In this thesis, we investigate individual molecular switches and metal-organic complexes on surfaces with scanning tunneling microscopy (STM) and spectroscopy (STS) at low temperatures. One focus addresses the switching ability and mechanism of diarylethene on Ag(111). The other focus lies on resolving and tuning magnetic interactions of individual molecules with superconductors. 4,4'-(4,4'-(perfluorocyclopent-1-ene-1,2-diyl)bis (5-methylthiophene-4,2-diyl)dip yridine (PDTE) is a prototypical photochromic switch. We can induce a structural change of individual PDTE molecules on Ag(111) with the STM tip. This change is accompanied by a reduction of the energy gap between the occupied and unoccupied molecular orbitals. Density functional theory (DFT) calculations reveal that the induced switching corresponds to a ring-closing reaction from an open isomer in a flat adsorption configuration to a ring-closed isomer with its methyl groups in a cis configuration. The final product is thermodynamically stabilized by strong dispersion interactions with the surface. A linear dependence of the switching threshold with the tip-sample distance with a minimal threshold of 1.4 V is found, which we assign to a combination of an electric-field induced process and a tunneling-electron contribution. DFT calculations suggest a large activation barrier for a ring-closing reaction from the open flat configuration into the closed cis configuration. The interaction of magnetic molecules with superconductors is studied on manganese phthalocyanine (MnPc) adsorbed on Pb(111). We find triplets of Shiba states inside the superconducting gap. Different adsorption sites of MnPc provide a large variety of exchange coupling strengths, which lead to a collective energy shift of the Shiba triplets. We can assign the splitting of the Shiba states to be an effect of magnetic anisotropy in the system. A quantum phase transition from a ''Kondo screened'' to a &apos

  7. Revealing molecular mechanisms by integrating high-dimensional functional screens with protein interaction data.

    Directory of Open Access Journals (Sweden)

    Angela Simeone

    2014-09-01

    Full Text Available Functional genomics screens using multi-parametric assays are powerful approaches for identifying genes involved in particular cellular processes. However, they suffer from problems like noise, and often provide little insight into molecular mechanisms. A bottleneck for addressing these issues is the lack of computational methods for the systematic integration of multi-parametric phenotypic datasets with molecular interactions. Here, we present Integrative Multi Profile Analysis of Cellular Traits (IMPACT. The main goal of IMPACT is to identify the most consistent phenotypic profile among interacting genes. This approach utilizes two types of external information: sets of related genes (IMPACT-sets and network information (IMPACT-modules. Based on the notion that interacting genes are more likely to be involved in similar functions than non-interacting genes, this data is used as a prior to inform the filtering of phenotypic profiles that are similar among interacting genes. IMPACT-sets selects the most frequent profile among a set of related genes. IMPACT-modules identifies sub-networks containing genes with similar phenotype profiles. The statistical significance of these selections is subsequently quantified via permutations of the data. IMPACT (1 handles multiple profiles per gene, (2 rescues genes with weak phenotypes and (3 accounts for multiple biases e.g. caused by the network topology. Application to a genome-wide RNAi screen on endocytosis showed that IMPACT improved the recovery of known endocytosis-related genes, decreased off-target effects, and detected consistent phenotypes. Those findings were confirmed by rescreening 468 genes. Additionally we validated an unexpected influence of the IGF-receptor on EGF-endocytosis. IMPACT facilitates the selection of high-quality phenotypic profiles using different types of independent information, thereby supporting the molecular interpretation of functional screens.

  8. Population reversal driven by unrestrained interactions in molecular dynamics simulations: A dialanine model

    Directory of Open Access Journals (Sweden)

    Filippo Pullara

    2015-10-01

    Full Text Available Standard Molecular Dynamics simulations (MD are usually performed under periodic boundary conditions using the well-established “Ewald summation”. This implies that the distance among each element in a given lattice cell and its corresponding element in another cell, as well as their relative orientations, are constant. Consequently, protein-protein interactions between proteins in different cells—important in many biological activities, such as protein cooperativity and physiological/pathological aggregation—are severely restricted, and features driven by protein-protein interactions are lost. The consequences of these restrictions, although conceptually understood and mentioned in the literature, have not been quantitatively studied before. The effect of protein-protein interactions on the free energy landscape of a model system, dialanine, is presented. This simple system features a free energy diagram with well-separated minima. It is found that, in the case of absence of peptide-peptide (p-p interactions, the ψ = 150° dihedral angle determines the most energetically favored conformation (global free-energy minimum. When strong p-p interactions are induced, the global minimum switches to the ψ = 0° conformation. This shows that the free-energy landscape of an individual molecule is dramatically affected by the presence of other freely interacting molecules of its same type. Results of the study suggest how taking into account p-p interactions in MD allows having a more realistic picture of system activity and functional conformations.

  9. Final Report on Investigation of the Electron Interactions in Graphene

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Philip [Columbia University

    2015-02-14

    In graphene, combined with the real spin degree of freedom, which exhibits SU(2) symmetry, the total internal degrees of freedom of graphene carriers is thus described by a larger SU(4) symmetry, which produces a richer space for potential phenomena of emergent correlated electron phenomena. The major part of this proposal is exploring this unique multicomponent correlated system in the quantum limit. In the current period of DOE BES support we have made several key advances that will serve as a foundation for the new studies in this proposal. Employing the high-mobility encapsulated graphene heterostructures developed during the current phase of research, we have investigated spin and valley quantum Hall ferromagnetism in graphene and discovered a spin phase transition leading to a quantum spin Hall analogue. We have also observed the fractal quantum Hall effect arising from the Hofstadter’s butterfly energy spectrum. In addition, we have discovered multiband transport phenomena in bilayer graphene at high carrier densities.

  10. Investigation of electron heating in laser-plasma interaction

    Directory of Open Access Journals (Sweden)

    A Parvazian

    2013-03-01

    Full Text Available  In this paper, stimulated Raman scattering (SRS and electron heating in laser plasma propagating along the plasma fusion is investigated by particle-in cell simulation. Applying an external magnetic field to plasma, production of whistler waves and electron heating associated with whistler waves in the direction perpendicular to external magnetic field was observed in this simulation. The plasma waves with low phase velocities, generated in backward-SRS and dominateing initially in time and space, accelerated the backward electrons by trapping them. Then these electrons promoted to higher energies by the forward-SRS plasma waves with high phase velocities. This tow-stage electron acceleration is more efficient due to the coexistence of these two instabilities.

  11. Investigation of electron heating in laser-plasma interaction

    International Nuclear Information System (INIS)

    Parvazian, A.; Haji Sharifi, K.

    2013-01-01

    In this paper, stimulated Raman scattering and electron heating in laser plasma propagating along the plasma fusion is investigated by particle-in cell simulation. Applying an external magnetic field to plasma, production of whistler waves and electron heating associated with whistler waves in the direction perpendicular to external magnetic field was observed in this simulation. The plasma waves with low phase velocities, generated in backward-stimulated Raman scattering and dominating initially in time and space, accelerated the backward electrons by trapping them. Then these electrons promoted to higher energies by the forward-stimulated Raman scattering plasma waves with high phase velocities. This two-stage electron acceleration is more efficient due to the coexistence of these two instabilities.

  12. Investigation of microbial-mineral interactions by Moessbauer spectroscopy

    International Nuclear Information System (INIS)

    Sawicki, J.A.; Brown, D.A.

    1998-01-01

    Moessbauer spectroscopy was used to investigate the reactions of microbes with iron minerals in aqueous solutions and as components of rocks in banded iron formations and granite. A microbial biofilm that formed on a wall of an excavated granite vault in a deep underground laboratory initiated this research. At the aerobic face of the biofilm, iron was found in a form of ferrihydrite; in the anaerobic face against the rock, iron was found as very small siderite particles. Laboratory incubations of the biofilm microbial consortium showed different mineral species could be formed. When the microbial consortium from the biofilm was incubated with magnetite grains, up to about 10% of the iron was altered in three weeks to hematite. The ability of the consortium to precipitate iron both as Fe 2+ and Fe 3+ in close proximity may have a bearing on the deposition of banded iron formations. These reactions could also be important in microbially induced corrosion

  13. Theoretical investigation of electron-positive ion/atom interactions

    International Nuclear Information System (INIS)

    Msezane, A.Z.

    1992-01-01

    Very brief summaries are given on three research topics. Electron impact elastic, excitation, and total cross sections for K were investigated by using elaborate Cl target wave functions in the close-coupling approximation. Photoionization cross sections from ground-state Na were calculated near the 2s 2 2p 5 3s and 2s2p 6 3s inner-shell thresholds; also, the photoionization cross sections of excited 3p 2 P o and 3d 2 D states were calculated with the R-matrix methodology near the 2s2p 6 3s thresholds. A numerical approach was developed to calculate the charge transfer matrix elements for ion-atom(ion) collisions; this was used for the proton-hydrogen collision problem as an illustration

  14. Molecular landscape of the interaction between the urease accessory proteins UreE and UreG.

    Science.gov (United States)

    Merloni, Anna; Dobrovolska, Olena; Zambelli, Barbara; Agostini, Federico; Bazzani, Micaela; Musiani, Francesco; Ciurli, Stefano

    2014-09-01

    Urease, the most efficient enzyme so far discovered, depends on the presence of nickel ions in the catalytic site for its activity. The transformation of inactive apo-urease into active holo-urease requires the insertion of two Ni(II) ions in the substrate binding site, a process that involves the interaction of four accessory proteins named UreD, UreF, UreG and UreE. This study, carried out using calorimetric and NMR-based structural analysis, is focused on the interaction between UreE and UreG from Sporosarcina pasteurii, a highly ureolytic bacterium. Isothermal calorimetric protein-protein titrations revealed the occurrence of a binding event between SpUreE and SpUreG, entailing two independent steps with positive cooperativity (Kd1=42±9μM; Kd2=1.7±0.3μM). This was interpreted as indicating the formation of the (UreE)2(UreG)2 hetero-oligomer upon binding of two UreG monomers onto the pre-formed UreE dimer. The molecular details of this interaction were elucidated using high-resolution NMR spectroscopy. The occurrence of SpUreE chemical shift perturbations upon addition of SpUreG was investigated and analyzed to establish the protein-protein interaction site. The latter appears to involve the Ni(II) binding site as well as mobile portions on the C-terminal and the N-terminal domains. Docking calculations based on the information obtained from NMR provided a structural basis for the protein-protein contact site. The high sequence and structural similarity within these protein classes suggests a generality of the interaction mode among homologous proteins. The implications of these results on the molecular details of the urease activation process are considered and analyzed. Copyright © 2014 Elsevier B.V. All rights reserved.

  15. Microstructure and molecular interaction in glycerol plasticized chitosan/poly(vinyl alcohol) blending films

    Science.gov (United States)

    Poly (vinyl alcohol) (PVA)/chitosan (CS) blended films plasticized by glycerol were investigated using mechanical testing, atomic force microscopy (AFM), differential scanning calorimetry (DSC) and FTIR spectroscopy, with primary emphasis on the effects of the glycerol content and the molecular weig...

  16. Molecular dynamics study of the influence of wall-gas interactions on heat flow in nanochannels

    NARCIS (Netherlands)

    Markvoort, Albert. J.; Hilbers, P.A.J.; Nedea, S.V.

    2005-01-01

    Especially at the nanometer scale interfaces play an important role. The effect of the wettability on the solid-liquid interface has already been studied with molecular dynamics. In this paper we study the dependence of wetting on the solid-gas interface for different density gases and investigate

  17. Comparative Investigation of Normal Modes and Molecular Dynamics of Hepatitis C NS5B Protein

    International Nuclear Information System (INIS)

    Asafi, M S; Tekpinar, M; Yildirim, A

    2016-01-01

    Understanding dynamics of proteins has many practical implications in terms of finding a cure for many protein related diseases. Normal mode analysis and molecular dynamics methods are widely used physics-based computational methods for investigating dynamics of proteins. In this work, we studied dynamics of Hepatitis C NS5B protein with molecular dynamics and normal mode analysis. Principal components obtained from a 100 nanoseconds molecular dynamics simulation show good overlaps with normal modes calculated with a coarse-grained elastic network model. Coarse-grained normal mode analysis takes at least an order of magnitude shorter time. Encouraged by this good overlaps and short computation times, we analyzed further low frequency normal modes of Hepatitis C NS5B. Motion directions and average spatial fluctuations have been analyzed in detail. Finally, biological implications of these motions in drug design efforts against Hepatitis C infections have been elaborated. (paper)

  18. Molecular investigations of a locally acquired case of melioidosis in Southern AZ, USA.

    Directory of Open Access Journals (Sweden)

    David M Engelthaler

    2011-10-01

    Full Text Available Melioidosis is caused by Burkholderia pseudomallei, a Gram-negative bacillus, primarily found in soils in Southeast Asia and northern Australia. A recent case of melioidosis in non-endemic Arizona was determined to be the result of locally acquired infection, as the patient had no travel history to endemic regions and no previous history of disease. Diagnosis of the case was confirmed through multiple microbiologic and molecular techniques. To enhance the epidemiological analysis, we conducted several molecular genotyping procedures, including multi-locus sequence typing, SNP-profiling, and whole genome sequence typing. Each technique has different molecular epidemiologic advantages, all of which provided evidence that the infecting strain was most similar to those found in Southeast Asia, possibly originating in, or around, Malaysia. Advancements in new typing technologies provide genotyping resolution not previously available to public health investigators, allowing for more accurate source identification.

  19. Towards a molecular level understanding of the sulfanilamide-soil organic matter-interaction

    Energy Technology Data Exchange (ETDEWEB)

    Ahmed, Ashour A., E-mail: ashour.ahmed@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany); Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Cairo, Faculty of Science, Department of Chemistry, 12613 Giza (Egypt); Thiele-Bruhn, Sören, E-mail: thiele@uni-trier.de [University of Trier, Soil Science, D-54286 Trier (Germany); Leinweber, Peter, E-mail: peter.leinweber@uni-rostock.de [Steinbeis GmbH & Co. KG für Technologietransfer, 70174 Stuttgart (Germany); University of Rostock, Soil Science, D-18051 Rostock (Germany); Kühn, Oliver, E-mail: oliver.kuehn@uni-rostock.de [University of Rostock, Institute of Physics, Albert-Einstein-Str. 23-24, D-18059 Rostock (Germany)

    2016-07-15

    Sorption experiments of sulfanilamide (SAA) on well-characterized samples of soil size-fractions were combined with the modeling of SAA-soil-interaction via quantum chemical calculations. Freundlich unit capacities were determined in batch experiments and it was found that they increase with the soil organic matter (SOM) content according to the order fine silt > medium silt > clay > whole soil > coarse silt > sand. The calculated binding energies for mass-spectrometrically quantified sorption sites followed the order ionic species > peptides > carbohydrates > phenols and lignin monomers > lignin dimers > heterocyclic compounds > fatty acids > sterols > aromatic compounds > lipids, alkanes, and alkenes. SAA forms H-bonds through its polar centers with the polar SOM sorption sites. In contrast dispersion and π-π-interactions predominate the interaction of the SAA aromatic ring with the non-polar moieties of SOM. Moreover, the dipole moment, partial atomic charges, and molecular volume of the SOM sorption sites are the main physical properties controlling the SAA-SOM-interaction. Further, reasonable estimates of the Freundlich unit capacities from the calculated binding energies have been established. Consequently, we suggest using this approach in forthcoming studies to disclose the interactions of a wide range of organic pollutants with SOM. - Highlights: • Experiment and theory showed that SAA obeys a site-specific sorption on soil surfaces. • SAA-SOM-interaction increases by increasing polarity of SOM sorption site. • H-bonds, dispersion, and π-π-interactions were observed for SAA-SOM-interaction. • Dipole moment and atomic charges of SOM sorption sites control SAA-SOM-interaction. • The Freundlich unit capacities were estimated from the calculated binding energies. • The current SOM model is flexible to describe interactions of SOM with other pollutants.

  20. A molecular dynamics investigation into the mechanisms of alectinib resistance of three ALK mutants.

    Science.gov (United States)

    He, Muyang; Li, Weikang; Zheng, Qingchuan; Zhang, Hongxing

    2018-01-11

    Alectinib, a highly selective next-genetation anaplastic lymphoma kinase (ALK) inhibitor, has demonstrated promising antitumor activity in patients with ALK-positive non-small cell lung carcinomas (NSCLC). However, the therapeutic benefits of alectinib is inescapably hampered by the development of acquired resistant mutations in ALK. Despite the availability of ample experimental mutagenesis data, the molecular origin and the structural motifs under alectinib binding affinity deficiencies are still ambiguous. Here, molecular dynamics (MD) simulations and molecular mechanics generalized born surface area (MM-GBSA) calculation approaches were employed to elucidate the mechanisms of alectinib resistance induced by the mutations I1171N, V1180L, and L1198F. The MD results reveal that the studied mutations could trigger the dislocation of alectinib as well as conformational changes at the inhibitor binding site, thus induce the interactional changes between alectinib and mutants. The most influenced regions are the ligand binding entrance and the hinge region, which are considered to be the dominant binding motifs accounting for the binding affinity loss in mutants. The "key and lock mechanism" between the ethyl group at position 9 of alectinib and a recognition cavity in the hinge region of ALK is presented to illustrate the major molecular origin of drug resistance. Our results provide mechanistic insight into the effect of ALK mutations resistant to alectinib, which could contribute to further rational design of inhibitors to combat the acquired resistance. © 2018 Wiley Periodicals, Inc.

  1. Interaction of the minocycline with extracelluar protein and intracellular protein by multi-spectral techniques and molecular docking

    Science.gov (United States)

    Fang, Qing; Wang, Yirun; Hu, Taoying; Liu, Ying

    2017-02-01

    The interaction of minocyeline (MNC) with extracelluar protein (lysozyme, LYSO) or intracellular protein (bovine hemoglobin, BHb) was investigated using multi-spectral techniques and molecular docking in vitro. Fluorescence studies suggested that MNC quenched LYSO/BHb fluorescence in a static mode with binding constants of 2.01 and 0.26 × 104 L•mol-1 at 298 K, respectively. The LYZO-MNC system was more easily influenced by temperature (298 and 310 K) than the BHb-MNC system. The thermodynamic parameters demonstrated that hydrogen bonds and van der Waals forces played the major role in the binding process. Based on the Förster theory of nonradiative energy transfer, the binding distances between MNC and the inner tryptophan residues of LYSO and BHb were calculated to be 4.34 and 3.49 nm, respectively. Furthermore, circular dichroism spectra (CD), Fourier transforms infrared (FTIR), UV-vis, and three-dimensional fluorescence spectra results indicated the secondary structures of LYSO and BHb were partially destroyed by MNC with the α-helix percentage of LYZO-MNC increased (17.8-28.6%) while that of BHb-MNC was decreased (41.6-39.6%). UV-vis spectral results showed these binding interactions could cause conformational and some micro-environmental changes of LYSO and BHb. In accordance with the results of molecular docking, In LYZO-MNC system, MNC was mainly bound in the active site hinge region where Trp-62 and Trp-63 are located, and in MNC-BHb system, MNC was close to the subunit α 1 of BHb, molecular docking analysis supported the thermodynamic results well. The work contributes to clarify the mechanism of MNC with two proteins at molecular level.

  2. Spectroscopic analysis of 8-hydroxyquinoline derivatives and investigation of its reactive properties by DFT and molecular dynamics simulations

    Science.gov (United States)

    Sureshkumar, B.; Mary, Y. Sheena; Resmi, K. S.; Panicker, C. Yohannan; Armaković, Stevan; Armaković, Sanja J.; Van Alsenoy, C.; Narayana, B.; Suma, S.

    2018-03-01

    Two 8-hydroxyquinoline derivatives, 5,7-dichloro-8-hydroxyquinoline (57DC8HQ) and 5-chloro-7-iodo-8-hydroxy quinoline (5CL7I8HQ) have been investigated in details by means of spectroscopic characterization and computational molecular modelling techniques. FT-IR and FT-Raman experimental spectroscopic approaches have been utilized in order to obtain detailed spectroscopic signatures of title compounds, while DFT calculations have been used in order to visualize and assign vibrations. The computed values of dipole moment, polarizability and hyperpolarizability indicate that the title molecules exhibit NLO properties. The evaluated HOMO and LUMO energies demonstrate the chemical stability of the molecules. NBO analysis is made to study the stability of the molecules arising from hyperconjugative interactions and charge delocalization. DFT calculations have been also used jointly with MD simulations in order to investigate in details global and local reactivity properties of title compounds. Also, molecular docking has been also used in order to investigate affinity of title compounds against decarboxylase inhibitor and quinoline derivatives can be a lead compounds for developing new antiparkinsonian drug.

  3. Molecular interactions between tomato and the leaf mold pathogen Cladosporium fulvum.

    Science.gov (United States)

    Rivas, Susana; Thomas, Colwyn M

    2005-01-01

    The interaction between tomato and the leaf mold pathogen Cladosporium fulvum is controlled in a gene-for-gene manner. This interaction has provided useful insights to the molecular basis of recognition specificity in plant disease resistance (R) proteins, disease resistance (R) gene evolution, R-protein mediated signaling, and cellular responses to pathogen attack. Tomato Cf genes encode type I membrane-associated receptor-like proteins (RLPs) comprised predominantly of extracellular leucine-rich repeats (eLRRs) and which are anchored in the plasma membrane. Cf proteins recognize fungal avirulence (Avr) peptides secreted into the leaf apoplast during infection. A direct interaction of Cf proteins with their cognate Avr proteins has not been demonstrated and the molecular mechanism of Avr protein perception is not known. Following ligand perception Cf proteins trigger a hypersensitive response (HR) and the arrest of pathogen development. Cf proteins lack an obvious signaling domain, suggesting that defense response activation is mediated through interactions with other partners. Avr protein perception results in the rapid accumulation of active oxygen species (AOS), changes in cellular ion fluxes, activation of protein kinase cascades, changes in gene expression and, possibly, targeted protein degradation. Here we review our current understanding of Cf-mediated responses in resistance to C. fulvum.

  4. AFD: an application for bi-molecular interaction using axial frequency distribution.

    Science.gov (United States)

    Raza, Saad; Azam, Syed Sikander

    2018-03-06

    Conformational flexibility and generalized structural features are responsible for specific phenomena existing in biological pathways. With advancements in computational chemistry, novel approaches and new methods are required to compare the dynamic nature of biomolecules, which are crucial not only to address dynamic functional relationships but also to gain detailed insights into the disturbance and positional fluctuation responsible for functional shifts. Keeping this in mind, axial frequency distribution (AFD) has been developed, designed, and implemented. AFD can profoundly represent distribution and density of ligand atom around a particular atom or set of atoms. It enabled us to obtain an explanation of local movements and rotations, which are not significantly highlighted by any other structural and dynamical parameters. AFD can be implemented on biological models representing ligand and protein interactions. It shows a comprehensive view of the binding pattern of ligand by exploring the distribution of atoms relative to the x-y plane of the system. By taking a relative centroid on protein or ligand, molecular interactions like hydrogen bonds, van der Waals, polar or ionic interaction can be analyzed to cater the ligand movement, stabilization or flexibility with respect to the protein. The AFD graph resulted in the residual depiction of bi-molecular interaction in gradient form which can yield specific information depending upon the system of interest.

  5. Investigation of the molecular conformations of ethanol using electron momentum spectroscopy

    International Nuclear Information System (INIS)

    Ning, C G; Luo, Z H; Huang, Y R; Liu, K; Zhang, S F; Deng, J K; Hajgato, B; Morini, F; Deleuze, M S

    2008-01-01

    The valence electronic structure and momentum-space electron density distributions of ethanol have been investigated with our newly constructed high-resolution electron momentum spectrometer. The measurements are compared to thermally averaged simulations based on Kohn-Sham (B3LYP) orbital densities as well as one-particle Green's function calculations of ionization spectra and Dyson orbital densities, assuming Boltzmann's statistical distribution of the molecular structure over the two energy minima defining the anti and gauche conformers. One-electron ionization energies and momentum distributions in the outer-valence region were found to be highly dependent upon the molecular conformation. Calculated momentum distributions indeed very sensitively reflect the distortions and topological changes that molecular orbitals undergo due to the internal rotation of the hydroxyl group, and thereby exhibit variations which can be traced experimentally. The B3LYP model Kohn-Sham orbital densities are overall in good agreement with the experimental distributions, and closely resemble benchmark ADC(3) Dyson orbital densities. Both approaches fail to quantitatively reproduce the experimental momentum distributions characterizing the highest occupied molecular orbital. Since electron momentum spectroscopy measurements at various electron impact energies indicate that the plane wave impulse approximation is valid, this discrepancy between theory and experiment is tentatively ascribed to thermal disorder, i.e. large-amplitude and thermally induced dynamical distortions of the molecular structure in the gas phase

  6. Separation and characterization of resins and asphaltenes coming from Castilla crude Evaluation of their molecular interaction

    International Nuclear Information System (INIS)

    Navarro, Lina; Alvarez, Mario; Grosso, Jorge Luis; Navarro, Uriel

    2004-01-01

    The study of resins and asphaltenes, the heaviest fractions of oil, has become an area of interest due to the abundance of heavy crude oils in Colombia and Latin America. We studied the chemical composition of the heavy fractions of Castilla crude oil, evaluated some of its molecular parameters and found evidence of the interaction between the resins extracted from the crude with the asphaltenes of the original crude. With this objective, we carried out at the pilot plant level precipitation of the resin-asphaltene (R-A) aggregate by adding and mixing under controlled conditions, a paraffin solvent, from the Apiay refinery, called Apiasol. By extracting Soxhlet with the same solvent, resin 1 of aggregate R-A was separated. Resin ll defined as the soluble fraction that is part of the maltenes, was separated from the deasphalted crude by open column chromatography, using alumina as support, according to the SAR method (Saturated, Aromatics, Resins). The fractions of resins and the asphaltenes obtained, were characterized by: Nuclear Magnetic Resonance (NMR), FT-lR, DRX, elementary analysis (C, H, N, S), metal content (Ni and V), distribution of molecular weight by GPC, and average molecular weight by VPO. The results obtained show evidence that resin l which is part of the aggregate has less average molecular weight than resin ll which is present in the fraction of maltenes. In addition, some changes were found in the elementary analysis of among the resins. On the one hand, and taking into account the existing theories of molecular interactions among these fractions, it was found that the resins l separated from the R-A aggregate, when added to the crude, they stabilize their asphaltenes. This evaluation was carried out by analyzing the flocculation point of the crude and its mixtures with 1,9% and 3,8% of resin l, when they are titrated with a precipitating agent in an NIR cell that works with high pressure and temperature

  7. Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

    Directory of Open Access Journals (Sweden)

    Cusick Michael E

    2007-10-01

    Full Text Available Abstract Background Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. Results The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. Conclusion The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel.

  8. Investigating hadronic resonances in pp interactions with HADES

    Directory of Open Access Journals (Sweden)

    Przygoda Witold

    2015-01-01

    Full Text Available In this paper we report on the investigation of baryonic resonance production in proton-proton collisions at the kinetic energies of 1.25 GeV and 3.5 GeV, based on data measured with HADES. Exclusive channels npπ+ and ppπ0 as well as ppe+e− were studied simultaneously in the framework of a one-boson exchange model. The resonance cross sections were determined from the one-pion channels for Δ(1232 and N(1440 (1.25 GeV as well as further Δ and N* resonances up to 2 GeV/c2 for the 3.5 GeV data. The data at 1.25 GeV energy were also analysed within the framework of the partial wave analysis together with the set of several other measurements at lower energies. The obtained solutions provided the evolution of resonance production with the beam energy, showing a sizeable non-resonant contribution but with still dominating contribution of Δ(1232P33. In the case of 3.5 GeV data, the study of the ppe+e− channel gave the insight on the Dalitz decays of the baryon resonances and, in particular, on the electromagnetic transition form-factors in the time-like region. We show that the assumption of a constant electromagnetic transition form-factors leads to underestimation of the yield in the dielectron invariant mass spectrum below the vector mesons pole. On the other hand, a comparison with various transport models shows the important role of intermediate ρ production, though with a large model dependency. The exclusive channels analysis done by the HADES collaboration provides new stringent restrictions on the parameterizations used in the models.

  9. Molecular Interaction Study of some ortho and para Substituted Anilines with 1-Octanol

    Directory of Open Access Journals (Sweden)

    M. S. Manjunatha

    2010-01-01

    Full Text Available Interactions between ortho and para substituents of anilines such as chloroaniline, methylaniline and methoxyaniline with 1-octanol have been studied in carbon tetrachloride. The most likely association of complex between 1-octanol and substituents of anilines is 1:1 stoichiometric complex, through hydroxyl group of 1-octanol and amine group of ortho and para substituents of anilines. Interactions are studied on the bases of formation constant and free energy changes. Formation constant of the complex has been calculated using Nash method. The result shows that molecular interaction of 1-octanol as proton donor with methyl and chloride substitution of anilines in ortho position is smaller than the para position substitution of anilines. The results shows, the ability of acceptors is in the order p-methoxyaniline < o-chloroaniline

  10. Thermodynamical analyses of molecular simulations of dislocation-defect interactions: simulations at 0 K

    International Nuclear Information System (INIS)

    Monnet, G.

    2008-01-01

    Full text of publication follows. Static molecular (SM) simulations of dislocation-defect interaction are analysed through a framework of different interaction regimes, in which the applied work has different roles. In most regimes, the applied work is transformed into elastic energy, a dissipative energy resulting from the lattice friction and a large quantity of energy needed to enable the dislocation to bow out when it is pinned by the defect. While the dissipative work is entirely evacuated in SM simulations, the elastic and curvature energies contribute to a large increase of the internal energy of the system. A method is presented in this work to evaluate the curvature energy and the result is compared to prediction of the line tension model. These analyses allow the determination of the dislocation-defect interaction energy. (author)

  11. Investigation of interactions between dendrimer-coated magnetite nanoparticles and bovine serum albumin

    International Nuclear Information System (INIS)

    Pan Bifeng; Gao Feng; Ao Limei

    2005-01-01

    We investigated the interactions between dendrimer-coated magnetite nanoparticles (MNPs) and the protein serum albumin. The investigation was based on the fluorescence quenching of tryptophan residue of serum albumin after binding with the dendrimer-coated magnetite nanoparticles. The extent of the interactions between bovine serum albumin and dendrimer-coated MNPs strongly depends on their surface groups and pH value

  12. Synthesis, vibrational spectroscopic investigations, molecular docking, antibacterial studies and molecular dynamics study of 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole

    Science.gov (United States)

    Sheena Mary, Y.; Al-Shehri, Mona M.; Jalaja, K.; Al-Omary, Fatmah A. M.; El-Emam, Ali A.; Yohannan Panicker, C.; Armaković, Stevan; Armaković, Sanja J.; Temiz-Arpaci, Ozlem; Van Alsenoy, C.

    2017-04-01

    Antimicrobial active 5-[(4-nitrophenyl)acetamido]-2-(4-tert-butylphenyl)benzoxazole (NATPB) was synthesized and observed IR, Raman bands are compared with the theoretically predicted wave numbers. In the IR spectrum the NH stretching wave number splits into a doublet with a noted difference and is red shifted from the computed value, which indicates the weakening of NH bond resulting in proton transfer to the neighbouring oxygen atom. The HOMO-LUMO plots reveal the charge transfer in the molecular system through the conjugated paths. The electrophilic and nucleophilic reactive sites are identified from the MEP plot. Mapping of average local ionization energy (ALIE) values to the electron density surface served us as a tool for prediction of molecule sites possibly prone to electrophilic attacks. Other important reactive centres of the title molecule were detected by calculations of Fukui functions. Calculations of bond dissociation energies (BDE) for hydrogen abstraction were used in order to assess whether the NATPB molecules is prone to autoxidation mechanism or not, while BDE of the remaining single acyclic bonds were used in order to determine the weakest bond. Interaction properties with water were investigated by molecular dynamics (MD) simulations and calculations of radial distribution functions (RDFs). The compound possessed broad spectrum activity against all of the tested Gram-positive and Gram-negative bacteria and yeasts, their minimum inhibitory concentrations (MICs) ranging between 32 and 128 μg/ml. The compound exhibited significant antibacterial activity (32 μg/ml) against an antibiotic resistant E. faecalis isolate, at same potency with the compared standard drugs vancomycin and gentamycin sulfate. The molecular docking studies show that the compound might exhibit inhibitory activity against CDK inhibitors.

  13. The Molecular Basis of Polyunsaturated Fatty Acid Interactions with the Shaker Voltage-Gated Potassium Channel.

    Directory of Open Access Journals (Sweden)

    Samira Yazdi

    2016-01-01

    Full Text Available Voltage-gated potassium (KV channels are membrane proteins that respond to changes in membrane potential by enabling K+ ion flux across the membrane. Polyunsaturated fatty acids (PUFAs induce channel opening by modulating the voltage-sensitivity, which can provide effective treatment against refractory epilepsy by means of a ketogenic diet. While PUFAs have been reported to influence the gating mechanism by electrostatic interactions to the voltage-sensor domain (VSD, the exact PUFA-protein interactions are still elusive. In this study, we report on the interactions between the Shaker KV channel in open and closed states and a PUFA-enriched lipid bilayer using microsecond molecular dynamics simulations. We determined a putative PUFA binding site in the open state of the channel located at the protein-lipid interface in the vicinity of the extracellular halves of the S3 and S4 helices of the VSD. In particular, the lipophilic PUFA tail covered a wide range of non-specific hydrophobic interactions in the hydrophobic central core of the protein-lipid interface, while the carboxylic head group displayed more specific interactions to polar/charged residues at the extracellular regions of the S3 and S4 helices, encompassing the S3-S4 linker. Moreover, by studying the interactions between saturated fatty acids (SFA and the Shaker KV channel, our study confirmed an increased conformational flexibility in the polyunsaturated carbon tails compared to saturated carbon chains, which may explain the specificity of PUFA action on channel proteins.

  14. MOLECULAR DYNAMICS STUDY OF INTERACTIONS OF POLYMYXIN B3 AND ITS ALA-MUTANTS WITH LIPOPOLYSACCHARIDE

    Directory of Open Access Journals (Sweden)

    Lisnyak Yu. V.

    2015-12-01

    Full Text Available Introduction. Emergence of nosocomial bacterial pathogens (especially Gram-negative bacteria with multiple resistance against almost all available antibiotics is a growing medical problem. No novel drugs targeting multidrug-resistant Gram-negative bacteria have been developed in recent years. In this context, there has been greatly renewed interest to cyclic lipodecapeptides polymyxins. Polymyxins exhibit rapid bactericidal activity, they are specific and highly potent against Gramnegative bacteria, but have potential nephrotoxic side effects. So polymyxins are attractive lead compounds to develop analogues with improved microbiological, pharmacological and toxicological properties. A detailed knowledge of the molecular mechanisms of polymyxin interactions with its cell targets is a prerequisite for the purposeful improvement of its therapeutic properties. The primary cell target of a polymyxin is a lipopolysaccharide (LPS in the outer membrane of Gram-negative bacteria. The binding site of polymyxin on LPS has been supposed to be Kdo2-lipid A fragment. Methods. For all molecular modeling and molecular dynamics simulation experiments the YASARA suite of programs was used. Complex of antimicrobial peptide polymyxin В3 (PmB3 with Kdo2-lipid A portion of E. coli lipopolysaccharide was constructed by rigid docking with flexible side chains of the peptide. By alanine scanning of polymyxin В3 bound to LPS followed by simulated annealing minimization of the complexes in explicit water environment, the molecular aspects of PmB3-LPS binding have been studied by 20 ns molecular dynamics simulations at 298 K and pH 7.0. The AMBER03 force field was used with a 1.05 nm force cutoff. To treat long range electrostatic interactions the Particle Mesh Ewald algorithm was used. Results. Ala-mutations of polymyxin’s residues Dab1, Dab3, Dab5, Dab8 and Dab9 in the PmB3-LPS complex caused sustained structural changes resulting in the notable loss in stability of

  15. Properties of Energy Spectra of Molecular Crystals Investigated by Nonlinear Theory

    Science.gov (United States)

    Pang, Xiao-Feng; Zhang, Huai-Wu

    We calculate the quantum energy spectra of molecular crystals, such as acetanilide, by using discrete nonlinear Schrodinger equation, containing various interactions, appropriate to the systems. The energy spectra consist of many energy bands, in each energy band there are a lot of energy levels including some higher excited states. The result of energy spectrum is basically consistent with experimental values obtained by infrared absorption and Raman scattering in acetanilide and can also explain some experimental results obtained by Careri et al. Finally, we further discuss the influences of variously characteristic parameters on the energy spectra of the systems.

  16. Investigation of the heparin-thrombin interaction by dynamic force spectroscopy.

    Science.gov (United States)

    Wang, Congzhou; Jin, Yingzi; Desai, Umesh R; Yadavalli, Vamsi K

    2015-06-01

    The interaction between heparin and thrombin is a vital step in the blood (anti)coagulation process. Unraveling the molecular basis of the interactions is therefore extremely important in understanding the mechanisms of this complex biological process. In this study, we use a combination of an efficient thiolation chemistry of heparin, a self-assembled monolayer-based single molecule platform, and a dynamic force spectroscopy to provide new insights into the heparin-thrombin interaction from an energy viewpoint at the molecular scale. Well-separated single molecules of heparin covalently attached to mixed self-assembled monolayers are demonstrated, whereby interaction forces with thrombin can be measured via atomic force microscopy-based spectroscopy. Further these interactions are studied at different loading rates and salt concentrations to directly obtain kinetic parameters. An increase in the loading rate shows a higher interaction force between the heparin and thrombin, which can be directly linked to the kinetic dissociation rate constant (koff). The stability of the heparin/thrombin complex decreased with increasing NaCl concentration such that the off-rate was found to be driven primarily by non-ionic forces. These results contribute to understanding the role of specific and nonspecific forces that drive heparin-thrombin interactions under applied force or flow conditions. Copyright © 2015 Elsevier B.V. All rights reserved.

  17. Exploring molecular and spin interactions of Tellurium adatom in reduced graphene oxide

    Energy Technology Data Exchange (ETDEWEB)

    Alegaonkar, Ashwini [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India); Alegaonkar, Prashant [Department of Applied Physics, Defence Institute of Advance Technology, Girinagar, Pune, 411 025, MS (India); Pardeshi, Satish, E-mail: skpar@chem.unipune.ac.in [Department of Chemistry, Savitribai Phule Pune University (Formerly University of Pune), Ganeshkhind, Pune, 411 007, MS (India)

    2017-07-01

    The transport of spin information fundamentally requires favourable molecular architecture and tunable spin moments to make the medium pertinent for spintronic. We report on achieving coherent molecular-spin parameters for rGO due to Tellurium (Te) adatom. Initially, GO prepared using graphite, was modified into rGO by in situ incorporation of 1 (w/w)% of Te. Both the systems were subjected to ESCA, FTIR, Raman dispersion, ESR spectroscopy, and electron microscopy. Analysis revealed that, Te substantially reacted with epoxides, carbonyl, and carboxylate groups that improved C-to-O ratio by twice. However, the spin splitting character, between Te and C, seems to be quenched. Moreover, Te altered the dynamical force constant between C-C and C=C that generated the mechanical stress within rGO network. The layer conjugation, nature of folding, symmetry, and electronic states of the edges were also affected by precipitation and entrapment of Te. The calculated dynamic molecular Raman and ESR spin parameters indicated that, Te acted as a bridging element for long range spin transport. This is particularly due to, the p-orbital moments of Te contributing, vectorially, to spin relaxation process operative at broken inversion symmetry sites. Our study suggests that, facile addition of Te in rGO is useful to achieve favourable spintronic properties. - Highlights: • Spin interactions and molecular dynamics modification due to Tellurium adatom in rGO. • Molecular level manipulation of Tellurium adatom for favourable spintronic properties. • Bychocov-Rashaba coupling are the operative channels in rGO. • Extrinsic coupling component get added vectorially by Tellurium. • Te-rGO is a viable medium for molecular spintronics.

  18. Interactions of Borneol with DPPC Phospholipid Membranes: A Molecular Dynamics Simulation Study

    Directory of Open Access Journals (Sweden)

    Qianqian Yin

    2014-11-01

    Full Text Available Borneol, known as a “guide” drug in traditional Chinese medicine, is widely used as a natural penetration enhancer in modern clinical applications. Despite a large number of experimental studies on borneol’s penetration enhancing effect, the molecular basis of its action on bio-membranes is still unclear. We carried out a series of coarse-grained molecular dynamics simulations with the borneol concentration ranging from 3.31% to 54.59% (v/v, lipid-free basis to study the interactions of borneol with aDPPC(1,2-dipalmitoylsn-glycero-3-phosphatidylcholine bilayer membrane, and the temperature effects were also considered. At concentrations below 21.89%, borneol’s presence only caused DPPC bilayer thinning and an increase in fluidity; A rise in temperature could promote the diffusing progress of borneol. When the concentration was 21.89% or above, inverted micelle-like structures were formed within the bilayer interior, which led to increased bilayer thickness, and an optimum temperature was found for the interaction of borneol with the DPPC bilayer membrane. These findings revealed that the choice of optimal concentration and temperature is critical for a given application in which borneol is used as a penetration enhancer. Our results not only clarify some molecular basis for borneol’s penetration enhancing effects, but also provide some guidance for the development and applications of new preparations containing borneol.

  19. Modeling the intermolecular interactions: molecular structure of N-3-hydroxyphenyl-4-methoxybenzamide.

    Science.gov (United States)

    Karabulut, Sedat; Namli, Hilmi; Kurtaran, Raif; Yildirim, Leyla Tatar; Leszczynski, Jerzy

    2014-03-01

    The title compound, N-3-hydroxyphenyl-4-methoxybenzamide (3) was prepared by the acylation reaction of 3-aminophenol (1) and 4-metoxybenzoylchloride (2) in THF and characterized by ¹H NMR, ¹³C NMR and elemental analysis. Molecular structure of the crystal was determined by single crystal X-ray diffraction and DFT calculations. 3 crystallizes in monoclinic P2₁/c space group. The influence of intermolecular interactions (dimerization and crystal packing) on molecular geometry has been evaluated by calculations performed for three different models; monomer (3), dimer (4) and dimer with added unit cell contacts (5). Molecular structure of 3, 4 and 5 was optimized by applying B3LYP method with 6-31G+(d,p) basis set in gas phase and compared with X-ray crystallographic data including bond lengths, bond angles and selected dihedral angles. It has been concluded that although the crystal packing and dimerization have a minor effect on bond lengths and angles, however, these interactions are important for the dihedral angles and the rotational conformation of aromatic rings. Copyright © 2013 Elsevier Inc. All rights reserved.

  20. Pressure Enhancement in Confined Fluids: Effect of Molecular Shape and Fluid-Wall Interactions.

    Science.gov (United States)

    Srivastava, Deepti; Santiso, Erik E; Gubbins, Keith E

    2017-10-24

    Recently, several experimental and simulation studies have found that phenomena that normally occur at extremely high pressures in a bulk phase can occur in nanophases confined within porous materials at much lower bulk phase pressures, thus providing an alternative route to study high-pressure phenomena. In this work, we examine the effect on the tangential pressure of varying the molecular shape, strength of the fluid-wall interactions, and pore width, for carbon slit-shaped pores. We find that, for multisite molecules, the presence of additional rotational degrees of freedom leads to unique changes in the shape of the tangential pressure profile, especially in larger pores. We show that, due to the direct relationship between the molecular density and the fluid-wall interactions, the latter have a large impact on the pressure tensor. The molecular shape and pore size have a notable impact on the layering of molecules in the pore, greatly influencing both the shape and scale of the tangential pressure profile.

  1. Molecular identification of blow flies recovered from human cadavers during crime scene investigations in Malaysia.

    Science.gov (United States)

    Kavitha, Rajagopal; Nazni, Wasi Ahmad; Tan, Tian Chye; Lee, Han Lim; Isa, Mohd Noor Mat; Azirun, Mohd Sofian

    2012-12-01

    Forensic entomology applies knowledge about insects associated with decedent in crime scene investigation. It is possible to calculate a minimum postmortem interval (PMI) by determining the age and species of the oldest blow fly larvae feeding on decedent. This study was conducted in Malaysia to identify maggot specimens collected during crime scene investigations. The usefulness of the molecular and morphological approach in species identifications was evaluated in 10 morphologically identified blow fly larvae sampled from 10 different crime scenes in Malaysia. The molecular identification method involved the sequencing of a total length of 2.2 kilo base pairs encompassing the 'barcode' fragments of the mitochondrial cytochrome oxidase I (COI), cytochrome oxidase II (COII) and t-RNA leucine genes. Phylogenetic analyses confirmed the presence of Chrysomya megacephala, Chrysomya rufifacies and Chrysomya nigripes. In addition, one unidentified blow fly species was found based on phylogenetic tree analysis.

  2. Molecular Dynamics Investigation of Cl− and Water Transport through a Eukaryotic CLC Transporter

    OpenAIRE

    Cheng, Mary Hongying; Coalson, Rob D.

    2012-01-01

    Early crystal structures of prokaryotic CLC proteins identified three Cl– binding sites: internal (Sint), central (Scen), and external (Sext). A conserved external GLU (GLUex) residue acts as a gate competing for Sext. Recently, the first crystal structure of a eukaryotic transporter, CmCLC, revealed that in this transporter GLUex competes instead for Scen. Here, we use molecular dynamics simulations to investigate Cl– transport through CmCLC. The gating and Cl–/H+ transport cycle are inferre...

  3. Molecular and Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017)

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-14-1-0399 TITLE: Molecular & Genetic Investigation of Tau in Chronic Traumatic Encephalopathy (Log No. 13267017) PRINCIPAL...this collection of information is estimated to average 1 hour per response, including the time for reviewing instructions, searching existing data ...sources, gathering and maintaining the data needed, and completing and reviewing the collection of information. Send comments regarding this burden

  4. Analytical and molecular dynamical investigations of the influence of molecular vibrations upon the (e,2e) electron momentum distributions of furan

    International Nuclear Information System (INIS)

    Morini, F; Deleuze, M S; Watanabe, N; Takahashi, M

    2015-01-01

    The role of molecular vibrations has been theoretically investigated in the electronic ground state on the (e, 2e) valence orbital momentum profiles of furan by means of two complementary approaches. The first one relies upon the principles of Born-Oppenheimer Molecular Dynamics (BOMD), whereas the second one, referred as Harmonic Analytical Quantum Mechanical (HAQM) approach, includes on quantum-mechanical (paper)

  5. Density-Dependent Formulation of Dispersion-Repulsion Interactions in Hybrid Multiscale Quantum/Molecular Mechanics (QM/MM) Models.

    Science.gov (United States)

    Curutchet, Carles; Cupellini, Lorenzo; Kongsted, Jacob; Corni, Stefano; Frediani, Luca; Steindal, Arnfinn Hykkerud; Guido, Ciro A; Scalmani, Giovanni; Mennucci, Benedetta

    2018-03-13

    Mixed multiscale quantum/molecular mechanics (QM/MM) models are widely used to explore the structure, reactivity, and electronic properties of complex chemical systems. Whereas such models typically include electrostatics and potentially polarization in so-called electrostatic and polarizable embedding approaches, respectively, nonelectrostatic dispersion and repulsion interactions are instead commonly described through classical potentials despite their quantum mechanical origin. Here we present an extension of the Tkatchenko-Scheffler semiempirical van der Waals (vdW TS ) scheme aimed at describing dispersion and repulsion interactions between quantum and classical regions within a QM/MM polarizable embedding framework. Starting from the vdW TS expression, we define a dispersion and a repulsion term, both of them density-dependent and consistently based on a Lennard-Jones-like potential. We explore transferable atom type-based parametrization strategies for the MM parameters, based on either vdW TS calculations performed on isolated fragments or on a direct estimation of the parameters from atomic polarizabilities taken from a polarizable force field. We investigate the performance of the implementation by computing self-consistent interaction energies for the S22 benchmark set, designed to represent typical noncovalent interactions in biological systems, in both equilibrium and out-of-equilibrium geometries. Overall, our results suggest that the present implementation is a promising strategy to include dispersion and repulsion in multiscale QM/MM models incorporating their explicit dependence on the electronic density.

  6. Characterizing the binding interaction between antimalarial artemether (AMT) and bovine serum albumin (BSA): Spectroscopic and molecular docking methods.

    Science.gov (United States)

    Shi, Jie-Hua; Pan, Dong-Qi; Wang, Xiou-Xiou; Liu, Ting-Ting; Jiang, Min; Wang, Qi

    2016-09-01

    Artemether (AMT), a peroxide sesquiterpenoides, has been widely used as an antimalarial for the treatment of multiple drug-resistant strains of plasmodium falciparum malaria. In this work, the binding interaction of AMT with bovine serum albumin (BSA) under the imitated physiological conditions (pH7.4) was investigated by UV spectroscopy, fluorescence emission spectroscopy, synchronous fluorescence spectroscopy, Fourier transform infrared spectroscopy (FT-IR), circular dichroism (CD), three-dimensional fluorescence spectroscopy and molecular docking methods. The experimental results indicated that there was a change in UV absorption of BSA along with a slight red shift of absorption wavelength, indicating that the interaction of AMT with BSA occurred. The intrinsic fluorescence of BSA was quenched by AMT due to the formation of AMT-BSA complex. The number of binding sites (n) and binding constant of AMT-BSA complex were about 1 and 2.63×10(3)M(-1) at 298K, respectively, suggesting that there was stronger binding interaction of AMT with BSA. Based on the analysis of the signs and magnitudes of the free energy change (ΔG(0)), enthalpic change (ΔH(0)) and entropic change (ΔS(0)) in the binding process, it can be concluded that the binding of AMT with BSA was enthalpy-driven process due to |ΔH°|>|TΔS°|. The results of experiment and molecular docking confirmed the main interaction forces between AMT and BSA were van der Waals force. And, there was a slight change in the BSA conformation after binding AMT but BSA still retains its secondary structure α-helicity. However, it had been confirmed that AMT binds on the interface between sub-domain IIA and IIB of BSA. Copyright © 2016 Elsevier B.V. All rights reserved.

  7. Characterization of interactions of simvastatin, pravastatin, fluvastatin, and pitavastatin with bovine serum albumin: multiple spectroscopic and molecular docking.

    Science.gov (United States)

    Shi, Jie-Hua; Wang, Qi; Pan, Dong-Qi; Liu, Ting-Ting; Jiang, Min

    2017-05-01

    The binding interactions of simvastatin (SIM), pravastatin (PRA), fluvastatin (FLU), and pitavastatin (PIT) with bovine serum albumin (BSA) were investigated for determining the affinity of four statins with BSA through multiple spectroscopic and molecular docking methods. The experimental results showed that SIM, PRA, FLU, and PIT statins quenched the intrinsic fluorescence of BSA through a static quenching process and the stable stains-BSA complexes with the binding constants in the order of 10 4  M -1 at 298 K were formed through intermolecular nonbond interaction. The values of ΔH 0 , ΔS 0 and ΔG 0 in the binding process of SIM, PRA, FLU, and PIT with BSA were negative at the studied temperature range, suggesting that the binding process of four statins and BSA was spontaneous and the main interaction forces were van der Waals force and hydrogen-bonding interactions. Moreover, the binding of four statins with BSA was enthalpy-driven process due to |ΔH°|>|TΔS°| under the studied temperature range. From the results of site marker competitive experiments and molecular docking, subdomain IIIA (site II) was the primary binding site for SIM, PRA, FLU, and PIT on BSA. The results of UV-vis absorption, synchronous fluorescence, 3D fluorescence and FT-IR spectra proved that the slight change in the conformation of BSA, while the significant changes in the conformation of SIM, PRA, FLU, and PIT drug in statin-BSA complexes, indicating that the flexibility of statin molecules plays an important role in increasing the stability of statin-BSA complexes.

  8. 2012 Gordon Research Conference and Seminar on Atomic and Molecular Interactions - Formal Schedule and Speaker/Poster Program

    Energy Technology Data Exchange (ETDEWEB)

    Zwier, Timothy S. [Purdue Univ., West Lafayette, IN (United States)

    2012-07-20

    The Gordon Research Conference on ATOMIC & MOLECULAR INTERACTIONS was held at Stonehill College Easton, Massachusetts, July 15-20, 2012. The Conference was well-attended with 121 participants (attendees list attached). The attendees represented the spectrum of endeavor in this field coming from academia, industry, and government laboratories, both U.S. and foreign scientists, senior researchers, young investigators, and students. Of the 121 attendees, 64 voluntarily responded to a general inquiry regarding ethnicity which appears on our registration forms. Of the 64 respondents, 11% were Minorities – 2% Hispanic, 9% Asian and 0% African American. Approximately 20% of the participants at the 2012 meeting were women. The Gordon Research SEMINAR on ATOMIC & MOLECULAR INTERACTIONS was held at Stonehill College Easton, Mas