Inter-subunit interactions across the upper voltage sensing-pore domain interface contribute to the concerted pore opening transition of Kv channels.

Science.gov (United States)

Shem-Ad, Tzilhav; Irit, Orr; Yifrach, Ofer

2013-01-01

The tight electro-mechanical coupling between the voltage-sensing and pore domains of Kv channels lies at the heart of their fundamental roles in electrical signaling. Structural data have identified two voltage sensor pore inter-domain interaction surfaces, thus providing a framework to explain the molecular basis for the tight coupling of these domains. While the contribution of the intra-subunit lower domain interface to the electro-mechanical coupling that underlies channel opening is relatively well understood, the contribution of the inter-subunit upper interface to channel gating is not yet clear. Relying on energy perturbation and thermodynamic coupling analyses of tandem-dimeric Shaker Kv channels, we show that mutation of upper interface residues from both sides of the voltage sensor-pore domain interface stabilizes the closed channel state. These mutations, however, do not affect slow inactivation gating. We, moreover, find that upper interface residues form a network of state-dependent interactions that stabilize the open channel state. Finally, we note that the observed residue interaction network does not change during slow inactivation gating. The upper voltage sensing-pore interaction surface thus only undergoes conformational rearrangements during channel activation gating. We suggest that inter-subunit interactions across the upper domain interface mediate allosteric communication between channel subunits that contributes to the concerted nature of the late pore opening transition of Kv channels.

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.

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.

Synchronization and Inter-Layer Interactions of Noise-Driven Neural Networks.

Science.gov (United States)

Yuniati, Anis; Mai, Te-Lun; Chen, Chi-Ming

2017-01-01

In this study, we used the Hodgkin-Huxley (HH) model of neurons to investigate the phase diagram of a developing single-layer neural network and that of a network consisting of two weakly coupled neural layers. These networks are noise driven and learn through the spike-timing-dependent plasticity (STDP) or the inverse STDP rules. We described how these networks transited from a non-synchronous background activity state (BAS) to a synchronous firing state (SFS) by varying the network connectivity and the learning efficacy. In particular, we studied the interaction between a SFS layer and a BAS layer, and investigated how synchronous firing dynamics was induced in the BAS layer. We further investigated the effect of the inter-layer interaction on a BAS to SFS repair mechanism by considering three types of neuron positioning (random, grid, and lognormal distributions) and two types of inter-layer connections (random and preferential connections). Among these scenarios, we concluded that the repair mechanism has the largest effect for a network with the lognormal neuron positioning and the preferential inter-layer connections.

Interactions of oxytetracycline with a smectite clay: a spectroscopic study with molecular simulations.

Science.gov (United States)

Aristilde, Ludmilla; Marichal, Claire; Miéhé-Brendlé, Jocelyne; Lanson, Bruno; Charlet, Laurent

2010-10-15

Binding of antibiotics to clay minerals can decrease both their physical and biological availability in soils. To elucidate the binding mechanisms of tetracycline antibiotics on smectite clays as a function of pH, we probed the interactions of oxytetracycline (OTC) with Na-montmorillonite (MONT) using X-ray diffraction (XRD), infrared (IR), and solid-state nuclear magnetic resonance (NMR) spectroscopies, and Monte Carlo molecular simulations. The XRD patterns demonstrate the presence of OTC in the MONT interlayer space at acidic pH whereas complexation of OTC by external basal and edge sites seems to prevail at pH 8. At both pH, the (1)H-(13)C NMR profile indicates restricted mobility of the adsorbed OTC species; and, -CH(3) deformation and C-N stretching IR vibration bands confirm a binding mechanism involving the protonated dimethylamino group of OTC. Changes in the (23)Na NMR environments are consistent with cation-exchange and cation complexation reactions at the different sites of adsorption. Molecular simulations indicate that MONT interlayer spacing and structural charge localization dictate favorable binding conformations of the intercalated OTC, facilitating multiple interactions in agreement with the spectroscopic data. Our results present complementary insights into the mechanisms of adsorption of TETs on smectites important for their retention in natural and engineered soil environments.

Modulation of intra- and inter-sheet interactions in short peptide self-assembly by acetonitrile in aqueous solution

International Nuclear Information System (INIS)

Deng Li; Zhao Yurong; Zhou Peng; Xu Hai; Wang Yanting

2016-01-01

Besides our previous experimental discovery (Zhao Y R, et al . 2015 Langmuir , 31, 12975) that acetonitrile (ACN) can tune the morphological features of nanostructures self-assembled by short peptides KIIIIK (KI4K) in aqueous solution, further experiments reported in this work demonstrate that ACN can also tune the mass of the self-assembled nanostructures. To understand the microscopic mechanism how ACN molecules interfere peptide self-assembly process, we conducted a series of molecular dynamics simulations on a monomer, a cross- β sheet structure, and a proto-fibril of KI4K in pure water, pure ACN, and ACN-water mixtures, respectively. The simulation results indicate that ACN enhances the intra-sheet interaction dominated by the hydrogen bonding (H-bonding) interactions between peptide backbones, but weakens the inter-sheet interaction dominated by the interactions between hydrophobic side chains. Through analyzing the correlations between different groups of solvent and peptides and the solvent behaviors around the proto-fibril, we have found that both the polar and nonpolar groups of ACN play significant roles in causing the opposite effects on intermolecular interactions among peptides. The weaker correlation of the polar group of ACN than water molecule with the peptide backbone enhances H-bonding interactions between peptides in the proto-fibril. The stronger correlation of the nonpolar group of ACN than water molecule with the peptide side chain leads to the accumulation of ACN molecules around the proto-fibril with their hydrophilic groups exposed to water, which in turn allows more water molecules close to the proto-fibril surface and weakens the inter-sheet interactions. The two opposite effects caused by ACN form a microscopic mechanism clearly explaining our experimental observations. (paper)

Role of plasma membrane surface charges in dictating the feasibility of membrane-nanoparticle interactions

Science.gov (United States)

Sinha, Shayandev; Jing, Haoyuan; Sachar, Harnoor Singh; Das, Siddhartha

2017-12-01

Receptor-ligand (R-L) binding mediated interactions between the plasma membrane (PM) and a nanoparticle (NP) require the ligand-functionalized NPs to come to a distance of separation (DOS) of at least dRL (length of the R-L complex) from the receptor-bearing membranes. In this letter, we establish that the membrane surface charges and the surrounding ionic environment dictate whether or not the attainment of such a critical DOS is possible. The negatively charged membrane invariably induces a negative electrostatic potential at the NP surface, repelling the NP from the membrane. This is countered by the attractive influences of the thermal fluctuations and van der Waals (vdw) interactions that drive the NP close to the membrane. For a NP approaching the membrane from a distance, the ratio of the repulsive (electrostatic) and attractive (thermal and vdW) effects balances at a critical NP-membrane DOS of dg,c. For a given set of parameters, there can be two possible values of dg,c, namely, dg,c,1 and dg,c,2 with dg,c,1 ≫ dg,c,2. We establish that any R-L mediated NP-membrane interaction is possible only if dRL > dg,c,1. Therefore, our study proposes a design criterion for engineering ligands for a NP that will ensure the appropriate length of the R-L complex in order to ensure the successful membrane-NP interaction in the presence of a given electrostatic environment. Finally, we discuss the manner in which our theory can help designing ligand-grafted NPs for targeted drug delivery, design biomimetics NPs, and also explain various experimental results.

Graphene Edges Dictate the Morphology of Nanoparticles during Catalytic Channeling

DEFF Research Database (Denmark)

Pizzocchero, Filippo; Vanin, Marco; Kling, Jens

2014-01-01

We perform in-situ transmission electron microscopy (TEM) experiments of silver nanoparticles channeling on mono-, bi-, and few-layer graphene and discover that the interactions in the one-dimensional particle–graphene contact line are sufficiently strong so as to dictate the three-dimensional sh......We perform in-situ transmission electron microscopy (TEM) experiments of silver nanoparticles channeling on mono-, bi-, and few-layer graphene and discover that the interactions in the one-dimensional particle–graphene contact line are sufficiently strong so as to dictate the three......-dimensional shape of the nanoparticles. We find a characteristic faceted shape in particles channeling along graphene ⟨100⟩ directions that is lost during turning and thus represents a dynamic equilibrium state of the graphene–particle system. We propose a model for the mechanism of zigzag edge formation...... and an explanation of the rate-limiting step for this process, supported by density functional theory (DFT) calculations, and obtain a good agreement between the DFT-predicted and experimentally obtained activation energies of 0.39 and 0.56 eV, respectively. Understanding the origin of the channels' orientation...

Correlation between inter-spin interaction and molecular dynamics of organic radicals in organic 1D nanochannels

Energy Technology Data Exchange (ETDEWEB)

Kobayashi, Hirokazu [Department of Chemistry, College of Humanities and Sciences, Nihon University 3-25-40, Sakura-jo-sui, Setagaya-ku, Tokyo, 156-8550 (Japan)

2015-12-31

One-dimensional (1D) molecular chains of 4-substituted-2,2,6,6-tetramethyl-1-piperidinyloxyl (4-X-TEMPO) radicals were constructed in the crystalline 1D nanochannels of 2,4,6-tris(4-chlorophenoxy)-1,3,5-triazine (CLPOT) used as a template. The ESR spectra of CLPOT inclusion compounds (ICs) using 4-X-TEMPO were examined on the basis of spectral simulation using EasySpin program package for simulating and fitting ESR spectra. The ESR spectra of [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC were isotropic in the total range of temperatures. The peak-to-peak line width (ΔB{sub pp}) became monotonically narrower from 2.8 to 1.3 mT with increase in temperature in the range of 4.2–298 K. The effect of the rotational diffusion motion of TEMPO radicals in the CLPOT nanochannels for the inter-spin interaction of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC was found to be smaller than the case of [(TPP){sub 2}−(TEMPO){sub 1.0}] IC (TPP = tris(o-phenylenedioxy)cyclotriphosphazene) reported in our previous study. The ΔB{sub pp} of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC in the whole range of temperatures was much narrower than the estimation to be based on the Van Vleck’s formula for the second moment of the rigid lattice model where the electron spin can be considered as fixed; 11 mT of Gaussian line-width component. This suggests the possibility of exchange narrowing in the 1D organic-radical chains of the [(CLPOT){sub 2}-(TEMPO){sub 1.0}] IC. On the other hand, the ESR spectra of [(CLPOT){sub 2}-(MeO-TEMPO){sub 0.41}] IC (MeO-TEMPO = 4-methoxy-TEMPO) were reproduced by a superposition of major broad isotropic adsorption line and minor temperature-dependent modulated triplet component. This suggests that the IC has the part of 1D organic-radical chains and MeO-TEMPO molecules isolated in the CLPOT nanochannels.

InterProSurf: a web server for predicting interacting sites on protein surfaces

Science.gov (United States)

Negi, Surendra S.; Schein, Catherine H.; Oezguen, Numan; Power, Trevor D.; Braun, Werner

2009-01-01

Summary A new web server, InterProSurf, predicts interacting amino acid residues in proteins that are most likely to interact with other proteins, given the 3D structures of subunits of a protein complex. The prediction method is based on solvent accessible surface area of residues in the isolated subunits, a propensity scale for interface residues and a clustering algorithm to identify surface regions with residues of high interface propensities. Here we illustrate the application of InterProSurf to determine which areas of Bacillus anthracis toxins and measles virus hemagglutinin protein interact with their respective cell surface receptors. The computationally predicted regions overlap with those regions previously identified as interface regions by sequence analysis and mutagenesis experiments. PMID:17933856

InterCUBE: a study into merging action and interaction spaces

NARCIS (Netherlands)

Salem, B.I.; Peeters, H.; Baranauskas, C.; Palanque, P.

2007-01-01

We describe the development of a novel tangible interface we call the InterCUBE, a cube-shaped device with no external buttons or widgets. We study the implications of such a shape in terms of interactions, notably the degrees of freedom available and the manipulations possible. We also explain and

Hubbard-Stratonovich-like Transformations for Few-Body Inter-actions

Directory of Open Access Journals (Sweden)

Körber Christopher

2018-01-01

Full Text Available Through the development of many-body methodology and algorithms, it has become possible to describe quantum systems composed of a large number of particles with great accuracy. Essential to all these methods is the application of auxiliary fields via the Hubbard-Stratonovich transformation. This transformation effectively reduces two-body interactions to interactions of one particle with the auxiliary field, thereby improving the computational scaling of the respective algorithms. The relevance of collective phenomena and interactions grows with the number of particles. For many theories, e.g. Chiral Perturbation Theory, the inclusion of three-body forces has become essential in order to further increase the accuracy on the many-body level. In this proceeding, the an-alytical framework for establishing a Hubbard-Stratonovich-like transformation, which allows for the systematic and controlled inclusion of contact three-and more-body inter-actions, is presented.

Locus of word frequency effects in spelling to dictation: Still at the orthographic level!

Science.gov (United States)

Bonin, Patrick; Laroche, Betty; Perret, Cyril

2016-11-01

The present study was aimed at testing the locus of word frequency effects in spelling to dictation: Are they located at the level of spoken word recognition (Chua & Rickard Liow, 2014) or at the level of the orthographic output lexicon (Delattre, Bonin, & Barry, 2006)? Words that varied on objective word frequency and on phonological neighborhood density were orally presented to adults who had to write them down. Following the additive factors logic (Sternberg, 1969, 2001), if word frequency in spelling to dictation influences a processing level, that is, the orthographic output level, different from that influenced by phonological neighborhood density, that is, spoken word recognition, the impact of the 2 factors should be additive. In contrast, their influence should be overadditive if they act at the same processing level in spelling to dictation, namely the spoken word recognition level. We found that both factors had a reliable influence on the spelling latencies but did not interact. This finding is in line with an orthographic output locus hypothesis of word frequency effects in spelling to dictation. (PsycINFO Database Record (c) 2016 APA, all rights reserved).

Automatic Measurement of Play-out Differences for Social TV, Interactive TV, Gaming and Inter-destination Synchronization,

NARCIS (Netherlands)

Mekuria, R.N.; Stokking, H.M.; Deventer, M.O. van

2011-01-01

Inter-destination media (play-out) synchronization for social TV has gained attention from research and industry in recent years. Applications include social TV and interactive game shows. To motivate further research of inter-destination synchronization technologies, pilot measurements of play-out

Calculation of inter-plane thermal resistance of few-layer graphene from equilibrium molecular dynamics simulations

International Nuclear Information System (INIS)

Ni, Y; Chalopin, Y; Volz, S

2012-01-01

Inter-plane thermal resistance in 5-layer graphene is calculated from equilibrium molecular dynamics (EMD) by calculating the autocorrelation function of temperature difference. Our simulated inter-plane resistance for 5-layer graphene is 4.83 × 10 −9 m 2 K/W. This data is in the same order of magnitude with the reported values from NEMD simulations and Debye model calculations, and the possible reasons for the slight differences are discussed in details. The inter-plane resistance is not dependent on temperature, according to the results of the EMD simulation. Phonon density of states (DOSs) were plotted to better understand the mechanism behind the obtained values. These results provide a better insight in the heat transfer across a few layer graphene and yield useful information on the design of graphene based thermal materials.

Selecting Molecular Recognition. What Can Existing Aptamers Tell Us about Their Inherent Recognition Capabilities and Modes of Interaction?

Directory of Open Access Journals (Sweden)

Ralf Landgraf

2012-05-01

Full Text Available The use of nucleic acid derived aptamers has rapidly expanded since the introduction of SELEX in 1990. Nucleic acid aptamers have demonstrated their ability to target a broad range of molecules in ways that rival antibodies, but advances have been very uneven for different biochemical classes of targets, and clinical applications have been slow to emerge. What sets different aptamers apart from each other and from rivaling molecular recognition platforms, specifically proteins? What advantages do aptamers as a reagent class offer, and how do the chemical properties and selection procedures of aptamers influence their function? Do the building blocks of nucleic acid aptamers dictate inherent limitations in the nature of molecular targets, and do existing aptamers give us insight in how these challenges might be overcome? This review is written as an introduction for potential endusers of aptamer technology who are evaluating the advantages of aptamers as a versatile, affordable, yet highly expandable platform to target a broad range of biological processes or interactions.

Dynamics of Moment Neuronal Networks with Intra- and Inter-Interactions

Directory of Open Access Journals (Sweden)

Xuyan Xiang

2015-01-01

Full Text Available A framework of moment neuronal networks with intra- and inter-interactions is presented. It is to show how the spontaneous activity is propagated across the homogeneous and heterogeneous network. The input-output firing relationship and the stability are first explored for a homogeneous network. For heterogeneous network without the constraint of the correlation coefficients between neurons, a more sophisticated dynamics is then explored. With random interactions, the network gets easily synchronized. However, desynchronization is produced by a lateral interaction such as Mexico hat function. It is the external intralayer input unit that offers a more sophisticated and unexpected dynamics over the predecessors. Hence, the work further opens up the possibility of carrying out a stochastic computation in neuronal networks.

Extinction and the Allee Effect in an Age-structured Ricker Population Model with Inter-stage Interaction

OpenAIRE

Lazaryan, N.; Sedaghat, H.

2017-01-01

We study the evolution in discrete time of certain age-structured populations, such as adults and juveniles, with a Ricker fitness function. We determine conditions for the convergence of orbits to the origin (extinction) in the presence of the Allee effect and time-dependent vital rates. We show that when stages interact, they may survive in the absence of interior fixed points, a surprising situation that is impossible without inter-stage interactions. We also examine the shift in the inter...

All-or-Nothing Dictator Games : A Field Experiment

NARCIS (Netherlands)

Bekkers, R.

2006-01-01

The dictator game has become well known for its results violating predictions based on ‘rational choice’ models of human behavior with orthodox assumptions on self-interest (Colin F. Camerer, 2003). Prosocial allocations in dictator games seem to suggest that there is some altruism in ‘human

Inter-particle Interactions in Composites of Antiferromagnetic Nanoparticles

DEFF Research Database (Denmark)

Frandsen, Cathrine; Mørup, Steen

2003-01-01

-Fe2O3 and Fe-57-doped NiO particles. The effect of NiO particles on alpha-FeA particles was a shorter relaxation time and an induced Morin transition, which usually is absent in alpha-Fe2O3 nanoparticles. Spectra of alpha-Fe2O3 particles, prepared by drying suspensions with added Co2+ and Ni2+ ions......We have prepared mixtures of alpha-Fe2O3, CoO, and NiO nanoparticles by drying aqueous suspensions of the particles. The magnetic properties were studied by Mossbauer spectroscopy. The measurements showed that interactions with CoO particles suppress the superparamagnetic relaxation of both alpha......, showed that the suspension medium can affect the magnetic properties of the alpha-FeA particles significantly, but not in the same way as the CoO or NiO nanoparticles. Therefore, a strong inter-particle exchange interaction between particles of different materials seems to be responsible for the magnetic...

Goal-based dictator game

Science.gov (United States)

Zaibidi, Nerda Zura; Ibrahim, Adyda; Abidin, Norhaslinda Zainal

2014-12-01

A considerable number of studies have been conducted to study fairness issues using two-player game. Dictator Game is one of the two-player games that receive much attention. In this paper, we develop an evolutionary approach to the Dictator Game by using Goal programming to build a model of human decision-making for cooperation. The model is formulated based on the theories of cognitive neuroscience that is capable in capturing a more realistic fairness concerns between players in the games. We show that fairness will evolve by taking into account players' aspirations and preferences explicitly in terms of profit and fairness concerns. The model is then simulated to investigate any possible effective strategy for people in economics to deal with fairness coalition. Parallels are drawn between the approach and concepts of human decision making from the field of cognitive neuroscience and psychology. The proposed model is also able to help decision makers to plan or enhance the effective strategies for business purposes.

Effects of Two Listening Strategies for Melodic Dictation

Science.gov (United States)

Buonviri, Nathan O.

2017-01-01

The purpose of this research was to examine effects of two listening strategies on melodic dictation scores. Fifty-four undergraduate music majors completed short tonal melodic dictations in a within-subjects design with three conditions: (a) no specified strategy in the instructions, (b) required listening before writing, and (c) required writing…

The values of ex-ante and ex-post communication in dictator games

OpenAIRE

Pascal Langenbach

2014-01-01

In the dictator game, the recipient's opportunity to send a message to the dictator increases giving. This paperreports two experimentswhich study how the timing of messages affects dictators' decisions (experiment 1) and which value recipients attach to communication opportunities (experiment 2). The first experiment shows that the effect of communication on dictator giving is equally strong when the recipient can send a message before or after the dictator has decided. However, recipients i...

Adapting a Computerized Medical Dictation System to Prepare Academic Papers in Radiology.

Science.gov (United States)

Sánchez, Yadiel; Prabhakar, Anand M; Uppot, Raul N

2017-09-14

Everyday radiologists use dictation software to compose clinical reports of imaging findings. The dictation software is tailored for medical use and to the speech pattern of each radiologist. Over the past 10 years we have used dictation software to compose academic manuscripts, correspondence letters, and texts of educational exhibits. The advantages of using voice dictation is faster composition of manuscripts. However, use of such software requires preparation. The purpose of this article is to review the steps of adapting a clinical dictation software for dictating academic manuscripts and detail the advantages and limitations of this technique. Copyright © 2017 Elsevier Inc. All rights reserved.

Uncovering patterns of inter-urban trip and spatial interaction from social media check-in data.

Directory of Open Access Journals (Sweden)

Yu Liu

Full Text Available The article revisits spatial interaction and distance decay from the perspective of human mobility patterns and spatially-embedded networks based on an empirical data set. We extract nationwide inter-urban movements in China from a check-in data set that covers half a million individuals within 370 cities to analyze the underlying patterns of trips and spatial interactions. By fitting the gravity model, we find that the observed spatial interactions are governed by a power law distance decay effect. The obtained gravity model also closely reproduces the exponential trip displacement distribution. The movement of an individual, however, may not obey the same distance decay effect, leading to an ecological fallacy. We also construct a spatial network where the edge weights denote the interaction strengths. The communities detected from the network are spatially cohesive and roughly consistent with province boundaries. We attribute this pattern to different distance decay parameters between intra-province and inter-province trips.

Uncovering patterns of inter-urban trip and spatial interaction from social media check-in data.

Science.gov (United States)

Liu, Yu; Sui, Zhengwei; Kang, Chaogui; Gao, Yong

2014-01-01

The article revisits spatial interaction and distance decay from the perspective of human mobility patterns and spatially-embedded networks based on an empirical data set. We extract nationwide inter-urban movements in China from a check-in data set that covers half a million individuals within 370 cities to analyze the underlying patterns of trips and spatial interactions. By fitting the gravity model, we find that the observed spatial interactions are governed by a power law distance decay effect. The obtained gravity model also closely reproduces the exponential trip displacement distribution. The movement of an individual, however, may not obey the same distance decay effect, leading to an ecological fallacy. We also construct a spatial network where the edge weights denote the interaction strengths. The communities detected from the network are spatially cohesive and roughly consistent with province boundaries. We attribute this pattern to different distance decay parameters between intra-province and inter-province trips.

Uncovering Patterns of Inter-Urban Trip and Spatial Interaction from Social Media Check-In Data

Science.gov (United States)

Liu, Yu; Sui, Zhengwei; Kang, Chaogui; Gao, Yong

2014-01-01

The article revisits spatial interaction and distance decay from the perspective of human mobility patterns and spatially-embedded networks based on an empirical data set. We extract nationwide inter-urban movements in China from a check-in data set that covers half a million individuals within 370 cities to analyze the underlying patterns of trips and spatial interactions. By fitting the gravity model, we find that the observed spatial interactions are governed by a power law distance decay effect. The obtained gravity model also closely reproduces the exponential trip displacement distribution. The movement of an individual, however, may not obey the same distance decay effect, leading to an ecological fallacy. We also construct a spatial network where the edge weights denote the interaction strengths. The communities detected from the network are spatially cohesive and roughly consistent with province boundaries. We attribute this pattern to different distance decay parameters between intra-province and inter-province trips. PMID:24465849

Moral distance in dictator games

Directory of Open Access Journals (Sweden)

Fernando Aguiar

2008-04-01

Full Text Available We perform an experimental investigation using a dictator game in which individuals must make a moral decision --- to give or not to give an amount of money to poor people in the Third World. A questionnaire in which the subjects are asked about the reasons for their decision shows that, at least in this case, moral motivations carry a heavy weight in the decision: the majority of dictators give the money for reasons of a consequentialist nature. Based on the results presented here and of other analogous experiments, we conclude that dicator behavior can be understood in terms of moral distance rather than social distance and that it systematically deviates from the egoism assumption in economic models and game theory. %extit{JEL}: A13, C72, C91

Non-covalent interaction between polyubiquitin and GTP cyclohydrolase 1 dictates its degradation.

Directory of Open Access Journals (Sweden)

Yu Zhao

Full Text Available GTP cyclohydrolase 1 (GTPCH1 is the rate-limiting enzyme in the de novo synthesis of tetrahydrobiopterin (BH4. GTPCH1 protein degradation has been reported in animal models of several diseases, including diabetes mellitus and hypertension. However, the molecular mechanisms by which GTPCH1 is degraded remain uncharacterized. Here we report a novel non-covalent interaction between polyubiquitin and GTPCH1 in vitro and in vivo. The non-covalent binding of GTPCH1 to polyubiquitin via an ubiquitin-binding domain (UBD results in ubiquitination and degradation. Ectopic expression of ubiquitin in cultured cells accelerated GTPCH1 degradation. In cultured cells and in vitro assays, Lys48-linked ubiquitin chains, but not Lys63-linked chains, interacted with GTPCH1 and targeted it for degradation. Consistently, proteasome inhibition attenuated GTPCH1 degradation. Finally, direct mutagenesis of an isoleucine (Ile131 in the hydrophobic patch of the GTPCH1 UBD affected its ubiquitin binding and the enzyme stability. Taken together, we conclude that GTPCH1 non-covalently interacts with polyubiquitin via an ubiquitin-binding domain. The polyubiquitin binding directs GTPCH1 ubiquitination and proteasome degradation.

When Ignorance is Bliss - Information Asymmetries Enhance Prosocial Behavior in Dictator Games

OpenAIRE

Evguenia Winschel; Philipp Zahn

2014-01-01

In most laboratory experiments concerning prosocial behavior subjects are fully informed how their decision influences the payoff of other players. Outside the laboratory, however, individuals typically have to decide without such detailed knowledge. To assess the effect of information asymmetries on prosocial behavior, we conduct a laboratory experiment with a simple non-strategic interaction. A dictator has only limited knowledge about the benefits his prosocial action generates for a recip...

Dynamic inter-subunit interactions in thermophilic F1-ATPase subcomplexes studied by cross-correlated relaxation-enhanced polarization transfer NMR

International Nuclear Information System (INIS)

Kobayashi, Masumi; Yagi, Hiromasa; Yamazaki, Toshio; Yoshida, Masasuke; Akutsu, Hideo

2008-01-01

F 1 -ATPase is a unique enzyme in terms of its rotational catalytic activity. The smallest unit showing this property is the α 3 β 3 γ complex (351 kDa). For investigation of such a huge system by means of solution NMR, we have explored a suitable NMR method using F 1 -ATPase subcomplexes from a thermophilic Bacillus PS3 including an α 3 β 3 hexamer (319 kDa). Pulse sequences for large molecules, effects of deuteration and simplification of the spectra were examined in this work. Since the β subunit includes the catalytic site, this was the target of the analysis in this work. The combination of [ 15 N, 1 H]-CRINEPT-HMQC-[ 1 H]-TROSY, deuteration of both α and β subunits, and segmental isotope-labeling was found essential to analyze such a huge and complex molecular system. Utilizing this method, subcomplexes composed of α and β subunits were investigated in terms of inter-subunit interactions. It turned out that there is equilibrium among monomers, heterodimers and the α 3 β 3 hexamers in solution. The rate of exchange between the dimer and hexamer is in the slow regime on the NMR time scale. In chemical shift perturbation experiments, the N-terminal domain was found to be involved in strong inter-subunit interactions. In contrast, the C-terminal domain was found to be mobile even in the hexamer

Social Preferences and Cognitive Reflection: Evidence from Dictator Game Experiment

Directory of Open Access Journals (Sweden)

Giovanni Benedetto Ponti

2015-06-01

Full Text Available This paper provides experimental evidence on the relationship between social preferences and cognitive abilities, which we measure using the Cognitive Reflection Test (CRT. We elicit social preferences by way of 24 dictatorial situations, in which the Dictator’s choice sets include i standard Dictator games, where increasing the Dictator’s payoff yields a loss for the Recipient, ii efficient Dicator games, where increasing the Dictator’s payoff also increases that the Recipient’s; as well as other situations in which iii either the Dictator’s or iv the Recipient’s monetary payoff is held constant. We partition our subject pool in three groups: reflective (scoring 2 or more in the CRT, impulsive (opting twice or more for the intuitive but wrong answers in the CRT and the remainder. We find that impulsive Dictators show a marked inequity aversion attitude, especially in standard Dictator Games. By contrast, reflective Dictators show lower distributional concerns, except for the situations in which the Dictators’ payoff is held constant. In this case, reflective Dictators give significantly more.

Calculation of the inter-nuclei separation of HD+

International Nuclear Information System (INIS)

Zhu Zhousen; Shi Miangong; Tang Ayou; Yang Baifang; Miao Jingwei

1993-01-01

With the Ritz variational principle, the authors calculate the inter nuclei separation of the HD + molecular ion, and introduces a method to calculate the inter nuclei separations of other simple non-symmetry two-atom molecular ions. One way to work out the trial wave function is provided

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

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.

Project InterActions: A Multigenerational Robotic Learning Environment

Science.gov (United States)

Bers, Marina U.

2007-12-01

This paper presents Project InterActions, a series of 5-week workshops in which very young learners (4- to 7-year-old children) and their parents come together to build and program a personally meaningful robotic project in the context of a multigenerational robotics-based community of practice. The goal of these family workshops is to teach both parents and children about the mechanical and programming aspects involved in robotics, as well as to initiate them in a learning trajectory with and about technology. Results from this project address different ways in which parents and children learn together and provide insights into how to develop educational interventions that would educate parents, as well as children, in new domains of knowledge and skills such as robotics and new technologies.

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....

A positive effect of flowers rather than eye images in a large-scale, cross-cultural dictator game.

Science.gov (United States)

Raihani, Nichola J; Bshary, Redouan

2012-09-07

People often consider how their behaviour will be viewed by others, and may cooperate to avoid gaining a bad reputation. Sensitivity to reputation may be elicited by subtle social cues of being watched: previous studies have shown that people behave more cooperatively when they see images of eyes rather than control images. Here, we tested whether eye images enhance cooperation in a dictator game, using the online labour market Amazon Mechanical Turk (AMT). In contrast to our predictions and the results of most previous studies, dictators gave away more money when they saw images of flowers rather than eye images. Donations in response to eye images were not significantly different to donations under control treatments. Dictator donations varied significantly across cultures but there was no systematic variation in responses to different image types across cultures. Unlike most previous studies, players interacting via AMT may feel truly anonymous when making decisions and, as such, may not respond to subtle social cues of being watched. Nevertheless, dictators gave away similar amounts as in previous studies, so anonymity did not erase helpfulness. We suggest that eye images might only promote cooperative behaviour in relatively public settings and that people may ignore these cues when they know their behaviour is truly anonymous.

Long-range interaction between dust grains in plasma

Directory of Open Access Journals (Sweden)

D.Yu. Mishagli

2014-03-01

Full Text Available The nature of long-range interactions between dust grains in plasma is discussed. The dust grain interaction potential within a cell model of dusty plasma is introduced. The attractive part of inter-grain potential is described by multipole interaction between two electro-neutral cells. This allowed us to draw an analogy with molecular liquids where attraction between molecules is determined by dispersion forces. Also main ideas of the fluctuation theory for electrostatic field in cell model are formulated, and the dominating contribution to attractive part of inter-grain potential is obtained.

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.

Study of inter species diversity and population structure by molecular genetic method in Iranian Artemia

OpenAIRE

Hajirostamloo, Mahbobeh

2005-01-01

Artemia is a small crustacean that adapted to live in brine water and has been seen in different brine water sources in Iran. Considering the importance of genetic studies manifest inter population differences in species, to estimate genetic structure, detect difference at molecular level and separate different Artemia populations of Iran, also study of phylogenic relationships among them, samples of Artemia were collected from nine region: Urmia lake in West Azerbaijan, Sh...

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.

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.

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

Self-Assembly of Molecular Threads into Reversible Gels

Science.gov (United States)

Sayar, Mehmet; Stupp, Samuel I.

2001-03-01

Reversible gels formed by low concentrations of molecular gelators that self-assemble into fibers with molecular width and extremely long length have been studied via Monte Carlo simulations. The gelators of interest have two kinds of interactions, one governs self-assembly into fibers and the other provides inter-fiber connectivity to drive the formation of a network. The off-lattice Monte Carlo simulation presented here is based on a point particle representation of gelators. In this model each particle can form only two strong bonds, that enable linear fiber formation, but a variable number of weak bonds which provide inter-fiber connectivity. The gel formation has been studied as a function of concentration of monomers, the strength of interactions, number of bonding sites per particle for weak interactions, and the stiffness of the fibers. The simulation results are compared with two experimental systems synthesized in our group in order to understand gelation mechanisms.

Effects of a Preparatory Singing Pattern on Melodic Dictation Success

Science.gov (United States)

Buonviri, Nathan O.

2015-01-01

The purpose of this study was to investigate effects of a preparatory contextual singing pattern on melodic dictation test scores. Forty-nine undergraduate music education majors took melodic dictations under three conditions. After hearing an orienting chord sequence, they (1) sang a preparatory solfége pattern in the key, meter, and tempo of the…

Resiliency to social defeat stress relates to the inter-strain social interaction and is influenced by season variation.

Science.gov (United States)

Han, Qiuqin; Yang, Liu; Liu, Yan; Lv, Ning; Yu, Jin; Wu, Gencheng; Zhang, Yuqiu

2014-02-21

Exposure to social defeat (SD) stress exerts social avoidance and depressive disorders. Little is known about the relationship between resiliency to stressors and the inter-strain social interaction (SI) level. We hypothesized that SD resiliency is correlated with a high SI between the same strain. C57BL/6J mice experienced a 10-day period of SD stress by repeated CD-1 mice offensive. The susceptible mice exhibited significant social-avoidance behaviors with less time in interaction-zone (IZ) and lower social interaction ratio (SIR) toward the Target (CD-1 mice), while resilient ones exhibited similar social interaction to control mice. When the Target was C57BL/6J mouse, either susceptible or resilient mice spent more time in IZ and the inter-strain SI in the resilient group was significantly higher than the susceptible. Correlation analysis revealed a significantly non-zero slope of the linear relationship between SIRs toward two strains. But different groups had a similar baseline of the inter-strain SI before stress, indicating a SD-induced defect in both types of SI. In addition, in four different seasons, animals exhibited a significant resiliency to the stress in summer. These data suggest that SD resiliency is related to a higher SI toward the same-strain, and may be regulated by seasonal variations. Copyright © 2013 Elsevier Ireland Ltd. All rights reserved.

Modeling Inequity Aversion in a Dictator Game with Production

Directory of Open Access Journals (Sweden)

Ismael Rodriguez-Lara

2012-10-01

Full Text Available We expand upon the previous models of inequity aversion of Fehr and Schmidt [1], and Frohlich et al. [2], which assume that dictators get disutility if the final allocation of surplus deviates from the equal split (egalitarian principle or from the subjects' production (libertarian principle. In our model, dictators may also account for the way in which the surplus was generated. More precisely, our model incorporates the idea of liberal egalitarian ethics into the analysis, making it possible for dictators to divide the surplus according to the accountability principle, which states that subjects should only be rewarded for factors under their control. This fairness ideal does not hold subjects responsible for factors beyond their control in the production of the surplus, an idea that is absent in the models of inequity aversion cited above (JEL Codes: D3, D6, D63.

The Cold Shock Domain of YB-1 Segregates RNA from DNA by Non-Bonded Interactions.

Directory of Open Access Journals (Sweden)

Vladislav Kljashtorny

Full Text Available The human YB-1 protein plays multiple cellular roles, of which many are dictated by its binding to RNA and DNA through its Cold Shock Domain (CSD. Using molecular dynamics simulation approaches validated by experimental assays, the YB1 CSD was found to interact with nucleic acids in a sequence-dependent manner and with a higher affinity for RNA than DNA. The binding properties of the YB1 CSD were close to those observed for the related bacterial Cold Shock Proteins (CSP, albeit some differences in sequence specificity. The results provide insights in the molecular mechanisms whereby YB-1 interacts with nucleic acids.

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.

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.

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

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.

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.

Empathy and Prosocial Behaviours. Insights from Intra- and Inter-species Interactions

Directory of Open Access Journals (Sweden)

Maria elide Vanutelli

2015-04-01

Full Text Available It has been suggested that “sharing the same body” between the observer and the observed subject allows for a direct form of understanding and emotional attuning by a process of simulation. Then, what happens when we don’t share the same body? The aim of the present paper is to review available evidence of intra- and inter-species empathic and prosocial behaviours, with respect to within-human, within-animals and cross-specifies interactions. Similarities and differences will be evaluated using a comparative perspective, and some possible moral and ethical implications for human-animal interactions will be discussed. According to Charles Darwin’s work, the perceived differences between human and animal empathy could be more quantitative than qualitative, suggesting a common affective core which allows both categories to mirror and tune to conspecifics’ feelings, where in the case of humans it can be integrated with more complex cognitive processes.

Inter-cluster coupling effects in high-spin molecular magnets

International Nuclear Information System (INIS)

Affronte, M.; Lasjaunias, J.C.; Wernsdorfer, W.; Sessoli, R.; Gatteschi, D.; Heath, S.L.; Fort, A.; Rettori, A.

2004-01-01

We report evidences of antiferromagnetic (AF) transition in Fe 19 metheidi, a new molecular nanomagnet with a total spin S=((33)/(2)), among the highest known so far. The temperature (T) dependence of specific heat (C) shows a λ-anomaly at 1.19 K and at the same temperature an anomaly is also observed in the low field (B<0.12 T) magnetization M-vs.-T curves. Since the dipolar interaction between clusters is estimated to be ∼190 mK, the origin of the AF transition is probably due to superexchange

Inter-cluster coupling effects in high-spin molecular magnets

Energy Technology Data Exchange (ETDEWEB)

Affronte, M.; Lasjaunias, J.C.; Wernsdorfer, W.; Sessoli, R.; Gatteschi, D.; Heath, S.L.; Fort, A. E-mail: fort@fi.infn.it; Rettori, A

2004-05-01

We report evidences of antiferromagnetic (AF) transition in Fe{sub 19}metheidi, a new molecular nanomagnet with a total spin S=((33)/(2)), among the highest known so far. The temperature (T) dependence of specific heat (C) shows a {lambda}-anomaly at 1.19 K and at the same temperature an anomaly is also observed in the low field (B<0.12 T) magnetization M-vs.-T curves. Since the dipolar interaction between clusters is estimated to be {approx}190 mK, the origin of the AF transition is probably due to superexchange.

Anonymity versus privacy in the dictator game: revealing donor decisions to recipients does not substantially impact donor behavior.

Directory of Open Access Journals (Sweden)

Jeffrey Winking

Full Text Available Anonymity is often offered in economic experiments in order to eliminate observer effects and induce behavior that would be exhibited under private circumstances. However, anonymity differs from privacy in that interactants are only unaware of each others' identities, while having full knowledge of each others' actions. Such situations are rare outside the laboratory and anonymity might not meet the requirements of some participants to psychologically engage as if their actions were private. In order to explore the impact of a lack of privacy on prosocial behaviors, I expand on a study reported in Dana et al. (2006 in which recipients were left unaware of the Dictator Game and given donations as "bonuses" to their show-up fees for other tasks. In the current study, I explore whether differences between a private Dictator Game (sensu Dana et al. (2006 and a standard anonymous one are due to a desire by dictators to avoid shame or to pursue prestige. Participants of a Dictator Game were randomly assigned to one of four categories-one in which the recipient knew of (1 any donation by an anonymous donor (including zero donations, (2 nothing at all, (3 only zero donations, and (4 and only non-zero donations. The results suggest that a lack of privacy increases the shame that selfish-acting participants experience, but that removing such a cost has only minimal effects on actual behavior.

A feeling of flow: exploring junior scientists' experiences with dictation of scientific articles.

Science.gov (United States)

Spanager, Lene; Danielsen, Anne Kjaergaard; Pommergaard, Hans-Christian; Burcharth, Jakob; Rosenberg, Jacob

2013-08-10

Science involves publishing results, but many scientists do not master this. We introduced dictation as a method of producing a manuscript draft, participating in writing teams and attending a writing retreat to junior scientists in our department. This study aimed to explore the scientists' experiences with this process. Four focus group interviews were conducted and comprised all participating scientists (n = 14). Each transcript was transcribed verbatim and coded independently by two interviewers. The coding structure was discussed until consensus and from this the emergent themes were identified. Participants were 7 PhD students, 5 scholarship students and 2 clinical research nurses. Three main themes were identified: 'Preparing and then letting go' indicated that dictating worked best when properly prepared. 'The big dictation machine' described benefits of writing teams when junior scientists got feedback on both content and structure of their papers. 'Barriers to and drivers for participation' described flow-like states that participants experienced during the dictation. Motivation and a high level of preparation were pivotal to be able to dictate a full article in one day. The descriptions of flow-like states seemed analogous to the theoretical model of flow which is interesting, as flow is usually deemed a state reserved to skilled experts. Our findings suggest that other academic groups might benefit from using the concept including dictation of manuscripts to encourage participants' confidence in their writing skills.

Dictator games: A meta study

OpenAIRE

Engel, Christoph

2010-01-01

Over the last 25 years, more than a hundred dictator game experiments have been published. This meta study summarizes the evidence. Exploiting the fact that most experiments had to fix parameters they did not intend to test, in multiple regression the meta study is able to assess the effect of single manipulations, controlling for a host of alternative explanatory factors. The resulting rich dataset also provides a testbed for comparing alternative specifications of the statistical model for ...

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.

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.)

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.

An Observation of Diamond-Shaped Particle Structure in a Soya Phosphatidylcohline and Bacteriorhodopsin Composite Langmuir Blodgett Film Fabricated by Multilayer Molecular Thin Film Method

Science.gov (United States)

Tsujiuchi, Y.; Makino, Y.

A composite film of soya phosphatidylcohline (soya PC) and bacteriorhodopsin (BR) was fabricated by the multilayer molecular thin film method using fatty acid and lipid on a quartz substrate. Direct Force Microscopy (DFM), UV absorption spectra and IR absorption spectra of the film were characterized on the detail of surface structure of the film. The DFM data revealed that many rhombus (diamond-shaped) particles were observed in the film. The spectroscopic data exhibited the yield of M-intermediate of BR in the film. On our modelling of molecular configuration indicate that the coexistence of the strong inter-molecular interaction and the strong inter-molecular interaction between BR trimmers attributed to form the particles.

Symmetry-dictated trucation: Solutions of the spherical shell model for heavy nuclei

International Nuclear Information System (INIS)

Guidry, M.W.

1992-01-01

Principles of dynamical symmetry are used to simplify the spherical shell model. The resulting symmetry-dictated truncation leads to dynamical symmetry solutions that are often in quantitative agreement with a variety of observables. Numerical calculations, including terms that break the dynamical symmetries, are shown that correspond to shell model calculations for heavy deformed nuclei. The effective residual interaction is simple, well-behaved, and can be determined from basic observables. With this approach, we intend to apply the shell model in systematic fashion to all nuclei. The implications for nuclear structure far from stability and for nuclear masses and other quantities of interest in astrophysics are discussed

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

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)

The Compact and Biologically Relevant Structure of Inter-α-inhibitor Is Maintained by the Chondroitin Sulfate Chain and Divalent Cations.

Science.gov (United States)

Scavenius, Carsten; Nikolajsen, Camilla Lund; Stenvang, Marcel; Thøgersen, Ida B; Wyrożemski, Łukasz; Wisniewski, Hans-Georg; Otzen, Daniel E; Sanggaard, Kristian W; Enghild, Jan J

2016-02-26

Inter-α-inhibitor is a proteoglycan of unique structure. The protein consists of three subunits, heavy chain 1, heavy chain 2, and bikunin covalently joined by a chondroitin sulfate chain originating at Ser-10 of bikunin. Inter-α-inhibitor interacts with an inflammation-associated protein, tumor necrosis factor-inducible gene 6 protein, in the extracellular matrix. This interaction leads to transfer of the heavy chains from the chondroitin sulfate of inter-α-inhibitor to hyaluronan and consequently to matrix stabilization. Divalent cations and heavy chain 2 are essential co-factors in this transfer reaction. In the present study, we have investigated how divalent cations in concert with the chondroitin sulfate chain influence the structure and stability of inter-α-inhibitor. The results showed that Mg(2+) or Mn(2+), but not Ca(2+), induced a conformational change in inter-α-inhibitor as evidenced by a decrease in the Stokes radius and a bikunin chondroitin sulfate-dependent increase of the thermodynamic stability. This structure was shown to be essential for the ability of inter-α-inhibitor to participate in extracellular matrix stabilization. In addition, the data revealed that bikunin was positioned adjacent to both heavy chains and that the two heavy chains also were in close proximity. The chondroitin sulfate chain interacted with all protein components and inter-α-inhibitor dissociated when it was degraded. Conventional purification protocols result in the removal of the Mg(2+) found in plasma and because divalent cations influence the conformation and affect function it is important to consider this when characterizing the biological activity of inter-α-inhibitor. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.

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.

Improving the Dictation in Attention Deficit Hyperactivity Disorder by Using Computer Based Interventions: A Clinical Trial

Directory of Open Access Journals (Sweden)

Mahdi Tehranidoost

2006-07-01

Full Text Available Objective: The aim of the current study was to assess the impact of computer games and computer-assisted type instruction on dictation scores of elementary school children with attention deficit – hyperactivity disorder (ADHD. Method: In this single-blind clinical trial, 37 elementary school children with ADHD, selected by convenience sampling and divided into group I (n=17 and group II (n=20, underwent eight one-hour sessions (3 sessions per week of intervention by computer games versus computer-assisted type instruction, respectively. 12 school dictation scores were considered: 4 scores preintervention, 4 scores during interventions, and 4 scores post-intervention. Dictation test was taken during each session. Data was analyzed using repeated measure ANOVA. Results: Two groups were matched for age, gender, school grade, medication, IQ, parent’s and teacher’s Conners’ scale scores, having computer at home, history of working with computer, and mean dictation scores. There was no significant difference in dictation scores before and after interventions and also between the study groups. The improvement in school dictation scores had no significant correlation with age, gender, Ritalin use, owning a computer at home and past history of computer work, baseline dictation scores, Ritalin dose, educational status, IQ, and the total score of parent’s and teacher’s Conners’ rating scale. Conclusion: Absence of significant improvement in dictation scores in study groups may be due to the confounding effect of other variables with known impact on dictation scores. Further studies in this field should also assess the change of attention and memory.

Consistency and Stability of Italian Children's Spelling in Dictation versus Composition Assessments

Science.gov (United States)

Bigozzi, Lucia; Tarchi, Christian; Pinto, Giuliana

2017-01-01

The purpose of this study was to investigate consistency in spelling skills across 2 different tasks of written production (dictation vs. composition) and stability of performance across 4 different grades. We assessed 2nd, 3rd, 4th, and 5th graders' spelling performance through 4 tasks: 2 dictation tasks (passage and sentences) and 2 composition…

Dipole-Oriented Molecular Solids Can Undergo a Phase Change and Still Maintain Electrical Polarization

Energy Technology Data Exchange (ETDEWEB)

Glavic, Artur G [ORNL; Cassidy, Andrew M [ORNL; Jorgensen, Mads Ry Ry [University of Aarhus, Denmark; Lauter, Valeria [ORNL; Rosu-Finsen, Alexander [Heriot-Watt University, Edinburgh, UK; Lasne, Jérôme [Heriot-Watt University, Edinburgh, UK; Jorgensen, Jakob [Aarhus University, Denmark; Iversen, Bo [ORNL; McCoustra, Martin [Heriot-Watt University, Edinburgh, UK; Field, David [University of Aarhus, Denmark

2016-10-02

It has recently been demonstrated that nanoscale molecular films can spontaneously assemble to self-generate intrinsic electric fields that can exceed 10⁸ V/m. These electric fields originate from polarization charges in the material that arise because the films self-assemble to orient molecular dipole moments. This has been called the spontelectric effect. Such growth of spontaneously polarized layers of molecular solids has implications for our understanding of how intermolecular interactions dictate the structure of molecular materials used in a range of applications, for example, molecular semiconductors, sensors, and catalysts. In this paper, we present the first in situ structural characterization of a representative spontelectric solid, nitrous oxide. Infrared spectroscopy, temperature-programmed desorption, and neutron reflectivity measurements demonstrate that polarized films of nitrous oxide undergo a structural phase transformation upon heating above 48 K. A mean-field model can be used to describe quantitatively the magnitude of the spontaneously generated field as a function of film-growth temperature, and this model also recreates the phase change. Finally, this reinforces the spontelectric model as a means of describing long-range dipole–dipole interactions and points to a new type of ordering in molecular thin films.

How cancer cells dictate their microenvironment: present roles of extracellular vesicles.

Science.gov (United States)

Naito, Yutaka; Yoshioka, Yusuke; Yamamoto, Yusuke; Ochiya, Takahiro

2017-02-01

Intercellular communication plays an important role in cancer initiation and progression through secretory molecules, including growth factors and cytokines. Recent advances have revealed that small membrane vesicles, termed extracellular vesicles (EVs), served as a regulatory agent in the intercellular communication of cancer. EVs enable the transfer of functional molecules, including proteins, mRNA and microRNAs (miRNAs), into recipient cells. Cancer cells utilize EVs to dictate the unique phenotype of surrounding cells, thereby promoting cancer progression. Against such "education" by cancer cells, non-tumoral cells suppress cancer initiation and progression via EVs. Therefore, researchers consider EVs to be important cues to clarify the molecular mechanisms of cancer biology. Understanding the functions of EVs in cancer progression is an important aspect of cancer biology that has not been previously elucidated. In this review, we summarize experimental data that indicate the pivotal roles of EVs in cancer progression.

Written object naming, spelling to dictation, and immediate copying: Different tasks, different pathways?

Science.gov (United States)

Bonin, Patrick; Méot, Alain; Lagarrigue, Aurélie; Roux, Sébastien

2015-01-01

We report an investigation of cross-task comparisons of handwritten latencies in written object naming, spelling to dictation, and immediate copying. In three separate sessions, adults had to write down a list of concrete nouns from their corresponding pictures (written naming), from their spoken (spelling to dictation) and from their visual presentation (immediate copying). Linear mixed models without random slopes were performed on the latencies in order to study and compare within-task fixed effects. By-participants random slopes were then included to investigate individual differences within and across tasks. Overall, the findings suggest that written naming, spelling to dictation, and copying all involve a lexical pathway, but that written naming relies on this pathway more than the other two tasks do. Only spelling to dictation strongly involves a nonlexical pathway. Finally, the analyses performed at the level of participants indicate that, depending on the type of task, the slower participants are more or less influenced by certain psycholinguistic variables.

The effect of $1, $5 and $10 stakes in an online dictator game.

Science.gov (United States)

Raihani, Nichola J; Mace, Ruth; Lamba, Shakti

2013-01-01

The decision rules underpinning human cooperative behaviour are often investigated under laboratory conditions using monetary incentives. A major concern with this approach is that stake size may bias subjects' decisions. This concern is particularly acute in online studies, where stakes are often far lower than those used in laboratory or field settings. We address this concern by conducting a Dictator Game using Amazon Mechanical Turk. In this two-player game, one player (the dictator) determines the division of an endowment between himself and the other player. We recruited subjects from India and the USA to play an online Dictator Game. Dictators received endowments of $1, $5 or $10. We collected two batches of data over two consecutive years. We found that players from India were less generous when playing with a $10 stake. By contrast, the effect of stake size among players from the USA was very small. This study indicates that the effects of stake size on decision making in economic games may vary across populations.

Reconciling patterns of inter-ocean molecular variance from four classes of molecular markers in blue marlin (Makaira nigricans).

Science.gov (United States)

Buonaccorsi, V P; McDowell, J R; Graves, J E

2001-05-01

Different classes of molecular markers occasionally yield discordant views of population structure within a species. Here, we examine the distribution of molecular variance from 14 polymorphic loci comprising four classes of molecular markers within approximately 400 blue marlin individuals (Makaira nigricans). Samples were collected from the Atlantic and Pacific Oceans over 5 years. Data from five hypervariable tetranucleotide microsatellite loci and restriction fragment length polymorphism (RFLP) analysis of whole molecule mitochondrial DNA (mtDNA) were reported and compared with previous analyses of allozyme and single-copy nuclear DNA (scnDNA) loci. Temporal variance in allele frequencies was nonsignificant in nearly all cases. Mitochondrial and microsatellite loci revealed striking phylogeographic partitioning among Atlantic and Pacific Ocean samples. A large cluster of alleles was present almost exclusively in Atlantic individuals at one microsatellite locus and for mtDNA, suggesting that, if gene flow occurs, it is likely to be unidirectional from Pacific to Atlantic oceans. Mitochondrial DNA inter-ocean divergence (FST) was almost four times greater than microsatellite or combined nuclear divergences including allozyme and scnDNA markers. Estimates of Neu varied by five orders of magnitude among marker classes. Using mathematical and computer simulation approaches, we show that substantially different distributions of FST are expected from marker classes that differ in mode of inheritance and rate of mutation, without influence of natural selection or sex-biased dispersal. Furthermore, divergent FST values can be reconciled by quantifying the balance between genetic drift, mutation and migration. These results illustrate the usefulness of a mitochondrial analysis of population history, and relative precision of nuclear estimates of gene flow based on a mean of several loci.

Molecular mechanics work station for protein conformational studies

International Nuclear Information System (INIS)

Fine, R.; Levinthal, C.; Schoenborn, B.; Dimmier, G.; Rankowitz, C.

1984-01-01

Interest in computational problems in Biology has intensified over the last few years, partly due to the development of techniques for the rapid cloning, sequencing, and mutagenesis of genes from organisims ranging from E. coli to Man. The central dogma of molecular biology; that DNA codes for mRNA which codes for protein, has been understood in a linear programming sense since the genetic code was cracked. But what is not understood at present is how a protein, once assembled as a long sequence of amino acids, folds back on itself to produce a three-dimensional structure which is unique to that protein and which dictates its chemical and biological activity. This folding process is purely physics, and involves the time evolution of a system of several thousand atoms which interact with each other and with atoms from the surrounding solvent. Molecular dynamics simulations on smaller molecules suggest that approaches which treat the protein as a classical ensemble of atoms interacting with each other via an empirical Hamiltonian can yield the kind of predictive results one would like when applied to proteins

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'.

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.

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.

Evolution of altruism in spatial prisoner's dilemma: Intra- and inter-cellular interactions

Science.gov (United States)

Yokoi, Hiroki; Uehara, Takashi; Sakata, Tomoyuki; Naito, Hiromi; Morita, Satoru; Tainaka, Kei-ichi

2014-12-01

Iterated prisoner's dilemma game is carried out on lattice with “colony” structure. Each cell is regarded as a colony which contains plural players with an identical strategy. Both intra- and inter-cellular interactions are assumed. In the former a player plays with all other players in the same colony, while in the latter he plays with one player each from adjacent colonies. Spatial patterns among four typical strategies exhibit various dynamics and winners. Both theory and simulation reveal that All Cooperation (AC) wins, when the members of colony or the intensity of noise increases. This result explains the evolution of altruism in animal societies, even though errors easily occur in animal communications.

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...

Genotyping and Molecular Identification of Date Palm Cultivars Using Inter-Simple Sequence Repeat (ISSR) Markers.

Science.gov (United States)

Ayesh, Basim M

2017-01-01

Molecular markers are credible for the discrimination of genotypes and estimation of the extent of genetic diversity and relatedness in a set of genotypes. Inter-simple sequence repeat (ISSR) markers rapidly reveal high polymorphic fingerprints and have been used frequently to determine the genetic diversity among date palm cultivars. This chapter describes the application of ISSR markers for genotyping of date palm cultivars. The application involves extraction of genomic DNA from the target cultivars with reliable quality and quantity. Subsequently the extracted DNA serves as a template for amplification of genomic regions flanked by inverted simple sequence repeats using a single primer. The similarity of each pair of samples is measured by calculating the number of mono- and polymorphic bands revealed by gel electrophoresis. Matrices constructed for similarity and genetic distance are used to build a phylogenetic tree and cluster analysis, to determine the molecular relatedness of cultivars. The protocol describes 3 out of 9 tested primers consistently amplified 31 loci in 6 date palm cultivars, with 28 polymorphic loci.

Teaching Melodic Dictation in Advanced Placement Music Theory

Science.gov (United States)

Paney, Andrew S.; Buonviri, Nathan O.

2014-01-01

In this study approaches to teaching melodic dictation skills used by Advanced Placement (AP) Music Theory teachers were examined. Twelve high school teachers from four states were interviewed. Four themes emerged from the interview transcripts: cognitive frameworks, processing strategies, rhythm, and course design. Participants generally…

Genetic plasticity of the Shigella virulence plasmid is mediated by intra- and inter-molecular events between insertion sequences.

Science.gov (United States)

Pilla, Giulia; McVicker, Gareth; Tang, Christoph M

2017-09-01

Acquisition of a single copy, large virulence plasmid, pINV, led to the emergence of Shigella spp. from Escherichia coli. The plasmid encodes a Type III secretion system (T3SS) on a 30 kb pathogenicity island (PAI), and is maintained in a bacterial population through a series of toxin:antitoxin (TA) systems which mediate post-segregational killing (PSK). The T3SS imposes a significant cost on the bacterium, and strains which have lost the plasmid and/or genes encoding the T3SS grow faster than wild-type strains in the laboratory, and fail to bind the indicator dye Congo Red (CR). Our aim was to define the molecular events in Shigella flexneri that cause loss of Type III secretion (T3S), and to examine whether TA systems exert positional effects on pINV. During growth at 37°C, we found that deletions of regions of the plasmid including the PAI lead to the emergence of CR-negative colonies; deletions occur through intra-molecular recombination events between insertion sequences (ISs) flanking the PAI. Furthermore, by repositioning MvpAT (which belongs to the VapBC family of TA systems) near the PAI, we demonstrate that the location of this TA system alters the rearrangements that lead to loss of T3S, indicating that MvpAT acts both globally (by reducing loss of pINV through PSK) as well as locally (by preventing loss of adjacent sequences). During growth at environmental temperatures, we show for the first time that pINV spontaneously integrates into different sites in the chromosome, and this is mediated by inter-molecular events involving IS1294. Integration leads to reduced PAI gene expression and impaired secretion through the T3SS, while excision of pINV from the chromosome restores T3SS function. Therefore, pINV integration provides a reversible mechanism for Shigella to circumvent the metabolic burden imposed by pINV. Intra- and inter-molecular events between ISs, which are abundant in Shigella spp., mediate plasticity of S. flexneri pINV.

The effect of $1, $5 and $10 stakes in an online dictator game.

Directory of Open Access Journals (Sweden)

Nichola J Raihani

Full Text Available The decision rules underpinning human cooperative behaviour are often investigated under laboratory conditions using monetary incentives. A major concern with this approach is that stake size may bias subjects' decisions. This concern is particularly acute in online studies, where stakes are often far lower than those used in laboratory or field settings. We address this concern by conducting a Dictator Game using Amazon Mechanical Turk. In this two-player game, one player (the dictator determines the division of an endowment between himself and the other player. We recruited subjects from India and the USA to play an online Dictator Game. Dictators received endowments of $1, $5 or $10. We collected two batches of data over two consecutive years. We found that players from India were less generous when playing with a $10 stake. By contrast, the effect of stake size among players from the USA was very small. This study indicates that the effects of stake size on decision making in economic games may vary across populations.

Inter-library Service Brokerage in LicenseScript

NARCIS (Netherlands)

Chong, C.N.; Etalle, Sandro; Hartel, Pieter H.; Joosten, Rieks; Kleinhuis, Geert

Inter-library loan involves interaction among a dynamic number of digital libraries and users. Therefore, inter-library service management is complex. We need to handle different and conflicting requirements of services from the digital libraries and users. To resolve this problem, we present the

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems

Science.gov (United States)

Kruse, Holger; Grimme, Stefan

2012-04-01

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

A geometrical correction for the inter- and intra-molecular basis set superposition error in Hartree-Fock and density functional theory calculations for large systems.

Science.gov (United States)

Kruse, Holger; Grimme, Stefan

2012-04-21

A semi-empirical counterpoise-type correction for basis set superposition error (BSSE) in molecular systems is presented. An atom pair-wise potential corrects for the inter- and intra-molecular BSSE in supermolecular Hartree-Fock (HF) or density functional theory (DFT) calculations. This geometrical counterpoise (gCP) denoted scheme depends only on the molecular geometry, i.e., no input from the electronic wave-function is required and hence is applicable to molecules with ten thousands of atoms. The four necessary parameters have been determined by a fit to standard Boys and Bernadi counterpoise corrections for Hobza's S66×8 set of non-covalently bound complexes (528 data points). The method's target are small basis sets (e.g., minimal, split-valence, 6-31G*), but reliable results are also obtained for larger triple-ζ sets. The intermolecular BSSE is calculated by gCP within a typical error of 10%-30% that proves sufficient in many practical applications. The approach is suggested as a quantitative correction in production work and can also be routinely applied to estimate the magnitude of the BSSE beforehand. The applicability for biomolecules as the primary target is tested for the crambin protein, where gCP removes intramolecular BSSE effectively and yields conformational energies comparable to def2-TZVP basis results. Good mutual agreement is also found with Jensen's ACP(4) scheme, estimating the intramolecular BSSE in the phenylalanine-glycine-phenylalanine tripeptide, for which also a relaxed rotational energy profile is presented. A variety of minimal and double-ζ basis sets combined with gCP and the dispersion corrections DFT-D3 and DFT-NL are successfully benchmarked on the S22 and S66 sets of non-covalent interactions. Outstanding performance with a mean absolute deviation (MAD) of 0.51 kcal/mol (0.38 kcal/mol after D3-refit) is obtained at the gCP-corrected HF-D3/(minimal basis) level for the S66 benchmark. The gCP-corrected B3LYP-D3/6-31G* model

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.

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.

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 ...

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

Propagator formalism and computer simulation of restricted diffusion behaviors of inter-molecular multiple-quantum coherences

International Nuclear Information System (INIS)

Cai Congbo; Chen Zhong; Cai Shuhui; Zhong Jianhui

2005-01-01

In this paper, behaviors of single-quantum coherences and inter-molecular multiple-quantum coherences under restricted diffusion in nuclear magnetic resonance experiments were investigated. The propagator formalism based on the loss of spin phase memory during random motion was applied to describe the diffusion-induced signal attenuation. The exact expression of the signal attenuation under the short gradient pulse approximation for restricted diffusion between two parallel plates was obtained using this propagator method. For long gradient pulses, a modified formalism was proposed. The simulated signal attenuation under the effects of gradient pulses of different width based on the Monte Carlo method agrees with the theoretical predictions. The propagator formalism and computer simulation can provide convenient, intuitive and precise methods for the study of the diffusion behaviors

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.

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.

Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

Directory of Open Access Journals (Sweden)

Gabrielle Stetz

2017-01-01

Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

Heat conduction in chain polymer liquids: molecular dynamics study on the contributions of inter- and intramolecular energy transfer.

Science.gov (United States)

Ohara, Taku; Yuan, Tan Chia; Torii, Daichi; Kikugawa, Gota; Kosugi, Naohiro

2011-07-21

In this paper, the molecular mechanisms which determine the thermal conductivity of long chain polymer liquids are discussed, based on the results observed in molecular dynamics simulations. Linear n-alkanes, which are typical polymer molecules, were chosen as the target of our studies. Non-equilibrium molecular dynamics simulations of bulk liquid n-alkanes under a constant temperature gradient were performed. Saturated liquids of n-alkanes with six different chain lengths were examined at the same reduced temperature (0.7T(c)), and the contributions of inter- and intramolecular energy transfer to heat conduction flux, which were identified as components of heat flux by the authors' previous study [J. Chem. Phys. 128, 044504 (2008)], were observed. The present study compared n-alkane liquids with various molecular lengths at the same reduced temperature and corresponding saturated densities, and found that the contribution of intramolecular energy transfer to the total heat flux, relative to that of intermolecular energy transfer, increased with the molecular length. The study revealed that in long chain polymer liquids, thermal energy is mainly transferred in the space along the stiff intramolecular bonds. This finding implies a connection between anisotropic thermal conductivity and the orientation of molecules in various organized structures with long polymer molecules aligned in a certain direction, which includes confined polymer liquids and self-organized structures such as membranes of amphiphilic molecules in water.

Social evaluation-induced amylase elevation and economic decision-making in the dictator game in humans.

Science.gov (United States)

Takahashi, Taiki; Ikeda, Koki; Hasegawa, Toshikazu

2007-10-01

Little is known regarding the relationship between social evaluation-induced neuroendocrine responses and generosity in game-theoretic situations. Previous studies demonstrated that reputation formation plays a pivotal role in prosocial behavior. This study aimed to examine the relationships between a social evaluation-induced salivary alpha-amylase (sAA) response and generosity in the dictator game. The relationship is potentially important in neuroeconomics of altruism and game theory. We assessed sAA and allocated money in the dictator game in male students with and without social evaluation. RESULTS Social evaluation-responders allocated significantly more money than controls; while there was no significant correlation between social evaluation-induced sAA elevation and the allocated money. Social evaluation significantly increases generosity in the dictator game, and individual differences in trait characteristics such as altruism and reward sensitivity may be important determinants of generosity in the dictator game task.

Management accounting as the inter-organisational boundary

DEFF Research Database (Denmark)

Jakobsen, Morten

2010-01-01

Purpose - The literature on managing inter-organisational relationships typically suggests managing these relationships based on the formalised exchange of information across the organisational boundary with due respect to trust build-up through successive interactions. This article argues...... that a focus on trust reduces the flexibility and accessibility of resources and hence ruins the advantages of inter-organisational relationships. The article focuses on power as a means for absorbing uncertainty when managing inter-organisational relationships. Methodology - The article is based on findings...... from a case study of inter-organisational relationships. Governmentality is used as a framework for analysing the practise of managing inter-organisational relationships. Findings - A number of representations are employed along the boundary between the case study parties and thereby the boundary...

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

Solid state synthesis, structural, physicochemical and optical properties of an inter-molecular compound: 2-hydroxy-1, 2-diphenylethanone-4-nitro-o-phenylenediamine system

Science.gov (United States)

Rai, U. S.; Singh, Manjeet; Rai, R. N.

2017-09-01

The phase diagram of 2-hydroxy-1, 2-diphenylethanone (HDPE)-4-nitro-o-phenylenediamine (NOPDA) system, determined by the thaw-melt method, gives two eutectics E1 (m p = 66.0 °C) and E2 (m p = 155.0 °C) with 0.30 and 0.55 mol fractions of NOPDA, respectively, and an 1:1 inter-molecular compound (IMC) (m p 162.0 °C). This IMC was synthesized by adopting the green synthetic method of solid state reaction. While its formation and structure were confirmed by the X-ray diffraction and spectroscopic methods, the ORTEP view gives mode of crystal packing, C‒H…O, C‒H…N, π-π stacking and the inter-molecular hydrogen bonding in the compound. The single crystal of the IMC shows 53% transmission and emits significantly higher dual fluorescence, and the band gap was computed to be 3.04 eV. The values of solubility of the IMC, measured in the temperature range 304-322 K, satisfy the mole fraction (X) and temperature equation: Xeq= 5.1324 × 10-7 e 0.01356T.

Reversible Self-Assembly of Supramolecular Vesicles and Nanofibers Driven by Chalcogen-Bonding Interactions.

Science.gov (United States)

Chen, Liang; Xiang, Jun; Zhao, Yue; Yan, Qiang

2018-05-29

Chalcogen-bonding interactions have been viewed as new noncovalent forces in supramolecular chemistry. However, harnessing chalcogen bonds to drive molecular self-assembly processes is still unexplored. Here we report for the first time a novel class of supra-amphiphiles formed by Te···O or Se···O chalcogen-bonding interactions, and their self-assembly into supramolecular vesicles and nanofibers. A quasi-calix[4]chalcogenadiazole (C4Ch) as macrocyclic donor and a tailed pyridine N-oxide surfactant as molecular acceptor are designed to construct the donor-acceptor complex via chalcogen-chalcogen connection between the chalcogenadiazole moieties and oxide anion. The affinity of such chalcogen-bonding can dictate the geometry of supra-amphiphiles, driving diverse self-assembled morphologies. Furthermore, the reversible disassembly of these nanostructures can be promoted by introducing competing anions, such as halide ions, or by decreasing the systemic pH value.

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.

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.

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

The locus of word frequency effects in skilled spelling-to-dictation.

Science.gov (United States)

Chua, Shi Min; Liow, Susan J Rickard

2014-01-01

In spelling-to-dictation tasks, skilled spellers consistently initiate spelling of high-frequency words faster than that of low-frequency words. Tainturier and Rapp's model of spelling shows three possible loci for this frequency effect: spoken word recognition, orthographic retrieval, and response execution of the first letter. Thus far, researchers have attributed the effect solely to orthographic retrieval without considering spoken word recognition or response execution. To investigate word frequency effects at each of these three loci, Experiment 1 involved a delayed spelling-to-dictation task and Experiment 2 involved a delayed/uncertain task. In Experiment 1, no frequency effect was found in the 1200-ms delayed condition, suggesting that response execution is not affected by word frequency. In Experiment 2, no frequency effect was found in the delayed/uncertain task that reflects the orthographic retrieval, whereas a frequency effect was found in the comparison immediate/uncertain task that reflects both spoken word recognition and orthographic retrieval. The results of this two-part study suggest that frequency effects in spoken word recognition play a substantial role in skilled spelling-to-dictation. Discrepancies between these findings and previous research, and the limitations of the present study, are discussed.

4. Assessment Typologies Used Within the Discipline Theory, Solfeggio, Musical Dictation

Directory of Open Access Journals (Sweden)

Duţică Luminiţa

2018-03-01

Full Text Available Assessment is a distinct stage within the teaching process, aiming to measure the level of the knowledge, skills and competences acquired within a given time frame. The discipline Theory, Solfeggio, Musical Dictation involves a synthesis between the theoretical and the practical side of the matter, and, as a result, it uses specific assessment tools for each side. Modern assessment methods involve personalized systems based on the diversification of types of docimological tests, quizzes, practical tests, etc. In this study we will present a series of personal contributions referring to the contents specific to the discipline Theory, Solfeggio, Musical Dictation taught at university.

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.

Interactions inter/intra stades de développement et régénération de ...

African Journals Online (AJOL)

SARAH

31 janv. 2014 ... Objectifs : Cette étude a été réalisée dans l'objectif de comprendre la dynamique de régénération via la répartition spatiale et interaction inter/intra stade ... mécanismes de recrutement dans les populations d'arbres indigènes du miombo katangais et de l'autre d'approfondir les connaissances concernant ...

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.

Molecular diversity analysis of Tetradium ruticarpum (WuZhuYu) in China based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers.

Science.gov (United States)

Xu, Jing-Yuan; Zhu, Yan; Yi, Ze; Wu, Gang; Xie, Guo-Yong; Qin, Min-Jian

2018-01-01

"Wu zhu yu", which is obtained from the dried unripe fruits of Tetradium ruticarpum (A. Jussieu) T. G. Hartley, has been used as a traditional Chinese medicine for treatment of headaches, abdominal colic, and hypertension for thousands of years. The present study was designed to assess the molecular genetic diversity among 25 collected accessions of T. ruticarpum (Wu zhu yu in Chinese) from different areas of China, based on inter-primer binding site (iPBS) markers and inter-simple sequence repeat (ISSR) markers. Thirteen ISSR primers generated 151 amplification bands, of which 130 were polymorphic. Out of 165 bands that were amplified using 10 iPBS primers, 152 were polymorphic. The iPBS markers displayed a higher proportion of polymorphic loci (PPL = 92.5%) than the ISSR markers (PPL = 84.9%). The results showed that T. ruticarpum possessed high loci polymorphism and genetic differentiation occurred in this plant. The combined data of iPBS and ISSR markers scored on 25 accessions produced five clusters that approximately matched the geographic distribution of the species. The results indicated that both iPBS and ISSR markers were reliable and effective tools for analyzing the genetic diversity in T. ruticarpum. Copyright © 2018 China Pharmaceutical University. Published by Elsevier B.V. All rights reserved.

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.

Outlining and dictating scientific manuscripts is a useful method for health researchers: A focus group interview.

Science.gov (United States)

Andresen, Kristoffer; Laursen, Jannie; Rosenberg, Jacob

2018-01-01

Young researchers may experience difficulties when writing scientific articles for publication in biomedical journals. Various methods may facilitate the writing process including outlining the paper before the actual writing and using dictation instead of writing the first draft. The aim of this study was to investigate the experiences and difficulties for young, experienced researchers when writing articles using a detailed outline and dictation of the first draft. We used qualitative focus group interviews and the study was reported according to the COnsolidated criteria for REporting Qualitative research guideline. Participants were sampled from a group of researchers participating in a writing retreat/course. The interviews were recorded on a digital recorder and transcribed. The text was analyzed according to content analysis and coded and condensed into themes and subthemes. Groups of participants were added until data saturation was reached. A total of 14 researchers participated (9 women and 5 men). Their clinical experience was median (range) of 6 (1-11) years since graduation from medical school. Two themes arose during the analyses of the data: "Process guidance with the outline as the map" and "arrival at dictation." The outline was used in the preparation phase leading up to the day of dictation and was used in collaboration with co-authors and supervisors. The participants found it to be a useful tool for preparing the manuscript and dictating their initial first full draft. Experienced young researchers found beneficial effects of using a structured outline to prepare for dictation of scientific articles. The outline was a tool that would develop in close collaboration with co-authors and mentors. With dictation, a full first draft of a manuscript can be produced in a few hours. Participants positively evaluated this structured and reproducible way of producing scientific articles.

A molecular dynamics study of the structure and inter-particle interactions of polyethylene glycol-conjugated PAMAM dendrimers

OpenAIRE

Lee, Hwankyu; Larson, Ronald G.

2009-01-01

We performed molecular dynamics (MD) simulations of one or two copies of polyethylene glycol of molecular weight 550 (PEG550) and 5000 (PEG5000) Daltons, conjugated to generation 3 (G3) to 5 (G5) polyamidoamine (PAMAM) dendrimers with explicit water using a coarse-grained model. We found the radii of gyration of these dendrimer-PEG molecules to be close to those measured in experiments by Hedden and Bauer (Macromolecules 2003, 36, 1829). Densely grafted PEG ligands (>50% of the dendrimer surf...

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.

English-to-Japanese Translation vs. Dictation vs. Post-editing

DEFF Research Database (Denmark)

Carl, Michael; Aizawa, Akiko; Yamada, Masaru

2016-01-01

of text production. This paper introduces and evaluates a corpus of more than 55 hours of English-to-Japanese user activity data that were collected within the ENJA15 project, in which translators were observed while writing and speaking translations (translation dictation) and during machine translation...

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

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.

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.

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

Specific acoustic models for spontaneous and dictated style in indonesian speech recognition

Science.gov (United States)

Vista, C. B.; Satriawan, C. H.; Lestari, D. P.; Widyantoro, D. H.

2018-03-01

The performance of an automatic speech recognition system is affected by differences in speech style between the data the model is originally trained upon and incoming speech to be recognized. In this paper, the usage of GMM-HMM acoustic models for specific speech styles is investigated. We develop two systems for the experiments; the first employs a speech style classifier to predict the speech style of incoming speech, either spontaneous or dictated, then decodes this speech using an acoustic model specifically trained for that speech style. The second system uses both acoustic models to recognise incoming speech and decides upon a final result by calculating a confidence score of decoding. Results show that training specific acoustic models for spontaneous and dictated speech styles confers a slight recognition advantage as compared to a baseline model trained on a mixture of spontaneous and dictated training data. In addition, the speech style classifier approach of the first system produced slightly more accurate results than the confidence scoring employed in the second system.

Give and Take in Dictator Games

DEFF Research Database (Denmark)

Cappelen, Alexander W.; Nielsen, Ulrik Haagen; Sørensen, Erik Ø.

2014-01-01

It has been shown that participants in the dictator game are less willing to give money to the other participant when their choice set also includes the option to take money. We examine whether this effect is due to the choice set providing a signal about entitlements in a setting where...... entitlements initially may be considered unclear. We find that the share of positive transfers depends on the choice set even when there is no uncertainty about entitlements, and that this choice-set effect is robust across a heterogenous group of participants recruited from the general adult population...

The bystander effect in an N-person dictator game

NARCIS (Netherlands)

Panchanathan, K.; Frankenhuis, W.E.; Silk, J.B.

2013-01-01

Dozens of studies show that bystanders are less likely to help victims as bystander number increases. However, these studies model one particular situation, in which victims need only one helper. Using a multi-player dictator game, we study a different but common situation, in which a recipient’s

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

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.

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

The molecular nature of photovoltage losses in organic solar cells

KAUST Repository

Schlenker, Cody W.

2011-01-01

Since the inception of heterojunction organic photovoltaic research the organic/organic interface has been thought to play a crucial role in determining the magnitude of the open-circuit voltage. Yet, the task of defining the molecular properties dictating the photovoltage delivered by these devices, that employ mixed or neat layers of different organic molecules to convert incident photons to electricity, is still an active area of research. This will likely be a key step in designing the new materials required for improving future device efficiencies. With the intent to underscore the importance of considering both thermodynamic and kinetic factors, this article highlights recent progress in elucidating molecular characteristics dictating photovoltage losses in heterojunction organic photovoltaics. © The Royal Society of Chemistry.

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...

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.

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.

Efficient small molecule bulk heterojunction solar cells with high fill factors via pyrene-directed molecular self-assembly

KAUST Repository

Lee, Olivia P.; Yiu, Alan T.; Beaujuge, Pierre; Woo, Claire; Holcombe, Thomas W.; Millstone, Jill E.; Douglas, Jessica D.; Chen, Mark S.; Frechet, Jean

2011-01-01

Efficient organic photovoltaic (OPV) materials are constructed by attaching completely planar, symmetric end-groups to donor-acceptor electroactive small molecules. Appending C2-pyrene as the small molecule end-group to a diketopyrrolopyrrole core leads to materials with a tight, aligned crystal packing and favorable morphology dictated by π-π interactions, resulting in high power conversion efficiencies and high fill factors. The use of end-groups to direct molecular self-assembly is an effective strategy for designing high-performance small molecule OPV devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Efficient small molecule bulk heterojunction solar cells with high fill factors via pyrene-directed molecular self-assembly

KAUST Repository

Lee, Olivia P.

2011-10-21

Efficient organic photovoltaic (OPV) materials are constructed by attaching completely planar, symmetric end-groups to donor-acceptor electroactive small molecules. Appending C2-pyrene as the small molecule end-group to a diketopyrrolopyrrole core leads to materials with a tight, aligned crystal packing and favorable morphology dictated by π-π interactions, resulting in high power conversion efficiencies and high fill factors. The use of end-groups to direct molecular self-assembly is an effective strategy for designing high-performance small molecule OPV devices. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

A novel epistatic interaction at two loci causing hybrid male sterility in an inter-subspecific cross of rice (Oryza sativa L.).

Science.gov (United States)

Kubo, Takahiko; Yamagata, Yoshiyuki; Eguchi, Maki; Yoshimura, Atsushi

2008-12-01

Postzygotic reproductive isolation (RI) often arises in inter-subspecific crosses as well as inter-specific crosses of rice (Oryza sativa L.). To further understand the genetic architecture of the postzygotic RI, we analyzed genes causing hybrid sterility and hybrid breakdown in a rice inter-subspecific cross. Here we report hybrid male sterility caused by epistatic interaction between two novel genes, S24 and S35, which were identified on rice chromosomes 5 and 1, respectively. Genetic analysis using near-isogenic lines (NILs) carrying IR24 (ssp. indica) segments with Asominori (ssp. japonica) genetic background revealed a complicated aspect of the epistasis. Allelic interaction at the S24 locus in the heterozygous plants caused abortion of male gametes carrying the Asominori allele (S24-as) independent of the S35 genotype. On the other hand, male gametes carrying the Asominori allele at the S35 locus (S35-as) showed abortion only when the IR24 allele at the S24 locus (S24-ir) was concurrently introgressed into the S35 heterozygous plants, indicating that the sterility phenotype due to S35 was dependent on the S24 genotype through negative epistasis between S24-ir and S35-as alleles. Due to the interaction between S24 and S35, self-pollination of the double heterozygous plants produced pollen-sterile progeny carrying the S24-ir/S24-ir S35-as/S35-ir genotype in addition to the S24 heterozygous plants. This result suggests that the S35 gene might function as a modifier of S24. This study presents strong evidence for the importance of epistatic interaction as a part of the genetic architecture of hybrid sterility in rice. In addition, it suggests that diverse systems have been developed as postzygotic RI mechanisms within the rice.

Partner Selection and the Division of Surplus: Evidence from Ultimatum and Dictator Experiments

Directory of Open Access Journals (Sweden)

Priyodorshi Banerjee

2016-01-01

Full Text Available We study ultimatum and dictator environments with one-way, unenforceable pre-play communication from the proposer to the recipient, semantically framed as a promise. After observing this promise regarding how much the proposer will offer if selected, in our treatment conditions, recipients choose whether or not to select a particular proposer. We find that offers can increase in the ultimatum game both with non-competitive selection with a single potential proposer, and more so with competition, where the recipient chooses one of two potential proposers, as compared to the no selection baseline. Furthermore, the offer is rejected with higher probability if the promisemade by the selected proposer is higher than the eventual offer. Our dictator environment does not give the power to reject offers, thus selection power carries no benefits in the dictator game. Finally, independent of the game institution or proposer selection mechanism, promises provide credible signals for offers.

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.

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.

Molecular characterization of Fagaceae species using inter-primer binding site (iPBS) markers.

Science.gov (United States)

Coutinho, João Paulo; Carvalho, Ana; Martín, Antonio; Lima-Brito, José

2018-04-01

Retrotransposons (RTNs) contribute for genome evolution, influencing its size and structure. We investigated the utility of the RTN-based markers inter-primer binding site (iPBS) for the molecular characterization of 25 Fagaceae species from genera Castanea, Fagus and Quercus. The assessment of genetic diversity, relationships and structure, as well as taxonomic classification of Fagaceae based on molecular data is important for definition of conservation, forestry management strategies and discrimination among natural hybrids and their parents since natural hybridization may increase with the climate changes. Here, iPBS primers designed by other authors were tested alone and combined. Some of them were discriminative, revealed polymorphism within and among taxa allowing the production of a total of 150 iPBS markers. In addition, several monomorphic iPBS markers were also amplified in each taxon. The UPGMA dendrogram based on the pooled iPBS data revealed 27% of genetic similarity among species. The individuals were clustered per genus and most of the oaks per infrageneric group corroborating the adopted taxonomy. Globally, the iPBS markers demonstrated suitability for DNA fingerprinting, determination of phylogenies and taxonomic discrimination in Fagaceae, and could constitute a useful and alternative tool for germplasm characterization, and for definition of conservation strategies and forestry management. Moreover, these markers would be useful for fingerprinting natural hybrids that share morphological similarities with their parents. Since iPBS markers could also enable insights about RTNs evolution, an eventual correlation among iPBS polymorphism, variability of RTN insertions and/or genome size in Fagaceae is discussed.

Parallel inter channel interaction mechanisms

International Nuclear Information System (INIS)

Jovic, V.; Afgan, N.; Jovic, L.

1995-01-01

Parallel channels interactions are examined. For experimental researches of nonstationary regimes flow in three parallel vertical channels results of phenomenon analysis and mechanisms of parallel channel interaction for adiabatic condition of one-phase fluid and two-phase mixture flow are shown. (author)

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.

Future directions for radiological physics: An interface with molecular biology

International Nuclear Information System (INIS)

Braby, L.A.

1987-01-01

Recent experiments with low energy x-rays and fast molecular ions have shown that the products of the interaction of several ionizations within a few nanometers dominate radiation effects. However, the authors still can only make assumptions about the physical and chemical nature of this initial damage. Enzymatic repair of DNA damage is another key factor, but they have little idea of what governs the success or failure (misrepair) of these processes. Unresolved problems like these dictate the future direction of radiological physics. Molecular biology techniques are being applied to determine molecular alterations which result in observed damage. Interpretation of these experiments will require new data on the physics of energy transfer to macromolecules and the stochastics of energy deposition in time. Future studies will attempt to identify the initial damage, before biological processes have amplified it. This will require a detailed understanding of the role of chromatin structure in governing gene expression, the transport of energy within macromolecules, the transport of ions and radicals in the semiordered environment near DNA strands, and many other physical characteristics within the living cell

Inter-disciplinary Interactions in Underground Laboratories

Science.gov (United States)

Wang, J. S.; Bettini, A.

2010-12-01

facilities needed for next generation of underground assessments and experiments. There are growing interests in developing multi-disciplinary programs in DULs and some URLs have rooms set aside for physics experiments. Examples of DULs and URLs with interactions between earth sciences and physics include Gran Sasso in Italy, Kaimioka in Japan, Canfranc in Spain, LSBB in France, WIPP in New Mexico, DUSEL in South Dakota, and Jing Ping deep tunnel underground laboratory proposal in China. Instruments of common interests include interferometers, laser strain meters, seismic networks, tiltmeters, gravimeters, magnetometers, and other sensors to detect signals over different frequencies and water chemical analyses, including radon concentrations. Radon emissions are of concern for physics experiments and are studied as possible precursors of earthquakes. Measuring geoneutrino flux and energy spectrum in different locations is of interests to both physics and earth sciences. The contributions of U and Th in the crust and the mantle to the energy production in the Earth can be studied. One final note is that our ongoing reviews are aimed to contribute to technological innovations anticipated through inter-disciplinary interactions.

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.

Distinct Functional Domains of Ubc9 Dictate Cell Survival and Resistance to Genotoxic Stress

Science.gov (United States)

van Waardenburg, Robert C. A. M.; Duda, David M.; Lancaster, Cynthia S.; Schulman, Brenda A.; Bjornsti, Mary-Ann

2006-01-01

Covalent modification with SUMO alters protein function, intracellular localization, or protein-protein interactions. Target recognition is determined, in part, by the SUMO E2 enzyme, Ubc9, while Siz/Pias E3 ligases may facilitate select interactions by acting as substrate adaptors. A yeast conditional Ubc9P123L mutant was viable at 36°C yet exhibited enhanced sensitivity to DNA damage. To define functional domains in Ubc9 that dictate cellular responses to genotoxic stress versus those necessary for cell viability, a 1.75-Å structure of yeast Ubc9 that demonstrated considerable conservation of backbone architecture with human Ubc9 was solved. Nevertheless, differences in side chain geometry/charge guided the design of human/yeast chimeras, where swapping domains implicated in (i) binding residues within substrates that flank canonical SUMOylation sites, (ii) interactions with the RanBP2 E3 ligase, and (iii) binding of the heterodimeric E1 and SUMO had distinct effects on cell growth and resistance to DNA-damaging agents. Our findings establish a functional interaction between N-terminal and substrate-binding domains of Ubc9 and distinguish the activities of E3 ligases Siz1 and Siz2 in regulating cellular responses to genotoxic stress. PMID:16782883

Human immunodeficiencies related to APC/T cell interaction

Directory of Open Access Journals (Sweden)

Marinos eKallikourdis

2015-08-01

Full Text Available The primary event for initiating adaptive immune responses is the encounter between T lymphocytes and antigen presenting cells (APC in the T cell area of secondary lymphoid organs and the formation of highly organized inter-cellular junctions referred to as the immune synapses. In vivo live-cell imaging of APC-T cell interactions combined to functional studies unveiled that T cell fate is dictated, in large part, by the stability of the initial contact. Immune cell interaction is equally important during delivery of T cell help to B cells and for the killing of target cells by cytotoxic T cells and NK cells. The critical role of contact dynamics and synapse stability on the immune response is well illustrated by human immune deficiencies in which disease pathogenesis is linked to altered adhesion or defective cross-talk between the synaptic partners. Here we will discuss in details the mechanisms of defective APC-T cell communications in Wiskott-Aldrich syndrome (WAS and in warts, hypogammaglobulinemia, infections, myelokathexis syndrome (WHIM. In addition, we will summarize the evidences pointing to a compromised conjugate formation in WIP deficiency, DOCK8 deficiency and X-linked lymphoproliferative syndrome.

Factors responsible for the aggregation behavior of hydrophobic polyelectrolyte PEA in aqueous solution studied by molecular dynamics simulations.

Science.gov (United States)

Sappidi, Praveenkumar; Natarajan, Upendra

2017-08-01

Self-association (i.e. interchain aggregation) behavior of atactic poly(ethacrylic acid) PEA in dilute aqueous solution as function of degree-of-neutralization by Na + counter-ions (i.e. charge fraction f) was investigated by molecular dynamics simulations. Aggregation is found to occur in the range 0≤f≤0.7 in agreement with experimental results compared at specified polymer concentration C p =0.36mol/l in dilute solution. The macromolecular solution was characterized and analysed for radius-of-gyration, torsion angle distribution, inter and intra-molecular hydrogen bonds, radial distribution functions of intermolecular and inter-atomic pairs, inter-chain contacts and solvation enthalpy. The PEA chains form aggregate through attractive inter-chain interaction via hydrogen bonding, in the range fenthalpy. The PEA solvation enthalpy becomes increasingly favorable with increase in f. The transition enthalpy change, in going from uncharged (acid) state to fully charged state (f=1) is unfavorable towards aggregate formation. Copyright © 2017 Elsevier Inc. All rights reserved.

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.

The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation

DEFF Research Database (Denmark)

Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu

2017-01-01

clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been....... Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur....... proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes...

Report on achievements in fiscal 1998. Development of a technology to measure biological molecular interactions; 1998 nendo seitai bunshi sogo sayo no keisoku gijutsu no kaihatsu seika hokokusho

Energy Technology Data Exchange (ETDEWEB)

NONE

2000-03-01

It has been indicated possible in principle in recent years to measure biological molecular interactions with the molecules in the living state by combining the technologies called the co-focussing optical system and the fluorescence correlation spectroscopy (FCS). The FCS method is a method capable of analyzing concentrations, sizes, and inter-molecule interactions through detection of fluorescence fluctuation in single molecules in submicron zones. In spite of the FCS method being a very effective method to measure interactions in biological molecules, the technology has not reached a level that allows easy utilization under the present condition. The present research and development is intended to solve the technological problems in the FCS method in the co-focussing optical system, and perform as many research and development works as possible in a short time to establish a technological foundation that can be provided to bio-industrial and medical sites. Particularly, in order to make the utilization thereof possible in measuring biological molecular interactions in cells, a measuring technology using the bi-photon excited fluorescence correlation spectroscopy was established with an objective to reduce damages to cells and their internal micro organs, and minimize effects of interference signals from the own fluorescence. (NEDO)

Conceptual strategies and inter-theory relations: The case of nanoscale cracks

Science.gov (United States)

Bursten, Julia R.

2018-05-01

This paper introduces a new account of inter-theory relations in physics, which I call the conceptual strategies account. Using the example of a multiscale computer simulation model of nanoscale crack propagation in silicon, I illustrate this account and contrast it with existing reductive, emergent, and handshaking approaches. The conceptual strategies account develops the notion that relations among physical theories, and among their models, are constrained but not dictated by limitations from physics, mathematics, and computation, and that conceptual reasoning within those limits is required both to generate and to understand the relations between theories. Conceptual strategies result in a variety of types of relations between theories and models. These relations are themselves epistemic objects, like theories and models, and as such are an under-recognized part of the epistemic landscape of science.

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.

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.

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.

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...

Inter-relationships of haplosporidians deduced from ultrastructural studies

NARCIS (Netherlands)

Hine, P.M.; Carnegie, R.B.; Burreson, E.M.; Engelsma, M.Y.

2009-01-01

We reviewed papers reporting haplosporidian ultrastructure to compare inter-relationships based on ultrastructure with those based on molecular data, to identify features that may be important in haplosporidian taxonomy, and to consider parasite taxonomy in relation to host taxonomy. There were

Limitations of the Dual-Process-Theory regarding the Writing of Words and Non-Words to Dictation

Science.gov (United States)

Tucha, Oliver; Trumpp, Christian; Lange, Klaus W.

2004-01-01

It is generally assumed that the lexical and phonological systems are involved in writing to dictation. In an experiment concerned with the writing of words and non-words to dictation, the handwriting of female students was registered using a digitising tablet. The data contradict the assumption that the phonological system represents an alexical…

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 ...

Molecular determinants of tetramerization in the KcsA cytoplasmic domain.

Science.gov (United States)

Kamnesky, Guy; Hirschhorn, Orel; Shaked, Hadassa; Chen, Jingfei; Yao, Lishan; Chill, Jordan H

2014-10-01

The cytoplasmic C-terminal domain (CTD) of KcsA, a bacterial homotetrameric potassium channel, is an amphiphilic domain that forms a helical bundle with four-fold symmetry mediated by hydrophobic and electrostatic interactions. Previously we have established that a CTD-derived 34-residue peptide associates into a tetramer in a pH-dependent manner (Kamnesky et al., JMB 2012;418:237-247). Here we further investigate the molecular determinants of tetramer formation in the CTD by characterizing the kinetics of monomer-tetramer equilibrium for 10 alanine mutants using NMR, sedimentation equilibrium (SE) and molecular dynamics simulation. NMR and SE concur in finding single-residue contributions to tetramer stability to be in the 0.5 to 3.5 kcal/mol range. Hydrophobic interactions between residues lining the tetramer core generally contributed more to formation of tetramer than electrostatic interactions between residues R147, D149 and E152. In particular, alanine replacement of residue R147, a key contributor to inter-subunit salt bridges, resulted in only a minor effect on tetramer dissociation. Mutations outside of the inter-subunit interface also influenced tetramer stability by affecting the tetramerization on-rate, possibly by changing the inherent helical propensity of the peptide. These findings are interpreted in the context of established paradigms of protein-protein interactions and protein folding, and lay the groundwork for further studies of the CTD in full-length KcsA channels. © 2014 The Protein Society.

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...

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.)

Inter-brain synchronization during social interaction.

Directory of Open Access Journals (Sweden)

Guillaume Dumas

Full Text Available During social interaction, both participants are continuously active, each modifying their own actions in response to the continuously changing actions of the partner. This continuous mutual adaptation results in interactional synchrony to which both members contribute. Freely exchanging the role of imitator and model is a well-framed example of interactional synchrony resulting from a mutual behavioral negotiation. How the participants' brain activity underlies this process is currently a question that hyperscanning recordings allow us to explore. In particular, it remains largely unknown to what extent oscillatory synchronization could emerge between two brains during social interaction. To explore this issue, 18 participants paired as 9 dyads were recorded with dual-video and dual-EEG setups while they were engaged in spontaneous imitation of hand movements. We measured interactional synchrony and the turn-taking between model and imitator. We discovered by the use of nonlinear techniques that states of interactional synchrony correlate with the emergence of an interbrain synchronizing network in the alpha-mu band between the right centroparietal regions. These regions have been suggested to play a pivotal role in social interaction. Here, they acted symmetrically as key functional hubs in the interindividual brainweb. Additionally, neural synchronization became asymmetrical in the higher frequency bands possibly reflecting a top-down modulation of the roles of model and imitator in the ongoing interaction.

Statistical discovery of site inter-dependencies in sub-molecular hierarchical protein structuring.

Science.gov (United States)

Durston, Kirk K; Chiu, David Ky; Wong, Andrew Kc; Li, Gary Cl

2012-07-13

Much progress has been made in understanding the 3D structure of proteins using methods such as NMR and X-ray crystallography. The resulting 3D structures are extremely informative, but do not always reveal which sites and residues within the structure are of special importance. Recently, there are indications that multiple-residue, sub-domain structural relationships within the larger 3D consensus structure of a protein can be inferred from the analysis of the multiple sequence alignment data of a protein family. These intra-dependent clusters of associated sites are used to indicate hierarchical inter-residue relationships within the 3D structure. To reveal the patterns of associations among individual amino acids or sub-domain components within the structure, we apply a k-modes attribute (aligned site) clustering algorithm to the ubiquitin and transthyretin families in order to discover associations among groups of sites within the multiple sequence alignment. We then observe what these associations imply within the 3D structure of these two protein families. The k-modes site clustering algorithm we developed maximizes the intra-group interdependencies based on a normalized mutual information measure. The clusters formed correspond to sub-structural components or binding and interface locations. Applying this data-directed method to the ubiquitin and transthyretin protein family multiple sequence alignments as a test bed, we located numerous interesting associations of interdependent sites. These clusters were then arranged into cluster tree diagrams which revealed four structural sub-domains within the single domain structure of ubiquitin and a single large sub-domain within transthyretin associated with the interface among transthyretin monomers. In addition, several clusters of mutually interdependent sites were discovered for each protein family, each of which appear to play an important role in the molecular structure and/or function. Our results

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

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.

Probing stochastic inter-galactic magnetic fields using blazar-induced gamma ray halo morphology

Energy Technology Data Exchange (ETDEWEB)

Duplessis, Francis [Physics Department, Arizona State University, Tempe, AZ 85287 (United States); Vachaspati, Tanmay, E-mail: fdupless@asu.edu, E-mail: tvachasp@asu.edu [Maryland Center for Fundamental Physics, University of Maryland, College Park, MD 20742 (United States)

2017-05-01

Inter-galactic magnetic fields can imprint their structure on the morphology of blazar-induced gamma ray halos. We show that the halo morphology arises through the interplay of the source's jet and a two-dimensional surface dictated by the magnetic field. Through extensive numerical simulations, we generate mock halos created by stochastic magnetic fields with and without helicity, and study the dependence of the halo features on the properties of the magnetic field. We propose a sharper version of the Q-statistics and demonstrate its sensitivity to the magnetic field strength, the coherence scale, and the handedness of the helicity. We also identify and explain a new feature of the Q-statistics that can further enhance its power.

In situ study of the impact of inter- and intra-reader variability on region of interest (ROI) analysis in preclinical molecular imaging.

Science.gov (United States)

Habte, Frezghi; Budhiraja, Shradha; Keren, Shay; Doyle, Timothy C; Levin, Craig S; Paik, David S

2013-01-01

We estimated reader-dependent variability of region of interest (ROI) analysis and evaluated its impact on preclinical quantitative molecular imaging. To estimate reader variability, we used five independent image datasets acquired each using microPET and multispectral fluorescence imaging (MSFI). We also selected ten experienced researchers who utilize molecular imaging in the same environment that they typically perform their own studies. Nine investigators blinded to the data type completed the ROI analysis by drawing ROIs manually that delineate the tumor regions to the best of their knowledge and repeated the measurements three times, non-consecutively. Extracted mean intensities of voxels within each ROI are used to compute the coefficient of variation (CV) and characterize the inter- and intra-reader variability. The impact of variability was assessed through random samples iterated from normal distributions for control and experimental groups on hypothesis testing and computing statistical power by varying subject size, measured difference between groups and CV. The results indicate that inter-reader variability was 22.5% for microPET and 72.2% for MSFI. Additionally, mean intra-reader variability was 10.1% for microPET and 26.4% for MSFI. Repeated statistical testing showed that a total variability of CV variability has been observed mainly due to differences in the ROI placement and geometry drawn between readers, which may adversely affect statistical power and erroneously lead to negative study outcomes.

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

The structure of molecular liquids. Neutron diffraction and molecular dynamics simulations

International Nuclear Information System (INIS)

Bianchi, L.

2000-05-01

Neutron diffraction (ND) measurements on liquid methanol (CD 3 OD, CD 3 O(H/D), CD 3 OH) under ambient conditions were performed to obtain the distinct (intra- + inter-molecular), G dist (r) and inter-molecular, G inter (r) radial distribution functions (rdfs) for the three samples. The H/D substitution on hydroxyl-hydrogen (Ho) has been used to extract the partial distribution functions, G XHo (r) (X=C, O, and H - a methyl hydrogen) and G XX (r) at both the distinct and inter-molecular levels from the difference techniques of ND. The O-Ho bond length, which has been the subject of controversy in the past, is found purely from the distinct partial distribution function, G XHo (r) to be 0.98 ± 0.01 A. The C-H distance obtained from the distinct G XX (r) partial is 1.08 ± 0.01 A. These distances determined by fitting an intra-molecular model to the total distinct structure functions are 0.961 ± 0.001 A and 1.096 ± 0.001 A, respectively. The inter-molecular G XX (r) function, dominated by contributions from the methyl groups, apart from showing broad oscillations extending up to ∼14 A is featureless, mainly because of cancellation effects from six contributing pairs. The Ho-Ho partial pair distribution function (pdf), g HoHo (r), determined from the second order difference, shows that only one other Ho atom can be found within a mean Ho-Ho separation of 2.36 A. The average position of the O-Ho hydrogen bond determined for the first time purely from experimental inter-molecular G XHo (r) partial distribution function is found to be at 1.75 ± 0.03 A. The experimental structural results at the partial distribution level are compared with those obtained from molecular dynamics (MD) simulations performed in NVE ensemble by using both 3- and 6-site force field models for the first time in this study. The MD simulations with both the models reproduce the ND rdfs rather well. However, discrepancies begin to appear between the simulated and the experimental partial

Influence of the inter-ion interaction on the phase diagrams of the 1D Falicov-Kimball system

Science.gov (United States)

Gajek, Z.; Lemański, R.

2004-05-01

A model of itinerant, spinless electrons interacting with ions via the on-site Coulomb potential U, modified by the inter-ionic nearest-neighbour interaction V, is studied on the one-dimensional infinite lattice. Only periodical configurations of the ions with a limited number of lattice sites in a unit cell and their mixtures are taken into account. Phases whose energies reach minimum values for given electron and ion chemical potentials are selected and depicted for a set of model parameters. Then the results are translated into the ion density-electron density canonical phase diagrams and summarized in the electrondensity-U plane. The diagrams clearly show how various kinds of charge ordering evolve with V, starting from V=0 case, that represents the standard Falicov-Kimball model discussed previously.

Influence of the inter-ion interaction on the phase diagrams of the 1D Falicov-Kimball system

International Nuclear Information System (INIS)

Gajek, Z.; Lemanski, R.

2004-01-01

A model of itinerant, spinless electrons interacting with ions via the on-site Coulomb potential U, modified by the inter-ionic nearest-neighbour interaction V, is studied on the one-dimensional infinite lattice. Only periodical configurations of the ions with a limited number of lattice sites in a unit cell and their mixtures are taken into account. Phases whose energies reach minimum values for given electron and ion chemical potentials are selected and depicted for a set of model parameters. Then the results are translated into the ion density-electron density canonical phase diagrams and summarized in the electron density-U plane. The diagrams clearly show how various kinds of charge ordering evolve with V, starting from V=0 case, that represents the standard Falicov-Kimball model discussed previously

Influence of the inter-ion interaction on the phase diagrams of the 1D Falicov-Kimball system

Energy Technology Data Exchange (ETDEWEB)

Gajek, Z. E-mail: gajek@int.pan.wroc.pl; Lemanski, R

2004-05-01

A model of itinerant, spinless electrons interacting with ions via the on-site Coulomb potential U, modified by the inter-ionic nearest-neighbour interaction V, is studied on the one-dimensional infinite lattice. Only periodical configurations of the ions with a limited number of lattice sites in a unit cell and their mixtures are taken into account. Phases whose energies reach minimum values for given electron and ion chemical potentials are selected and depicted for a set of model parameters. Then the results are translated into the ion density-electron density canonical phase diagrams and summarized in the electron density-U plane. The diagrams clearly show how various kinds of charge ordering evolve with V, starting from V=0 case, that represents the standard Falicov-Kimball model discussed previously.

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

Molecular Recognition in the Colloidal World.

Science.gov (United States)

Elacqua, Elizabeth; Zheng, Xiaolong; Shillingford, Cicely; Liu, Mingzhu; Weck, Marcus

2017-11-21

Colloidal self-assembly is a bottom-up technique to fabricate functional nanomaterials, with paramount interest stemming from programmable assembly of smaller building blocks into dynamic crystalline domains and photonic materials. Multiple established colloidal platforms feature diverse shapes and bonding interactions, while achieving specific orientations along with short- and long-range order. A major impediment to their universal use as building blocks for predesigned architectures is the inability to precisely dictate and control particle functionalization and concomitant reversible self-assembly. Progress in colloidal self-assembly necessitates the development of strategies that endow bonding specificity and directionality within assemblies. Methodologies that emulate molecular and polymeric three-dimensional (3D) architectures feature elements of covalent bonding, while high-fidelity molecular recognition events have been installed to realize responsive reconfigurable assemblies. The emergence of anisotropic 'colloidal molecules', coupled with the ability to site-specifically decorate particle surfaces with supramolecular recognition motifs, has facilitated the formation of superstructures via directional interactions and shape recognition. In this Account, we describe supramolecular assembly routes to drive colloidal particles into precisely assembled architectures or crystalline lattices via directional noncovalent molecular interactions. The design principles are based upon the fabrication of colloidal particles bearing surface-exposed functional groups that can undergo programmable conjugation to install recognition motifs with high fidelity. Modular and versatile by design, our strategy allows for the introduction and integration of molecular recognition principles into the colloidal world. We define noncovalent molecular interactions as site-specific forces that are predictable (i.e., feature selective and controllable complementary bonding partners

NaviCell: a web-based environment for navigation, curation and maintenance of large molecular interaction maps.

Science.gov (United States)

Kuperstein, Inna; Cohen, David P A; Pook, Stuart; Viara, Eric; Calzone, Laurence; Barillot, Emmanuel; Zinovyev, Andrei

2013-10-07

Molecular biology knowledge can be formalized and systematically represented in a computer-readable form as a comprehensive map of molecular interactions. There exist an increasing number of maps of molecular interactions containing detailed and step-wise description of various cell mechanisms. It is difficult to explore these large maps, to organize discussion of their content and to maintain them. Several efforts were recently made to combine these capabilities together in one environment, and NaviCell is one of them. NaviCell is a web-based environment for exploiting large maps of molecular interactions, created in CellDesigner, allowing their easy exploration, curation and maintenance. It is characterized by a combination of three essential features: (1) efficient map browsing based on Google Maps; (2) semantic zooming for viewing different levels of details or of abstraction of the map and (3) integrated web-based blog for collecting community feedback. NaviCell can be easily used by experts in the field of molecular biology for studying molecular entities of interest in the context of signaling pathways and crosstalk between pathways within a global signaling network. NaviCell allows both exploration of detailed molecular mechanisms represented on the map and a more abstract view of the map up to a top-level modular representation. NaviCell greatly facilitates curation, maintenance and updating the comprehensive maps of molecular interactions in an interactive and user-friendly fashion due to an imbedded blogging system. NaviCell provides user-friendly exploration of large-scale maps of molecular interactions, thanks to Google Maps and WordPress interfaces, with which many users are already familiar. Semantic zooming which is used for navigating geographical maps is adopted for molecular maps in NaviCell, making any level of visualization readable. In addition, NaviCell provides a framework for community-based curation of maps.

Inter-cellular transport of ran GTPase.

Directory of Open Access Journals (Sweden)

Deepak Khuperkar

Full Text Available Ran, a member of the Ras-GTPase superfamily, has a well-established role in regulating the transport of macromolecules across the nuclear envelope (NE. Ran has also been implicated in mitosis, cell cycle progression, and NE formation. Over-expression of Ran is associated with various cancers, although the molecular mechanism underlying this phenomenon is unclear. Serendipitously, we found that Ran possesses the ability to move from cell-to-cell when transiently expressed in mammalian cells. Moreover, we show that the inter-cellular transport of Ran is GTP-dependent. Importantly, Ran displays a similar distribution pattern in the recipient cells as that in the donor cell and co-localizes with the Ran binding protein Nup358 (also called RanBP2. Interestingly, leptomycin B, an inhibitor of CRM1-mediated export, or siRNA mediated depletion of CRM1, significantly impaired the inter-cellular transport of Ran, suggesting a function for CRM1 in this process. These novel findings indicate a possible role for Ran beyond nucleo-cytoplasmic transport, with potential implications in inter-cellular communication and cancers.

Dopamine D4 receptor gene and religious affiliation correlate with dictator game altruism in males and not females: evidence for gender-sensitive gene × culture interaction.

Science.gov (United States)

Jiang, Yushi; Bachner-Melman, Rachel; Chew, Soo Hong; Ebstein, Richard P

2015-01-01

On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-)selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion) based on self-reports, and genotyped for the dopamine D4 receptor (DRD4) gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer) than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R "susceptibility" genotype is more responsive to a positive environment provided by some religions.

Effects of molecular structure on microscopic heat transport in chain polymer liquids

International Nuclear Information System (INIS)

Matsubara, Hiroki; Kikugawa, Gota; Ohara, Taku; Bessho, Takeshi; Yamashita, Seiji

2015-01-01

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T c ) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs

Effects of molecular structure on microscopic heat transport in chain polymer liquids

Energy Technology Data Exchange (ETDEWEB)

Matsubara, Hiroki, E-mail: matsubara@microheat.ifs.tohoku.ac.jp; Kikugawa, Gota; Ohara, Taku [Institute of Fluid Science, Tohoku University, 2-1-1 Katahira, Aoba-ku, Sendai 980-8577 (Japan); Bessho, Takeshi; Yamashita, Seiji [Higashifuji Technical Center, Toyota Motor Corporation, 1200 Mishuku, Susono, Shizuoka 410-1193 (Japan)

2015-04-28

In this paper, we discuss the molecular mechanism of the heat conduction in a liquid, based on nonequilibrium molecular dynamics simulations of a systematic series of linear- and branched alkane liquids, as a continuation of our previous study on linear alkane [T. Ohara et al., J. Chem. Phys. 135, 034507 (2011)]. The thermal conductivities for these alkanes in a saturated liquid state at the same reduced temperature (0.7T{sub c}) obtained from the simulations are compared in relation to the structural difference of the liquids. In order to connect the thermal energy transport characteristics with molecular structures, we introduce the new concept of the interatomic path of heat transfer (atomistic heat path, AHP), which is defined for each type of inter- and intramolecular interaction. It is found that the efficiency of intermolecular AHP is sensitive to the structure of the first neighbor shell, whereas that of intramolecular AHP is similar for different alkane species. The dependence of thermal conductivity on different lengths of the main and side chain can be understood from the natures of these inter- and intramolecular AHPs.

The Pay-What-You-Want game: What can be learned from the experimental evidence on Dictator and Trust Games?

Directory of Open Access Journals (Sweden)

Greiff Matthias

2017-03-01

Full Text Available This paper introduces the Pay-What-You-Want game which represents the interaction between a buyer and a seller in a Pay-What-You-Want (PWYW situation. The PWYW game embeds the dictator game and the trust game as subgames. This allows us to use previous experimental studies with the dictator and the trust game to identify three factors that can influence the success of PWYW pricing in business practice: (i social context, (ii social information, and (iii deservingness. Only few cases of PWYW pricing for a longer period of time have been documented. By addressing repeated games, we isolate two additional factors which are likely to contribute to successful implementations of PWYW as a long term pricing strategy. These are (iv communication and (v the reduction of goal conflicts. The central contribution of this study is an attempt to bridge the gap between laboratory experiments and the research on PWYW pricing, which relies largely on evidence from the field. By reviewing the relevant experiments, this study identifies factors crucial for the success of PWYW pricing and provides guidance to developing long-term applications of PWYW pricing.

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.

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

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.

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

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.

Inter-Corporeity

Directory of Open Access Journals (Sweden)

Algis Mickūnas

2011-02-01

Full Text Available The essay explicates the phenomenological problematic of intersubjectivity on the level of bodily interaction with the world and with others. On this level, the concept of visibility is transformed in terms of the primacy of bodily “I can” and the kinaesthetic awareness that pervades all perceptual fields. In addition, the investigations into kinaesthetic awareness lead to the understanding that one’s own bodily action is extended as well as varied by the kinaesthetic activities of others and thus form an inter-corporeal field wherein visibility is located. Such an extended awareness is the bodily counterpart of transcendental domain. 

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.

18 Dictation as a Veritable Tool for Language Proficiency on Project ...

African Journals Online (AJOL)

User

Dictation is a valuable language teaching and learning device that has been used for centuries ... English language among the second learners of English language in a ... through effective study English by developing the language curriculum and ... language teachers need to be abreast with different methods of language.

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.

Giant magnetoresistance in cluster-assembled nanostructures: on the influence of inter-particle interactions

International Nuclear Information System (INIS)

Oyarzún, Simón; Domingues Tavares de Sa, Artur; Tuaillon-Combes, Juliette; Tamion, Alexandre; Hillion, Arnaud; Boisron, Olivier; Mosset, Alexis; Pellarin, Michel; Dupuis, Véronique; Hillenkamp, Matthias

2013-01-01

The giant magnetoresistance response of granular systems has since its discovery been described by a simple model based on the geometric orientation of the magnetic moments of adjacent nanoparticles. This model has been proven quite successful in many cases but its being based on decoupled neighboring grains has never been verified as all available studies rely on samples with too high concentration. Here we report on magnetic and magnetotransport measurements of cluster-assembled nanostructures with cobalt clusters around 2.3 nm diameter embedded in copper matrices at different concentrations. The thorough magnetic characterization based on the recently developed “triple fit” method allows the detection of measurable inter-particle interactions and thus assures true superparamagnetic behavior in the most dilute sample. The spintronic response is compared to theory and we show that only at low concentration (0.5 at.% Co) all experiments are consistent and the common theoretical description is appropriate. Increasing the concentration to 2.5 and 5 at.% implies deviations between magnetometry and magnetotransport

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.

Inter-varietal interactions among plants in genotypically diverse mixtures tend to decrease herbivore performance.

Science.gov (United States)

Grettenberger, Ian M; Tooker, John F

2016-09-01

Much research has explored the effects of plant species diversity on herbivore populations, but far less has considered effects of plant genotypic diversity, or how abiotic stressors, like drought, can modify effects. Mechanisms by which plant genotypic diversity affects herbivore populations remain largely unresolved. We used greenhouse studies with a model system of wheat (Triticum aestivum L.) and bird cherry-oat aphid (Rhopalosiphum padi L.) to determine whether the genotypic diversity of a plant's neighborhood influences performance and fitness of herbivores on a focal plant and if drought changes the influence of neighborhood diversity. Taken across all varieties we tested, plant-plant interactions in diverse neighborhoods reduced aphid performance and generated associational resistance, although effects on aphids depended on variety identity. In diverse mixtures, drought stress greatly diminished the genotypic diversity-driven reduction in aphid performance. Neighborhood diversity influenced mother aphid size, and appeared to partially explain how plant-plant interactions reduced the number of offspring produced in mixtures. Plant size did not mediate effects on aphid performance, although neighborhood diversity reduced plant mass across varieties and watering treatments. Our results suggest inter-varietal interactions in genotypic mixtures can affect herbivore performance in the absence of herbivore movement and that abiotic stress may diminish any effects. Accounting for how neighborhood diversity influences resistance of an individual plant to herbivores will help aid development of mixtures of varieties for managing insect pests and clarify the role of plant genotypic diversity in ecosystems.

The dictator effect: how long years in office affect economic development

NARCIS (Netherlands)

Papaioannou, Kostadis; van Zanden, Jan Luiten

This paper contributes to the growing literature on the links between political regimes and economic development by studying the effects of years in office on economic development. The hypothesis is that dictators who stay in office for a long time period will find it increasingly difficult to carry

The dictator effect: how long years in office affect economic development

NARCIS (Netherlands)

Papaioannou, K.I.; Zanden, van J.L.

2015-01-01

This paper contributes to the growing literature on the links between political regimes and economic development by studying the effects of years in office on economic development. The hypothesis is that dictators who stay in office for a long time period will find it increasingly difficult to carry

Melodic Dictation Instruction: A Survey of Advanced Placement Music Theory Teachers

Science.gov (United States)

Buonviri, Nathan O.; Paney, Andrew S.

2015-01-01

Based on relevant literature and recent qualitative findings, the purpose of this survey research was to identify pedagogical approaches to melodic dictation employed by Advanced Placement (AP) Music Theory teachers across the United States. The researcher-designed survey questions focused on pitch and rhythm skills, instructional resources,…

Interaction of amyloid inhibitor proteins with amyloid beta peptides: insight from molecular dynamics simulations.

Directory of Open Access Journals (Sweden)

Payel Das

Full Text Available Knowledge of the detailed mechanism by which proteins such as human αB- crystallin and human lysozyme inhibit amyloid beta (Aβ peptide aggregation is crucial for designing treatment for Alzheimer's disease. Thus, unconstrained, atomistic molecular dynamics simulations in explicit solvent have been performed to characterize the Aβ17-42 assembly in presence of the αB-crystallin core domain and of lysozyme. Simulations reveal that both inhibitor proteins compete with inter-peptide interaction by binding to the peptides during the early stage of aggregation, which is consistent with their inhibitory action reported in experiments. However, the Aβ binding dynamics appear different for each inhibitor. The binding between crystallin and the peptide monomer, dominated by electrostatics, is relatively weak and transient due to the heterogeneous amino acid distribution of the inhibitor surface. The crystallin-bound Aβ oligomers are relatively long-lived, as they form more extensive contact surface with the inhibitor protein. In contrast, a high local density of arginines from lysozyme allows strong binding with Aβ peptide monomers, resulting in stable complexes. Our findings not only illustrate, in atomic detail, how the amyloid inhibitory mechanism of human αB-crystallin, a natural chaperone, is different from that of human lysozyme, but also may aid de novo design of amyloid inhibitors.

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.

Pumping requirements and options for molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

International Nuclear Information System (INIS)

McCollum, M.J.; Plano, M.A.; Haase, M.A.; Robbins, V.M.; Jackson, S.L.; Cheng, K.Y.; Stillman, G.E.

1989-01-01

This paper discusses the use of gas sources in growth by MBE as a result of current interest in growth of InP/InGaAsP/InGaAs lattice matched to InP. For gas flows greater than a few sccm, pumping speed requirements dictate the use of turbomolecular or diffusion pumps. GaAs samples with high p-type mobilities have been grown with diffusion pumped molecular beam epitaxial system. According to the authors, this demonstration of the inherent cleanliness of a properly designed diffusion pumping system indicates that a diffusion pump is an excellent inexpensive and reliable choice for growth by molecular beam epitaxy and gas source molecular beam epitaxy/chemical beam epitaxy

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.

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.

The Impact of Morphological Awareness on Word Reading and Dictation in Chinese Early Adolescent Readers With and Without Dyslexia.

Science.gov (United States)

Kalindi, Sylvia Chanda; Chung, Kevin Kien Hoa

2018-01-01

This study investigated the role of morphological awareness in understanding Chinese word reading and dictation among Chinese-speaking adolescent readers in Hong Kong as well as the cognitive-linguistic profile of early adolescent readers with dyslexia. Fifty-four readers with dyslexia in Grades 5 and 6 were compared with 54 chronological age-matched (CA) typical readers on the following measures of cognitive-linguistic and literacy skills: morphological awareness, phonological awareness, visual-orthographic knowledge, rapid naming, vocabulary knowledge, verbal short-term memory (STM), Chinese word reading, and dictation (or spelling). The results indicated that early adolescent readers with dyslexia performed less well than the typical readers on all cognitive-linguistic and literacy measures except the phonological measures. Both groups' scores showed substantial correlations between morphological awareness and Chinese word reading and dictation. Visual-orthographic knowledge and rapid naming were also associated with dictation in early adolescent readers with and without dyslexia, respectively. Moderated multiple regression analyses further revealed that morphological awareness and rapid naming explained unique variance in word reading and dictation for the readers with dyslexia and typical readers separately after controlling readers' age and group effect. These results highlight the potential importance of morphological awareness and rapid naming in Chinese word reading and writing in Chinese early adolescents' literacy development and impairment.

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.

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.

Child-centered reading intervention: See, talk, dictate, read, write!

Directory of Open Access Journals (Sweden)

Muhammet BAŞTUĞ

2016-06-01

Full Text Available Poor reading achievement of children in elementary schools has been one of the major concerns in education. The aim of this study is to examine the effectiveness of a child-centered reading intervention in eliminating the reading problems of a student with poor reading achievement. The research was conducted with a student having difficulty in reading. A reading intervention was designed that targeted multiple areas of reading and aimed to improve reading skills through the use of multiple strategies. This intervention is child-centered and includes visual aids, talking, dictating, reading and writing stages. The study was performed in 35 sessions consisting of stages of a single sentence (5 sessions, two sentences (5 sessions, three sentences (20 sessions and the text stage (5 sessions. The intervention sessions were audio-taped. These recordings and the written responses to the reading comprehension questions provided the data for analysis. The findings on the reading intervention revealed positive outcomes. The student exhibited certain improvements at the levels of reading, reading rate and reading comprehension. These results were discussed in the literature and the findings suggest that child-centered reading strategies such as talking, dictating and writing should be the main focus of instruction for students with low reading literacy achievement to enable these students to meet the demands of the curriculum.

Dopamine D4 Receptor Gene and Religious Affiliation Correlate with Dictator Game Altruism in Males and not Females: Evidence for Gender-sensitive Gene x Culture Interaction

Directory of Open Access Journals (Sweden)

Yushi eJiang

2015-09-01

Full Text Available On a large sample of 2288 Han Chinese undergraduates, we investigated how religion and DRD4 are related to human altruistic giving behavior as measured with the Andreoni-Miller Dictator Game. This game enables us to clearly specify (non-selfishness, efficiency, and fairness motives for sharing. Participants were further classified into religious categories (Christian, Buddhist-Tao, and No Religion based on self-reports, and genotyped for the dopamine D4 receptor (DRD4 gene exon III VNTR. Our analysis revealed a significant interaction between religion and DRD4 correlated with giving behavior solely among males: Whereas no significant association between religion and sharing decisions was observed in the majority 4R/4R genotype group, a significant difference in giving behavior between Christian and non-Christian males was seen in the non-4R/4R group, with Christian men being overall more altruistic (less selfish and fairer than non-Christian men. These results support the vantage sensitivity hypothesis regarding DRD4 that the non-4R/4R ‘susceptibility’ genotype is more responsive to a positive environment provided by some religions.

Medizinbibliotheken: inter:disziplinär – inter:national –inter:aktiv

Directory of Open Access Journals (Sweden)

Bauer, Bruno

2017-12-01

Full Text Available The focus of the current issue 3/2017 of GMS Medizin – Bibliothek – Information is the annual conference 2017 of the German Medical Libraries Association in Vienna. The motto of the conference was “Medical Libraries: inter:disciplinary – inter:national – inter:active”. The authors in this issue are Bruno Bauer (Austrian Transition to Open Access 2017–2020, Beata Górczynska (Development and structure of Polish veterinary school system and its libraries, Katharina Heldt, Henriette Senst & Jessica Riedel (Salon on the institute’s history: outstanding artifacts. 28.01.2016 to 15.12.2016, Jutta Matrisciano, Martina Semmler-Schmetz & Saskia Rohmer (Advice – From info snack to special menu: Solutions of the MedMA-Bib, Stefan Nortmann (The ‘Ersti-Café’ of the Medical Branch Library Münster, Sandra Rümmele (Toolbox: The new teaching library project of the Central Medical Library of the University Medical Center Hamburg-Eppendorf, Eva Seidlmayer & Christoph Poley (One Health – Transdisciplinarity at ZB MED and Heike Andermann (“Medical Libraries: inter:disciplinary – inter:national – inter:active”. Annual Meeting of the German Medical Library Association (AGMB, September 25 to 27, 2017 in Vienna. Furthermore this focus issue features articles from Stefan Grün & Christoph Poley (Statistical evaluation of semantic entities from metadata and full text on German Medical Science corpora and Iris Reimann (German MLA News; Competition of the German MLA Pioneer projects in medical libraries 2017: Introduction of the winners; Competition of the German MLA (AGMB Pioneer projects in medical libraries 2018 – Announcement.

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

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.

The neural basis for writing from dictation in the temporoparietal cortex.

Science.gov (United States)

Roux, Franck-Emmanuel; Durand, Jean-Baptiste; Réhault, Emilie; Planton, Samuel; Draper, Louisa; Démonet, Jean-François

2014-01-01

Cortical electrical stimulation mapping was used to study neural substrates of the function of writing in the temporoparietal cortex. We identified the sites involved in oral language (sentence reading and naming) and writing from dictation, in order to spare these areas during removal of brain tumours in 30 patients (23 in the left, and 7 in the right hemisphere). Electrostimulation of the cortex impaired writing ability in 62 restricted cortical areas (.25 cm2). These were found in left temporoparietal lobes and were mostly located along the superior temporal gyrus (Brodmann's areas 22 and 42). Stimulation of right temporoparietal lobes in right-handed patients produced no writing impairments. However there was a high variability of location between individuals. Stimulation resulted in combined symptoms (affecting oral language and writing) in fourteen patients, whereas in eight other patients, stimulation-induced pure agraphia symptoms with no oral language disturbance in twelve of the identified areas. Each detected area affected writing in a different way. We detected the various different stages of the auditory-to-motor pathway of writing from dictation: either through comprehension of the dictated sentences (word deafness areas), lexico-semantic retrieval, or phonologic processing. In group analysis, barycentres of all different types of writing interferences reveal a hierarchical functional organization along the superior temporal gyrus from initial word recognition to lexico-semantic and phonologic processes along the ventral and the dorsal comprehension pathways, supporting the previously described auditory-to-motor process. The left posterior Sylvian region supports different aspects of writing function that are extremely specialized and localized, sometimes being segregated in a way that could account for the occurrence of pure agraphia that has long-been described in cases of damage to this region. Copyright © 2013 Elsevier Ltd. All rights reserved.

Low-field spin dynamics of Cr₇Ni and Cr₇Ni-Cu-Cr₇Ni molecular rings as detected by μsR

OpenAIRE

Sanna, S.; Arosio, P.; Bordonali, L.; Adelnia, F.; Mariani, M.; Garlatti, E.; Baines, C.; Amato, A.; Sabareesh, K. P.V.; Timco, G.; Winpenny, R. E.P.; Blundell, S. J.; Lascialfari, A.

2017-01-01

Muon spin rotation measurements were used to investigate the spin dynamics of heterometallic Cr7Ni and Cr7Ni-Cu-Cr7Ni molecular clusters. In Cr7Ni the magnetic ions are arranged in a quasiplanar ring and interact via an antiferromagnetic exchange coupling constant J, while Cr7Ni-Cu-Cr7Ni is composed of two Cr7Ni linked by a bridging moiety containing one Cu ion, that induces an inter-ring ferromagnetic interaction J ≪ J. The longitudinal muon relaxation rate λ collected at low magnetic fields...

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.

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.

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

The Traditional Chinese Philosophies in Inter-cultural Leadership

DEFF Research Database (Denmark)

Lin, Li; Li, Peter Ping; Roelfsema, Hein

2018-01-01

cultural distance. To fill the gap in the literature concerning the leadership challenges for expatriate managers in an inter-cultural context, the purpose of this paper is to elucidate the leadership styles of Chinese expatriate managers from the perspectives of three traditional Chinese philosophies (i...... that the leadership style of Chinese expatriate managers is deeply rooted in the three traditional Chinese philosophies of Confucianism, Taoism, and Legalism, even in an inter-cultural context. Specifically, the study reveals two salient aspects of how Chinese expatriate managers frame and interact with a foreign...... managers also reported that their interactions with the Dutch culture are best described as a balance between partial conflict and partial complementarity (thus, a duality). In this sense, the leadership style of Chinese expatriate managers is influenced jointly by the three traditional Chinese...

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.

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.

Magnetic relaxation phenomena and inter-particle interactions in nanosized gamma-Fe sub 2 O sub 3 systems

CERN Document Server

Predoi, D; Tronc, E; Nogues, M; Russo, U; Principi, G; Filoti, G

2003-01-01

Samples of gamma-Fe sub 2 O sub 3 nano-particles with a mean size of 4.0(3) nm and with different hydration and surfactant degrees were prepared by sol-gel methods. Morphology and structural data were obtained by transmission electron microscopy and x-ray diffraction, whereas the surface effects and hyperfine interactions were analysed mainly by Moessbauer spectroscopy. The relative number of surface iron positions was found to be proportional to the amount of OH sup - and SO sub 4 sup 2 sup - groups on the particle surface, which in turn is strictly dependent on the preparation conditions. Strong relaxation processes versus temperature were evidenced in the analysed systems. New criteria for the evaluation of the blocking temperature via Moessbauer measurements are proposed. The results are in good agreement with blocking temperatures obtained by magnetic measurements. Moreover, it was shown that the inter-particle magnetic interactions decrease with the number of iron surface states.

Collapse and revival in inter-band oscillations of a two-band Bose-Hubbard model

Energy Technology Data Exchange (ETDEWEB)

Ploetz, Patrick; Wimberger, Sandro [Institut fuer Theoretische Physik, Universitaet Heidelberg, Philosophenweg 19, 69120 Heidelberg (Germany); Madronero, Javier, E-mail: ploetz@thphys.uni-heidelberg.d [Physik Department, Technische Universitaet Muenchen, James-Franck-Str. 1, 85748 Garching (Germany)

2010-04-28

We study the effect of a many-body interaction on inter-band oscillations in a two-band Bose-Hubbard model with an external Stark force. Weak and strong inter-band oscillations are observed, where the latter arise from a resonant coupling of the bands. These oscillations collapse and revive due to a weak two-body interaction between the atoms. Effective models for oscillations in and out of resonance are introduced that provide predictions for the system's behaviour, particularly for the time scales for the collapse and revival of the resonant inter-band oscillations. (fast track communication)

Ab initio quantum chemical calculations of the interaction between radioactive elements and imidazolium based ionic liquids

Science.gov (United States)

Saravanan, A. V. Sai; Abishek, B.; Anantharaj, R.

2018-04-01

The fundamental natures of the molecular level interaction and charge transfer between specific radioactive elements and ionic liquids of 1-butyl-3-methylimidazolium bis (trifluoromethylsulfonyl) imide ([BMIM]+[NTf2]-), 1-Butyl-3-methylimidazolium ethylsulfate ([BMIM]+[ES]-) and 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM]+[BF4]-) were investigated utilising HF theory and B3LYP hybrid DFT. The ambiguity in reaction mechanism of the interacting species dictates to employ Effective Core Potential (ECP) basis sets such as UGBS, SDD, and SDDAll to account for the relativistic effects of deep core electrons in the system involving potential, heavy and hazardous radioactive elements present in nuclear waste. The SCF energy convergence of each system validates the characterisation of the molecular orbitals as a linear combination of atomic orbitals utilising fixed MO coefficients and the optimized geometry of each system is visualised based on which Mulliken partial charge analysis is carried out to account for the polarising behaviour of the radioactive element and charge transfer between the IL phase by comparison with the bare IL species.

Measuring Altruistic Behavior in Surveys: The All-or-Nothing Dictator Game

Directory of Open Access Journals (Sweden)

Rene Bekkers

2007-12-01

Full Text Available A field study of altruistic behaviour is presented using a modification of the dictator game in a large random sample survey in the netherlands (n=1,964. In line with laboratory experiments, only 5.7% donated money. In line with other survey research on giving, generosity increased with age, education, income, trust, and prosocial value orientation.

Do gray wolves (Canis lupus) support pack mates during aggressive inter-pack interactions?

Science.gov (United States)

Cassidy, Kira A; McIntyre, Richard T

2016-09-01

For group-living mammals, social coordination increases success in everything from hunting and foraging (Crofoot and Wrangham in Mind the Gap, Springer, Berlin, 2010; Bailey et al. in Behav Ecol Sociobiol 67:1-17, 2013) to agonism (Mosser and Packer in Anim Behav 78:359-370, 2009; Wilson et al. in Anim Behav 83:277-291, 2012; Cassidy et al. in Behav Ecol 26:1352-1360, 2015). Cooperation is found in many species and, due to its low costs, likely is a determining factor in the evolution of living in social groups (Smith in Anim Behav 92:291-304, 2014). Beyond cooperation, many mammals perform costly behaviors for the benefit of group mates (e.g., parental care, food sharing, grooming). Altruism is considered the most extreme case of cooperation where the altruist increases the fitness of the recipient while decreasing its own fitness (Bell in Selection: the mechanism of evolution. Oxford University Press, Oxford 2008). Gray wolf life history requires intra-pack familiarity, communication, and cooperation in order to succeed in hunting (MacNulty et al. in Behav Ecol doi: 10.1093/beheco/arr159 2011) and protecting group resources (Stahler et al. in J Anim Ecol 82: 222-234, 2013; Cassidy et al. in Behav Ecol 26:1352-1360, 2015). Here, we report 121 territorial aggressive inter-pack interactions in Yellowstone National Park between 1 April 1995 and 1 April 2011 (>5300 days of observation) and examine each interaction where one wolf interferes when its pack mate is being attacked by a rival group. This behavior was recorded six times (17.6 % of interactions involving an attack) and often occurred between dyads of closely related individuals. We discuss this behavior as it relates to the evolution of cooperation, sociality, and altruism.

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

Using business intelligence for efficient inter-facility patient transfer.

Science.gov (United States)

Haque, Waqar; Derksen, Beth Ann; Calado, Devin; Foster, Lee

2015-01-01

In the context of inter-facility patient transfer, a transfer operator must be able to objectively identify a destination which meets the needs of a patient, while keeping in mind each facility's limitations. We propose a solution which uses Business Intelligence (BI) techniques to analyze data related to healthcare infrastructure and services, and provides a web based system to identify optimal destination(s). The proposed inter-facility transfer system uses a single data warehouse with an Online Analytical Processing (OLAP) cube built on top that supplies analytical data to multiple reports embedded in web pages. The data visualization tool includes map based navigation of the health authority as well as an interactive filtering mechanism which finds facilities meeting the selected criteria. The data visualization is backed by an intuitive data entry web form which safely constrains the data, ensuring consistency and a single version of truth. The overall time required to identify the destination for inter-facility transfers is reduced from hours to a few minutes with this interactive solution.

Translucent Radiosity: Efficiently Combining Diffuse Inter-Reflection and Subsurface Scattering.

Science.gov (United States)

Sheng, Yu; Shi, Yulong; Wang, Lili; Narasimhan, Srinivasa G

2014-07-01

It is hard to efficiently model the light transport in scenes with translucent objects for interactive applications. The inter-reflection between objects and their environments and the subsurface scattering through the materials intertwine to produce visual effects like color bleeding, light glows, and soft shading. Monte-Carlo based approaches have demonstrated impressive results but are computationally expensive, and faster approaches model either only inter-reflection or only subsurface scattering. In this paper, we present a simple analytic model that combines diffuse inter-reflection and isotropic subsurface scattering. Our approach extends the classical work in radiosity by including a subsurface scattering matrix that operates in conjunction with the traditional form factor matrix. This subsurface scattering matrix can be constructed using analytic, measurement-based or simulation-based models and can capture both homogeneous and heterogeneous translucencies. Using a fast iterative solution to radiosity, we demonstrate scene relighting and dynamically varying object translucencies at near interactive rates.

Ranking multiple docking solutions based on the conservation of inter-residue contacts

KAUST Repository

Oliva, Romina M.

2013-06-17

Molecular docking is the method of choice for investigating the molecular basis of recognition in a large number of functional protein complexes. However, correctly scoring the obtained docking solutions (decoys) to rank native-like (NL) conformations in the top positions is still an open problem. Herein we present CONSRANK, a simple and effective tool to rank multiple docking solutions, which relies on the conservation of inter-residue contacts in the analyzed decoys ensemble. First it calculates a conservation rate for each inter-residue contact, then it ranks decoys according to their ability to match the more frequently observed contacts. We applied CONSRANK to 102 targets from three different benchmarks, RosettaDock, DOCKGROUND, and Critical Assessment of PRedicted Interactions (CAPRI). The method performs consistently well, both in terms of NL solutions ranked in the top positions and of values of the area under the receiver operating characteristic curve. Its ideal application is to solutions coming from different docking programs and procedures, as in the case of CAPRI targets. For all the analyzed CAPRI targets where a comparison is feasible, CONSRANK outperforms the CAPRI scorers. The fraction of NL solutions in the top ten positions in the RosettaDock, DOCKGROUND, and CAPRI benchmarks is enriched on average by a factor of 3.0, 1.9, and 9.9, respectively. Interestingly, CONSRANK is also able to specifically single out the high/medium quality (HMQ) solutions from the docking decoys ensemble: it ranks 46.2 and 70.8% of the total HMQ solutions available for the RosettaDock and CAPRI targets, respectively, within the top 20 positions. © 2013 Wiley Periodicals, Inc.

Transitional grain boundary structures and the influence on thermal, mechanical and energy properties from molecular dynamics simulations

International Nuclear Information System (INIS)

Burbery, N.J.; Das, R.; Ferguson, W.G.

2016-01-01

The thermo-kinetic characteristics that dictate the activation of atomistic crystal defects significantly influence the mechanical properties of crystalline materials. Grain boundaries (GBs) primarily influence the plastic deformation of FCC metals through their interaction with mobile dislocation defects. The activation thresholds and atomic mechanisms that dictate the thermo-kinetic properties of grain boundaries have been difficult to study due to complex and highly variable GB structure. This paper presents a new approach for modelling GBs which is based on a systematic structural analysis of metastable and stable GBs. GB structural transformation accommodates defect interactions at the interface. The activation energy for such structural transformations was evaluated with nudged elastic band analysis of bi-crystals with several metastable 0 K grain boundary structures in pure FCC Aluminium (Al). The resultant activation energy was used to evaluate the thermal stability of the metastable grain boundary structures, with predictions of transition time based on transition state theory. The predictions are in very good agreement with the minimum time for irreversible structure transformation at 300 K obtained with molecular dynamics simulations. Analytical methods were used to evaluate the activation volume, which in turn was used to predict and explain the influence of stress and strain rate on the thermal and mechanical properties. Results of molecular dynamics simulations show that the GB structure is more closely related to the elastic strength at 0 K than the GB energy. Furthermore, the thermal instability of the GB structure directly influences the relationship between bi-crystal strength, temperature and strain rate. Hence, theoretically consistent models are established on the basis of activation criteria, and used to make predictions of temperature-dependent yield stress at a low strain rate, in agreement with experimental results.

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.

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.

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.

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.

Molecular dynamics approaches to the design and synthesis of PCB targeting molecularly imprinted polymers: interference to monomer-template interactions in imprinting of 1,2,3-trichlorobenzene.

Science.gov (United States)

Cleland, Dougal; Olsson, Gustaf D; Karlsson, Björn C G; Nicholls, Ian A; McCluskey, Adam

2014-02-07

The interactions between each component of the pre-polymerisation mixtures used in the synthesis of molecularly imprinted polymers (MIP) specific for 1,2,3,4,5-pentachlorobenzene (1) and 1,2,3-trichlorobenzene (2) were examined in four molecular dynamics simulations. These simulations revealed that the relative frequency of functional monomer-template (FM-T) interactions was consistent with results obtained by the synthesis and evaluation of the actual MIPs. The higher frequency of 1 interaction with trimethylstyrene (TMS; 54.7%) than 1 interaction with pentafluorostyrene (PFS; 44.7%) correlated with a higher imprinting factor (IF) of 2.1 vs. 1.7 for each functional monomer respectively. The higher frequency of PFS interactions with 2 (29.6%) than TMS interactions with 2 (1.9%) also correlated well with the observed differences in IF (3.7) of 2 MIPs imprinted using PFS as the FM than the IF (2.8) of 2 MIPs imprinted using TMS as the FM. The TMS-1 interaction dominated the molecular simulation due to high interaction energies, but the weaker TMS-2 resulted in low interaction maintenance, and thus lower IF values. Examination of the other pre-polymerisation mixture components revealed that the low levels of TMS-2 interaction was, in part, due to interference caused by the cross linker (CL) ethyleneglycol dimethylacrylate (EGDMA) interactions with TMS. The main reason was, however, attributed to MeOH interactions with TMS in both a hydrogen bond and perpendicular configuration. This positioned a MeOH directly above the π-orbital of all TMS for an average of 63.8% of MD2 creating significant interference to π-π stacking interactions between 2 and TMS. These findings are consistent with the deviation from the 'normal' molecularly imprinted polymer synthesis ratio of 1 : 4 : 20 (T : FM : CL) of 20 : 1 : 29 and 15 : 6 : 29 observed with 2 and TMS and PFS respectively. Our molecular dynamics simulations correctly predicted the high level

An Inter-Disciplinary Language for Inter-Disciplinary Communication: Academic Globalization, Ethos, Pathos, and Logos

Directory of Open Access Journals (Sweden)

Marta Szabo White

2014-08-01

Full Text Available Inspired by the intersection of character, emotions, and logic, much like a Hungarian Rhapsody which is beautifully sad; this paper explores ethos, pathos, and logos in the context of Academic Globalization. As students of the world, an inter-disciplinary language is pivotal for inter-disciplinary communication. Given that the current state of the world stems primarily from miscommunications, it is imperative to launch a cognitive language tool which underscores global commonalities and mitigates cultural differences. Such a platform would foster interdisciplinary research, education, and communication. New paradigms would evolve, grounded in ethos, pathos, and logos. Like yin and yang, these states are interrelated, interacting, and interchanging learning spheres. Just as day and night blend at some point; just as the Parthenon epitomized Greek thought, celebrated the birthplace of democracy, and for the first time, depicted everyday citizens in friezes- underscoring their impactful role- ethos, pathos, and logos represent cross-disciplinary communication devices which synergistically transform and ignite academic globalization. The Literature Review links the concepts of ethos, pathos, and logos with the seminal work Lewis and his LMR framework, which has given birth to Cultureactive and subsequently to ICE [InterCultural Edge]. http://www.fuqua.duke.edu/ciber/programs/we_organize/ice/ Accessed February 14, 2014

Lattice topology dictates photon statistics.

Science.gov (United States)

Kondakci, H Esat; Abouraddy, Ayman F; Saleh, Bahaa E A

2017-08-21

Propagation of coherent light through a disordered network is accompanied by randomization and possible conversion into thermal light. Here, we show that network topology plays a decisive role in determining the statistics of the emerging field if the underlying lattice is endowed with chiral symmetry. In such lattices, eigenmode pairs come in skew-symmetric pairs with oppositely signed eigenvalues. By examining one-dimensional arrays of randomly coupled waveguides arranged on linear and ring topologies, we are led to a remarkable prediction: the field circularity and the photon statistics in ring lattices are dictated by its parity while the same quantities are insensitive to the parity of a linear lattice. For a ring lattice, adding or subtracting a single lattice site can switch the photon statistics from super-thermal to sub-thermal, or vice versa. This behavior is understood by examining the real and imaginary fields on a lattice exhibiting chiral symmetry, which form two strands that interleave along the lattice sites. These strands can be fully braided around an even-sited ring lattice thereby producing super-thermal photon statistics, while an odd-sited lattice is incommensurate with such an arrangement and the statistics become sub-thermal.

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

Energy Technology Data Exchange (ETDEWEB)

Fischer, Sean A.; Apra, Edoardo; Govind, Niranjan; Hess, Wayne P.; El-Khoury, Patrick Z.

2017-02-03

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

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.

Cross dimerization of amyloid-β and αsynuclein proteins in aqueous environment: a molecular dynamics simulations study.

Directory of Open Access Journals (Sweden)

Jaya C Jose

Full Text Available Self-assembly of the intrinsically unstructured proteins, amyloid beta (Aβ and alpha synclein (αSyn, are associated with Alzheimer's Disease, and Parkinson's and Lewy Body Diseases, respectively. Importantly, pathological overlaps between these neurodegenerative diseases, and the possibilities of interactions between Aβ and αSyn in biological milieu emerge from several recent clinical reports and in vitro studies. Nevertheless, there are very few molecular level studies that have probed the nature of spontaneous interactions between these two sequentially dissimilar proteins and key characteristics of the resulting cross complexes. In this study, we have used atomistic molecular dynamics simulations to probe the possibility of cross dimerization between αSyn1-95 and Aβ1-42, and thereby gain insights into their plausible early assembly pathways in aqueous environment. Our analyses indicate a strong probability of association between the two sequences, with inter-protein attractive electrostatic interactions playing dominant roles. Principal component analysis revealed significant heterogeneity in the strength and nature of the associations in the key interaction modes. In most, the interactions of repeating Lys residues, mainly in the imperfect repeats 'KTKEGV' present in αSyn1-95 were found to be essential for cross interactions and formation of inter-protein salt bridges. Additionally, a hydrophobicity driven interaction mode devoid of salt bridges, where the non-amyloid component (NAC region of αSyn1-95 came in contact with the hydrophobic core of Aβ1-42 was observed. The existence of such hetero complexes, and therefore hetero assembly pathways may lead to polymorphic aggregates with variations in pathological attributes. Our results provide a perspective on development of therapeutic strategies for preventing pathogenic interactions between these proteins.

Temperature dependence of magnetotransport behavior and its correlation with inter-particle interaction in Cu100−xCox granular films

International Nuclear Information System (INIS)

Kumar, Dinesh; Chaudhary, Sujeet; Pandya, Dinesh K.

2013-01-01

Granular Cu 100−x Co x (x=15.1-30.9) films were deposited by magnetron co-sputtering and their magnetotransport properties were investigated as a function of temperature. We observed that with increasing cobalt content the room temperature magnetoresistance (MR) shows a maximum at x=20.9. With decreasing temperature, it is observed that the cobalt concentration at which the maximum MR occurs shifts progressively towards lower Co concentration. This behavior has been discussed in terms of the inter-particle magnetic interactions.

X-ray computed tomography uncovers root-root interactions: quantifying spatial relationships between interacting root systems in three dimensions.

Science.gov (United States)

Paya, Alexander M; Silverberg, Jesse L; Padgett, Jennifer; Bauerle, Taryn L

2015-01-01

Research in the field of plant biology has recently demonstrated that inter- and intra-specific interactions belowground can dramatically alter root growth. Our aim was to answer questions related to the effect of inter- vs. intra-specific interactions on the growth and utilization of undisturbed space by fine roots within three dimensions (3D) using micro X-ray computed tomography. To achieve this, Populus tremuloides (quaking aspen) and Picea mariana (black spruce) seedlings were planted into containers as either solitary individuals, or inter-/intra-specific pairs, allowed to grow for 2 months, and 3D metrics developed in order to quantify their use of belowground space. In both aspen and spruce, inter-specific root interactions produced a shift in the vertical distribution of the root system volume, and deepened the average position of root tips when compared to intra-specifically growing seedlings. Inter-specific interactions also increased the minimum distance between root tips belonging to the same root system. There was no effect of belowground interactions on the radial distribution of roots, or the directionality of lateral root growth for either species. In conclusion, we found that significant differences were observed more often when comparing controls (solitary individuals) and paired seedlings (inter- or intra-specific), than when comparing inter- and intra-specifically growing seedlings. This would indicate that competition between neighboring seedlings was more responsible for shifting fine root growth in both species than was neighbor identity. However, significant inter- vs. intra-specific differences were observed, which further emphasizes the importance of biological interactions in competition studies.

Cohesion between two clay lamellae: From Primitive Model to Full Molecular Simulation

International Nuclear Information System (INIS)

Carrier, Benoit; Vandamme, Matthieu; Pellenq, Roland; Van Damme, Henri

2012-01-01

Document available in extended abstract form only. The objective of this work is to investigate the range of validity of various models to describe accurately the cohesion between two charged clay lamellae. These models, in order of increasing complexity, are the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory, the primitive model, the explicit solvent primitive model and the full molecular model. We aim at providing a clear picture of which physical mechanisms play a significant role for various interlayer spacings, surface charges and cationic charges. The up-scaling of the mechanical properties starting from the lamellar microstructure of a smectite is usually performed within the framework of the DLVO theory. In this case, the interaction between two charged lamellae with cations between them is the sum of the repulsive double layer electrostatic interaction and of the attractive Van der Waals interaction. However, the Primitive Model shows that concentration fluctuations of counter-ions can generate a strongly attractive ionic correlation force. The Primitive Model is a Monte-Carlo simulation of hydrated counter-ions between two infinite charges surfaces and the water is implicitly modeled by scaling all electrostatic interactions by the dielectric permittivity of bulk water. Nevertheless, for very small inter-layer spacings (1 nm), molecular simulations and experiments show that water is organized in a layered structure and does not behave like bulk water. Therefore, we investigate the role of the solvent in the cohesion of clay lamellae. For this purpose, we use a modified version of the original Primitive Model in which the solvent is modeled by point-dipoles: This model is called the Explicit Solvent Primitive Model. We consider four different systems: A Na + -montmorillonite, a Ca 2+ -montmorillonite, a Na + -vermiculite, a Ca 2+ -vermiculite. The vermiculite layers are twice as charged as the montmorillonite layers. We use a full molecular model as a

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.

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.

Direct observation, study and control of molecular super rotors

Science.gov (United States)

Korobenko, Aleksey; Milner, Alexander; Hepburn, John; Milner, Valery

2014-05-01

Extremely fast rotating molecules whose rotational energy is comparable with or exceeds the molecular bond strength are known as ``super rotors''. It has been speculated that super rotors may exhibit a number of unique properties, yet only indirect evidence of these molecular objects has been reported to date. We demonstrate the first direct observation of molecular super rotors by detecting coherent unidirectional molecular rotation with extreme frequencies exceeding 10 THz. The technique of an ``optical centrifuge'' is used to control the degree of rotational excitation in an ultra-broad range of rotational quantum numbers, reaching as high as N = 95 in oxygen and N = 60 in nitrogen. State-resolved detection enables us to determine the shape of the excited rotational wave packet and quantify the effect of centrifugal distortion on the rotational spectrum. Femtosecond time resolution reveals coherent rotational dynamics with increasing coherence times at higher angular momentum. We demonstrate that molecular super rotors can be created and observed in dense samples under normal conditions where the effects of ultrafast rotation on many-body interactions, inter-molecular collisions and chemical reactions can be readily explored.

Writing to dictation and handwriting performance among Chinese children with dyslexia: relationships with orthographic knowledge and perceptual-motor skills.

Science.gov (United States)

Cheng-Lai, Alice; Li-Tsang, Cecilia W P; Chan, Alan H L; Lo, Amy G W

2013-10-01

The purpose of this study was to investigate the relationships between writing to dictation, handwriting, orthographic, and perceptual-motor skills among Chinese children with dyslexia. A cross-sectional design was used. A total of 45 third graders with dyslexia were assessed. Results of stepwise multiple regression models showed that Chinese character naming was the only predictor associated with word dictation (β=.32); handwriting speed was related to deficits in rapid automatic naming (β=-.36) and saccadic efficiency (β=-.29), and visual-motor integration predicted both of the number of characters exceeded grid (β=-.41) and variability of character size (β=-.38). The findings provided support to a multi-stage working memory model of writing for explaining the possible underlying mechanism of writing to dictation and handwriting difficulties. Copyright © 2013 Elsevier Ltd. All rights reserved.

What Behaviors are Disapproved? Experimental Evidence from Five Dictator Games

Directory of Open Access Journals (Sweden)

Marc Vorsatz

2012-04-01

Full Text Available The literature on social norms has often stressed that social disapproval is crucial to foster compliance with norms and promote fair and cooperative behavior. With this in mind, we explore the disapproval of allocation decisions using experimental data from five dictator games with a feedback stage. Our data suggests that subjects are heterogeneous in their disapproval patterns, distinguishing two main groups: (1 Subjects who only disapprove choices that harm them, and (2 subjects who disapprove socially inefficient choices.

Density functional theory study of inter-layer coupling in bulk tin selenide

Science.gov (United States)

Song, Hong-Yue; Lü, Jing-Tao

2018-03-01

We study the inter-layer coupling in bulk tin selenide (SnSe) through density functional theory based calculations. Different approximations for the exchange-correlation functionals and the van der Waals interaction are employed. By performing comparison with graphite, MoS2 and black phosphorus, we analyze the inter-layer coupling from different points of view, including the binding energy, the low frequency inter-layer optical phonons, and the inter-layer charge transfer. We find that, there is a strong charge transfer between layers of SnSe, resulting in the strongest inter-layer coupling. Moreover, the charge transfer renders the inter-layer coupling in SnSe not of van der Waals type. Mechanical exfoliation has been used to fabricate mono- or few-layer graphene, MoS2 and black phosphorus. But, our results show that it may be difficult to apply similar technique to SnSe.

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.

Parameterization of the prosthetic redox centers of the bacterial cytochrome bc(1) complex for atomistic molecular dynamics simulations

DEFF Research Database (Denmark)

Kaszuba, K.; Postila, P. A.; Cramariuc, O.

2013-01-01

studied in large-scale classical molecular dynamics (MD) simulations. In part, this is due to lack of suitable force field parameters, centered atomic point charges in particular, for the complex's prosthetic redox centers. Accurate redox center charges are needed to depict realistically the inter-molecular...... interactions at different redox stages of the cyt bc(1) complex. Accordingly, here we present high-precision atomic point charges for the metal centers of the cyt bc(1) complex of Rhodobacter capsulatus derived from extensive density functional theory calculations, fitted using the restrained electrostatic...

Molecular tweezers modulate 14-3-3 protein-protein interactions

Science.gov (United States)

Bier, David; Rose, Rolf; Bravo-Rodriguez, Kenny; Bartel, Maria; Ramirez-Anguita, Juan Manuel; Dutt, Som; Wilch, Constanze; Klärner, Frank-Gerrit; Sanchez-Garcia, Elsa; Schrader, Thomas; Ottmann, Christian

2013-03-01

Supramolecular chemistry has recently emerged as a promising way to modulate protein functions, but devising molecules that will interact with a protein in the desired manner is difficult as many competing interactions exist in a biological environment (with solvents, salts or different sites for the target biomolecule). We now show that lysine-specific molecular tweezers bind to a 14-3-3 adapter protein and modulate its interaction with partner proteins. The tweezers inhibit binding between the 14-3-3 protein and two partner proteins—a phosphorylated (C-Raf) protein and an unphosphorylated one (ExoS)—in a concentration-dependent manner. Protein crystallography shows that this effect arises from the binding of the tweezers to a single surface-exposed lysine (Lys214) of the 14-3-3 protein in the proximity of its central channel, which normally binds the partner proteins. A combination of structural analysis and computer simulations provides rules for the tweezers' binding preferences, thus allowing us to predict their influence on this type of protein-protein interactions.

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

Allowing for Reflection Time does not Change Behavior in Dictator and Cheating Games

DEFF Research Database (Denmark)

Andersen, Steffen; Gneezy, Uri; Kajackaite, Agne

2018-01-01

Reaction time, usually measured in seconds, has been shown to be correlated with decisions in experimental games. In this paper, we study how allowing for a full day of “reflection time” alters behavior. We compare behavior in dictator and cheating games when participants make immediate choices...

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

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.

Bronchial Mucus as a Complex Fluid: Molecular Interactions and Influence of Nanostructured Particles on Rheological and Transport Properties

Directory of Open Access Journals (Sweden)

Odziomek Marcin

2017-06-01

Full Text Available Transport properties of bronchial mucus are investigated by two-stage experimental approach focused on: (a rheological properties and (b mass transfer rate through the stagnant layer of solutions of mucus components (mucine, DNA, proteins and simulated multi-component mucus. Studies were done using thermostated horizontal diffusion cells with sodium cromoglycate and carminic acid as transferred solutes. Rheological properties of tested liquids was studied by a rotational viscometer and a cone-plate rheometer (dynamic method. First part of the studies demonstrated that inter-molecular interactions in these complex liquids influence both rheological and permeability characteristics. Transfer rate is governed not only by mucus composition and concentration but also by hydrophobic/hydrophilic properties of transported molecules. Second part was focused on the properties of such a layer in presence of selected nanostructured particles (different nanoclays and graphene oxide which may be present in lungs after inhalation. It was shown that most of such particles increase visco-elasticity of the mucus and reduce the rate of mass transfer of model drugs. Measured effects may have adverse impact on health, since they will reduce mucociliary clearance in vivo and slow down drug penetration to the bronchial epithelium during inhalation therapy.

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.

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

Inter-firm Networks, Organizational Learning and Knowledge Updating: An Empirical Study

Science.gov (United States)

Zhang, Su-rong; Wang, Wen-ping

In the era of knowledge-based economy which information technology develops rapidly, the rate of knowledge updating has become a critical factor for enterprises to gaining competitive advantage .We build an interactional theoretical model among inter-firm networks, organizational learning and knowledge updating thereby and demonstrate it with empirical study at last. The result shows that inter-firm networks and organizational learning is the source of knowledge updating.

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.

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.

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...

PET-based molecular nuclear neuro-imaging

International Nuclear Information System (INIS)

Kim, Jong Ho

2004-01-01

Molecular nuclear neuro-imaging in CNS drug discovery and development can be divided into four categories that are clearly inter-related. (1) Neuroreceptor mapping to examine the involvement of specific neurotransmitter system in CNS diseases, drug occupancy characteristics and perhaps examine mechanisms of action;(2) Structural and spectroscopic imaging to examine morphological changes and their consequences;(3) Metabolic mapping to provide evidence of central activity and CNS fingerprinting the neuroanatomy of drug effects;(4) Functional mapping to examine disease-drug interactions. In addition, targeted delivery of therapeutic agents could be achieved by modifying stem cells to release specific drugs at the site of transplantation('stem cell pharmacology'). Future exploitation of stem cell biology, including enhanced release of therapeutic factors through genetic stem cell engineering might thus constitute promising pharmaceutical approaches to treating diseases of the nervous system. With continued improvements in instrumentation, identification of better imaging probes by innovative chemistry, molecular nuclear neuro-imaging promise to play increasingly important roles in disease diagnosis and therapy

PET-based molecular nuclear neuro-imaging

Energy Technology Data Exchange (ETDEWEB)

Kim, Jong Ho [Gil Medical Center, Gachon (Korea, Republic of)

2004-04-01

Molecular nuclear neuro-imaging in CNS drug discovery and development can be divided into four categories that are clearly inter-related. (1) Neuroreceptor mapping to examine the involvement of specific neurotransmitter system in CNS diseases, drug occupancy characteristics and perhaps examine mechanisms of action;(2) Structural and spectroscopic imaging to examine morphological changes and their consequences;(3) Metabolic mapping to provide evidence of central activity and CNS fingerprinting the neuroanatomy of drug effects;(4) Functional mapping to examine disease-drug interactions. In addition, targeted delivery of therapeutic agents could be achieved by modifying stem cells to release specific drugs at the site of transplantation('stem cell pharmacology'). Future exploitation of stem cell biology, including enhanced release of therapeutic factors through genetic stem cell engineering might thus constitute promising pharmaceutical approaches to treating diseases of the nervous system. With continued improvements in instrumentation, identification of better imaging probes by innovative chemistry, molecular nuclear neuro-imaging promise to play increasingly important roles in disease diagnosis and therapy.

Hierarchical folding of multiple sequence alignments for the prediction of structures and RNA-RNA interactions

DEFF Research Database (Denmark)

Seemann, Ernst Stefan; Richter, Andreas S.; Gorodkin, Jan

2010-01-01

of that used for individual multiple alignments. Results: We derived a rather extensive algorithm. One of the advantages of our approach (in contrast to other RNARNA interaction prediction methods) is the application of covariance detection and prediction of pseudoknots between intra- and inter-molecular base...... pairs. As a proof of concept, we show an example and discuss the strengths and weaknesses of the approach....

New aspects of π–d interactions in magnetic molecular conductors

Science.gov (United States)

Sugimoto, Toyonari; Fujiwara, Hideki; Noguchi, Satoru; Murata, Keizo

2009-01-01

The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO), ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO), ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS), ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO) and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS) with FeX4− (X = Cl, Br) ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III) d spins of FeX4− ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d–d interaction between the d spins and an indirect π–d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π–d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π–d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π–d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO)2•FeBr4 is a ferromagnetic semiconductor, (EDT-DSDTFVO)2•FeX4 (X = Cl, Br) and (EDT-DSDTFVSDS)2•FeBr4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO)2•FeCl4 and (EDO-TTFVODS)2•FeBr4•(DCE)0.5 (DCE =-dichloroethane) are

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

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.

Molecular genetic gene-environment studies using candidate genes in schizophrenia: a systematic review.

Science.gov (United States)

Modinos, Gemma; Iyegbe, Conrad; Prata, Diana; Rivera, Margarita; Kempton, Matthew J; Valmaggia, Lucia R; Sham, Pak C; van Os, Jim; McGuire, Philip

2013-11-01

The relatively high heritability of schizophrenia suggests that genetic factors play an important role in the etiology of the disorder. On the other hand, a number of environmental factors significantly influence its incidence. As few direct genetic effects have been demonstrated, and there is considerable inter-individual heterogeneity in the response to the known environmental factors, interactions between genetic and environmental factors may be important in determining whether an individual develops the disorder. To date, a considerable number of studies of gene-environment interactions (G×E) in schizophrenia have employed a hypothesis-based molecular genetic approach using candidate genes, which have led to a range of different findings. This systematic review aims to summarize the results from molecular genetic candidate studies and to review challenges and opportunities of this approach in psychosis research. Finally, we discuss the potential of future prospects, such as new studies that combine hypothesis-based molecular genetic candidate approaches with agnostic genome-wide association studies in determining schizophrenia risk. © 2013 Elsevier B.V. All rights reserved.

Developing Students' Listening Metacognitive Strategies Using Online Videotext Self-Dictation-Generation Learning Activity

Science.gov (United States)

Chang, Ching; Chang, Chih-Kai

2014-01-01

The study is based on the use of a flexible learning framework to help students improve information processes underlying strategy instruction in EFL listening. By exploiting the online videotext self-dictation-generation (video-SDG) learning activity implemented on the YouTube caption manager platform, the learning cycle was emphasized to promote…

The Neural Basis of Social Influence in a Dictator Decision

Directory of Open Access Journals (Sweden)

Zhenyu Wei

2017-12-01

Full Text Available Humans tend to reduce inequitable distributions. Previous neuroimaging studies have shown that inequitable decisions are related to brain regions that associated with negative emotion and signaling conflict. In the highly complex human social environment, our opinions and behaviors can be affected by social information. In current study, we used a modified dictator game to investigate the effect of social influence on making an equitable decision. We found that the choices of participants in present task was influenced by the choices of peers. However, participants’ decisions were influenced by equitable rather than inequitable group choices. fMRI results showed that brain regions that related to norm violation and social conflict were related to the inequitable social influence. The neural responses in the dorsomedial prefrontal cortex, rostral cingulate zone, and insula predicted subsequent conforming behavior in individuals. Additionally, psychophysiological interaction analysis revealed that the interconnectivity between the dorsal striatum and insula was elevated in advantageous inequity influence versus no-social influence conditions. We found decreased functional connectivity between the medial prefrontal cortex and insula, supplementary motor area, posterior cingulate gyrus and dorsal anterior cingulate cortex in the disadvantageous inequity influence versus no-social influence conditions. This suggests that a disadvantageous inequity influence may decrease the functional connectivity among brain regions that are related to reward processes. Thus, the neural mechanisms underlying social influence in an equitable decision may be similar to those implicated in social norms and reward processing.

The Neural Basis of Social Influence in a Dictator Decision.

Science.gov (United States)

Wei, Zhenyu; Zhao, Zhiying; Zheng, Yong

2017-01-01

Humans tend to reduce inequitable distributions. Previous neuroimaging studies have shown that inequitable decisions are related to brain regions that associated with negative emotion and signaling conflict. In the highly complex human social environment, our opinions and behaviors can be affected by social information. In current study, we used a modified dictator game to investigate the effect of social influence on making an equitable decision. We found that the choices of participants in present task was influenced by the choices of peers. However, participants' decisions were influenced by equitable rather than inequitable group choices. fMRI results showed that brain regions that related to norm violation and social conflict were related to the inequitable social influence. The neural responses in the dorsomedial prefrontal cortex, rostral cingulate zone, and insula predicted subsequent conforming behavior in individuals. Additionally, psychophysiological interaction analysis revealed that the interconnectivity between the dorsal striatum and insula was elevated in advantageous inequity influence versus no-social influence conditions. We found decreased functional connectivity between the medial prefrontal cortex and insula, supplementary motor area, posterior cingulate gyrus and dorsal anterior cingulate cortex in the disadvantageous inequity influence versus no-social influence conditions. This suggests that a disadvantageous inequity influence may decrease the functional connectivity among brain regions that are related to reward processes. Thus, the neural mechanisms underlying social influence in an equitable decision may be similar to those implicated in social norms and reward processing.

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.

A multilevel-skin neighbor list algorithm for molecular dynamics simulation

Science.gov (United States)

Zhang, Chenglong; Zhao, Mingcan; Hou, Chaofeng; Ge, Wei

2018-01-01

Searching of the interaction pairs and organization of the interaction processes are important steps in molecular dynamics (MD) algorithms and are critical to the overall efficiency of the simulation. Neighbor lists are widely used for these steps, where thicker skin can reduce the frequency of list updating but is discounted by more computation in distance check for the particle pairs. In this paper, we propose a new neighbor-list-based algorithm with a precisely designed multilevel skin which can reduce unnecessary computation on inter-particle distances. The performance advantages over traditional methods are then analyzed against the main simulation parameters on Intel CPUs and MICs (many integrated cores), and are clearly demonstrated. The algorithm can be generalized for various discrete simulations using neighbor lists.

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.

The Effect of the Tuning System and Instrument Variables on Modal Dictation Performance

Science.gov (United States)

Demirbatir, Rasim Erol; Çeliktas, Hatice; Engür, Doruk

2018-01-01

Ear training and musical literacy (ETML) education is one of the main dimensions of the bachelor degree program of music teacher education departments, which provides professional music education. In ETML education, hearing, sight-reading and dictation studies for Turkish music makams have an important place. In this study, it was aimed to…

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...

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.

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

Molecular cooperativity and compatibility via full atomistic simulation

Science.gov (United States)

Kwan Yang, Kenny

Civil engineering has customarily focused on problems from a large-scale perspective, encompassing structures such as bridges, dams, and infrastructure. However, present day challenges in conjunction with advances in nanotechnology have forced a re-focusing of expertise. The use of atomistic and molecular approaches to study material systems opens the door to significantly improve material properties. The understanding that material systems themselves are structures, where their assemblies can dictate design capacities and failure modes makes this problem well suited for those who possess expertise in structural engineering. At the same time, a focus has been given to the performance metrics of materials at the nanoscale, including strength, toughness, and transport properties (e.g., electrical, thermal). Little effort has been made in the systematic characterization of system compatibility -- e.g., how to make disparate material building blocks behave in unison. This research attempts to develop bottom-up molecular scale understanding of material behavior, with the global objective being the application of this understanding into material design/characterization at an ultimate functional scale. In particular, it addresses the subject of cooperativity at the nano-scale. This research aims to define the conditions which dictate when discrete molecules may behave as a single, functional unit, thereby facilitating homogenization and up-scaling approaches, setting bounds for assembly, and providing a transferable assessment tool across molecular systems. Following a macro-scale pattern where the compatibility of deformation plays a vital role in the structural design, novel geometrical cooperativity metrics based on the gyration tensor are derived with the intention to define nano-cooperativity in a generalized way. The metrics objectively describe the general size, shape and orientation of the structure. To validate the derived measures, a pair of ideal macromolecules

Nuances of Morphology in Myelodysplastic Diseases in the Age of Molecular Diagnostics.

Science.gov (United States)

Shaver, Aaron C; Seegmiller, Adam C

2017-10-01

Morphologic dysplasia is an important factor in diagnosis of myelodysplastic syndrome (MDS). However, the role of dysplasia is changing as new molecular genetic and genomic technologies take a more prominent place in diagnosis. This review discusses the role of morphology in the diagnosis of MDS and its interactions with cytogenetic and molecular testing. Recent changes in diagnostic criteria have attempted to standardize approaches to morphologic diagnosis of MDS, recognizing significant inter-observer variability in assessment of dysplasia. Definitive correlates between cytogenetic/molecular and morphologic findings have been described in only a small set of cases. However, these genetic and morphologic tools do play a complementary role in the diagnosis of both MDS and other myeloid neoplasms. Diagnosis of MDS requires a multi-factorial approach, utilizing both traditional morphologic as well as newer molecular genetic techniques. Understanding these tools, and the interplay between them, is crucial in the modern diagnosis of myeloid neoplasms.

Analysis of pattern formation in systems with competing range interactions

International Nuclear Information System (INIS)

Zhao, H J; Misko, V R; Peeters, F M

2012-01-01

We analyzed pattern formation and identified various morphologies in a system of particles interacting through a non-monotonic potential with a competing range interaction characterized by a repulsive core (r c ) and an attractive tail (r > r c ), using molecular-dynamics simulations. Depending on parameters, the interaction potential models the inter-particle interaction in various physical systems ranging from atoms, molecules and colloids to vortices in low κ type-II superconductors and in recently discovered ‘type-1.5’ superconductors. We constructed a ‘morphology diagram’ in the plane ‘critical radius r c -density n’ and proposed a new approach to characterizing the different types of patterns. Namely, we elaborated a set of quantitative criteria in order to identify the different pattern types, using the radial distribution function (RDF), the local density function and the occupation factor. (paper)

TOPICAL REVIEW: New aspects of π-d interactions in magnetic molecular conductors

Science.gov (United States)

Sugimoto, Toyonari; Fujiwara, Hideki; Noguchi, Satoru; Murata, Keizo

2009-04-01

The 2 : 1 cation radical salts of bent donor molecules of ethylenedithio-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDT-TTFVO), ethylenedithio-diselenadithiafulvalenoquinone-1,3-dithiolemethide (EDT-DSDTFVO), ethylenedithio-diselenadithiafulvalenothioquinone-1,3-diselenolemethide (EDT-DSDTFVSDS), ethylenedioxy-tetrathiafulvalenoquinone-1,3-dithiolemethide (EDO-TTFVO) and ethylenedioxy-tetrathiafulvalenoquinone-1,3-diselenolemethide (EDO-TTFVODS) with FeX4- (X = Cl, Br) ions are prepared by electrocrystallization. The crystal structures of these salts are composed of alternately stacked donor molecule and magnetic anion layers. The band structures of the donor molecule layers are calculated using the overlap integrals between neighboring donor molecules and are compared with the observed electronic transport properties. The magnetic ordering of the Fe(III) d spins of FeX4- ions is determined from magnetization and heat capacity measurements. The magnetic ordering temperatures are estimated by considering a combination of a direct d-d interaction between the d spins and an indirect π-d interaction between the conduction π electron and the d spins, whose magnitudes are separately calculated from the crystal structures with an extended Hückel molecular orbital method. The occurrence of a π-d interaction is proved by the negative magnetoresistance, and the magnitude of magnetoresistance reflects the strength of the π-d interaction. The effect of pressure on the magnetoresistance is studied, and the result indicates that the magnitude of magnetoresistance increases, namely, the π-d interaction is enhanced with increasing pressure. From these experimental results it is shown that (EDT-TTFVO)2•FeBr4 is a ferromagnetic semiconductor, (EDT-DSDTFVO)2•FeX4 (X = Cl, Br) and (EDT-DSDTFVSDS)2•FeBr4 are metals exhibiting antiferromagnetic ordering of the d spins, and (EDO-TTFVO)2•FeCl4 and (EDO-TTFVODS)2•FeBr4•(DCE)0.5 (DCE =-dichloroethane) are genuine

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...

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

Evidence for the robustness of protein complexes to inter-species hybridization.

Directory of Open Access Journals (Sweden)

Jean-Baptiste Leducq

Full Text Available Despite the tremendous efforts devoted to the identification of genetic incompatibilities underlying hybrid sterility and inviability, little is known about the effect of inter-species hybridization at the protein interactome level. Here, we develop a screening platform for the comparison of protein-protein interactions (PPIs among closely related species and their hybrids. We examine in vivo the architecture of protein complexes in two yeast species (Saccharomyces cerevisiae and Saccharomyces kudriavzevii that diverged 5-20 million years ago and in their F1 hybrids. We focus on 24 proteins of two large complexes: the RNA polymerase II and the nuclear pore complex (NPC, which show contrasting patterns of molecular evolution. We found that, with the exception of one PPI in the NPC sub-complex, PPIs were highly conserved between species, regardless of protein divergence. Unexpectedly, we found that the architecture of the complexes in F1 hybrids could not be distinguished from that of the parental species. Our results suggest that the conservation of PPIs in hybrids likely results from the slow evolution taking place on the very few protein residues involved in the interaction or that protein complexes are inherently robust and may accommodate protein divergence up to the level that is observed among closely related species.

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.

Fluctuation Solution Theory Properties from Molecular Simulation

DEFF Research Database (Denmark)

Abildskov, Jens; Wedberg, R.; O’Connell, John P.

2013-01-01

The thermodynamic properties obtained in the Fluctuation Solution Theory are based on spatial integrals of molecular TCFs between component pairs in the mixture. Molecular simulation, via either MD or MC calculations, can yield these correlation functions for model inter- and intramolecular...

An investigation of the inter-clonal variation of the interactive effects of cadmium and Microcystis aeruginosa on the reproductive performance of Daphnia magna

International Nuclear Information System (INIS)

De Coninck, Dieter I.M.; Janssen, Colin R.; De Schamphelaere, Karel A.C.

2013-01-01

all clones were analyzed together (F-test, p = 0.07), suggesting no inter-clonal variation of the interactive effect between Cd and Microcystis. However, when the same data were quantitatively analyzed on a clone-by-clone scale, we found a relatively wide range of deviations between observed and IA-model-predicted reproduction in combined Cd + Microcystis treatments (both in direction and magnitude), suggesting some biological significance of inter-clonal variation of interactive effects. In one of the twenty clones this deviation was statistically significant (two-way ANOVA, F-test, p = 0.005), indicating an interactive Cd × Microcystis effect in this clone. Together, these two observations caution against the extrapolation of conclusions about mixed stressor data obtained with single clones to the level of the entire species and to the level of natural, genetically diverse populations

An investigation of the inter-clonal variation of the interactive effects of cadmium and Microcystis aeruginosa on the reproductive performance of Daphnia magna

Energy Technology Data Exchange (ETDEWEB)

De Coninck, Dieter I.M., E-mail: Dieter.DeConinck@UGent.be; Janssen, Colin R.; De Schamphelaere, Karel A.C.

2013-09-15

all clones were analyzed together (F-test, p = 0.07), suggesting no inter-clonal variation of the interactive effect between Cd and Microcystis. However, when the same data were quantitatively analyzed on a clone-by-clone scale, we found a relatively wide range of deviations between observed and IA-model-predicted reproduction in combined Cd + Microcystis treatments (both in direction and magnitude), suggesting some biological significance of inter-clonal variation of interactive effects. In one of the twenty clones this deviation was statistically significant (two-way ANOVA, F-test, p = 0.005), indicating an interactive Cd × Microcystis effect in this clone. Together, these two observations caution against the extrapolation of conclusions about mixed stressor data obtained with single clones to the level of the entire species and to the level of natural, genetically diverse populations.

Effect of inter-species selective interactions on the thermodynamics and nucleation free-energy barriers of a tessellating polyhedral compound

International Nuclear Information System (INIS)

Escobedo, Fernando A.

2016-01-01

The phase behavior and the homogeneous nucleation of an equimolar mixture of octahedra and cuboctahedra are studied using thermodynamic integration, Gibbs-Duhem integration, and umbrella sampling simulations. The components of this mixture are modeled as polybead objects of equal edge lengths so that they can assemble into a space-filling compound with the CsCl crystal structure. Taking as reference the hard-core system where the compound crystal does not spontaneously nucleate, we quantified the effect of inter-species selective interactions on facilitating the disorder-to-order transition. Facet selective and facet non-selective inter-species attractions were considered, and while the former was expectedly more favorable toward the target tessellating structure, the latter was found to be similarly effective in nucleating the crystal compound. Ranges for the strength of attractions and degree of supersaturation were identified where the nucleation free-energy barrier was small enough to foretell a fast process but large enough to prevent spinodal fluctuations that can trap the system in dense metastable states lacking long-range order. At those favorable conditions, the tendency toward the local orientational order favored by packing entropy is amplified and found to play a key role seeding nuclei with the CsCl structure.

A peptide extension dictates IgM assembly.

Science.gov (United States)

Pasalic, Dzana; Weber, Benedikt; Giannone, Chiara; Anelli, Tiziana; Müller, Roger; Fagioli, Claudio; Felkl, Manuel; John, Christine; Mossuto, Maria Francesca; Becker, Christian F W; Sitia, Roberto; Buchner, Johannes

2017-10-10

Professional secretory cells can produce large amounts of high-quality complex molecules, including IgM antibodies. Owing to their multivalency, polymeric IgM antibodies provide an efficient first-line of defense against pathogens. To decipher the mechanisms of IgM assembly, we investigated its biosynthesis in living cells and faithfully reconstituted the underlying processes in vitro. We find that a conserved peptide extension at the C-terminal end of the IgM heavy (Ig-μ) chains, termed the tailpiece, is necessary and sufficient to establish the correct geometry. Alanine scanning revealed that hydrophobic amino acids in the first half of the tailpiece contain essential information for generating the correct topology. Assembly is triggered by the formation of a disulfide bond linking two tailpieces. This induces conformational changes in the tailpiece and the adjacent domain, which drive further polymerization. Thus, the biogenesis of large and topologically challenging IgM complexes is dictated by a local conformational switch in a peptide extension.

Application of TensorFlow to recognition of visualized results of fragment molecular orbital (FMO) calculations

OpenAIRE

Saitou, Sona; Iijima, Jun; Fujimoto, Mayu; Mochizuki, Yuji; Okuwaki, Koji; Doi, Hideo; Komeiji, Yuto

2018-01-01

We have applied Google's TensorFlow deep learning toolkit to recognize the visualized results of the fragment molecular orbital (FMO) calculations. Typical protein structures of alpha-helix and beta-sheet provide some characteristic patterns in the two-dimensional map of inter-fragment interaction energy termed as IFIE-map (Kurisaki et al., Biophys. Chem. 130 (2007) 1). A thousand of IFIE-map images with labels depending on the existences of alpha-helix and beta-sheet were prepared by employi...

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.

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.

Protein-binding RNA aptamers affect molecular interactions distantly from their binding sites.

Directory of Open Access Journals (Sweden)

Daniel M Dupont

Full Text Available Nucleic acid aptamer selection is a powerful strategy for the development of regulatory agents for molecular intervention. Accordingly, aptamers have proven their diligence in the intervention with serine protease activities, which play important roles in physiology and pathophysiology. Nonetheless, there are only a few studies on the molecular basis underlying aptamer-protease interactions and the associated mechanisms of inhibition. In the present study, we use site-directed mutagenesis to delineate the binding sites of two 2´-fluoropyrimidine RNA aptamers (upanap-12 and upanap-126 with therapeutic potential, both binding to the serine protease urokinase-type plasminogen activator (uPA. We determine the subsequent impact of aptamer binding on the well-established molecular interactions (plasmin, PAI-1, uPAR, and LRP-1A controlling uPA activities. One of the aptamers (upanap-126 binds to the area around the C-terminal α-helix in pro-uPA, while the other aptamer (upanap-12 binds to both the β-hairpin of the growth factor domain and the kringle domain of uPA. Based on the mapping studies, combined with data from small-angle X-ray scattering analysis, we construct a model for the upanap-12:pro-uPA complex. The results suggest and highlight that the size and shape of an aptamer as well as the domain organization of a multi-domain protein such as uPA, may provide the basis for extensive sterical interference with protein ligand interactions considered distant from the aptamer binding site.

TCM grammar systems: an approach to aid the interpretation of the molecular interactions in Chinese herbal medicine.

Science.gov (United States)

Yan, Jing; Wang, Yun; Luo, Si-Jun; Qiao, Yan-Jiang

2011-09-01

Interpreting the molecular interactions in Chinese herbal medicine will help to understand the molecular mechanisms of Traditional Chinese medicines (TCM) and predict the new pharmacological effects of TCM. Yet, we still lack a method which could integrate the concerned pieces of parsed knowledge about TCM. To solve the problem, a new method named TCM grammar systems was proposed in the present article. The possibility to study the interactions of TCM at the molecular level using TCM grammar systems was explored using Herba Ephedrae Decoction (HED) as an example. A platform was established based on the formalism of TCM grammar systems. The related molecular network of Herba Ephedrae Decoction (HED) can be extracted automatically. The molecular network indicates that Beta2 adrenergic receptor, Glucocorticoid receptor and Interleukin12 are the relatively important targets for the anti-anaphylaxis asthma function of HED. Moreover, the anti-anaphylaxis asthma function of HED is also related with suppressing inflammation process. The results show the feasibility using TCM grammar systems to interpret the molecular mechanism of TCM. Although the results obtained depend on the database absolutely, recombination of existing knowledge in this method provides new insight for interpreting the molecular mechanism of TCM. TCM grammar systems could aid the interpretation of the molecular interactions in TCM to some extent. Moreover, it might be useful to predict the new pharmacological effects of TCM. The method is an in silico technology. In association with the experimental techniques, this method will play an important role in the understanding of the molecular mechanisms of TCM. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

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...

Molecular basis for the interplay of apoptosis and proliferation mediated by Bcl-xL:Bim interactions in pancreatic cancer cells

International Nuclear Information System (INIS)

Abrol, Ravinder; Edderkaoui, Mouad; Goddard, William A.; Pandol, Stephen J.

2012-01-01

Highlights: ► Direct role of Bcl-2 protein interactions in cell proliferation is not clear. ► Designed Bcl-xL mutants show opposite effects on apoptosis and proliferation. ► Disrupting Bcl-xL:Bim interaction increased apoptosis in pancreatic cancer. ► Disrupting Bcl-xL:Bim interaction decreased proliferation in pancreatic cancer. ► Bcl-xL:Bim interaction can control both apoptosis and proliferation. -- Abstract: A major mechanism through which cancer cells avoid apoptosis is by promoting the association of anti-apoptotic members of the pro-survival Bcl-2 protein family (like Bcl-2 and Bcl-xL) with BH 3 domain-only proteins (like Bim and Bid). Apoptosis and cell proliferation have been shown to be linked for many cancers but the molecular basis for this link is far from understood. We have identified the Bcl-xL:Bim protein–protein interface as a direct regulator of proliferation and apoptosis in pancreatic cancer cells. We were able to predict and subsequently verify experimentally the effect of various Bcl-xL single-point mutants (at the position A142) on binding to Bim by structural analysis and computational modeling of the inter-residue interactions at the Bcl-xL:Bim protein–protein interface. The mutants A142N, A142Q, and A142Y decreased binding of Bim to Bcl-xL and A142S increased this binding. The Bcl-xL mutants, with decreased affinity for Bim, caused an increase in apoptosis and a corresponding decrease in cell proliferation. However, we could prevent these effects by introducing a small interfering RNA (siRNA) targeted at Bim. These results show a novel role played by the Bcl-xL:Bim interaction in regulating proliferation of pancreatic cancer cells at the expense of apoptosis. This study presents a physiologically relevant model of the Bcl-xL:Bim interface that can be used for rational therapeutic design for the inhibition of proliferation and cancer cell resistance to apoptosis.

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

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.

Molecular Design of Branched and Binary Molecules at Ordered Interfaces

Energy Technology Data Exchange (ETDEWEB)

Genson, Kirsten Larson [Iowa State Univ., Ames, IA (United States)

2005-01-01

This study examined five different branched molecular architectures to discern the effect of design on the ability of molecules to form ordered structures at interfaces. Photochromic monodendrons formed kinked packing structures at the air-water interface due to the cross-sectional area mismatch created by varying number of alkyl tails and the hydrophilic polar head group. The lower generations formed orthorhombic unit cell with long range ordering despite the alkyl tails tilted to a large degree. Favorable interactions between liquid crystalline terminal groups and the underlying substrate were observed to compel a flexible carbosilane dendrimer core to form a compressed elliptical conformation which packed stagger within lamellae domains with limited short range ordering. A twelve arm binary star polymer was observed to form two dimensional micelles at the air-water interface attributed to the higher polystyrene block composition. Linear rod-coil molecules formed a multitude of packing structures at the air-water interface due to the varying composition. Tree-like rod-coil molecules demonstrated the ability to form one-dimensional structures at the air-water interface and at the air-solvent interface caused by the preferential ordering of the rigid rod cores. The role of molecular architecture and composition was examined and the influence chemically competing fragments was shown to exert on the packing structure. The amphiphilic balance of the different molecular series exhibited control on the ordering behavior at the air-water interface and within bulk structures. The shell nature and tail type was determined to dictate the preferential ordering structure and molecular reorganization at interfaces with the core nature effect secondary.

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

Synthesis and studies on structural, optical and nonlinear optical properties of novel organic inter-molecular compounds: 4-chloro-3-nitroaniline-3-hydroxy benzaldehyde and urea-4-dimethylaminopyridine

Science.gov (United States)

Pandey, Priyanka; Rai, R. N.

2018-05-01

Two novel organic inter-molecular compounds (IMCs), (3-(4-chloro-3-nitrophenylimino) methyl) phenol) (CNMP) and urea ̶ 4-dimethylaminopyridine complex (UDMAP), have been synthesized by solid state reaction. These two IMCs were identified by phase diagram study of CNA-HB and U-DMAP systems. The single crystals of newly obtained IMCs were grown by slow solvent evaporation technique at room temperature. Both the IMCs were further studied for their thermal, spectral, single crystal XRD for their atomic packing in molecule, crystallinity, optical and nonlinear optical behaviour. In both the cases, melting point of inter-molecular compounds was found to be higher than that of their parent components, CNMP was found to be thermally stable up to 158 °C while UDMAP was stable up to 144 °C, which indicate their extra stability than their parents. The single crystal XRD studies confirmed that CNMP has crystallized in orthorhombic unit cell with non-centrosymmetric space group P212121 while UDMAP has crystallized in monoclinic unit cell with centrosymmetric space group C2/c. The absorption spectrum of CNMP was found to be in between the absorption of parents, while broadening of peak and red shift was observed in UDMAP as compared to the parents. Second order nonlinear optical property of CNMP and UDMAP was studied using Kurtz Perry powder technique and intense green light emission was observed with CNMP on excitation with 1064 nm of Nd:YAG laser while no emission was observed with UDMAP.

Head-head interactions of resting myosin crossbridges in intact frog skeletal muscles, revealed by synchrotron x-ray fiber diffraction.

Directory of Open Access Journals (Sweden)

Kanji Oshima

Full Text Available The intensities of the myosin-based layer lines in the x-ray diffraction patterns from live resting frog skeletal muscles with full thick-thin filament overlap from which partial lattice sampling effects had been removed were analyzed to elucidate the configurations of myosin crossbridges around the thick filament backbone to nanometer resolution. The repeat of myosin binding protein C (C-protein molecules on the thick filaments was determined to be 45.33 nm, slightly longer than that of myosin crossbridges. With the inclusion of structural information for C-proteins and a pre-powerstroke head shape, modeling in terms of a mixed population of regular and perturbed regions of myosin crown repeats along the filament revealed that the myosin filament had azimuthal perturbations of crossbridges in addition to axial perturbations in the perturbed region, producing pseudo-six-fold rotational symmetry in the structure projected down the filament axis. Myosin crossbridges had a different organization about the filament axis in each of the regular and perturbed regions. In the regular region that lacks C-proteins, there were inter-molecular interactions between the myosin heads in axially adjacent crown levels. In the perturbed region that contains C-proteins, in addition to inter-molecular interactions between the myosin heads in the closest adjacent crown levels, there were also intra-molecular interactions between the paired heads on the same crown level. Common features of the interactions in both regions were interactions between a portion of the 50-kDa-domain and part of the converter domain of the myosin heads, similar to those found in the phosphorylation-regulated invertebrate myosin. These interactions are primarily electrostatic and the converter domain is responsible for the head-head interactions. Thus multiple head-head interactions of myosin crossbridges also characterize the switched-off state and have an important role in the regulation

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.

Cross-Layer Design of the Inter-RAT Handover between UMTS and WiMAX

Directory of Open Access Journals (Sweden)

Bertin Philippe

2010-01-01

Full Text Available In future mobile networks, different radio access technologies will have to coexist. IEEE 802.21 MIH (Media-Independent Handover provides primitive mechanisms that ease the implementation of a seamless vertical handover (inter-RAT handover between different radio access technologies. However, it does not specify any handover execution mechanism. The first objective of this paper is to propose a novel MIHF (Media-Independent Handover Function variant, which is renamed interworking (IW sublayer. IW sublayer provides a seamless inter-RAT handover procedure between UMTS and WiMAX systems. It relies on a new intersystem retransmission mechanism with cross-layer interaction ability providing lossless handover while keeping acceptable delays. The second objective of this paper is to design a new TCP snoop agent (TCP Snoop, which interacts with the IW layer in order to mitigate BDP (Bandwidth Delay Product mismatch and to solve spurious RTO (Retransmission TimeOut problems. The cross-layer effects on the handover performance are evaluated by simulations. Our results show that cross-layer interaction between IW layer and TCP Snoop smoothes the handover procedure for TCP traffics. Additionally, this novel inter-RAT cross-layer scheme has the merit of keeping existing TCP protocol stacks unchanged.

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

(4S)-4-(3,4-Dichloro?phen?yl)-1?-methyl-4?-phenyl-3,4-dihydronaphthalene-2-spiro-3?-pyrrolidine-2?-spiro-1??-acenaphthyl?ene-1,2??(2H,1??H)-dione

OpenAIRE

Murugan, R.; Gunasekaran, B.; Narayanan, S. Sriman; Manivannan, V.

2008-01-01

In the title compound, C37H27Cl2NO2, the 3,4-dichloro?phenyl ring makes a dihedral angle of 46.66?(6)? with the phenyl ring. The mol?ecular structure is stabilized by weak intra?molecular C?H?O inter?actions and the crystal structure is stabilized by weak inter?molecular C?H?O inter?actions. The C?C?C?C?C five-membered ring is planar, while the C?C?C?C?N five-membered ring adopts a half-chair conformation.

Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

KAUST Repository

Chawla, Mohit; Chermak, Edrisse; Zhang, Qingyun; Bujnicki, Janusz M.; Oliva, Romina; Cavallo, Luigi

2017-01-01

The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4′ atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose–base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair–π stacking interactions also occur between ribose and aromatic amino acids in RNA–protein complexes.

Occurrence and stability of lone pair–π stacking interactions between ribose and nucleobases in functional RNAs

KAUST Repository

Chawla, Mohit

2017-08-18

The specific folding pattern and function of RNA molecules lies in various weak interactions, in addition to the strong base-base pairing and stacking. One of these relatively weak interactions, characterized by the stacking of the O4′ atom of a ribose on top of the heterocycle ring of a nucleobase, has been known to occur but has largely been ignored in the description of RNA structures. We identified 2015 ribose–base stacking interactions in a high-resolution set of non-redundant RNA crystal structures. They are widespread in structured RNA molecules and are located in structural motifs other than regular stems. Over 50% of them involve an adenine, as we found ribose-adenine contacts to be recurring elements in A-minor motifs. Fewer than 50% of the interactions involve a ribose and a base of neighboring residues, while approximately 30% of them involve a ribose and a nucleobase at least four residues apart. Some of them establish inter-domain or inter-molecular contacts and often implicate functionally relevant nucleotides. In vacuo ribose-nucleobase stacking interaction energies were calculated by quantum mechanics methods. Finally, we found that lone pair–π stacking interactions also occur between ribose and aromatic amino acids in RNA–protein complexes.

Molecular interactions of agonist and inverse agonist ligands at serotonin 5-HT2C G protein-coupled receptors: computational ligand docking and molecular dynamics studies validated by experimental mutagenesis results

Science.gov (United States)

Córdova-Sintjago, Tania C.; Liu, Yue; Booth, Raymond G.

2015-02-01

To understand molecular determinants for ligand activation of the serotonin 5-HT2C G protein-coupled receptor (GPCR), a drug target for obesity and neuropsychiatric disorders, a 5-HT2C homology model was built according to an adrenergic β2 GPCR (β2AR) structure and validated using a 5-HT2B GPCR crystal structure. The models were equilibrated in a simulated phosphatidyl choline membrane for ligand docking and molecular dynamics studies. Ligands included (2S, 4R)-(-)-trans-4-(3'-bromo- and trifluoro-phenyl)-N,N-dimethyl-1,2,3,4-tetrahydronaphthalene-2-amine (3'-Br-PAT and 3'-CF3-PAT), a 5-HT2C agonist and inverse agonist, respectively. Distinct interactions of 3'-Br-PAT and 3'-CF3-PAT at the wild-type (WT) 5-HT2C receptor model were observed and experimental 5-HT2C receptor mutagenesis studies were undertaken to validate the modelling results. For example, the inverse agonist 3'-CF3-PAT docked deeper in the WT 5-HT2C binding pocket and altered the orientation of transmembrane helices (TM) 6 in comparison to the agonist 3'-Br-PAT, suggesting that changes in TM orientation that result from ligand binding impact function. For both PATs, mutation of 5-HT2C residues S3.36, T3.37, and F5.47 to alanine resulted in significantly decreased affinity, as predicted from modelling results. It was concluded that upon PAT binding, 5-HT2C residues T3.37 and F5.47 in TMs 3 and 5, respectively, engage in inter-helical interactions with TMs 4 and 6, respectively. The movement of TMs 5 and 6 upon agonist and inverse agonist ligand binding observed in the 5-HT2C receptor modelling studies was similar to movements reported for the activation and deactivation of the β2AR, suggesting common mechanisms among aminergic neurotransmitter GPCRs.

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.

Crossing ethnic lines? The impact of in-group favouritism and acculturation preferences on inter-ethnic contacts

Directory of Open Access Journals (Sweden)

Joachim Brüb

2014-11-01

Full Text Available Starting from the notion that making individuals in-teract across ethnic lines seems to be a major difficulty (Amir,1976, this comparative field study offers two explanations for the differences in inter-ethnic contacts among German, Turkish and Aussiedler (Resettler adolescents. One assumption is based on Social Identity Theory research with its central proposition that in group affiliation is likely to trigger out-group rejection. Thus in group favouritism is expected to decrease the frequency of inter-ethnic encounters. The other assumption is built on acculturation research and argues that certain dispositions towards acculturation facilitate or inhibit inter-ethnic contacts considerably. A preference for interaction is supposed to function as a facilitating factor where as assimilation is likely to prevent inter-ethnic encounters.On the whole the findings of this field study corroborate the assumptionsfor in-group favouritism and acculturation preferences.Further, young men tend more often to approve of in-group favouritism which prohibits inter-ethnic contact, while in contrast, young women more often agree with notions of dissimilation orinteraction which facilitate encounters with out-group members.Finally, subgroup analyses point to the importance of religious affiliation sand their consequences for inter-ethnic contacts under certain conditions.

Inter-Korean military confidence building after 2003.

Energy Technology Data Exchange (ETDEWEB)

Tae-woo, Kim (Korea Institute for Defense Analyses, Seoul, Republic of Korea); Littlefield, Adriane C.; Vannoni, Michael Geoffrey; Sang-beom, Kim (Korea Institute for Defense Analyses, Seoul, Republic of Korea); Koelm, Jennifer Gay; Olsen, John Norman; Myong-jin, Kim (Korea Institute for Defense Analyses, Seoul, Republic of Korea); Sung-tack, Shin (Korea Institute for Defense Analyses, Seoul, Republic of Korea)

2003-08-01

Tensions on the Korean Peninsula remain high despite a long-term strategy by South Korea to increase inter-Korean exchanges in economics, culture, sports, and other topics. This is because the process of reconciliation has rarely extended to military and security topics and those initiatives that were negotiated have been ineffective. Bilateral interactions must include actions to reduce threats and improve confidence associated with conventional military forces (land, sea, and air) as well as nuclear, chemical, and biological activities that are applicable to developing and producing weapons of mass destruction (WMD). The purpose of this project is to develop concepts for inter-Korean confidence building measures (CBMs) for military and WMD topics that South Korea could propose to the North when conditions are right. This report describes the historical and policy context for developing security-related CBMs and presents an array of bilateral options for conventional military and WMD topics within a consistent framework. The conceptual CBMs address two scenarios: (1) improved relations where construction of a peace regime becomes a full agenda item in inter-Korean dialogue, and (2) continued tense inter-Korean relations. Some measures could be proposed in the short term under current conditions, others might be implemented in a series of steps, while some require a higher level of cooperation than currently exists. To support decision making by political leaders, this research focuses on strategies and policy options and does not include technical details.

Growth of bi- and tri-layered graphene on silicon carbide substrate via molecular dynamics simulation

Energy Technology Data Exchange (ETDEWEB)

Min, Tjun Kit; Yoon, Tiem Leong [School of Physics, Universiti Sains Malaysia, 11800 USM, Penang (Malaysia); Lim, Thong Leng [Faculty of Engineering and Technology, Multimedia University, Melaka Campus, 75450 Melaka (Malaysia)

2015-04-24

Molecular dynamics (MD) simulation with simulated annealing method is used to study the growth process of bi- and tri-layered graphene on a 6H-SiC (0001) substrate via molecular dynamics simulation. Tersoff-Albe-Erhart (TEA) potential is used to describe the inter-atomic interactions among the atoms in the system. The formation temperature, averaged carbon-carbon bond length, pair correlation function, binding energy and the distance between the graphene formed and the SiC substrate are quantified. The growth mechanism, graphitization of graphene on the SiC substrate and characteristics of the surface morphology of the graphene sheet obtained in our MD simulation compare well to that observed in epitaxially grown graphene experiments and other simulation works.

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.

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.

Noncovalent Intermolecular Interactions in Organic Electronic Materials: Implications for the Molecular Packing vs Electronic Properties of Acenes

KAUST Repository

Sutton, Christopher

2015-10-30

Noncovalent intermolecular interactions, which can be tuned through the toolbox of synthetic chemistry, determine not only the molecular packing but also the resulting electronic, optical, and mechanical properties of materials derived from π-conjugated molecules, oligomers, and polymers. Here, we provide an overview of the theoretical underpinnings of noncovalent intermolecular interactions and briefly discuss the computational chemistry approaches used to understand the magnitude of these interactions. These methodologies are then exploited to illustrate how noncovalent intermolecular interactions impact important electronic properties-such as the electronic coupling between adjacent molecules, a key parameter for charge-carrier transport-through a comparison between the prototype organic semiconductor pentacene with a series of N-substituted heteropentacenes. Incorporating an understanding of these interactions into the design of organic semiconductors can assist in developing novel materials systems from this fascinating molecular class. © 2015 American Chemical Society.

Electrochemical control of quantum interference in anthraquinone-based molecular switches

DEFF Research Database (Denmark)

Markussen, Troels; Schiøtz, Jakob; Thygesen, Kristian Sommer

2010-01-01

Using first-principles calculations we analyze the electronic transport properties of a recently proposed anthraquinone-based electrochemical switch. Robust conductance on/off ratios of several orders of magnitude are observed due to destructive quantum interference present in the anthraquinone...... of hopping via the localized orbitals. The topology of the tight-binding model, which is dictated by the symmetries of the molecular orbitals, determines the amount of quantum interference....

PyBioMed: a python library for various molecular representations of chemicals, proteins and DNAs and their interactions.

Science.gov (United States)

Dong, Jie; Yao, Zhi-Jiang; Zhang, Lin; Luo, Feijun; Lin, Qinlu; Lu, Ai-Ping; Chen, Alex F; Cao, Dong-Sheng

2018-03-20

With the increasing development of biotechnology and informatics technology, publicly available data in chemistry and biology are undergoing explosive growth. Such wealthy information in these data needs to be extracted and transformed to useful knowledge by various data mining methods. Considering the amazing rate at which data are accumulated in chemistry and biology fields, new tools that process and interpret large and complex interaction data are increasingly important. So far, there are no suitable toolkits that can effectively link the chemical and biological space in view of molecular representation. To further explore these complex data, an integrated toolkit for various molecular representation is urgently needed which could be easily integrated with data mining algorithms to start a full data analysis pipeline. Herein, the python library PyBioMed is presented, which comprises functionalities for online download for various molecular objects by providing different IDs, the pretreatment of molecular structures, the computation of various molecular descriptors for chemicals, proteins, DNAs and their interactions. PyBioMed is a feature-rich and highly customized python library used for the characterization of various complex chemical and biological molecules and interaction samples. The current version of PyBioMed could calculate 775 chemical descriptors and 19 kinds of chemical fingerprints, 9920 protein descriptors based on protein sequences, more than 6000 DNA descriptors from nucleotide sequences, and interaction descriptors from pairwise samples using three different combining strategies. Several examples and five real-life applications were provided to clearly guide the users how to use PyBioMed as an integral part of data analysis projects. By using PyBioMed, users are able to start a full pipelining from getting molecular data, pretreating molecules, molecular representation to constructing machine learning models conveniently. PyBioMed provides

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.

Reduced density matrix embedding. General formalism and inter-domain correlation functional.

Science.gov (United States)

Pernal, Katarzyna

2016-08-03

An embedding method for a one-electron reduced density matrix (1-RDM) is proposed. It is based on partitioning of 1-RDM into domains and describing each domain in the effective potential of the other ones. To assure N-representability of the total 1-RDM N-representability and strong-orthogonality conditions are imposed on the domains. The total energy is given as a sum of single-domain energies and domain-domain electron interaction contributions. Higher than two-body inter-domain interaction terms are neglected. The two-body correlation terms are approximated by deriving inter-domain correlation from couplings of density fluctuations of two domains at a time. Unlike in most density embedding methods kinetic energy is treated exactly and it is not required that densities pertaining to the domains are only weakly overlapping. We propose to treat each domain by a corrected perfect-pairing functional. On a few examples it is shown that the embedding reduced density matrix functional method (ERDMF) yields excellent results for molecules that are well described by a single Lewis structure even if strong static intra-domain or dynamic inter-domain correlation effects must be accounted for.

The molecular mechanism of bisphenol A (BPA as an endocrine disruptor by interacting with nuclear receptors: insights from molecular dynamics (MD simulations.

Directory of Open Access Journals (Sweden)

Lanlan Li

Full Text Available Bisphenol A (BPA can interact with nuclear receptors and affect the normal function of nuclear receptors in very low doses, which causes BPA to be one of the most controversial endocrine disruptors. However, the detailed molecular mechanism about how BPA interferes the normal function of nuclear receptors is still undiscovered. Herein, molecular dynamics simulations were performed to explore the detailed interaction mechanism between BPA with three typical nuclear receptors, including hERα, hERRγ and hPPARγ. The simulation results and calculated binding free energies indicate that BPA can bind to these three nuclear receptors. The binding affinities of BPA were slightly lower than that of E2 to these three receptors. The simulation results proved that the binding process was mainly driven by direct hydrogen bond and hydrophobic interactions. In addition, structural analysis suggested that BPA could interact with these nuclear receptors by mimicking the action of natural hormone and keeping the nuclear receptors in active conformations. The present work provided the structural evidence to recognize BPA as an endocrine disruptor and would be important guidance for seeking safer substitutions of BPA.

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.

Characterization of the hydrogen bond in molecular systems of biological interest by neutron scattering

International Nuclear Information System (INIS)

Cavillon, F.

2004-10-01

This work presents a methodology for the analysis of the scattering spectra of neutrons on molecular liquids. This method is based on the adjustment of the molecular form factor concerning great momentum transfer. The subtraction of the intra-molecular contributions gives access to information on inter-molecular interactions such as the hydrogen bond. 3 systems with increasing levels of difficulty have been studied: the ammonia molecule, the N-methyl-formamide (NMF) and the N-methyl-acetamide (NMA). The value we get for the N-D intermolecular distance of the liquid ammonia molecule is 1.7 angstrom, this value is different from the value generally admitted (2.3 angstrom) but we have validated it by studying the isotopic substitution N 14 /N 15 . The adjustment to the NMF is obtained with a good accuracy but the characterization of the hydrogen bound is more delicate to infer. A preliminary study of the NMA molecule shows that this method can give relevant results on complex molecules

Conductance and thermopower in molecular nanojunctions

Science.gov (United States)

Sen, Arijit

2013-02-01

Electronic transport through short channels in a molecular junction is an intricate quantum scattering problem [1]. To garner insight on how the structure and the electrical properties of a nanoscale junction are correlated is thus of both fundamental and technological interest [1-3]. As observed experimentally in the last couple of years by several independent research groups [4-5], a two-terminal molecular junction comprising of a simple alkane chain with varying length can exhibit high as well as low conductance. However, what causes the simultaneous unveiling of multiple conductances remained largely obscure. We have recently demonstrated [6] that the binary conductance in these heterostructures is due mainly to two distinct electrode orientations that control the electrode-molecule coupling as well as the tunneling strength through quantum interference following diversity in the electrode band structures. Our detailed analysis on the transmission spectra indicates that even a single-molecule nanojunction can potentially serve as a realistic double-quantum-dot kind of system to yield tunable Fano resonance, as often desired for nanoscale switching. In this talk, I intend to give a brief account of molecular electronics and its future applications along with the challenges and possibilities in the current perspective. A few deliberations may as well include how the inter-dot tunneling strength may affect the non-equilibrium charge transport and thermoelectricity in a myriad of molecular junctions based on different molecular conformations and electrode structures. Finally, I shall try to touch upon the effect of electron-phonon interaction on the nanoscale charge transport, and also, the phonon-mediated thermal transport in molecular nanodevices.

Written Spelling to Dictation: Sound-To-Spelling Regularity Affects Both Writing Latencies and Durations

Science.gov (United States)

Delattre, Marie; Bonin, Patrick; Barry, Christopher

2006-01-01

The authors examined the effect of sound-to-spelling regularity on written spelling latencies and writing durations in a dictation task in which participants had to write each target word 3 times in succession. The authors found that irregular words (i.e., those containing low-probability phoneme-to-grapheme mappings) were slower both to…

Locus of Word Frequency Effects in Spelling to Dictation: Still at the Orthographic Level!

Science.gov (United States)

Bonin, Patrick; Laroche, Betty; Perret, Cyril

2016-01-01

The present study was aimed at testing the locus of word frequency effects in spelling to dictation: Are they located at the level of spoken word recognition (Chua & Rickard Liow, 2014) or at the level of the orthographic output lexicon (Delattre, Bonin, & Barry, 2006)? Words that varied on objective word frequency and on phonological…

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.

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.

Inter-Professional Practices of Private-Sector Physiotherapists for Low Back Pain Management: Who, How, and When?

Science.gov (United States)

Perreault, Kadija; Dionne, Clermont E; Rossignol, Michel; Poitras, Stéphane; Morin, Diane

Purpose : Although there have been increasing demands for health care providers to take part in inter-professional practices in recent years, very little attention has been paid to the actualization of such practices in the private sector. This study describes private-sector physiotherapists' inter-professional practices regarding low back pain (LBP) management and identifies organizational and provider-level variables associated with the intensity of such practices. Method : A total of 327 randomly selected physiotherapists were surveyed in the province of Quebec. Data were analyzed using descriptive and multiple regression analyses. Results : Physiotherapists reported frequent interactions with other physiotherapists (daily/weekly for 52.6%), family physicians (51.0%), and physiotherapy (PT) assistants (45.2%), but infrequent interactions with psychologists (3.6%), neurosurgeons (0.9%), and chiropractors (0.3%). Frequently reported means of interactions were written and oral messages sent through clients (55.1% and 24.1%, respectively), face-to-face unplanned discussions (41.9%), and faxed or mailed letters (23.2%). Variables associated with the intensity of inter-professional practices (mean of 6.7 [ SD 1.7] out of 10 on the Intensity of Interprofessional Practices Questionnaire for Private Sector Physiotherapists) were related to physiotherapists' clientele, social activities with other providers, and perceptions of inter-professional practices as well as organizational models, vision, and provision of PT training. Conclusions: There is room to improve inter-professional practices with private-sector physiotherapists involved in managing LBP. Targets for action include physiotherapists and their workplaces.

Interplay of vacuum-mediated inter- and intra-atomic couplings in a pair of atoms

International Nuclear Information System (INIS)

Schmid, Sandra Isabelle; Evers, Joerg

2010-01-01

The resonance fluorescence emitted by a system of two dipole-dipole interacting nearby four-level atoms in a J=1/2↔J=1/2 configuration is studied. This setup is the simplest realistic model system which provides a complete description of the (inter-atomic) dipole-dipole interaction for arbitrary orientation of the inter-atomic distance vector, and at the same time allows for intra-atomic spontaneously generated coherences. Our main interest is the interplay of both these different coupling mechanisms. We discuss different methods to analyze the contribution of the various vacuum-induced coupling constants to the total resonance fluorescence spectrum. These allow us to find a dressed state interpretation of the contribution of the different inter-atomic dipole-dipole couplings to the total spectrum. We further study the role of the spontaneously generated coherences, and identify two different contributions to the single-particle vacuum-induced couplings. We show that they have a noticeable impact on the total resonance fluorescence spectrum down to small inter-atomic distances, even though the dipole-dipole coupling constants then are much larger in magnitude than the the single-particle coupling constants. Interestingly, we find that the inter-atomic couplings can induce an effect of the intra-atomic spontaneously generated coherences on the observed spectra which is not present in single-atom systems.

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...

Scanning number and brightness yields absolute protein concentrations in live cells: a crucial parameter controlling functional bio-molecular interaction networks.

Science.gov (United States)

Papini, Christina; Royer, Catherine A

2018-02-01

Biological function results from properly timed bio-molecular interactions that transduce external or internal signals, resulting in any number of cellular fates, including triggering of cell-state transitions (division, differentiation, transformation, apoptosis), metabolic homeostasis and adjustment to changing physical or nutritional environments, amongst many more. These bio-molecular interactions can be modulated by chemical modifications of proteins, nucleic acids, lipids and other small molecules. They can result in bio-molecular transport from one cellular compartment to the other and often trigger specific enzyme activities involved in bio-molecular synthesis, modification or degradation. Clearly, a mechanistic understanding of any given high level biological function requires a quantitative characterization of the principal bio-molecular interactions involved and how these may change dynamically. Such information can be obtained using fluctation analysis, in particular scanning number and brightness, and used to build and test mechanistic models of the functional network to define which characteristics are the most important for its regulation.

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.

Computational analysis and prediction of the binding motif and protein interacting partners of the Abl SH3 domain.

Directory of Open Access Journals (Sweden)

Tingjun Hou

2006-01-01

Full Text Available Protein-protein interactions, particularly weak and transient ones, are often mediated by peptide recognition domains, such as Src Homology 2 and 3 (SH2 and SH3 domains, which bind to specific sequence and structural motifs. It is important but challenging to determine the binding specificity of these domains accurately and to predict their physiological interacting partners. In this study, the interactions between 35 peptide ligands (15 binders and 20 non-binders and the Abl SH3 domain were analyzed using molecular dynamics simulation and the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. The calculated binding free energies correlated well with the rank order of the binding peptides and clearly distinguished binders from non-binders. Free energy component analysis revealed that the van der Waals interactions dictate the binding strength of peptides, whereas the binding specificity is determined by the electrostatic interaction and the polar contribution of desolvation. The binding motif of the Abl SH3 domain was then determined by a virtual mutagenesis method, which mutates the residue at each position of the template peptide relative to all other 19 amino acids and calculates the binding free energy difference between the template and the mutated peptides using the Molecular Mechanics/Poisson-Boltzmann Solvent Area method. A single position mutation free energy profile was thus established and used as a scoring matrix to search peptides recognized by the Abl SH3 domain in the human genome. Our approach successfully picked ten out of 13 experimentally determined binding partners of the Abl SH3 domain among the top 600 candidates from the 218,540 decapeptides with the PXXP motif in the SWISS-PROT database. We expect that this physical-principle based method can be applied to other protein domains as well.

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.

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.

Defining the molecular basis of BubR1 kinetochore interactions and APC/C-CDC20 inhibition.

Science.gov (United States)

D'Arcy, Sheena; Davies, Owen R; Blundell, Tom L; Bolanos-Garcia, Victor M

2010-05-07

BubR1 is essential for the mitotic checkpoint that prevents aneuploidy in cellular progeny by triggering anaphase delay in response to kinetochores incorrectly/not attached to the mitotic spindle. Here, we define the molecular architecture of the functionally significant N-terminal region of human BubR1 and present the 1.8 A crystal structure of its tetratricopeptide repeat (TPR) domain. The structure reveals divergence from the classical TPR fold and is highly similar to the TPR domain of budding yeast Bub1. Shared distinctive features include a disordered loop insertion, a 3(10)-helix, a tight turn involving glycine positive Phi angles, and noncanonical packing of and between the TPR motifs. We also define the molecular determinants of the interaction between BubR1 and kinetochore protein Blinkin. We identify a shallow groove on the concave surface of the BubR1 TPR domain that forms multiple discrete and potentially cooperative interactions with Blinkin. Finally, we present evidence for a direct interaction between BubR1 and Bub1 mediated by regions C-terminal to their TPR domains. This interaction provides a mechanism for Bub1-dependent kinetochore recruitment of BubR1. We thus present novel molecular insights into the structure of BubR1 and its interactions at the kinetochore-microtubule interface. Our studies pave the way for future structure-directed engineering aimed at dissecting the roles of kinetochore-bound and other pools of BubR1 in vivo.

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...

Proxemic interactions from theory to practice

CERN Document Server

Marquardt, Nicolai

2015-01-01

In the everyday world, much of what we do as social beings is dictated by how we perceive and manage our interpersonal space. This is called proxemics. At its simplest, people naturally correlate physical distance to social distance. We believe that people's expectations of proxemics can be exploited in interaction design to mediate their interactions with devices (phones, tablets, computers, appliances, large displays) contained within a small ubiquitous computing ecology. Just as people expect increasing engagement and intimacy as they approach others, so should they naturally expect increas

Syntheses, spectroscopic properties and molecular structure of silver phytate complexes - IR, UV-VIS studies and DFT calculations

Science.gov (United States)

Zając, A.; Dymińska, L.; Lorenc, J.; Ptak, M.; Hanuza, J.

2018-03-01

Silver phytate IP6, IP6Ag, IP6Ag2 and IP6Ag3 complexes in the solid state have been synthesized changing the phosphate to metal mole ratio. The obtained products have been characterized by means of chemical and spectroscopic studies. Attenuated total reflection Fourier transform infrared technique and Raman microscope were used in the measurements. These results were discussed in terms of DFT (Density Functional Theory) quantum chemical calculations using the B3LYP/6-31G(d,p) approach. The molecular structures of these compounds have been proposed on the basis of group theory and geometry optimization taking into account the shape and the number of the observed bands corresponding to the stretching and bending vibrations of the phosphate group and metal-oxygen polyhedron. The role of inter- and intra-hydrogen bonds in stabilization of the structure has been discussed. It was found that three types of hydrogen bonds appear in the studied compounds: terminal, and those engaged in the inter- and intra-molecular interactions. The Fermi resonance as a result of the strong intra-molecular Osbnd H⋯O hydrogen bonds was discovered. Electron absorption spectra have been measured to characterize the electron properties of the studied complexes and their local symmetry.

Molecular modeling of interactions in electronic nose sensors for environmental monitoring

Science.gov (United States)

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

2002-01-01

We report a study aimed at understanding analyte interactions with sensors made from polymer-carbon black composite films. The sensors are used in an Electronic Nose (ENose) which is used for monitoring the breathing air quality in human habitats. The model mimics the experimental conditions of the composite film deposition and formation and was developed using molecular modeling and simulation tools. The Dreiding 2.21 Force Field was used for the polymer and analyte molecules while graphite parameters were assigned to the carbon black atoms. The polymer considered for this work is methyl vinyl ether / maleic acid copolymer. The target analytes include both inorganic (NH3) and organic (methanol) types of compound. Results indicate different composite-analyte interaction behavior.

The interaction properties of the human Rab GTPase family--comparative analysis reveals determinants of molecular binding selectivity.

Directory of Open Access Journals (Sweden)

Matthias Stein

Full Text Available Rab GTPases constitute the largest subfamily of the Ras protein superfamily. Rab proteins regulate organelle biogenesis and transport, and display distinct binding preferences for effector and activator proteins, many of which have not been elucidated yet. The underlying molecular recognition motifs, binding partner preferences and selectivities are not well understood.Comparative analysis of the amino acid sequences and the three-dimensional electrostatic and hydrophobic molecular interaction fields of 62 human Rab proteins revealed a wide range of binding properties with large differences between some Rab proteins. This analysis assists the functional annotation of Rab proteins 12, 14, 26, 37 and 41 and provided an explanation for the shared function of Rab3 and 27. Rab7a and 7b have very different electrostatic potentials, indicating that they may bind to different effector proteins and thus, exert different functions. The subfamily V Rab GTPases which are associated with endosome differ subtly in the interaction properties of their switch regions, and this may explain exchange factor specificity and exchange kinetics.We have analysed conservation of sequence and of molecular interaction fields to cluster and annotate the human Rab proteins. The analysis of three dimensional molecular interaction fields provides detailed insight that is not available from a sequence-based approach alone. Based on our results, we predict novel functions for some Rab proteins and provide insights into their divergent functions and the determinants of their binding partner selectivity.

Interaction webs in arctic ecosystems

DEFF Research Database (Denmark)

Schmidt, Niels M.; Hardwick, Bess; Gilg, Olivier

2017-01-01

How species interact modulate their dynamics, their response to environmental change, and ultimately the functioning and stability of entire communities. Work conducted at Zackenberg, Northeast Greenland, has changed our view on how networks of arctic biotic interactions are structured, how...... they vary in time, and how they are changing with current environmental change: firstly, the high arctic interaction webs are much more complex than previously envisaged, and with a structure mainly dictated by its arthropod component. Secondly, the dynamics of species within these webs reflect changes...... that the combination of long-term, ecosystem-based monitoring, and targeted research projects offers the most fruitful basis for understanding and predicting the future of arctic ecosystems....

Exploring the Interaction Mechanism Between Cyclopeptide DC3 and Androgen Receptor Using Molecular Dynamics Simulations and Free Energy Calculations

Directory of Open Access Journals (Sweden)

Huimin Zhang

2018-04-01

Full Text Available Androgen receptor (AR is a key target in the discovery of anti-PCa (Prostate Cancer drugs. Recently, a novel cyclopeptide Diffusa Cyclotide-3 (DC3, isolated from Hedyotisdiffusa, has been experimentally demonstrated to inhibit the survival and growth of LNCap cells, which typically express T877A-mutated AR, the most frequently detected point mutation of AR in castration-resistant prostate cancer (CRPC. But the interaction mechanism between DC3 and AR is not clear. Here in this study we aim to explore the possible binding mode of DC3 to T877A-mutated AR from molecular perspective. Firstly, homology modeling was employed to construct the three-dimensional structure of the cyclopeptide DC3 using 2kux.1.A as the template. Then molecular docking, molecular dynamics (MD simulations, and molecular mechanics/generalized Born surface area (MM-GBSA methods were performed to determine the bind site and explore the detailed interaction mechanism of DC3-AR complex. The obtained results suggested that the site formed by H11, loop888-893, and H12 (site 2 was the most possible position of DC3 binding to AR. Besides, hydrogen bonds, hydrophobic, and electrostatic interactions play dominant roles in the recognition and combination of DC3-AR complex. The essential residues dominant in each interaction were specifically revealed. This work facilitates our understanding of the interaction mechanism of DC3 binding to AR at the molecular level and contributes to the rational cyclopeptide drug design for prostate cancer.

Intra-molecular selectivity of muonium towards chlorinated aromatic compounds

International Nuclear Information System (INIS)

Venkateswaran, K.; Stadlbauer, J.M.; Laing, M.E.; Klugkist, J.; Chong, D.P.; Porter, G.B.; Walker, D.C.

1994-01-01

Muon resonance studies show that muonium atoms (Mu) in ethanol add selectively to certain C-sites of aromatic compounds containing -Cl and -OH substituents. The sites chosen seem to be those carrying the lowest electron density. This helps to characterize Mu as a nucleophile in addition reactions and, in this respect, Mu differs from ordinary H-atoms. The study shows no apparent inter-molecular selectivity between a pair of aromatic solutes in an equimolar mixture, but strong intra-molecular selectivity in an ether composed of those two aromatic rings. This difference between intra- and inter-molecular selectivity is interpreted as kinetic in origin - arising from the 'caging effect' of the solvent and peculiar to reactions close to the diffusion-controlled limit. (orig.)

Deuterium-labelled N-acyl-l-homoserine lactones (AHLs) - inter-kingdom signalling molecules - synthesis, structural studies, and interactions with model lipid membranes

International Nuclear Information System (INIS)

Jakubczyk, Dorota; Barth, Christoph; Anastassacos, Frances; Koelsch, Patrick; Schepers, Ute; Kubas, Adam; Fink, Karin; Brenner-Weiss, Gerald; Braese, Stefan

2012-01-01

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum's acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein. (orig.)

Predicting the influence of long-range molecular interactions on macroscopic-scale diffusion by homogenization of the Smoluchowski equation

Energy Technology Data Exchange (ETDEWEB)

Kekenes-Huskey, P. M., E-mail: pkekeneshuskey@ucsd.edu [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Gillette, A. K. [Department of Mathematics, University of Arizona, Tucson, Arizona 85721-0089 (United States); McCammon, J. A. [Department of Pharmacology, University of California San Diego, La Jolla, California 92093-0636 (United States); Department of Chemistry, Howard Hughes Medical Institute, University of California San Diego, La Jolla, California 92093-0636 (United States)

2014-05-07

The macroscopic diffusion constant for a charged diffuser is in part dependent on (1) the volume excluded by solute “obstacles” and (2) long-range interactions between those obstacles and the diffuser. Increasing excluded volume reduces transport of the diffuser, while long-range interactions can either increase or decrease diffusivity, depending on the nature of the potential. We previously demonstrated [P. M. Kekenes-Huskey et al., Biophys. J. 105, 2130 (2013)] using homogenization theory that the configuration of molecular-scale obstacles can both hinder diffusion and induce diffusional anisotropy for small ions. As the density of molecular obstacles increases, van der Waals (vdW) and electrostatic interactions between obstacle and a diffuser become significant and can strongly influence the latter's diffusivity, which was neglected in our original model. Here, we extend this methodology to include a fixed (time-independent) potential of mean force, through homogenization of the Smoluchowski equation. We consider the diffusion of ions in crowded, hydrophilic environments at physiological ionic strengths and find that electrostatic and vdW interactions can enhance or depress effective diffusion rates for attractive or repulsive forces, respectively. Additionally, we show that the observed diffusion rate may be reduced independent of non-specific electrostatic and vdW interactions by treating obstacles that exhibit specific binding interactions as “buffers” that absorb free diffusers. Finally, we demonstrate that effective diffusion rates are sensitive to distribution of surface charge on a globular protein, Troponin C, suggesting that the use of molecular structures with atomistic-scale resolution can account for electrostatic influences on substrate transport. This approach offers new insight into the influence of molecular-scale, long-range interactions on transport of charged species, particularly for diffusion-influenced signaling events

Inter-Series Interactions on the Atomic Photoionization Spectra Studied by the Phase-Shifted Multichannel-Quantum Defect Theory

Directory of Open Access Journals (Sweden)

Chun-Woo Lee

2017-05-01

Full Text Available Development in mathematical formulations of parameterizing the resonance structures using the phase-shifted multichannel quantum defect theory (MQDT and their use in analyzing the effect of inter-series interactions on the autoionizing Rydberg spectra is reviewed. Reformulation of the short-range scattering matrix into the form analogous to S = SBSR in scattering theory are the crucial step in this development. Formulation adopts different directions and goals depending on whether autoionizing series converge to the same limit (degenerate or to different limits (nondegenerate because of the different nature of the perturbation. For the nondegenerate case, finding the simplest form of profile index functions of the autoionizing spectra with the minimal number of parameters is the main goal and some results are reviewed. For the degenerate case where perturbation acts uniformly throughout the entire series, isolation of the overlapped autoionizing series into the unperturbed autoionizing series is the key objective in research and some results in that direction are reviewed.

Molecular Networking As a Drug Discovery, Drug Metabolism, and Precision Medicine Strategy.

Science.gov (United States)

Quinn, Robert A; Nothias, Louis-Felix; Vining, Oliver; Meehan, Michael; Esquenazi, Eduardo; Dorrestein, Pieter C

2017-02-01

Molecular networking is a tandem mass spectrometry (MS/MS) data organizational approach that has been recently introduced in the drug discovery, metabolomics, and medical fields. The chemistry of molecules dictates how they will be fragmented by MS/MS in the gas phase and, therefore, two related molecules are likely to display similar fragment ion spectra. Molecular networking organizes the MS/MS data as a relational spectral network thereby mapping the chemistry that was detected in an MS/MS-based metabolomics experiment. Although the wider utility of molecular networking is just beginning to be recognized, in this review we highlight the principles behind molecular networking and its use for the discovery of therapeutic leads, monitoring drug metabolism, clinical diagnostics, and emerging applications in precision medicine. Copyright © 2016. Published by Elsevier Ltd.

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.

When biomolecules meet graphene: from molecular level interactions to material design and applications.

Science.gov (United States)

Li, Dapeng; Zhang, Wensi; Yu, Xiaoqing; Wang, Zhenping; Su, Zhiqiang; Wei, Gang

2016-12-01

Graphene-based materials have attracted increasing attention due to their atomically-thick two-dimensional structures, high conductivity, excellent mechanical properties, and large specific surface areas. The combination of biomolecules with graphene-based materials offers a promising method to fabricate novel graphene-biomolecule hybrid nanomaterials with unique functions in biology, medicine, nanotechnology, and materials science. In this review, we focus on a summarization of the recent studies in functionalizing graphene-based materials using different biomolecules, such as DNA, peptides, proteins, enzymes, carbohydrates, and viruses. The different interactions between graphene and biomolecules at the molecular level are demonstrated and discussed in detail. In addition, the potential applications of the created graphene-biomolecule nanohybrids in drug delivery, cancer treatment, tissue engineering, biosensors, bioimaging, energy materials, and other nanotechnological applications are presented. This review will be helpful to know the modification of graphene with biomolecules, understand the interactions between graphene and biomolecules at the molecular level, and design functional graphene-based nanomaterials with unique properties for various applications.

Improving the Accuracy of Laplacian Estimation with Novel Variable Inter-Ring Distances Concentric Ring Electrodes

Directory of Open Access Journals (Sweden)

Oleksandr Makeyev

2016-06-01

Full Text Available Noninvasive concentric ring electrodes are a promising alternative to conventional disc electrodes. Currently, the superiority of tripolar concentric ring electrodes over disc electrodes, in particular, in accuracy of Laplacian estimation, has been demonstrated in a range of applications. In our recent work, we have shown that accuracy of Laplacian estimation can be improved with multipolar concentric ring electrodes using a general approach to estimation of the Laplacian for an (n + 1-polar electrode with n rings using the (4n + 1-point method for n ≥ 2. This paper takes the next step toward further improving the Laplacian estimate by proposing novel variable inter-ring distances concentric ring electrodes. Derived using a modified (4n + 1-point method, linearly increasing and decreasing inter-ring distances tripolar (n = 2 and quadripolar (n = 3 electrode configurations are compared to their constant inter-ring distances counterparts. Finite element method modeling and analytic results are consistent and suggest that increasing inter-ring distances electrode configurations may decrease the truncation error resulting in more accurate Laplacian estimates compared to respective constant inter-ring distances configurations. For currently used tripolar electrode configuration, the truncation error may be decreased more than two-fold, while for the quadripolar configuration more than a six-fold decrease is expected.

Improving the Accuracy of Laplacian Estimation with Novel Variable Inter-Ring Distances Concentric Ring Electrodes

Science.gov (United States)

Makeyev, Oleksandr; Besio, Walter G.

2016-01-01

Noninvasive concentric ring electrodes are a promising alternative to conventional disc electrodes. Currently, the superiority of tripolar concentric ring electrodes over disc electrodes, in particular, in accuracy of Laplacian estimation, has been demonstrated in a range of applications. In our recent work, we have shown that accuracy of Laplacian estimation can be improved with multipolar concentric ring electrodes using a general approach to estimation of the Laplacian for an (n + 1)-polar electrode with n rings using the (4n + 1)-point method for n ≥ 2. This paper takes the next step toward further improving the Laplacian estimate by proposing novel variable inter-ring distances concentric ring electrodes. Derived using a modified (4n + 1)-point method, linearly increasing and decreasing inter-ring distances tripolar (n = 2) and quadripolar (n = 3) electrode configurations are compared to their constant inter-ring distances counterparts. Finite element method modeling and analytic results are consistent and suggest that increasing inter-ring distances electrode configurations may decrease the truncation error resulting in more accurate Laplacian estimates compared to respective constant inter-ring distances configurations. For currently used tripolar electrode configuration, the truncation error may be decreased more than two-fold, while for the quadripolar configuration more than a six-fold decrease is expected. PMID:27294933

Power transformations improve interpolation of grids for molecular mechanics interaction energies.

Science.gov (United States)

Minh, David D L

2018-02-18

A common strategy for speeding up molecular docking calculations is to precompute nonbonded interaction energies between a receptor molecule and a set of three-dimensional grids. The grids are then interpolated to compute energies for ligand atoms in many different binding poses. Here, I evaluate a smoothing strategy of taking a power transformation of grid point energies and inverse transformation of the result from trilinear interpolation. For molecular docking poses from 85 protein-ligand complexes, this smoothing procedure leads to significant accuracy improvements, including an approximately twofold reduction in the root mean square error at a grid spacing of 0.4 Å and retaining the ability to rank docking poses even at a grid spacing of 0.7 Å. © 2018 Wiley Periodicals, Inc. © 2018 Wiley Periodicals, Inc.

A Comparison of the Incremental Difference between the Beginning and Ending Heart Rate When Shorthand Writers Are Informed and Not Informed of Speeds of Dictation.

Science.gov (United States)

Dickey, Patsy A.

1980-01-01

Forty female students were used to compare the incremental difference in heart rate of shorthand writers when they were informed and not informed of shorthand speeds prior to dictation. It was concluded that students' performances were enhanced by receiving instructions as to speed of dictation prior to the take. (Author/CT)

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.

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...

Effect of Sequence Blockiness on the Morphologies of Surface-grafted Elastin-like Polypeptides

Science.gov (United States)

Albert, Julie; Sintavanon, Kornkanok; Mays, Robin; MacEwan, Sarah; Chilkoti, Ashutosh; Genzer, Jan

2014-03-01

The inter- and intra- molecular interactions among monomeric units of copolymers and polypeptides depend strongly on monomer sequence distribution and dictate the phase behavior of these species both in solution and on surfaces. To study the relationship between sequence and phase behavior, we have designed a series of elastin-like polypeptides (ELPs) with controlled monomer sequences that mimic copolymers with various co-monomer sequence distributions and attached them covalently to silicon substrates from buffer solutions at temperatures below and above the bulk ELPs' lower critical solution temperatures (LCSTs). The dependence of ELP grafting density on solution temperature was examined by ellipsometry and the resultant surface morphologies were examined in air and under water with atomic force microscopy. Depositions performed above the LCST resulted in higher grafting densities and greater surface roughness of ELPs relative to depositions carried out below the LCST. In addition, we are using gradient substrates to examine the effect of ELP grafting density on temperature responsiveness.

Ultrafast spectroscopy on DNA-cleavage by endonuclease in molecular crowding.

Science.gov (United States)

Singh, Priya; Choudhury, Susobhan; Dutta, Shreyasi; Adhikari, Aniruddha; Bhattacharya, Siddhartha; Pal, Debasish; Pal, Samir Kumar

2017-10-01

The jam-packed intracellular environments differ the activity of a biological macromolecule from that in laboratory environments (in vitro) through a number of mechanisms called molecular crowding related to structure, function and dynamics of the macromolecule. Here, we have explored the structure, function and dynamics of a model enzyme protein DNase I in molecular crowing of polyethylene glycol (PEG; MW 3350). We have used steady state and picosecond resolved dynamics of a well-known intercalator ethidium bromide (EB) in a 20-mer double-stranded DNA (dsDNA) to monitor the DNA-cleavage by the enzyme in absence and presence PEG. We have also labelled the enzyme by a well-known fluorescent probe 8-anilino-1-naphthalenesulfonic acid ammonium salt (ANS) to study the molecular mechanism of the protein-DNA association through exited state relaxation of the probe in absence (dictated by polarity) and presence of EB in the DNA (dictated by Förster resonance energy transfer (FRET)). The overall and local structures of the protein in presence of PEG have been followed by circular dichroism and time resolved polarization gated spectroscopy respectively. The enhanced dynamical flexibility of protein in presence of PEG as revealed from excited state lifetime and polarization gated anisotropy of ANS has been correlated with the stronger DNA-binding for the higher nuclease activity. We have also used conventional experimental strategy of agarose gel electrophoresis to monitor DNA-cleavage and found consistent results of enhanced nuclease activities both on synthetic 20-mer oligonucleotide and long genomic DNA from calf thymus. Copyright © 2017 Elsevier B.V. All rights reserved.

Inter-observer and inter-examination variability of manual vertebral bone attenuation measurements on computed tomography

International Nuclear Information System (INIS)

Pompe, Esther; Lammers, Jan-Willem J.; Jong, Pim A. de; Jong, Werner U. de; Takx, Richard A.P.; Eikendal, Anouk L.M.; Willemink, Martin J.; Mohamed Hoesein, Firdaus A.A.; Oudkerk, Matthijs; Budde, Ricardo P.J.

2016-01-01

To determine inter-observer and inter-examination variability of manual attenuation measurements of the vertebrae in low-dose unenhanced chest computed tomography (CT). Three hundred and sixty-seven lung cancer screening trial participants who underwent baseline and repeat unenhanced low-dose CT after 3 months because of an indeterminate lung nodule were included. The CT attenuation value of the first lumbar vertebrae (L1) was measured in all CTs by one observer to obtain inter-examination reliability. Six observers performed measurements in 100 randomly selected CTs to determine agreement with limits of agreement and Bland-Altman plots and reliability with intraclass correlation coefficients (ICCs). Reclassification analyses were performed using a threshold of 110 HU to define osteoporosis. Inter-examination reliability was excellent with an ICC of 0.92 (p < 0.001). Inter-examination limits of agreement ranged from -26 to 28 HU with a mean difference of 1 ± 14 HU. Inter-observer reliability ICCs ranged from 0.70 to 0.91. Inter-examination variability led to 11.2 % reclassification of participants and inter-observer variability led to 22.1 % reclassification. Vertebral attenuation values can be manually quantified with good to excellent inter-examination and inter-observer reliability on unenhanced low-dose chest CT. This information is valuable for early detection of osteoporosis on low-dose chest CT. (orig.)

Proportion offered in the Dictator and Ultimatum Games decreases with amount and social distance.

Science.gov (United States)

Bechler, Christopher; Green, Leonard; Myerson, Joel

2015-06-01

Behavior in both the Dictator Game and the Ultimatum Game is of special interest because proposers often violate the predictions of normative economic theory: On average, offers in both games are higher than what would be considered income-maximizing. In the present study, the initial amount provided to the proposer and the social distance between the proposer and the respondent were both varied across a wide range, and the effects of these manipulations on offers in the Dictator Game and the Ultimatum Game were examined in a broad sample of participants recruited via MTurk. Although the amount offered was consistently higher in the Ultimatum Game, the proportion of the amount offered decreased as the size of the initial amount increased in both games. Moreover, the proportion offered also decreased as a function of the social distance between the proposer and the responder. The present results extend our knowledge of the determinants of proposers' behavior in two-person economic games and emphasize the importance of social distance and the amount of money at stake as factors that affect people's economic decisions. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular basis for the interplay of apoptosis and proliferation mediated by Bcl-xL:Bim interactions in pancreatic cancer cells

Energy Technology Data Exchange (ETDEWEB)

Abrol, Ravinder, E-mail: abrol@wag.caltech.edu [Materials and Process Simulation Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States); Edderkaoui, Mouad [Veterans Affairs Greater Los Angeles Healthcare System and UCLA, Los Angeles, CA 90073 (United States); Goddard, William A. [Materials and Process Simulation Center, Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125 (United States); Pandol, Stephen J., E-mail: stephen.pandol@va.gov [Veterans Affairs Greater Los Angeles Healthcare System and UCLA, Los Angeles, CA 90073 (United States)

2012-06-15

Highlights: Black-Right-Pointing-Pointer Direct role of Bcl-2 protein interactions in cell proliferation is not clear. Black-Right-Pointing-Pointer Designed Bcl-xL mutants show opposite effects on apoptosis and proliferation. Black-Right-Pointing-Pointer Disrupting Bcl-xL:Bim interaction increased apoptosis in pancreatic cancer. Black-Right-Pointing-Pointer Disrupting Bcl-xL:Bim interaction decreased proliferation in pancreatic cancer. Black-Right-Pointing-Pointer Bcl-xL:Bim interaction can control both apoptosis and proliferation. -- Abstract: A major mechanism through which cancer cells avoid apoptosis is by promoting the association of anti-apoptotic members of the pro-survival Bcl-2 protein family (like Bcl-2 and Bcl-xL) with BH{sub 3} domain-only proteins (like Bim and Bid). Apoptosis and cell proliferation have been shown to be linked for many cancers but the molecular basis for this link is far from understood. We have identified the Bcl-xL:Bim protein-protein interface as a direct regulator of proliferation and apoptosis in pancreatic cancer cells. We were able to predict and subsequently verify experimentally the effect of various Bcl-xL single-point mutants (at the position A142) on binding to Bim by structural analysis and computational modeling of the inter-residue interactions at the Bcl-xL:Bim protein-protein interface. The mutants A142N, A142Q, and A142Y decreased binding of Bim to Bcl-xL and A142S increased this binding. The Bcl-xL mutants, with decreased affinity for Bim, caused an increase in apoptosis and a corresponding decrease in cell proliferation. However, we could prevent these effects by introducing a small interfering RNA (siRNA) targeted at Bim. These results show a novel role played by the Bcl-xL:Bim interaction in regulating proliferation of pancreatic cancer cells at the expense of apoptosis. This study presents a physiologically relevant model of the Bcl-xL:Bim interface that can be used for rational therapeutic design for the

Molecular interactions and thermal transport in ionic liquids with carbon nanomaterials.

Science.gov (United States)

França, João M P; Nieto de Castro, Carlos A; Pádua, Agílio A H

2017-07-05

We used molecular dynamics simulation to study the effect of suspended carbon nanomaterials, nanotubes and graphene sheets, on the thermal conductivity of ionic liquids, an issue related to understanding the properties of nanofluids. One important aspect that we developed is an atomistic model of the interactions between the organic ions and carbon nanomaterials, so we did not rely on existing force fields for small organic molecules or assume simple combining rules to describe the interactions at the liquid/material interface. Instead, we used quantum calculations with a density functional suitable for non-covalent interactions to parameterize an interaction model, including van der Waals terms and also atomic partial charges on the materials. We fitted a n-m interaction potential function with n values of 9 or 10 and m values between 5 and 8, so a 12-6 Lennard-Jones function would not fit the quantum calculations. For the atoms of ionic liquids and carbon nanomaterials interacting among themselves, we adopted existing models from the literature. We studied the imidazolium ionic liquids [C 4 C 1 im][SCN], [C 4 C 1 im][N(CN) 2 ], [C 4 C 1 im][C(CN) 3 ] and [C 4 C 1 im][(CF 3 SO 2 ) 2 N]. Attraction is stronger for cations (than for anions) above and below the π-system of the nanomaterials, whereas anions show stronger attraction for the hydrogenated edges. The ordering of ions around and inside (7,7) and (10,10) single-walled nanotubes, and near a stack of graphene sheets, was analysed in terms of density distribution functions. We verified that anions are found, as well as cations, in the first interfacial layer interacting with the materials, which is surprising given the interaction potential surfaces. The thermal conductivity of the ionic liquids and of composite systems containing one nanotube or one graphene stack in suspension was calculated using non-equilibrium molecular dynamics. Thermal conductivity was calculated along the axis of the nanotube and

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

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.

Regulatory T cell suppressive potency dictates the balance between bacterial proliferation and clearance during persistent Salmonella infection.

Directory of Open Access Journals (Sweden)

Tanner M Johanns

2010-08-01

Full Text Available The pathogenesis of persistent infection is dictated by the balance between opposing immune activation and suppression signals. Herein, virulent Salmonella was used to explore the role and potential importance of Foxp3-expressing regulatory T cells in dictating the natural progression of persistent bacterial infection. Two distinct phases of persistent Salmonella infection are identified. In the first 3-4 weeks after infection, progressively increasing bacterial burden was associated with delayed effector T cell activation. Reciprocally, at later time points after infection, reductions in bacterial burden were associated with robust effector T cell activation. Using Foxp3(GFP reporter mice for ex vivo isolation of regulatory T cells, we demonstrate that the dichotomy in infection tempo between early and late time points is directly paralleled by drastic changes in Foxp3(+ Treg suppressive potency. In complementary experiments using Foxp3(DTR mice, the significance of these shifts in Treg suppressive potency on infection outcome was verified by enumerating the relative impacts of regulatory T cell ablation on bacterial burden and effector T cell activation at early and late time points during persistent Salmonella infection. Moreover, Treg expression of CTLA-4 directly paralleled changes in suppressive potency, and the relative effects of Treg ablation could be largely recapitulated by CTLA-4 in vivo blockade. Together, these results demonstrate that dynamic regulation of Treg suppressive potency dictates the course of persistent bacterial infection.

Experimental study on inter-particle acoustic forces.

Science.gov (United States)

Garcia-Sabaté, Anna; Castro, Angélica; Hoyos, Mauricio; González-Cinca, Ricard

2014-03-01

A method for the experimental measurement of inter-particle forces (secondary Bjerknes force) generated by the action of an acoustic field in a resonator micro-channel is presented. The acoustic radiation force created by an ultrasonic standing wave moves suspended particles towards the pressure nodes and the acoustic pressure induces particle volume oscillations. Once particles are in the levitation plane, transverse and secondary Bjerknes forces become important. Experiments were carried out in a resonator filled with a suspension composed of water and latex particles of different size (5-15 μm) at different concentrations. Ultrasound was generated by means of a 2.5 MHz nominal frequency transducer. For the first time the acoustic force generated by oscillating particles acting on other particles has been measured, and the critical interaction distance in various cases has been determined. Inter-particle forces on the order of 10(-14) N have been measured by using this method.

Theoretical and experimental approach on the molecular interactions of the DL-Alanine with an electrolytic environment

Science.gov (United States)

Cantero-López, Plinio; Yañez-Osses, Osvaldo; Páez-Meza, Manuel Silvestre; López, Johana E.; Páez-Hernández, Dayán; Arratia-Pérez, Ramiro

2017-11-01

The molecular interactions that promote the stability of proteins and amino acids in saline solutions is a central topic of molecular biophysics. However, a well-supported molecular picture of the phenomena has not been established yet. In this paper, we studied as model system the mix between DL-Alanine in aqueous solutions of STP (Na2S2O3·5H2O) at different temperatures, from volumetric and viscometric properties. The thermophysical properties obtained indicate the presence of a strong preferential solvation, structure-making action and a possible salt in effect. Quantum chemical calculations and molecular dynamic (MD) simulations provide a new insight to support these arguments.

Pervasive orbital eccentricities dictate the habitability of extrasolar earths.

Science.gov (United States)

Kita, Ryosuke; Rasio, Frederic; Takeda, Genya

2010-09-01

The long-term habitability of Earth-like planets requires low orbital eccentricities. A secular perturbation from a distant stellar companion is a very important mechanism in exciting planetary eccentricities, as many of the extrasolar planetary systems are associated with stellar companions. Although the orbital evolution of an Earth-like planet in a stellar binary system is well understood, the effect of a binary perturbation on a more realistic system containing additional gas-giant planets has been very little studied. Here, we provide analytic criteria confirmed by a large ensemble of numerical integrations that identify the initial orbital parameters leading to eccentric orbits. We show that an extrasolar earth is likely to experience a broad range of orbital evolution dictated by the location of a gas-giant planet, which necessitates more focused studies on the effect of eccentricity on the potential for life.

Theoretical Views in Inter-religious Dialog in Iran

Directory of Open Access Journals (Sweden)

Mohammad Masjed Jamei

2015-08-01

Full Text Available It has almost passed one century from the emergence of the idea of the inter-religious dialog. The idea, being based on the assumption that no religion has the absolute truth, believes that there is the possibility of the dialog between all the existent religions in the social world. The dialog could make the coexistence and peace between the religions possible. The importance of this issue is increasingly growing and different ideas have been presented in the different religion departments worldwide. After the Iranian Islamic Revolution, a new image of Islam was offered to the world. An image whose true exposure made the use of the inter-religious dialog unavoidable. This also caused appearance of different views between the Muslim scholars. This article seeks to provide a presentation of three different approaches to the inter-religious dialog by exploring the works of three eminent scholars in the field; Mohaghegh Damad, Abolhassan Navab and Mohammad Masjed Jamei. These three approaches are:   · Inter-religious dialog as an interaction-oriented action    · Inter-religious dialog as a necessity-oriented action    · Inter-religious dialog as a backgroubd-oriented action    The necessity-oriented action is the approach taken by Mohaghegh Damad. He emphasizes on the acceptance of other religions. The active action referring to this acceptance is the foundation of this approach. This approach, accepting the developmental discourse in the meaning of inter-religious dialog, believes that this kind of dialog has been evolved from defensive and opposing to a new meaning. Hence, the inter-religious dialog in its new meaning possesses three conditions; the existence of common rights, emphasis on mutual respect and the effort for the two sides for religious exchange. This approach­ assumes that we must first establish a pattern from the current experiences of inter-religious dialogs in order to have an ideal cooperation and to fortify it. Then

Theoretical Views in Inter-religious Dialog in Iran

Directory of Open Access Journals (Sweden)

Majid Jafarian

2015-09-01

Full Text Available   It has almost passed one century from the emergence of the idea of the inter-religious dialog. The idea, being based on the assumption that no religion has the absolute truth, believes that there is the possibility of the dialog between all the existent religions in the social world. The dialog could make the coexistence and peace between the religions possible. The importance of this issue is increasingly growing and different ideas have been presented in the different religion departments worldwide. After the Iranian Islamic Revolution, a new image of Islam was offered to the world. An image whose true exposure made the use of the inter-religious dialog unavoidable. This also caused appearance of different views between the Muslim scholars. This article seeks to provide a presentation of three different approaches to the inter-religious dialog by exploring the works of three eminent scholars in the field; Mohaghegh Damad, Abolhassan Navab and Mohammad Masjed Jamei. These three approaches are:   · Inter-religious dialog as an interaction-oriented action    · Inter-religious dialog as a necessity-oriented action    · Inter-religious dialog as a backgroubd-oriented action    The necessity-oriented action is the approach taken by Mohaghegh Damad. He emphasizes on the acceptance of other religions. The active action referring to this acceptance is the foundation of this approach. This approach, accepting the developmental discourse in the meaning of inter-religious dialog, believes that this kind of dialog has been evolved from defensive and opposing to a new meaning. Hence, the inter-religious dialog in its new meaning possesses three conditions; the existence of common rights, emphasis on mutual respect and the effort for the two sides for religious exchange. This approach­ assumes that we must first establish a pattern from the current experiences of inter-religious dialogs in order to have an ideal cooperation and to fortify it

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.

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.

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.

[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.

A Molecular Dynamics Simulation of the Turbulent Couette Minimal Flow Unit

Science.gov (United States)

Smith, Edward

2016-11-01

What happens to turbulent motions below the Kolmogorov length scale? In order to explore this question, a 300 million molecule Molecular Dynamics (MD) simulation is presented for the minimal Couette channel in which turbulence can be sustained. The regeneration cycle and turbulent statistics show excellent agreement to continuum based computational fluid dynamics (CFD) at Re=400. As MD requires only Newton's laws and a form of inter-molecular potential, it captures a much greater range of phenomena without requiring the assumptions of Newton's law of viscosity, thermodynamic equilibrium, fluid isotropy or the limitation of grid resolution. The fundamental nature of MD means it is uniquely placed to explore the nature of turbulent transport. A number of unique insights from MD are presented, including energy budgets, sub-grid turbulent energy spectra, probability density functions, Lagrangian statistics and fluid wall interactions. EPSRC Post Doctoral Prize Fellowship.

A Systems Biology Approach to the Coordination of Defensive and Offensive Molecular Mechanisms in the Innate and Adaptive Host-Pathogen Interaction Networks.

Science.gov (United States)

Wu, Chia-Chou; Chen, Bor-Sen

2016-01-01

Infected zebrafish coordinates defensive and offensive molecular mechanisms in response to Candida albicans infections, and invasive C. albicans coordinates corresponding molecular mechanisms to interact with the host. However, knowledge of the ensuing infection-activated signaling networks in both host and pathogen and their interspecific crosstalk during the innate and adaptive phases of the infection processes remains incomplete. In the present study, dynamic network modeling, protein interaction databases, and dual transcriptome data from zebrafish and C. albicans during infection were used to infer infection-activated host-pathogen dynamic interaction networks. The consideration of host-pathogen dynamic interaction systems as innate and adaptive loops and subsequent comparisons of inferred innate and adaptive networks indicated previously unrecognized crosstalk between known pathways and suggested roles of immunological memory in the coordination of host defensive and offensive molecular mechanisms to achieve specific and powerful defense against pathogens. Moreover, pathogens enhance intraspecific crosstalk and abrogate host apoptosis to accommodate enhanced host defense mechanisms during the adaptive phase. Accordingly, links between physiological phenomena and changes in the coordination of defensive and offensive molecular mechanisms highlight the importance of host-pathogen molecular interaction networks, and consequent inferences of the host-pathogen relationship could be translated into biomedical applications.

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.

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.

Correction of gene expression data: Performance-dependency on inter-replicate and inter-treatment biases.

Science.gov (United States)

Darbani, Behrooz; Stewart, C Neal; Noeparvar, Shahin; Borg, Søren

2014-10-20

This report investigates for the first time the potential inter-treatment bias source of cell number for gene expression studies. Cell-number bias can affect gene expression analysis when comparing samples with unequal total cellular RNA content or with different RNA extraction efficiencies. For maximal reliability of analysis, therefore, comparisons should be performed at the cellular level. This could be accomplished using an appropriate correction method that can detect and remove the inter-treatment bias for cell-number. Based on inter-treatment variations of reference genes, we introduce an analytical approach to examine the suitability of correction methods by considering the inter-treatment bias as well as the inter-replicate variance, which allows use of the best correction method with minimum residual bias. Analyses of RNA sequencing and microarray data showed that the efficiencies of correction methods are influenced by the inter-treatment bias as well as the inter-replicate variance. Therefore, we recommend inspecting both of the bias sources in order to apply the most efficient correction method. As an alternative correction strategy, sequential application of different correction approaches is also advised. Copyright © 2014 Elsevier B.V. All rights reserved.

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

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.

Small Angle Neutron Scattering Studies of the Counterion Effects on the Molecular Conformation and Structure of Charged G4 PAMAM Dendrimers in Aqueous Solutions

International Nuclear Information System (INIS)

Chen, Wei-Ren

2007-01-01

The structural properties of generation 4 (G4) poly(amidoamine) starburst dendrimers (PAMAM) with an ethylenediamine ne (EDA) central core in D O 2 solutions have been studied by small angle neutron scattering. Upon the addition of DCl , SANS patterns show a pronounced inter-particle 2 correlation peaks due to the strong repulsion introduced by the protonation of the amino groups of the dendrimers. By solving the Ornstein-Zernike integral equation (OZ) with hypernetted chain closure (HNC), the dendrimer-dendrimer er structure factor S(Q) is determined and used to fit the experimental data. Quantitative information such as the effective charge per dendrimer and its conformational change at different conditions can be obtained. The results obtained show clear evidence that significant counterion association occurs, strongly mediating the inter-dendrimer interaction. The influence of interplay between counterions and molecular protonation of dendrimers has strong effect on the dendrimer conformation and effective interaction.

Insight into the binding interactions of CYP450 aromatase inhibitors with their target enzyme: a combined molecular docking and molecular dynamics study.

Science.gov (United States)

Galeazzi, Roberta; Massaccesi, Luca

2012-03-01

CYP450 aromatase catalyzes the terminal and rate-determining step in estrogen synthesis, the aromatization of androgens, and its inhibition is an efficient approach to treating estrogen-dependent breast cancer. Insight into the molecular basis of the interaction at the catalytic site between CYP450 aromatase inhibitors and the enzyme itself is required in order to design new and more active compounds. Hence, a combined molecular docking-molecular dynamics study was carried out to obtain the structure of the lowest energy association complexes of aromatase with some third-generation aromatase inhibitors (AIs) and with other novel synthesized letrozole-derived compounds which showed high in vitro activity. The results obtained clearly demonstrate the role of the pharmacophore groups present in the azaheterocyclic inhibitors (NSAIs)-namely the triazolic ring and highly functionalized aromatic moieties carrying H-bond donor or acceptor groups. In particular, it was pointed out that all of them can contribute to inhibition activity by interacting with residues of the catalytic cleft, but the amino acids involved are different for each compound, even if they belong to the same class. Furthermore, the azaheterocyclic group strongly coordinates with the Fe(II) of heme cysteinate in the most active NSAI complexes, while it prefers to adopt another orientation in less active ones.

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

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.

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

Clinical Simulation and Workflow by use of two Clinical Information Systems, the Electronic Health Record and Digital Dictation

DEFF Research Database (Denmark)

Schou Jensen, Iben; Koldby, Sven

2013-01-01

digital dictation and the EHR (electronic health record) were simulated in realistic and controlled clinical environments. Useful information dealing with workflow and patient safety were obtained. The clinical simulation demonstrated that the EHR locks during use of the integration of digital dictation......Clinical information systems do not always support clinician workflows. An increasing number of unintended clinical inci-dents might be related to implementation of clinical infor-mation systems and to a new registration praxis of unin-tended clinical incidents. Evidence of performing clinical...... simulations before implementation of new clinical information systems provides the basis for use of this method. The intention has been to evaluate patient safety issues, functionality, workflow, and usefulness of a new solution before implementation in the hospitals. Use of a solution which integrates...

Molecular orbitals for properties and spectroscopies

Energy Technology Data Exchange (ETDEWEB)

Robert, Vincent [Laboratoire de Chimie Quantique, Institut de Chimie, Université de Strasbourg, 1 rue Blaise Pascal 67000 Strasbourg-France (France); Domingo, Alex [Quantum Chemistry and Physical Chemistry Celestijnenlaan 200f, 3001 Heverlee - Belgium (Belgium); Braunstein, Pierre; Danopoulos, Andreas; Monakhov, Kirill [Laboratoire de Chimie de Coordination, Institut de Chimie, Université de Strasbourg, 4 rue Blaise Pascal 67081 Strasbourg-France (France)

2015-12-31

The description and clarification of spectroscopies and properties goes through ab initio calculations. Wave function based calculations (CASSCF/CASPT2) are particularly appealing since they offer spectroscopic accuracy and means of interpretation. we performed such calculations to elucidate the origin of unusual structural changes and intramolecular electron transfer phenomenon. Based on optimized molecular orbitals and a reading of the multireference wave function, it is suggested that intimate interactions are likely to considerably modify the standard pictures. A so-called PIMA (polarization-induced metalâĹŠarene) interaction similar to the more familiar anion-π interaction is responsible for a significant deviation from sp{sup 3} geometry and an energetic stabilization of 50 kJ/mol in Cr(II) benzyl organometallic complexes. In a similar fashion, it is proposed that the energetic profile of the IVCT (inter valence charge transfer) exhibits strong similarities to the Marcus’ theory, suggesting a response behaviour of the ensemble of electrons as electron transfer occurs in Fe{sup 2+}/Fe{sup 3+} bimetallic compound. The electronic reorganization induced by the IVCT process accounts for 11.8 eV, a very large effect that reduces the transfer energy down to 0.89 eV, in very good agreement with experiments.

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.

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.

Thermodynamic Molecular Switch in Sequence-Specific Hydrophobic Interaction: Two Computational Models Compared

Directory of Open Access Journals (Sweden)

Paul Chun

2003-01-01

Full Text Available We have shown in our published work the existence of a thermodynamic switch in biological systems wherein a change of sign in ΔCp°(Treaction leads to a true negative minimum in the Gibbs free energy change of reaction, and hence, a maximum in the related Keq. We have examined 35 pair-wise, sequence-specific hydrophobic interactions over the temperature range of 273–333 K, based on data reported by Nemethy and Scheraga in 1962. A closer look at a single example, the pair-wise hydrophobic interaction of leucine-isoleucine, will demonstrate the significant differences when the data are analyzed using the Nemethy-Scheraga model or treated by the Planck-Benzinger methodology which we have developed. The change in inherent chemical bond energy at 0 K, ΔH°(T0 is 7.53 kcal mol-1 compared with 2.4 kcal mol-1, while ‹ts› is 365 K as compared with 355 K, for the Nemethy-Scheraga and Planck-Benzinger model, respectively. At ‹tm›, the thermal agitation energy is about five times greater than ΔH°(T0 in the Planck-Benzinger model, that is 465 K compared to 497 K in the Nemethy-Scheraga model. The results imply that the negative Gibbs free energy minimum at a well-defined ‹ts›, where TΔS° = 0 at about 355 K, has its origin in the sequence-specific hydrophobic interactions, which are highly dependent on details of molecular structure. The Nemethy-Scheraga model shows no evidence of the thermodynamic molecular switch that we have found to be a universal feature of biological interactions. The Planck-Benzinger method is the best known for evaluating the innate temperature-invariant enthalpy, ΔH°(T0, and provides for better understanding of the heat of reaction for biological molecules.

Effect of inter-fibre bonding on the fracture of fibrous networks with strong interactions

DEFF Research Database (Denmark)

Goutianos, Stergios; Mao, Rui; Peijs, Ton

2017-01-01

Abstract The mechanical response of cellulose nanopaper composites is investigated using a three-dimensional (3D) finite element fibrous network model with focus on the effect of inter-fibre bonds. It is found that the Young’s modulus and strength, for fixed fibre properties, are mainly controlle...

Deuterium-labelled N-acyl-l-homoserine lactones (AHLs) - inter-kingdom signalling molecules - synthesis, structural studies, and interactions with model lipid membranes

Energy Technology Data Exchange (ETDEWEB)

Jakubczyk, Dorota [Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe (Germany); Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Barth, Christoph; Anastassacos, Frances; Koelsch, Patrick; Schepers, Ute [Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Kubas, Adam; Fink, Karin [Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Brenner-Weiss, Gerald [Institute of Functional Interfaces, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen (Germany); Braese, Stefan [Institute of Organic Chemistry, Karlsruhe Institute of Technology, Karlsruhe (Germany)

2012-04-15

N-Acyl-l-homoserine lactones (AHLs) are synthesized by Gram-negative bacteria. These quorum-sensing molecules play an important role in the context of bacterial infection and biofilm formation. They also allow communication between microorganisms and eukaryotic cells (inter-kingdom signalling). However, very little is known about the entire mechanism of those interactions. Precise structural studies are required to analyse the different AHL isomers as only one form is biologically most active. Theoretical studies combined with experimental infrared and Raman spectroscopic data are therefore undertaken to characterise the obtained compounds. To mimic interactions between AHL and cell membranes, we studied the insertion of AHL in supported lipid bilayers, using vibrational sum-frequency-generation spectroscopy. Deuterium-labelled AHLs were thus synthesized. Starting from readily available deuterated fatty acids, a two-step procedure towards deuterated N-acyl-l-homoserine lactones with varying chain lengths is described. This included the acylation of Meldrum's acid followed by amidation. Additionally, the detailed analytical evaluation of the products is presented herein. (orig.)

Structural analysis of inter-genus complexes of V-antigen and its regulator and their stabilization by divalent metal ions.

Science.gov (United States)

Basu, Abhishek; Das, Atanu; Mondal, Abhisek; Datta, Saumen

2016-03-01

Gram-negative bacteria like Yersinia, Pseudomonas, and Aeromonas need type III secretion system (T3SS) for their pathogenicity. V-antigen and its regulator are essential for functioning of T3SS. There is significant functional conservation amongst V-antigen and its regulator belonging to the Ysc family. In this study, we have structurally characterized the inter-genus complexes of V-antigen and its regulator. ConSurf analysis demonstrates that V-antigens belonging to the Ysc family show high structural identity predominantly confined to the two long helical regions. The regulator of V-antigen shows high conservation in its first intramolecular coiled-coil domain, responsible for interaction with V-antigen. ∆LcrG(1-70) localizes within the groove formed by long helices of LcrV, as observed in PcrV-∆PcrG(13-72) interaction. Inter-genus complexes of LcrV-PcrG and PcrV-LcrG exhibited elongated conformation and 1:1 heterodimeric state like the native complex of PcrV-PcrG and LcrV-LcrG. Both native and inter-genus complexes showed rigid tertiary structure, solvent-exposed hydrophobic patches, and cooperative melting behavior with high melting temperature. LcrV-PcrG and PcrV-LcrG showed nanomolar affinity of interaction, identical to PcrV-PcrG interaction, but stronger than LcrV-LcrG interaction. Calcium (a secretion blocker of T3SS) propels all the complexes towards a highly monodisperse form. Calcium and magnesium increase the helicity of the native and inter-genus complexes, and causes helix-helix stabilization. Stabilization of helices leads to a slight increase in the melting temperature by 1.5-2.0 °C. However, calcium does not alter the affinity of interaction of V-antigen and its regulator, emphasizing the effect of divalent of cations at the structural level without any regulatory implications. Therefore, the structural conservation of these inter-genus complexes could be the basis for their functional complementation.

Inter-operator and inter-device agreement and reliability of the SEM Scanner.

Science.gov (United States)

Clendenin, Marta; Jaradeh, Kindah; Shamirian, Anasheh; Rhodes, Shannon L

2015-02-01

The SEM Scanner is a medical device designed for use by healthcare providers as part of pressure ulcer prevention programs. The objective of this study was to evaluate the inter-rater and inter-device agreement and reliability of the SEM Scanner. Thirty-one (31) volunteers free of pressure ulcers or broken skin at the sternum, sacrum, and heels were assessed with the SEM Scanner. Each of three operators utilized each of three devices to collect readings from four anatomical sites (sternum, sacrum, left and right heels) on each subject for a total of 108 readings per subject collected over approximately 30 min. For each combination of operator-device-anatomical site, three SEM readings were collected. Inter-operator and inter-device agreement and reliability were estimated. Over the course of this study, more than 3000 SEM Scanner readings were collected. Agreement between operators was good with mean differences ranging from -0.01 to 0.11. Inter-operator and inter-device reliability exceeded 0.80 at all anatomical sites assessed. The results of this study demonstrate the high reliability and good agreement of the SEM Scanner across different operators and different devices. Given the limitations of current methods to prevent and detect pressure ulcers, the SEM Scanner shows promise as an objective, reliable tool for assessing the presence or absence of pressure-induced tissue damage such as pressure ulcers. Copyright © 2015 Bruin Biometrics, LLC. Published by Elsevier Ltd.. All rights reserved.

Interactions between proteins and carbon-based nanoparticles: exploring the origin of nanotoxicity at the molecular level.

Science.gov (United States)

Zuo, Guanghong; Kang, Seung-Gu; Xiu, Peng; Zhao, Yuliang; Zhou, Ruhong

2013-05-27

The widespread application of nanomaterials has spurred an interest in the study of interactions between nanoparticles and proteins due to the biosafety concerns of these nanomaterials. In this review, a summary is presented of some of the recent studies on this important subject, especially on the interactions of proteins with carbon nanotubes (CNTs) and metallofullerenols. Two potential molecular mechanisms have been proposed for CNTs' inhibition of protein functions. The driving forces of CNTs' adsorption onto proteins are found to be mainly hydrophobic interactions and the so-called π-π stacking between CNTs' carbon rings and proteins' aromatic residues. However, there is also recent evidence showing that endohedral metallofullerenol Gd@C82 (OH)22 can be used to inhibit tumor growth, thus acting as a potential nanomedicine. These recent findings have provided a better understanding of nanotoxicity at the molecular level and also suggested therapeutic potential by using nanoparticles' cytotoxicity against cancer cells. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

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.

VirHostNet 2.0: surfing on the web of virus/host molecular interactions data.

Science.gov (United States)

Guirimand, Thibaut; Delmotte, Stéphane; Navratil, Vincent

2015-01-01

VirHostNet release 2.0 (http://virhostnet.prabi.fr) is a knowledgebase dedicated to the network-based exploration of virus-host protein-protein interactions. Since the previous VirhostNet release (2009), a second run of manual curation was performed to annotate the new torrent of high-throughput protein-protein interactions data from the literature. This resource is shared publicly, in PSI-MI TAB 2.5 format, using a PSICQUIC web service. The new interface of VirHostNet 2.0 is based on Cytoscape web library and provides a user-friendly access to the most complete and accurate resource of virus-virus and virus-host protein-protein interactions as well as their projection onto their corresponding host cell protein interaction networks. We hope that the VirHostNet 2.0 system will facilitate systems biology and gene-centered analysis of infectious diseases and will help to identify new molecular targets for antiviral drugs design. This resource will also continue to help worldwide scientists to improve our knowledge on molecular mechanisms involved in the antiviral response mediated by the cell and in the viral strategies selected by viruses to hijack the host immune system. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

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

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)

Investigating the structural impacts of I64T and P311S mutations in APE1-DNA complex: a molecular dynamics approach.

Directory of Open Access Journals (Sweden)

C George Priya Doss

Full Text Available Elucidating the molecular dynamic behavior of Protein-DNA complex upon mutation is crucial in current genomics. Molecular dynamics approach reveals the changes on incorporation of variants that dictate the structure and function of Protein-DNA complexes. Deleterious mutations in APE1 protein modify the physicochemical property of amino acids that affect the protein stability and dynamic behavior. Further, these mutations disrupt the binding sites and prohibit the protein to form complexes with its interacting DNA.In this study, we developed a rapid and cost-effective method to analyze variants in APE1 gene that are associated with disease susceptibility and evaluated their impacts on APE1-DNA complex dynamic behavior. Initially, two different in silico approaches were used to identify deleterious variants in APE1 gene. Deleterious scores that overlap in these approaches were taken in concern and based on it, two nsSNPs with IDs rs61730854 (I64T and rs1803120 (P311S were taken further for structural analysis.Different parameters such as RMSD, RMSF, salt bridge, H-bonds and SASA applied in Molecular dynamic study reveals that predicted deleterious variants I64T and P311S alters the structure as well as affect the stability of APE1-DNA interacting functions. This study addresses such new methods for validating functional polymorphisms of human APE1 which is critically involved in causing deficit in repair capacity, which in turn leads to genetic instability and carcinogenesis.

The significance of the amorphous potential energy landscape for dictating glassy dynamics and driving solid-state crystallisation.

Science.gov (United States)

Ruggiero, Michael T; Krynski, Marcin; Kissi, Eric Ofosu; Sibik, Juraj; Markl, Daniel; Tan, Nicholas Y; Arslanov, Denis; van der Zande, Wim; Redlich, Britta; Korter, Timothy M; Grohganz, Holger; Löbmann, Korbinian; Rades, Thomas; Elliott, Stephen R; Zeitler, J Axel

2017-11-15

The fundamental origins surrounding the dynamics of disordered solids near their characteristic glass transitions continue to be fiercely debated, even though a vast number of materials can form amorphous solids, including small-molecule organic, inorganic, covalent, metallic, and even large biological systems. The glass-transition temperature, T g , can be readily detected by a diverse set of techniques, but given that these measurement modalities probe vastly different processes, there has been significant debate regarding the question of why T g can be detected across all of them. Here we show clear experimental and computational evidence in support of a theory that proposes that the shape and structure of the potential-energy surface (PES) is the fundamental factor underlying the glass-transition processes, regardless of the frequency that experimental methods probe. Whilst this has been proposed previously, we demonstrate, using ab initio molecular-dynamics (AIMD) simulations, that it is of critical importance to carefully consider the complete PES - both the intra-molecular and inter-molecular features - in order to fully understand the entire range of atomic-dynamical processes in disordered solids. Finally, we show that it is possible to utilise this dependence to directly manipulate and harness amorphous dynamics in order to control the behaviour of such solids by using high-powered terahertz pulses to induce crystallisation and preferential crystal-polymorph growth in glasses. Combined, these findings provide compelling evidence that the PES landscape, and the corresponding energy barriers, are the ultimate controlling feature behind the atomic and molecular dynamics of disordered solids, regardless of the frequency at which they occur.

The effect of amount and tangibility of endowment and certainty of recipients on selfishness in a modified dictator game.

Science.gov (United States)

Chang, Shao-Chuan; Lin, Li-Yun; Horng, Ruey-Yun; Wang, Yau-De

2014-06-01

Taiwanese college students (N = 101) participated in the study to examine the effects of the amount of an endowment, the tangibility of an endowment, and the certainty of the recipient on selfishness in a modified dictator game. Results showed that dictators were more selfish when allocating tangible (money) than less tangible (honor credits) endowments. Selfishness was higher when large amounts of money were involved. The certainty of the recipient was manipulated by whether the recipient was chosen and announced before or after the decision. Unexpectedly, participants were more self-interested in the certain-recipient condition than in the uncertain-recipient condition. In the honor condition, the amount of an endowment and the certainty of the recipient did not affect participants' allocations.

Binding interaction of ramipril with bovine serum albumin (BSA): Insights from multi-spectroscopy and molecular docking methods.

Science.gov (United States)

Shi, Jie-Hua; Pan, Dong-Qi; Jiang, Min; Liu, Ting-Ting; Wang, Qi

2016-11-01

The binding interaction between a typical angiotensin-converting enzyme inhibitor (ACEI), ramipril, and a transport protein, bovine serum albumin (BSA), was studied in vitro using UV-vis absorption spectroscopy, steady-state fluorescence spectroscopic titration, synchronous fluorescence spectroscopy, three dimensional fluorescence spectroscopy, circular dichroism and molecular docking under the imitated physiological conditions (pH=7.4). The experimental results suggested that the intrinsic fluorescence of BSA was quenched by ramipril thought a static quenching mechanism, indicating that the stable ramipril-BSA complex was formed by the intermolecular interaction. The number of binding sites (n) and binding constant of ramipril-BSA complex were about 1 and 3.50×10 4 M -1 at 298K, respectively, suggesting that there was stronger binding interaction of ramipril with BSA. The thermodynamic parameters together with molecular docking study revealed that both van der Waal's forces and hydrogen bonding interaction dominated the formation of the ramipril-BSA complex and the binding interaction of BSA with ramipril is enthalpy-driven processes due to |ΔH°|>|TΔS°| and ΔG°<0. The spatial distance between ramipril and BSA was calculated to be 3.56nm based on Förster's non-radiative energy transfer theory. The results of the competitive displacement experiments and molecular docking confirmed that ramipril inserted into the subdomain IIA (site I) of BSA, resulting in a slight change in the conformation of BSA but BSA still retained its secondary structure α-helicity. Copyright © 2016 Elsevier B.V. All rights reserved.

Spectroscopic and molecular modeling study on the interaction of ctDNA with 3′-deoxy-3′-azido doxorubicin

International Nuclear Information System (INIS)

Geng, Shaoguang; Cui, Yanrui; Liu, Qingfeng; Cui, Fengling; Zhang, Guisheng; Chi, Yanwei; Peng, Hao

2013-01-01

The method of synthesizing 3′-deoxy-3′-azido doxorubicin (ADOX) directly from doxorubicin has been developed. This study presents the interaction between ADOX and calf thymus deoxyribonucleic acid (ctDNA) by using spectroscopic methods and molecular modeling techniques. Iodide quenching, fluorescence polarization, viscosity and molecular modeling studies of ADOX–ctDNA interactions indicated that ADOX was an intercalator of ctDNA and preferentially bound to C–G rich regions of ctDNA. Simultaneously, spectroscopic results indicated that the quenching mechanism of ADOX–ctDNA was a static quenching. According to thermodynamic parameters, electrostatic force played roles in the interaction of ADOX with ctDNA. -- Highlights: ●An approach to 3′-deoxy-3′-azido doxorubicin (ADOX) from doxorubicin was developed. ●The quenching mechanism of ADOX with ctDNA was a static quenching type. ●The binding mode between ADOX and ctDNA was intercalative binding. ●The results of molecular docking corroborated results of spectra investigations

Facilitating Students' Interaction with Real Gas Properties Using a Discovery-Based Approach and Molecular Dynamics Simulations

Science.gov (United States)

Sweet, Chelsea; Akinfenwa, Oyewumi; Foley, Jonathan J., IV

2018-01-01

We present an interactive discovery-based approach to studying the properties of real gases using simple, yet realistic, molecular dynamics software. Use of this approach opens up a variety of opportunities for students to interact with the behaviors and underlying theories of real gases. Students can visualize gas behavior under a variety of…

Intergranular and inter-phased boundaries in the materials

International Nuclear Information System (INIS)

Aslanides, A.; Backhaus-Ricoult, M.; Bayle-Guillemaud, P.

2000-01-01

This document collects the abstracts of the talks presented during the colloquium J2IM on the intergranular and inter-phased boundaries in the materials. Around the themes of the interfaces behaviour and grain boundaries defects in materials, these days dealt with the microstructure behaviour in many domains such as the interfaces in batteries, the irradiation damages and the special case of the fuel-cladding interactions, the stressed interfaces, the alumina or silicon carbides substrates. (A.L.B.)

IAEA activities on atomic, molecular and plasma-material interaction data for fusion

Science.gov (United States)

Braams, Bastiaan J.; Chung, Hyun-Kyung

2013-09-01

The IAEA Atomic and Molecular Data Unit (http://www-amdis.iaea.org/) aims to provide internationally evaluated and recommended data for atomic, molecular and plasma-material interaction (A+M+PMI) processes in fusion research. The Unit organizes technical meetings and coordinates an A+M Data Centre Network (DCN) and a Code Centre Network (CCN). In addition the Unit organizes Coordinated Research Projects (CRPs), for which the objectives are mixed between development of new data and evaluation and recommendation of existing data. In the area of A+M data we are placing new emphasis in our meeting schedule on data evaluation and especially on uncertainties in calculated cross section data and the propagation of uncertainties through structure data and fundamental cross sections to effective rate coefficients. Following a recent meeting of the CCN it is intended to use electron scattering on Be, Ne and N2 as exemplars for study of uncertainties and uncertainty propagation in calculated data; this will be discussed further at the presentation. Please see http://www-amdis.iaea.org/CRP/ for more on our active and planned CRPs, which are concerned with atomic processes in core and edge plasma and with plasma interaction with beryllium-based surfaces and with irradiated tungsten.

[2,3,7,8,13,14,17,18-Octa-kis(ethyl-sulfan-yl)-5,10,15,20-porphyrazinato]zinc(II).

Science.gov (United States)

Akkurt, Mehmet; Coşkun, Naciye Yılmaz; Kılıçaslan, Fatma Aytan; Yalçın, Sabiha Manav; Büyükgüngör, Orhan; Gül, Ahmet

2010-07-24

In the title compound, [Zn(C(32)H(40)N(8)S(8))], the Zn(II) ion is coordinated by four N atoms in a slightly distorted square-planar environment. In addition, there is a Zn⋯S contact involving a symmetry-related S atom which, when considered, forms a pseudo-square-pyramidal coordination with respect to the Zn(II) ion. Three of the ethyl groups are disordered over two sites with occupancy ratios of 0.841 (10):0.159 (10), 0.802 (10):0.198 (10) and 0.457 (13):0.543 (13). Weak intra-molecular C-H⋯N and C-H⋯S inter-actions contribute to the stability of the mol-ecular conformation. Inter-molecular C-H⋯S contacts, weak C-H⋯π inter-actions and π-π stacking inter-actions [centroid-centriod distances = 3.832 (4) and 3.850 (5) Å] contribute to the stabilization of the crystal structure.

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.

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)

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.

Molecular weight (hydrodynamic volume) dictates the systemic pharmacokinetics and tumour disposition of PolyPEG star polymers.

Science.gov (United States)

Khor, Song Yang; Hu, Jinming; McLeod, Victoria M; Quinn, John F; Williamson, Mark; Porter, Christopher J H; Whittaker, Michael R; Kaminskas, Lisa M; Davis, Thomas P

2015-11-01

Herein we report for the first time the biological fate of poly[(oligoethylene glycol) acrylate] (POEGA) star polymers synthesised via a versatile arm-first reversible addition-fragmentation chain transfer (RAFT) polymerisation approach. The biopharmaceutical behaviour of three different molecular weight (49, 64 and 94kDa) POEGA stars was evaluated in rats and nude mice bearing human MDA MB-231 tumours after intravenous administration. The 94kDa star polymer exhibited a longer plasma exposure time than the 49kDa or 64kDa star polymer; an observation attributable to differences in the rates of both polymer biodegradation and urinary excretion. Tumour biodistribution also correlated with molecular weight and was greatest for the longest circulating 94kDa star. Different patterns of liver and spleen biodistribution were observed between mice and rats for the different sized polymers. The polymers were also well-tolerated in vivo and in vitro at therapeutic concentrations. Advances in nanotechnology has enabled scientists to produce nanoparticle as drug carriers in cancer therapeutics. In this article, the authors studied the biological fate of poly[(oligoethylene glycol) acrylate] (POEGA) star polymers of different size, after intravenous injections. This would allow the subsequent comparison to other drug delivery systems for better drug delivery. Copyright © 2015 Elsevier Inc. All rights reserved.

Evaluating Combinations of Ranked Lists and Visualizations of Inter-Document Similarity.

Science.gov (United States)

Allan, James; Leuski, Anton; Swan, Russell; Byrd, Donald

2001-01-01

Considers how ideas from document clustering can be used to improve retrieval accuracy of ranked lists in interactive systems and how to evaluate system effectiveness. Describes a TREC (Text Retrieval Conference) study that constructed and evaluated systems that present the user with ranked lists and a visualization of inter-document similarities.…

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.

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.

Assessing the initial adaptability and impact of a mobile dictation and reporting system in the radiology department of an academic hospital

Science.gov (United States)

Gali, Raja L.; Dave, Jaydev K.

2017-03-01

Mobile Radiologist 360, rolled out as part of the voice dictation system upgrade from Nuance Powerscribe 5.0 to PS360 allows an attending radiologist to edit and sign-off a report assigned by a trainee or that has been started by the radiologist on a workstation. The purpose of this study was to evaluate the adoptability and impact of this application. Report turnaround time data was extracted from the RIS (GE-Centricity RIS-IC) for 60 days before- (period-1) and 60 days after- (period-2) the application implementation and then, for 60 days after end of period-2 (period-3). Adoptability of the application was evaluated using two metrics; first, the number of attending radiologists who signed-off reports using the application in periods 2 and 3, and second, the proportion of reports signed-off by the top five users of the mobile application using the application. Impact of the application was evaluated by comparing the time from initial dictation to final sign-off (time_PF) for the top five users of the mobile application to the time_PF by other five radiologists who did not use the application. 41% radiologists used the mobile application at least once during the study period; the proportion of cases signed-off using the mobile application ranged from 1% to 20%. ANOVA revealed no statistically significant effect of the mobile application system on time_PF (p=0.842). In conclusion, there was low initial adoptability and no impact of the mobile dictation and reporting system in reducing the time from initial dictation to final sign-off on a radiology report.

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.

Computational Analysis of Molecular Interaction Networks Underlying Change of HIV-1 Resistance to Selected Reverse Transcriptase Inhibitors.

Science.gov (United States)

Kierczak, Marcin; Dramiński, Michał; Koronacki, Jacek; Komorowski, Jan

2010-12-12

Despite more than two decades of research, HIV resistance to drugs remains a serious obstacle in developing efficient AIDS treatments. Several computational methods have been developed to predict resistance level from the sequence of viral proteins such as reverse transcriptase (RT) or protease. These methods, while powerful and accurate, give very little insight into the molecular interactions that underly acquisition of drug resistance/hypersusceptibility. Here, we attempt at filling this gap by using our Monte Carlo feature selection and interdependency discovery method (MCFS-ID) to elucidate molecular interaction networks that characterize viral strains with altered drug resistance levels. We analyzed a number of HIV-1 RT sequences annotated with drug resistance level using the MCFS-ID method. This let us expound interdependency networks that characterize change of drug resistance to six selected RT inhibitors: Abacavir, Lamivudine, Stavudine, Zidovudine, Tenofovir and Nevirapine. The networks consider interdependencies at the level of physicochemical properties of mutating amino acids, eg,: polarity. We mapped each network on the 3D structure of RT in attempt to understand the molecular meaning of interacting pairs. The discovered interactions describe several known drug resistance mechanisms and, importantly, some previously unidentified ones. Our approach can be easily applied to a whole range of problems from the domain of protein engineering. A portable Java implementation of our MCFS-ID method is freely available for academic users and can be obtained at: http://www.ipipan.eu/staff/m.draminski/software.htm.

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.

Kosovo, the beginning and end of the adventure of a dictator in Europe

Directory of Open Access Journals (Sweden)

Xhavit Sadrijaj

2016-07-01

Full Text Available When desires are not based in reality, the result is the only one that can be expected from such desires. In such games winning is actually called losing. That also happened with the consuming desires of the late dictator in Europe, Milošević. The permanent Yugoslav president Tito, was known for his philosophy: “We decline what is not ours; ours we will relinquish not”. Although it was not like that, this philosophy had its success. It kept the morale of strength and the existence of a state of over 30 nations who lived in it and who remained steadfast and unbeaten throughout the Cold War. With Tito's death his country died too, altogether with the philosophy. The fact that it really was just philosophy was shown several years later, when in the absence of a successor to Tito, but also through new anticommunist movements in the world, the state collapsed becoming involved in war and chaos that was manifested by bloody tragedies of very large dimensions. Of course all this tragedy was preceded by Serbian chauvinist passions and desires which were planned for a century in all forms, and which were implemented by a dictator who also will remain in history as such, Slobodan Milošević and his clique. This executioner chose Kosovo as the most appropriate level for its establishment in the peaks of power and certainly had not imagined then that was also his end.

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

Molecular mechanisms of nematode-nematophagous microbe interactions: basis for biological control of plant-parasitic nematodes.

Science.gov (United States)

Li, Juan; Zou, Chenggang; Xu, Jianping; Ji, Xinglai; Niu, Xuemei; Yang, Jinkui; Huang, Xiaowei; Zhang, Ke-Qin

2015-01-01

Plant-parasitic nematodes cause significant damage to a broad range of vegetables and agricultural crops throughout the world. As the natural enemies of nematodes, nematophagous microorganisms offer a promising approach to control the nematode pests. Some of these microorganisms produce traps to capture and kill the worms from the outside. Others act as internal parasites to produce toxins and virulence factors to kill the nematodes from within. Understanding the molecular basis of microbe-nematode interactions provides crucial insights for developing effective biological control agents against plant-parasitic nematodes. Here, we review recent advances in our understanding of the interactions between nematodes and nematophagous microorganisms, with a focus on the molecular mechanisms by which nematophagous microorganisms infect nematodes and on the nematode defense against pathogenic attacks. We conclude by discussing several key areas for future research and development, including potential approaches to apply our recent understandings to develop effective biocontrol strategies.

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.

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

Conceptualizing inter-organizational triads

DEFF Research Database (Denmark)

Vedel, Mette; Holma, Anne-Maria; Havila, Virpi

2016-01-01

of inter-organizational phenomena. However, not all studies involving a context of three actors are actually examining triads. This paper offers a robust definition of three-actor constellations qualifying as triads. Moreover, it elaborates on different types of inter-organizational triads, based on two...... aspects of collectivity; cohesion and the ability to act as a single entity. The definition of inter-organizational triads and the categorization of different types of triads will hopefully encourage further studies of triads; the smallest and simplest network which offers insights, which cannot...

Interaction of VUV-photons with molecules. Spectroscopy and dynamics of molecular superexcited states

International Nuclear Information System (INIS)

Hatano, Y.

2002-01-01

Complete text of publication follows. A survey is given of recent progress in experimental studies of the interaction of VUV-photons with molecules, i.e., those of photoabsorption, photoionization, and photodissociation of molecules in the excitation photon energy range of 10-50 eV, with a particular emphasis placed on current understanding of the spectroscopy and dynamics of formed molecular superexcited states. These studies are of great importance in understanding the interaction of ionizing radiation with matter. Molecules studied are ranged from simple diatomic and triatomic molecules to polyatomic molecules such as hydrocarbons. Most of the observed molecular superexcited states are assigned to high Rydber states which are vibrationally, doubly, or inner-core excited and converge to each of ion states. Non-Rydberg superexcited states are also observed. Dissociation into neutral fragments in comparison with ionization is of unexpectedly great importance in the observed decay of each of these state-assigned superexcited molecules. Dissociation dynamics as well as its products of superexcited states are remarkably different from those of lower excited states below about ionization thresholds. Some remarks are also presented of molecules in the condensed phase

Molecular dynamics on diffusive time scales from the phase-field-crystal equation.

Science.gov (United States)

Chan, Pak Yuen; Goldenfeld, Nigel; Dantzig, Jon

2009-03-01

We extend the phase-field-crystal model to accommodate exact atomic configurations and vacancies by requiring the order parameter to be non-negative. The resulting theory dictates the number of atoms and describes the motion of each of them. By solving the dynamical equation of the model, which is a partial differential equation, we are essentially performing molecular dynamics simulations on diffusive time scales. To illustrate this approach, we calculate the two-point correlation function of a fluid.

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.

On the interconnection of stable protein complexes: inter-complex hubs and their conservation in Saccharomyces cerevisiae and Homo sapiens networks.

Science.gov (United States)

Guerra, Concettina

2015-01-01

Protein complexes are key molecular entities that perform a variety of essential cellular functions. The connectivity of proteins within a complex has been widely investigated with both experimental and computational techniques. We developed a computational approach to identify and characterise proteins that play a role in interconnecting complexes. We computed a measure of inter-complex centrality, the crossroad index, based on disjoint paths connecting proteins in distinct complexes and identified inter-complex hubs as proteins with a high value of the crossroad index. We applied the approach to a set of stable complexes in Saccharomyces cerevisiae and in Homo sapiens. Just as done for hubs, we evaluated the topological and biological properties of inter-complex hubs addressing the following questions. Do inter-complex hubs tend to be evolutionary conserved? What is the relation between crossroad index and essentiality? We found a good correlation between inter-complex hubs and both evolutionary conservation and essentiality.

Development of an inter-atomic potential for the Pd-H binary system.

Energy Technology Data Exchange (ETDEWEB)

Zimmerman, Jonathan A.; Hoyt, Jeffrey John (McMaster University, Hamilton, Ontario, Canada); Leonard, Francois Leonard; Griffin, Joshua D.; Zhou, Xiao Wang

2007-09-01

Ongoing research at Sandia National Laboratories has been in the area of developing models and simulation methods that can be used to uncover and illuminate the material defects created during He bubble growth in aging bulk metal tritides. Previous efforts have used molecular dynamics calculations to examine the physical mechanisms by which growing He bubbles in a Pd metal lattice create material defects. However, these efforts focused only on the growth of He bubbles in pure Pd and not on bubble growth in the material of interest, palladium tritide (PdT), or its non-radioactive isotope palladium hydride (PdH). The reason for this is that existing inter-atomic potentials do not adequately describe the thermodynamics of the Pd-H system, which includes a miscibility gap that leads to phase separation of the dilute (alpha) and concentrated (beta) alloys of H in Pd at room temperature. This document will report the results of research to either find or develop inter-atomic potentials for the Pd-H and Pd-T systems, including our efforts to use experimental data and density functional theory calculations to create an inter-atomic potential for this unique metal alloy system.

A Molecular Dynamics Approach for Nucleation-Growth of Cryogenic Cavitation