Chemical reactivity and spectroscopy explored from QM/MM molecular dynamics simulations using the LIO code

NASA Astrophysics Data System (ADS)

Marcolongo, Juan P.; Zeida, Ari; Semelak, Jonathan A.; Foglia, Nicolás O.; Morzan, Uriel N.; Estrin, Dario A.; González Lebrero, Mariano C.; Scherlis, Damián A.

2018-03-01

In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.

Magnetically engineered smart thin films: toward lab-on-chip ultra-sensitive molecular imaging.

PubMed

Hassan, Muhammad A; Saqib, Mudassara; Shaikh, Haseeb; Ahmad, Nasir M; Elaissari, Abdelhamid

2013-03-01

Magnetically responsive engineered smart thin films of nanoferrites as contrast agent are employed to develop surface based magnetic resonance imaging to acquire simple yet fast molecular imaging. The work presented here can be of significant potential for future lab-on-chip point-of-care diagnostics from the whole blood pool on almost any substrates to reduce or even prevent clinical studies involve a living organism to enhance the non-invasive imaging to advance the '3Rs' of work in animals-replacement, refinement and reduction.

Studies of chain substitution caused sub-fibril level differences in stiffness and ultrastructure of wildtype and oim/oim collagen fibers using multifrequency-AFM and molecular modeling.

PubMed

Li, Tao; Chang, Shu-Wei; Rodriguez-Florez, Naiara; Buehler, Markus J; Shefelbine, Sandra; Dao, Ming; Zeng, Kaiyang

2016-11-01

Molecular alteration in type I collagen, i.e., substituting the α2 chain with α1 chain in tropocollagen molecule, can cause osteogenesis imperfecta (OI), a brittle bone disease, which can be represented by a mouse model (oim/oim). In this work, we use dual-frequency Atomic Force Microscopy (AFM) and incorporated with molecular modeling to quantify the ultrastructure and stiffness of the individual native collagen fibers from wildtype (+/+) and oim/oim diseased mice humeri. Our work presents direct experimental evidences that the +/+ fibers have highly organized and compact ultrastructure and corresponding ordered stiffness distribution. In contrast, oim/oim fibers have ordered but loosely packed ultrastructure with uncorrelated stiffness distribution, as well as local defects. The molecular model also demonstrates the structural and molecular packing differences between +/+ and oim/oim collagens. The molecular mutation significantly altered sub-fibril structure and mechanical property of collagen fibers. This study can give the new insight for the mechanisms and treatment of the brittle bone disease. Copyright © 2016 Elsevier Ltd. All rights reserved.

Marine Biotoxins: Laboratory Culture and Molecular Structure

DTIC Science & Technology

1988-10-11

has been known for several years. has so far been isolated from toxic zoanthid corals. Palv~tha sp. Preliminary evidence suggests that the producer of...epiphyte of the zoanthid coral has not been realized. C. Purpose of Present Work The purposes of this work are the successful culture of G_. toxicus

Theoretical Insight into Shocked Gases

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

Leiding, Jeffery Allen

2016-09-29

I present the results of statistical mechanical calculations on shocked molecular gases. This work provides insight into the general behavior of shock Hugoniots of gas phase molecular targets with varying initial pressures. The dissociation behavior of the molecules is emphasized. Impedance matching calculations are performed to determine the maximum degree of dissociation accessible for a given flyer velocity as a function of initial gas pressure.

Self-Assembly and Drug Release Capacities of Organogels via Some Amide Compounds with Aromatic Substituent Headgroups

PubMed Central

Zhang, Lexin; Jiao, Tifeng; Ma, Kai; Xing, Ruirui; Liu, Yamei; Xiao, Yong; Zhou, Jingxin; Zhang, Qingrui; Peng, Qiuming

2016-01-01

In this work, some amide compounds with different aromatic substituent headgroups were synthesized and their gelation self-assembly behaviors in 22 solvents were characterized as new gelators. The obtained results indicated that the size of aromatic substituent headgroups in molecular skeletons in gelators showed crucial effect in the gel formation and self-assembly behavior of all compounds in the solvents used. Larger aromatic headgroups in molecular structures in the synthesized gelator molecules are helpful to form various gel nanostructures. Morphological investigations showed that the gelator molecules can self-assembly and stack into various organized aggregates with solvent change, such as wrinkle, belt, rod, and lamella-like structures. Spectral characterizations suggested that there existed various weak interactions including π-π stacking, hydrogen bonding, and hydrophobic forces due to aromatic substituent headgroups and alkyl substituent chains in molecular structures. In addition, the drug release capacities experiments demonstrated that the drug release rate in present obtained gels can be tuned by adjusting the concentrations of dye. The present work would open up enormous insight to design and investigate new kind of soft materials with designed molecular structures and tunable drug release performance. PMID:28773663

Calculation of surface potentials at the silica–water interface using molecular dynamics: Challenges and opportunities

NASA Astrophysics Data System (ADS)

Lowe, Benjamin M.; Skylaris, Chris-Kriton; Green, Nicolas G.; Shibuta, Yasushi; Sakata, Toshiya

2018-04-01

Continuum-based methods are important in calculating electrostatic properties of interfacial systems such as the electric field and surface potential but are incapable of providing sufficient insight into a range of fundamentally and technologically important phenomena which occur at atomistic length-scales. In this work a molecular dynamics methodology is presented for interfacial electric field and potential calculations. The silica–water interface was chosen as an example system, which is highly relevant for understanding the response of field-effect transistors sensors (FET sensors). Detailed validation work is presented, followed by the simulated surface charge/surface potential relationship. This showed good agreement with experiment at low surface charge density but at high surface charge density the results highlighted challenges presented by an atomistic definition of the surface potential. This methodology will be used to investigate the effect of surface morphology and biomolecule addition; both factors which are challenging using conventional continuum models.

Molecular computational elements encode large populations of small objects

NASA Astrophysics Data System (ADS)

Prasanna de Silva, A.; James, Mark R.; McKinney, Bernadine O. F.; Pears, David A.; Weir, Sheenagh M.

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1nm) and large `on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100μm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a `wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.

Molecular computational elements encode large populations of small objects.

PubMed

de Silva, A Prasanna; James, Mark R; McKinney, Bernadine O F; Pears, David A; Weir, Sheenagh M

2006-10-01

Since the introduction of molecular computation, experimental molecular computational elements have grown to encompass small-scale integration, arithmetic and games, among others. However, the need for a practical application has been pressing. Here we present molecular computational identification (MCID), a demonstration that molecular logic and computation can be applied to a widely relevant issue. Examples of populations that need encoding in the microscopic world are cells in diagnostics or beads in combinatorial chemistry (tags). Taking advantage of the small size (about 1 nm) and large 'on/off' output ratios of molecular logic gates and using the great variety of logic types, input chemical combinations, switching thresholds and even gate arrays in addition to colours, we produce unique identifiers for members of populations of small polymer beads (about 100 microm) used for synthesis of combinatorial libraries. Many millions of distinguishable tags become available. This method should be extensible to far smaller objects, with the only requirement being a 'wash and watch' protocol. Our focus on converting molecular science into technology concerning analog sensors, turns to digital logic devices in the present work.

Hard Sphere Simulation by Event-Driven Molecular Dynamics: Breakthrough, Numerical Difficulty, and Overcoming the issues

NASA Astrophysics Data System (ADS)

Isobe, Masaharu

Hard sphere/disk systems are among the simplest models and have been used to address numerous fundamental problems in the field of statistical physics. The pioneering numerical works on the solid-fluid phase transition based on Monte Carlo (MC) and molecular dynamics (MD) methods published in 1957 represent historical milestones, which have had a significant influence on the development of computer algorithms and novel tools to obtain physical insights. This chapter addresses the works of Alder's breakthrough regarding hard sphere/disk simulation: (i) event-driven molecular dynamics, (ii) long-time tail, (iii) molasses tail, and (iv) two-dimensional melting/crystallization. From a numerical viewpoint, there are serious issues that must be overcome for further breakthrough. Here, we present a brief review of recent progress in this area.

Cold Atomic Hydrogen, Narrow Self-Absorption, and the Age of Molecular Clouds

NASA Technical Reports Server (NTRS)

Goldsmith, Paul F.

2006-01-01

This viewgraph presentation reviews the history, and current work on HI and its importance in star formation. Through many observations of HI Narrow Self Absorption (HINSA) the conclusions are drawn and presented. Local molecular clouds have HI well-mixed with molecular constituents This HI is cold, quiescent, and must be well-shielded from the UV radiation field The density and fractional abundance (wrt H2) of the cold HI are close to steady state values The time required to convert these starless clouds from purely HI initial state to observed present composition is a few to ten million years This timescale is a lower limit - if dense clouds being swept up from lower density regions by shocks, the time to accumulate material to get A(sub v) is approximately 1 and provide required shielding may be comparable or longer

Synthesizing and databasing fossil calibrations: divergence dating and beyond

PubMed Central

Ksepka, Daniel T.; Benton, Michael J.; Carrano, Matthew T.; Gandolfo, Maria A.; Head, Jason J.; Hermsen, Elizabeth J.; Joyce, Walter G.; Lamm, Kristin S.; Patané, José S. L.; Phillips, Matthew J.; Polly, P. David; Van Tuinen, Marcel; Ware, Jessica L.; Warnock, Rachel C. M.; Parham, James F.

2011-01-01

Divergence dating studies, which combine temporal data from the fossil record with branch length data from molecular phylogenetic trees, represent a rapidly expanding approach to understanding the history of life. National Evolutionary Synthesis Center hosted the first Fossil Calibrations Working Group (3–6 March, 2011, Durham, NC, USA), bringing together palaeontologists, molecular evolutionists and bioinformatics experts to present perspectives from disciplines that generate, model and use fossil calibration data. Presentations and discussions focused on channels for interdisciplinary collaboration, best practices for justifying, reporting and using fossil calibrations and roadblocks to synthesis of palaeontological and molecular data. Bioinformatics solutions were proposed, with the primary objective being a new database for vetted fossil calibrations with linkages to existing resources, targeted for a 2012 launch. PMID:21525049

The principle of respect for autonomy--concordant with the experience of oncology physicians and molecular biologists in their daily work?

PubMed

Ebbesen, Mette; Pedersen, Birthe D

2008-03-26

This article presents results from a qualitative empirical investigation of how Danish oncology physicians and Danish molecular biologists experience the principle of respect for autonomy in their daily work. This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. We found that that molecular biologists consider the principle of respect for autonomy as a negative obligation, where the informed consent of patients or research subjects should be respected. Furthermore, molecular biologists believe that very sick patients are constraint by the circumstances to a certain choice. However, in contrast to molecular biologists, oncology physicians experience the principle of respect for autonomy as a positive obligation, where the physician in dialogue with the patient performs a medical prognosis based on the patient's wishes and ideas, mutual understanding and respect. Oncology physicians believe that they have a positive obligation to adjust to the level of the patient when providing information making sure that the patient understands. Oncology physicians experience situations where the principle of respect for autonomy does not apply because the patient is in a difficult situation. In this study we explore the moral views and attitudes of oncology physicians and molecular biologists and compare these views with bioethical theories of the American bioethicists Tom L. Beauchamp & James F. Childress and the Danish philosophers Jakob Rendtorff & Peter Kemp. This study shows that essential parts of the two bioethical theories are reflected in the daily work of Danish oncology physicians and Danish molecular biologists. However, the study also explores dimensions where the theories can be developed further to be concordant with biomedical practice. The hope is that this study enhances the understanding of the principle of respect for autonomy and the way it is practiced.

Molecular Force Spectroscopy on Cells

NASA Astrophysics Data System (ADS)

Liu, Baoyu; Chen, Wei; Zhu, Cheng

2015-04-01

Molecular force spectroscopy has become a powerful tool to study how mechanics regulates biology, especially the mechanical regulation of molecular interactions and its impact on cellular functions. This force-driven methodology has uncovered a wealth of new information of the physical chemistry of molecular bonds for various biological systems. The new concepts, qualitative and quantitative measures describing bond behavior under force, and structural bases underlying these phenomena have substantially advanced our fundamental understanding of the inner workings of biological systems from the nanoscale (molecule) to the microscale (cell), elucidated basic molecular mechanisms of a wide range of important biological processes, and provided opportunities for engineering applications. Here, we review major force spectroscopic assays, conceptual developments of mechanically regulated kinetics of molecular interactions, and their biological relevance. We also present current challenges and highlight future directions.

How molecular motors work – insights from the molecular machinist's toolbox: the Nobel prize in Chemistry 2016

PubMed Central

Astumian, R. D.

2017-01-01

The Nobel prize in Chemistry for 2016 was awarded to Jean Pierre Sauvage, Sir James Fraser Stoddart, and Bernard (Ben) Feringa for their contributions to the design and synthesis of molecular machines. While this field is still in its infancy, and at present there are no commercial applications, many observers have stressed the tremendous potential of molecular machines to revolutionize technology. However, perhaps the most important result so far accruing from the synthesis of molecular machines is the insight provided into the fundamental mechanisms by which molecular motors, including biological motors such as kinesin, myosin, FoF1 ATPase, and the flagellar motor, function. The ability to “tinker” with separate components of molecular motors allows asking, and answering, specific questions about mechanism, particularly with regard to light driven vs. chemistry driven molecular motors. PMID:28572896

Free energy surface of an intrinsically disordered protein: comparison between temperature replica exchange molecular dynamics and bias-exchange metadynamics.

PubMed

Zerze, Gül H; Miller, Cayla M; Granata, Daniele; Mittal, Jeetain

2015-06-09

Intrinsically disordered proteins (IDPs), which are expected to be largely unstructured under physiological conditions, make up a large fraction of eukaryotic proteins. Molecular dynamics simulations have been utilized to probe structural characteristics of these proteins, which are not always easily accessible to experiments. However, exploration of the conformational space by brute force molecular dynamics simulations is often limited by short time scales. Present literature provides a number of enhanced sampling methods to explore protein conformational space in molecular simulations more efficiently. In this work, we present a comparison of two enhanced sampling methods: temperature replica exchange molecular dynamics and bias exchange metadynamics. By investigating both the free energy landscape as a function of pertinent order parameters and the per-residue secondary structures of an IDP, namely, human islet amyloid polypeptide, we found that the two methods yield similar results as expected. We also highlight the practical difference between the two methods by describing the path that we followed to obtain both sets of data.

Exact dynamic properties of molecular motors

NASA Astrophysics Data System (ADS)

Boon, N. J.; Hoyle, R. B.

2012-08-01

Molecular motors play important roles within a biological cell, performing functions such as intracellular transport and gene transcription. Recent experimental work suggests that there are many plausible biochemical mechanisms that molecules such as myosin-V could use to achieve motion. To account for the abundance of possible discrete-stochastic frameworks that can arise when modeling molecular motor walks, a generalized and straightforward graphical method for calculating their dynamic properties is presented. It allows the calculation of the velocity, dispersion, and randomness ratio for any proposed system through analysis of its structure. This article extends work of King and Altman ["A schematic method of deriving the rate laws of enzyme-catalyzed reactions," J. Phys. Chem. 60, 1375-1378 (1956)], 10.1021/j150544a010 on networks of enzymatic reactions by calculating additional dynamic properties for spatially hopping systems. Results for n-state systems are presented: single chain, parallel pathway, divided pathway, and divided pathway with a chain. A novel technique for combining multiple system architectures coupled at a reference state is also demonstrated. Four-state examples illustrate the effectiveness and simplicity of these methods.

Molecular Growth Inside of Polycyclic Aromatic Hydrocarbon Clusters Induced by Ion Collisions.

PubMed

Delaunay, Rudy; Gatchell, Michael; Rousseau, Patrick; Domaracka, Alicja; Maclot, Sylvain; Wang, Yang; Stockett, Mark H; Chen, Tao; Adoui, Lamri; Alcamí, Manuel; Martín, Fernando; Zettergren, Henning; Cederquist, Henrik; Huber, Bernd A

2015-05-07

The present work combines experimental and theoretical studies of the collision between keV ion projectiles and clusters of pyrene, one of the simplest polycyclic aromatic hydrocarbons (PAHs). Intracluster growth processes induced by ion collisions lead to the formation of a wide range of new molecules with masses larger than that of the pyrene molecule. The efficiency of these processes is found to strongly depend on the mass and velocity of the incoming projectile. Classical molecular dynamics simulations of the entire collision process-from the ion impact (nuclear scattering) to the formation of new molecular species-reproduce the essential features of the measured molecular growth process and also yield estimates of the related absolute cross sections. More elaborate density functional tight binding calculations yield the same growth products as the classical simulations. The present results could be relevant to understand the physical chemistry of the PAH-rich upper atmosphere of Saturn's moon Titan.

Determination of the Temperature Dependence of Heat Capacity for Some Molecular Crystals of Nitro Compounds

NASA Astrophysics Data System (ADS)

Kovalev, Yu. M.; Kuropatenko, V. F.

2018-05-01

An analysis of the existing approximations used for describing the dependence of heat capacity at a constant volume on the temperature of a molecular crystal has been carried out. It is shown that the considered Debye and Einstein approximations do not enable one to adequately describe the dependence of heat capacity at a constant volume on the temperature of the molecular crystals of nitro compounds. This inference requires the development of special approximations that would describe both low-frequency and high-frequency parts of the vibrational spectra of molecular crystals. This work presents a universal dependence allowing one to describe the dependence of heat capacity at a constant volume on temperature for a number of molecular crystals of nitro compounds.

Molecular-Level Computational Investigation of Mechanical Transverse Behavior of p-Phenylene Terephthalamide (PPTA) Fibers

DTIC Science & Technology

2013-01-01

fabricated today are based on polymer matrix composites containing Kevlarw KM2 reinforcements , the present work will deal with generic PPTA fibers . In...Multi-length scale enriched continuum-level material model for Kevlarw- fiber reinforced polymer-matrix composites”, Journal of Materials...mechanical transverse behavior of p-phenylene terephthalamide (PPTA) fibers Purpose – A series of all-atom molecular-level computational analyses is

Force field development with GOMC, a fast new Monte Carlo molecular simulation code

NASA Astrophysics Data System (ADS)

Mick, Jason Richard

In this work GOMC (GPU Optimized Monte Carlo) a new fast, flexible, and free molecular Monte Carlo code for the simulation atomistic chemical systems is presented. The results of a large Lennard-Jonesium simulation in the Gibbs ensemble is presented. Force fields developed using the code are also presented. To fit the models a quantitative fitting process is outlined using a scoring function and heat maps. The presented n-6 force fields include force fields for noble gases and branched alkanes. These force fields are shown to be the most accurate LJ or n-6 force fields to date for these compounds, capable of reproducing pure fluid behavior and binary mixture behavior to a high degree of accuracy.

Molecular chirality: language, history, and significance.

PubMed

Gal, Joseph

2013-01-01

In this chapter some background material concerning molecular chirality and enantiomerism is presented. First some basic chemical-molecular aspects of chirality are reviewed, after which certain relevant terminology whose use in the literature has been problematic is discussed. Then an overview is provided of some of the early discoveries that laid the foundations of the science of molecular chirality in chemistry and biology, including the discovery of the phenomenon of molecular chirality by L. Pasteur, the proposals for the asymmetric carbon atom by J.H. van 't Hoff and J.A. Lebel, Pasteur's discovery of biological enantioselectivity, the discovery of enantioselectivity at biological receptors by A. Piutti, the studies of enzymatic stereoselectivity by E. Fischer, and the work on enantioselectivity in pharmacology by A. Cushny. Finally, the role of molecular chirality in pharmacotherapy and new-drug development, arguably one of the main driving forces for the current intense interest in the phenomenon of molecular chirality, is discussed.

Delocalized electrons in atomic and molecular nanoclusters

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

Kresin, Vitaly

The aim of the award (Program director: Dr. Mark Pederson) was to facilitate the attendance of researchers, students, and postdocs from the U.S. at the international workshop co-organized by the applicant. The award succeeded in making it possible for a number of US attendees to present their work and participate in the meeting, which was a significant event in the research community at the interdisciplinary interface of physical chemistry, nanoscience, atomic and molecular physics, condensed matter physics, and spectroscopy. The workshop did not issue proceedings, but the present report includes present the schedule, the abstracts, and the attendance list ofmore » the July 2016 Workshop. DOE sponsorship is gratefully acknowledged in the program.« less

Molecular similarity measures.

PubMed

Maggiora, Gerald M; Shanmugasundaram, Veerabahu

2011-01-01

Molecular similarity is a pervasive concept in chemistry. It is essential to many aspects of chemical reasoning and analysis and is perhaps the fundamental assumption underlying medicinal chemistry. Dissimilarity, the complement of similarity, also plays a major role in a growing number of applications of molecular diversity in combinatorial chemistry, high-throughput screening, and related fields. How molecular information is represented, called the representation problem, is important to the type of molecular similarity analysis (MSA) that can be carried out in any given situation. In this work, four types of mathematical structure are used to represent molecular information: sets, graphs, vectors, and functions. Molecular similarity is a pairwise relationship that induces structure into sets of molecules, giving rise to the concept of chemical space. Although all three concepts - molecular similarity, molecular representation, and chemical space - are treated in this chapter, the emphasis is on molecular similarity measures. Similarity measures, also called similarity coefficients or indices, are functions that map pairs of compatible molecular representations that are of the same mathematical form into real numbers usually, but not always, lying on the unit interval. This chapter presents a somewhat pedagogical discussion of many types of molecular similarity measures, their strengths and limitations, and their relationship to one another. An expanded account of the material on chemical spaces presented in the first edition of this book is also provided. It includes a discussion of the topography of activity landscapes and the role that activity cliffs in these landscapes play in structure-activity studies.

Empirical investigation of the ethical reasoning of physicians and molecular biologists - the importance of the four principles of biomedical ethics.

PubMed

Ebbesen, Mette; Pedersen, Birthe D

2007-10-25

This study presents an empirical investigation of the ethical reasoning and ethical issues at stake in the daily work of physicians and molecular biologists in Denmark. The aim of this study was to test empirically whether there is a difference in ethical considerations and principles between Danish physicians and Danish molecular biologists, and whether the bioethical principles of the American bioethicists Tom L. Beauchamp and James F. Childress are applicable to these groups. This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. In this sample, the authors found that oncology physicians and molecular biologists employed in a private biopharmaceutical company have the specific principle of beneficence in mind in their daily work. Both groups are motivated to help sick patients. According to the study, molecular biologists explicitly consider nonmaleficence in relation to the environment, the researchers' own health, and animal models; and only implicitly in relation to patients or human subjects. In contrast, considerations of nonmaleficence by oncology physicians relate to patients or human subjects. Physicians and molecular biologists both consider the principle of respect for autonomy as a negative obligation in the sense that informed consent of patients should be respected. However, in contrast to molecular biologists, physicians experience the principle of respect for autonomy as a positive obligation as the physician, in dialogue with the patient, offers a medical prognosis based upon the patients wishes and ideas, mutual understanding, and respect. Finally, this study discloses utilitarian characteristics in the overall conception of justice as conceived by oncology physicians and molecular biologists from the private biopharmaceutical company. Molecular biologists employed at a public university are, in this study, concerned with allocation, however, they do not propose a specific theory of justice. This study demonstrates that each of the four bioethical principles of the American bioethicists Tom L. Beauchamp & James F. Childress - respect for autonomy, beneficence, nonmaleficence and justice - are reflected in the daily work of physicians and molecular biologists in Denmark. Consequently, these principles are applicable in the Danish biomedical setting.

Empirical investigation of the ethical reasoning of physicians and molecular biologists – the importance of the four principles of biomedical ethics

PubMed Central

Ebbesen, Mette; Pedersen, Birthe D

2007-01-01

Background This study presents an empirical investigation of the ethical reasoning and ethical issues at stake in the daily work of physicians and molecular biologists in Denmark. The aim of this study was to test empirically whether there is a difference in ethical considerations and principles between Danish physicians and Danish molecular biologists, and whether the bioethical principles of the American bioethicists Tom L. Beauchamp and James F. Childress are applicable to these groups. Method This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. Results In this sample, the authors found that oncology physicians and molecular biologists employed in a private biopharmaceutical company have the specific principle of beneficence in mind in their daily work. Both groups are motivated to help sick patients. According to the study, molecular biologists explicitly consider nonmaleficence in relation to the environment, the researchers' own health, and animal models; and only implicitly in relation to patients or human subjects. In contrast, considerations of nonmaleficence by oncology physicians relate to patients or human subjects. Physicians and molecular biologists both consider the principle of respect for autonomy as a negative obligation in the sense that informed consent of patients should be respected. However, in contrast to molecular biologists, physicians experience the principle of respect for autonomy as a positive obligation as the physician, in dialogue with the patient, offers a medical prognosis based upon the patients wishes and ideas, mutual understanding, and respect. Finally, this study discloses utilitarian characteristics in the overall conception of justice as conceived by oncology physicians and molecular biologists from the private biopharmaceutical company. Molecular biologists employed at a public university are, in this study, concerned with allocation, however, they do not propose a specific theory of justice. Conclusion This study demonstrates that each of the four bioethical principles of the American bioethicists Tom L. Beauchamp & James F. Childress – respect for autonomy, beneficence, nonmaleficence and justice – are reflected in the daily work of physicians and molecular biologists in Denmark. Consequently, these principles are applicable in the Danish biomedical setting. PMID:17961251

OptoBase: A web platform for molecular optogenetics.

PubMed

Kolar, Katja; Knobloch, Christian; Stork, Hendrik; Žnidarič, Matej; Weber, Wilfried

2018-06-18

OptoBase is an online platform for molecular optogenetics. At its core is a hand-annotated and ontology-supported database that aims to cover all existing optogenetic switches and publications, which is further complemented with a collection of convenient optogenetics-related web tools. OptoBase is meant for both expert optogeneticists, to easily keep track of the field, as well as for all researchers who find optogenetics inviting as a powerful tool to address their biological questions of interest. It is available at https://www.optobase.org. This work also presents OptoBase-based analysis of the trends in molecular optogenetics.

Electron transport in molecular wires with transition metal contacts

NASA Astrophysics Data System (ADS)

Dalgleish, Hugh

A molecular wire is an organic molecule that forms a conducting bridge between electronic contacts. Single molecules are likely to be the smallest entities to conduct electricity and thus molecular wires present many interesting challenges to fundamental science as well as enormous potential for nanoelectronic technological applications. A particular challenge stems from the realization that the properties of molecular wires are strongly influenced by the combined characteristics of the molecule and the metal contacts. While gold has been the most studied contact material to date, interest in molecular wires with transition metal contacts that are electronically more complex than gold is growing. This thesis presents a theoretical investigation of electron transport and associated phenomena in molecular wires with transition metal contacts. An appropriate methodology is developed on the basis of Landauer theory and ab initio and semi-empirical considerations and new, physically important systems are identified. Spin-dependent transport mechanisms and device characteristics are explored for molecular wires with ferromagnetic iron contacts, systems that have not been considered previously, either theoretically or experimentally. Electron transport between iron point contacts bridged by iron atoms is also investigated. Spin-dependent transport is also studied for molecules bridging nickel contacts and a possible explanation of some experimentally observed phenomena is proposed. A novel physical phenomenon termed strong spin current rectification and a new controllable negative differential resistance mechanism with potential applications for molecular electronic technology are introduced. The phenomena predicted in this thesis should be accessible to present day experimental techniques and this work is intended to stimulate experiments directed at observing them. Keywords. molecular electronics; spintronics; electron transport; interface states.

COPRED: prediction of fold, GO molecular function and functional residues at the domain level.

PubMed

López, Daniel; Pazos, Florencio

2013-07-15

Only recently the first resources devoted to the functional annotation of proteins at the domain level started to appear. The next step is to develop specific methodologies for predicting function at the domain level based on these resources, and to implement them in web servers to be used by the community. In this work, we present COPRED, a web server for the concomitant prediction of fold, molecular function and functional sites at the domain level, based on a methodology for domain molecular function prediction and a resource of domain functional annotations previously developed and benchmarked. COPRED can be freely accessed at http://csbg.cnb.csic.es/copred. The interface works in all standard web browsers. WebGL (natively supported by most browsers) is required for the in-line preview and manipulation of protein 3D structures. The website includes a detailed help section and usage examples. pazos@cnb.csic.es.

High-pressure/high-temperature polymorphs of energetic materials by first-principles simulations

NASA Astrophysics Data System (ADS)

Le, Nam; Schweigert, Igor

2017-06-01

Energetic molecular crystals exhibit complex phase diagrams that include solid-solid phase transitions, melting, and decomposition. Sorescu and Rice have recently demonstrated that first-principles molecular dynamics (MD) simulations based on dispersion-corrected density functional theory (DFT) can capture the α to γ phase transition in hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX) on time scales of several picoseconds. Motivated by their work, we are using DFT-based MD to model the relative stability of solid phases in several molecular crystals. In this presentation, we report simulations of pentaerythritol tetranitrate (PETN) and 2,4,6-trinitrotoluene (TNT) under high pressures and temperatures and compare them with experimentally observed polymorphs. This work was supported by the U.S. Naval Research Laboratory via the National Research Council and by the Office of Naval Research through the U.S. Naval Research Laboratory.

Theoretical and Experimental Triple Differential Cross Sections for Electron Impact Ionization of SF6

NASA Astrophysics Data System (ADS)

Chaluvadi, Hari; Nixon, Kate; Murray, Andrew; Ning, Chuangang; Colgan, James; Madison, Don

2014-10-01

Experimental and theoretical Triply Differential Cross Sections (TDCS) will be presented for electron-impact ionization of sulfur hexafluoride (SF6) for the molecular orbital 1t1g. M3DW (molecular 3-body distorted wave) results will be compared with experiment for coplanar geometry and for perpendicular plane geometry (a plane which is perpendicular to the incident beam direction). In both cases, the final state electron energies and observation angles are symmetric and the final state electron energies range from 5 eV to 40 eV. It will be shown that there is a large difference between using the OAMO (orientation averaged molecular orbital) approximation and the proper average over all orientations and also that the proper averaged results are in much better agreement with experiment. Work supported by NSF under Grant Number PHY-1068237. Computational work was performed with Institutional resources made available through Los Alamos National Laboratory.

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

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

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

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

Cold Gas in High-z Galaxies: The CO Gas Excitation Ladder and the need for the ngVLA

NASA Astrophysics Data System (ADS)

Casey, Caitlin M.; Champagne, Jaclyn; Narayanan, Desika; Davé, Romeel; Hung, Chao-Ling; Carilli, Chris; Murphy, Eric Joseph; Decarli, Roberto; Popping, Gergo; Riechers, Dominik A.; Somerville, Rachel; Walter, Fabian

2018-01-01

We will present updated results on a community study led to understand the observable molecular gas properties of high-z galaxies. This work uses a series of high-resolution, hydrodynamic, cosmological zoom-in simulations from MUFASA, the Despotic radiative transfer code that uses simultaneous thermal and statistical equilibrium in calculating molecular and atomic level populations, and a CASA simulator which generates mock ngVLA and ALMA observations. Our work reveals a stark contrast in gas characteristics (geometry and kinematics) as measured from low-J transitions of CO to high-J transitions, demonstrating the need for the ngVLA in probing the cold gas reservoir in the highest-redshift galaxies.

Theoretical study of a molecular turbine.

PubMed

Perez-Carrasco, R; Sancho, J M

2013-10-01

We present an analytic and stochastic simulation study of a molecular engine working with a flux of particles as a turbine. We focus on the physical observables of velocity, flux, power, and efficiency. The control parameters are the external conservative force and the particle densities. We revise a simpler previous study by using a more realistic model containing multiple equidistant vanes complemented by stochastic simulations of the particles and the turbine. Here we show that the effect of the thermal fluctuations into the flux and the efficiency of these nanometric devices are relevant to the working scale of the system. The stochastic simulations of the Brownian motion of the particles and turbine support the simplified analytical calculations performed.

Saponification equivalent of dasamula taila.

PubMed

Saxena, R B

1994-07-01

Saponification equivalent values of Dasamula taila are very useful for the technical and analytical work. It gives the mean molecular weight of the glycerides and acids present in Dasamula Taila. Saponification equivalent values of Dasamula taila are reported in different packings.

Molecular dynamics approach to probe PKCβII-ligand interactions and influence of crystal water molecules on these interactions.

PubMed

Grewal, Baljinder K; Bhat, Jyotsna; Sobhia, Masilamani Elizabeth

2015-01-01

PKCβII is a potential target for therapeutic intervention against pandemic diabetic complications. Present study probes the molecular interactions of PKCβII with its clinically important ligands, viz. ruboxistaurin, enzastaurin and co-crystallized ligand, 2-methyl-1H-indol-3-yl-BIM-1. The essentials of PKCβII-ligand interaction, crystal water-induced alterations in these interactions and key interacting flexible residues are analyzed. Computational methodologies, viz. molecular docking and molecular simulation coupled with molecular mechanics-Poisson-Boltzmann surface area and generalized born surface area (MM-PB[GB]SA) are employed. The structural changes in the presence and absence of crystal water molecules in PKCβII ATP binding site residues, and its interaction with bound ligand, are identified. Difference in interaction of selective and nonselective ligand with ATP binding site residues of PKCβII is reported. The study showed that the nonbonding interactions contribute significantly in PKCβII-ligand binding and presence of crystal water molecules affects the interactions. The findings of present work may integrate the new aspects in the drug design process of PKCβII inhibitors.

Molecular Beam Epitaxial Growth of GaAs on (631) Oriented Substrates

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

Cruz Hernandez, Esteban; Rojas Ramirez, Juan-Salvador; Contreras Hernandez, Rocio

2007-02-09

In this work, we report the study of the homoepitaxial growth of GaAs on (631) oriented substrates by molecular beam epitaxy (MBE). We observed the spontaneous formation of a high density of large scale features on the surface. The hilly like features are elongated towards the [-5, 9, 3] direction. We show the dependence of these structures with the growth conditions and we present the possibility of to create quantum wires structures on this surface.

The principle of respect for autonomy – Concordant with the experience of oncology physicians and molecular biologists in their daily work?

PubMed Central

Ebbesen, Mette; Pedersen, Birthe D

2008-01-01

Background This article presents results from a qualitative empirical investigation of how Danish oncology physicians and Danish molecular biologists experience the principle of respect for autonomy in their daily work. Methods This study is based on 12 semi-structured interviews with three groups of respondents: a group of oncology physicians working in a clinic at a public hospital and two groups of molecular biologists conducting basic research, one group employed at a public university and the other in a private biopharmaceutical company. Results We found that that molecular biologists consider the principle of respect for autonomy as a negative obligation, where the informed consent of patients or research subjects should be respected. Furthermore, molecular biologists believe that very sick patients are constraint by the circumstances to a certain choice. However, in contrast to molecular biologists, oncology physicians experience the principle of respect for autonomy as a positive obligation, where the physician in dialogue with the patient performs a medical prognosis based on the patient's wishes and ideas, mutual understanding and respect. Oncology physicians believe that they have a positive obligation to adjust to the level of the patient when providing information making sure that the patient understands. Oncology physicians experience situations where the principle of respect for autonomy does not apply because the patient is in a difficult situation. Conclusion In this study we explore the moral views and attitudes of oncology physicians and molecular biologists and compare these views with bioethical theories of the American bioethicists Tom L. Beauchamp & James F. Childress and the Danish philosophers Jakob Rendtorff & Peter Kemp. This study shows that essential parts of the two bioethical theories are reflected in the daily work of Danish oncology physicians and Danish molecular biologists. However, the study also explores dimensions where the theories can be developed further to be concordant with biomedical practice. The hope is that this study enhances the understanding of the principle of respect for autonomy and the way it is practiced. PMID:18366749

Super-Earths, Warm Neptunes, and Hot Jupiters: Transmission Spectroscopy for Comparative Planetology

NASA Astrophysics Data System (ADS)

Fraine, Jonathan D.; Deming, Drake; Jordan, Andres; Knutson, Heather

2015-01-01

The detections and non-detections of molecular species in transiting planets-- such as water, methane, and carbon monoxide-- lead to greater understanding of planet formation and evolution. Recent significant advances in both theoretical and observational discoveries from planets like HD189733b, HD209458b, GJ436b, as well as our own work with HAT-P-11b and GJ1214b, have shown that the range of measurable atmospheric properties spans from clear, molecular absorption dominated worlds to opaque worlds, with cloudy, hazy, or high mean molecular weight atmospheres. Characterization of significant non-detections allowed us to infer the existence of opaque cloud layers at very high altitudes or mean molecular weights upwards of ~1000x solar. The prevalence of these atmospheres was unexpected from extrapolations of solar system analogs. I will present our published results from GJ1214b and HAT-P-11b, as well as our recent work using both Spitzer and Magellan. Our results, combined with transmission spectra obtained for other similar planets, connect to develop a better understanding about the nature of these distant and alien worlds

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

Rizzi, Silvio; Hereld, Mark; Insley, Joseph

In this work we perform in-situ visualization of molecular dynamics simulations, which can help scientists to visualize simulation output on-the-fly, without incurring storage overheads. We present a case study to couple LAMMPS, the large-scale molecular dynamics simulation code with vl3, our parallel framework for large-scale visualization and analysis. Our motivation is to identify effective approaches for covisualization and exploration of large-scale atomistic simulations at interactive frame rates.We propose a system of coupled libraries and describe its architecture, with an implementation that runs on GPU-based clusters. We present the results of strong and weak scalability experiments, as well as future researchmore » avenues based on our results.« less

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

Inokuti, M.; Rau, A. R. P.; Physics

With the passing of Ugo Fano on 13 February 2001, Comments on Atomic and Molecular Physics lost a longtime correspondent since its founding in 1969. A broader community dearly misses a great theoretical physicist. The present tribute is designed in a special way appropriate for this journal, in view of other documents describing Fano's life and work. It is accompanied by a curriculum vitae, which shows the span of a rich professional life. We shall concentrate on his accomplishments in atomic and molecular physics, leaving aside contributions to radiation physics and other areas. We also present a list of hismore » publications, which should be useful as a resource material.« less

Conference summary & recent advances: The 8th Conference on Metal Toxicity and Carcinogenesis

PubMed Central

Zhou, Xixi; Burchiel, Scott W.; Hudson, Laurie G.; Liu, Ke Jian

2015-01-01

Diseases caused by occupational and environmental exposure to metals are a public health concern. The underlying molecular mechanisms of metal toxicity and carcinogenicity remain largely unknown. Over 130 scientists attended the 8th Conference on Metal Toxicity and Carcinogenesis, presenting their various research concerns and recent findings to stimulate interactions and collaborations among scientists in the field. Several major areas were emphasized, including human & population studies, molecular & cellular mechanisms, biological targets, epigenetic effects, metabolism, and metal mixtures. Here we summarize presentations at the conference sessions and highlight the attendees’ latest work published in this special issue of Biological Trace Element Research. PMID:25975949

Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

PubMed Central

2013-01-01

In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures. PMID:24083361

Spacer effect on nanostructures and self-assembly in organogels via some bolaform cholesteryl imide derivatives with different spacers

NASA Astrophysics Data System (ADS)

Jiao, Tifeng; Gao, Fengqing; Zhang, Qingrui; Zhou, Jingxin; Gao, Faming

2013-10-01

In this paper, new bolaform cholesteryl imide derivatives with different spacers were designed and synthesized. Their gelation behaviors in 23 solvents were investigated, and some of them were found to be low molecular mass organic gelators. The experimental results indicated that these as-formed organogels can be regulated by changing the flexible/rigid segments in spacers and organic solvents. Suitable combination of flexible/rigid segments in molecular spacers in the present cholesteryl gelators is favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle and belt to fiber with the change of spacers and solvents. Spectral studies indicated that there existed different H-bond formations between imide groups and assembly modes, depending on the substituent spacers in molecular skeletons. The present work may give some insight into the design and character of new organogelators and soft materials with special molecular structures.

Theoretical Characterization of the Spectral Density of the Water-Soluble Chlorophyll-Binding Protein from Combined Quantum Mechanics/Molecular Mechanics Molecular Dynamics Simulations.

PubMed

Rosnik, Andreana M; Curutchet, Carles

2015-12-08

Over the past decade, both experimentalists and theorists have worked to develop methods to describe pigment-protein coupling in photosynthetic light-harvesting complexes in order to understand the molecular basis of quantum coherence effects observed in photosynthesis. Here we present an improved strategy based on the combination of quantum mechanics/molecular mechanics (QM/MM) molecular dynamics (MD) simulations and excited-state calculations to predict the spectral density of electronic-vibrational coupling. We study the water-soluble chlorophyll-binding protein (WSCP) reconstituted with Chl a or Chl b pigments as the system of interest and compare our work with data obtained by Pieper and co-workers from differential fluorescence line-narrowing spectra (Pieper et al. J. Phys. Chem. B 2011, 115 (14), 4042-4052). Our results demonstrate that the use of QM/MM MD simulations where the nuclear positions are still propagated at the classical level leads to a striking improvement of the predicted spectral densities in the middle- and high-frequency regions, where they nearly reach quantitative accuracy. This demonstrates that the so-called "geometry mismatch" problem related to the use of low-quality structures in QM calculations, not the quantum features of pigments high-frequency motions, causes the failure of previous studies relying on similar protocols. Thus, this work paves the way toward quantitative predictions of pigment-protein coupling and the comprehension of quantum coherence effects in photosynthesis.

Nonequilibrium, steady-state electron transport with N-representable density matrices from the anti-Hermitian contracted Schrödinger equation

NASA Astrophysics Data System (ADS)

Rothman, Adam E.; Mazziotti, David A.

2010-03-01

We study molecular conductivity for a one-electron, bath-molecule-bath model Hamiltonian. The primary quantum-mechanical variable is the one-electron reduced density matrix (1-RDM). By identifying similarities between the steady-state Liouville equation and the anti-Hermitian contracted Schrödinger equation (ACSE) [D. A. Mazziotti, Phys. Rev. A 75, 022505 (2007)], we develop a way of enforcing nonequilibrium, steady-state behavior in a time-independent theory. Our results illustrate the relationship between current and voltage in molecular junctions assuming that the total number of electrons under consideration can be fixed across all driving potentials. The impetus for this work is a recent study by Subotnik et al. that also uses the 1-RDM to study molecular conductivity under different assumptions regarding the total number of electrons [J. E. Subotnik et al., J. Chem. Phys. 130, 144105 (2009)]. Unlike calculations in the previous study, our calculations result in 1-RDMs that are fully N-representable. The present work maintains N-representability through a bath-bath mixing that is related to a time-independent relaxation of the baths in the absence of the molecule, as governed by the ACSE. A lack of N-representability can be important since it corresponds to occupying energy states in the molecule or baths with more than one electron or hole (the absence of an electron) in violation of the Pauli principle. For this reason the present work may serve as an important, albeit preliminary, step in designing a 2-RDM/ACSE method for studying steady-state molecular conductivity with an explicit treatment of electron correlation.

SAPONIFICATION EQUIVALENT OF DASAMULA TAILA

PubMed Central

Saxena, R. B.

1994-01-01

Saponification equivalent values of Dasamula taila are very useful for the technical and analytical work. It gives the mean molecular weight of the glycerides and acids present in Dasamula Taila. Saponification equivalent values of Dasamula taila are reported in different packings. PMID:22556683

Molecular dynamics computer simulation of permeation in solids

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

Pohl, P.I.; Heffelfinger, G.S.; Fisler, D.K.

1997-12-31

In this work the authors simulate permeation of gases and cations in solid models using molecular mechanics and a dual control volume grand canonical molecular dynamics technique. The molecular sieving nature of microporous zeolites are discussed and compared with that for amorphous silica made by sol-gel methods. One mesoporous and one microporous membrane model are tested with Lennard-Jones gases corresponding to He, H{sub 2}, Ar and CH{sub 4}. The mesoporous membrane model clearly follows a Knudsen diffusion mechanism, while the microporous model having a hard-sphere cutoff pore diameter of {approximately}3.4 {angstrom} demonstrates molecular sieving of the methane ({sigma} = 3.8more » {angstrom}) but anomalous behavior for Ar ({sigma} = 3.4 {angstrom}). Preliminary results of Ca{sup +} diffusion in calcite and He/H{sub 2} diffusion in polyisobutylene are also presented.« less

Preventing iron(ii) precipitation in aqueous systems using polyacrylic acid: some molecular insights.

PubMed

Artola, Pierre-Arnaud; Rousseau, Bernard; Clavaguéra, Carine; Roy, Marion; You, Dominique; Plancque, Gabriel

2018-06-22

We present molecular dynamics simulations of aqueous iron(ii) systems in the presence of polyacrylic acid (PAA) under the extreme conditions that take place in the secondary coolant circuit of a nuclear power plant. The aim of this work is to understand how the oligomer can prevent iron(ii) deposits, and to provide molecular interpretation. We show how, to this end, not only the complexant ability is necessary, but also the chain length compared to iron(ii) concentration. When the chain is long enough, a hyper-complexation phenomenon occurs that can explain the specific capacity of the polymer to prevent iron(ii) precipitation.

Planetary Biology and Microbial Ecology: Molecular Ecology and the Global Nitrogen cycle

NASA Technical Reports Server (NTRS)

Nealson, Molly Stone (Editor); Nealson, Kenneth H. (Editor)

1993-01-01

This report summarizes the results of the Planetary Biology and Molecular Ecology's summer 1991 program, which was held at the Marine Biological Laboratory in Woods Hole, Massachusetts. The purpose of the interdisciplinary PBME program is to integrate, via lectures and laboratory work, the contributions of university and NASA scientists and student interns. The goals of the 1991 program were to examine several aspects of the biogeochemistry of the nitrogen cycle and to teach the application of modern methods of molecular genetics to field studies of organisms. Descriptions of the laboratory projects and protocols and abstracts and references of the lectures are presented.

Electronic excitations in molecular solids: bridging theory and experiment.

PubMed

Skelton, Jonathan M; da Silva, E Lora; Crespo-Otero, Rachel; Hatcher, Lauren E; Raithby, Paul R; Parker, Stephen C; Walsh, Aron

2015-01-01

As the spatial and temporal resolution accessible to experiment and theory converge, computational chemistry is an increasingly powerful tool for modelling and interpreting spectroscopic data. However, the study of molecular processes, in particular those related to electronic excitations (e.g. photochemistry), frequently pushes quantum-chemical techniques to their limit. The disparity in the level of theory accessible to periodic and molecular calculations presents a significant challenge when modelling molecular crystals, since accurate calculations require a high level of theory to describe the molecular species, but must also take into account the influence of the crystalline environment on their properties. In this article, we briefly review the different classes of quantum-chemical techniques, and present an overview of methods that account for environmental influences with varying levels of approximation. Using a combination of solid-state and molecular calculations, we quantitatively evaluate the performance of implicit-solvent models for the [Ni(Et4dien)(η2-O,ON)(η1-NO2)] linkage-isomer system as a test case. We focus particularly on the accurate reproduction of the energetics of the isomerisation, and on predicting spectroscopic properties to compare with experimental results. This work illustrates how the synergy between periodic and molecular calculations can be exploited for the study of molecular crystals, and forms a basis for the investigation of more challenging phenomena, such as excited-state dynamics, and for further methodological developments.

Imaging and Force Recognition of Single Molecular Behaviors Using Atomic Force Microscopy

PubMed Central

Li, Mi; Dang, Dan; Liu, Lianqing; Xi, Ning; Wang, Yuechao

2017-01-01

The advent of atomic force microscopy (AFM) has provided a powerful tool for investigating the behaviors of single native biological molecules under physiological conditions. AFM can not only image the conformational changes of single biological molecules at work with sub-nanometer resolution, but also sense the specific interactions of individual molecular pair with piconewton force sensitivity. In the past decade, the performance of AFM has been greatly improved, which makes it widely used in biology to address diverse biomedical issues. Characterizing the behaviors of single molecules by AFM provides considerable novel insights into the underlying mechanisms guiding life activities, contributing much to cell and molecular biology. In this article, we review the recent developments of AFM studies in single-molecule assay. The related techniques involved in AFM single-molecule assay were firstly presented, and then the progress in several aspects (including molecular imaging, molecular mechanics, molecular recognition, and molecular activities on cell surface) was summarized. The challenges and future directions were also discussed. PMID:28117741

Joint adsorption of light hydrogen by CuO and 5A molecular sieves

NASA Astrophysics Data System (ADS)

Wang, J.; Zhan, Y.; Wang, W.; Wang, R. S.

2018-03-01

H2 is the primary cause of the deteriorating vacuum degree of high-vacuum multilayer insulation tank (HVMLIT). At present, the precious metal PdO is used to adsorb H2 and maintain the high vacuum of HVMLIT. In this study, CA, a compound hydrogen adsorbent integrated with the cheap metal CuO and 5A molecular sieves, is adopted to jointly adsorb light hydrogen in HVMLIT. This work also investigates the adsorption characteristics and mechanisms of CA.

Floating-point performance of ARM cores and their efficiency in classical molecular dynamics

NASA Astrophysics Data System (ADS)

Nikolskiy, V.; Stegailov, V.

2016-02-01

Supercomputing of the exascale era is going to be inevitably limited by power efficiency. Nowadays different possible variants of CPU architectures are considered. Recently the development of ARM processors has come to the point when their floating point performance can be seriously considered for a range of scientific applications. In this work we present the analysis of the floating point performance of the latest ARM cores and their efficiency for the algorithms of classical molecular dynamics.

Overcoming Ehrlich-Schwöbel barrier in (1 1 1)A GaAs molecular beam epitaxy

NASA Astrophysics Data System (ADS)

Ritzmann, Julian; Schott, Rüdiger; Gross, Katherine; Reuter, Dirk; Ludwig, Arne; Wieck, Andreas D.

2018-01-01

In this work, we first study the effect of different growth parameters on the molecular beam epitaxy (MBE) growth of GaAs layers on (1 1 1)A oriented substrates. After that we present a method for the MBE growth of atomically smooth layers by sequences of growth and annealing phases. The samples exhibit low surface roughness and good electrical properties shown by atomic force microscopy (AFM), scanning electron microscopy (SEM) and van-der-Pauw Hall measurements.

Free-energy landscape of glycerol permeation through aquaglyceroporin GlpF determined from steered molecular dynamics simulations.

PubMed

Chen, L Y

2010-10-01

The free-energy landscape of glycerol permeation through the aquaglyceroporin GlpF has been estimated in the literature by the nonequilibrium method of steered molecular dynamics (SMD) simulations and by the equilibrium method of adaptive biasing force (ABF) simulations. However, the ABF results qualitatively disagree with the SMD results that were based on the Jarzynski equality (JE) relating the equilibrium free-energy difference to the nonequilibrium work of the irreversible pulling experiments. In this paper, I present a new SMD study of the glycerol permeation through GlpF to explore the free-energy profile of glycerol along the permeation channel. Instead of the JE in terms of thermodynamic work, I use the fluctuation-dissipation theorem (FDT) of Brownian dynamics (BD), in terms of mechanical work, for extracting the free-energy difference from the nonequilibrium work of irreversible pulling experiments. The results of this new SMD-BD-FDT study are in agreement with the experimental data and with the ABF results. 2010 Elsevier B.V. All rights reserved.

Rectified Brownian movement in molecular and cell biology

NASA Astrophysics Data System (ADS)

Fox, Ronald F.

1998-02-01

A unified model is presented for rectified Brownian movement as the mechanism for a variety of putatively chemomechanical energy conversions in molecular and cell biology. The model is established by a detailed analysis of ubiquinone transport in electron transport chains and of allosteric conformation changes in proteins. It is applied to P-type ATPase ion transporters and to a variety of rotary arm enzyme complexes. It provides a basis for the dynamics of actin-myosin cross-bridges in muscle fibers. In this model, metabolic free energy does no work directly, but instead biases boundary conditions for thermal diffusion. All work is done by thermal energy, which is harnessed at the expense of metabolic free energy through the establishment of the asymmetric boundary conditions.

Molecular simulation of separation of CO{sub 2} from flue gases in Cu-BTC metal-organic framework

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

Yang, Q.Y.; Xue, C.Y.; Zhong, C.L.

2007-11-15

In this work, a computational study was performed on the adsorption separation of CO{sub 2} from flue gases (mixtures of CO{sub 2}/N{sub 2}/O{sub 2}) in Cu-BTC metal-organic framework (MOF) to investigate the applicability of MOFs to this important industrial system. The computational results showed that Cu-BTC is a promising material for separation of CO{sub 2} from flue gases, and the macroscopic separation behaviors of the MOF were elucidated at a molecular level to give insight into the underlying mechanisms. The present work not only provided useful information for understanding the separation characteristics of MOFs, but also showed their potential applicationsmore » in chemical industry.« less

New methods for accelerating the convergence of molecular electronic integrals over exponential type orbitals

NASA Astrophysics Data System (ADS)

Safouhi, Hassan; Hoggan, Philip

2003-01-01

This review on molecular integrals for large electronic systems (MILES) places the problem of analytical integration over exponential-type orbitals (ETOs) in a historical context. After reference to the pioneering work, particularly by Barnett, Shavitt and Yoshimine, it focuses on recent progress towards rapid and accurate analytic solutions of MILES over ETOs. Software such as the hydrogenlike wavefunction package Alchemy by Yoshimine and collaborators is described. The review focuses on convergence acceleration of these highly oscillatory integrals and in particular it highlights suitable nonlinear transformations. Work by Levin and Sidi is described and applied to MILES. A step by step description of progress in the use of nonlinear transformation methods to obtain efficient codes is provided. The recent approach developed by Safouhi is also presented. The current state of the art in this field is summarized to show that ab initio analytical work over ETOs is now a viable option.

Insights from molecular modeling and dynamics simulation of pathogen resistance (R) protein from brinjal.

PubMed

Shrivastava, Dipty; Nain, Vikrant; Sahi, Shakti; Verma, Anju; Sharma, Priyanka; Sharma, Prakash Chand; Kumar, Polumetla Ananda

2011-01-22

Resistance (R) protein recognizes molecular signature of pathogen infection and activates downstream hypersensitive response signalling in plants. R protein works as a molecular switch for pathogen defence signalling and represent one of the largest plant gene family. Hence, understanding molecular structure and function of R proteins has been of paramount importance for plant biologists. The present study is aimed at predicting structure of R proteins signalling domains (CC-NBS) by creating a homology model, refining and optimising the model by molecular dynamics simulation and comparing ADP and ATP binding. Based on sequence similarity with proteins of known structures, CC-NBS domains were initially modelled using CED- 4 (cell death abnormality protein) and APAF-1 (apoptotic protease activating factor) as multiple templates. The final CC-NBS structural model was built and optimized by molecular dynamic simulation for 5 nanoseconds (ns). Docking of ADP and ATP at active site shows that both ligand bind specifically with same residues and with minor difference (1 Kcal/mol) in binding energy. Sharing of binding site by ADP and ATP and low difference in their binding site makes CC-NBS suitable for working as molecular switch. Furthermore, structural superimposition elucidate that CC-NBS and CARD (caspase recruitment domains) domain of CED-4 have low RMSD value of 0.9 A° Availability of 3D structural model for both CC and NBS domains will . help in getting deeper insight in these pathogen defence genes.

An official American Thoracic Society Workshop Report: presentations and discussion of the fifth Jack Pepys Workshop on Asthma in the Workplace. Comparisons between asthma in the workplace and non-work-related asthma.

PubMed

Malo, Jean-Luc; Tarlo, Susan M; Sastre, Joaquin; Martin, James; Jeebhay, Mohamed F; Le Moual, Nicole; Heederik, Dick; Platts-Mills, Thomas; Blanc, Paul D; Vandenplas, Olivier; Moscato, Gianna; de Blay, Frédéric; Cartier, André

2015-07-01

The fifth Jack Pepys Workshop on Asthma in the Workplace focused on the similarities and differences of work-related asthma (WRA) and non-work-related asthma (non-WRA). WRA includes occupational asthma (OA) and work-exacerbated asthma (WEA). There are few biological differences in the mechanisms of sensitization to environmental and occupational allergens. Non-WRA and OA, when due to high-molecular-weight agents, are both IgE mediated; it is uncertain whether OA due to low-molecular-weight agents is also IgE mediated. Risk factors for OA include female sex, a history of upper airway symptoms, and a history of bronchial hyperresponsiveness. Atopy is a risk factor for OA due to high-molecular-weight agents, and exposure to cleaning agents is a risk factor for both OA and non-WRA. WEA is important among workers with preexisting asthma and may overlap with irritant-induced asthma, a type of OA. Induced sputum cytology can confirm airway inflammation, but specific inhalation challenge is the reference standard diagnostic test. Inhalation challenges are relatively safe, with the most severe reactions occurring with low-molecular-weight agents. Indirect health care costs account for about 50% of total asthma costs. Workers with poor asthma control (WRA or non-WRA) are less likely to be employed. Income loss is a major contributor to the indirect costs of WRA. Overall, asthma outcomes probably are worse for adult-onset than for childhood-onset asthma but better for OA than adult-onset non-WRA. Important aspects of management of OA are rapid and proper confirmation of the diagnosis and reduction of exposure to sensitizers or irritants at work and home.

An Official American Thoracic Society Workshop Report: Presentations and Discussion of the Fifth Jack Pepys Workshop on Asthma in the Workplace. Comparisons between Asthma in the Workplace and Non–Work-related Asthma

PubMed Central

Malo, Jean-Luc; Sastre, Joaquin; Martin, James; Jeebhay, Mohamed F.; Le Moual, Nicole; Heederik, Dick; Platts-Mills, Thomas; Blanc, Paul D.; Vandenplas, Olivier; Moscato, Gianna; de Blay, Frédéric; Cartier, André

2015-01-01

The fifth Jack Pepys Workshop on Asthma in the Workplace focused on the similarities and differences of work-related asthma (WRA) and non–work-related asthma (non-WRA). WRA includes occupational asthma (OA) and work-exacerbated asthma (WEA). There are few biological differences in the mechanisms of sensitization to environmental and occupational allergens. Non-WRA and OA, when due to high-molecular-weight agents, are both IgE mediated; it is uncertain whether OA due to low-molecular-weight agents is also IgE mediated. Risk factors for OA include female sex, a history of upper airway symptoms, and a history of bronchial hyperresponsiveness. Atopy is a risk factor for OA due to high-molecular-weight agents, and exposure to cleaning agents is a risk factor for both OA and non-WRA. WEA is important among workers with preexisting asthma and may overlap with irritant-induced asthma, a type of OA. Induced sputum cytology can confirm airway inflammation, but specific inhalation challenge is the reference standard diagnostic test. Inhalation challenges are relatively safe, with the most severe reactions occurring with low-molecular-weight agents. Indirect health care costs account for about 50% of total asthma costs. Workers with poor asthma control (WRA or non-WRA) are less likely to be employed. Income loss is a major contributor to the indirect costs of WRA. Overall, asthma outcomes probably are worse for adult-onset than for childhood-onset asthma but better for OA than adult-onset non-WRA. Important aspects of management of OA are rapid and proper confirmation of the diagnosis and reduction of exposure to sensitizers or irritants at work and home. PMID:26203621

Molecular Targeted Drugs and Biomarkers in NSCLC, the Evolving Role of Individualized Therapy

PubMed Central

Domvri, Kalliopi; Zarogoulidis, Paul; Darwiche, Kaid; Browning, Robert F.; Li, Qiang; Turner, J. Francis; Kioumis, Ioannis; Spyratos, Dionysios; Porpodis, Konstantinos; Papaiwannou, Antonis; Tsiouda, Theodora; Freitag, Lutz; Zarogoulidis, Konstantinos

2013-01-01

Lung cancer first line treatment has been directed from the non-specific cytotoxic doublet chemotherapy to the molecular targeted. The major limitation of the targeted therapies still remains the small number of patients positive to gene mutations. Furthermore, the differentiation between second line and maintenance therapy has not been fully clarified and differs in the clinical practice between cancer centers. The authors present a segregation between maintenance treatment and second line and present a possible definition for the term “maintenance” treatment. In addition, cancer cell evolution induces mutations and therefore either targeted therapies or non-specific chemotherapy drugs in many patients become ineffective. In the present work pathways such as epidermal growth factor, anaplastic lymphoma kinase, met proto-oncogene and PI3K are extensively presented and correlated with current chemotherapy treatment. Future, perspectives for targeted treatment are presented based on the current publications and ongoing clinical trials. PMID:24312144

Skeletal dosimetry models for alpha-particles for use in molecular radiotherapy

NASA Astrophysics Data System (ADS)

Watchman, Christopher J.

Molecular radiotherapy is a cancer treatment methodology whereby a radionuclide is combined with a biologically active molecule to preferentially target cancer cells. Alpha-particle emitting radionuclides show significant potential for use in molecular radiotherapy due to the short range of the alpha-particles in tissue and their high rates of energy deposition. Current radiation dosimetry models used to assess alpha emitter dose in the skeleton were developed originally for occupational applications. In medical dosimetry, individual variability in uptake, translocation and other biological factors can result in poor correlation of clinical outcome with marrow dose estimates determined using existing skeletal models. Methods presented in this work were developed in response to the need for dosimetry models which account for these biological and patient-specific factors. Dosimetry models are presented for trabecular bone alpha particle dosimetry as well as a model for cortical bone dosimetry. These radiation transport models are the 3D chord-based infinite spongiosa transport model (3D-CBIST) and the chord-based infinite cortical transport model (CBICT), respectively. Absorbed fraction data for several skeletal tissues for several subjects are presented. Each modeling strategy accounts for biological parameters, such as bone marrow cellularity, not previously incorporated into alpha-particle skeletal dosimetry models used in radiation protection. Using these data a study investigating the variability in alpha-particle absorbed fractions in the human skeleton is also presented. Data is also offered relating skeletal tissue masses in individual bone sites for a range of ages. These data are necessary for dose calculations and have previously only been available as whole body tissue masses. A revised 3D-CBIST model is also presented which allows for changes in endosteum thickness to account for revised target cell location of tissues involved in the radiological induction of bone cancer. In addition, new data are presented on the location of bone-marrow stem cells within the marrow cavities of trabecular bone of the pelvis. All results presented in this work may be applied to occupational exposures, but their greatest utility lies in dose assessments for alpha-emitters in molecular radiotherapy.

Rotation Detection Using the Precession of Molecular Electric Dipole Moment

NASA Astrophysics Data System (ADS)

Ke, Yi; Deng, Xiao-Bing; Hu, Zhong-Kun

2017-11-01

We present a method to detect the rotation by using the precession of molecular electric dipole moment in a static electric field. The molecular electric dipole moments are polarized under the static electric field and a nonzero electric polarization vector emerges in the molecular gas. A resonant radio-frequency pulse electric field is applied to realize a 90° flip of the electric polarization vector of a particular rotational state. After the pulse electric field, the electric polarization vector precesses under the static electric field. The rotation induces a shift in the precession frequency which is measured to deduce the angular velocity of the rotation. The fundamental sensitivity limit of this method is estimated. This work is only a proposal and does not involve experimental results.

Regulation of substituent groups on morphologies and self-assembly of organogels based on some azobenzene imide derivatives

NASA Astrophysics Data System (ADS)

Jiao, Tifeng; Wang, Yujin; Zhang, Qingrui; Zhou, Jingxin; Gao, Faming

2013-04-01

In this paper, new azobenzene imide derivatives with different substituent groups were designed and synthesized. Their gelation behaviors in 21 solvents were tested as novel low-molecular-mass organic gelators. It was shown that the alkyl substituent chains and headgroups of azobenzene residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle, lamella, and belt to fiber with the change of solvents. Spectral studies indicated that there existed different H-bond formations between amide groups and conformations of methyl chains. The present work may give some insight to the design and character of new organogelators and soft materials with special molecular structures.

Regulation of substituent groups on morphologies and self-assembly of organogels based on some azobenzene imide derivatives

PubMed Central

2013-01-01

In this paper, new azobenzene imide derivatives with different substituent groups were designed and synthesized. Their gelation behaviors in 21 solvents were tested as novel low-molecular-mass organic gelators. It was shown that the alkyl substituent chains and headgroups of azobenzene residues in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. More alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscopy and atomic force microscopy observations revealed that the gelator molecules self-assemble into different aggregates, from wrinkle, lamella, and belt to fiber with the change of solvents. Spectral studies indicated that there existed different H-bond formations between amide groups and conformations of methyl chains. The present work may give some insight to the design and character of new organogelators and soft materials with special molecular structures. PMID:23566628

Ethical issues in molecular medicine of relevance to surgeons

PubMed Central

Bernstein, Mark; Bampoe, Joseph; Daar, Abdallah S.

2004-01-01

The technology associated with the care of surgical patients and the level of sophistication of biomedical research accompanying it are evolving at a rapid pace. Both new and old bioethical issues are assuming increasing levels of prominence and importance, particularly in this age of molecular medicine. The authors explore bioethical issues pertinent and relevant to surgeons. Four specific areas that are exemplary by presenting both major scientific and ethical challenges are briefly addressed: privacy of information, stem cells, gene therapy, and conflict of interest in biomedical research. All of these can be generalized to all surgeons. As bioethical issues today play a greater role in surgical practice than they did even a decade ago, it is hoped that this brief review on ethical issues in molecular medicine will help stimulate present and future generations of surgeons in thinking about the ethical dimensions of their work. PMID:15646439

The importance of molecular analyses for understanding the genetic diversity of Histoplasma capsulatum: an overview.

PubMed

Vite-Garín, Tania; Estrada-Bárcenas, Daniel Alfonso; Cifuentes, Joaquín; Taylor, Maria Lucia

2014-01-01

Advances in the classification of the human pathogen Histoplasma capsulatum (H. capsulatum) (ascomycete) are sustained by the results of several genetic analyses that support the high diversity of this dimorphic fungus. The present mini-review highlights the great genetic plasticity of H. capsulatum. Important records with different molecular tools, mainly single- or multi-locus sequence analyses developed with this fungus, are discussed. Recent phylogenetic data with a multi-locus sequence analysis using 5 polymorphic loci support a new clade and/or phylogenetic species of H. capsulatum for the Americas, which was associated with fungal isolates obtained from the migratory bat Tadarida brasiliensis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Activity coefficients from molecular simulations using the OPAS method

NASA Astrophysics Data System (ADS)

Kohns, Maximilian; Horsch, Martin; Hasse, Hans

2017-10-01

A method for determining activity coefficients by molecular dynamics simulations is presented. It is an extension of the OPAS (osmotic pressure for the activity of the solvent) method in previous work for studying the solvent activity in electrolyte solutions. That method is extended here to study activities of all components in mixtures of molecular species. As an example, activity coefficients in liquid mixtures of water and methanol are calculated for 298.15 K and 323.15 K at 1 bar using molecular models from the literature. These dense and strongly interacting mixtures pose a significant challenge to existing methods for determining activity coefficients by molecular simulation. It is shown that the new method yields accurate results for the activity coefficients which are in agreement with results obtained with a thermodynamic integration technique. As the partial molar volumes are needed in the proposed method, the molar excess volume of the system water + methanol is also investigated.

Noncovalent Molecular Electronics.

PubMed

Gryn'ova, G; Corminboeuf, C

2018-05-03

Molecular electronics covers several distinctly different conducting architectures, including organic semiconductors and single-molecule junctions. The noncovalent interactions, abundant in the former, are also often found in the latter, i.e., the dimer junctions. In the present work, we draw the parallel between the two types of noncovalent molecular electronics for a range of π-conjugated heteroaromatic molecules. In silico modeling allows us to distill the factors that arise from the chemical nature of their building blocks and from their mutual arrangement. We find that the same compounds are consistently the worst and the best performers in the two types of electronic assemblies, emphasizing the universal imprint of the underlying chemistry of the molecular cores on their diverse charge transport characteristics. The interplay between molecular and intermolecular factors creates a spectrum of noncovalent conductive architectures, which can be manipulated using the design strategies based upon the established relationships between chemistry and transport.

Comparative Analysis of the Molecular Adjuvants and Their Binding Efficiency with CR1.

PubMed

Saranya, B; Saxena, Shweta; Saravanan, K M; Shakila, H

2016-03-01

There are so many obstacles in developing a vaccine or vaccine technology for diseases like cancer and human immunodeficiency virus infection. While developing vaccines that target specific infection, molecular adjuvants are indispensable. These molecular adjuvants act as a vaccine delivery vehicle to the immune system to increase the effectiveness of the specific antigens. In the present work, a computational study has been done on molecular adjuvants like IgGFc, GMCSF and C3d to find out how efficiently they are binding to CR1. Sequence, structure and mutational analysis are performed on the molecular adjuvants to understand the features important for their binding with the receptor. Results obtained from our study indicate that the adjuvant IgGFc complexed with the receptor CR1 has the best binding efficiency, which can be used further to develop better vaccine technologies.

Molecular ion battery: a rechargeable system without using any elemental ions as a charge carrier

PubMed Central

Yao, Masaru; Sano, Hikaru; Ando, Hisanori; Kiyobayashi, Tetsu

2015-01-01

Is it possible to exceed the lithium redox potential in electrochemical systems? It seems impossible to exceed the lithium potential because the redox potential of the elemental lithium is the lowest among all the elements, which contributes to the high voltage characteristics of the widely used lithium ion battery. However, it should be possible when we use a molecule-based ion which is not reduced even at the lithium potential in principle. Here we propose a new model system using a molecular electrolyte salt with polymer-based active materials in order to verify whether a molecular ion species serves as a charge carrier. Although the potential of the negative-electrode is not yet lower than that of lithium at present, this study reveals that a molecular ion can work as a charge carrier in a battery and the system is certainly a molecular ion-based “rocking chair” type battery. PMID:26043147

V-Shaped Molecular Configuration of Wax Esters of Jojoba Oil in a Langmuir Film Model.

PubMed

Caruso, Benjamín; Martini, M Florencia; Pickholz, Mónica; Perillo, María A

2018-06-19

The aim of the present work was to understand the interfacial properties of a complex mixture of wax esters (WEs) obtained from Jojoba oil (JO). Previously, on the basis of molecular area measurements, a hairpin structure was proposed as the hypothetical configuration of WEs, allowing their organization as compressible monolayers at the air-water interface. In the present work, we contributed with further experimental evidence by combining surface pressure (π), surface potential (Δ V), and PM-IRRAS measurements of JO monolayers and molecular dynamic simulations (MD) on a modified JO model. WEs were self-assembled in Langmuir films. Compression isotherms exhibited π lift-off at 100 Å 2 /molecule mean molecular area ( A lift-off ) and a collapse point at π c ≈ 2.2 mN/m and A c ≈ 77 Å 2 /molecule. The Δ V profile reflected two dipolar reorganizations, with one of them at A > A lift-off due to the release of loosely bound water molecules and another one at A c < A < A lift-off possibly due to reorientations of a more tightly bound water population. This was consistent with the maximal SP value that was calculated according to a model that considered two populations of oriented water and was very close to the experimental value. The orientation of the ester group that was assumed in that calculation was coherent with the PM-IRRAS behavior of the carbonyl group with the C═O oriented toward the water and the C-O oriented parallel to the surface and was in accordance with their orientational angles (∼45 and ∼90°, respectively) determined by MD simulations. Taken together, the present results confirm a V shape rather than a hairpin configuration of WEs at the air-water interface.

A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules.

PubMed

Martínez-Araya, Jorge I

2016-09-30

By means of the conceptual density functional theory, the so-called dual descriptor (DD) has been adapted to be used in any closed-shell molecule that presents degeneracy in its frontier molecular orbitals. The latter is of paramount importance because a correct description of local reactivity will allow to predict the most favorable sites on a molecule to undergo nucleophilic or electrophilic attacks; on the contrary, an incomplete description of local reactivity might have serio us consequences, particularly for those experimental chemists that have the need of getting an insight about reactivity of chemical reagents before using them in synthesis to obtain a new compound. In the present work, the old approach based only on electronic densities of frontier molecular orbitals is replaced by the most accurate procedure that implies the use of total electronic densities thus keeping consistency with the essential principle of the DFT in which the electronic density is the fundamental variable and not the molecular orbitals. As a result of the present work, the DD will be able to properly describe local reactivities only in terms of total electronic densities. To test the proposed operational formula, 12 very common molecules were selected as the original definition of the DD was not able to describe their local reactivities properly. The ethylene molecule was additionally used to test the capability of the proposed operational formula to reveal a correct local reactivity even in absence of degeneracy in frontier molecular orbitals. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

Biochemical and functional characterization of an albumin protein belonging to the hemopexin superfamily from Lens culinaris seeds.

PubMed

Scarafoni, Alessio; Gualtieri, Elisa; Barbiroli, Alberto; Carpen, Aristodemo; Negri, Armando; Duranti, Marcello

2011-09-14

The present paper reports the purification and biochemical characterization of an albumin identified in mature lentil seeds with high sequence similarity to pea PA2. These proteins are found in many edible seeds and are considered potentially detrimental for human health due to the potential allergenicity and lectin-like activity. Thus, the description of their possible presence in food and the assessment of the molecular properties are relevant. The M(r), pI, and N-terminal sequence of this protein have been determined. The work included the study of (i) the binding properties to hemine to assess the presence of hemopexin structural domains and (ii) the binding properties of the protein to thiamin. In addition, the structural changes induced by heating have been evaluated by means of spectroscopic techniques. Denaturation temperature has also been determined. The present work provides new insights about the structural molecular features and the ligand-binding properties and dynamics of this kind of seed albumin.

The impact of computer science in molecular medicine: enabling high-throughput research.

PubMed

de la Iglesia, Diana; García-Remesal, Miguel; de la Calle, Guillermo; Kulikowski, Casimir; Sanz, Ferran; Maojo, Víctor

2013-01-01

The Human Genome Project and the explosion of high-throughput data have transformed the areas of molecular and personalized medicine, which are producing a wide range of studies and experimental results and providing new insights for developing medical applications. Research in many interdisciplinary fields is resulting in data repositories and computational tools that support a wide diversity of tasks: genome sequencing, genome-wide association studies, analysis of genotype-phenotype interactions, drug toxicity and side effects assessment, prediction of protein interactions and diseases, development of computational models, biomarker discovery, and many others. The authors of the present paper have developed several inventories covering tools, initiatives and studies in different computational fields related to molecular medicine: medical informatics, bioinformatics, clinical informatics and nanoinformatics. With these inventories, created by mining the scientific literature, we have carried out several reviews of these fields, providing researchers with a useful framework to locate, discover, search and integrate resources. In this paper we present an analysis of the state-of-the-art as it relates to computational resources for molecular medicine, based on results compiled in our inventories, as well as results extracted from a systematic review of the literature and other scientific media. The present review is based on the impact of their related publications and the available data and software resources for molecular medicine. It aims to provide information that can be useful to support ongoing research and work to improve diagnostics and therapeutics based on molecular-level insights.

Molecular shear heating and vortex dynamics in thermostatted two dimensional Yukawa liquids

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

Gupta, Akanksha; Ganesh, Rajaraman, E-mail: ganesh@ipr.res.in; Joy, Ashwin

2016-07-15

It is well known that two-dimensional macroscale shear flows are susceptible to instabilities leading to macroscale vortical structures. The linear and nonlinear fate of such a macroscale flow in a strongly coupled medium is a fundamental problem. A popular example of a strongly coupled medium is a dusty plasma, often modelled as a Yukawa liquid. Recently, laboratory experiments and molecular dynamics (MD) studies of shear flows in strongly coupled Yukawa liquids indicated the occurrence of strong molecular shear heating, which is found to reduce the coupling strength exponentially leading to the destruction of macroscale vorticity. To understand the vortex dynamicsmore » of strongly coupled molecular fluids undergoing macroscale shear flows and molecular shear heating, MD simulation has been performed, which allows the macroscopic vortex dynamics to evolve, while at the same time “removes” the microscopically generated heat without using the velocity degrees of freedom. We demonstrate that by using a configurational thermostat in a novel way, the microscale heat generated by shear flow can be thermostatted out efficiently without compromising the large scale vortex dynamics. In the present work, using MD simulations, a comparative study of shear flow evolution in Yukawa liquids in the presence and absence of molecular or microscopic heating is presented for a prototype shear flow, namely, Kolmogorov flow.« less

Subset of Kappa and Lambda Germline Sequences Result in Light Chains with a Higher Molecular Mass Phenotype.

PubMed

Barnidge, David R; Lundström, Susanna L; Zhang, Bo; Dasari, Surendra; Murray, David L; Zubarev, Roman A

2015-12-04

In our previous work, we showed that electrospray ionization of intact polyclonal kappa and lambda light chains isolated from normal serum generates two distinct, Gaussian-shaped, molecular mass distributions representing the light-chain repertoire. During the analysis of a large (>100) patient sample set, we noticed a low-intensity molecular mass distribution with a mean of approximately 24 250 Da, roughly 800 Da higher than the mean of the typical kappa molecular-mass distribution mean of 23 450 Da. We also observed distinct clones in this region that did not appear to contain any typical post-translational modifications that would account for such a large mass shift. To determine the origin of the high molecular mass clones, we performed de novo bottom-up mass spectrometry on a purified IgM monoclonal light chain that had a calculated molecular mass of 24 275.03 Da. The entire sequence of the monoclonal light chain was determined using multienzyme digestion and de novo sequence-alignment software and was found to belong to the germline allele IGKV2-30. The alignment of kappa germline sequences revealed ten IGKV2 and one IGKV4 sequences that contained additional amino acids in their CDR1 region, creating the high-molecular-mass phenotype. We also performed an alignment of lambda germline sequences, which showed additional amino acids in the CDR2 region, and the FR3 region of functional germline sequences that result in a high-molecular-mass phenotype. The work presented here illustrates the ability of mass spectrometry to provide information on the diversity of light-chain molecular mass phenotypes in circulation, which reflects the germline sequences selected by the immunoglobulin-secreting B-cell population.

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies.

PubMed

Dries, Daniel R; Dean, Diane M; Listenberger, Laura L; Novak, Walter R P; Franzen, Margaret A; Craig, Paul A

2017-01-02

A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three-dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure-function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69-75, 2017. © 2016 The Authors Biochemistry and Molecular Biology Education published by Wiley Periodicals, Inc. on behalf of International Union of Biochemistry and Molecular Biology.

Identification of the Molecular Clockwork of the Oyster Crassostrea gigas

PubMed Central

Perrigault, Mickael; Tran, Damien

2017-01-01

Molecular clock system constitutes the origin of biological rhythms that allow organisms to anticipate cyclic environmental changes and adapt their behavior and physiology. Components of the molecular clock are largely conserved across a broad range of species but appreciable diversity in clock structure and function is also present especially in invertebrates. The present work aimed at identify and characterize molecular clockwork components in relationship with the monitoring of valve activity behavior in the oyster Crassostrea gigas. Results provided the characterization of most of canonical clock gene including clock, bmal/cycle, period, timeless, vertebrate-type cry, rev-erb, ror as well as other members of the cryptochrome/photolyase family (plant-like cry, 6–4 photolyase). Analyses of transcriptional variations of clock candidates in oysters exposed to light / dark regime and to constant darkness led to the generation of a putative and original clockwork model in C. gigas, intermediate of described systems in vertebrates and insects. This study is the first characterization of a mollusk clockwork. It constitutes essential bases to understand interactions of the different components of the molecular clock in C. gigas as well as the global mechanisms associated to the generation and the synchronization of biological rhythms in oysters. PMID:28072861

Visible light-harvesting photoanodes for solar energy conversion: A comparison of anchoring groups to titanium dioxide

NASA Astrophysics Data System (ADS)

Martini, Lauren A.

Environmental concerns related to climate change and geopolitical issues related to energy security have led to a widespread pursuit of alternative, non-fossil fuel energy sources capable of meeting our increasing global energy demands. Solar energy, which strikes the earth's surface at a rate vastly exceeding our current worldwide power demand, presents itself as a promising source of clean, abundant and renewable energy. The capture and conversion of solar energy into electricity as well as storable, transportable chemical fuels has therefore become major area of chemical research. Inspired by photosynthesis in nature, in which plants and algae convert sunlight, water, and carbon dioxide into oxygen and stored chemical fuel in the form of sugars, recent work has focused on visible light-driven water-splitting technologies for the production of solar fuels. Honda and Fujishima reported the first example of photoelectrochemical water oxidation in 1972. In their system, an inexpensive titanium dioxide semiconductor irradiated with ultraviolet light produced oxygen at the photoanode surface and hydrogen at the surface of a platinum counter electrode. In attempt to harness visible light instead, titanium dioxide and other inexpensive wide band gap photoanodes have been functionalized with visible light-absorbing molecular dyes. These dye-sensitized photoanodes have been used successfully to convert solar energy into electrical current, as in dye-sensitized solar cells, and to drive chemical processes like water oxidation, as in photocatalytic cells. In both systems, a long-lived charge separation is established upon illumination of the photoanode surface when a photoexcited molecular chromophore transfers an electron to the semiconductor conduction band. Following this electron injection process, a nearby redox-active species is oxidized and refills the hole left behind on the molecular chromophore. While the steps of this scheme are relatively straightforward, the integration of efficient visible-light absorption, ultrafast forward electron transfer, and stable charge separation is quite complicated. The work presented here is devoted to the design, synthesis, spectroscopy, and computational study of dye-sensitized photoanodes. In particular, we explore the relative stability and performance of different anchoring groups for the surface attachment of light-harvesting molecular dyes to titanium dioxide. Here we present the first systematic study that directly compares carboxylate, phosphonate, acetylacetonate, and hydroxamate anchors using the same molecular chromophore framework. We discuss a number of novel methods for the incorporation of anchoring group functionalities on each chromophore framework. We also assess the relative water stability of each of the anchoring groups on titanium dioxide as well as the relative efficiency of electron transfer from photoexcited molecular chromophores through each anchoring group into the conduction band of titanium dioxide. We hope that the work presented here will contribute to the rational design of better photoanodes for light-driven water splitting.

Single Spore Isolation as a Simple and Efficient Technique to obtain fungal pure culture

NASA Astrophysics Data System (ADS)

Noman, E.; Al-Gheethi, AA; Rahman, N. K.; Talip, B.; Mohamed, R.; H, N.; Kadir, O. A.

2018-04-01

The successful identification of fungi by phenotypic methods or molecular technique depends mainly on the using an advanced technique for purifying the isolates. The most efficient is the single spore technique due to the simple requirements and the efficiency in preventing the contamination by yeast, mites or bacteria. The method described in the present work is depends on the using of a light microscope to transfer one spore into a new culture medium. The present work describes a simple and efficient procedure for single spore isolation to purify of fungi recovered from the clinical wastes.

Molecular mechanisms of antibiotic resistance in Acinetobacter baumannii with a special focus on its epidemiology in Lebanon.

PubMed

Jamal, Sabah; Atrouni, Ahmad Al; Rafei, Rayane; Dabboussi, Fouad; Hamze, Monzer; Osman, Marwan

2018-05-30

Acinetobacter baumannii is an opportunistic bacterium involved in several types of infection with high mortality and morbidity, especially in intensive care units. Treatment of these infections remains a challenge due to the worldwide emergence of broad-spectrum resistance to many antibiotics. Following the implementation of molecular techniques to study A. baumannii outbreaks, it has been shown that they are mainly caused by specific clones like international clone 1, 2 and 3. The present work aims to review the available data on the mechanisms underlying the antimicrobial resistance in A. baumannii with a special focus on the molecular epidemiology of this species in Lebanon. Copyright © 2018. Published by Elsevier Ltd.

Synthesis and CV Studies of Dithiol-terminated Metal Terpyridine Complexes

NASA Technical Reports Server (NTRS)

Asano, Sylvia; Fan, Wendy; Ng, Hou-Tee; Han, Jie; Meyyappan, M.

2003-01-01

Transition metal coordination complexes possess unique electronic structures that should be a good model for studying electronic transport behavior at a molecular level. The discrete, multiple redox states, low redox potential and the superb ability to establish contact with other molecular and electronic components by coordination chemistry have made this a subject of investigation for their possible application as active electronic components in molecular devices. We present the synthesis and electrochemical characterization of 4'-thioacetylphenyl-2'2:6',2"-terpyridine iron(II) complex and compare it with a model bis-terpyridine iron(II) complex by cyclic voltammetry. With the use of different working electrodes, the behavior of these complexes show different electron transfer rates.

Molecular Detection of Chilo infuscatellus

PubMed Central

Wang, Weizhong; Wang, Rong; Zheng, Haotian; Gao, Sanji

2017-01-01

Abstract The Chilo infuscatellus (Snellen; Lepidoptera: Pyralidae) is the main pest of sugarcane in China. The shortage of easily distinguishable morphological characters especially in early stage make it challenging to diagnosed and promptly take steps for pest management. In the present study, we described a PCR method for the molecular identification of based on barcode region of COI sequences between C. infuscatellus and four other sugarcane borer species. A 285bp fragment was successfully amplified from all life stages and different geographical populations. Sensitivity tests revealed that diagnostic bands were generated as low as the DNA template concentration of 5 ng/µl. Our work demonstrated a rapid and accurate way for the molecular diagnosis of C. infuscatellus. PMID:29117377

Molecular dynamics approach to water structure of HII mesophase of monoolein

NASA Astrophysics Data System (ADS)

Kolev, Vesselin; Ivanova, Anela; Madjarova, Galia; Aserin, Abraham; Garti, Nissim

2012-02-01

The goal of the present work is to study theoretically the structure of water inside the water cylinder of the inverse hexagonal mesophase (HII) of glyceryl monooleate (monoolein, GMO), using the method of molecular dynamics. To simplify the computational model, a fixed structure of the GMO tube is maintained. The non-standard cylindrical geometry of the system required the development and application of a novel method for obtaining the starting distribution of water molecules. A predictor-corrector schema is employed for generation of the initial density of water. Molecular dynamics calculations are performed at constant volume and temperature (NVT ensemble) with 1D periodic boundary conditions applied. During the simulations the lipid structure is kept fixed, while the dynamics of water is unrestrained. Distribution of hydrogen bonds and density as well as radial distribution of water molecules across the water cylinder show the presence of water structure deep in the cylinder (about 6 Å below the GMO heads). The obtained results may help understanding the role of water structure in the processes of insertion of external molecules inside the GMO/water system. The present work has a semi-quantitative character and it should be considered as the initial stage of more comprehensive future theoretical studies.

Fast molecular shocks. I - Reformation of molecules behind a dissociative shock

NASA Technical Reports Server (NTRS)

Neufeld, David A.; Dalgarno, A.

1989-01-01

The physical and chemical processes that operate in the cooling gas behind a fast, dissociative, single-fluid shock propagating in a dense interstellar cloud are discussed. The treatment extends previous theoretical work on fast molecular shocks by including the effects of the conversion of Ly-alpha photons into radiation of the two-photon continuum and into H2 Lyman band emission lines, the effects of CO photodissociation following line absorption, and the formation and destruction of molecules containing the elements nitrogen, silicon, and sulphur, and of the complex hydrocarbons. Abundance profiles for the molecular species of interest are presented. After molecular hydrogen begins to reform, by means of gas phase and grain surface processes, the neutral species OH, H2O, O2, CO, CN, HCN, N2, NO, SO, and SiO reach substantial abundances. The molecular ions HeH(+), OH(+), SO(+), CH(+), H2(+), and H3(+), are produced while the gas is still hot and partially ionized. Emissions from them provide a possible diagnostic probe of fast molecular shocks.

Flexible bent rod model with a saturating induced dipole moment to study the electric linear dichroism of DNA fragments

NASA Astrophysics Data System (ADS)

Bertolotto, Jorge A.; Umazano, Juan P.

2016-06-01

In the present work we make a theoretical study of the steady state electric linear dichroism of DNA fragments in aqueous solution. The here developed theoretical approach considers a flexible bent rod model with a saturating induced dipole moment. The electric polarizability tensor of bent DNA fragments is calculated considering a phenomenological model which theoretical and experimental backgroung is presented here. The model has into account the electric polarizability longitudinal and transversal to the macroion. Molecular flexibility is described using an elastic potential. We consider DNA fragments originally bent with bending fluctuations around an average bending angle. The induced dipole moment is supposed constant once the electric field strength grows up at critical value. To calculate the reduced electric linear dichroism we determine the optical factor considering the basis of the bent DNA perpendicular to the molecular axis. The orientational distribution function has into account the anisotropic electric properties and the molecule flexibility. We applied the present theoretical background to fit electric dichroism experimental data of DNA fragments reported in the bibliography in a wide range of molecular weight and electric field. From these fits, values of DNA physical properties are estimated. We compare and discuss the results here obtained with the theoretical and experimental data presented by other authors. The original contributions of this work are: the inclusion of the transversal electric polarizability saturating with the electric field, the description of the electric properties with an electric polarizability tensor dependant on the bending angle and the use of an arc model originally bent.

Middle molecules and small-molecular-weight proteins in ESRD: properties and strategies for their removal.

PubMed

Clark, William R; Winchester, James F

2003-10-01

Molecular weight has traditionally been the parameter most commonly used to classify uremic toxins, with a value of approximately 500 Da frequently used as a demarcation point below which the molecular weights of small nitrogenous waste products fall. This toxin group, the most extensively studied from a clinical perspective, is characterized by a high degree of water solubility and the absence of protein binding. However, uremia is mediated by the retention of a plethora of other compounds having characteristics that differ significantly from those of the previously mentioned group. As opposed to the relative homogeneity of the nitrogenous metabolite class, other uremic toxins collectively are a very heterogeneous group, not only with respect to molecular weight but also other characteristics, such as protein binding and hydrophobicity. A recently proposed classification scheme by the European Uraemic Toxin Work Group subdivides the remainder of molecules into 2 categories: protein-bound solutes and middle molecules. For the latter group, the Work Group proposes a molecular weight range (500-60,000 Da) that incorporates many toxins identified since the original middle molecule hypothesis, for which the upper molecular weight limit was approximately 2,000 Da. In fact, low-molecular-weight peptides and proteins (LMWPs) comprise nearly the entire middle molecule category in the new scheme. The purpose of this article is to provide an overview of the middle molecule class of uremic toxins, with the focus on LMWPs. A brief review of LMWP metabolism under conditions of normal (and in a few cases, abnormal) renal function will be presented. The physical characteristics of several LMWPs will also be presented, including molecular weight, conformation, and charge. Specific LMWPs to be covered will include beta 2-microglobulin, complement proteins (C3a and Factor D), leptin, and proinflammatory cytokines. The article will also include a discussion of the treatment-related factors influencing dialytic removal of middle molecules. Once these factors, which include membrane characteristics, protein-membrane interactions, and solute removal mechanisms, are discussed, an overview of the different therapeutic strategies used to enhance clearance of these compounds is provided.

In silico modelling of thiazolidine derivatives with antioxidant potency: Models quantify the degree of contribution of molecular fragments towards the free radical scavenging ability

NASA Astrophysics Data System (ADS)

De, Biplab; Adhikari, Indrani; Nandy, Ashis; Saha, Achintya; Goswami, Binoy Behari

2017-06-01

Design and development of antioxidant supplements constitute an essential aspect of research in order to derive molecules that would help to combat the free radical invasion to the human body and curb oxidative stress related diseases. The present work deals with the development of in silico models for a series of thiazolidine derivatives having antioxidant potential. The objective of the work is to obtain models that would help to design new thazolidine derivatives based on substituent modification and thereby predict their activity profile. The QSAR model thus developed helps in quantification of the extent of contribution of the various molecular fragments towards the activity of the molecules, while the 3D pharmacophore model provides a brief idea of the essential molecular features that help the molecules to interact with the neighbouring free radicals. Both the models have been extensively validated which ensures their predictive ability as well the potential to search molecular databases for selection of thiazolidine derivatives with potent antioxidant activity. The models can thus be utilised effectively for database searching with the aim to isolate active antioxidants belonging to the thiazolidine group.

Molecular modeling of field-driven ion emission from ionic liquids

NASA Astrophysics Data System (ADS)

Zhang, Fei; He, Yadong; Qiao, Rui

2017-11-01

Traditionally, operating electrosprays in the purely ionic mode is challenging, but recent experiments confirmed that such operation can be achieved using room-temperature ionic liquids as working electrolytes. Such electrosprays have shown promise in applications including chemical analysis, nanomanufacturing, and space propulsion. The mechanistic and quantitative understanding of such electrosprays at the molecular level, however, remain limited at present. In this work, we simulated ion emission from EMIM-PF6 ionic liquid films using the molecular dynamics method. We show that, when the surface electric field is smaller than 1.5V/nm, the ion emission current predicted using coarse-grained ionic liquid model observes the classical scaling law by J. V. Iribarne and B. A. Thomson, i.e., ln(Je/ σ) En1/2. These simulations, however, cannot capture the co-emission of cations and anions from ionic liquid surface observed in some experiments. Such co-emission was successfully captured when united-atom models were adopted for the ionic liquids. By examining the co-emission events with picosecond, sub-angstrom resolution, we clarified the origins of the co-emission phenomenon and delineate the molecular events leading to ion emission.

A molecular quantum spin network controlled by a single qubit.

PubMed

Schlipf, Lukas; Oeckinghaus, Thomas; Xu, Kebiao; Dasari, Durga Bhaktavatsala Rao; Zappe, Andrea; de Oliveira, Felipe Fávaro; Kern, Bastian; Azarkh, Mykhailo; Drescher, Malte; Ternes, Markus; Kern, Klaus; Wrachtrup, Jörg; Finkler, Amit

2017-08-01

Scalable quantum technologies require an unprecedented combination of precision and complexity for designing stable structures of well-controllable quantum systems on the nanoscale. It is a challenging task to find a suitable elementary building block, of which a quantum network can be comprised in a scalable way. We present the working principle of such a basic unit, engineered using molecular chemistry, whose collective control and readout are executed using a nitrogen vacancy (NV) center in diamond. The basic unit we investigate is a synthetic polyproline with electron spins localized on attached molecular side groups separated by a few nanometers. We demonstrate the collective readout and coherent manipulation of very few (≤ 6) of these S = 1/2 electronic spin systems and access their direct dipolar coupling tensor. Our results show that it is feasible to use spin-labeled peptides as a resource for a molecular qubit-based network, while at the same time providing simple optical readout of single quantum states through NV magnetometry. This work lays the foundation for building arbitrary quantum networks using well-established chemistry methods, which has many applications ranging from mapping distances in single molecules to quantum information processing.

Behavioral response of Daphnia magna to silver salt and nanoparticle exposure

EPA Science Inventory

Endpoints in the investigation of the toxicity of metallic nanoparticles have varied from genetic and molecular through whole organism responses such as death and reproduction. The work presented here is an effort to quantify behavioral responses of Daphnia magna to exposure to s...

Molecular dynamics studies of a hexameric purine nucleoside phosphorylase.

PubMed

Zanchi, Fernando Berton; Caceres, Rafael Andrade; Stabeli, Rodrigo Guerino; de Azevedo, Walter Filgueira

2010-03-01

Purine nucleoside phosphorylase (PNP) (EC.2.4.2.1) is an enzyme that catalyzes the cleavage of N-ribosidic bonds of the purine ribonucleosides and 2-deoxyribonucleosides in the presence of inorganic orthophosphate as a second substrate. This enzyme is involved in purine-salvage pathway and has been proposed as a promising target for design and development of antimalarial and antibacterial drugs. Recent elucidation of the three-dimensional structure of PNP by X-ray protein crystallography left open the possibility of structure-based virtual screening initiatives in combination with molecular dynamics simulations focused on identification of potential new antimalarial drugs. Most of the previously published molecular dynamics simulations of PNP were carried out on human PNP, a trimeric PNP. The present article describes for the first time molecular dynamics simulations of hexameric PNP from Plasmodium falciparum (PfPNP). Two systems were simulated in the present work, PfPNP in ligand free form, and in complex with immucillin and sulfate. Based on the dynamical behavior of both systems the main results related to structural stability and protein-drug interactions are discussed.

Self-assembly of organogels via new luminol imide derivatives: diverse nanostructures and substituent chain effect

PubMed Central

2013-01-01

Luminol is considered as an efficient sycpstem in electrochemiluminescence (ECL) measurements for the detection of hydrogen peroxide. In this paper, new luminol imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 26 solvents were tested as novel low molecular mass organic gelators. It was shown that the length and number of alkyl substituent chains linked to a benzene ring in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. Longer alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscope and atomic force microscope observations revealed that the gelator molecules self-assemble into different micro/nanoscale aggregates from a dot, flower, belt, rod, and lamella to wrinkle with change of solvents. Spectral studies indicated that there existed different H-bond formations and hydrophobic forces, depending on the alkyl substituent chains in molecular skeletons. The present work may give some insight to the design and characteristic of new versatile soft materials and potential ECL biosensors with special molecular structures. PMID:23758979

Self-assembly of organogels via new luminol imide derivatives: diverse nanostructures and substituent chain effect

NASA Astrophysics Data System (ADS)

Jiao, Tifeng; Huang, Qinqin; Zhang, Qingrui; Xiao, Debao; Zhou, Jingxin; Gao, Faming

2013-06-01

Luminol is considered as an efficient sycpstem in electrochemiluminescence (ECL) measurements for the detection of hydrogen peroxide. In this paper, new luminol imide derivatives with different alkyl substituent chains were designed and synthesized. Their gelation behaviors in 26 solvents were tested as novel low molecular mass organic gelators. It was shown that the length and number of alkyl substituent chains linked to a benzene ring in gelators played a crucial role in the gelation behavior of all compounds in various organic solvents. Longer alkyl chains in molecular skeletons in present gelators are favorable for the gelation of organic solvents. Scanning electron microscope and atomic force microscope observations revealed that the gelator molecules self-assemble into different micro/nanoscale aggregates from a dot, flower, belt, rod, and lamella to wrinkle with change of solvents. Spectral studies indicated that there existed different H-bond formations and hydrophobic forces, depending on the alkyl substituent chains in molecular skeletons. The present work may give some insight to the design and characteristic of new versatile soft materials and potential ECL biosensors with special molecular structures.

Protecting High Energy Barriers: A New Equation to Regulate Boost Energy in Accelerated Molecular Dynamics Simulations.

PubMed

Sinko, William; de Oliveira, César Augusto F; Pierce, Levi C T; McCammon, J Andrew

2012-01-10

Molecular dynamics (MD) is one of the most common tools in computational chemistry. Recently, our group has employed accelerated molecular dynamics (aMD) to improve the conformational sampling over conventional molecular dynamics techniques. In the original aMD implementation, sampling is greatly improved by raising energy wells below a predefined energy level. Recently, our group presented an alternative aMD implementation where simulations are accelerated by lowering energy barriers of the potential energy surface. When coupled with thermodynamic integration simulations, this implementation showed very promising results. However, when applied to large systems, such as proteins, the simulation tends to be biased to high energy regions of the potential landscape. The reason for this behavior lies in the boost equation used since the highest energy barriers are dramatically more affected than the lower ones. To address this issue, in this work, we present a new boost equation that prevents oversampling of unfavorable high energy conformational states. The new boost potential provides not only better recovery of statistics throughout the simulation but also enhanced sampling of statistically relevant regions in explicit solvent MD simulations.

Superatom spectroscopy and the electronic state correlation between elements and isoelectronic molecular counterparts.

PubMed

Peppernick, Samuel J; Gunaratne, K D Dasitha; Castleman, A W

2010-01-19

Detailed in the present investigation are results pertaining to the photoelectron spectroscopy of negatively charged atomic ions and their isoelectronic molecular counterparts. Experiments utilizing the photoelectron imaging technique are performed on the negative ions of the group 10 noble metal block (i.e. Ni-, Pd-, and Pt-) of the periodic table at a photon energy of 2.33 eV (532 nm). The accessible electronic transitions, term energies, and orbital angular momentum components of the bound electronic states in the atom are then compared with photoelectron images collected for isoelectronic early transition metal heterogeneous diatomic molecules, M-X- (M = Ti,Zr,W; X = O or C). A superposition principle connecting the spectroscopy between the atomic and molecular species is observed, wherein the electronic structure of the diatomic is observed to mimic that present in the isoelectronic atom. The molecular ions studied in this work, TiO-, ZrO-, and WC- can then be interpreted as possessing superatomic electronic structures reminiscent of the isoelectronic elements appearing on the periodic table, thereby quantifying the superatom concept.

An orbital localization criterion based on the theory of "fuzzy" atoms.

PubMed

Alcoba, Diego R; Lain, Luis; Torre, Alicia; Bochicchio, Roberto C

2006-04-15

This work proposes a new procedure for localizing molecular and natural orbitals. The localization criterion presented here is based on the partitioning of the overlap matrix into atomic contributions within the theory of "fuzzy" atoms. Our approach has several advantages over other schemes: it is computationally inexpensive, preserves the sigma/pi-separability in planar systems and provides a straightforward interpretation of the resulting orbitals in terms of their localization indices and atomic occupancies. The corresponding algorithm has been implemented and its efficiency tested on selected molecular systems. (c) 2006 Wiley Periodicals, Inc.

Nanotechnology Presentation Agenda

NASA Technical Reports Server (NTRS)

2005-01-01

Working at the atomic, molecular and supra-molecular levels, in the length scale of approximately 1 - 100 nm range, in order to understand, create and use materials, devices and systems with fundamentally new properties and functions because of their small structure. NNI definition encourages new contributions that were not possible.before. Novel phenomena, properties and functions at nanoscale,which are non scalable outside of the nm domain. The ability to measure / control / manipulate matter at the nanoscale in order to change those properties and functions. Integration along length scales, and fields of application.

Investigations of the Formation of Molecular Hydrogen on Dust Grain Analogues

NASA Technical Reports Server (NTRS)

Vidali, Gianfranco; Roser, Joseph E.; Manico, Giulio; Pirronello, Valerio

2002-01-01

In the last four years we have been working to investigate the formation of molecular hydrogen on surfaces of materials of astrophysical interest, such as silicates, carbonaceous particles and ices, and in conditions approximating the ones present in a variety of astrophysical environments. Our experimental studies - the first of their kind and complemented with computer simulations and theoretical analyses - have given not only hydrogen recombination rates under different ISM conditions, but they have also offered new insights into this fundamental astrophysical problem. Here we summarize our experimental methods and most significant results.

Fast parallel molecular algorithms for DNA-based computation: factoring integers.

PubMed

Chang, Weng-Long; Guo, Minyi; Ho, Michael Shan-Hui

2005-06-01

The RSA public-key cryptosystem is an algorithm that converts input data to an unrecognizable encryption and converts the unrecognizable data back into its original decryption form. The security of the RSA public-key cryptosystem is based on the difficulty of factoring the product of two large prime numbers. This paper demonstrates to factor the product of two large prime numbers, and is a breakthrough in basic biological operations using a molecular computer. In order to achieve this, we propose three DNA-based algorithms for parallel subtractor, parallel comparator, and parallel modular arithmetic that formally verify our designed molecular solutions for factoring the product of two large prime numbers. Furthermore, this work indicates that the cryptosystems using public-key are perhaps insecure and also presents clear evidence of the ability of molecular computing to perform complicated mathematical operations.

How effective are simulated molecular-level experiments for teaching diffusion and osmosis?

PubMed

Meir, Eli; Perry, Judith; Stal, Derek; Maruca, Susan; Klopfer, Eric

2005-01-01

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger et al., 2001; and results herein). Students have deep-rooted misconceptions about how diffusion and osmosis work, especially at the molecular level. We hypothesized that this might be in part due to the inability to see and explore these processes at the molecular level. In order to investigate this, we developed new software, OsmoBeaker, which allows students to perform inquiry-based experiments at the molecular level. Here we show that these simulated laboratories do indeed teach diffusion and osmosis and help overcome some, but not all, student misconceptions.

How Effective Are Simulated Molecular-level Experiments for Teaching Diffusion and Osmosis?

PubMed Central

2005-01-01

Diffusion and osmosis are central concepts in biology, both at the cellular and organ levels. They are presented several times throughout most introductory biology textbooks (e.g., Freeman, 2002), yet both processes are often difficult for students to understand (Odom, 1995; Zuckerman, 1994; Sanger et al., 2001; and results herein). Students have deep-rooted misconceptions about how diffusion and osmosis work, especially at the molecular level. We hypothesized that this might be in part due to the inability to see and explore these processes at the molecular level. In order to investigate this, we developed new software, OsmoBeaker, which allows students to perform inquiry-based experiments at the molecular level. Here we show that these simulated laboratories do indeed teach diffusion and osmosis and help overcome some, but not all, student misconceptions. PMID:16220144

Ab Initio Simulation Beryllium in Solid Molecular Hydrogen: Elastic Constant

NASA Astrophysics Data System (ADS)

Guerrero, Carlo L.; Perlado, Jose M.

2016-03-01

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

Positron scattering from molecular hydrogen

NASA Astrophysics Data System (ADS)

Machacek, J. R.; Anderson, E. K.; Makochekanwa, C.; Buckman, S. J.; Sullivan, J. P.

2013-10-01

We present results for total and partial cross sections for positron scattering from H2. The total scattering and positronium formation cross sections are reported between 0.5 and 200 eV. Total quasielastic and inelastic scattering cross sections are reported for energies between the positronium formation threshold and 50 eV, with quasielastic differential scattering cross sections reported at 1, 3, 5, 7, and 10 eV. Our results are compared with previous work, both experimental and theoretical, with particular attention paid to the region below the positronium formation threshold, where there are apparent discrepancies in previous work. A discussion of possible reasons for discrepancies between this and previous work is presented, including a focus on known systematic effects in the experimental results.

Post-exercise ingestion of a unique, high molecular weight glucose polymer solution improves performance during a subsequent bout of cycling exercise.

PubMed

Stephens, Francis B; Roig, Marc; Armstrong, Gerald; Greenhaff, Paul L

2008-01-15

The aim of the present study was to determine the effect of post-exercise ingestion of a unique, high molecular weight glucose polymer solution, known to augment gastric emptying and post-exercise muscle glycogen re-synthesis, on performance during a subsequent bout of intense exercise. On three randomized visits, eight healthy men cycled to exhaustion at 73.0% (s = 1.3) maximal oxygen uptake (90 min, s = 15). Immediately after this, participants consumed a one-litre solution containing sugar-free flavoured water (control), 100 g of a low molecular weight glucose polymer or 100 g of a very high molecular weight glucose polymer, and rested on a bed for 2 h. After recovery, a 15-min time-trial was performed on a cycle ergometer, during which work output was determined. Post-exercise ingestion of the very high molecular weight glucose polymer solution resulted in faster and greater increases in blood glucose (P < 0.001) and serum insulin (P < 0.01) concentrations than the low molecular weight glucose polymer solution, and greater work output during the 15-min time-trial (164.1 kJ, s = 21.1) than both the sugar-free flavoured water (137.5 kJ, s = 24.2; P < 0.05) and the low molecular weight glucose polymer (149.4 kJ, s = 21.8; P < 0.05) solutions. These findings could be of practical importance for athletes wishing to optimize performance by facilitating rapid re-synthesis of the muscle glycogen store during recovery following prolonged sub-maximal exercise.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure.

PubMed

Chang, Wendi; Akselrod, Gleb M; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole-dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopant molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole-dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole-dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.

Solid-State Solvation and Enhanced Exciton Diffusion in Doped Organic Thin Films under Mechanical Pressure

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

Chang, Wendi; Akselrod, Gleb M.; Bulović, Vladimir

2015-04-28

Direct modification of exciton energy has been previously used to optimize the operation of organic optoelectronic devices. One demonstrated method for exciton energy modification is through the use of the solvent dielectric effects in doped molecular films. To gain a deeper appreciation of the underlying physical mechanisms, in this work we test the solid-state solvation effect in molecular thin films under applied external pressure. We observe that external mechanical pressure increases dipole–dipole interactions, leading to shifts in the Frenkel exciton energy and enhancement of the time-resolved spectral red shift associated with the energy-transfer-mediated exciton diffusion. Measurements are performed on host:dopantmore » molecular thin films, which show bathochromic shifts in photoluminescence (PL) under increasing pressure. This is in agreement with a simple solvation theory model of exciton energetics with a fitting parameter based on the mechanical properties of the host matrix material. We measure no significant change in exciton lifetime with increasing pressure, consistent with unchanged aggregation in molecular films under compression. However, we do observe an increase in exciton spectral thermalization rate for compressed molecular films, indicating enhanced exciton diffusion for increased dipole–dipole interactions under pressure. The results highlight the contrast between molecular energy landscapes obtained when dipole–dipole interactions are increased by the pressure technique versus the conventional dopant concentration variation methods, which can lead to extraneous effects such as aggregation at higher doping concentrations. The present work demonstrates the use of pressure-probing techniques in studying energy disorder and exciton dynamics in amorphous molecular thin films.« less

VizieR Online Data Catalog: NGC 3503 YSO candidates (Duronea+, 2014)

NASA Astrophysics Data System (ADS)

Duronea, N. U.; Vasquez, J.; Romero, G. A.; Cappa, C. E.; Barba, R.; Bronfman, L.

2014-07-01

The molecular observations presented in this paper were made during October 2011, with APEX at Llano de Chajnantor (Chilean Andes). In this work we use unpublished images of ATLASGAL at 870um (345GHz) (Schuller et al. 2009A&A...504..415S). (2 data files).

Molecular Dynamics Studies of Proton Transport in Hydrogenase and Hydrogenase Mimics.

PubMed

Ginovska, B; Raugei, S; Shaw, W J

2016-01-01

There is extensive interest in hydrogenases based on their ability to rapidly and efficiently interconvert H2 with protons and electrons, and their (typically) superior function relative to molecular mimics. Understanding the function of enzymes is one approach to implementing design features to make better catalysts and is an approach we have implemented in our work. In this review, we will discuss our efforts to develop design principles from enzymes, with specific focus on proton transport. We will also present computational studies of the mimics we have investigated with similar methodologies. We will discuss the mechanisms used by small scaffolds on molecular mimics which in many cases are surprisingly similar to those used by nature, while in other cases, computational analysis allowed us to reveal an unexpected role. Computational methods provide one of the best ways, and in some cases, the only way, to gain insight into the mechanistic details of enzymes. In this review, we illustrate the general computational strategy we used to study the proton pathway of [FeFe]-hydrogenase, and the similar strategy to investigate small molecules. We present the main results we obtained and how our computational work stimulated or worked in concert with experimental investigations. We also focus on estimation of errors and convergence of properties in the simulations. These studies demonstrate the powerful results that can be obtained by the close pairing of experimental and theoretical approaches. Copyright © 2016 Elsevier Inc. All rights reserved. Battelle, operator of PNNL, under Contract No: DE-AC05-76RL01830 with US DoE.

Molecular investigations of β-thalassemic children in Erbil governorate

NASA Astrophysics Data System (ADS)

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

2017-09-01

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

PETROLEUM RESIDUA SOLUBILITY PARAMETER/POLARITY MAP: STABILITY STUDIES OF RESIDUA PYROLYSIS

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

John F. Schabron; A. Troy Pauli; Joseph F. Rovani, Jr.

1999-04-30

A new molecular weight/polarity map based on the Scatchard-Hildebrand solubility equation has been developed for petroleum residua. A series of extractions are performed with solvents of increasing solubility parameter, and the fractions are analyzed by vapor pressure osmometry for number average molecular weight and by analytical-scale size exclusion chromatography for molecular weight spread. Work was performed for a heavy oil material subjected to three increasing severities of thermal treatment prior to and through the onset of coke formation. The results are diagnostic of the layers of solvations by resin-type molecules around a central asphaltene core. Two additional stability diagnostic methodsmore » were also used. These were the Heithaus titration ''P-index'' and Gaestel ''G'' index, which have been applied to paving asphalts for decades. The Heithaus titration involves the titration of three toluene solutions of a residuum at three concentrations with a poor solvent, such as isooctane, to the point of asphaltene flocculation. In the present work, the significance of the data are developed in terms of the Hildebrand solubility parameter. The Heithaus results are combined with data from the new molecular weight/polarity map. The solubility parameters for the toluene-soluble asphaltene components are measured, and the solubility parameters of the maltenes can be calculated. As thermal treatment progresses, the solubility parameters of asphaltene materials increase and the molecular weights decrease. A new coking index is proposed based on Heithaus titration data. Preliminary results suggest that an alternative, simpler coking index may be developed by measuring the weight percent of cyclohexane solubles in heptane asphaltenes. Coking onset appears to coincide with the depletion of these resin-type asphaltene solubilizing components of residua. The objective of the present study was to develop a mapping tool that will enhance understanding of the changes that occur in residua during upgrading and support the industry-sponsored work in which Western Research Institute is engaged. WRI performs proprietary industry-sponsored residua and heavy oil upgrading process development and optimization research. The new mapping tool can be used for evaluating heavy oils and residua in both upstream and downstream operations.« less

Investigation and reduction of sub-microgram peptide loss using molecular weight cut-off fractionation prior to mass spectrometric analysis

PubMed Central

Cunningham, Robert; Wang, Jingxin; Wellner, Daniel; Li, Lingjun

2013-01-01

This work investigates the suitability of molecular weight cut-off membrane-based centrifugal filter devices (MWCO) for sub-microgram peptide enrichment passing through the membrane by introduction of methanol and a salt modifier. Using a neuropeptide standard, bradykinin, a reduction in sample loss of over two orders of magnitude is demonstrated with and without undigested protein present. Additionally, a bovine serum albumin (BSA) tryptic digestion was investigated and 27 tryptic peptides were identified using MALDI mass spectrometry whereas only two BSA tryptic peptides were identified after MWCO separation using H2O. The protocol presented here enhances recovery from MWCO separation for sub-μg peptide samples. PMID:23019164

Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching

NASA Astrophysics Data System (ADS)

Engstrom, James R.; Kummel, Andrew C.

2017-02-01

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

Preface: Special Topic on Atomic and Molecular Layer Processing: Deposition, Patterning, and Etching.

PubMed

Engstrom, James R; Kummel, Andrew C

2017-02-07

Thin film processing technologies that promise atomic and molecular scale control have received increasing interest in the past several years, as traditional methods for fabrication begin to reach their fundamental limits. Many of these technologies involve at their heart phenomena occurring at or near surfaces, including adsorption, gas-surface reactions, diffusion, desorption, and re-organization of near-surface layers. Moreover many of these phenomena involve not just reactions occurring under conditions of local thermodynamic equilibrium but also the action of energetic species including electrons, ions, and hyperthermal neutrals. There is a rich landscape of atomic and molecular scale interactions occurring in these systems that is still not well understood. In this Special Topic Issue of The Journal of Chemical Physics, we have collected recent representative examples of work that is directed at unraveling the mechanistic details concerning atomic and molecular layer processing, which will provide an important framework from which these fields can continue to develop. These studies range from the application of theory and computation to these systems to the use of powerful experimental probes, such as X-ray synchrotron radiation, probe microscopies, and photoelectron and infrared spectroscopies. The work presented here helps in identifying some of the major challenges and direct future activities in this exciting area of research involving atomic and molecular layer manipulation and fabrication.

Structural analysis, molecular docking and molecular dynamics of an edematogenic lectin from Centrolobium microchaete seeds.

PubMed

Neco, Antonio Hadson Bastos; Pinto-Junior, Vanir Reis; Araripe, David Alencar; Santiago, Mayara Queiroz; Osterne, Vinicius Jose Silva; Lossio, Claudia Figueiredo; Nobre, Clareane Avelino Simplicio; Oliveira, Messias Vital; Silva, Mayara Torquato Lima; Martins, Maria Gleiciane Queiroz; Cajazeiras, Joao Batista; Marques, Gabriela Fernandes Oliveira; Costa, Diego Rabelo; Nascimento, Kyria Santiago; Assreuy, Ana Maria Sampaio; Cavada, Benildo Sousa

2018-05-24

Lectins represent a class of proteins or glycoproteins capable of reversibly binding to carbohydrates. Seed lectins from the Dalbergieae tribe (Leguminosae) have structural variability, carbohydrate specificity, and biological effects, such as inflammation, vasorelaxation and cancer antigen binding. To comprehensively address these factors, the present work aimed to establish and characterize the three-dimensional structure of Centrolobium microchaete lectin (CML) by homology modeling, investigate protein-carbohydrate interactions and evaluate its inflammatory effect on mice. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and N-glycans. Two dimannosides, methyl mannose-1,3-α-D-mannose (MDM) and mannose-1,3-α-D-mannose (M13), were used in molecular dynamics (MD) simulations to study the behavior of the carbohydrate-recognition domain (CRD) over time. Results showed an expanded domain within which hydrophobic interactions with the methyl group in the MDM molecule were established, thus revealing novel interactions for mannose-specific Dalbergieae lectins. To examine its biological activities, CML was purified in a single step by affinity chromatography on Sepharose-mannose matrix. The lectin demonstrated inflammatory response in the paw edema model and stimulated leukocyte migration to the animal peritoneal cavities, an effect elicited by CRD. For the first time, this work reports the molecular dynamics of a lectin from the Dalbergieae tribe. Copyright © 2018 Elsevier B.V. All rights reserved.

Improved Infrastucture for Cdms and JPL Molecular Spectroscopy Catalogues

NASA Astrophysics Data System (ADS)

Endres, Christian; Schlemmer, Stephan; Drouin, Brian; Pearson, John; Müller, Holger S. P.; Schilke, P.; Stutzki, Jürgen

2014-06-01

Over the past years a new infrastructure for atomic and molecular databases has been developed within the framework of the Virtual Atomic and Molecular Data Centre (VAMDC). Standards for the representation of atomic and molecular data as well as a set of protocols have been established which allow now to retrieve data from various databases through one portal and to combine the data easily. Apart from spectroscopic databases such as the Cologne Database for Molecular Spectroscopy (CDMS), the Jet Propulsion Laboratory microwave, millimeter and submillimeter spectral line catalogue (JPL) and the HITRAN database, various databases on molecular collisions (BASECOL, KIDA) and reactions (UMIST) are connected. Together with other groups within the VAMDC consortium we are working on common user tools to simplify the access for new customers and to tailor data requests for users with specified needs. This comprises in particular tools to support the analysis of complex observational data obtained with the ALMA telescope. In this presentation requests to CDMS and JPL will be used to explain the basic concepts and the tools which are provided by VAMDC. In addition a new portal to CDMS will be presented which has a number of new features, in particular meaningful quantum numbers, references linked to data points, access to state energies and improved documentation. Fit files are accessible for download and queries to other databases are possible.

pH-Induced Modulation of One- and Two-Photon Absorption Properties in a Naphthalene-Based Molecular Probe.

PubMed

Murugan, N Arul; Kongsted, Jacob; Ågren, Hans

2013-08-13

Presently, there is a great demand for small probe molecules that can be used for two-photon excitation microscopy (TPM)-based monitoring of intracellular and intraorganelle activity and pH. The candidate molecules should ideally possess a large two-photon absorption cross section with optical properties sensitive to pH changes. In the present work, we investigate the potential of a methoxy napthalene (MONAP) derivative for its suitability to serve as a pH sensor using TPM. Using an integrated approach rooted in hybrid quantum mechanics/molecular mechanics, the structures, dynamics, and the one- and two-photon properties of the probe in dimethylformamide solvent are studied. It is found that the protonated form is responsible for the optical property of MONAP at moderately low pH, for which the calculated pH-induced red shift is in good agreement with experiments. A 2-fold increase in the two-photon absorption cross section in the IR region of the spectrum is predicted for the moderately low pH form of the probe, suggesting that this can be a potential probe for pH monitoring of living cells. We also propose some design principles aimed at obtaining control of the absorption spectral range of the probe by structural tuning. Our work indicates that the integrated approach employed is capable of capturing the pH-induced changes in structure and optical properties of organic molecular probes and that such in silico tools can be used to draw structure-property relationships to design novel molecular probes suitable for a specific application.

Molecularly Imprinted Microrods via Mesophase Polymerization.

PubMed

Parisi, Ortensia Ilaria; Scrivano, Luca; Candamano, Sebastiano; Ruffo, Mariarosa; Vattimo, Anna Francesca; Spanedda, Maria Vittoria; Puoci, Francesco

2017-12-28

The aim of the present research work was the synthesis of molecularly imprinted polymers (MIPs) with a rod-like geometry via "mesophase polymerization". The ternary lyotropic system consisting of sodium dodecyl sulfate (SDS), water, and decanol was chosen to prepare a hexagonal mesophase to direct the morphology of the synthesized imprinted polymers using theophylline, methacrylic acid, and ethylene glycol dimethacrylate as a drug model template, a functional monomer, and a crosslinker, respectively. The obtained molecularly imprinted microrods (MIMs) were assessed by performing binding experiments and in vitro release studies, and the obtained results highlighted good selective recognition abilities and sustained release properties. In conclusion, the adopted synthetic strategy involving a lyotropic mesophase system allows for the preparation of effective MIPs characterized by a rod-like morphology.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program

NASA Astrophysics Data System (ADS)

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A.

2017-12-01

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

Optimization and benchmarking of a perturbative Metropolis Monte Carlo quantum mechanics/molecular mechanics program.

PubMed

Feldt, Jonas; Miranda, Sebastião; Pratas, Frederico; Roma, Nuno; Tomás, Pedro; Mata, Ricardo A

2017-12-28

In this work, we present an optimized perturbative quantum mechanics/molecular mechanics (QM/MM) method for use in Metropolis Monte Carlo simulations. The model adopted is particularly tailored for the simulation of molecular systems in solution but can be readily extended to other applications, such as catalysis in enzymatic environments. The electrostatic coupling between the QM and MM systems is simplified by applying perturbation theory to estimate the energy changes caused by a movement in the MM system. This approximation, together with the effective use of GPU acceleration, leads to a negligible added computational cost for the sampling of the environment. Benchmark calculations are carried out to evaluate the impact of the approximations applied and the overall computational performance.

A Framework for Globular Proteins

NASA Astrophysics Data System (ADS)

Lezon, Timothy

2006-03-01

Due to their remarkable chemical specificity and diversity, globular proteins play a crucial role in the network of molecular interactions of life. Over the past several decades, much experimental data has been accumulated on proteins, but the overarching principles that govern the general features of proteins remain largely unknown. Here, a novel framework for understanding many key attributes of globular proteins is presented. This framework suggests that the characteristics of globular proteins that make them well-suited for biological function are the emergent properties of a unique phase of matter. Implications of this picture include the provision of a fixed backdrop for molecular evolution and natural selection and design restrictions on molecular machinery. The work described here was carried out in collaboration with Jayanth Banavar and Amos Maritan.

[Changes in molecular forms of sex hormone binding globulin during menstrual cycle and menopause].

PubMed

Fonseca, M E; Masón, M; Ochoa, R; Hernández-V, M; Zárate, A

1996-11-01

Sex hormone binding globulin (SHBG) is a glycoprotein that transports mainly androgens and estrogens regulating the amount of free and bound hormone which in turn plays a role in the metabolic balance. It is also known that estrogens increase the hepatic production of SHBG which circulates in various molecular forms containing different amounts of sialic acid as the main component of carbohydrates. In the present work we studied physiological variations of molecular forms of SHBG during the normal menstrual cycle and the menopause. During the follicular phase the form 54 KD was the predominant variant, in the periovulatory period was isomers 90 KD, and during the luteal phase corresponded to both 54 and 90 KD. In the menopause dimeric form of 90 KD corresponded to the major proportion and was present a higher molecular forms of 115-135 KD. Following estrogen therapy the chromatographic profile changed as to that observed during the menstrual cycle. Important changes in the proportion of sialic acid were observed in each of the phases of menstrual cycle and following estrogen replacement. And increase in the amount of sialic acid corresponded to higher estrogen concentrations. It is concluded that SHBG concentrations varies during the menstrual cycle according the estrogen levels which in addition regulates the proportion of molecular forms and sialic acid containt.

The integrity of welded interfaces in ultra-high molecular weight polyethylene: Part 2--interface toughness.

PubMed

Haughie, David W; Buckley, C Paul; Wu, Junjie

2006-07-01

In Part 2 of a study of welding of ultra-high molecular weight polyethylene (UHMWPE), experiments were conducted to measure the interfacial fracture energy of butt welds, for various welding times and temperatures above the melting point. Their toughness was investigated at 37 degrees C in terms of their fracture energy, obtained by adapting the essential work of fracture (EWF) method. However, a proportion of the welded samples (generally decreasing with increasing welding time or temperature) failed in dual ductile/brittle mode, hence invalidating the EWF test. Even those failing in purely ductile mode showed a measurable interface work of fracture only for the highest weld temperature and time: 188 degrees C and 90 min. Results from the model presented in Part 1 show that this corresponds to the maximum reptated molecular weight reaching close to the peak in the molar mass distribution. Hence this work provides the first experimental evidence that the slow rate of self-diffusion in UHMWPE leads to welded interfaces acting as low-toughness crack paths. Since such interfaces exist around every powder particle in processed UHMWPE this problem cannot be avoided, and it must be accommodated in design of hip and knee bearing surfaces made from this polymer.

Examining the Self-Assembly of Rod-Coil Block Copolymers via Physics Based Polymer Models and Polarized X-Ray Scattering

NASA Astrophysics Data System (ADS)

Hannon, Adam; Sunday, Daniel; Windover, Donald; Liman, Christopher; Bowen, Alec; Khaira, Gurdaman; de Pablo, Juan; Delongchamp, Dean; Kline, R. Joseph

Photovoltaics, flexible electronics, and stimuli-responsive materials all require enhanced methodology to examine their nanoscale molecular orientation. The mechanical, electronic, optical, and transport properties of devices made from these materials are all a function of this orientation. The polymer chains in these materials are best modeled as semi-flexible to rigid rods. Characterizing the rigidity and molecular orientation of these polymers non-invasively is currently being pursued by using polarized resonant soft X-ray scattering (P-RSoXS). In this presentation, we show recent work on implementing such a characterization process using a rod-coil block copolymer system in the rigid-rod limit. We first demonstrate how we have used physics based models such as self-consistent field theory (SCFT) in non-polarized RSoXS work to fit scattering profiles for thin film coil-coil PS- b-PMMA block copolymer systems. We then show by using a wormlike chain partition function in the SCFT formulism to model the rigid-rod block, the methodology can be used there as well to extract the molecular orientation of the rod block from a simulated P-RSoXS experiment. The results from the work show the potential of the technique to extract thermodynamic and morphological sample information.

Structure and atomic correlations in molecular systems probed by XAS reverse Monte Carlo refinement

NASA Astrophysics Data System (ADS)

Di Cicco, Andrea; Iesari, Fabio; Trapananti, Angela; D'Angelo, Paola; Filipponi, Adriano

2018-03-01

The Reverse Monte Carlo (RMC) algorithm for structure refinement has been applied to x-ray absorption spectroscopy (XAS) multiple-edge data sets for six gas phase molecular systems (SnI2, CdI2, BBr3, GaI3, GeBr4, GeI4). Sets of thousands of molecular replicas were involved in the refinement process, driven by the XAS data and constrained by available electron diffraction results. The equilibrated configurations were analysed to determine the average tridimensional structure and obtain reliable bond and bond-angle distributions. Detectable deviations from Gaussian models were found in some cases. This work shows that a RMC refinement of XAS data is able to provide geometrical models for molecular structures compatible with present experimental evidence. The validation of this approach on simple molecular systems is particularly important in view of its possible simple extension to more complex and extended systems including metal-organic complexes, biomolecules, or nanocrystalline systems.

MAIN software for density averaging, model building, structure refinement and validation

PubMed Central

Turk, Dušan

2013-01-01

MAIN is software that has been designed to interactively perform the complex tasks of macromolecular crystal structure determination and validation. Using MAIN, it is possible to perform density modification, manual and semi-automated or automated model building and rebuilding, real- and reciprocal-space structure optimization and refinement, map calculations and various types of molecular structure validation. The prompt availability of various analytical tools and the immediate visualization of molecular and map objects allow a user to efficiently progress towards the completed refined structure. The extraordinary depth perception of molecular objects in three dimensions that is provided by MAIN is achieved by the clarity and contrast of colours and the smooth rotation of the displayed objects. MAIN allows simultaneous work on several molecular models and various crystal forms. The strength of MAIN lies in its manipulation of averaged density maps and molecular models when noncrystallographic symmetry (NCS) is present. Using MAIN, it is possible to optimize NCS parameters and envelopes and to refine the structure in single or multiple crystal forms. PMID:23897458

Dissipation dynamics of field-free molecular alignment for symmetric-top molecules: Ethane (C2H6)

NASA Astrophysics Data System (ADS)

Zhang, H.; Billard, F.; Yu, X.; Faucher, O.; Lavorel, B.

2018-03-01

The field-free molecular alignment of symmetric-top molecules, ethane, induced by intense non-resonant linearly polarized femtosecond laser pulses is investigated experimentally in the presence of collisional relaxation. The dissipation dynamics of field-free molecular alignment are measured by the balanced detection of ultrafast molecular birefringence of ethane gas samples at high pressures. By separating the molecular alignment into the permanent alignment and the transient alignment, the decay time-constants of both components are quantified at the same pressure. It is observed that the permanent alignment always decays slower compared to the transient alignment within the measured pressure range. This demonstrates that the propensity of molecules to conserve the orientation of angular momentum during collisions, previously observed for linear species, is also applicable to symmetric-top molecules. The results of this work provide valuable information for further theoretical understanding of collisional relaxation within nonlinear polyatomic molecules, which are expected to present interesting and nontrivial features due to an extra rotational degree of freedom.

Simulation of the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin foils

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

Barriga-Carrasco, Manuel D.; Garcia-Molina, Rafael

2004-09-01

This work presents the results of computer simulations for the energy spectra of original versus recombined H{sub 2}{sup +} molecular ions transmitted through thin amorphous carbon foils, for a broad range of incident energies. A detailed description of the projectile motion through the target has been done, including nuclear scattering and Coulomb repulsion as well as electronic self-retarding and wake forces; the two latter are calculated in the dielectric formalism framework. Differences in the energy spectra of recombined and original transmitted H{sub 2}{sup +} molecular ions clearly appear in the simulations, in agreement with the available experimental data. Our simulationmore » code also differentiates the contributions due to original and to recombined H{sub 2}{sup +} molecular ions when the energy spectra contain both contributions, a feature that could be used for experimental purposes in estimating the ratio between the number of original and recombined H{sub 2}{sup +} molecular ions transmitted through thin foils.« less

Oxidation of Carbon Nanotubes in an Ionizing Environment.

PubMed

Koh, Ai Leen; Gidcumb, Emily; Zhou, Otto; Sinclair, Robert

2016-02-10

In this work, we present systematic studies on how an illuminating electron beam which ionizes molecular gas species can influence the mechanism of carbon nanotube oxidation in an environmental transmission electron microscope (ETEM). We found that preferential attack of the nanotube tips is much more prevalent than for oxidation in a molecular gas environment. We establish the cumulative electron doses required to damage carbon nanotubes from 80 keV electron beam irradiation in gas versus in high vacuum. Our results provide guidelines for the electron doses required to study carbon nanotubes within or without a gas environment, to determine or ameliorate the influence of the imaging electron beam. This work has important implications for in situ studies as well as for the oxidation of carbon nanotubes in an ionizing environment such as that occurring during field emission.

Pyrene functionalized molecular beacon with pH-sensitive i-motif in a loop.

PubMed

Dembska, Anna; Juskowiak, Bernard

2015-01-01

In this work, we present a spectral characterization of pH-sensitive system, which combines the i-motif properties with the spatially sensitive fluorescence signal of pyrene molecules attached to hairpin ends. The excimer production (fluorescence max. ∼480 nm) by pyrene labels at the ends of the molecular beacon is driven by pH-dependent i-motif formation in the loop. To illustrate the performance and reversible work of our systems, we performed the experiments with repeatedly pH cycling between pH values of 7.5±0.3 and 6.5±0.3. The sensor gives analytical response in excimer-monomer switching mode in narrow pH range (1.5 pH units) and exhibits high pH resolution (0.1 pH unit). Copyright © 2015 Elsevier B.V. All rights reserved.

4-Mercaptophenylboronic acid: conformation, FT-IR, Raman, OH stretching and theoretical studies.

PubMed

Parlak, Cemal; Ramasami, Ponnadurai; Tursun, Mahir; Rhyman, Lydia; Kaya, Mehmet Fatih; Atar, Necip; Alver, Özgür; Şenyel, Mustafa

2015-06-05

4-Mercaptophenylboronic acid (4-mpba, C6H7BO2S) was investigated experimentally by vibrational spectroscopy. The molecular structure and spectroscopic parameters were studied by computational methods. The molecular dimer was investigated for intermolecular hydrogen bonding. Potential energy distribution analysis of normal modes was performed to identify characteristic frequencies. The present work provides a simple physical picture of the OH stretch vibrational spectra of 4-mpba and analogues of the compound studied. When the different computational methods are compared, there is a strong evidence of the better performance of the BLYP functional than the popular B3LYP functional to describe hydrogen bonding in the dimer. The findings of this research work should be useful to experimentalists in their quests for functionalised 4-mpba derivatives. Copyright © 2015 Elsevier B.V. All rights reserved.

SketchBio: a scientist's 3D interface for molecular modeling and animation.

PubMed

Waldon, Shawn M; Thompson, Peter M; Hahn, Patrick J; Taylor, Russell M

2014-10-30

Because of the difficulties involved in learning and using 3D modeling and rendering software, many scientists hire programmers or animators to create models and animations. This both slows the discovery process and provides opportunities for miscommunication. Working with multiple collaborators, a tool was developed (based on a set of design goals) to enable them to directly construct models and animations. SketchBio is presented, a tool that incorporates state-of-the-art bimanual interaction and drop shadows to enable rapid construction of molecular structures and animations. It includes three novel features: crystal-by-example, pose-mode physics, and spring-based layout that accelerate operations common in the formation of molecular models. Design decisions and their consequences are presented, including cases where iterative design was required to produce effective approaches. The design decisions, novel features, and inclusion of state-of-the-art techniques enabled SketchBio to meet all of its design goals. These features and decisions can be incorporated into existing and new tools to improve their effectiveness.

Dipole and nondipole photoionization of molecular hydrogen

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

Zimmermann, B.; McKoy, V.; Southworth, S. H.

2015-05-01

We describe a theoretical approach to molecular photoionization that includes first-order corrections to the dipole approximation. The theoretical formalism is presented and applied to photoionization of H-2 over the 20-to 180-eV photon energy range. The angle-integrated cross section sigma, the electric dipole anisotropy parameter beta(e), the molecular alignment anisotropy parameter beta(m), and the first-order nondipole asymmetry parameters gamma and delta were calculated within the single-channel, static-exchange approximation. The calculated parameters are compared with previous measurements of sigma and beta(m) and the present measurements of beta(e) and gamma + 3 delta. The dipole and nondipole angular distribution parameters were determined simultaneouslymore » using an efficient, multiangle measurement technique. Good overall agreement is observed between the magnitudes and spectral variations of the calculated and measured parameters. The nondipole asymmetries of He 1s and Ne 2p photoelectrons were also measured in the course of this work.« less

Effect of Molecular Rotation on Charge Transport Phenomena

NASA Astrophysics Data System (ADS)

Garg, O. P.; Lamba, Vijay Kr; Kaushik, D. K.

2015-12-01

The study of electron transport properties of molecular systems could be explained on the basis of the Landauer formalism. Unfortunately, due to the complexity of the experimental setup, most of these measurements have no control over the details of the electrode geometry, rotation of molecules, variation in angle of contacts, effect of fano resonances associated with side groups attached to rigid backbones, which results in a spectrum of IV-characteristics. Theoretical models can therefore help to understand and helps to develop new applications such as molecular sensors, etc. Thus we used simulation methods that generate the required structural ensemble, which is then analyzed with Green’s function methods to characterize the electronic transport properties. In present work we had discussed applications of this approach to understand the conductance in molecular system in the direction of controlling electron transport through molecules and studied the effect of rotation of sandwiched molecule.

Molecular logic gates: the past, present and future.

PubMed

Erbas-Cakmak, Sundus; Kolemen, Safacan; Sedgwick, Adam C; Gunnlaugsson, Thorfinnur; James, Tony D; Yoon, Juyoung; Akkaya, Engin U

2018-04-03

The field of molecular logic gates originated 25 years ago, when A. P. de Silva published a seminal article in Nature. Stimulated by this ground breaking research, scientists were inspired to join the race to simulate the workings of the fundamental components of integrated circuits using molecules. The rules of this game of mimicry were flexible, and have evolved and morphed over the years. This tutorial review takes a look back on and provides an overview of the birth and growth of the field of molecular logics. Spinning-off from chemosensor research, molecular logic gates quickly proved themselves to be more than intellectual exercises and are now poised for many potential practical applications. The ultimate goal of this vein of research became clearer only recently - to "boldly go where no silicon-based logic gate has gone before" and seek out a new deeper understanding of life inside tissues and cells.

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium.

PubMed

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-12-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Molecular Dynamics Modeling and Simulation of Diamond Cutting of Cerium

NASA Astrophysics Data System (ADS)

Zhang, Junjie; Zheng, Haibing; Shuai, Maobing; Li, Yao; Yang, Yang; Sun, Tao

2017-07-01

The coupling between structural phase transformations and dislocations induces challenges in understanding the deformation behavior of metallic cerium at the nanoscale. In the present work, we elucidate the underlying mechanism of cerium under ultra-precision diamond cutting by means of molecular dynamics modeling and simulations. The molecular dynamics model of diamond cutting of cerium is established by assigning empirical potentials to describe atomic interactions and evaluating properties of two face-centered cubic cerium phases. Subsequent molecular dynamics simulations reveal that dislocation slip dominates the plastic deformation of cerium under the cutting process. In addition, the analysis based on atomic radial distribution functions demonstrates that there are trivial phase transformations from the γ-Ce to the δ-Ce occurred in both machined surface and formed chip. Following investigations on machining parameter dependence reveal the optimal machining conditions for achieving high quality of machined surface of cerium.

Internal force corrections with machine learning for quantum mechanics/molecular mechanics simulations.

PubMed

Wu, Jingheng; Shen, Lin; Yang, Weitao

2017-10-28

Ab initio quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulation is a useful tool to calculate thermodynamic properties such as potential of mean force for chemical reactions but intensely time consuming. In this paper, we developed a new method using the internal force correction for low-level semiempirical QM/MM molecular dynamics samplings with a predefined reaction coordinate. As a correction term, the internal force was predicted with a machine learning scheme, which provides a sophisticated force field, and added to the atomic forces on the reaction coordinate related atoms at each integration step. We applied this method to two reactions in aqueous solution and reproduced potentials of mean force at the ab initio QM/MM level. The saving in computational cost is about 2 orders of magnitude. The present work reveals great potentials for machine learning in QM/MM simulations to study complex chemical processes.

Exploring unimolecular dissociation kinetics of ethyl dibromide through electronic structure calculations

NASA Astrophysics Data System (ADS)

Gulvi, Nitin R.; Patel, Priyanka; Badani, Purav M.

2018-04-01

Pathway for dissociation of multihalogenated alkyls is observed to be competitive between molecular and atomic elimination products. Factors such as molecular structure, temperature and pressure are known to influence the same. Hence present work is focussed to explore mechanism and kinetics of atomic (Br) and molecular (HBr and Br2) elimination upon pyrolysis of 1,1- and 1,2-ethyl dibromide (EDB). For this purpose, electronic structure calculations were performed at DFT and CCSD(T) level of theory. In addition to concerted mechanism, an alternate energetically efficient isomerisation pathway has been exploited for molecular elimination. Energy calculations are further complimented by detailed kinetic investigation, over wide range of temperature and pressure, using suitable models like Canonical Transition State Theory, Statistical Adiabatic Channel Model and Troe's formalism. Our calculations suggest high branching ratio for dehydrohalogentation reaction, from both isomers of EDB. Fall off curve depicts good agreement between theoretically estimated and experimentally reported values.

A morphological and molecular study of Clinostomid metacercariae from African fish with a redescription of Clinostomum tilapiae.

PubMed

Caffara, Monica; Locke, Sean A; Echi, Paul C; Halajian, Ali; Benini, Deborah; Luus-Powell, Wilmien J; Tavakol, Sareh; Fioravanti, Maria L

2017-09-01

The genus Clinostomum Leidy, 1856 (Digenea: Clinostomidae) has been reported in all ecozones of the world and a clear separation between the species of the 'Old World' and 'New World' has been recognized based on molecular studies. Recent works on Afrotropical species include redescriptions of C. cutaneum and C. phalacrocoracis, while C. tilapiae has yet to be studied using modern taxonomic approaches. In the present research, morphological redescription of C. tilapiae metacercariae from a new host, Synodontis batensoda sampled at Anambra River Basin, Nigeria, together with molecular analysis of nuclear internal transcribed spacer rDNA and cytochrome c oxidase 1 mtDNA are reported. We also provide morphological and molecular data from four further putative species of Clinostomum (morphotypes 1-4) from different areas of Africa, as well as the first report of C. phalacrocoracis in South Africa.

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

PubMed

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

2014-12-01

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

Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell.

PubMed

Cordova, Caio M M; Hoeltgebaum, Daniela L; Machado, Laís D P N; Santos, Larissa Dos

2016-01-01

Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.

Realistic simulations of the coupling between the protomotive force and the mechanical rotation of the F0-ATPase

PubMed Central

Mukherjee, Shayantani; Warshel, Arieh

2012-01-01

The molecular origin of the action of the F0 proton gradient-driven rotor presents a major puzzle despite significant structural advances. Although important conceptual models have provided guidelines of how such systems should work, it has been challenging to generate a structure-based molecular model using physical principles that will consistently lead to the unidirectional proton-driven rotational motion during ATP synthesis. This work uses a coarse-grained (CG) model to simulate the energetics of the F0-ATPase system in the combined space defined by the rotational coordinate and the proton transport (PTR) from the periplasmic side (P) to the cytoplasmic side (N). The model establishes the molecular origin of the rotation, showing that this effect is due to asymmetry in the energetics of the proton path rather than only the asymmetry of the interaction of the Asp on the c-ring helices and Arg on the subunit-a. The simulation provides a clear conceptual background for further exploration of the electrostatic basis of proton-driven mechanochemical systems. PMID:22927379

Transport properties at fluids interfaces: a molecular study for a macroscopic modelling

NASA Astrophysics Data System (ADS)

Russo, Antonio; Morciano, Matteo; Sibley, David N.; Nold, Andreas; Goddard, Benjamin D.; Asinari, Pietro; Kalliadasis, Serafim

2017-11-01

Rapid developments in the field of micro- and nano-fluidics require detailed analysis of the properties of matter at the molecular level. But despite numerous works in the literature, appropriate macroscopic relations able to integrate a microscopic description of fluid and soft matter properties at liquid-vapour and multi-fluid interfaces are missing. As a consequence, studies on interfacial phenomena and micro-device designs often rely on oversimplified assumptions, e.g. that the viscosities can be considered constant across interfaces. In our work, we present non-equilibrium MD simulations to scrutinise efficiently and systematically, through the tools of statistical mechanics, the anisotropic properties of fluids, namely density variations, stress tensor, and shear viscosity, at the fluid interfaces between liquid and vapour and between two partially miscible fluids. Our analysis has led to the formulation of a general relation between shear viscosity and density variations validated for a wide spectrum of interfacial fluid problems. In addition, it provides a rational description of other interfacial quantities of interest, including surface tension and its origins, and more generally, it offers valuable insight of molecular transport phenomena at interfaces.

Structural Biology of Tumor Necrosis Factor Demonstrated for Undergraduates Instruction by Computer Simulation

ERIC Educational Resources Information Center

Roy, Urmi

2016-01-01

This work presents a three-dimensional (3D) modeling exercise for undergraduate students in chemistry and health sciences disciplines, focusing on a protein-group linked to immune system regulation. Specifically, the exercise involves molecular modeling and structural analysis of tumor necrosis factor (TNF) proteins, both wild type and mutant. The…

Research Studies on Radiative Collision Lasers

DTIC Science & Technology

1980-06-01

34Branching Ratios for TlBr Photodissocia- tion with 2660 X Radiation." Abstract: Selective molecular photodi:ssociation as a pumping mechanism to invert...following the flash photolysis of CF I. In the present work we examine the selective 3 photodissociation of TlBr into the Tl(6p 2 P3 / 2 ) metastable state

Autophagy at sea.

PubMed

Martens, Sascha; Rusten, Tor Erik; Kraft, Claudine

2013-09-01

The 3rd EMBO Conference on, "Autophagy: Molecular mechanism, physiology and pathology" organized by Anne Simonsen and Sharon Tooze, was held in May 2013 on a sea cruise along the Norwegian coastline from Bergen to Tromsø. Researchers from all corners of the world presented work covering autophagosome biogenesis, physiological regulation of autophagy, selective autophagy and disease.

Proteomic analysis of a model fish species exposed to individual pesticides and a binary mixture--Presentation

EPA Science Inventory

Pesticides are nearly ubiquitous in surface waters of the United States, where they often are found as mixtures. The molecular mechanisms underlying the toxic effects of sub-lethal exposure to pesticides as both individual and mixtures are unclear. The current work aims to ident...

Role of magnetic and diamagnetic interactions in molecular optics and scattering

NASA Astrophysics Data System (ADS)

Forbes, Kayn A.

2018-05-01

This paper aims to explicitly clarify the role and interpretation of diamagnetic interactions between molecules and light in quantum electrodynamics. In contrast to their electric and magnetic counterparts, the diamagnetic couplings between light and matter have received relatively little interest in the field of molecular optics. This intriguing disregard of an interaction term is puzzling. The diamagnetic couplings possess unique physical properties that warrant their inclusion in any multiphoton process, and the lack of gauge invariance for paramagnetic and diamagnetic susceptibilities necessitates their inclusion. Their role and importance within nonrelativistic molecular quantum electrodynamics in the Coulomb gauge is illuminated, and it is highlighted how for any multiphoton process their inclusion should be implicit. As an indicative example of the theory presented, the diamagnetic contributions to both forward and nonforward Rayleigh scattering are derived and put into context alongside the electric and magnetic molecular responses. The work represents clarification of diamagnetic couplings in molecular quantum electrodynamics, which subsequently should proffer the study of diamagnetic interactions in molecular optics due to their unique physical attributes and necessary inclusion in multiphoton processes.

A method for fast safety screening of explosives in terms of crystal packing and molecular stability.

PubMed

Hu, Xiaohua; Chen, Nana; Li, Weichen

2016-07-01

Safety prediction is crucial to the molecular design or the material design of explosives, and the predictions based on any single factor alone will cause much inaccuracy, leading to a desire for a method on multi-bases. The presented proposes an improved method for fast screening explosive safety by combining a crystal packing factor and a molecular one, that is, steric hindrance against shear slide in crystal and molecular stability, denoted by intermolecular friction symbol (IFS) and bond dissociation energy (BDE) of trigger linkage respectively. Employing this BDE-IFS combined method, we understand the impact sensitivities of 24 existing explosives, and predict those of two energetic-energetic cocrystals of the observed CL-20/BTF and the supposed HMX/TATB. As a result, a better understanding is implemented by the combined method relative to molecular stability alone, verifying its improvement of more accurate predictions and the feasibility of IFS to graphically reflect molecular stacking in crystals. Also, this work verifies that the explosive safety is strongly related with its crystal stacking, which determines steric hindrance and influences shear slide.

Molecular modeling: An open invitation for applied mathematics

NASA Astrophysics Data System (ADS)

Mezey, Paul G.

2013-10-01

Molecular modeling methods provide a very wide range of challenges for innovative mathematical and computational techniques, where often high dimensionality, large sets of data, and complicated interrelations imply a multitude of iterative approximations. The physical and chemical basis of these methodologies involves quantum mechanics with several non-intuitive aspects, where classical interpretation and classical analogies are often misleading or outright wrong. Hence, instead of the everyday, common sense approaches which work so well in engineering, in molecular modeling one often needs to rely on rather abstract mathematical constraints and conditions, again emphasizing the high level of reliance on applied mathematics. Yet, the interdisciplinary aspects of the field of molecular modeling also generates some inertia and perhaps too conservative reliance on tried and tested methodologies, that is at least partially caused by the less than up-to-date involvement in the newest developments in applied mathematics. It is expected that as more applied mathematicians take up the challenge of employing the latest advances of their field in molecular modeling, important breakthroughs may follow. In this presentation some of the current challenges of molecular modeling are discussed.

Synthesis of 4-aminophenyl substituted indole derivatives for the instrumental analysis and molecular docking evaluation studies

NASA Astrophysics Data System (ADS)

Singh, Navneet; Kumar, Keshav

2017-07-01

The Indole has been known to maintain celebrity status since so many decades and has been a centre point at the spectrum of pharmacological research. The present work stimulates an idea of generating a pool of library of lead compounds. The data collected can be used for the mapping of biologically active compounds. The reported derivatives of 4-aminophenyl substituted Indole were prepared by the methods of Fischer Indole synthesis and Vilsemeier reaction followed by screening for instrumental analysis and molecular docking studies. The synthesized compounds 4-(1-(2-phenylhydrazono)ethyl)aniline, 1, 4-(1H-indol-2-yl)aniline, 2 and 2-(4-aminophenyl)-1H-indole-3-carbaldehyde, 3 were found to have remarkable yield and instrumental data analysis and also showed remarkable docked characteristic. The molecular docking studies revealed that ligand (amino acids) of comp. 1, 2 and 3 had been docked successfully on the binding site of the 3JUS protein selected from PDB with H bonding. The molecular docking data showed that compound 1, would possess remarkable biological activity and compd. 2 and 3 would possess mild to moderate biological activity. Thus this research work paves the way to synthesize new derivatives and thus to develop new compounds in future with accurate prediction.

Fiber sensors for molecular detection

NASA Astrophysics Data System (ADS)

Gu, Claire; Yang, Xuan; Zhang, Jin; Newhouse, Rebecca; Cao, Liangcai

2010-11-01

The demand on sensors for detecting chemical and biological agents is greater than ever before, including medical, environmental, food safety, military, and security applications. At present, most detection or sensing techniques tend to be either non-molecular specific, bulky, expensive, relatively inaccurate, or unable to provide real time data. Clearly, alternative sensing technologies are urgently needed. Recently, we have been working to develop a compact fiber optic surface enhanced Raman scattering (SERS) sensor system that integrates various novel ideas to achieve compactness, high sensitivity and consistency, molecular specificity, and automatic preliminary identification capabilities. The unique sensor architecture is expected to bring SERS sensors to practical applications due to a combination of 1) novel SERS substrates that provide the high sensitivity and consistency, molecular specificity, and applicability to a wide range of compounds; 2) a unique hollow core optical fiber probe with double SERS substrate structure that provides the compactness, reliability, low cost, and ease of sampling; and 3) an innovative matched spectral filter set that provides automatic preliminary molecule identification. In this paper, we will review the principle of operation and some of the important milestones of fiber SERS sensor development with emphasis on our recent work to integrate photonic crystal fiber SERS probes with a portable Raman spectrometer and to demonstrate a matched spectral filter for molecule identification.

An expanded framework for biomolecular visualization in the classroom: Learning goals and competencies

PubMed Central

Dries, Daniel R.; Dean, Diane M.; Listenberger, Laura L.; Novak, Walter R.P.

2016-01-01

Abstract A thorough understanding of the molecular biosciences requires the ability to visualize and manipulate molecules in order to interpret results or to generate hypotheses. While many instructors in biochemistry and molecular biology use visual representations, few indicate that they explicitly teach visual literacy. One reason is the need for a list of core content and competencies to guide a more deliberate instruction in visual literacy. We offer here the second stage in the development of one such resource for biomolecular three‐dimensional visual literacy. We present this work with the goal of building a community for online resource development and use. In the first stage, overarching themes were identified and submitted to the biosciences community for comment: atomic geometry; alternate renderings; construction/annotation; het group recognition; molecular dynamics; molecular interactions; monomer recognition; symmetry/asymmetry recognition; structure‐function relationships; structural model skepticism; and topology and connectivity. Herein, the overarching themes have been expanded to include a 12th theme (macromolecular assemblies), 27 learning goals, and more than 200 corresponding objectives, many of which cut across multiple overarching themes. The learning goals and objectives offered here provide educators with a framework on which to map the use of molecular visualization in their classrooms. In addition, the framework may also be used by biochemistry and molecular biology educators to identify gaps in coverage and drive the creation of new activities to improve visual literacy. This work represents the first attempt, to our knowledge, to catalog a comprehensive list of explicit learning goals and objectives in visual literacy. © 2016 by The International Union of Biochemistry and Molecular Biology, 45(1):69–75, 2017. PMID:27486685

A molecular dynamics study of lithium-containing aprotic heterocyclic ionic liquid electrolytes

NASA Astrophysics Data System (ADS)

Lourenço, Tuanan C.; Zhang, Yong; Costa, Luciano T.; Maginn, Edward J.

2018-05-01

Classical molecular dynamics simulations were performed on twelve different ionic liquids containing aprotic heterocyclic anions doped with Li+. These ionic liquids have been shown to be promising electrolytes for lithium ion batteries. Self-diffusivities, lithium transference numbers, densities, and free volumes were computed as a function of lithium concentration. The dynamics and free volume decreased with increasing lithium concentration, and the trends were rationalized by examining the changes to the liquid structure. Of those examined in the present work, it was found that (methyloxymethyl)triethylphosphonium triazolide ionic liquids have the overall best performance.

Molecular Dynamics Modeling of Thermal Properties of Aluminum Near Melting Line

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

Karavaev, A. V.; Dremov, V. V.; Sapozhnikov, F. A.

2006-08-03

In this work we present results of calculations of thermal properties of solid and liquid phases of aluminum at different densities and temperatures using classical molecular dynamics with EAM potential function. Dependencies of heat capacity CV on temperature and density have been analyzed. It was shown that when temperature increases, heat capacity CV behavior deviates from that by Dulong-Petit law. It may be explained by influence of anharmonicity of crystal lattice vibrations. Comparison of heat capacity CV of liquid phase with Grover's model has been performed. Dependency of aluminum melting temperature on pressure has been acquired.

Toxicodynamics of Mycotoxins in the Framework of Food Risk Assessment—An In Silico Perspective

PubMed Central

Dall’Asta, Chiara

2018-01-01

Mycotoxins severely threaten the health of humans and animals. For this reason, many countries have enforced regulations and recommendations to reduce the dietary exposure. However, even though regulatory actions must be based on solid scientific knowledge, many aspects of their toxicological activity are still poorly understood. In particular, deepening knowledge on the primal molecular events triggering the toxic stimulus may be relevant to better understand the mechanisms of action of mycotoxins. The present work presents the use of in silico approaches in studying the mycotoxins toxicodynamics, and discusses how they may contribute in widening the background of knowledge. A particular emphasis has been posed on the methods accounting the molecular initiating events of toxic action. In more details, the key concepts and challenges of mycotoxins toxicology have been introduced. Then, topical case studies have been presented and some possible practical implementations of studying mycotoxins toxicodynamics have been discussed. PMID:29360783

Co-infection with arthropod-borne pathogens in domestic cats.

PubMed

André, Marcos Rogério; Filgueira, Kilder Dantas; Calchi, Ana Cláudia; Sousa, Keyla Carstens Marques de; Gonçalves, Luiz Ricardo; Medeiros, Vitor Brasil; Ximenes, Poliana Araújo; Lelis, Ivana Cristina Nunes Gadelha; Meireles, Maria Vanuza Nunes de; Machado, Rosangela Zacarias

2017-01-01

The role of several feline vector-borne pathogens (FVBP) as a cause of disease in cats has not been clearly determined. In fact, with the exception of Bartonella spp. and hemoplasmas, FVBP in cats has not been clearly determined in Brazil yet. The present study aimed at identifying, by using molecular methods, the presence of FVBP in three cats showing non-specific clinical signs and inclusions suggestive of hemoparasites in blood smears. Cytauxzoon felis, 'Candidatus Mycoplasma haemominutum', Ehrlichia sp. closely related to Ehrlichia canis, and Anaplasma sp. closely related to Anaplasma phagocytophilum were detected in blood samples from two out of three sampled cats. Both cats positive for multiple FVBP did not show hematological and biochemical abnormalities. The present work emphasizes the need for molecular confirmation of co-infection by multiple FVBP in cats presenting non-specific clinical signs and inclusions resembling hemoparasites in blood smears.

Enacting the molecular imperative: How gene-environment interaction research links bodies and environments in the Post-Genomic Age

PubMed Central

Darling, Katherine Weatherford; Ackerman, Sara L.; Hiatt, Robert H.; Lee, Sandra Soo-Jin; Shim, Janet K.

2016-01-01

Despite a proclaimed shift from ‘nature versus nurture’ to ‘genes and environment’ paradigms within biomedical and genomic science, capturing the environment and identifying gene-environment interactions (GEIs) has remained a challenge. What does ‘the environment’ mean in the post-genomic age? In this paper, we present qualitative data from a study of 33 principal investigators funded by the U.S. National Institutes of Health to conduct etiological research on three complex diseases (cancer, cardiovascular disease and diabetes). We examine their research practices and perspectives on the environment through the concept of molecularization: the social processes and transformations through which phenomena (diseases, identities, pollution, food, racial/ethnic classifications) are re-defined in terms of their molecular components and described in the language of molecular biology. We show how GEI researchers’ expansive conceptualizations of the environment ultimately yield to the imperative to molecularize and personalize the environment. They seek to ‘go into the body’ and re-work the boundaries between bodies and environments. In the process, they create epistemic hinges to facilitate a turn from efforts to understand social and environmental exposures outside the body, to quantifying their effects inside the body. GEI researchers respond to these emergent imperatives with a mixture of excitement, ambivalence and frustration. We reflect on how GEI researchers struggle to make meaning of molecules in their work, and how they grapple with molecularization as a methodological and rhetorical imperative as well as a process transforming biomedical research practices. PMID:26994357

Enacting the molecular imperative: How gene-environment interaction research links bodies and environments in the post-genomic age.

PubMed

Darling, Katherine Weatherford; Ackerman, Sara L; Hiatt, Robert H; Lee, Sandra Soo-Jin; Shim, Janet K

2016-04-01

Despite a proclaimed shift from 'nature versus nurture' to 'genes and environment' paradigms within biomedical and genomic science, capturing the environment and identifying gene-environment interactions (GEIs) has remained a challenge. What does 'the environment' mean in the post-genomic age? In this paper, we present qualitative data from a study of 33 principal investigators funded by the U.S. National Institutes of Health to conduct etiological research on three complex diseases (cancer, cardiovascular disease and diabetes). We examine their research practices and perspectives on the environment through the concept of molecularization: the social processes and transformations through which phenomena (diseases, identities, pollution, food, racial/ethnic classifications) are re-defined in terms of their molecular components and described in the language of molecular biology. We show how GEI researchers' expansive conceptualizations of the environment ultimately yield to the imperative to molecularize and personalize the environment. They seek to 'go into the body' and re-work the boundaries between bodies and environments. In the process, they create epistemic hinges to facilitate a turn from efforts to understand social and environmental exposures outside the body, to quantifying their effects inside the body. GEI researchers respond to these emergent imperatives with a mixture of excitement, ambivalence and frustration. We reflect on how GEI researchers struggle to make meaning of molecules in their work, and how they grapple with molecularization as a methodological and rhetorical imperative as well as a process transforming biomedical research practices. Copyright © 2016 Elsevier Ltd. All rights reserved.

Understanding allosteric interactions in G protein-coupled receptors using Supervised Molecular Dynamics: A prototype study analysing the human A3 adenosine receptor positive allosteric modulator LUF6000.

PubMed

Deganutti, Giuseppe; Cuzzolin, Alberto; Ciancetta, Antonella; Moro, Stefano

2015-07-15

The search for G protein-coupled receptors (GPCRs) allosteric modulators represents an active research field in medicinal chemistry. Allosteric modulators usually exert their activity only in the presence of the orthosteric ligand by binding to protein sites topographically different from the orthosteric cleft. They therefore offer potentially therapeutic advantages by selectively influencing tissue responses only when the endogenous agonist is present. The prediction of putative allosteric site location, however, is a challenging task. In facts, they are usually located in regions showing more structural variation among the family members. In the present work, we applied the recently developed Supervised Molecular Dynamics (SuMD) methodology to interpret at the molecular level the positive allosteric modulation mediated by LUF6000 toward the human adenosine A3 receptor (hA3 AR). Our data suggest at least two possible mechanisms to explain the experimental data available. This study represent, to the best of our knowledge, the first case reported of an allosteric recognition mechanism depicted by means of molecular dynamics simulations. Copyright © 2015 Elsevier Ltd. All rights reserved.

Probing Electronic and Thermoelectric Properties of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Widawsky, Jonathan R.

In an effort to further understand electronic and thermoelectric phenomenon at the nanometer scale, we have studied the transport properties of single molecule junctions. To carry out these transport measurements, we use the scanning tunneling microscope-break junction (STM-BJ) technique, which involves the repeated formation and breakage of a metal point contact in an environment of the target molecule. Using this technique, we are able to create gaps that can trap the molecules, allowing us to sequentially and reproducibly create a large number of junctions. By applying a small bias across the junction, we can measure its conductance and learn about the transport mechanisms at the nanoscale. The experimental work presented here directly probes the transmission properties of single molecules through the systematic measurement of junction conductance (at low and high bias) and thermopower. We present measurements on a variety of molecular families and study how conductance depends on the character of the linkage (metal-molecule bond) and the nature of the molecular backbone. We start by describing a novel way to construct single molecule junctions by covalently connecting the molecular backbone to the electrodes. This eliminates the use of linking substituents, and as a result, the junction conductance increases substantially. Then, we compare transport across silicon chains (silanes) and saturated carbon chains (alkanes) while keeping the linkers the same and find a stark difference in their electronic transport properties. We extend our studies of molecular junctions by looking at two additional aspects of quantum transport -- molecular thermopower and molecular current-voltage characteristics. Each of these additional parameters gives us further insight into transport properties at the nanoscale. Evaluating the junction thermopower allows us to determine the nature of charge carriers in the system and we demonstrate this by contrasting the measurement of amine-terminated and pyridine-terminated molecules (which exhibit hole transport and electron transport, respectively). We also report the thermopower of the highly conducting, covalently bound molecular junctions that we have recently been able to form, and learn that, because of their unique transport properties, the junction power factors, GS2, are extremely high. Finally, we discuss the measurement of molecular current-voltage curves and consider the electronic and physical effects of applying a large bias to the system. We conclude with a summary of the work discussed and an outlook on related scientific studies.

Multiscale geometric modeling of macromolecules II: Lagrangian representation

PubMed Central

Feng, Xin; Xia, Kelin; Chen, Zhan; Tong, Yiying; Wei, Guo-Wei

2013-01-01

Geometric modeling of biomolecules plays an essential role in the conceptualization of biolmolecular structure, function, dynamics and transport. Qualitatively, geometric modeling offers a basis for molecular visualization, which is crucial for the understanding of molecular structure and interactions. Quantitatively, geometric modeling bridges the gap between molecular information, such as that from X-ray, NMR and cryo-EM, and theoretical/mathematical models, such as molecular dynamics, the Poisson-Boltzmann equation and the Nernst-Planck equation. In this work, we present a family of variational multiscale geometric models for macromolecular systems. Our models are able to combine multiresolution geometric modeling with multiscale electrostatic modeling in a unified variational framework. We discuss a suite of techniques for molecular surface generation, molecular surface meshing, molecular volumetric meshing, and the estimation of Hadwiger’s functionals. Emphasis is given to the multiresolution representations of biomolecules and the associated multiscale electrostatic analyses as well as multiresolution curvature characterizations. The resulting fine resolution representations of a biomolecular system enable the detailed analysis of solvent-solute interaction, and ion channel dynamics, while our coarse resolution representations highlight the compatibility of protein-ligand bindings and possibility of protein-protein interactions. PMID:23813599

Inverse transport problems in quantitative PAT for molecular imaging

NASA Astrophysics Data System (ADS)

Ren, Kui; Zhang, Rongting; Zhong, Yimin

2015-12-01

Fluorescence photoacoustic tomography (fPAT) is a molecular imaging modality that combines photoacoustic tomography with fluorescence imaging to obtain high-resolution imaging of fluorescence distributions inside heterogeneous media. The objective of this work is to study inverse problems in the quantitative step of fPAT where we intend to reconstruct physical coefficients in a coupled system of radiative transport equations using internal data recovered from ultrasound measurements. We derive uniqueness and stability results on the inverse problems and develop some efficient algorithms for image reconstructions. Numerical simulations based on synthetic data are presented to validate the theoretical analysis. The results we present here complement these in Ren K and Zhao H (2013 SIAM J. Imaging Sci. 6 2024-49) on the same problem but in the diffusive regime.

Charge Transport Processes in Molecular Junctions

NASA Astrophysics Data System (ADS)

Smith, Christopher Eugene

Molecular electronics (ME) has evolved into a rich area of exploration that combines the fields of chemistry, materials, electronic engineering and computational modeling to explore the physics behind electronic conduction at the molecular level. Through studying charge transport properties of single molecules and nanoscale molecular materials the field has gained the potential to bring about new avenues for the miniaturization of electrical components where quantum phenomena are utilized to achieve solid state molecular device functionality. Molecular junctions are platforms that enable these studies and consist of a single molecule or a small group of molecules directly connected to electrodes. The work presented in this thesis has built upon the current understanding of the mechanisms of charge transport in ordered junctions using self-assembled monolayer (SAM) molecular thin films. Donor and acceptor compounds were synthesized and incorporated into SAMs grown on metal substrates then the transport properties were measured with conducting probe atomic force microscopy (CP-AFM). In addition to experimentally measured current-voltage (I-V) curves, the transport properties were addressed computationally and modeled theoretically. The key objectives of this project were to 1) investigate the impact of molecular structure on hole and electron charge transport, 2) understand the nature of the charge carriers and their structure-transport properties through long (<4 nm) conjugated molecular wires, and 3) quantitatively extract interfacial properties characteristic to macroscopic junctions, such as energy level alignment and molecule-contact electronic coupling from experimental I-V curves. Here, we lay ground work for creating a more complete picture of charge transport in macroscopically ordered molecular junctions of controlled architecture, length and charge carrier. The polaronic nature of hopping transport has been predicted in long, conjugated molecular wires. Using quantum-based calculations, we modeled 'p-type' polaron transport through oligophenylenethiophene (OPTI) wires and assigned transport activation energies to specific modes of nuclear motion. We also show control over 'n-type', LUMO-mediated transport in short ( 2 nm) redox-active perylenediimide (PDI) SAMs bound to contacts through isocyano linkers. By changing the contact work function (φ) and temperature, we were able to verify thermally-assisted LUMO transport. Transition voltage spectroscopy and the single level model was employed to fit the experimental I-V curves and extract the electronic coupling (epsilon) and the EF-LUMO offset (epsilonl). It was found that epsilonl does not change with φ (LUMO pinning), while Gamma changes with both φ and temperature. Further, the PDI SAMs could be reversibly chemically gated to modulate the transport. These results help advance our understanding of transport behavior in semiconducting molecular thin films, and open opportunities to engineer improved electronic functionality into molecular devices.

Clinicopathological parameters associated with histological background and recurrence after surgical intervention of vocal cord leukoplakia.

PubMed

Cui, Weixin; Xu, Wen; Yang, Qingwen; Hu, Rong

2017-06-01

Histological examination of biopsy shows usefulness in the diagnosis of vocal cord leukoplakia; however, in considerable amount of cases, the examination cannot provide definitive diagnosis of malignancy from benign conditions such as hyperplasia and dysplasia. The present work therefore was aimed to identify clinicopathological factors and molecular markers predictive of recurrence and malignant transformation of vocal cord leukoplakia.Clinical data of 555 cases of vocal cord leukoplakia enrolled from July 1999 to June 2014 were analyzed. The cohort consisted of keratosis (n = 137), hyperplasia (n = 139), dysplasia (n = 177), and primary (n = 10) and invasive (n = 46) carcinoma. Correlations between patients' backgrounds, clinicopathological factors, molecular markers (p53, p16, Ki67, cytokeratin, and proliferating cell nuclear antigen), and histology backgrounds were examined using by Pearson Chi-squared or Fisher exact test. Reflux symptom index (RSI) and reflux finding score (RFS) before and after treatment were compared using Wilcoxon signed-rank test. Risk factors for disease recurrence were identified using Cox proportional hazards models of multivariate analysis. Time to recurrence was analyzed using log-rank test of Kaplan-Meier method.In the present cohort, alcohol drinking was found associated with GRBAS grade (P = .0258) and the site (P = .0298) of leukoplakia. For the different disease types, chief complaint (P = .0179), GRBAS grade (P = .0101), mucosal wave (P < .0001), and molecular markers p53 (P < .0001) and Ki67 (P < .0001) were identified as correlates. RSI and RFS were significantly lowered by surgical intervention. A single side of leukoplakia was predictive of a lower risk of recurrence (odds ratio, 0.378; 95% confidence interval, 0.197-0.723; P = .0033). Absence of mucosal wave was associated with a shorter time-to-recurrence (P = .0357).The present work identified clinicopathological factors and molecular markers associated with the different histology of vocal cord leukoplakia, and also the prognostic factor for the low risk of recurrence after surgery.

QSAR Study and Molecular Design of Open-Chain Enaminones as Anticonvulsant Agents

PubMed Central

Garro Martinez, Juan C.; Duchowicz, Pablo R.; Estrada, Mario R.; Zamarbide, Graciela N.; Castro, Eduardo A.

2011-01-01

Present work employs the QSAR formalism to predict the ED50 anticonvulsant activity of ringed-enaminones, in order to apply these relationships for the prediction of unknown open-chain compounds containing the same types of functional groups in their molecular structure. Two different modeling approaches are applied with the purpose of comparing the consistency of our results: (a) the search of molecular descriptors via multivariable linear regressions; and (b) the calculation of flexible descriptors with the CORAL (CORrelation And Logic) program. Among the results found, we propose some potent candidate open-chain enaminones having ED50 values lower than 10 mg·kg−1 for corresponding pharmacological studies. These compounds are classified as Class 1 and Class 2 according to the Anticonvulsant Selection Project. PMID:22272137

Interactive molecular dynamics

NASA Astrophysics Data System (ADS)

Schroeder, Daniel V.

2015-03-01

Physics students now have access to interactive molecular dynamics simulations that can model and animate the motions of hundreds of particles, such as noble gas atoms, that attract each other weakly at short distances but repel strongly when pressed together. Using these simulations, students can develop an understanding of forces and motions at the molecular scale, nonideal fluids, phases of matter, thermal equilibrium, nonequilibrium states, the Boltzmann distribution, the arrow of time, and much more. This article summarizes the basic features and capabilities of such a simulation, presents a variety of student exercises using it at the introductory and intermediate levels, and describes some enhancements that can further extend its uses. A working simulation code, in html5 and javascript for running within any modern Web browser, is provided as an online supplement.

A model of early formation of uranium molecular oxides in laser-ablated plasmas

NASA Astrophysics Data System (ADS)

Finko, Mikhail S.; Curreli, Davide; Weisz, David G.; Crowhurst, Jonathan C.; Rose, Timothy P.; Koroglu, Batikan; Radousky, Harry B.; Armstrong, Michael R.

2017-12-01

In this work, we present a newly constructed U x O y reaction mechanism that consists of 30 reaction channels (21 of which are reversible channels) for 11 uranium molecular species (including ions). Both the selection of reaction channels and calculation of corresponding rate coefficients is accomplished via a comprehensive literature review and application of basic reaction rate theory. The reaction mechanism is supplemented by a detailed description of oxygen plasma chemistry (19 species and 142 reaction channels) and is used to model an atmospheric laser ablated uranium plume via a 0D (global) model. The global model is used to analyze the evolution of key uranium molecular species predicted by the reaction mechanism, and the initial stage of formation of uranium oxide species.

Effect of carbon spacer length on zwitterionic carboxybetaines.

PubMed

Shao, Qing; Jiang, Shaoyi

2013-02-07

Zwitterionic carboxybetaines (CBs) are ubiquitous in nature and considered promising materials for biological and chemical applications. A thorough understanding of the effect of carbon spacer length (CSL) on molecular properties is important. In this work, using molecular dynamics simulation and quantum chemical calculation, we investigated the effect of CSL on the molecular properties of CB molecules. The hydration number, structure, and dynamics of carboxylic and trimethyl ammonium groups were investigated and found to present different behaviors in regards to the variation of CSL. The simulation results with partial charges developed from quantum chemical calculations were compared with those with partial charges from the OPLS all atom (OPLSAA) force field. The hydration free energy of CB molecules and CB-Na(+) association was also studied as a function of CSL.

Exploring the science of thinking independently together: Faraday Discussion Volume 204 - Complex Molecular Surfaces and Interfaces, Sheffield, UK, July 2017.

PubMed

Samperi, M; Hirsch, B E; Diaz Fernandez, Y A

2017-11-23

The 2017 Faraday Discussion on Complex Molecular Surfaces and Interfaces brought together theoreticians and experimentalists from both physical and chemical backgrounds to discuss the relevant applied and fundamental research topics within the broader field of chemical surface analysis and characterization. Main discussion topics from the meeting included the importance of "disordered" two-dimensional (2D) molecular structures and the utility of kinetically trapped states. An emerging need for new experimental tools to address dynamics and kinetic pathways involved in self-assembled systems, as well as the future prospects and current limitations of in silico studies were also discussed. The following article provides a brief overview of the work presented and the challenges discussed during the meeting.

Super-Earths, Warm-Neptunes, and Hot-Jupiters: Transmission Spectroscopy for Comparative Planetology

NASA Astrophysics Data System (ADS)

Fraine, Jonathan D.; Deming, Drake; Knutson, Heather; Jordán, Andrés

2014-11-01

We used the Kepler, Hubble, and Spitzer Space Telescopes to probe the diversity of exoplanetary atmospheres with transmission spectroscopy, constraining atomic and molecular absorption in Jupiter- and Neptune-sized exoplanets. The detections and non-detections of molecular species such as water, methane, and carbon monoxide lead to greater understanding of planet formation and evolution. Recent significant advances in both theoretical and observational discoveries from planets like HD189733b, HD209458b, GJ436, as well as our own work with HAT-P-11b and GJ1214b, have shown that the range of measurable atmospheric properties spans from clear, molecular absorption dominated worlds to opaque worlds, with cloudy, hazy, or high mean molecular weight atmospheres. Characterization of these significant non-detections allows us to infer the existence of cloud compositions at high altitudes, or mean molecular weights upwards of ~1000x solar. Neither scenario was expected from extrapolations of solar system analogs. We present here our published results from GJ1214b and HAT-P-11b, as well as our recent work on HAT-P-7b and HAT-P-13b. We search for evidence of atmospheric hazes and clouds, and place constraints on the relative abundance of water vapor, methane, and carbon monoxide-- in the case of cloud-free atmospheres. We conclude by discussing how our results compare to transmission spectra obtained for other similar planets, and use these combined data to develop a better understanding for the nature of these distant and alien worlds.

Quantum chemical and statistical study of megazol-derived compounds with trypanocidal activity

NASA Astrophysics Data System (ADS)

Rosselli, F. P.; Albuquerque, C. N.; da Silva, A. B. F.

In this work we performed a structure-activity relationship (SAR) study with the aim to correlate molecular properties of the megazol compound and 10 of its analogs with the biological activity against Trypanosoma cruzi (trypanocidal or antichagasic activity) presented by these molecules. The biological activity indication was obtained from in vitro tests and the molecular properties (variables or descriptors) were obtained from the optimized chemical structures by using the PM3 semiempirical method. It was calculated ˜80 molecular properties selected among steric, constitutional, electronic, and lipophilicity properties. In order to reduce dimensionality and investigate which subset of variables (descriptors) would be more effective in classifying the compounds studied, according to their degree of trypanocidal activity, we employed statistical methodologies (pattern recognition and classification techniques) such as principal component analysis (PCA), hierarchical cluster analysis (HCA), K-nearest neighbor (KNN), and discriminant function analysis (DFA). These methods showed that the descriptors molecular mass (MM), energy of the second lowest unoccupied molecular orbital (LUMO+1), charge on the first nitrogen at substituent 2 (qN'), dihedral angles (D1 and D2), bond length between atom C4 and its substituent (L4), Moriguchi octanol-partition coefficient (MLogP), and length-to-breadth ratio (L/Bw) were the variables responsible for the separation between active and inactive compounds against T. cruzi. Afterwards, the PCA, KNN, and DFA models built in this work were used to perform trypanocidal activity predictions for eight new megazol analog compounds.

Effects of surface functionalization on the electronic and structural properties of carbon nanotubes: A computational approach

NASA Astrophysics Data System (ADS)

Ribeiro, M. S.; Pascoini, A. L.; Knupp, W. G.; Camps, I.

2017-12-01

Carbon nanotubes (CNTs) have important electronic, mechanical and optical properties. These features may be different when comparing a pristine nanotube with other presenting its surface functionalized. These changes can be explored in areas of research and application, such as construction of nanodevices that act as sensors and filters. Following this idea, in the current work, we present the results from a systematic study of CNT's surface functionalized with hydroxyl and carboxyl groups. Using the entropy as selection criterion, we filtered a library of 10k stochastically generated complexes for each functional concentration (5, 10, 15, 20 and 25%). The structurally related parameters (root-mean-square deviation, entropy, and volume/area) have a monotonic relationship with functionalization concentration. Differently, the electronic parameters (frontier molecular orbital energies, electronic gap, molecular hardness, and electrophilicity index) present and oscillatory behavior. For a set of concentrations, the nanotubes present spin polarized properties that can be used in spintronics.

Combustion chemistry and flame structure of furan group biofuels using molecular-beam mass spectrometry and gas chromatography – Part III: 2,5-Dimethylfuran

PubMed Central

Togbé, Casimir; Tran, Luc-Sy; Liu, Dong; Felsmann, Daniel; Oßwald, Patrick; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Fournet, René; Battin-Leclerc, Frédérique; Kohse-Höinghaus, Katharina

2013-01-01

This work is the third part of a study focusing on the combustion chemistry and flame structure of furan and selected alkylated derivatives, i.e. furan in Part I, 2-methylfuran (MF) in Part II, and 2,5-dimethylfuran (DMF) in the present work. Two premixed low-pressure (20 and 40 mbar) flat argon-diluted (50%) flames of DMF were studied with electron-ionization molecular-beam mass spectrometry (EI-MBMS) and gas chromatography (GC) under two equivalence ratios (φ=1.0 and 1.7). Mole fractions of reactants, products, and stable and radical intermediates were measured as a function of the distance to the burner. Kinetic modeling was performed using a reaction mechanism that was further developed in the present series, including Part I and Part II. A reasonable agreement between the present experimental results and the simulation is observed. The main reaction pathways of DMF consumption were derived from a reaction flow analysis. Also, a comparison of the key features for the three flames is presented, as well as a comparison between these flames of furanic compounds and those of other fuels. An a priori surprising ability of DMF to form soot precursors (e.g. 1,3-cyclopentadiene or benzene) compared to less substituted furans and to other fuels has been experimentally observed and is well explained in the model. PMID:24518851

Combustion chemistry and flame structure of furan group biofuels using molecular-beam mass spectrometry and gas chromatography - Part III: 2,5-Dimethylfuran.

PubMed

Togbé, Casimir; Tran, Luc-Sy; Liu, Dong; Felsmann, Daniel; Oßwald, Patrick; Glaude, Pierre-Alexandre; Sirjean, Baptiste; Fournet, René; Battin-Leclerc, Frédérique; Kohse-Höinghaus, Katharina

2014-03-01

This work is the third part of a study focusing on the combustion chemistry and flame structure of furan and selected alkylated derivatives, i.e. furan in Part I, 2-methylfuran (MF) in Part II, and 2,5-dimethylfuran (DMF) in the present work. Two premixed low-pressure (20 and 40 mbar) flat argon-diluted (50%) flames of DMF were studied with electron-ionization molecular-beam mass spectrometry (EI-MBMS) and gas chromatography (GC) under two equivalence ratios (φ=1.0 and 1.7). Mole fractions of reactants, products, and stable and radical intermediates were measured as a function of the distance to the burner. Kinetic modeling was performed using a reaction mechanism that was further developed in the present series, including Part I and Part II. A reasonable agreement between the present experimental results and the simulation is observed. The main reaction pathways of DMF consumption were derived from a reaction flow analysis. Also, a comparison of the key features for the three flames is presented, as well as a comparison between these flames of furanic compounds and those of other fuels. An a priori surprising ability of DMF to form soot precursors (e.g. 1,3-cyclopentadiene or benzene) compared to less substituted furans and to other fuels has been experimentally observed and is well explained in the model.

Overview of Piezoelectric Biosensors, Immunosensors and DNA Sensors and Their Applications.

PubMed

Pohanka, Miroslav

2018-03-19

Piezoelectric biosensors are a group of analytical devices working on a principle of affinity interaction recording. A piezoelectric platform or piezoelectric crystal is a sensor part working on the principle of oscillations change due to a mass bound on the piezoelectric crystal surface. In this review, biosensors having their surface modified with an antibody or antigen, with a molecularly imprinted polymer, with genetic information like single stranded DNA, and biosensors with bound receptors of organic of biochemical origin, are presented and discussed. The mentioned recognition parts are frequently combined with use of nanoparticles and applications in this way are also introduced. An overview of the current literature is given and the methods presented are commented upon.

Molecular Electronic Angular Motion Transducer Broad Band Self-Noise.

PubMed

Zaitsev, Dmitry; Agafonov, Vadim; Egorov, Egor; Antonov, Alexander; Shabalina, Anna

2015-11-20

Modern molecular electronic transfer (MET) angular motion sensors combine high technical characteristics with low cost. Self-noise is one of the key characteristics which determine applications for MET sensors. However, until the present there has not been a model describing the sensor noise in the complete operating frequency range. The present work reports the results of an experimental study of the self-noise level of such sensors in the frequency range of 0.01-200 Hz. Based on the experimental data, a theoretical model is developed. According to the model, self-noise is conditioned by thermal hydrodynamic fluctuations of the operating fluid flow in the frequency range of 0.01-2 Hz. At the frequency range of 2-100 Hz, the noise power spectral density has a specific inversely proportional dependence of the power spectral density on the frequency that could be attributed to convective processes. In the high frequency range of 100-200 Hz, the noise is conditioned by the voltage noise of the electronics module input stage operational amplifiers and is heavily reliant to the sensor electrical impedance. The presented results allow a deeper understanding of the molecular electronic sensor noise nature to suggest the ways to reduce it.

Reagent-Free Programming of Shape-Memory Behavior in Gelatin by Electron Beams: Experiments and Modeling

NASA Astrophysics Data System (ADS)

Riedel, Stefanie; Mayr, Stefan G.

2018-02-01

Recent years have seen a paradigm shift in biomaterials toward stimuli-responsive switchable systems that actively interact with their environment. This work demonstrates how to turn the ubiquitous off-the-shelf material gelatin into such a smart biomaterial. This is achieved by realizing the shape-memory effect, viz., a temperature-induced transition from a secondary into a primary shape that has been programmed in the first place merely by exposure to energetic electrons without addition of potentially hazardous cross-linkers. While this scenario is experimentally quantified for exemplary actuators, a theoretical framework capable of unraveling the molecular foundations and predicting experiments is also presented. It particularly employs molecular dynamics modeling based on force fields that are also derived within this work. Implementing this functionality into a highly accepted material, these findings open an avenue for large-scale application in a broad range of areas.

Development of molecular based optical techniques for thermometry and velocimetry for fluorocarbon media

NASA Astrophysics Data System (ADS)

Pouya, Shahram; Blanchard, Gary; Koochesfahani, Manoochehr

2016-11-01

Fluorocarbon solvents are very stable inert fluids with unique physical properties that make them attractive compounds as refrigerant and several medical applications such as contrast enhanced ultrasound imaging. Since they do not mix with typical organic solvents or water, most luminescent (fluorescent or phosphorescent) probes cannot be used as tracers for optical diagnostic techniques. Perfluoropentane, a compound from this family, is used as a simulant fluid by NASA for two-phase heat transfer/mixing experiments under micro-gravity condition due to its low boiling temperature. Here we study the feasibility of employing non-intrusive optical methods for measurements of temperature and/or velocity within Perfluoropentane as the working fluid. Preliminary results of temperature and velocity measurement using Laser Induced Fluorescence and Molecular Tagging Velocimetry are presented. This work was supported by NASA Grant Number NNX16AD52A.

Braving the attitude of altitude: Caragana jubata at work in cold desert of Himalaya

PubMed Central

Bhardwaj, Pardeep Kumar; Kapoor, Ritu; Mala, Deep; Bhagwat, Geetika; Acharya, Vishal; Singh, Anil Kumar; Vats, Surender Kumar; Ahuja, Paramvir Singh; Kumar, Sanjay

2013-01-01

The present work was conducted to understand the basis of adaptation in Caragana jubata in its niche environment at high altitude cold desert of Himalaya. Molecular data showed predominance of genes encoding chaperones and those involved in growth and development at low temperature (LT), a major cue operative at high altitude. Importantly, these genes expressed in C. jubata in its natural habitat. Their homologues in Arabidopsis thaliana, Oryza sativa, and Glycine max did not exhibit similar trend of gene expression at LT. Constitutive expression and a quick up-regulation of the above genes suggested the ability of C. jubata to adjust its cellular machinery to maintain growth and development in its niche. This was reflected in LT50 (the temperature at which 50% injury occurred) and LT mediated photosynthetic acclimatory response. Such molecular and physiological plasticity enables C. jubata to thrive in the high altitude cold desert of Himalayas. PMID:23289064

Molecular biology of testicular germ cell tumors.

PubMed

Gonzalez-Exposito, R; Merino, M; Aguayo, C

2016-06-01

Testicular germ cell tumors (TGCTs) are the most common solid tumors in young adult men. They constitute a unique pathology because of their embryonic and germ origin and their special behavior. Genetic predisposition, environmental factors involved in their development and genetic aberrations have been under study in many works throughout the last years trying to explain the susceptibility and the transformation mechanism of TGCTs. Despite the high rate of cure in this type of tumors because its particular sensitivity to cisplatin, there are tumors resistant to chemotherapy for which it is needed to find new therapies. In the present work, it has been carried out a literature review on the most important molecular aspects involved in the onset and development of such tumors, as well as a review of the major developments regarding prognostic factors, new prognostic biomarkers and the possibility of new targeted therapies.

Organosiloxane working fluids for the liquid droplet radiator

NASA Technical Reports Server (NTRS)

Buch, R. R.; Huntress, A. R.

1985-01-01

Siloxane-based working fluids for advanced space radiators requiring direct fluid exposure to the space environment are evaluated. Isolation of five candidate fluids by vacuum distillation from existing siloxane polymers is discussed. The five fluids recovered include a polydimethylsiloxane, three phenyl-containing siloxanes, and a methylhexylsiloxane. Vapor pressures and viscosities for the five fluids are reported over the temperature range of 250 to 400 K. Use of thermal-gravimetric analysis to reliably estimate vapor pressures of 10 to the -8 power Pascals is described. Polydimethylsiloxane (PDMS) and polymethylphenylsiloxane (PMPS) are selected from the five candidate fluids based on favorable vapor pressure and viscosity, as well as perceived stability in low-Earth orbit environments. Characterization of these fluids by infrared spectroscopy, Si-29 NMR, gel-permeation chromatography, and liquid chromatography is presented. Both fluids consist of narrow molecular weight distributions, with average molecular weights of about 2500 for PDMS and 1300 for PMPS.

A Single Reaction Thread Ties Multiple Core Concepts in an Introductory Chemistry Course

ERIC Educational Resources Information Center

Barbee, Meredith H.; Carden, Robert G.; Johnson, Julia H. R.; Brown, Cameron L.; Canelas, Dorian A.; Craig, Stephen L.

2018-01-01

This work describes the use of a single chemical reaction to teach and connect a number of standard general chemistry course topics while also introducing students to polymer concepts. Through the study of the reaction that converts spiropyran into merocyanine, we are able to present and connect molecular orbital theory, quantum mechanics,…

Solving the Nose-Hoover thermostat for Nuclear Pasta

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

Perez Garcia, M. Angeles

2006-06-19

At densities just below nuclear saturation density, there may be possible non-uniform spatial configurations of neutron rich matter. In this work we present a calculation using molecular dynamics techniques for a nuclear system interacting via a semiclassical potential depending on both positions and momenta and kept at fixed temperature by using the Nose-Hoover Thermostat.

Recent theoretical chemical dynamics at Rochester in the paths of Joseph O. Hirschfelder

NASA Technical Reports Server (NTRS)

George, T. F.; Lam, K.-S.; Bhattacharyya, D. K.; Hutchinson, M.; Zimmerman, I. H.; Devries, P. L.; Yuan, J.-M.

1982-01-01

A review of recent theoretical studies of gas-phase molecular rate processes, including various effects of laser radiation, is presented in the context of the extensive and influential work of Joseph O. Hirschfelder during the past half-century. The topics addressed are energy transfer, chemical reactions, unimolecular dissociation, transition states, and bound-continuum interactions.

Coarse-Grained Molecular Monte Carlo Simulations of Liquid Crystal-Nanoparticle Mixtures

NASA Astrophysics Data System (ADS)

Neufeld, Ryan; Kimaev, Grigoriy; Fu, Fred; Abukhdeir, Nasser M.

Coarse-grained intermolecular potentials have proven capable of capturing essential details of interactions between complex molecules, while substantially reducing the number of degrees of freedom of the system under study. In the domain of liquid crystals, the Gay-Berne (GB) potential has been successfully used to model the behavior of rod-like and disk-like mesogens. However, only ellipsoid-like interaction potentials can be described with GB, making it a poor fit for many real-world mesogens. In this work, the results of Monte Carlo simulations of liquid crystal domains using the Zewdie-Corner (ZC) potential are presented. The ZC potential is constructed from an orthogonal series of basis functions, allowing for potentials of essentially arbitrary shapes to be modeled. We also present simulations of mixtures of liquid crystalline mesogens with nanoparticles. Experimentally these mixtures have been observed to exhibit microphase separation and formation of long-range networks under some conditions. This highlights the need for a coarse-grained approach which can capture salient details on the molecular scale while simulating sufficiently large domains to observe these phenomena. We compare the phase behavior of our simulations with that of a recently presented continuum theory. This work was made possible by the Natural Sciences and Engineering Research Council of Canada and Compute Ontario.

Organic contamination of ground water at Gas Works Park, Seattle, Washington

USGS Publications Warehouse

Turney, G.L.; Goerlitz, D.F.

1990-01-01

Gas Works Park, in Seattle, Washington, is located on the site of a coal and oil gasification plant that ceased operation in 1956. During operation, many types of wastes, including coal, tar, and oil, accumulated on-site. The park soil is currently (1986) contaminated with compounds such as polynuclear aromatic hydrocarbons, volatile organic compounds, trace metals, and cyanide. Analyses of water samples from a network of observation wells in the park indicate that these compounds are also present in the ground water. Polynuclear aromatic hydrocarbons and volatile organic compounds were identified in ground water samples in concentrations as large as 200 mg/L. Concentrations of organic compounds were largest where ground water was in contact with a non-aqueous phase liquid in the soil. Where no non-aqueous phase liquid was present, concentrations were much smaller, even if the ground water was in contact with contaminated soils. This condition is attributed to weathering processes in which soluble, low-molecular-weight organic compounds are preferentially dissolved from the non-aqueous phase liquid into the ground water. Where no non-aqueous phase liquid is present, only stained soils containing relatively insoluble, high-molecular-weight compounds remain. Concentrations of organic contaminants in the soils may still remain large.

Understanding thio-effects in simple phosphoryl systems: role of solvent effects and nucleophile charge† †Electronic supplementary information (ESI) available: A breakdown of calculated activation free energies shown in Table 1, as well as absolute energies and Cartesian coordinates of all key species in this work are presented as ESI. See DOI: 10.1039/c5ob00309a Click here for additional data file.

PubMed Central

Carvalho, Alexandra T. P.; O'Donoghue, AnnMarie C.; Hodgson, David R. W.

2015-01-01

Recent experimental work (J. Org. Chem., 2012, 77, 5829) demonstrated pronounced differences in measured thio-effects for the hydrolysis of (thio)phosphodichloridates by water and hydroxide nucleophiles. In the present work, we have performed detailed quantum chemical calculations of these reactions, with the aim of rationalizing the molecular bases for this discrimination. The calculations highlight the interplay between nucleophile charge and transition state solvation in SN2(P) mechanisms as the basis of these differences, rather than a change in mechanism. PMID:25797408

A genetic fingerprint of Amphipoda from Icelandic waters – the baseline for further biodiversity and biogeography studies

PubMed Central

Jażdżewska, Anna M.; Corbari, Laure; Driskell, Amy; Frutos, Inmaculada; Havermans, Charlotte; Hendrycks, Ed; Hughes, Lauren; Lörz, Anne-Nina; Bente Stransky; Tandberg, Anne Helene S.; Vader, Wim; Brix, Saskia

2018-01-01

Abstract Amphipods constitute an abundant part of Icelandic deep-sea zoobenthos yet knowledge of the diversity of this fauna, particularly at the molecular level, is scarce. The present work aims to use molecular methods to investigate genetic variation of the Amphipoda sampled during two IceAGE collecting expeditions. The mitochondrial cytochrome oxidase subunit 1 (COI) of 167 individuals originally assigned to 75 morphospecies was analysed. These targeted morhospecies were readily identifiable by experts using light microscopy and representative of families where there is current ongoing taxonomic research. The study resulted in 81 Barcode Identity Numbers (BINs) (of which >90% were published for the first time), while Automatic Barcode Gap Discovery revealed the existence of 78 to 83 Molecular Operational Taxonomic Units (MOTUs). Six nominal species (Rhachotropis helleri, Arrhis phyllonyx, Deflexilodes tenuirostratus, Paroediceros propinquus, Metopa boeckii, Astyra abyssi) appeared to have a molecular variation higher than the 0.03 threshold of both p-distance and K2P usually used for amphipod species delineation. Conversely, two Oedicerotidae regarded as separate morphospecies clustered together with divergences in the order of intraspecific variation. The incongruence between the BINs associated with presently identified species and the publicly available data of the same taxa was observed in case of Paramphithoe hystrix and Amphilochus manudens. The findings from this research project highlight the necessity of supporting molecular studies with thorough morphology species analyses. PMID:29472762

Transport mirages in single-molecule devices

NASA Astrophysics Data System (ADS)

Gaudenzi, R.; Misiorny, M.; Burzurí, E.; Wegewijs, M. R.; van der Zant, H. S. J.

2017-03-01

Molecular systems can exhibit a complex, chemically tailorable inner structure which allows for targeting of specific mechanical, electronic, and optical properties. At the single-molecule level, two major complementary ways to explore these properties are molecular quantum-dot structures and scanning probes. This article outlines comprehensive principles of electron-transport spectroscopy relevant to both these approaches and presents a new, high-resolution experiment on a high-spin single-molecule junction exemplifying these principles. Such spectroscopy plays a key role in further advancing our understanding of molecular and atomic systems, in particular, the relaxation of their spin. In this joint experimental and theoretical analysis, particular focus is put on the crossover between the resonant regime [single-electron tunneling] and the off-resonant regime [inelastic electron (co)tunneling spectroscopy (IETS)]. We show that the interplay of these two processes leads to unexpected mirages of resonances not captured by either of the two pictures alone. Although this turns out to be important in a large fraction of the possible regimes of level positions and bias voltages, it has been given little attention in molecular transport studies. Combined with nonequilibrium IETS—four-electron pump-probe excitations—these mirages provide crucial information on the relaxation of spin excitations. Our encompassing physical picture is supported by a master-equation approach that goes beyond weak coupling. The present work encourages the development of a broader connection between the fields of molecular quantum-dot and scanning probe spectroscopy.

Molecular dynamics analysis of the influence of Coulomb and van der Waals interactions on the work of adhesion at the solid-liquid interface

NASA Astrophysics Data System (ADS)

Surblys, Donatas; Leroy, Frédéric; Yamaguchi, Yasutaka; Müller-Plathe, Florian

2018-04-01

We investigated the solid-liquid work of adhesion of water on a model silica surface by molecular dynamics simulations, where a methodology previously developed to determine the work of adhesion through thermodynamic integration was extended to a system with long-range electrostatic interactions between solid and liquid. In agreement with previous studies, the work of adhesion increased when the magnitude of the surface polarity was increased. On the other hand, we found that when comparing two systems with and without solid-liquid electrostatic interactions, which were set to have approximately the same total solid-liquid interfacial energy, former had a significantly smaller work of adhesion and a broader distribution in the interfacial energies, which has not been previously reported in detail. This was explained by the entropy contribution to the adhesion free energy; i.e., the former with a broader energy distribution had a larger interfacial entropy than the latter. While the entropy contribution to the work of adhesion has already been known, as a work of adhesion itself is free energy, these results indicate that, contrary to common belief, wetting behavior such as the contact angle is not only governed by the interfacial energy but also significantly affected by the interfacial entropy. Finally, a new interpretation of interfacial entropy in the context of solid-liquid energy variance was offered, from which a fast way to qualitatively estimate the work of adhesion was also presented.

A molecular dynamics study of ethanol-water hydrogen bonding in binary structure I clathrate hydrate with CO2

NASA Astrophysics Data System (ADS)

Alavi, Saman; Ohmura, Ryo; Ripmeester, John A.

2011-02-01

Guest-host hydrogen bonding in clathrate hydrates occurs when in addition to the hydrophilic moiety which causes the molecule to form hydrates under high pressure-low temperature conditions, the guests contain a hydrophilic, hydrogen bonding functional group. In the presence of carbon dioxide, ethanol clathrate hydrate has been synthesized with 10% of large structure I (sI) cages occupied by ethanol. In this work, we use molecular dynamics simulations to study hydrogen bonding structure and dynamics in this binary sI clathrate hydrate in the temperature range of 100-250 K. We observe that ethanol forms long-lived (>500 ps) proton-donating and accepting hydrogen bonds with cage water molecules from both hexagonal and pentagonal faces of the large cages while maintaining the general cage integrity of the sI clathrate hydrate. The presence of the nondipolar CO2 molecules stabilizes the hydrate phase, despite the strong and prevalent alcohol-water hydrogen bonding. The distortions of the large cages from the ideal form, the radial distribution functions of the guest-host interactions, and the ethanol guest dynamics are characterized in this study. In previous work through dielectric and NMR relaxation time studies, single crystal x-ray diffraction, and molecular dynamics simulations we have observed guest-water hydrogen bonding in structure II and structure H clathrate hydrates. The present work extends the observation of hydrogen bonding to structure I hydrates.

Study of Comets Composition and Structure

NASA Astrophysics Data System (ADS)

Khalaf, S. Z.; Selman, A. A.; Ali, H. S.

2008-12-01

The present paper focuses on the nature of the different interactions between cometary nucleus and tail with solar wind. The dynamics of the comet will impose many features that provide unique behavior of the comet when entering the solar system. These features are reviewed in this paper and few investigations are made. The calculations made in this work represent the analysis and interpretation of the different features of the comet, such as perihelion and eccentricity dependence on the gas production rate, and the dependence of the latter on the composition of the comet nucleus. The dependences of the heliocentric, bow shock, contact surface, and stand-off distances with gas production rate for many types of comets that cover linear and non-linear types are studied in this work. Important results are obtained which indicated the different physical interactions between cometary ions and solar wind. Furthermore, the important relation between mean molecular weight and gas production rate are analyzed and studied in this work and a conclusion is made that, as the gas production rate increases, the mean molecular weight will decrease exponentially. A detailed discussion for this unique relation is given.

An electromechanical model of myosin molecular motors.

PubMed

Masuda, Tadashi

2003-12-21

There is a long-running debate on the working mechanism of myosin molecular motors, which, by interacting with actin filaments, convert the chemical energy of ATP into a variety of mechanical work. After the development of technologies for observing and manipulating individual working molecules, experimental results negating the widely accepted 'lever-arm hypothesis' have been reported. In this paper, based on the experimental results so far accumulated, an alternative hypothesis is proposed, in which motor molecules are modelled as electromechanical components that interact with each other through electrostatic force. Electrostatic attractive force between myosin and actin is assumed to cause a conformational change in the myosin head during the attachment process. An elastic energy resulting from the conformational change then produces the power stroke. The energy released at the ATP hydrolysis is mainly used to detach the myosin head from actin filaments. The mechanism presented in this paper is compatible with the experimental results contradictory to the previous theories. It also explains the behavior of myosins V and VI, which are engaged in cellular transport and move processively along actin filaments.

Structural Rearrangement of Au-Pd Nanoparticles under Reaction Conditions: An ab Initio Molecular Dynamics Study.

PubMed

Xu, Cong-Qiao; Lee, Mal-Soon; Wang, Yang-Gang; Cantu, David C; Li, Jun; Glezakou, Vassiliki-Alexandra; Rousseau, Roger

2017-02-28

The structure, composition, and atomic distribution of nanoalloys under operating conditions are of significant importance for their catalytic activity. In the present work, we use ab initio molecular dynamics simulations to understand the structural behavior of Au-Pd nanoalloys supported on rutile TiO 2 under different conditions. We find that the Au-Pd structure is strongly dependent on the redox properties of the support, originating from strong metal-support interactions. Under reducing conditions, Pd atoms are inclined to move toward the metal/oxide interface, as indicated by a significant increase of Pd-Ti bonds. This could be attributed to the charge localization at the interface that leads to Coulomb attractions to positively charged Pd atoms. In contrast, under oxidizing conditions, Pd atoms would rather stay inside or on the exterior of the nanoparticle. Moreover, Pd atoms on the alloy surface can be stabilized by hydrogen adsorption, forming Pd-H bonds, which are stronger than Au-H bonds. Our work offers critical insights into the structure and redox properties of Au-Pd nanoalloy catalysts under working conditions.

Advanced plastic scintillators for fast neutron discrimination

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

Feng, Patrick L; Anstey, Mitchell; Doty, F. Patrick

2014-09-01

The present work addresses the need for solid-state, fast neutron discriminating scintillators that possess higher light yields and faster decay kinetics than existing organic scintillators. These respective attributes are of critical importance for improving the gamma-rejection capabilities and increasing the neutron discrimination performance under high-rate conditions. Two key applications that will benefit from these improvements include large-volume passive detection scenarios as well as active interrogation search for special nuclear materials. Molecular design principles were employed throughout this work, resulting in synthetically tailored materials that possess the targeted scintillation properties.

Discovery of the photosynthetic relatives of the "Maltese mushroom" Cynomorium

PubMed Central

Nickrent, Daniel L; Der, Joshua P; Anderson, Frank E

2005-01-01

Background Although recent molecular phylogenetic studies have identified the photosynthetic relatives of several enigmatic holoparasitic angiosperms, uncertainty remains for the last parasitic plant order, Balanophorales, often considered to include two families, Balanophoraceae and Cynomoriaceae. The nonphotosynthetic (holoparasitic) flowering plant Cynomorium coccineum has long been known to the Muslim world as "tarthuth" and to Europeans as the "Maltese mushroom"; C. songaricum is known in Chinese medicine as "suo yang." Interest in these plants is increasing and they are being extensively collected from wild populations for use in herbal medicines. Results Here we report molecular phylogenetic analyses of nuclear ribosomal DNA and mitochondrial matR sequence data that strongly support the independent origin of Balanophoraceae and Cynomoriaceae. Analyses of single gene and combined gene data sets place Cynomorium in Saxifragales, possibly near Crassulaceae (stonecrop family). Balanophoraceae appear related to Santalales (sandalwood order), a position previously suggested from morphological characters that are often assumed to be convergent. Conclusion Our work shows that Cynomorium and Balanophoraceae are not closely related as indicated in all past and present classifications. Thus, morphological features, such as inflorescences bearing numerous highly reduced flowers, are convergent and were attained independently by these two holoparasite lineages. Given the widespread harvest of wild Cynomorium species for herbal medicines, we here raise conservation concerns and suggest that further molecular phylogenetic work is needed to identify its photosynthetic relatives. These relatives, which will be easier to cultivate, should then be examined for phytochemical activity purported to be present in the more sensitive Cynomorium. PMID:15969755

Electron tomography and 3D molecular simulations of platinum nanocrystals

NASA Astrophysics Data System (ADS)

Florea, Ileana; Demortière, Arnaud; Petit, Christophe; Bulou, Hervé; Hirlimann, Charles; Ersen, Ovidiu

2012-07-01

This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface.This work reports on the morphology of individual platinum nanocrystals with sizes of about 5 nm. By using the electron tomography technique that gives 3D spatial selectivity, access to quantitative information in the real space was obtained. The morphology of individual nanoparticles was characterized using HAADF-STEM tomography and it was shown to be close to a truncated octahedron. Using molecular dynamics simulations, this geometrical shape was found to be the one minimizing the nanocrystal energy. Starting from the tomographic reconstruction, 3D crystallographic representations of the studied Pt nanocrystals were obtained at the nanometer scale, allowing the quantification of the relative amount of the crystallographic facets present on the particle surface. Electronic supplementary information (ESI) available. See DOI: 10.1039/c2nr30990d

Raman Spectroscopy Detects Cardiac Allograft Rejection with Molecular Specificity

PubMed Central

Chung, Yoon Gi; Tu, Qiang; Cao, Dianjun; Harada, Shuko; Eisen, Howard J; Chang, Chang

2009-01-01

Abstract Spatially resolved Raman spectroscopy is shown here to be capable of molecular‐specific detection without exogenous labeling. This molecular specificity is achieved by detecting the strong and characteristic Raman spectral signature of an indole derivative, serotonin, whose selective existence in rejected heart transplants serves as the biomarker. The study also corroborates the increasingly recognized role of serotonin receptors in various immune responses, including cardiac allograft rejection. Combining both medical and physical sciences, this work demonstrates the potential use of Raman spectroscopy in replacing the invasive endomyocardial biopsy as the standard for post‐transplantation rejection surveillance and presents a new paradigm in advancing clinical care through interdisciplinary studies. PMID:20443894

Atomistic simulation of graphene-based polymer nanocomposites

NASA Astrophysics Data System (ADS)

Rissanou, Anastassia N.; Bačová, Petra; Harmandaris, Vagelis

2016-05-01

Polymer/graphene nanostructured systems are hybrid materials which have attracted great attention the last years both for scientific and technological reasons. In the present work atomistic Molecular Dynamics simulations are performed for the study of graphene-based polymer nanocomposites composed of pristine, hydrogenated and carboxylated graphene sheets dispersed in polar (PEO) and nonpolar (PE) short polymer matrices (i.e., matrices containing chains of low molecular weight). Our focus is twofold; the one is the study of the structural and dynamical properties of short polymer chains and the way that they are affected by functionalized graphene sheets while the other is the effect of the polymer matrices on the behavior of graphene sheets.

Molecular Modeling on the PC (by Matthew F. Schlecht)

NASA Astrophysics Data System (ADS)

Rioux, Reviewed Frank

2000-06-01

"Computeraided molecular modeling doesn't exist for its own sake, but to contribute to scientific endeavor, and enable the scientist to work smarter." This is the last sentence of Schlecht's preface and it says something very important about contemporary scientific research in the academic and industrial venues. Owing to the accelerating improvement in computer technology (hardware and software) and its widespread availability, molecular modeling has become a reliable and important tool in chemical research. Consequently, experimentalists have incorporated molecular modeling techniques in their research, and partnerships with computational chemists have become common. This is a wellorganized and thorough monograph that devotes its attention to one type of molecular modeling, molecular mechanics, and one molecular modeling software package, PCMODEL. Schlecht targets two reader-user groups, the novice and the journeyman modeler, and articulates three goals. He wants to provide the novice with an introduction to molecular mechanics, and after that with some practical examples of the use of empirical force field calculations. His third goal is to provide the journeyman modeler with a reference work that will aid "further study and practice". These are potentially conflicting goals, but Schlecht is, in my opinion, successful because of the way his book is organized. A comprehensive treatment such as this one is not meant to be read from cover to cover, because it is both an exposition of basic principles and a user's manual. Therefore, the novice and the experienced modeler will undoubtedly use this book in different ways. For example, a novice modeler might be advised to read the Preface and Chapter 1, which together provide a broad introduction to the historical development and goals of molecular mechanics. From there the novice could go to Chapter 5 and read section 5.1 on the components of the molecular mechanics force field, which is presented in 22 pages with plenty of graphical support. The reader is now ready to move to Chapter 6 on applications and work through the 32 exercises (Chapters 3 and 4 have an additional 11 exercises) designed to illustrate the current uses of molecular modeling in academic and industrial research. Chapter 3 (Input and Output), Chapter 4 (File Formats), and the balance of Chapter 5 can be consulted as needed. For example, Chapter 5 contains 160 pages on the evolution of the various empirical force fields in use today and important information in each case on parameterization and implementation. Besides finding a clearly written, wellorganized, thorough presentation, the reader will appreciate a number of other important features. There are numerous references (993) to the primary literature covering the field of molecular mechanics from its beginnings to mid1997, when the book went to press. There is a complete glossary of PCMODEL commands, and a comprehensive and valuable glossary (77 pages) of frequently used computer terms. There are 392 figures (many of them screen captures) providing illustrations of the PCMODEL interface in use and examples of input and output files. To aid the reader/user in obtaining expertise as a modeler, a diskette containing all the structure files for all the exercises accompanies the text. In addition, the author provides, on the same diskette, a browserreadable HTML file that contains links to a large number of pertinent resources on the World Wide Web. In summary, Molecular Modeling on the PC, by Matthew Schlecht, is a very impressive contribution to the molecular modeling literature. Schlecht's book should be in every college and university library and in the personal libraries of those who want to learn more about molecular mechanics or who anticipate its use in their teaching or research.

Topological analysis of long-chain branching patterns in polyolefins.

PubMed

Bonchev, D; Markel, E; Dekmezian, A

2001-01-01

Patterns in molecular topology and complexity for long-chain branching are quantitatively described. The Wiener number, the topological complexity index, and a new index of 3-starness are used to quantify polymer structure. General formulas for these indices were derived for the cases of 3-arm star, H-shaped, and B-arm comb polymers. The factors affecting complexity in monodisperse polymer systems are ranked as follows: number of arms > arm length > arm central position approximately equal to arm clustering > total molecular weight approximately equal to backbone molecular weight. Topological indices change rapidly and then plateau as the molecular weight of branches on a polyolefin backbone increases from 0 to 5 kD. Complexity calculations relate 2-arm or 3-arm comb structures to the corresponding 3-arm stars of equivalent complexity but much higher molecular weight. In a subsequent paper, we report the application of topological analysis for developing structure/property relationships for monodisperse polymers. While the focus of the present work is on the description of monodisperse, well-defined architectures, the methods may be extended to the description of polydisperse systems.

Quantum chemical study of a derivative of 3-substituted dithiocarbamic flavanone

NASA Astrophysics Data System (ADS)

Gosav, Steluta; Paduraru, Nicoleta; Maftei, Dan; Birsa, Mihail Lucian; Praisler, Mirela

2017-02-01

The aim of this work is to characterize a quite novel 3-dithiocarbamic flavonoid by vibrational spectroscopy in conjunction with Density Functional Theory (DFT) calculations. Quantum mechanics calculations of energies, geometries and vibrational wavenumbers in the ground state were carried out by using hybrid functional B3LYP with 6-311G(d,p) as basis set. The results indicate a remarkable agreement between the calculated molecular geometries, as well as vibrational frequencies, and the corresponding experimental data. In addition, a complete assignment of all the absorption bands present in the vibrational spectrum has been performed. In order to assess its chemical potential, quantum molecular descriptors characterizing the interactions between the 3-dithiocarbamic flavonoid and its biological receptors have been computed. The frontier molecular orbitals and the HOMO-LUMO energy gap have been used in order to explain the way in which the new molecule can interact with other species and to characterize its molecular chemical stability/reactivity. The molecular electrostatic potential (MEP) map, computed in order to identify the sites of the studied flavonoid that are most likely to interact with electrophilic and nucleophilic species, is discussed.

Accessing the molecular frame through strong-field alignment of distributions of gas phase molecules

NASA Astrophysics Data System (ADS)

Reid, Katharine L.

2018-03-01

A rationale for creating highly aligned distributions of molecules is that it enables vector properties referenced to molecule-fixed axes (the molecular frame) to be determined. In the present work, the degree of alignment that is necessary for this to be achieved in practice is explored. Alignment is commonly parametrized in experiments by a single parameter, ?, which is insufficient to enable predictive calculations to be performed. Here, it is shown that, if the full distribution of molecular axes takes a Gaussian form, this single parameter can be used to determine the complete set of alignment moments needed to characterize the distribution. In order to demonstrate the degree of alignment that is required to approach the molecular frame, the alignment moments corresponding to a few chosen values of ? are used to project a model molecular frame photoelectron angular distribution into the laboratory frame. These calculations show that ? needs to approach 0.9 in order to avoid significant blurring to be caused by averaging. This article is part of the theme issue `Modern theoretical chemistry'.

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

Sahu, Nityananda; Gadre, Shridhar R., E-mail: gadre@iitk.ac.in

The present work reports the calculation of vibrational infrared (IR) and Raman spectra of large molecular systems employing molecular tailoring approach (MTA). Further, it extends the grafting procedure for the accurate evaluation of IR and Raman spectra of large molecular systems, employing a new methodology termed as Fragments-in-Fragments (FIF), within MTA. Unlike the previous MTA-based studies, the accurate estimation of the requisite molecular properties is achieved without performing any full calculations (FC). The basic idea of the grafting procedure is implemented by invoking the nearly basis-set-independent nature of the MTA-based error vis-à-vis the respective FCs. FIF has been tested outmore » for the estimation of the above molecular properties for three isomers, viz., β-strand, 3{sub 10}- and α-helix of acetyl(alanine){sub n}NH{sub 2} (n = 10, 15) polypeptides, three conformers of doubly protonated gramicidin S decapeptide and trpzip2 protein (PDB id: 1LE1), respectively, employing BP86/TZVP, M06/6-311G**, and M05-2X/6-31G** levels of theory. For most of the cases, a maximum difference of 3 cm{sup −1} is achieved between the grafted-MTA frequencies and the corresponding FC values. Further, a comparison of the BP86/TZVP level IR and Raman spectra of α-helical (alanine){sub 20} and its N-deuterated derivative shows an excellent agreement with the existing experimental spectra. In view of the requirement of only MTA-based calculations and the ability of FIF to work at any level of theory, the current methodology provides a cost-effective solution for obtaining accurate spectra of large molecular systems.« less

Chemotion ELN: an Open Source electronic lab notebook for chemists in academia.

PubMed

Tremouilhac, Pierre; Nguyen, An; Huang, Yu-Chieh; Kotov, Serhii; Lütjohann, Dominic Sebastian; Hübsch, Florian; Jung, Nicole; Bräse, Stefan

2017-09-25

The development of an electronic lab notebook (ELN) for researchers working in the field of chemical sciences is presented. The web based application is available as an Open Source software that offers modern solutions for chemical researchers. The Chemotion ELN is equipped with the basic functionalities necessary for the acquisition and processing of chemical data, in particular the work with molecular structures and calculations based on molecular properties. The ELN supports planning, description, storage, and management for the routine work of organic chemists. It also provides tools for communicating and sharing the recorded research data among colleagues. Meeting the requirements of a state of the art research infrastructure, the ELN allows the search for molecules and reactions not only within the user's data but also in conventional external sources as provided by SciFinder and PubChem. The presented development makes allowance for the growing dependency of scientific activity on the availability of digital information by providing Open Source instruments to record and reuse research data. The current version of the ELN has been using for over half of a year in our chemistry research group, serves as a common infrastructure for chemistry research and enables chemistry researchers to build their own databases of digital information as a prerequisite for the detailed, systematic investigation and evaluation of chemical reactions and mechanisms.

Effects of substrate orientation on the growth of InSb nanostructures by molecular beam epitaxy

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

Chou, C. Y.; Torfi, A.; Pei, C.

2016-05-09

In this work, the effects of substrate orientation on InSb quantum structure growth by molecular beam epitaxy (MBE) are presented. Motivated by the observation that (411) evolves naturally as a stable facet during MBE crystal growth, comparison studies have been carried out to investigate the effects of the crystal orientation of the underlying GaSb substrate on the growth of InSb by MBE. By depositing InSb on a number of different substrate orientations, namely: (100), (311), (411), and (511), a higher nanostructure density was observed on the (411) surface compared with the other orientations. This result suggests that the (411) orientationmore » presents a superior surface in MBE growth to develop a super-flat GaSb buffer surface, naturally favorable for nanostructure growth.« less

Discriminating Drug-Like Compounds by Partition Trees with Quantum Similarity Indices and Graph Invariants.

PubMed

Julián-Ortiz, Jesus V de; Gozalbes, Rafael; Besalú, Emili

2016-01-01

The search for new drug candidates in databases is of paramount importance in pharmaceutical chemistry. The selection of molecular subsets is greatly optimized and much more promising when potential drug-like molecules are detected a priori. In this work, about one hundred thousand molecules are ranked following a new methodology: a drug/non-drug classifier constructed by a consensual set of classification trees. The classification trees arise from the stochastic generation of training sets, which in turn are used to estimate probability factors of test molecules to be drug-like compounds. Molecules were represented by Topological Quantum Similarity Indices and their Graph Theoretical counterparts. The contribution of the present paper consists of presenting an effective ranking method able to improve the probability of finding drug-like substances by using these types of molecular descriptors.

Temperature estimation from molecular nitrogen UV spectra in atmospheric pressure plasmas

NASA Astrophysics Data System (ADS)

Pepper, Keenan; Kim, Yongho; Kim, Jihun

2008-11-01

Atmospheric pressure plasmas have many potential applications to fuel processing, surface treatment, and manipulation of chemical reactions. These plasmas are often non-thermal, which means different species are not in equilibrium and have different effective temperatures. This is critical for many applications because it allows high concentrations of reactive species to be produced without using a prohibitive amount of power. In the present work, numerical software was developed to estimate the vibrational and rotational temperatures (Tvib and Trot) of N2 molecules from their ultraviolet emission spectra. The electron temperature Te can also be estimated by comparing the N2 spectrum to that of the N2^+ molecular ion. This technique is applied to several plasma sources including audio frequency, RF, and microwave devices. The results are presented and their implications for practical applications are discussed.

A COMPUTER MODELING STUDY OF BINDING PROPERTIES OF CHIRAL NUCLEOPEPTIDE FOR BIOMEDICAL APPLICATIONS.

PubMed

Pirtskhalava, M; Egoyan, A; Mirtskhulava, M; Roviello, G

2017-12-01

Nucleopeptides often show interesting properties of molecular binding that render them good candidates for development of innovative drugs for anticancer and antiviral therapies. In this work we present results of computer modeling of interactions between the molecules of hexathymine nucleopeptide (T6) and poly rA RNA (A18). The results of geometry optimization calculated using Hyperchem software and our own computer program for molecular docking show that molecules establish stable complexes due to the complementary-nucleobase interaction and the electrostatic interaction between the negative phosphate group of poly rA and the positively-charged residues present in the cationic nucleopeptide structure. Computer modeling makes it possible to find the optimal binding configuration of the molecules of a nucleopeptide and poly rA RNA and to estimate the binding energy between the molecules.

Excess protons in water-acetone mixtures. II. A conductivity study.

PubMed

Semino, Rocío; Longinotti, M Paula

2013-10-28

In the present work we complement a previous simulation study [R. Semino and D. Laria, J. Chem. Phys. 136, 194503 (2012)] on the disruption of the proton transfer mechanism in water by the addition of an aprotic solvent, such as acetone. We provide experimental measurements of the mobility of protons in aqueous-acetone mixtures in a wide composition range, for water molar fractions, xw, between 0.05 and 1.00. Furthermore, new molecular dynamics simulation results are presented for rich acetone mixtures, which provide further insight into the proton transport mechanism in water-non-protic solvent mixtures. The proton mobility was analyzed between xw 0.05 and 1.00 and compared to molecular dynamics simulation data. Results show two qualitative changes in the proton transport composition dependence at xw ∼ 0.25 and 0.8. At xw < 0.25 the ratio of the infinite dilution molar conductivities of HCl and LiCl, Λ(0)(HCl).Λ(0)(LiCl)(-1), is approximately constant and equal to one, since the proton diffusion is vehicular and equal to that of Li(+). At xw ∼ 0.25, proton mobility starts to differ from that of Li(+) indicating that above this concentration the Grotthuss transport mechanism starts to be possible. Molecular dynamics simulation results showed that at this threshold concentration the probability of interconversion between two Eigen structures starts to be non-negligible. At xw ∼ 0.8, the infinite molar conductivity of HCl concentration dependence qualitatively changes. This result is in excellent agreement with the analysis presented in the previous simulation work and it has been ascribed to the interchange of water and acetone molecules in the second solvation shell of the hydronium ion.

Targeted Cancer Therapy: Vital Oncogenes and a New Molecular Genetic Paradigm for Cancer Initiation Progression and Treatment.

PubMed

Willis, Rudolph E

2016-09-14

It has been declared repeatedly that cancer is a result of molecular genetic abnormalities. However, there has been no working model describing the specific functional consequences of the deranged genomic processes that result in the initiation and propagation of the cancer process during carcinogenesis. We no longer need to question whether or not cancer arises as a result of a molecular genetic defect within the cancer cell. The legitimate questions are: how and why? This article reviews the preeminent data on cancer molecular genetics and subsequently proposes that the sentinel event in cancer initiation is the aberrant production of fused transcription activators with new molecular properties within normal tissue stem cells. This results in the production of vital oncogenes with dysfunctional gene activation transcription properties, which leads to dysfunctional gene regulation, the aberrant activation of transduction pathways, chromosomal breakage, activation of driver oncogenes, reactivation of stem cell transduction pathways and the activation of genes that result in the hallmarks of cancer. Furthermore, a novel holistic molecular genetic model of cancer initiation and progression is presented along with a new paradigm for the approach to personalized targeted cancer therapy, clinical monitoring and cancer diagnosis.

The Evolutionary Connection Bewtween z~2-3 Submillimeter Galaxies and AGN as Probed by Molecular Gas Excitation

NASA Astrophysics Data System (ADS)

Sharon, Chelsea E.; Riechers, Dominik A.; Carilli, Chris Luke; Hodge, Jacqueline; Walter, Fabian

2016-01-01

Theoretical work has suggested that active galactic nuclei (AGN) play an important role in quenching star formation in massive galaxies. Direct evidence for AGN affecting the molecular ISM has so far been limited to detections of molecular outflows in low-redshift systems and extreme excitation regions which represent a tiny fraction of the total gas. Indirect evidence for AGN's impact on their host galaxies' cold gas phase may be provided by measurements of the gas excitation and dynamics. At z~2-3, the peak epoch of star formation and AGN activity, previous observations of the CO(1-0) line revealed that submillimeter galaxies (SMGs) have multi-phase molecular gas, including substantial reservoirs of cold-phase gas. However, the entirety of the molecular gas in AGN-host galaxies appears highly excited, potentially supporting an evolutionary connection between these two populations. I will present a new VLA sample that nearly doubles the number of CO(1-0) detections in z~2-3 SMGs and AGN-host galaxies that allows us to better compare the cold gas properties of these systems and further investigate evidence for the effects of AGN on the star-forming molecular gas.

Predictive Mechanical Characterization of Macro-Molecular Material Chemistry Structures of Cement Paste at Nano Scale - Two-phase Macro-Molecular Structures of Calcium Silicate Hydrate, Tri-Calcium Silicate, Di-Calcium Silicate and Calcium Hydroxide

NASA Astrophysics Data System (ADS)

Padilla Espinosa, Ingrid Marcela

Concrete is a hierarchical composite material with a random structure over a wide range of length scales. At submicron length scale the main component of concrete is cement paste, formed by the reaction of Portland cement clinkers and water. Cement paste acts as a binding matrix for the other components and is responsible for the strength of concrete. Cement paste microstructure contains voids, hydrated and unhydrated cement phases. The main crystalline phases of unhydrated cement are tri-calcium silicate (C3S) and di-calcium silicate (C2S), and of hydrated cement are calcium silicate hydrate (CSH) and calcium hydroxide (CH). Although efforts have been made to comprehend the chemical and physical nature of cement paste, studies at molecular level have primarily been focused on individual components. Present research focuses on the development of a method to model, at molecular level, and analysis of the two-phase combination of hydrated and unhydrated phases of cement paste as macromolecular systems. Computational molecular modeling could help in understanding the influence of the phase interactions on the material properties, and mechanical performance of cement paste. Present work also strives to create a framework for molecular level models suitable for potential better comparisons with low length scale experimental methods, in which the sizes of the samples involve the mixture of different hydrated and unhydrated crystalline phases of cement paste. Two approaches based on two-phase cement paste macromolecular structures, one involving admixed molecular phases, and the second involving cluster of two molecular phases are investigated. The mechanical properties of two-phase macromolecular systems of cement paste consisting of key hydrated phase CSH and unhydrated phases C3S or C2S, as well as CSH with the second hydrated phase CH were calculated. It was found that these cement paste two-phase macromolecular systems predicted an isotropic material behavior. Also, these systems exhibited a high bulk modulus, compared to the elastic modulus. These results are an indication and concur with the high compression strength of cement paste seen at engineering length scale. In addition, the bulk modulus of two-phase systems consisting of hydrated CSH and unhydrated C3S or C2S was found to increase with higher levels of unhydrated components. The interaction energies of two-phase cement paste molecular structures studied in the present work were calculated, showing that a higher interaction is attained when the two phases are admixed as small components instead of cluster of phases. Finally, the mechanical behavior under shear deformation was predicted by using a quasi-static deformation method and analyzed for a representative two-phase (CSH and C2S) macromolecular structure of cement paste.

Automated Illustration of Molecular Flexibility.

PubMed

Bryden, A; Phillips, George N; Gleicher, M

2012-01-01

In this paper, we present an approach to creating illustrations of molecular flexibility using normal mode analysis (NMA). The output of NMA is a collection of points corresponding to the locations of atoms and associated motion vectors, where a vector for each point is known. Our approach abstracts the complex object and its motion by grouping the points, models the motion of each group as an affine velocity, and depicts the motion of each group by automatically choosing glyphs such as arrows. Affine exponentials allow the extrapolation of nonlinear effects such as near rotations and spirals from the linear velocities. Our approach automatically groups points by finding sets of neighboring points whose motions fit the motion model. The geometry and motion models for each group are used to determine glyphs that depict the motion, with various aspects of the motion mapped to each glyph. We evaluated the utility of our system in real work done by structural biologists both by utilizing it in our own structural biology work and quantitatively measuring its usefulness on a set of known protein conformation changes. Additionally, in order to allow ourselves and our collaborators to effectively use our techniques we integrated our system with commonly used tools for molecular visualization.

Adsorption and Dissociation of Molecular Hydrogen on the (0001) Surface of DHCP Americium

NASA Astrophysics Data System (ADS)

Dholabhai, Pratik; Ray, Asok

2009-03-01

Hydrogen molecule adsorption on the (0001) surface of double hexagonal closed packed americium has been studied in detail within the framework of density functional theory. Weak molecular hydrogen adsorptions were observed. The most stable configuration corresponded to a Hor2 approach molecular adsorption at the one-fold top site where the molecule's approach is perpendicular to a lattice vector. Adsorption energies and adsorption geometries for different adsorption sites will be discussed. The change in work functions, magnetic moments, partial charges inside muffin-tins, difference charge density distributions and density of states for the bare Am slab and the Am slab after adsorption of the hydrogen molecule will be discussed. Reaction barrier for the dissociation of hydrogen molecule will be presented. The implications of adsorption on Am 5f electron localization-delocalization will be summarized.

A model of early formation of uranium molecular oxides in laser-ablated plasmas

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

Finko, Mikhail S.; Curreli, Davide; Weisz, David G.

Here, in this work, we present a newly constructed U xO y reaction mechanism that consists of 30 reaction channels (21 of which are reversible channels) for 11 uranium molecular species (including ions). Both the selection of reaction channels and calculation of corresponding rate coefficients is accomplished via a comprehensive literature review and application of basic reaction rate theory. The reaction mechanism is supplemented by a detailed description of oxygen plasma chemistry (19 species and 142 reaction channels) and is used to model an atmospheric laser ablated uranium plume via a 0D (global) model. Finally, the global model is usedmore » to analyze the evolution of key uranium molecular species predicted by the reaction mechanism, and the initial stage of formation of uranium oxide species.« less

Quantum Mechanics/Molecular Mechanics Free Energy Maps and Nonadiabatic Simulations for a Photochemical Reaction in DNA: Cyclobutane Thymine Dimer.

PubMed

Mendieta-Moreno, Jesús I; Trabada, Daniel G; Mendieta, Jesús; Lewis, James P; Gómez-Puertas, Paulino; Ortega, José

2016-11-03

The absorption of ultraviolet radiation by DNA may result in harmful genetic lesions that affect DNA replication and transcription, ultimately causing mutations, cancer, and/or cell death. We analyze the most abundant photochemical reaction in DNA, the cyclobutane thymine dimer, using hybrid quantum mechanics/molecular mechanics (QM/MM) techniques and QM/MM nonadiabatic molecular dynamics. We find that, due to its double helix structure, DNA presents a free energy barrier between nonreactive and reactive conformations leading to the photolesion. Moreover, our nonadiabatic simulations show that most of the photoexcited reactive conformations return to standard B-DNA conformations after an ultrafast nonradiative decay to the ground state. This work highlights the importance of dynamical effects (free energy, excited-state dynamics) for the study of photochemical reactions in biological systems.

Application of molecular dynamics simulation to predict the compatability between water-insoluble drugs and self-associating poly(ethylene oxide)-b-poly(epsilon-caprolactone) block copolymers.

PubMed

Patel, Sarthak; Lavasanifar, Afsaneh; Choi, Phillip

2008-11-01

In the present work, molecular dynamics (MD) simulation was applied to study the solubility of two water-insoluble drugs, fenofibrate and nimodipine, in a series of micelle-forming PEO-b-PCL block copolymers with combinations of blocks having different molecular weights. The solubility predictions based on the MD results were then compared with those obtained from solubility experiments and by the commonly used group contribution method (GCM). The results showed that Flory-Huggins interaction parameters computed by the MD simulations are consistent with the solubility data of the drug/PEO-b-PCL systems, whereas those calculated by the GCM significantly deviate from the experimental observation. We have also accounted for the possibility of drug solubilization in the PEO block of PEO-b-PCL.

Communication: Molecular near-infrared transitions determined with sub-kHz accuracy.

PubMed

Wang, Jin; Sun, Yu R; Tao, Lei-Gang; Liu, An-Wen; Hu, Shui-Ming

2017-09-07

Precise molecular transition frequencies are needed in various studies including the test of fundamental physics. Two well isolated ro-vibrational transitions of 12 C 16 O at 1.57 μm, R(9) and R(10) in the second overtone band, were measured by a comb-locked cavity ring-down spectrometer. Despite the weakness of the lines (Einstein coefficient A≃0.008 s -1 ), Lamb-dip spectra were recorded with a signal-to-noise ratio over 1000, and the line positions were determined to be 191 360 212 761.1 and 191 440 612 662.2 kHz, respectively, with an uncertainty of 0.5 kHz (δν/ν=2.6×10 -12 ). The present work demonstrates the possibility to explore extensive molecular lines in the near-infrared with sub-kHz accuracy.

A model of early formation of uranium molecular oxides in laser-ablated plasmas

DOE PAGES

Finko, Mikhail S.; Curreli, Davide; Weisz, David G.; ...

2017-10-12

Here, in this work, we present a newly constructed U xO y reaction mechanism that consists of 30 reaction channels (21 of which are reversible channels) for 11 uranium molecular species (including ions). Both the selection of reaction channels and calculation of corresponding rate coefficients is accomplished via a comprehensive literature review and application of basic reaction rate theory. The reaction mechanism is supplemented by a detailed description of oxygen plasma chemistry (19 species and 142 reaction channels) and is used to model an atmospheric laser ablated uranium plume via a 0D (global) model. Finally, the global model is usedmore » to analyze the evolution of key uranium molecular species predicted by the reaction mechanism, and the initial stage of formation of uranium oxide species.« less

Convergence acceleration of molecular dynamics methods for shocked materials using velocity scaling

NASA Astrophysics Data System (ADS)

Taylor, DeCarlos E.

2017-03-01

In this work, a convergence acceleration method applicable to extended system molecular dynamics techniques for shock simulations of materials is presented. The method uses velocity scaling to reduce the instantaneous value of the Rankine-Hugoniot conservation of energy constraint used in extended system molecular dynamics methods to more rapidly drive the system towards a converged Hugoniot state. When used in conjunction with the constant stress Hugoniostat method, the velocity scaled trajectories show faster convergence to the final Hugoniot state with little difference observed in the converged Hugoniot energy, pressure, volume and temperature. A derivation of the scale factor is presented and the performance of the technique is demonstrated using the boron carbide armour ceramic as a test material. It is shown that simulation of boron carbide Hugoniot states, from 5 to 20 GPa, using both a classical Tersoff potential and an ab initio density functional, are more rapidly convergent when the velocity scaling algorithm is applied. The accelerated convergence afforded by the current algorithm enables more rapid determination of Hugoniot states thus reducing the computational demand of such studies when using expensive ab initio or classical potentials.

Food for thought: Sub-fossil and fossil chelonian remains from Franchthi Cave and Megalopolis confirm a glacial refuge for Emys orbicularis in Peloponnesus (S. Greece)

NASA Astrophysics Data System (ADS)

Vlachos, Evangelos; Delfino, Massimo

2016-10-01

Peloponnesus peninsula (S. Greece) shows a remarkable extant chelonian fauna that has received considerable attention from a molecular and morphological point of view. Here we present new evidence from the fossil and sub-fossil record of two important sites in the area, Franchthi Cave and Megalopolis. The archaeological material from Franchthi Cave (Upper Paleolithic - Neolithic/latest Pleistocene - early Holocene) represents food remains from small game prey of the humans that inhabited the cave. The palaeontological material from Megalopolis (Late Pleistocene) comes from old and new excavations. The studied specimens, combined with information from molecular, climatic and zoological works, provide for the first time direct evidence for the presence of the European pond turtle, Emys orbicularis, in the glacial refuge of South Greece that was hypothesized on the basis of the results of molecular investigations. We also describe other chelonian taxa present in the localities, the Hermann's tortoise Testudo hermanni and the Balkan stripe-necked terrapin Mauremys rivulata, and review previously published chelonian material from Peloponnesus.

Molecular cytogenetics characterization of seven small supernumerary marker chromosomes derived from chromosome 19: Genotype-phenotype correlation and review of the literature.

PubMed

Recalcati, Maria Paola; Bonati, Maria Teresa; Beltrami, Nicola; Cardarelli, Laura; Catusi, Ilaria; Costa, Asia; Garzo, Maria; Mammi, Isabella; Mattina, Teresa; Nalesso, Elisa; Nardone, Anna Maria; Postorivo, Diana; Sajeva, Anna; Varricchio, Aminta; Verri, Annapia; Villa, Nicoletta; Larizza, Lidia; Giardino, Daniela

2018-03-01

Only a few subjects carrying supernumerary marker chromosomes derived from 19 chromosome (sSMC(19)) have been described to date and for a small portion of them the genic content has been defined at the molecular level. We present seven new different sSMCs(19) identified in eight individuals, seven of whom unrelated. The presence of the sSMC is associated with a clinical phenotype in five subjects, while the other three carriers, two of whom related, are normal. All sSMCs(19) have been characterized by means of conventional and molecular cytogenetics. We compare the sSMCs(19) carriers with a clinical phenotype to already described patients with gains (sSMCs or microduplications) of overlapping genomic regions with the aim to deepen the pathogenicity of the encountered imbalances and to assess the role of the involved genes on the phenotype. The present work supports the correlation between the gain of some chromosome 19 critical regions and specific phenotypes. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Stimulated Raman scattering (SRS) spectroscopic OCT (Conference Presentation)

NASA Astrophysics Data System (ADS)

Robles, Francisco E.; Zhou, Kevin C.; Fischer, Martin C.; Warren, Warren S.

2017-02-01

Optical coherence tomography (OCT) enables non-invasive, high-resolution, tomographic imaging of biological tissues by leveraging principles of low coherence interferometry; however, OCT lacks molecular specificity. Spectroscopic OCT (SOCT) overcomes this limitation by providing depth-resolved spectroscopic signatures of chromophores, but SOCT has been limited to a couple of endogenous molecules, namely hemoglobin and melanin. Stimulated Raman scattering, on the other hand, can provide highly specific molecular information of many endogenous species, but lacks the spatial and spectral multiplexing capabilities of SOCT. In this work we integrate the two methods, SRS and SOCT, to enable simultaneously multiplexed spatial and spectral imaging with sensitivity to many endogenous biochemical species that play an important role in biology and medicine. The method, termed SRS-SOCT, has the potential to achieve fast, volumetric, and highly sensitive label-free molecular imaging, which would be valuable for many applications. We demonstrate the approach by imaging excised human adipose tissue and detecting the lipids' Raman signatures in the high-wavenumber region. Details of this method along with validations and results will be presented.

Targeting CYP51 for drug design by the contributions of molecular modeling.

PubMed

Rabelo, Vitor W; Santos, Taísa F; Terra, Luciana; Santana, Marcos V; Castro, Helena C; Rodrigues, Carlos R; Abreu, Paula A

2017-02-01

CYP51 is an enzyme of sterol biosynthesis pathway present in animals, plants, protozoa and fungi. This enzyme is described as an important drug target that is still of interest. Therefore, in this work, we reviewed the structure and function of CYP51 and explored the molecular modeling approaches for the development of new antifungal and antiprotozoans that target this enzyme. Crystallographic structures of CYP51 of some organisms have already been described in the literature, which enable the construction of homology models of other organisms' enzymes and molecular docking studies of new ligands. The binding mode and interactions of some new series of azoles with antifungal or antiprotozoan activities has been studied and showed important residues of the active site. Molecular modeling is an important tool to be explored for the discovery and optimization of CYP51 inhibitors with better activities, pharmacokinetics, and toxicological profiles. © 2016 Société Française de Pharmacologie et de Thérapeutique.

Effect of Molecular Flexibility on the Nematic-to-Isotropic Phase Transition for Highly Biaxial Molecular Non-Symmetric Liquid Crystal Dimers

PubMed Central

Sebastián, Nerea; López, David Orencio; Diez-Berart, Sergio; de la Fuente, María Rosario; Salud, Josep; Pérez-Jubindo, Miguel Angel; Ros, María Blanca

2011-01-01

In this work, a study of the nematic (N)–isotropic (I) phase transition has been made in a series of odd non-symmetric liquid crystal dimers, the α-(4-cyanobiphenyl-4’-yloxy)-ω-(1-pyrenimine-benzylidene-4’-oxy) alkanes, by means of accurate calorimetric and dielectric measurements. These materials are potential candidates to present the elusive biaxial nematic (NB) phase, as they exhibit both molecular biaxiality and flexibility. According to the theory, the uniaxial nematic (NU)–isotropic (I) phase transition is first-order in nature, whereas the NB–I phase transition is second-order. Thus, a fine analysis of the critical behavior of the N–I phase transition would allow us to determine the presence or not of the biaxial nematic phase and understand how the molecular biaxiality and flexibility of these compounds influences the critical behavior of the N–I phase transition. PMID:28824100

The Effect of Molecular Weight on the Composite Properties of Cured Phenylethynyl Terminated Imide Oligomers

NASA Technical Reports Server (NTRS)

Smith, J. G., Jr.; Connell, J. W.; Hergenrother, P. M.

1997-01-01

As part of a program to develop high temperature/high performance structural resins for aeronautical applications, imide oligomers containing terminal phenylethynyl groups with calculated number average molecular weights of 1250, 2500 and 5000 g/mol were prepared, characterized, and evaluated as adhesives and composite matrix resins. The goal of this work was to develop resin systems that are processable using conventional processing equipment into void free composites that exhibit high mechanical properties with long term high temperature durability, and are not affected by exposure to common aircraft fluids. The imide oligomers containing terminal phenylethynyl groups were fabricated into titanium adhesive specimens and IM-7 carbon fiber laminates under 0.1 - 1.4 MPa for 1 hr at 350-371 C. The lower molecular weight oligomers exhibited higher cured Tg, better processability, and better retention of mechanical properties at elevated temperature without significantly sacrificing toughness or damage tolerance than the higher molecular weight oligomer. The neat resin, adhesive and composite properties of the cured polymers will be presented.

Analysis of low molecular weight compounds by MALDI-FTICR-MS.

PubMed

Wang, Hao-Yang; Chu, Xu; Zhao, Zhi-Xiong; He, Xiao-Shuang; Guo, Yin-Long

2011-05-15

This review focuses on recent applications of matrix-assisted laser desorption ionization-Fourier-transform ion cyclotron resonance mass spectrometry (MALDI-FTICR-MS) in qualitative and quantitative analysis of low molecular weight compounds. The scope of the work includes amino acids, small peptides, mono and oligosaccharides, lipids, metabolic compounds, small molecule phytochemicals from medicinal herbs and even the volatile organic compounds from tobacco. We discuss both direct analysis and analysis following derivatization. In addition we review sample preparation strategies to reduce interferences in the low m/z range and to improve sensitivities by derivatization with charge tags. We also present coupling of head space techniques with MALDI-FTICR-MS. Furthermore, omics analyses based on MALDI-FTICR-MS were also discussed, including proteomics, metabolomics and lipidomics, as well as the relative MS imaging for bio-active low molecular weight compounds. Finally, we discussed the investigations on dissociation/rearrangement processes of low molecular weight compounds by MALDI-FTICR-MS. Copyright © 2011 Elsevier B.V. All rights reserved.

Chemical sensors from the cooperative actuation of multistep electrochemical molecular machines of polypyrrole: potentiostatic study. Trying to replicate muscle’s fatigue signals

NASA Astrophysics Data System (ADS)

Beaumont, Samuel; Otero, Toribio F.

2018-07-01

Polypyrrole film electrodes are constituted by multielectronic electrochemical molecular machines (every polymeric molecule) counterions and water, mimicking the intracellular matrix of muscular cells. The influence of the electrolyte concentration on the reversible oxidation/reduction of polypyrrole films was studied in NaCl aqueous solutions by consecutive square potential waves. The consumed redox charge and the consumed electrical energy change as a function of the concentration. That means that the extension (the consumed charge) of the reaction involving conformational, or allosteric, movements of the reacting polymeric chains (molecular machines) responds to (senses) the chemical energy of the reaction ambient. A theoretical description of the attained empirical results is presented getting the sensing equations and the concomitant sensitivities. Those results could indicate the origin and nature of the neural signals sent to the brain from biological haptic muscles working by cooperative actuation of the actin-myosin molecular machines driven by chemical reactions and sensing, simultaneously, the fatigue state of the muscle.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations.

PubMed

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-14

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiC x O 6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young's modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young's modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Modeling of amorphous SiCxO6/5 by classical molecular dynamics and first principles calculations

NASA Astrophysics Data System (ADS)

Liao, Ningbo; Zhang, Miao; Zhou, Hongming; Xue, Wei

2017-02-01

Polymer-derived silicon oxycarbide (SiCO) presents excellent performance for high temperature and lithium-ion battery applications. Current experiments have provided some information on nano-structure of SiCO, while it is very challenging for experiments to take further insight into the molecular structure and its relationship with properties of materials. In this work, molecular dynamics (MD) based on empirical potential and first principle calculation were combined to investigate amorphous SiCxO6/5 ceramics. The amorphous structures of SiCO containing silicon-centered mix bond tetrahedrons and free carbon were successfully reproduced. The calculated radial distribution, angular distribution and Young’s modulus were validated by current experimental data, and more details on molecular structure were discussed. The change in the slope of Young’s modulus is related to the glass transition temperature of the material. The proposed modeling approach can be used to predict the properties of SiCO with different compositions.

Towards a high sensitivity small animal PET system based on CZT detectors (Conference Presentation)

NASA Astrophysics Data System (ADS)

Abbaszadeh, Shiva; Levin, Craig

2017-03-01

Small animal positron emission tomography (PET) is a biological imaging technology that allows non-invasive interrogation of internal molecular and cellular processes and mechanisms of disease. New PET molecular probes with high specificity are under development to target, detect, visualize, and quantify subtle molecular and cellular processes associated with cancer, heart disease, and neurological disorders. However, the limited uptake of these targeted probes leads to significant reduction in signal. There is a need to advance the performance of small animal PET system technology to reach its full potential for molecular imaging. Our goal is to assemble a small animal PET system based on CZT detectors and to explore methods to enhance its photon sensitivity. In this work, we reconstruct an image from a phantom using a two-panel subsystem consisting of six CZT crystals in each panel. For image reconstruction, coincidence events with energy between 450 and 570 keV were included. We are developing an algorithm to improve sensitivity of the system by including multiple interaction events.

Molecular organization, localization and orientation of antifungal antibiotic amphotericin B in a single lipid bilayer

PubMed Central

Grudzinski, Wojciech; Sagan, Joanna; Welc, Renata; Luchowski, Rafal; Gruszecki, Wieslaw I.

2016-01-01

Amphotericin B is a popular antifungal antibiotic, a gold standard in treatment of systemic mycotic infections, due to its high effectiveness. On the other hand, applicability of the drug is limited by its considerable toxicity to patients. Biomembranes are a primary target of physiological activity of amphotericin B and both the pharmacologically desired and toxic side effects of the drug relay on its molecular organization in the lipid phase. In the present work, molecular organization, localization and orientation of amphotericin B, in a single lipid bilayer system, was analysed simultaneously, thanks to application of a confocal fluorescence lifetime imaging microscopy of giant unilamellar vesicles. The results show that the presence of sterols, in the lipid phase, promotes formation of supramolecular structures of amphotericin B and their penetration into the membrane hydrophobic core. The fact that such an effect is substantially less pronounced in the case of cholesterol than ergosterol, the sterol of fungal membranes, provides molecular insight into the selectivity of the drug. PMID:27620838

Some Dynamical Features of Molecular Fragmentation by Electrons and Swift Ions

NASA Astrophysics Data System (ADS)

Montenegro, E. C.; Sigaud, L.; Wolff, W.; Luna, H.; Natalia, Ferreira

To date, the large majority of studies on molecular fragmentation by swift charged particles have been carried out using simple molecules, for which reliable Potential Energy Curves are available to interpret the measured fragmentation yields. For complex molecules the scenario is quite different and such guidance is not available, obscuring even a simple organization of the data which are currently obtained for a large variety of molecules of biological or technological interest. In this work we show that a general and relatively simple methodology can be used to obtain a broader picture of the fragmentation pattern of an arbitrary molecule. The electronic ionization or excitation cross section of a given molecular orbital, which is the first part of the fragmentation process, can be well scaled by a simple and general procedure at high projectile velocities. The fragmentation fractions arising from each molecular orbital can then be achieved by matching the calculated ionization with the measured fragmentation cross sections. Examples for Oxygen, Chlorodifluoromethane and Pyrimidine molecules are presented.

Investigation for Molecular Attraction Impact Between Contacting Surfaces in Micro-Gears

NASA Astrophysics Data System (ADS)

Yang, Ping; Li, Xialong; Zhao, Yanfang; Yang, Haiying; Wang, Shuting; Yang, Jianming

2013-10-01

The aim of this research work is to provide a systematic method to perform molecular attraction impact between contacting surfaces in micro-gear train. This method is established by integrating involute profile analysis and molecular dynamics simulation. A mathematical computation of micro-gear involute is presented based on geometrical properties, Taylor expression and Hamaker assumption. In the meantime, Morse potential function and the cut-off radius are introduced with a molecular dynamics simulation. So a hybrid computational method for the Van Der Waals force between the contacting faces in micro-gear train is developed. An example is illustrated to show the performance of this method. The results show that the change of Van Der Waals force in micro-gear train has a nonlinear characteristic with parameters change such as the modulus of the gear and the tooth number of gear etc. The procedure implies a potential feasibility that we can control the Van Der Waals force by adjusting the manufacturing parameters for gear train design.

Molecular cloning of toxins expressed by the venom gland of Lasiodora sp.

PubMed

Vieira, A L G; Moura, M B; Babá, E H; Chávez-Olórtegui, C; Kalapothakis, E; Castro, I M

2004-12-15

The present work describes the identification of toxins expressed by the venom gland of the spider Lasiodora sp. The toxins LTx1, LTx2 and LTx3 were identified by the screening of a cDNA library. These toxins showed significant similarity at the amino acid level with spider toxins from Lasiodora parahybana, Eurypelma californicum, Brachypelma smithii, Selenocosmia huwena.

Problem-Solving Test: RNA and Protein Synthesis in Bacteriophage-Infected "E. coli" Cells

ERIC Educational Resources Information Center

Szeberenyi, Jozsef

2008-01-01

The classic experiment presented in this problem-solving test was designed to identify the template molecules of translation by analyzing the synthesis of phage proteins in "Escherichia coli" cells infected with bacteriophage T4. The work described in this test led to one of the most seminal discoveries of early molecular biology: it dealt a…

Molecular-Simulation-Driven Fragment Screening for the Discovery of New CXCL12 Inhibitors.

PubMed

Martinez-Rosell, Gerard; Harvey, Matt J; De Fabritiis, Gianni

2018-03-26

Fragment-based drug discovery (FBDD) has become a mainstream approach in drug design because it allows the reduction of the chemical space and screening libraries while identifying fragments with high protein-ligand efficiency interactions that can later be grown into drug-like leads. In this work, we leverage high-throughput molecular dynamics (MD) simulations to screen a library of 129 fragments for a total of 5.85 ms against the CXCL12 monomer, a chemokine involved in inflammation and diseases such as cancer. Our in silico binding assay was able to recover binding poses, affinities, and kinetics for the selected library and was able to predict 8 mM-affinity fragments with ligand efficiencies higher than 0.3. All of the fragment hits present a similar chemical structure, with a hydrophobic core and a positively charged group, and bind to either sY7 or H1S68 pockets, where they share pharmacophoric properties with experimentally resolved natural binders. This work presents a large-scale screening assay using an exclusive combination of thousands of short MD adaptive simulations analyzed with a Markov state model (MSM) framework.

The effect of carbon-chain oxygenation in the carbon-carbon dissociation.

PubMed

Dos Santos, Lisandra Paulino; Baptista, Leonardo

2018-06-01

Currently, there is a trend of moving away from the use of fossil fuels to the use of biofuels. This modification changes the molecular structure of gasoline and diesel constituents, which should impact pollutant emissions and engine efficiency. An important property of automotive fuels is the resistance to autoignition. The goal of the present work is to evaluate thermochemical and kinetic parameters that govern the carbon-carbon bond dissociation and relate these parameters, in conjunction with molecular properties, to autoignition resistance. Three model reactions were investigated in the present work: dissociation of ethane, ethanol, and ethanal. All studies were conducted at the multiconfigurational level of theory, and the rate coefficients were evaluated from 300 to 2000 K. The comparison of dissociation energies and Arrhenius expressions indicates that autoignition resistance is related to the kinetic control of dissociation reactions and it is possible to relate the higher octane number of ethanol based fuels to the kinetics parameters of carbon-carbon bond fission. Graphical abstract Effect of the functional group in the Arrhenius parameters of the C-C dissociation. Arrhenius curves calculated at NEVPT2(6,6)/6-311G(2df,2pd).

Transport Phenomena of Water in Molecular Fluidic Channels

PubMed Central

Vo, Truong Quoc; Kim, BoHung

2016-01-01

In molecular-level fluidic transport, where the discrete characteristics of a molecular system are not negligible (in contrast to a continuum description), the response of the molecular water system might still be similar to the continuum description if the time and ensemble averages satisfy the ergodic hypothesis and the scale of the average is enough to recover the classical thermodynamic properties. However, even in such cases, the continuum description breaks down on the material interfaces. In short, molecular-level liquid flows exhibit substantially different physics from classical fluid transport theories because of (i) the interface/surface force field, (ii) thermal/velocity slip, (iii) the discreteness of fluid molecules at the interface and (iv) local viscosity. Therefore, in this study, we present the result of our investigations using molecular dynamics (MD) simulations with continuum-based energy equations and check the validity and limitations of the continuum hypothesis. Our study shows that when the continuum description is subjected to the proper treatment of the interface effects via modified boundary conditions, the so-called continuum-based modified-analytical solutions, they can adequately predict nanoscale fluid transport phenomena. The findings in this work have broad effects in overcoming current limitations in modeling/predicting the fluid behaviors of molecular fluidic devices. PMID:27650138

Development of a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees.

PubMed

Murphy, Michael J; Shahriari, Neda; Payette, Michael; Mnayer, Laila; Elaba, Zendee

2016-10-01

Results of molecular studies are redefining the diagnosis and management of a wide range of skin disorders. Dermatology training programs maintain a relative gap in relevant teaching. To develop a curriculum in molecular diagnostics, genomics and personalized medicine for dermatology trainees at our institution. The aim is to provide trainees with a specialty-appropriate, working knowledge in clinical molecular dermatology. The Departments of Dermatology and Pathology and Laboratory Medicine collaborated on the design and implementation of educational objectives and teaching modalities for the new curriculum. A multidisciplinary curriculum was developed. It comprises: (i) assigned reading from the medical literature and reference textbook; (ii) review of teaching sets; (iii) two 1 hour lectures; (iv) trainee presentations; (v) 1-week rotation in a clinical molecular pathology and cytogenetics laboratory; and (vi) assessments and feedback. Residents who participated in the curriculum to date have found the experience to be of value. Our curriculum provides a framework for other dermatology residency programs to develop their own specific approach to molecular diagnostics education. Such training will provide a foundation for lifelong learning as molecular testing evolves and becomes integral to the practice of dermatology. © 2016 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

Quantum Fragment Based ab Initio Molecular Dynamics for Proteins.

PubMed

Liu, Jinfeng; Zhu, Tong; Wang, Xianwei; He, Xiao; Zhang, John Z H

2015-12-08

Developing ab initio molecular dynamics (AIMD) methods for practical application in protein dynamics is of significant interest. Due to the large size of biomolecules, applying standard quantum chemical methods to compute energies for dynamic simulation is computationally prohibitive. In this work, a fragment based ab initio molecular dynamics approach is presented for practical application in protein dynamics study. In this approach, the energy and forces of the protein are calculated by a recently developed electrostatically embedded generalized molecular fractionation with conjugate caps (EE-GMFCC) method. For simulation in explicit solvent, mechanical embedding is introduced to treat protein interaction with explicit water molecules. This AIMD approach has been applied to MD simulations of a small benchmark protein Trpcage (with 20 residues and 304 atoms) in both the gas phase and in solution. Comparison to the simulation result using the AMBER force field shows that the AIMD gives a more stable protein structure in the simulation, indicating that quantum chemical energy is more reliable. Importantly, the present fragment-based AIMD simulation captures quantum effects including electrostatic polarization and charge transfer that are missing in standard classical MD simulations. The current approach is linear-scaling, trivially parallel, and applicable to performing the AIMD simulation of proteins with a large size.

Molecular detection via hybrid peptide-semiconductor photonic devices

NASA Astrophysics Data System (ADS)

Estephan, E.; Saab, M.-b.; Martin, M.; Cloitre, T.; Larroque, C.; Cuisinier, F. J. G.; Malvezzi, A. M.; Gergely, C.

2011-03-01

The aim of this work was to investigate the possibilities to support device functionality that includes strongly confined and localized light emission and detection processes within nano/micro-structured semiconductors for biosensing applications. The interface between biological molecules and semiconductor surfaces, yet still under-explored is a key issue for improving biomolecular recognition in devices. We report on the use of adhesion peptides, elaborated via combinatorial phage-display libraries for controlled placement of biomolecules, leading to user-tailored hybrid photonic systems for molecular detection. An M13 bacteriophage library has been used to screen 1010 different peptides against various semiconductors to finally isolate specific peptides presenting a high binding capacity for the target surfaces. When used to functionalize porous silicon microcavities (PSiM) and GaAs/AlGaAs photonic crystals, we observe the formation of extremely thin (<1nm) peptide layers, hereby preserving the nanostructuration of the crystals. This is important to assure the photonic response of these tiny structures when they are functionalized by a biotinylated peptide layer and then used to capture streptavidin. Molecular detection was monitored via both linear and nonlinear optical measurements. Our linear reflectance spectra demonstrate an enhanced detection resolution via PSiM devices, when functionalized with the Si-specific peptide. Molecular capture at even lower concentrations (femtomols) is possible via the second harmonic generation of GaAs/AlGaAs photonic crystals when functionalized with GaAs-specific peptides. Our work demonstrates the outstanding value of adhesion peptides as interface linkers between semiconductors and biological molecules. They assure an enhanced molecular detection via both linear and nonlinear answers of photonic crystals.

Discovery of an Unexplored Protein Structural Scaffold of Serine Protease from Big Blue Octopus (Octopus cyanea): A New Prospective Lead Molecule.

PubMed

Panda, Subhamay; Kumari, Leena

2017-01-01

Serine proteases are a group of enzymes that hydrolyses the peptide bonds in proteins. In mammals, these enzymes help in the regulation of several major physiological functions such as digestion, blood clotting, responses of immune system, reproductive functions and the complement system. Serine proteases obtained from the venom of Octopodidae family is a relatively unexplored area of research. In the present work, we tried to effectively utilize comparative composite molecular modeling technique. Our key aim was to propose the first molecular model structure of unexplored serine protease 5 derived from big blue octopus. The other objective of this study was to analyze the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis with the aid of different bioinformatic tools. In the present study, molecular model has been generated with the help of I-TASSER suite. Afterwards the refined structural model was validated with standard methods. For functional annotation of protein molecule we used Protein Information Resource (PIR) database. Serine protease 5 of big blue octopus was analyzed with different bioinformatical algorithms for the distribution of negatively and positively charged amino acid over molecular modeled structure, distribution of secondary structural elements, hydrophobicity molecular surface analysis and electrostatic potential analysis. The functionally critical amino acids and ligand- binding site (LBS) of the proteins (modeled) were determined using the COACH program. The molecular model data in cooperation to other pertinent post model analysis data put forward molecular insight to proteolytic activity of serine protease 5, which helps in the clear understanding of procoagulant and anticoagulant characteristics of this natural lead molecule. Our approach was to investigate the octopus venom protein as a whole or a part of their structure that may result in the development of new lead molecule. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Above-threshold ionization in multicenter molecules: The role of the initial state

NASA Astrophysics Data System (ADS)

Suárez, Noslen; Chacón, Alexis; Pisanty, Emilio; Ortmann, Lisa; Landsman, Alexandra S.; Picón, Antonio; Biegert, Jens; Lewenstein, Maciej; Ciappina, Marcelo F.

2018-03-01

A possible route to extract electronic and nuclear dynamics from molecular targets with attosecond temporal and nanometer spatial resolution is to employ recolliding electrons as "probes." The recollision process in molecules is, however, very challenging to treat using ab initio approaches. Even for the simplest diatomic systems, such as H2, today's computational capabilities are not enough to give a complete description of the electron and nuclear dynamics initiated by a strong laser field. As a consequence, approximate qualitative descriptions are called to play an important role. In this paper we extend the work presented in Suárez et al. [N. Suárez, A. Chacón, J. A. Pérez-Hernández, J. Biegert, M. Lewenstein, and M. F. Ciappina, High-order-harmonic generation in atomic and molecular systems, Phys. Rev. A 95, 033415 (2017), 10.1103/PhysRevA.95.033415] to three-center molecular targets. Additionally, we incorporate a more accurate description of the molecular ground state, employing information extracted from quantum chemistry software packages. This step forward allows us to include, in a detailed way, both the molecular symmetries and nodes present in the high-occupied molecular orbital. We are able, on the one hand, to keep our formulation as analytical as in the case of diatomics and, on the other hand, to still give a complete description of the underlying physics behind the above-threshold ionization process. The application of our approach to complex multicenter—with more than three centers—targets appears to be straightforward.

Path-space variational inference for non-equilibrium coarse-grained systems

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

Harmandaris, Vagelis, E-mail: harman@uoc.gr; Institute of Applied and Computational Mathematics; Kalligiannaki, Evangelia, E-mail: ekalligian@tem.uoc.gr

In this paper we discuss information-theoretic tools for obtaining optimized coarse-grained molecular models for both equilibrium and non-equilibrium molecular simulations. The latter are ubiquitous in physicochemical and biological applications, where they are typically associated with coupling mechanisms, multi-physics and/or boundary conditions. In general the non-equilibrium steady states are not known explicitly as they do not necessarily have a Gibbs structure. The presented approach can compare microscopic behavior of molecular systems to parametric and non-parametric coarse-grained models using the relative entropy between distributions on the path space and setting up a corresponding path-space variational inference problem. The methods can become entirelymore » data-driven when the microscopic dynamics are replaced with corresponding correlated data in the form of time series. Furthermore, we present connections and generalizations of force matching methods in coarse-graining with path-space information methods. We demonstrate the enhanced transferability of information-based parameterizations to different observables, at a specific thermodynamic point, due to information inequalities. We discuss methodological connections between information-based coarse-graining of molecular systems and variational inference methods primarily developed in the machine learning community. However, we note that the work presented here addresses variational inference for correlated time series due to the focus on dynamics. The applicability of the proposed methods is demonstrated on high-dimensional stochastic processes given by overdamped and driven Langevin dynamics of interacting particles.« less

Interface-Engineered Charge-Transport Properties in Benzenedithiol Molecular Electronic Junctions via Chemically p-Doped Graphene Electrodes.

PubMed

Jang, Yeonsik; Kwon, Sung-Joo; Shin, Jaeho; Jeong, Hyunhak; Hwang, Wang-Taek; Kim, Junwoo; Koo, Jeongmin; Ko, Taeg Yeoung; Ryu, Sunmin; Wang, Gunuk; Lee, Tae-Woo; Lee, Takhee

2017-12-06

In this study, we fabricated and characterized vertical molecular junctions consisting of self-assembled monolayers of benzenedithiol (BDT) with a p-doped multilayer graphene electrode. The p-type doping of a graphene film was performed by treating pristine graphene (work function of ∼4.40 eV) with trifluoromethanesulfonic (TFMS) acid, producing a significantly increased work function (∼5.23 eV). The p-doped graphene-electrode molecular junctions statistically showed an order of magnitude higher current density and a lower charge injection barrier height than those of the pristine graphene-electrode molecular junctions, as a result of interface engineering. This enhancement is due to the increased work function of the TFMS-treated p-doped graphene electrode in the highest occupied molecular orbital-mediated tunneling molecular junctions. The validity of these results was proven by a theoretical analysis based on a coherent transport model that considers asymmetric couplings at the electrode-molecule interfaces.

Developing Strategies to Block Beta-Catenin Action in Signaling and Cell Adhesion During Carcinogenesis

DTIC Science & Technology

2002-07-01

this section was published in a paper from our lab in Molecular Biology of the Cell (Simcha et al., 2001)--below we refer to Figures in this paper...work, both in yeast and in mammalian cells, were recently published in Molecular Biology of the Cell (Simcha et al., 2001), and the work from our lab ...detail genetic and molecular interactions between gro, wg ,arm and dTCF (task 2 and 4 above)- this work was a collaboration with the labs of Amy

Force and Conductance Spectroscopy of Single Molecule Junctions

NASA Astrophysics Data System (ADS)

Frei, Michael

Investigation of mechanical properties of single molecule junctions is crucial to develop an understanding and enable control of single molecular junctions. This work presents an experimental and analytical approach that enables the statistical evaluation of force and simultaneous conductance data of metallic atomic point contacts and molecular junctions. A conductive atomic force microscope based break junction technique is developed to form single molecular junctions and collect conductance and force data simultaneously. Improvements of the optical components have been achieved through the use of a super-luminescent diode, enabling tremendous increases in force resolution. An experimental procedure to collect data for various molecular junctions has been developed and includes deposition, calibration, and analysis methods. For the statistical analysis of force, novel approaches based on two dimensional histograms and a direct force identification method are presented. The two dimensional method allows for an unbiased evaluation of force events that are identified using corresponding conductance signatures. This is not always possible however, and in these situations, the force based identification of junction rearrangement events is an attractive alternative method. This combined experimental and analytical approach is then applied to three studies: First, the impact of molecular backbones to the mechanical behavior of single molecule junctions is investigated and it is found that junctions formed with identical linkers but different backbone structure result in junctions with varying breaking forces. All molecules used show a clear molecular signature and force data can be evaluated using the 2D method. Second, the effects of the linker group used to attach molecules to gold electrodes are investigated. A study of four alkane molecules with different linkers finds a drastic difference in the evolution of donor-acceptor and covalently bonded molecules respectively. In fact, the covalent bond is found to significantly distort the metal electrode rearrangement such that junction rearrangement events can no longer be identified with a clean and well defined conductance signature. For this case, the force based identification process is used. Third, results for break junction measurements with different metals are presented. It is found that silver and palladium junctions rupture with forces different from those of gold contacts. In the case of silver experiments in ambient conditions, we can also identify oxygen impurities in the silver contact formation process, leading to force and conductance measurements of silver-oxygen structures. For the future, this work provides an experimental and analytical foundation that will enable insights into single molecule systems not previously accessible.

OCT imaging of craniofacial anatomy in xenopus embryos (Conference Presentation)

NASA Astrophysics Data System (ADS)

Deniz, Engin; Jonas, Stephan M.; Griffin, John; Hooper, Michael C.; Choma, Michael A.; Khokha, Mustafa K.

2016-03-01

The etiology of craniofacial defects is incompletely understood. The ability to obtain large amounts of gene sequence data from families affected by craniofacial defects is opening up new ways to understand molecular genetic etiological factors. One important link between gene sequence data and clinical relevance is biological research into candidate genes and molecular pathways. We present our recent research using OCT as a nondestructive phenotyping modality of craniofacial morphology in Xenopus embryos, an important animal model for biological research in gene and pathway discovery. We define 2D and 3D scanning protocols for a standardized approach to craniofacial imaging in Xenopus embryos. We define standard views and planar reconstructions for visualizing normal anatomy and landmarks. We compare these views and reconstructions to traditional histopathology using alcian blue staining. In addition to being 3D, nondestructive, and having much faster throughout, OCT can identify craniofacial features that are lost during traditional histopathological preparation. We also identify quantitative morphometric parameters to define normative craniofacial anatomy. We also note that craniofacial and cardiac defects are not infrequently present in the same patient (e.g velocardiofacial syndrome). Given that OCT excels at certain aspects of cardiac imaging in Xenopus embryos, our work highlights the potential of using OCT and Xenopus to study molecular genetic factors that impact both cardiac and craniofacial development.

Diagnostic Yield of Next-Generation Sequencing in Very Early-Onset Inflammatory Bowel Diseases: A Multicenter Study.

PubMed

Charbit-Henrion, Fabienne; Parlato, Marianna; Hanein, Sylvain; Duclaux-Loras, Rémi; Nowak, Jan; Begue, Bernadette; Rakotobe, Sabine; Bruneau, Julie; Fourrage, Cécile; Alibeu, Olivier; Rieux-Laucat, Frédéric; Lévy, Eva; Stolzenberg, Marie-Claude; Mazerolles, Fabienne; Latour, Sylvain; Lenoir, Christelle; Fischer, Alain; Picard, Capucine; Aloi, Marina; Amil Dias, Jorge; Ben Hariz, Mongi; Bourrier, Anne; Breuer, Christian; Breton, Anne; Bronski, Jiri; Buderus, Stephan; Cananzi, Mara; Coopman, Stéphanie; Crémilleux, Clara; Dabadie, Alain; Dumant-Forest, Clémentine; Egritas Gurkan, Odul; Fabre, Alexandre; Fischer, Aude; German Diaz, Marta; Gonzalez-Lama, Yago; Goulet, Olivier; Guariso, Graziella; Gurcan, Neslihan; Homan, Matjaz; Hugot, Jean-Pierre; Jeziorski, Eric; Karanika, Evi; Lachaux, Alain; Lewindon, Peter; Lima, Rosa; Magro, Fernando; Major, Janos; Malamut, Georgia; Mas, Emmanuel; Mattyus, Istvan; Mearin, Luisa M; Melek, Jan; Navas-Lopez, Victor Manuel; Paerregaard, Anders; Pelatan, Cecile; Pigneur, Bénédicte; Pinto Pais, Isabel; Rebeuh, Julie; Romano, Claudio; Siala, Nadia; Strisciuglio, Caterina; Tempia-Caliera, Michela; Tounian, Patrick; Turner, Dan; Urbonas, Vaidotas; Willot, Stéphanie; Ruemmele, Frank M; Cerf-Bensussan, Nadine

2018-05-18

An expanding number of monogenic defects have been identified as causative of severe forms of very early-onset inflammatory bowel diseases (VEO-IBD). The present study aimed at defining how next-generation sequencing (NGS) methods can be used to improve identification of known molecular diagnosis and adapt treatment. 207 children were recruited in 45 Paediatric centres through an international collaborative network (ESPGHAN GENIUS working group) with a clinical presentation of severe VEO-IBD (n=185) or an anamnesis suggestive of a monogenic disorder (n=22). Patients were divided at inclusion into three phenotypic subsets: predominantly small bowel inflammation, colitis with perianal lesions, and colitis only. Methods to obtain molecular diagnosis included functional tests followed by specific Sanger sequencing, custom-made targeted NGS, and in selected cases whole exome sequencing (WES) of parents-child trios. Genetic findings were validated clinically and/or functionally. Molecular diagnosis was achieved in 66/207 children (32%): 61% with small bowel inflammation, 39% with colitis and perianal lesions and 18% with colitis only. Targeted NGS pinpointed gene mutations causative of atypical presentations and identified large exonic copy number variations previously missed by WES. Our results lead us to propose an optimised diagnostic strategy to identify known monogenic causes of severe IBD.

Molecular Electronic Angular Motion Transducer Broad Band Self-Noise

PubMed Central

Zaitsev, Dmitry; Agafonov, Vadim; Egorov, Egor; Antonov, Alexander; Shabalina, Anna

2015-01-01

Modern molecular electronic transfer (MET) angular motion sensors combine high technical characteristics with low cost. Self-noise is one of the key characteristics which determine applications for MET sensors. However, until the present there has not been a model describing the sensor noise in the complete operating frequency range. The present work reports the results of an experimental study of the self-noise level of such sensors in the frequency range of 0.01–200 Hz. Based on the experimental data, a theoretical model is developed. According to the model, self-noise is conditioned by thermal hydrodynamic fluctuations of the operating fluid flow in the frequency range of 0.01–2 Hz. At the frequency range of 2–100 Hz, the noise power spectral density has a specific inversely proportional dependence of the power spectral density on the frequency that could be attributed to convective processes. In the high frequency range of 100–200 Hz, the noise is conditioned by the voltage noise of the electronics module input stage operational amplifiers and is heavily reliant to the sensor electrical impedance. The presented results allow a deeper understanding of the molecular electronic sensor noise nature to suggest the ways to reduce it. PMID:26610502

A report template for molecular genetic tests designed to improve communication between the clinician and laboratory.

PubMed

Scheuner, Maren T; Hilborne, Lee; Brown, Julie; Lubin, Ira M

2012-07-01

Errors are most likely to occur during the pre- and postanalytic phases of the genetic testing process, which can contribute to underuse, overuse, and misuse of genetic tests. To mitigate these errors, we created a template for molecular genetic test reports that utilizes the combined features of synoptic reporting and narrative interpretation. A variation of the Delphi consensus process with an expert panel was used to create a draft report template, which was further informed by focus group discussions with primary care physicians. There was agreement that molecular genetic test reports should present information in groupings that flow in a logical manner, and most participants preferred the following order of presentation: patient and physician information, test performed, test results and interpretation, guidance on next steps, and supplemental information. We define data elements for the report as "required," "optional," "possible," and "not necessary"; provide recommendations regarding the grouping of these data elements; and describe the ideal design of the report template, including the preferred order of the report sections, formatting of data, and length of the report. With input from key stakeholders and building upon prior work, we created a template for molecular genetic test reports designed to improve clinical decision making at the point of care. The template design should lead to more effective communication between the laboratory and ordering clinician. Studies are needed to assess the usefulness and effectiveness of molecular genetic test reports generated using this template.

A quantitative analysis of IRAS maps of molecular clouds

NASA Technical Reports Server (NTRS)

Wiseman, Jennifer J.; Adams, Fred C.

1994-01-01

We present an analysis of IRAS maps of five molecular clouds: Orion, Ophiuchus, Perseus, Taurus, and Lupus. For the classification and description of these astrophysical maps, we use a newly developed technique which considers all maps of a given type to be elements of a pseudometric space. For each physical characteristic of interest, this formal system assigns a distance function (a pseudometric) to the space of all maps: this procedure allows us to measure quantitatively the difference between any two maps and to order the space of all maps. We thus obtain a quantitative classification scheme for molecular clouds. In this present study we use the IRAS continuum maps at 100 and 60 micrometer(s) to produce column density (or optical depth) maps for the five molecular cloud regions given above. For this sample of clouds, we compute the 'output' functions which measure the distribution of density, the distribution of topological components, the self-gravity, and the filamentary nature of the clouds. The results of this work provide a quantitative description of the structure in these molecular cloud regions. We then order the clouds according to the overall environmental 'complexity' of these star-forming regions. Finally, we compare our results with the observed populations of young stellar objects in these clouds and discuss the possible environmental effects on the star-formation process. Our results are consistent with the recently stated conjecture that more massive stars tend to form in more 'complex' environments.

Treatment of geometric singularities in implicit solvent models

NASA Astrophysics Data System (ADS)

Yu, Sining; Geng, Weihua; Wei, G. W.

2007-06-01

Geometric singularities, such as cusps and self-intersecting surfaces, are major obstacles to the accuracy, convergence, and stability of the numerical solution of the Poisson-Boltzmann (PB) equation. In earlier work, an interface technique based PB solver was developed using the matched interface and boundary (MIB) method, which explicitly enforces the flux jump condition at the solvent-solute interfaces and leads to highly accurate biomolecular electrostatics in continuum electric environments. However, such a PB solver, denoted as MIBPB-I, cannot maintain the designed second order convergence whenever there are geometric singularities, such as cusps and self-intersecting surfaces. Moreover, the matrix of the MIBPB-I is not optimally symmetrical, resulting in the convergence difficulty. The present work presents a new interface method based PB solver, denoted as MIBPB-II, to address the aforementioned problems. The present MIBPB-II solver is systematical and robust in treating geometric singularities and delivers second order convergence for arbitrarily complex molecular surfaces of proteins. A new procedure is introduced to make the MIBPB-II matrix optimally symmetrical and diagonally dominant. The MIBPB-II solver is extensively validated by the molecular surfaces of few-atom systems and a set of 24 proteins. Converged electrostatic potentials and solvation free energies are obtained at a coarse grid spacing of 0.5Å and are considerably more accurate than those obtained by the PBEQ and the APBS at finer grid spacings.

Ground states of linear rotor chains via the density matrix renormalization group

NASA Astrophysics Data System (ADS)

Iouchtchenko, Dmitri; Roy, Pierre-Nicholas

2018-04-01

In recent years, experimental techniques have enabled the creation of ultracold optical lattices of molecules and endofullerene peapod nanomolecular assemblies. It was previously suggested that the rotor model resulting from the placement of dipolar linear rotors in one-dimensional lattices at low temperature has a transition between ordered and disordered phases. We use the density matrix renormalization group (DMRG) to compute ground states of chains of up to 100 rotors and provide further evidence of the phase transition in the form of a diverging entanglement entropy. We also propose two methods and present some first steps toward rotational spectra of such molecular assemblies using DMRG. The present work showcases the power of DMRG in this new context of interacting molecular rotors and opens the door to the study of fundamental questions regarding criticality in systems with continuous degrees of freedom.

Controllable growth of layered selenide and telluride heterostructures and superlattices using molecular beam epitaxy

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

Vishwanath, Suresh; Liu, Xinyu; Rouvimov, Sergei

2016-01-06

Layered materials are an actively pursued area of research for realizing highly scaled technologies involving both traditional device structures as well as new physics. Lately, non-equilibrium growth of 2D materials using molecular beam epitaxy (MBE) is gathering traction in the scientific community and here we aim to highlight one of its strengths, growth of abrupt heterostructures, and superlattices (SLs). In this work we present several of the firsts: first growth of MoTe 2 by MBE, MoSe 2 on Bi 2Se 3 SLs, transition metal dichalcogenide (TMD) SLs, and lateral junction between a quintuple atomic layer of Bi 2Te 3 andmore » a triple atomic layer of MoTe 2. In conclusion, reflected high electron energy diffraction oscillations presented during the growth of TMD SLs strengthen our claim that ultrathin heterostructures with monolayer layer control is within reach.« less

Thermal properties of tannin extracted from Anacardium occidentale L. using TGA and FT-IR spectroscopy.

PubMed

Viswanath, Vinod; Leo, Vincent Vineeth; Prabha, S Sabna; Prabhakumari, C; Potty, V P; Jisha, M S

2016-01-01

The chemical nature of the polyphenols of cashew kernel testa has been determined. Testa contains tannins, which present large molecular complexity and has an ancient use as tanning agents. The use of tannins extracted from cashew testa, considered in many places as a waste, grants an extra value to the cashew. In this work we have analysed through high performance liquid chromatography, infrared spectroscopy (FT-IR) and thermo gravimetric analysis the average molecular weight, main functional groups and thermal properties of tannins extracted from Anacardium occidentale L. The results of these analyses are compared with the commercial grade tannic acid. The FT-IR spectra showed bands characteristic of C = C, C-C and OH bonds. This important bioactive compound present in the cashew nut kernel testa was suggested as an interesting economical source of antioxidants for use in the food and nutraceutical industry.

Improved Escherichia coli Bactofection and Cytotoxicity by Heterologous Expression of Bacteriophage ΦX174 Lysis Gene E.

PubMed

Chung, Tai-Chun; Jones, Charles H; Gollakota, Akhila; Kamal Ahmadi, Mahmoud; Rane, Snehal; Zhang, Guojian; Pfeifer, Blaine A

2015-05-04

Bactofection offers a gene delivery option particularly useful in the context of immune modulation. The bacterial host naturally attracts recognition and cellular uptake by antigen presenting cells (APCs) as the initial step in triggering an immune response. Moreover, depending on the bacterial vector, molecular biology tools are available to influence and/or overcome additional steps and barriers to effective antigen presentation. In this work, molecular engineering was applied using Escherichia coli as a bactofection vector. In particular, the bacteriophage ΦX174 lysis E (LyE) gene was designed for variable expression across strains containing different levels of lysteriolysin O (LLO). The objective was to generate a bacterial vector with improved attenuation and delivery characteristics. The resulting strains exhibited enhanced gene and protein release and inducible cellular death. In addition, the new vectors demonstrated improved gene delivery and cytotoxicity profiles to RAW264.7 macrophage APCs.

On the influence of the mixture of denaturants on protein structure stability: A molecular dynamics study

NASA Astrophysics Data System (ADS)

Shao, Qiang; Wang, Jinan; Zhu, Weiliang

2014-09-01

Mixtures of osmolytes and/or inorganic salts are present in the cell. Therefore, the understanding of the interplay of mixed osmolyte molecules and inorganic salts and their combined effects on protein structure is of fundamental importance. A novel test is presented to investigate the combined effects of urea and a chaotropic inorganic salt, potassium iodide (KI), on protein structure by using molecular dynamics simulation. It is found that the coexistence of KI and urea does not affect their respective distribution in solution. The solvation of KI salt in urea solution makes the electrostatic interactions of urea more favorable, promoting the hydrogen bonding between urea (and water) to protein backbone. The interactions from K+ and hydrogen bonding from urea and water to protein backbone work as the driving force for protein denaturation. The collaborative behavior of urea and KI salt thus enhances the denaturing ability of urea and KI mixed solution.

Molecular Simulations of Graphene-Based Electric Double-Layer Capacitors

NASA Astrophysics Data System (ADS)

Kalluri, Raja K.; Konatham, Deepthi; Striolo, Alberto

2011-03-01

Towards deploying renewable energy sources it is crucial to develop efficient and cost-effective technologies to store electricity. Traditional batteries are plagued by a number of practical problems that at present limit their widespread applicability. One possible solution is represented by electric double-layer capacitors (EDLCs). To deploy EDLCs at the large scale it is necessary to better understand how electrolytes pack and diffuse within narrow charged pores. We present here simulation results for the concentrated aqueous solutions of NaCl, CsCl, and NaI confined within charged graphene-based porous materials. We discuss how the structure of confined water, the salt concentration, the ions size, and the surface charge density determine the accumulation of electrolytes within the porous network. Our results, compared to data available for bulk systems, are critical for relating macroscopic observations to molecular-level properties of the confined working fluids. Research supported by the Department of Energy.

Proteolytic enzyme engineering: a tool for wool.

PubMed

Araújo, Rita; Silva, Carla; Machado, Raul; Casal, Margarida; Cunha, António M; Rodriguez-Cabello, José Carlos; Cavaco-Paulo, Artur

2009-06-08

One of the goals of protein engineering is to tailor the structure of enzymes to optimize industrial bioprocesses. In the present work, we present the construction of a novel high molecular weight subtilisin, based on the fusion of the DNA sequences coding for Bacillus subtilis prosubtilisin E and for an elastin-like polymer (ELP). The resulting fusion protein was biologically produced in Escherichia coli , purified and used for wool finishing assays. When compared to the commercial protease Esperase, the recombinant subtilisinE-VPAVG(220) activity was restricted to the cuticle of wool, allowing a significant reduction of pilling, weight loss and tensile strength loss of wool fibers. Here we report, for the first time, the microbial production of a functionalized high molecular weight protease for controlled enzymatic hydrolysis of wool surface. This original process overcomes the unrestrained diffusion and extended fiber damage which are the major obstacles for the use of proteases for wool finishing applications.

Characterization of landfill leachates by molecular size distribution, biodegradability, and inert chemical oxygen demand.

PubMed

Amaral, Míriam C S; Ferreira, Cynthia F A; Lange, Liséte Celina; Aquino, Sérgio F

2009-05-01

This work presents results from a detailed characterization of landfill leachates of different ages from a landfill in a major Brazilian city. This characterization consists of determining the molecular size distribution and the inert chemical oxygen demand (COD) and the biodegradability of both aerobic and anaerobic processes. Results show that leachate with a high COD concentration leachate has low biodegradability. A significant fraction of the COD is not characterized as protein, carbohydrate, or lipids, which reinforces the hypothesis that the remaining fraction was present in all leachate fractions (less than 1 kDa; between 1 and 10 kDa; between 10 and 100 kDa; and greater than 100 kDa) and is refractory. These results suggest that leachates with such characteristics require treatment systems that use physical-chemical processes as a pre- or post-treatment step to biological processes.

Studies on molecular structure and tautomerism of a vitamin B6 analog with density functional theory.

PubMed

Sahoo, Suban K; Sharma, Darshna; Bera, Rati Kanta

2012-05-01

This work presents a computational study on the molecular structure and tautomeric equilibria of a novel Schiff base L derived from pyridoxal (PL) and o-phenylenediamine by using the density functional method B3LYP with basis sets 6-31 G(d,p), 6-31++G(d,p), 6-311 G(d,p) and 6-311++G(d,p). The optimized geometrical parameters obtained by B3LYP/6-31 G(d,p) method showed the best agreement with the experimental values. Tautomeric stability study of L inferred that the enolimine form is more stable than its ketoenamine form in both gas phase and solution. However, protonation of the pyridoxal nitrogen atom (LH) have accelerated the formation of ketoenamine form, and therefore, both ketoenamine and enolimine forms could be present in acidic media.

Laser Diagnostics for Reacting Flows

DTIC Science & Technology

2007-01-30

image the exit region of an underexpanded jet. Background IRPLIF involves the excitation of molecular vibrational modes via infrared laser radiation (an...excitation wavelength of 2.0 pm is used for this work), followed by imaging of the subsequent vibrational fluorescence (fluorescence is collected...with an IR-active vibrational mode, such as CO2, are naturally present in sufficient abundance. Even in situations where they need to be added, small

An Interdisciplinary Approach for Designing Kinetic Models of the Ras/MAPK Signaling Pathway.

PubMed

Reis, Marcelo S; Noël, Vincent; Dias, Matheus H; Albuquerque, Layra L; Guimarães, Amanda S; Wu, Lulu; Barrera, Junior; Armelin, Hugo A

2017-01-01

We present in this article a methodology for designing kinetic models of molecular signaling networks, which was exemplarily applied for modeling one of the Ras/MAPK signaling pathways in the mouse Y1 adrenocortical cell line. The methodology is interdisciplinary, that is, it was developed in a way that both dry and wet lab teams worked together along the whole modeling process.

Linus Pauling and sickle cell disease.

PubMed

Eaton, William A

2003-01-01

The 1949 paper by Linus Pauling et al. [Science 110 (1949) 543-548] describing the discovery of sickle cell anemia as the first molecular disease had a major impact on biology and medicine. Inspired by the scholarly works of John Edsall on the history of hemoglobin research, I present a brief retrospective analysis of Pauling's paper. This is followed by some personal recollections of Edsall and Pauling.

A simple backscattering microscope for fast tracking of biological molecules

PubMed Central

Sowa, Yoshiyuki; Steel, Bradley C.; Berry, Richard M.

2010-01-01

Recent developments in techniques for observing single molecules under light microscopes have helped reveal the mechanisms by which molecular machines work. A wide range of markers can be used to detect molecules, from single fluorophores to micron sized markers, depending on the research interest. Here, we present a new and simple objective-type backscattering microscope to track gold nanoparticles with nanometer and microsecond resolution. The total noise of our system in a 55 kHz bandwidth is ∼0.6 nm per axis, sufficient to measure molecular movement. We found our backscattering microscopy to be useful not only for in vitro but also for in vivo experiments because of lower background scattering from cells than in conventional dark-field microscopy. We demonstrate the application of this technique to measuring the motion of a biological rotary molecular motor, the bacterial flagellar motor, in live Escherichia coli cells. PMID:21133475

The vibrational spectroscopic studies and molecular property analysis of Estradiol, Tamoxifen and their interaction by density functional theory

NASA Astrophysics Data System (ADS)

Borah, Mukunda Madhab; Gomti Devi, Th.

2018-07-01

In the present work Tamoxifen, Estradiol and their interaction are studied using the experimental and theoretical methodologies. The spectral characterization was made by using Raman, FTIR, DFT and VEDA calculation. The optimization of the molecules have been studied using basis set B3LYP/6-31 G(d,p). Complete vibrational assignment of Tamoxifen, Estradiol and Estradiol + Tamoxifen have been attempted and the potential energy distribution and normal mode analysis had also been carried out to determine the contributions of bond oscillators in each normal mode. We have optimized several binding modes of Estradiol and Tamoxifen and taken the lowest energy conformer in our interest. The molecular geometry, HOMO-LUMO energy gap, molecular hardness (η), ionization energy (IE), electron affinity (EA), total energy and dipole moment were analyzed. The observed experimental and the scaled theoretical results were found in good agreement.

How nanobubbles lose stability: Effects of surfactants

NASA Astrophysics Data System (ADS)

Xiao, Qianxiang; Liu, Yawei; Guo, Zhenjiang; Liu, Zhiping; Zhang, Xianren

2017-09-01

In contrast to stability theories of nanobubbles, the molecular mechanism of how nanobubbles lose stability is far from being understood. In this work, we try to interpret recent experimental observations that the addition of surfactants destabilizes nanobubbles with an unclear mechanism. Using molecular dynamics simulations, we identify two surfactant-induced molecular mechanisms for nanobubbles losing stability, either through depinning of a contact line or reducing vapor-liquid surface tension. One corresponds to the case with significant adsorption of surfactants on the substrates, which causes depinning of the nanobubble contact line and thus leads to nanobubble instability. The other stresses surfactant adsorption on the vapor-liquid interface of nanobubbles, especially for insoluble surfactants, which reduces the surface tension of the interface and leads to an irreversible liquid-to-vapor phase transition. Our finding can help improve our understanding in nanobubble stability, and the insight presented here has implications for surface nanobubbles involving with other amphiphilic molecules, such as proteins and contaminations.

A novel approach for the removal of radiocesium from aqueous solution by ZSM-5 molecular sieve.

PubMed

Gao, Xiaoqing; Zhang, Peng; Yang, Junqiang; Sun, Xuejie; Fu, Yi; Shi, Keliang; Chai, Zhifang; Wu, Wangsuo

2018-05-21

Finding an approach for pretreatment of radionuclides from contaminated water are interesting topics of research. In present work, the ZSM-5 molecular sieve was characterized with different techniques such as zeta potential, SEM, FT-IR and XRD to clarify the surface properties of sample and applied as a sorbent to concentrate and recover Cs(I) from aqueous solution. The effect of environmental conditions such as contact time, ionic strength, content of sorbent and solution pH on Cs(I) uptake were optimized using batch techniques. Different kinetic and isotherm models were utilized to evaluate the experimental data and the correlation parameters were obtained. Based on the sorption/desorption experiment, it can be deduced that the ZSM-5 molecular sieve has potential application for the rapid and quantitative recovery of radiocesium from wastewater. Copyright © 2018 Elsevier Ltd. All rights reserved.

[Microbiologic and molecular diagnostic of cariogenic bacteria in pregnant women from the Araucania Region of Chile].

PubMed

Herrera G, Christian L; Pantoja F, Patricio; De la M, Tomás de La Maza; Sanhueza C, Antonio; Salazar N, Luis A

2007-08-01

Dental caries is a transmissible infectious disease in which Streptococcus mutans is a principal protagonist. Although it is widely believed that pregnancy is harmful to teeth, the effect of pregnancy on the development of caries is not clear. Considering this situation, the aim of the present study was to evaluate the levels of infection and to differentiate bacterial species with cariogenic potential in pregnant women from the Araucania region in Chile, by bacteriological and molecular analysis. In this work, we evaluated 51 pregnant women aged 15 to 40 years. The results show that 100% of women are infected by mutans streptococci Group, and 70.6% exhibited high levels of infection (> 500.000 cfu/mL). The molecular analysis shows that Streptococcus mutans and Streptococcus sobrinus frequencies were 92.1% and 1.9%, respectively. In conclusion, our data suggest that pregnant women are a high risk group for caries development.

Protein dynamics in organic media at varying water activity studied by molecular dynamics simulation.

PubMed

Wedberg, Rasmus; Abildskov, Jens; Peters, Günther H

2012-03-01

In nonaqueous enzymology, control of enzyme hydration is commonly approached by fixing the thermodynamic water activity of the medium. In this work, we present a strategy for evaluating the water activity in molecular dynamics simulations of proteins in water/organic solvent mixtures. The method relies on determining the water content of the bulk phase and uses a combination of Kirkwood-Buff theory and free energy calculations to determine corresponding activity coefficients. We apply the method in a molecular dynamics study of Candida antarctica lipase B in pure water and the organic solvents methanol, tert-butyl alcohol, methyl tert-butyl ether, and hexane, each mixture at five different water activities. It is shown that similar water activity yields similar enzyme hydration in the different solvents. However, both solvent and water activity are shown to have profound effects on enzyme structure and flexibility.

Molecular-scale shear response of the organic semiconductor β -DBDCS (100) surface

NASA Astrophysics Data System (ADS)

Álvarez-Asencio, Rubén; Moreno-Ramírez, Jorge S.; Pimentel, Carlos; Casado, Santiago; Matta, Micaela; Gierschner, Johannes; Muccioli, Luca; Yoon, Seong-Jun; Varghese, Shinto; Park, Soo Young; Gnecco, Enrico; Pina, Carlos M.

2017-09-01

In this work we present friction-force microscopy (FFM) lattice-resolved images acquired on the (100) facet of the semiconductor organic oligomer (2 Z ,2'Z )-3 , 3' -(1,4-phenylene)bis(2-(4-butoxyphenyl)acrylonitrile) (β -DBDCS) crystal in water at room temperature. Stick-slip contrast, lateral contact stiffness, and friction forces are found to depend strongly on the sliding direction due to the anisotropic packing of the molecular chains forming the crystal surface along the [010] and [001] directions. The anisotropy also causes the maximum value of the normal force applicable before wearing to increase by a factor of 3 when the scan is performed along the [001] direction on the (100) face. Altogether, our results contribute to achieving a better understanding of the molecular origin of friction anisotropy on soft crystalline surfaces, which has been often hypothesized but rarely investigated in the literature.

A molecular and haematological study of Theileria equi in Balkan donkeys.

PubMed

Davitkov, Dajana; Davitkov, Darko; Vucicevic, Milos; Stanisic, Ljubodrag; Radakovic, Milena; Glavinic, Uros; Stanimirovic, Zoran

2017-06-01

Equine piroplasmosis in donkeys has been recognised as a serious problem of major economic importance. The present molecular study is the first investigation of the presence of Theileria equi and Babesia caballi in Balkan donkeys and of the possible haematological alterations related to it. A total of 70 apparently healthy donkeys from Serbia were included in this study. The overall prevalence of T. equi infection in donkeys tested with multiplex PCR was 50%. There was no B. caballi-positive sample. Infections in donkeys included in this study seem to be associated with decreased red blood cell count, haemoglobin concentration, haematocrit and platelet count, and with increased white blood cell count, mean corpuscular haemoglobin and mean corpuscular haemoglobin concentration. Altered haematological parameters in donkeys can lead to a decrease in working capacity and production performance. Further molecular research and long-term monitoring of equine piroplasmosis is needed in Serbia and throughout Europe.

CURVATURE-DRIVEN MOLECULAR FLOW ON MEMBRANE SURFACE*

PubMed Central

MIKUCKI, MICHAEL; ZHOU, Y. C.

2017-01-01

This work presents a mathematical model for the localization of multiple species of diffusion molecules on membrane surfaces. Morphological change of bilayer membrane in vivo is generally modulated by proteins. Most of these modulations are associated with the localization of related proteins in the crowded lipid environments. We start with the energetic description of the distributions of molecules on curved membrane surface, and define the spontaneous curvature of bilayer membrane as a function of the molecule concentrations on membrane surfaces. A drift-diffusion equation governs the gradient flow of the surface molecule concentrations. We recast the energetic formulation and the related governing equations by using an Eulerian phase field description to define membrane morphology. Computational simulations with the proposed mathematical model and related numerical techniques predict (i) the molecular localization on static membrane surfaces at locations with preferred mean curvatures, and (ii) the generation of preferred mean curvature which in turn drives the molecular localization. PMID:29056778

Molecular Blends of Methylated-Poly(ethylenimine) and Amorphous Porous Organic Cages for SO 2 Adsorption

DOE PAGES

Zhu, Guanghui; Carrillo, Jan-Michael Y.; Sujan, Achintya; ...

2018-05-30

Porous organic cages (POCs) are emerging porous materials that exhibit intriguing properties in the areas of self-assembly, host-guest interaction, and solution processability. Here in this work, we explore the applicability of POCs as molecular porous supports for polymeric amines. We find that primary amines in poly(ethylenimine) (PEI) can undergo metathesis with the imine bonds present in POCs, resulting in non-porous products. This problem can be overcome by transforming the primary amines in PEI to tertiary amines via methylation. The methylated PEI (mPEI) forms homogeneous composites with amorphous scrambled porous organic cages (ASPOCs) without undesired reactions or phase separation. The microscopicmore » structure of the composites is studied using molecular dynamics simulations. Finally, these composite materials are evaluated as adsorbents for low concentration SO2 (200 ppm) adsorption and show good thermal and cyclic stability.« less

Antimicrobial Polymers Prepared by ROMP with Unprecedented Selectivity: A Molecular Construction Kit Approach

PubMed Central

Lienkamp, Karen; Madkour, Ahmad E.; Musante, Ashlan; Nelson, Christopher F.; Nüsslein, Klaus

2014-01-01

Synthetic Mimics of Antimicrobial Peptides (SMAMPs) imitate natural host-defense peptides, a vital component of the body’s immune system. This work presents a molecular construction kit that allows the easy and versatile synthesis of a broad variety of facially amphiphilic oxanorbornene-derived monomers. Their ring-opening metathesis polymerization (ROMP) and deprotection provide several series of SMAMPs. Using amphiphilicity, monomer feed ratio, and molecular weight as parameters, polymers with 533 times higher selectivitiy (selecitviy = hemolytic concentration/minimum inhibitory concentration) for bacteria over mammalian cells were discovered. Some of these polymers were 50 times more selective for Gram-positive over Gram-negative bacteria while other polymers surprisingly showed the opposite preference. This kind of “double selectivity” (bacteria over mammalian and one bacterial type over another) is unprecedented in other polymer systems and is attributed to the monomer’s facial amphiphilicity. PMID:18593128

Light microscopy applications in systems biology: opportunities and challenges

PubMed Central

2013-01-01

Biological systems present multiple scales of complexity, ranging from molecules to entire populations. Light microscopy is one of the least invasive techniques used to access information from various biological scales in living cells. The combination of molecular biology and imaging provides a bottom-up tool for direct insight into how molecular processes work on a cellular scale. However, imaging can also be used as a top-down approach to study the behavior of a system without detailed prior knowledge about its underlying molecular mechanisms. In this review, we highlight the recent developments on microscopy-based systems analyses and discuss the complementary opportunities and different challenges with high-content screening and high-throughput imaging. Furthermore, we provide a comprehensive overview of the available platforms that can be used for image analysis, which enable community-driven efforts in the development of image-based systems biology. PMID:23578051

Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration.

PubMed

Furmanchuk, Al'ona; Isayev, Olexandr; Gorb, Leonid; Shishkin, Oleg V; Hovorun, Dmytro M; Leszczynski, Jerzy

2011-03-14

In the present work, the conventional static ab initio picture of a water-assisted mechanism of the tautomerization of Nucleic Acid Bases (NABs) in an aqueous environment is enhanced by the classical and Car-Parrinello molecular dynamics simulations. The inclusion of the dynamical contribution is vital because the formation and longevity of the NAB-water bridge complexes represent decisive factors for further tautomerization. The results of both molecular dynamic techniques indicate that the longest time when such complexes exist is significantly shorter than the time required for proton transfer suggested by the static ab initio level of theory. New rate constants of tautomerization corrected for the dynamic effect of environment are proposed based on the first principles molecular dynamics data. Those values are used for the evaluation of a water-assisted mechanism that is feasible in such biological systems as E. coli cell.

Molecular Blends of Methylated-Poly(ethylenimine) and Amorphous Porous Organic Cages for SO 2 Adsorption

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

Zhu, Guanghui; Carrillo, Jan-Michael Y.; Sujan, Achintya

Porous organic cages (POCs) are emerging porous materials that exhibit intriguing properties in the areas of self-assembly, host-guest interaction, and solution processability. Here in this work, we explore the applicability of POCs as molecular porous supports for polymeric amines. We find that primary amines in poly(ethylenimine) (PEI) can undergo metathesis with the imine bonds present in POCs, resulting in non-porous products. This problem can be overcome by transforming the primary amines in PEI to tertiary amines via methylation. The methylated PEI (mPEI) forms homogeneous composites with amorphous scrambled porous organic cages (ASPOCs) without undesired reactions or phase separation. The microscopicmore » structure of the composites is studied using molecular dynamics simulations. Finally, these composite materials are evaluated as adsorbents for low concentration SO2 (200 ppm) adsorption and show good thermal and cyclic stability.« less

Adaptively biased molecular dynamics for free energy calculations

NASA Astrophysics Data System (ADS)

Babin, Volodymyr; Roland, Christopher; Sagui, Celeste

2008-04-01

We present an adaptively biased molecular dynamics (ABMD) method for the computation of the free energy surface of a reaction coordinate using nonequilibrium dynamics. The ABMD method belongs to the general category of umbrella sampling methods with an evolving biasing potential and is inspired by the metadynamics method. The ABMD method has several useful features, including a small number of control parameters and an O(t ) numerical cost with molecular dynamics time t. The ABMD method naturally allows for extensions based on multiple walkers and replica exchange, where different replicas can have different temperatures and/or collective variables. This is beneficial not only in terms of the speed and accuracy of a calculation, but also in terms of the amount of useful information that may be obtained from a given simulation. The workings of the ABMD method are illustrated via a study of the folding of the Ace-GGPGGG-Nme peptide in a gaseous and solvated environment.

Molecular, metabolic, and genetic control: An introduction

NASA Astrophysics Data System (ADS)

Tyson, John J.; Mackey, Michael C.

2001-03-01

The living cell is a miniature, self-reproducing, biochemical machine. Like all machines, it has a power supply, a set of working components that carry out its necessary tasks, and control systems that ensure the proper coordination of these tasks. In this Special Issue, we focus on the molecular regulatory systems that control cell metabolism, gene expression, environmental responses, development, and reproduction. As for the control systems in human-engineered machines, these regulatory networks can be described by nonlinear dynamical equations, for example, ordinary differential equations, reaction-diffusion equations, stochastic differential equations, or cellular automata. The articles collected here illustrate (i) a range of theoretical problems presented by modern concepts of cellular regulation, (ii) some strategies for converting molecular mechanisms into dynamical systems, (iii) some useful mathematical tools for analyzing and simulating these systems, and (iv) the sort of results that derive from serious interplay between theory and experiment.

Molecular dynamics simulations of dislocations in TlBr crystals under an electrical field

DOE PAGES

Zhou, X. W.; Foster, M. E.; Yang, P.; ...

2016-07-13

TlBr crystals have superior radiation detection properties; however, their properties degrade in the range of hours to weeks when an operating electrical field is applied. To account for this rapid degradation using the widely-accepted vacancy migration mechanism, the vacancy concentration must be orders of magnitude higher than any conventional estimates. The present work has incorporated a new analytical variable charge model in molecular dynamics (MD) simulations to examine the structural changes of materials under electrical fields. Our simulations indicate that dislocations in TlBr move under electrical fields. As a result, this discovery can lead to new understanding of TlBr agingmore » mechanisms under external fields.« less

Using FT-IR Spectroscopy to Elucidate the Structures of Ablative Polymers

NASA Technical Reports Server (NTRS)

Fan, Wendy

2011-01-01

The composition and structure of an ablative polymer has a multifaceted influence on its thermal, mechanical and ablative properties. Understanding the molecular level information is critical to the optimization of material performance because it helps to establish correlations with the macroscopic properties of the material, the so-called structure-property relationship. Moreover, accurate information of molecular structures is also essential to predict the thermal decomposition pathways as well as to identify decomposition species that are fundamentally important to modeling work. In this presentation, I will describe the use of infrared transmission spectroscopy (FT-IR) as a convenient tool to aid the discovery and development of thermal protection system materials.

The structural properties of PbF2 by molecular dynamics

NASA Astrophysics Data System (ADS)

Chergui, Y.; Nehaoua, N.; Telghemti, B.; Guemid, S.; Deraddji, N. E.; Belkhir, H.; Mekki, D. E.

2010-08-01

This work presents the use of molecular dynamics (MD) and the code of Dl_Poly, in order to study the structure of fluoride glass after melting and quenching. We are realized the processing phase liquid-phase, simulating rapid quenching at different speeds to see the effect of quenching rate on the operation of the devitrification. This technique of simulation has become a powerful tool for investigating the microscopic behaviour of matter as well as for calculating macroscopic observable quantities. As basic results, we calculated the interatomic distance, angles and statistics, which help us to know the geometric form and the structure of PbF2. These results are in experimental agreement to those reported in literature.

eMolTox: prediction of molecular toxicity with confidence.

PubMed

Ji, Changge; Svensson, Fredrik; Zoufir, Azedine; Bender, Andreas

2018-03-07

In this work we present eMolTox, a web server for the prediction of potential toxicity associated with a given molecule. 174 toxicology-related in vitro/vivo experimental datasets were used for model construction and Mondrian conformal prediction was used to estimate the confidence of the resulting predictions. Toxic substructure analysis is also implemented in eMolTox. eMolTox predicts and displays a wealth of information of potential molecular toxicities for safety analysis in drug development. The eMolTox Server is freely available for use on the web at http://xundrug.cn/moltox. chicago.ji@gmail.com or ab454@cam.ac.uk. Supplementary data are available at Bioinformatics online.

Atomdroid: a computational chemistry tool for mobile platforms.

PubMed

Feldt, Jonas; Mata, Ricardo A; Dieterich, Johannes M

2012-04-23

We present the implementation of a new molecular mechanics program designed for use in mobile platforms, the first specifically built for these devices. The software is designed to run on Android operating systems and is compatible with several modern tablet-PCs and smartphones available in the market. It includes molecular viewer/builder capabilities with integrated routines for geometry optimizations and Monte Carlo simulations. These functionalities allow it to work as a stand-alone tool. We discuss some particular development aspects, as well as the overall feasibility of using computational chemistry software packages in mobile platforms. Benchmark calculations show that through efficient implementation techniques even hand-held devices can be used to simulate midsized systems using force fields.

Atomistic simulations of TeO₂-based glasses: interatomic potentials and molecular dynamics.

PubMed

Gulenko, Anastasia; Masson, Olivier; Berghout, Abid; Hamani, David; Thomas, Philippe

2014-07-21

In this work we present for the first time empirical interatomic potentials that are able to reproduce TeO2-based systems. Using these potentials in classical molecular dynamics simulations, we obtained first results for the pure TeO2 glass structure model. The calculated pair distribution function is in good agreement with the experimental one, which indicates a realistic glass structure model. We investigated the short- and medium-range TeO2 glass structures. The local environment of the Te atom strongly varies, so that the glass structure model has a broad Q polyhedral distribution. The glass network is described as weakly connected with a large number of terminal oxygen atoms.

CCC calculated differential cross sections of electron-H2 scattering

NASA Astrophysics Data System (ADS)

Fursa, Dmitry; Zammit, Mark; Savage, Jeremy; Bray, Igor

2016-09-01

Recently we applied the molecular convergent close-coupling (CCC) method to electron scattering from molecular hydrogen H2. Convergence of the major differential cross sections has been explicitly demonstrated in the fixed-nuclei approximation. A large close-coupling expansion that coupled highly excited states and ionization channels proved to be important to obtain convergent results. Here we present benchmark elastic and electronic excitation differential cross sections for b3Σu+ , a3Σg+ , c3Πu , B1Σu+ , EF1Σg+ , C1Πu , and e3Σu+ states and compare with available experiment and previous calculations. Work supported by Los Alamos National Laboratory and Curtin University.

Synergistic effect of high and low molecular weight molecules in the foamability and foam stability of sparkling wines.

PubMed

Coelho, Elisabete; Reis, Ana; Domingues, M Rosário M; Rocha, Sílvia M; Coimbra, Manuel A

2011-04-13

The foam of sparkling wines is a key parameter of their quality. However, the compounds that are directly involved in foam formation and stabilization are not yet completely established. In this work, seven sparkling wines were produced in Bairrada appellation (Portugal) under different conditions and their foaming properties evaluated using a Mosalux-based device. Fractionation of the sparkling wines into four independent fractions, (1) high molecular weight material, with molecular weight higher than 12 kDa (HMW), (2) hydrophilic material with molecular weigh between 1 and 12 kDa (AqIMW), (3) hydrophobic material with molecular weigh between 1 and 12 kDa (MeIMW), and (4) hydrophobic material with a molecular weight lower than 1 kDa (MeLMW), allowed the observation that the wines presenting the lower foam stability were those that presented lower amounts of the MeLMW fraction. The fraction that presented the best foam stability was HMW. When HMW is combined with MeLMW fraction, the foam stability largely increased. This increase was even larger, approaching the foam stability of the sparkling wine, when HMW was combined with the less hydrophobic subfraction of MeLMW (fraction 3). Electrospray tandem mass spectrometry (ESI-MS/MS) of fraction 3 allowed the assignment of polyethylene glycol oligomers (n = 5-11) and diethylene glycol 8-hydroxytridecanoate glyceryl acetate. To observe if these molecules occur in sparkling wine foam, the MeLMW was recovered directly from the sparkling wine foam and was also analyzed by ESI-MS/MS. The presence of monoacylglycerols of palmitic and stearic acids, as well as four glycerylethylene glycol fatty acid derivatives, was observed. These surface active compounds are preferentially partitioned by the sparkling wine foam rather than the liquid phase, allowing the inference of their role as key components in the promotion and stabilization of sparkling wine foam.

Proton cooling in ultracold low-density electron gas

NASA Astrophysics Data System (ADS)

Bobrov, A. A.; Bronin, S. Y.; Manykin, E. A.; Zelener, B. B.; Zelener, B. V.; Khikhlukha, D. R.

2015-11-01

A sole proton energy loss processes in an electron gas and the dependence of these processes on temperature and magnetic field are studied using molecular dynamics techniques in present work. It appears that for electron temperatures less than 100 K many body collisions affect the proton energy loss and these collisions must be taken into account. The influence of a strong magnetic field on the relaxation processes is also considered in this work. Calculations were performed for electron densities 10 cm-3, magnetic field 1-3 Tesla, electron temperatures 10-50 K, initial proton energies 100-10000 K.

Note: Work function change measurement via improved Anderson method

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

Sabik, A., E-mail: sabik@ifd.uni.wroc.pl; Gołek, F.; Antczak, G.

We propose the modification to the Anderson method of work function change (Δϕ) measurements. In this technique, the kinetic energy of the probing electrons is already low enough for non-destructive investigation of delicate molecular systems. However, in our implementation, all electrodes including filament of the electron gun are polarized positively. As a consequence, electron bombardment of any elements of experimental system is eliminated. Our modification improves cleanliness of the ultra-high vacuum system. As an illustration of the solution capabilities, we present Δϕ of the Ag(100) surface induced by cobalt phthalocyanine layers.

Analyzing Data for Systems Biology: Working at the Intersection of Thermodynamics and Data Analytics

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

Cannon, William R.; Baxter, Douglas J.

2012-08-15

Many challenges in systems biology have to do with analyzing data within the framework of molecular phenomena and cellular pathways. How does this relate to thermodynamics that we know govern the behavior of molecules? Making progress in relating data analysis to thermodynamics is essential in systems biology if we are to build predictive models that enable the field of synthetic biology. This report discusses work at the crossroads of thermodynamics and data analysis, and demonstrates that statistical mechanical free energy is a multinomial log likelihood. Applications to systems biology are presented.

Graphene-based nanomaterials for nanobiotechnology and biomedical applications.

PubMed

Krishna, K Vijaya; Ménard-Moyon, Cécilia; Verma, Sandeep; Bianco, Alberto

2013-10-01

Graphene family nanomaterials are currently being extensively explored for applications in the field of nanotechnology. The unique intrinsic properties treasured in their simple molecular design and their ability to work in coherence with other existing nanomaterials make graphene family nanomaterials the most promising candidates for different types of applications. This review highlights the scope and utility of these multifaceted nanomaterials in nanobiotechnology and biomedicine. In a tandem approach, this review presents the smooth inclusion of these nanomaterials into existing designs for creating efficient working models at the nanoscale level as well as discussing their broad future possibilities.

Chemoinformatic expedition of the chemical space of fungal products.

PubMed

González-Medina, Mariana; Prieto-Martínez, Fernando D; Naveja, J Jesús; Méndez-Lucio, Oscar; El-Elimat, Tamam; Pearce, Cedric J; Oberlies, Nicholas H; Figueroa, Mario; Medina-Franco, José L

2016-08-01

Fungi are valuable resources for bioactive secondary metabolites. However, the chemical space of fungal secondary metabolites has been studied only on a limited basis. Herein, we report a comprehensive chemoinformatic analysis of a unique set of 207 fungal metabolites isolated and characterized in a USA National Cancer Institute funded drug discovery project. Comparison of the molecular complexity of the 207 fungal metabolites with approved anticancer and nonanticancer drugs, compounds in clinical studies, general screening compounds and molecules Generally Recognized as Safe revealed that fungal metabolites have high degree of complexity. Molecular fingerprints showed that fungal metabolites are as structurally diverse as other natural products and have, in general, drug-like physicochemical properties. Fungal products represent promising candidates to expand the medicinally relevant chemical space. This work is a significant expansion of an analysis reported years ago for a smaller set of compounds (less than half of the ones included in the present work) from filamentous fungi using different structural properties.

The biophysical basis of Benveniste experiments: Entropy, structure, and information in water

NASA Astrophysics Data System (ADS)

Widom, Allan; Srivastava, Yogendra; Valenzi, Vincenzo

Benveniste had observed that highly dilute (and even in the absence of physical molecules) biological agents still triggered relevant biological systems. Some of these experiments were reproduced in three other laboratories who cosigned the article, (Davenas et al., Nature 1988, 333, 816). Further works, [(Medical Hypotheses 2000, 54, 33), (Rivista di Biologia/Biology Forum 97, 2004, 169)], showed that molecular activity in more than 50 biochemical systems and even in bacteria could be induced by electromagnetic signals transferred through water solutes. The sources of the electromagnetic signals were recordings of specific biological activities. These results suggest that electromagnetic transmission of biochemical information can be stored in the electric dipole moments of water in close analogy to the manner in which magnetic moments store information on a computer disk. The electromagnetic transmission would enable in vivo transmissions of the specific molecular information between two functional biomolecules. In the present work, the physical nature of such biological information storage and retrieval in ordered quantum electromagnetic domains of water will be discussed.

IADE: a system for intelligent automatic design of bioisosteric analogs

NASA Astrophysics Data System (ADS)

Ertl, Peter; Lewis, Richard

2012-11-01

IADE, a software system supporting molecular modellers through the automatic design of non-classical bioisosteric analogs, scaffold hopping and fragment growing, is presented. The program combines sophisticated cheminformatics functionalities for constructing novel analogs and filtering them based on their drug-likeness and synthetic accessibility using automatic structure-based design capabilities: the best candidates are selected according to their similarity to the template ligand and to their interactions with the protein binding site. IADE works in an iterative manner, improving the fitness of designed molecules in every generation until structures with optimal properties are identified. The program frees molecular modellers from routine, repetitive tasks, allowing them to focus on analysis and evaluation of the automatically designed analogs, considerably enhancing their work efficiency as well as the area of chemical space that can be covered. The performance of IADE is illustrated through a case study of the design of a nonclassical bioisosteric analog of a farnesyltransferase inhibitor—an analog that has won a recent "Design a Molecule" competition.

A 2MASS Analysis of the Stability and Star Formation in Southern Bok Globules

NASA Astrophysics Data System (ADS)

Racca, G. A.; de La Reza, R.

2006-06-01

Bok globules are the simplest molecular clouds in which the study of low-mass star formation is not affected by disruptive phenomena that occur in other clouds that are actively forming low- and high-mass stars. The Two Micron All Sky Survey (2MASS) offer a great possibility to survey these clouds in the near-infrared distributed along the Galaxy. In this work we present extinction maps of Southern Bok globules from the catalog of Bourke, Hyland & Robinson (1995) constructed from extincted background stars in the 2MASS JHK_s bands. The radial distribution of column density obtained from these maps are then modeled with different solutions that arise from several models of the gravitational collapse of molecular clouds cores. We adjust these profiles with Bonnor-Ebert spheres, negative-index polytropes and a simple power-law. This work will help constrain the early stages of the process of isolated star formation of low-mass stars.

IADE: a system for intelligent automatic design of bioisosteric analogs.

PubMed

Ertl, Peter; Lewis, Richard

2012-11-01

IADE, a software system supporting molecular modellers through the automatic design of non-classical bioisosteric analogs, scaffold hopping and fragment growing, is presented. The program combines sophisticated cheminformatics functionalities for constructing novel analogs and filtering them based on their drug-likeness and synthetic accessibility using automatic structure-based design capabilities: the best candidates are selected according to their similarity to the template ligand and to their interactions with the protein binding site. IADE works in an iterative manner, improving the fitness of designed molecules in every generation until structures with optimal properties are identified. The program frees molecular modellers from routine, repetitive tasks, allowing them to focus on analysis and evaluation of the automatically designed analogs, considerably enhancing their work efficiency as well as the area of chemical space that can be covered. The performance of IADE is illustrated through a case study of the design of a nonclassical bioisosteric analog of a farnesyltransferase inhibitor--an analog that has won a recent "Design a Molecule" competition.

Coupled Molecular Switching Processes in Ordered Mono- and Multilayers of Stimulus-Responsive Rotaxanes on Gold Surfaces

PubMed Central

2015-01-01

Interfaces provide the structural basis for function as, for example, encountered in nature in the membrane-embedded photosystem or in technology in solar cells. Synthetic functional multilayers of molecules cooperating in a coupled manner can be fabricated on surfaces through layer-by-layer self-assembly. Ordered arrays of stimulus-responsive rotaxanes undergoing well-controlled axle shuttling are excellent candidates for coupled mechanical motion. Such stimulus-responsive surfaces may help integrate synthetic molecular machines in larger systems exhibiting even macroscopic effects or generating mechanical work from chemical energy through cooperative action. The present work demonstrates the successful deposition of ordered mono- and multilayers of chemically switchable rotaxanes on gold surfaces. Rotaxane mono- and multilayers are shown to reversibly switch in a coupled manner between two ordered states as revealed by linear dichroism effects in angle-resolved NEXAFS spectra. Such a concerted switching process is observed only when the surfaces are well packed, while less densely packed surfaces lacking lateral order do not exhibit such effects. PMID:25782057

Highly sensitive and selective hyphenated technique (molecularly imprinted polymer solid-phase microextraction-molecularly imprinted polymer sensor) for ultra trace analysis of aspartic acid enantiomers.

PubMed

Prasad, Bhim Bali; Srivastava, Amrita; Tiwari, Mahavir Prasad

2013-03-29

The present work is related to combination of molecularly imprinted solid-phase microextraction and complementary molecularly imprinted polymer-sensor. The molecularly imprinted polymer grafted on titanium dioxide modified silica fiber was used for microextraction, while the same polymer immobilized on multiwalled carbon nanotubes/titanium dioxide modified pencil graphite electrode served as a detection tool. In both cases, the surface initiated polymerization was found to be advantageous to obtain a nanometer thin imprinted film. The modified silica fiber exhibited high adsorption capacity and enantioselective diffusion of aspartic acid isomers into respective molecular cavities. This combination enabled double preconcentrations of d- and l-aspartic acid that helped sensing both isomers in real samples, without any cross-selectivity and matrix complications. Taking into account 6×10(4)-fold dilution of serum and 2×10(3)-fold dilution of cerebrospinal fluid required by the proposed method, the limit of detection for l-aspartic acid is 0.031ngmL(-1). Also, taking into account 50-fold dilution required by the proposed method, the limit of detection for d-aspartic acid is 0.031ngmL(-1) in cerebrospinal fluid. Copyright © 2013 Elsevier B.V. All rights reserved.

[Research progress in molecular classification of gastric cancer].

PubMed

Zhou, Menglong; Li, Guichao; Zhang, Zhen

2016-09-25

Gastric cancer(GC) is a highly heterogeneous malignancy. The present widely used histopathological classifications have gradually failed to meet the needs of individualized diagnosis and treatment. Development of technologies such as microarray and next-generation sequencing (NGS) has allowed GC to be studied at the molecular level. Mechanisms about tumorigenesis and progression of GC can be elucidated in the aspects of gene mutations, chromosomal alterations, transcriptional and epigenetic changes, on the basis of which GC can be divided into several subtypes. The classifications of Tan's, Lei's, TCGA and ACRG are relatively comprehensive. Especially the TCGA and ACRG classifications have large sample size and abundant molecular profiling data, thus, the genomic characteristics of GC can be depicted more accurately. However, significant differences between both classifications still exist so that they cannot be substituted for each other. So far there is no widely accepted molecular classification of GC. Compared with TCGA classification, ACRG system may have more clinical significance in Chinese GC patients since the samples are mostly from Asian population and show better association with prognosis. The molecular classification of GC may provide the theoretical and experimental basis for early diagnosis, therapeutic efficacy prediction and treatment stratification while their clinical application is still limited. Future work should involve the application of molecular classifications in the clinical settings for improving the medical management of GC.

Molecular Gas Excitation and the Evolutionary Connection Between Submillimeter Galaxies and AGN at z~2-3

NASA Astrophysics Data System (ADS)

Sharon, Chelsea; Riechers, Dominik Alexander; Carilli, Christopher; Hodge, Jacqueline; Walter, Fabian

2015-08-01

Theoretical work has suggested that active galactic nuclei (AGN) may play an important role in quenching star formation in massive galaxies. Due to sensitivity demands, direct evidence for AGN affecting the molecular ISM (the gas phase that fuels star formation) has so far been limited to detections of molecular outflows in low-redshift systems. Indirect evidence for an interplay between AGN and their host galaxies' cold gas phase may be provided by measurements of the gas excitation (and dynamics). At z~2-3, the peak epoch of star formation and AGN activity, previous observations of the CO(1-0) line revealed that submillimeter galaxies have substantial reservoirs of cold molecular gas. However, the molecular gas in AGN-host galaxies appears highly excited, potentially supporting an evolutionary connection between these two populations. We will present a new larger Karl G. Jansky Very Large Array sample that nearly doubles the number of CO(1-0) detections in z~2-3 submillimeter galaxies and AGN-host galaxies with existing CO(3-2) detections (from 13 to 23, plus four new upper limits) that allows us to better compare the low-excitation molecular gas properties of these systems and further investigate potential evidence for gas excitation due to active black holes.

Regulated release of serotonin from axonal growth cones isolated from the fetal rat brain.

PubMed

Mercado, R; Floran, B; Hernandez, J

1998-01-01

In the present work we propose an hypothetical model related to a molecular recognizing system for serotonin in isolated growth cone particles. This model is supported by previous results from our laboratory plus new ones which show that growth cones release serotonin tonically and such release can be stimulated by potassium in a calcium-dependent manner. The present results, together with other author's data, suggest a physiological basis for the putative role of serotonin as a trophic factor during nervous system development.

Research at a Liberal Arts College: Make Sure you have a Net for your High Wire Act

NASA Astrophysics Data System (ADS)

Marshall, Mark D.; Leung, Helen O.

2015-06-01

A career as a spectroscopist at a primarily (or exclusively) undergraduate institution presents both great rewards and significant challenges. Strategies that we have found helpful in meeting some of the challenges are presented along with some of the work we have been able to accomplish with undergraduate students. The most important resource is a network of colleagues who can provide mentoring and collaboration, and the role of the International Symposium on Molecular Spectroscopy in facilitating this support is highlighted.

An introduction to genetic quality in the context of sexual selection.

PubMed

Pitcher, Trevor E; Mays, Herman L

2008-09-01

This special issue of Genetica brings together empirical researchers and theoreticians to present the latest on the evolutionary ecology of genetic quality in the context of sexual selection. The work comes from different fields of study including behavioral ecology, quantitative genetics and molecular genetics on a diversity of organisms using different approaches from comparative studies, mathematical modeling, field studies and laboratory experiments. The papers presented in this special issue primarily focus on genetic quality in relation to (1) sources of genetic variation, (2) polyandry, (3) new theoretical developments and (4) comprehensive reviews.

Exploring infrared neural stimulation with multimodal nonlinear imaging (Conference Presentation)

NASA Astrophysics Data System (ADS)

Adams, Wilson R.; Mahadevan-Jansen, Anita

2017-02-01

Infrared neural stimulation (INS) provides optical control of neural excitability using near to mid-infrared (mid-IR) light, which allows for spatially selective, artifact-free excitation without the introduction of exogenous agents or genetic modification. Although neural excitability is mediated by a transient temperature increase due to water absorption of IR energy, the molecular nature of IR excitability in neural tissue remains unknown. Current research suggests that transient changes in local tissue temperature give rise to a myriad of cellular responses that have been individually attributed to IR mediated excitability. To further elucidate the underlying biophysical mechanisms, we have begun work towards employing a novel multimodal nonlinear imaging platform to probe the molecular underpinnings of INS. Our imaging system performs coherent anti-Stokes Raman scattering (CARS), stimulated Raman scattering (SRS), two-photon excitation fluorescence (TPEF), second-harmonic generation (SHG) and thermal imaging into a single platform that allows for unprecedented co-registration of thermal and biochemical information in real-time. Here, we present our work leveraging CARS and SRS in acute thalamocortical brain slice preparations. We observe the evolution of lipid and protein-specific Raman bands during INS and electrically evoked activity in real-time. Combined with two-photon fluorescence and second harmonic generation, we offer insight to cellular metabolism and membrane dynamics during INS. Thermal imaging allows for the coregistration of acquired biochemical information with temperature information. Our work previews the versatility and capabilities of coherent Raman imaging combined with multiphoton imaging to observe biophysical phenomena for neuroscience applications.

Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

USGS Publications Warehouse

Lee, M.W.; Meuwly, M.

2013-01-01

The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly.

PubMed

Martín-Rodríguez, Juan F; Muñoz-Bravo, Jose L; Ibañez-Costa, Alejandro; Fernandez-Maza, Laura; Balcerzyk, Marcin; Leal-Campanario, Rocío; Luque, Raúl M; Castaño, Justo P; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso; Cano, David A

2015-11-09

Acromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic, and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors.

Molecular Characterization of Growth Hormone-producing Tumors in the GC Rat Model of Acromegaly

PubMed Central

Martín-Rodríguez, Juan F.; Muñoz-Bravo, Jose L.; Ibañez-Costa, Alejandro; Fernandez-Maza, Laura; Balcerzyk, Marcin; Leal-Campanario, Rocío; Luque, Raúl M.; Castaño, Justo P.; Venegas-Moreno, Eva; Soto-Moreno, Alfonso; Leal-Cerro, Alfonso; Cano, David A.

2015-01-01

Acromegaly is a disorder resulting from excessive production of growth hormone (GH) and consequent increase of insulin-like growth factor 1 (IGF-I), most frequently caused by pituitary adenomas. Elevated GH and IGF-I levels results in wide range of somatic, cardiovascular, endocrine, metabolic, and gastrointestinal morbidities. Subcutaneous implantation of the GH-secreting GC cell line in rats leads to the formation of tumors. GC tumor-bearing rats develop characteristics that resemble human acromegaly including gigantism and visceromegaly. However, GC tumors remain poorly characterized at a molecular level. In the present work, we report a detailed histological and molecular characterization of GC tumors using immunohistochemistry, molecular biology and imaging techniques. GC tumors display histopathological and molecular features of human GH-producing tumors, including hormone production, cell architecture, senescence activation and alterations in cell cycle gene expression. Furthermore, GC tumors cells displayed sensitivity to somatostatin analogues, drugs that are currently used in the treatment of human GH-producing adenomas, thus supporting the GC tumor model as a translational tool to evaluate therapeutic agents. The information obtained would help to maximize the usefulness of the GC rat model for research and preclinical studies in GH-secreting tumors. PMID:26549306

Mapping the Transmission Functions of Single-Molecule Junctions

DOE PAGES

Capozzi, Brian; Low, Jonathan Z.; Xia, Jianlong; ...

2016-06-08

Charge transport characteristics of single-molecule junctions are often governed by a transmission function that dictates the probability of electrons or holes tunneling across the junction. Here, we present a new and simple technique for measuring the transmission function of molecular junctions in the coherent tunneling limit, over an energy range of 2 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different areas exposed, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junctionmore » Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction’s transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed ab initio. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale.« less

Mapping the Transmission Functions of Single-Molecule Junctions

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

Capozzi, Brian; Low, Jonathan Z.; Xia, Jianlong

Charge transport characteristics of single-molecule junctions are often governed by a transmission function that dictates the probability of electrons or holes tunneling across the junction. Here, we present a new and simple technique for measuring the transmission function of molecular junctions in the coherent tunneling limit, over an energy range of 2 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different areas exposed, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junctionmore » Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction’s transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed ab initio. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale.« less

Mapping the Transmission Functions of Single-Molecule Junctions.

PubMed

Capozzi, Brian; Low, Jonathan Z; Xia, Jianlong; Liu, Zhen-Fei; Neaton, Jeffrey B; Campos, Luis M; Venkataraman, Latha

2016-06-08

Charge transport phenomena in single-molecule junctions are often dominated by tunneling, with a transmission function dictating the probability that electrons or holes tunnel through the junction. Here, we present a new and simple technique for measuring the transmission functions of molecular junctions in the coherent tunneling limit, over an energy range of 1.5 eV around the Fermi energy. We create molecular junctions in an ionic environment with electrodes having different exposed areas, which results in the formation of electric double layers of dissimilar density on the two electrodes. This allows us to electrostatically shift the molecular resonance relative to the junction Fermi levels in a manner that depends on the sign of the applied bias, enabling us to map out the junction's transmission function and determine the dominant orbital for charge transport in the molecular junction. We demonstrate this technique using two groups of molecules: one group having molecular resonance energies relatively far from EF and one group having molecular resonance energies within the accessible bias window. Our results compare well with previous electrochemical gating data and with transmission functions computed from first principles. Furthermore, with the second group of molecules, we are able to examine the behavior of a molecular junction as a resonance shifts into the bias window. This work provides a new, experimentally simple route for exploring the fundamentals of charge transport at the nanoscale.

An historical overview of cavity-enhanced methods

NASA Astrophysics Data System (ADS)

Paldus, B. A.; Kachanov, A. A.

2005-10-01

An historical overview of laser-based, spectroscopic methods that employ high-finesse optical resonators is presented. The overview begins with the early work in atomic absorption (1962) and optical cavities (1974) that led to the first mirror reflectivity measurements in 1980. This paper concludes with very recent extensions of cavity-enhanced methods for the study of condensed-phase media and biological systems. Methods described here include cavity ring-down spectroscopy, integrated cavity output spectroscopy, and noise-immune cavity-enhanced optical heterodyne molecular spectroscopy. Given the explosive growth of the field over the past decade, this review does not attempt to present a comprehensive bibliography of all work published in cavity-enhanced spectroscopy, but rather strives to illustrate the rich history, creative diversity, and broad applications potential of these methods.

Cascading of molecular logic gates for advanced functions: a self-reporting, activatable photosensitizer.

PubMed

Erbas-Cakmak, Sundus; Akkaya, Engin U

2013-10-18

Logical progress: Independent molecular logic gates have been designed and characterized. Then, the individual molecular logic gates were coerced to work together within a micelle. Information relay between the two logic gates was achieved through the intermediacy of singlet oxygen. Working together, these concatenated logic gates result in a self-reporting and activatable photosensitizer. GSH=glutathione. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Feature extraction using molecular planes for fuzzy relational clustering of a flexible dopamine reuptake inhibitor.

PubMed

Banerjee, Amit; Misra, Milind; Pai, Deepa; Shih, Liang-Yu; Woodley, Rohan; Lu, Xiang-Jun; Srinivasan, A R; Olson, Wilma K; Davé, Rajesh N; Venanzi, Carol A

2007-01-01

Six rigid-body parameters (Shift, Slide, Rise, Tilt, Roll, Twist) are commonly used to describe the relative displacement and orientation of successive base pairs in a nucleic acid structure. The present work adapts this approach to describe the relative displacement and orientation of any two planes in an arbitrary molecule-specifically, planes which contain important pharmacophore elements. Relevant code from the 3DNA software package (Nucleic Acids Res. 2003, 31, 5108-5121) was generalized to treat molecular fragments other than DNA bases as input for the calculation of the corresponding rigid-body (or "planes") parameters. These parameters were used to construct feature vectors for a fuzzy relational clustering study of over 700 conformations of a flexible analogue of the dopamine reuptake inhibitor, GBR 12909. Several cluster validity measures were used to determine the optimal number of clusters. Translational (Shift, Slide, Rise) rather than rotational (Tilt, Roll, Twist) features dominate clustering based on planes that are relatively far apart, whereas both types of features are important to clustering when the pair of planes are close by. This approach was able to classify the data set of molecular conformations into groups and to identify representative conformers for use as template conformers in future Comparative Molecular Field Analysis studies of GBR 12909 analogues. The advantage of using the planes parameters, rather than the combination of atomic coordinates and angles between molecular planes used in our previous fuzzy relational clustering of the same data set (J. Chem. Inf. Model. 2005, 45, 610-623), is that the present clustering results are independent of molecular superposition and the technique is able to identify clusters in the molecule considered as a whole. This approach is easily generalizable to any two planes in any molecule.

Adhesive Properties of Cured Phenylethynyl Containing Imides

NASA Technical Reports Server (NTRS)

Jensen, Brian J.; Chang, Alice C.

1997-01-01

Considerable attention has been directed towards acetylene terminated oligomers over the last 20 years' and recent work has focused on phenylethynyl terminated imide (PETI) oligomers. These reactive oligomers possess several features which make them attractive candidates for use as composite matrices and adhesives. The phenylethynyl group can be readily incorporated into many different functionalized oligomers. The reactive oligomers possess relatively low melt viscosities and thermally cure without the evolution of volatile by-products. Once cured, they typically display high glass transition temperatures (Tgs), excellent solvent resistance and high mechanical properties. new modified phenylethynyl-terminated imide (LaRC MPEI) oligomers were synthesized at various molecular weights utilizing a small amount of trifunctional amine. As long as the amount of triamine is relatively small, this approach produces a mixture of linear, star-shaped and branched polymer chains that has lower melt and solution viscosity than an equivalent molecular weight linear phenylethynyl terminated imide oligomers. The work reported herein involves the synthesis and characterization of a copolymer using this approach and the preparation of blends utilizing a phenylethynyl containing reactive plasticizer of lower molecular weight called LaRC LV-121. The chemistry and properties of this new MPEI as well as some blends of MPEI with LV-121, are presented and compared to the linear version, LARC-PETI-5.

Developing a molecular picture for polymer glasses under large deformation

NASA Astrophysics Data System (ADS)

Wang, Shi-Qing; Cheng, Shiwang; Wang, Panpan

2014-03-01

Polymer glasses differ from most other types of glassy materials because they can be ductile under tensile extension. Remarkably, a ductile polymer can turn brittle and vice versa. For example, upon cooling, the glass changes from ductile to brittle at a temperature known as the brittle-ductile transition temperature (BDT). Aging causes the ductile glass to be brittle. Mechanical ``rejuvenation'' or pressurization brings a brittle glass into a ductile state. Finally, one glass can be ductile 100 degrees below Tg while another polymer is already brittle even just 10 degree below Tg. Polystyrene and bisphenol A polycarbonate are at the two extremes in the family of polymer glasses. How to rationale such a wide range of behavior in terms of a molecular picture has been a challenging task. What is the role of ``chain entanglement''? Since many of the procedures including the temperature change do not alter the ``chain entanglement'', it is clearly insufficient to explain the nature of the BDT in terms of the entanglement density. Our work attempts to answer the question of what then is the role of chain networking. We have formulated a molecular picture that presents a unifying and coherent explanation for all the known phenomenology concerning the BDT and condition for crazing. This work is supported, in part, by NSF (CMMI-0926522 and DMR-1105135).

ION IRRADIATION OF ETHANE AND WATER MIXTURE ICE AT 15 K: IMPLICATIONS FOR THE SOLAR SYSTEM AND THE ISM

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

Barros, A. L. F. de; Silveira, E. F da; Fulvio, D.

2016-06-20

Solid water has been observed on the surface of many different astronomical objects and is the dominant ice present in the universe, from the solar system (detected on the surface of some asteroids, planets and their satellites, trans-Neptunian objects [TNOs], comets, etc.) to dense cold interstellar clouds (where interstellar dust grains are covered with water-rich ices). Ethane has been detected across the solar system, from the atmosphere of the giant planets and the surface of Saturn’s satellite Titan to various comets and TNOs. To date, there were no experiments focused on icy mixtures of C{sub 2}H{sub 6} and H{sub 2}Omore » exposed to ion irradiation simulating cosmic rays, a case study for many astronomical environments in which C{sub 2}H{sub 6} has been detected. In this work, the radiolysis of a C{sub 2}H{sub 6}:H{sub 2}O (2:3) ice mixture bombarded by a 40 MeV{sup 58}Ni{sup 11+} ion beam is studied. The chemical evolution of the molecular species existing in the sample is monitored by a Fourier transform infrared spectrometer. The analysis of ethane, water, and molecular products in solid phase was performed. Induced chemical reactions in C{sub 2}H{sub 6}:H{sub 2}O ice produce 13 daughter molecular species. Their formation and dissociation cross sections are determined. Furthermore, atomic carbon, oxygen, and hydrogen budgets are determined and used to verify the stoichiometry of the most abundantly formed molecular species. The results are discussed in the view of solar system and interstellar medium chemistry. The study presented here should be regarded as a first step in laboratory works dedicated to simulate the effect of cosmic radiation on multicomponent mixtures involving C{sub 2}H{sub 6} and H{sub 2}O.« less

Prediction and validation of diffusion coefficients in a model drug delivery system using microsecond atomistic molecular dynamics simulation and vapour sorption analysis.

PubMed

Forrey, Christopher; Saylor, David M; Silverstein, Joshua S; Douglas, Jack F; Davis, Eric M; Elabd, Yossef A

2014-10-14

Diffusion of small to medium sized molecules in polymeric medical device materials underlies a broad range of public health concerns related to unintended leaching from or uptake into implantable medical devices. However, obtaining accurate diffusion coefficients for such systems at physiological temperature represents a formidable challenge, both experimentally and computationally. While molecular dynamics simulation has been used to accurately predict the diffusion coefficients, D, of a handful of gases in various polymers, this success has not been extended to molecules larger than gases, e.g., condensable vapours, liquids, and drugs. We present atomistic molecular dynamics simulation predictions of diffusion in a model drug eluting system that represent a dramatic improvement in accuracy compared to previous simulation predictions for comparable systems. We find that, for simulations of insufficient duration, sub-diffusive dynamics can lead to dramatic over-prediction of D. We present useful metrics for monitoring the extent of sub-diffusive dynamics and explore how these metrics correlate to error in D. We also identify a relationship between diffusion and fast dynamics in our system, which may serve as a means to more rapidly predict diffusion in slowly diffusing systems. Our work provides important precedent and essential insights for utilizing atomistic molecular dynamics simulations to predict diffusion coefficients of small to medium sized molecules in condensed soft matter systems.

Crystal structure of Pisum arvense seed lectin (PAL) and characterization of its interaction with carbohydrates by molecular docking and dynamics.

PubMed

Pinto-Junior, Vanir Reis; Santiago, Mayara Queiroz; Nobre, Camila Bezerra; Osterne, Vinicius Jose Silva; Leal, Rodrigo Bainy; Cajazeiras, Joao Batista; Lossio, Claudia Figueiredo; Rocha, Bruno Anderson Matias; Martins, Maria Gleiciane Queiroz; Nobre, Clareane Avelino Simplicio; Silva, Mayara Torquato Lima; Nascimento, Kyria Santiago; Cavada, Benildo Sousa

2017-09-15

The Pisum arvense lectin (PAL), a legume protein belonging to the Vicieae tribe, is capable of specific recognition of mannose, glucose and its derivatives without altering its structure. In this work, the three-dimensional structure of PAL was determined by X-ray crystallography and studied in detail by a combination of molecular docking and molecular dynamics (MD). Crystals belonging to monoclinic space group P2 1 were grown by the vapor diffusion method at 293 K. The structure was solved at 2.16 Å and was similar to that of other Vicieae lectins. The structure presented R factor and R free of 17.04% and 22.08%, respectively, with all acceptable geometric parameters. Molecular docking was performed to analyze interactions of the lectin with monosaccharides, disaccharides and high-mannose N-glycans. PAL demonstrated different affinities on carbohydrates, depending on bond orientation and glycosidic linkage present in ligands. Furthermore, the lectin interacted with representative N-glycans in a manner consistent with the biological effects described for Vicieae lectins. Carbohydrate-recognition domain (CRD) in-depth analysis was performed by MD, describing the behavior of CRD residues in complex with ligand, stability, flexibility of the protein over time, CRD volume and topology. This is a first report of its kind for a lectin of the Vicieae tribe. Copyright © 2017 Elsevier Inc. All rights reserved.

Investigations of vibrational spectra and bioactivity of novel anticancer drug N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid ethyl ester

NASA Astrophysics Data System (ADS)

Sudhi, Geethu; Rajina, S. R.; Praveen, S. G.; Xavier, T. S.; Kenny, Peter T. M.; Jaiswal-Nagar, D.; Binoy, J.

2017-10-01

The bioactivity of compounds is mainly dependent on molecular structure and the present work aims to explore the bonding features responsible for biological activity of novel anticancer drug N-(6-ferrocenyl-2-naphthoyl)-gamma-amino butyric acid ethyl ester (FNGABEE). In the present study, we investigate the molecular structural properties of newly synthesized title compound through experimental and quantum chemical studies. The detailed vibrational analysis has been performed using FT IR and FT Raman spectrum, aided by DFT computed geometry, vibrational spectrum, Eigen vector distribution and PED, at B3LYP/6-311 ++G(d,p) level. The resonance structure of naphthalene, different from that of benzene, revealed by molecular structure has been investigated using Csbnd C and Cdbnd C stretching modes. The proton transfer in amide has been analyzed to obtain spectral distinction between different carbonyl and Csbnd N groups which point to the reactive sites responsible for binding with DNA and bovine serum albumin (BSA). The spectral distinction between eclipsed and staggered form of ferrocene has been analyzed. The molecular docking of FNGABEE with BSA and DNA has been performed to find the strength of binding and the moieties responsible for the interactions. The experimental binding studies of FNGABEE with BSA and DNA has been performed using UV absorption spectroscopy and fluorometric assay, to find the nature and strength of binding.

Exploiting molecular dynamics in Nested Sampling simulations of small peptides

NASA Astrophysics Data System (ADS)

Burkoff, Nikolas S.; Baldock, Robert J. N.; Várnai, Csilla; Wild, David L.; Csányi, Gábor

2016-04-01

Nested Sampling (NS) is a parameter space sampling algorithm which can be used for sampling the equilibrium thermodynamics of atomistic systems. NS has previously been used to explore the potential energy surface of a coarse-grained protein model and has significantly outperformed parallel tempering when calculating heat capacity curves of Lennard-Jones clusters. The original NS algorithm uses Monte Carlo (MC) moves; however, a variant, Galilean NS, has recently been introduced which allows NS to be incorporated into a molecular dynamics framework, so NS can be used for systems which lack efficient prescribed MC moves. In this work we demonstrate the applicability of Galilean NS to atomistic systems. We present an implementation of Galilean NS using the Amber molecular dynamics package and demonstrate its viability by sampling alanine dipeptide, both in vacuo and implicit solvent. Unlike previous studies of this system, we present the heat capacity curves of alanine dipeptide, whose calculation provides a stringent test for sampling algorithms. We also compare our results with those calculated using replica exchange molecular dynamics (REMD) and find good agreement. We show the computational effort required for accurate heat capacity estimation for small peptides. We also calculate the alanine dipeptide Ramachandran free energy surface for a range of temperatures and use it to compare the results using the latest Amber force field with previous theoretical and experimental results.

Theoretical and experimental examination of SFG polarization analysis at acetonitrile-water solution surfaces.

PubMed

Saito, Kengo; Peng, Qiling; Qiao, Lin; Wang, Lin; Joutsuka, Tatsuya; Ishiyama, Tatsuya; Ye, Shen; Morita, Akihiro

2017-03-29

Sum frequency generation (SFG) spectroscopy is widely used to observe molecular orientation at interfaces through a combination of various types of polarization. The present work thoroughly examines the relation between the polarization dependence of SFG signals and the molecular orientation, by comparing SFG measurements and molecular dynamics (MD) simulations of acetonitrile/water solutions. The present SFG experiment and MD simulations yield quite consistent results on the ratios of χ (2) elements, supporting the reliability of both means. However, the subsequent polarization analysis tends to derive more upright tilt angles of acetonitrile than the direct MD calculations. The reasons for discrepancy are examined in terms of three issues; (i) anisotropy of the Raman tensor, (ii) cross-correlation, and (iii) orientational distribution. The analysis revealed that the issues (i) and (iii) are the main causes of errors in the conventional polarization analysis of SFG spectra. In methyl CH stretching, the anisotropy of Raman tensor cannot be estimated from the simple bond polarizability model. The neglect of the orientational distribution is shown to systematically underestimate the tilt angle of acetonitrile. Further refined use of polarization analysis in collaboration with MD simulations should be proposed.

Synthesis of N-(β-D-glycuronopyranosyl)alkanamides and 1-(β-D-glycuronopyranosyl)-4-phenyl-[1,2,3]-triazoles as N-glycoprotein linkage region analogs: examination of the effect of C5 substituent on the N-glycosidic torsion (ΦN) based on X-ray crystallography.

PubMed

Mathiselvam, Manoharan; Loganathan, Duraikkannu; Varghese, Babu

2013-10-18

The torsion angle around the N-glycoprotein linkage region (GlcNAc-Asn) is an important factor for presenting sugar on the cell surface which is crucial for many biological processes. Earlier studies using model and analogs showed that this important torsion angle is greatly influenced by substitutions in the sugar part. In the present work, uronic acid alkanamides and triazole derivatives have been designed and synthesized as newer analogs of N-glycoprotein linkage region to understand the influence of the carboxylic group on linkage region torsion as well as on molecular packing. Crystal structure of N-(β-D-galacturonopyranosyl)acetamide is solved with the space group of P22121. Comparison of the torsion angle and molecular packing of this compound with N-(β-D-galactopyranosyl)acetamide showed that changing the C6-hydoxymethyl group to the carboxylic acid group has minimum influence on the N-glycosidic torsion angle, ΦN and significant influence on the molecular packing. Copyright © 2013 Elsevier Ltd. All rights reserved.

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

PubMed

Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

2009-03-14

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

High Molecular Weight Proteins of Trypanosoma cruzi Reduce Cross-Reaction with Leishmania spp. in Serological Diagnosis Tests

PubMed Central

Cervantes-Landín, Alejandra Yunuen; Martínez, Ignacio; Schabib, Muslim; Espinoza, Bertha

2014-01-01

Chagas disease is caused by the parasite Trypanosoma cruzi. Because of its distribution throughout Latin America, sometimes it can overlap with other parasitic diseases, such as leishmaniasis, caused by Leishmania spp. This might represent a problem when performing serological diagnosis, because both parasites share antigens, resulting in cross-reactions. In the present work we evaluated Mexican sera samples: 83.8% of chagasic patients recognized at least one antigen of high molecular weight (>95 kDa) when evaluated by Western blot. Proteins of 130 kDa and 160 kDa are predominantly being recognized by asymptomatic chagasic patients. When the proteins were extracted using Triton X-100 detergent, a larger number of specific T. cruzi proteins were obtained. This protein fraction can be used to increase specificity to 100% in Western blot assays without losing sensitivity of the test. High molecular weight proteins of T. cruzi include glycoproteins with a great amount of αMan (α-mannose), αGlc (α-glucose), GlcNAc (N-acetylglucosamine), and αGal (α-galactose) content and these structures play an essential role in antigens recognition by antibodies present in patients' sera. PMID:25136581

Bounding the electrostatic free energies associated with linear continuum models of molecular solvation

NASA Astrophysics Data System (ADS)

Bardhan, Jaydeep P.; Knepley, Matthew G.; Anitescu, Mihai

2009-03-01

The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

Multiple e-pharmacophore modelling pooled with high-throughput virtual screening, docking and molecular dynamics simulations to discover potential inhibitors of Plasmodium falciparum lactate dehydrogenase (PfLDH).

PubMed

Saxena, Shalini; Durgam, Laxman; Guruprasad, Lalitha

2018-05-14

Development of new antimalarial drugs continues to be of huge importance because of the resistance of malarial parasite towards currently used drugs. Due to the reliance of parasite on glycolysis for energy generation, glycolytic enzymes have played important role as potential targets for the development of new drugs. Plasmodium falciparum lactate dehydrogenase (PfLDH) is a key enzyme for energy generation of malarial parasites and is considered to be a potential antimalarial target. Presently, there are nearly 15 crystal structures bound with inhibitors and substrate that are available in the protein data bank (PDB). In the present work, we attempted to consider multiple crystal structures with bound inhibitors showing affinity in the range of 1.4 × 10 2 -1.3 × 10 6  nM efficacy and optimized the pharmacophore based on the energy involved in binding termed as e-pharmacophore mapping. A high throughput virtual screening (HTVS) combined with molecular docking, ADME predictions and molecular dynamics simulation led to the identification of 20 potential compounds which could be further developed as novel inhibitors for PfLDH.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-01

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400 cm-1) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

A hydro/organo/hybrid gelator: a peptide lipid with turning aspartame head groups.

PubMed

Mukai, Masaru; Minamikawa, Hiroyuki; Aoyagi, Masaru; Asakawa, Masumi; Shimizu, Toshimi; Kogiso, Masaki

2013-04-01

This work presents a novel bola-type peptide lipid which can gelate water, organic solvents, and water/organic-solvent mixtures. In its molecular structure, an amphiphilic dipeptide aspartame (L-α-aspartyl-L-phenylalanine methyl ester) is connected at both ends of an alkylene linker. The different morphologies in the hydrogel (helical nanotapes) and the organogel (tape-like nanostructures) were visualized by energy-filtering transmission electron microscopy (EF-TEM) and energy-filtering scanning electron microscopy (FE-SEM), and the molecular arrangement was examined using X-ray diffraction (XRD), infrared (IR) spectroscopy, and circular dichroism (CD) spectroscopy. Possessing a hydrophilic aspartic acid group and a (relatively) hydrophobic phenylalanine methyl ester group, the dipeptide head group can turn about in response to solvent polarity. As a consequence, the solvent condition changed the molecular packing of the gelator and affected the overall supramolecular structure of the gel. It is noted that the peptide lipid gelated mixed solvents of water and organic solvents such as dichloromethane, liquid-paraffin, olive-oil, silicone-oils, and so on. The present hybrid gel can simultaneously hold hydrophilic and hydrophobic functional materials. Copyright © 2013 Elsevier Inc. All rights reserved.

Tabletop Molecular Communication: Text Messages through Chemical Signals

PubMed Central

Farsad, Nariman; Guo, Weisi; Eckford, Andrew W.

2013-01-01

In this work, we describe the first modular, and programmable platform capable of transmitting a text message using chemical signalling – a method also known as molecular communication. This form of communication is attractive for applications where conventional wireless systems perform poorly, from nanotechnology to urban health monitoring. Using examples, we demonstrate the use of our platform as a testbed for molecular communication, and illustrate the features of these communication systems using experiments. By providing a simple and inexpensive means of performing experiments, our system fills an important gap in the molecular communication literature, where much current work is done in simulation with simplified system models. A key finding in this paper is that these systems are often nonlinear in practice, whereas current simulations and analysis often assume that the system is linear. However, as we show in this work, despite the nonlinearity, reliable communication is still possible. Furthermore, this work motivates future studies on more realistic modelling, analysis, and design of theoretical models and algorithms for these systems. PMID:24367571

Molecular vibrational investigation [FT-IR, FT-Raman, UV-Visible and NMR] on Bis(thiourea) Nickel chloride using HF and DFT calculations.

PubMed

Anand, S; Sundararajan, R S; Ramachandraraja, C; Ramalingam, S; Durga, R

2015-03-05

In the present research work, the FT-IR, FT-Raman spectra of the Bis(thiourea) Nickel chloride (BTNC) were recorded and analyzed. The observed fundamental frequencies in finger print and functional group regions were assigned according to their uniqueness region. The computational calculations were carried out by HF and DFT (B3LYP and B3PW91) methods with 6-31++G(d,p) and 6-311++G(d,p) basis sets and the corresponding results were tabulated. The present organo-metallic compound was made up of covalent and coordination covalent bonds. The modified vibrational pattern of the complex molecule associated with ligand group was analyzed. Furthermore, the (13)C NMR and (1)H NMR spectral data were calculated by using the gauge independent atomic orbital (GIAO) method with B3LYP/6-311++G(d,p) basis set and their spectra were simulated and the chemical shifts linked to TMS were compared. A investigation on the electronic and optical properties; absorption wavelengths, excitation energy, dipole moment and frontier molecular orbital energies were carried out. The kubo gap of the present compound was calculated related to HOMO and LUMO energies which confirm the occurring of charge transformation between the base and ligand. Besides frontier molecular orbitals (FMO), molecular electrostatic potential (MEP) was performed. The NLO properties related to Polarizability and hyperpolarizability based on the finite-field approach were also discussed. Crown Copyright © 2014. Published by Elsevier B.V. All rights reserved.

Structural alterations by five disease-causing mutations in the low-pH conformation of human dihydrolipoamide dehydrogenase (hLADH) analyzed by molecular dynamics - Implications in functional loss and modulation of reactive oxygen species generation by pathogenic hLADH forms.

PubMed

Ambrus, Attila; Mizsei, Reka; Adam-Vizi, Vera

2015-07-01

Human dihydrolipoamide dehydrogenase (hLADH) is a flavoenzyme component (E3) of the human alpha-ketoglutarate dehydrogenase complex (α-KGDHc) and few other dehydrogenase complexes. Pathogenic mutations of hLADH cause severe metabolic diseases (atypical forms of E3 deficiency) that often escalate to cardiological or neurological presentations and even premature death; the pathologies are generally accompanied by lactic acidosis. hLADH presents a distinct conformation under acidosis (pH 5.5-6.8) with lower physiological activity and the capacity of generating reactive oxygen species (ROS). It has been shown by our laboratory that selected pathogenic mutations, besides lowering the physiological activity of hLADH, significantly stimulate ROS generation by hLADH, especially at lower pH, which might play a role in the pathogenesis of E3-deficiency in respective cases. Previously, we generated by molecular dynamics (MD) simulation the low-pH hLADH structure and analyzed the structural changes induced in this structure by eight of the pathogenic mutations of hLADH. In the absence of high resolution mutant structures these pieces of information are crucial for the mechanistic investigation of the molecular pathogeneses of the hLADH protein. In the present work we analyzed by molecular dynamics simulation the structural changes induced in the low-pH conformation of hLADH by five pathogenic mutations of hLADH; the structures of these disease-causing mutants of hLADH have never been examined before.

Universal optimal working cycles of molecular motors.

PubMed

Efremov, Artem; Wang, Zhisong

2011-04-07

Molecular motors capable of directional track-walking or rotation are abundant in living cells, and inspire the emerging field of artificial nanomotors. Some biomotors can convert 90% of free energy from chemical fuels into usable mechanical work, and the same motors still maintain a speed sufficient for cellular functions. This study exposed a new regime of universal optimization that amounts to a thermodynamically best working regime for molecular motors but is unfamiliar in macroscopic engines. For the ideal case of zero energy dissipation, the universally optimized working cycle for molecular motors is infinitely slow like Carnot cycle for heat engines. But when a small amount of energy dissipation reduces energy efficiency linearly from 100%, the speed is recovered exponentially due to Boltzmann's law. Experimental data on a major biomotor (kinesin) suggest that the regime of universal optimization has been largely approached in living cells, underpinning the extreme efficiency-speed trade-off in biomotors. The universal optimization and its practical approachability are unique thermodynamic advantages of molecular systems over macroscopic engines in facilitating motor functions. The findings have important implications for the natural evolution of biomotors as well as the development of artificial counterparts.

Comment on "Spontaneous liquid-liquid phase separation of water".

PubMed

Limmer, David T; Chandler, David

2015-01-01

Yagasaki et al. [Phys. Rev. E 89, 020301 (2014)] present results from a molecular dynamics trajectory illustrating coarsening of ice, which they interpret as evidence of transient coexistence between two distinct supercooled phases of liquid water. We point out that neither two distinct liquids nor criticality are demonstrated in this simulation study. Instead, the illustrated trajectory is consistent with coarsening behaviors analyzed and predicted in earlier work by others.

Application of Renyi entropy for ultrasonic molecular imaging.

PubMed

Hughes, M S; Marsh, J N; Arbeit, J M; Neumann, R G; Fuhrhop, R W; Wallace, K D; Thomas, L; Smith, J; Agyem, K; Lanza, G M; Wickline, S A; McCarthy, J E

2009-05-01

Previous work has demonstrated that a signal receiver based on a limiting form of the Shannon entropy is, in certain settings, more sensitive to subtle changes in scattering architecture than conventional energy-based signal receivers [M. S. Hughes et al., J. Acoust. Soc. Am. 121, 3542-3557 (2007)]. In this paper new results are presented demonstrating further improvements in sensitivity using a signal receiver based on the Renyi entropy.

Nanoparticle light scattering on interferometric surfaces

NASA Astrophysics Data System (ADS)

Hayrapetyan, K.; Arif, K. M.; Savran, C. A.; Nolte, D. D.

2011-03-01

We present a model based on Mie Surface Double Interaction (MSDI) to explore bead-based detection mechanisms using imaging and scanning. The application goal of this work is to explore the trade-offs between the sensitivity and throughput among various detection methods. Experimentally we use thermal oxide on silicon to establish and control surface interferometric conditions. Surface-captured gold beads are detected using Molecular Interferometric Imaging (MI2) and Spinning-Disc Interferometry (SDI).

USSR and Eastern Europe Scientific Abstracts, Biomedical and Behavioral Sciences, Number 81.

DTIC Science & Technology

1977-11-28

Hydrobiology 21 Industrial Microbiology 22 Industrial Toxicology 31 Marine Mammals 35 Microbiology 36 Molecular Biology 38 Neuros ciences...in progress. Factors involved in increasing productivity were calculated and presented in 4 tables: duration of use of equipment in 1 day (hours...machines no longer in production but omits materials on some new equipment and some new forms of organization of the work of the agrochemical

Directional Darwinian Selection in proteins.

PubMed

McClellan, David A

2013-01-01

Molecular evolution is a very active field of research, with several complementary approaches, including dN/dS, HON90, MM01, and others. Each has documented strengths and weaknesses, and no one approach provides a clear picture of how natural selection works at the molecular level. The purpose of this work is to present a simple new method that uses quantitative amino acid properties to identify and characterize directional selection in proteins. Inferred amino acid replacements are viewed through the prism of a single physicochemical property to determine the amount and direction of change caused by each replacement. This allows the calculation of the probability that the mean change in the single property associated with the amino acid replacements is equal to zero (H0: μ = 0; i.e., no net change) using a simple two-tailed t-test. Example data from calanoid and cyclopoid copepod cytochrome oxidase subunit I sequence pairs are presented to demonstrate how directional selection may be linked to major shifts in adaptive zones, and that convergent evolution at the whole organism level may be the result of convergent protein adaptations. Rather than replace previous methods, this new method further complements existing methods to provide a holistic glimpse of how natural selection shapes protein structure and function over evolutionary time.

A generalized any particle propagator theory: Assessment of nuclear quantum effects on electron propagator calculations

NASA Astrophysics Data System (ADS)

Romero, Jonathan; Posada, Edwin; Flores-Moreno, Roberto; Reyes, Andrés

2012-08-01

In this work we propose an extended propagator theory for electrons and other types of quantum particles. This new approach has been implemented in the LOWDIN package and applied to sample calculations of atomic and small molecular systems to determine its accuracy and performance. As a first application of the method we have studied the nuclear quantum effects on electron ionization energies. We have observed that ionization energies of atoms are similar to those obtained with the electron propagator approach. However, for molecular systems containing hydrogen atoms there are improvements in the quality of the results with the inclusion of nuclear quantum effects. An energy term analysis has allowed us to conclude that nuclear quantum effects are important for zero order energies whereas propagator results correct the electron and electron-nuclear correlation terms. Results presented for a series of n-alkanes have revealed the potential of this method for the accurate calculation of ionization energies of a wide variety of molecular systems containing hydrogen nuclei. The proposed methodology will also be applicable to exotic molecular systems containing positrons or muons.

Effect of molecular properties on the performance of polymer light-emitting diodes

NASA Astrophysics Data System (ADS)

Ramos, Marta M. D.; Almeida, A. M.; Correia, Helena M. G.; Ribeiro, R. Mendes; Stoneham, A. M.

2004-11-01

The performance of a single layer polymer light-emitting diode depends on several interdependent factors, although recombination between electrons and holes within the polymer layer is believed to play an important role. Our aim is to carry out computer experiments in which bipolar charge carriers are injected in polymer networks made of poly(p-phenylene vinylene) chains randomly oriented. In these simulations, we follow the charge evolution in time from some initial state to the steady state. The intra-molecular properties of the polymer molecules obtained from self-consistent quantum molecular dynamics calculations are used in the mesoscopic model. The purpose of the present work is to clarify the effects of intra-molecular charge mobility and energy disorder on recombination efficiency. In particular, we find that charge mobility along the polymer chains has a serious influence on recombination within the polymer layer. Our results also show that energy disorder due to differences in ionization potential and electron affinity of neighbouring molecules affects mainly recombinations that occur near the electrodes at polymer chains parallel to them.

Chain exchange in triblock copolymer micelles

NASA Astrophysics Data System (ADS)

Lu, Jie; Lodge, Timothy; Bates, Frank

2015-03-01

Block polymer micelles offer a host of technological applications including drug delivery, viscosity modification, toughening of plastics, and colloidal stabilization. Molecular exchange between micelles directly influences the stability, structure and access to an equilibrium state in such systems and this property recently has been shown to be extraordinarily sensitive to the core block molecular weight in diblock copolymers. The dependence of micelle chain exchange dynamics on molecular architecture has not been reported. The present work conclusively addresses this issue using time-resolved small-angle neutron scattering (TR-SANS) applied to complimentary S-EP-S and EP-S-EP triblock copolymers dissolved in squalane, a selective solvent for the EP blocks, where S and EP refer to poly(styrene) and poly(ethylenepropylene), respectively. Following the overall SANS intensity as a function of time from judiciously deuterium labelled polymer and solvent mixtures directly probes the rate of molecular exchange. Remarkably, the two triblocks display exchange rates that differ by approximately ten orders of magnitude, even though the solvophobic S blocks are of comparable size. This discovery is considered in the context of a model that successfully explains S-EP diblock exchange dynamics.

Anatomy of a Photodissociation Region: High angular resolution images of molecular emission in the Orion Bar

NASA Technical Reports Server (NTRS)

Tauber, Jan A.; Tielens, A. G. G. M.; Meixner, Margaret; Foldsmith, Paul F.

1994-01-01

We present observations of the molecular component of the Orion Bar, a prototypical Photodissociation Region (PDR) illuminated by the Trapezium cluster. The high angular resolution (6 sec-10 sec) that we have achieved by combining single-dish and interferometric observations has allowed us to examine in detail the spatial and kinematic morphology of this region and to estimate the physical characteristics of the molecular gas it contains. Our observations indicate that this PDR can be essentially described as a homogeneously distributed slab of moderately dense material (approximately 5 x 10(exp 4)/cu cm), in which are embedded a small number of dense (greater than 10(exp 6)/cu cm) clumps. The latter play little or no role in determining the thickness and kinetic temperature structure of this PDR. This observational picture is largely supported by PDR model calculations for this region, which we describe in detail in this work. We also find our model predictions of the intensities of a variety of atomic and molecular lines to be in good general agreement with a number of previous observations.

Single-Molecule Real-Time 3D Imaging of the Transcription Cycle by Modulation Interferometry.

PubMed

Wang, Guanshi; Hauver, Jesse; Thomas, Zachary; Darst, Seth A; Pertsinidis, Alexandros

2016-12-15

Many essential cellular processes, such as gene control, employ elaborate mechanisms involving the coordination of large, multi-component molecular assemblies. Few structural biology tools presently have the combined spatial-temporal resolution and molecular specificity required to capture the movement, conformational changes, and subunit association-dissociation kinetics, three fundamental elements of how such intricate molecular machines work. Here, we report a 3D single-molecule super-resolution imaging study using modulation interferometry and phase-sensitive detection that achieves <2 nm axial localization precision, well below the few-nanometer-sized individual protein components. To illustrate the capability of this technique in probing the dynamics of complex macromolecular machines, we visualize the movement of individual multi-subunit E. coli RNA polymerases through the complete transcription cycle, dissect the kinetics of the initiation-elongation transition, and determine the fate of σ 70 initiation factors during promoter escape. Modulation interferometry sets the stage for single-molecule studies of several hitherto difficult-to-investigate multi-molecular transactions that underlie genome regulation. Copyright © 2016 Elsevier Inc. All rights reserved.

Fractography of poly(methyl methacrylates).

PubMed

Kusy, R P; Turner, D T

1975-07-01

For convenience in clinical manipulation, it is the practice to fabricate PMMA protheses from mixtures of powder and monomer. When the monomer is subsequently polymerized an unusual 2-phase polymeric material results in which grains of PMMA are dispersed in a matrix of the same polymer. The mechanical properties of the 2-phase materials are inferior in certain respects relative to 1-phase polymers. The purpose of the present work is to evaluate the failure of 2-phase materials by microscopical examination of their fracture surfaces. A granular microstructure was clearly distinguishable and a distinction made between materials which fail exclusively by transgranular fracture and others which additionally exhibit intergranular fracture. In order to interpret markings observed on the fracture surfaces of the complex 2-phase systems a study was made of the influence of molecular weight on the fractography of 1-phase PMMA. Molecular weight was reduced by degradation of samples by exposure to gamma-rays. The spacing of periodic rib markings on fracture surfaces was found to decrease with molecular weight and this relationship used to provide an estimate of the molecular weight of polymer in the matrix of 2-phase materials.

Control of metallic corrosion through microbiological route.

PubMed

Maruthamuthu, S; Ponmariappan, S; Mohanan, S; Palaniswamy, N; Palaniappan, R; Rengaswamy, N S

2003-09-01

Involvement of biofilm or microorganisms in corrosion processes is widely acknowledged. Although majority of the studies on microbiologically induced corrosion (MIC) have concentrated on aerobic/anaerobic bacteria. There are numerous aerobic bacteria, which could hinder the corrosion process. The microbiologically produced exopolymers provide the structural frame work for the biofilm. These polymers combine with dissolved metal ions and form organometallic complexes. Generally heterotrophic bacteria contribute to three major processes: (i) synthesis of polymers (ii) accumulation of reserve materials like poly-beta-hydroxy butrate (iii) production of high molecular weight extracellular polysaccharides. Poly-beta-hydroxy butyrate is a polymer of D(-)beta-hydroxy butrate and has a molecular weight between 60,000 and 2,50,000. Some extracellular polymers also have higher molecular weights. It seems that higher molecular weight polymer acts as biocoating. In the present review, role of biochemistry on corrosion inhibition and possibilities of corrosion inhibition by various microbes are discussed. The role of bacteria on current demand during cathodic protection is also debated. In addition, some of the significant contributions made by CECRI in this promising area are highlighted.

The Effect of Molecular Contamination on the Emissivity Spectral Index in Orion A

NASA Astrophysics Data System (ADS)

Coudé, Simon; Bastien, Pierre; Drabek, Emily; Johnstone, Doug; Hatchell, Jennifer

2013-07-01

The emissivity spectral index is a critical component in the study of the physical properties of dust grains in cold and optically thin interstellar star forming regions. Since submillimeter astronomy is an ideal tool to measure the thermal emission of those dust grains, it can be used to characterize this important parameter. We present the SCUBA-2 shared risks observations at 450 μm and 850 μm of the Orion A molecular cloud obtained at the James-Clerk-Maxwell telescope. Previous studies showed that molecular emission lines can also contribute significantly to the measured fluxes in those continuum bands. We use HARP 12CO 3-2 maps to evaluate the total molecular line contamination in the SCUBA-2 maps and its effect on the determination of the spectral index in highly contaminated areas. With the corrected fluxes, we have obtained new spectral index maps for different regions of the well-known integral-shaped filament. This work is part of an ongoing effort to characterize the properties of star forming regions in the Gould belt with the new instruments available at the JCMT.

Lighting the dark molecular gas and a Bok globule

NASA Astrophysics Data System (ADS)

Togi, Aditya G.

Stars are the building blocks of galaxies. The gas present in galaxies is the primary fuel for star formation. Galaxy evolution depends on the amount of gas present in the interstellar medium (ISM). Stars are born mainly from molecular gas in the GMCs. Robust knowledge of the molecular hydrogen H2 gas distribution is necessary to understand star formation in galaxies. Since H2 is not readily observable in the cold interstellar medium (ISM), the molecular gas content has traditionally been inferred using indirect tracers like carbon-monoxide (CO), dust emission, gamma ray interactions, and star formation efficiency. Physical processes resulting in enhancement and reduction of these indirect tracers can result in misleading estimates of molecular gas masses. My dissertation work is based on devising a new temperature power law distribution model for H2, a direct tracer, to calculate the total molecular gas mass in galaxies. The model parameters are estimated using mid infrared (MIR) H2 rotational line fluxes obtained from IRS-Spitzer (Infrared Spectrograph-Spitzer) instrument and the model is extrapolated to a suitable lower temperature to recover the total molecular gas mass. The power law model is able to recover the dark molecular gas, undetected by CO, in galaxies at metallicity as low as one-tenth of our Milky Way value. I have applied the power law model in U/LIRGs and shocks of Stephan's Quintet to understand molecular gas properties, where shocks play an important role in exciting H2. Comparing the molecular gas content derived through our power law model can be useful in studying the application of our model in mergers. The parameters derived by our model is useful in understanding variation in molecular gas properties in shock regions of Stephan's Quintet. Low mass stars are formed in small isolated dense cores known as Bok globules. Multiple star formation events are seen in a Bok globule. In my thesis I also studied a Bok globule, B207, and determined the physical properties and future evolutionary stage of the cloud. My thesis spans studying ISM properties in galaxies from kpc to sub-pc scales. Using the power law model in the coming era of James Webb Space Telescope (JWST) with the high sensitivity MIR Instrument (MIRI) spectrograph we will be able to understand the properties of molecular gas at low and high redshifts.

Shigeru Tsuiki: a pioneer in the research fields of complex carbohydrates and protein phosphatases.

PubMed

Miyagi, Taeko; Kikuchi, Kunimi; Tamura, Shinri

2011-11-01

Dr Tsuiki made three major contributions during his illustrious career as a biochemist. First, he developed the procedure for mucin isolation from bovine submaxillary glands. His work became the basis for mucin biochemistry. Second, he identified four distinct molecular species of mammalian sialidase. Subsequent studies based on his work led to the discovery that sialidase plays a unique role as an intracellular signalling factor involved in the regulation of a variety of cellular functions. Finally, he established the molecular basis for the diversity of mammalian protein phosphatases through protein purification and molecular cloning. His work prompted the functional studies of protein phosphatases.

Targeted Approach to Overcoming Treatment Resistance in Advanced Prostate Cancer

DTIC Science & Technology

2013-07-01

molecular   dynamics  as  in  our  previous  works  (Vasilyeva,  A  et  al,  2009;  Vasilyeva,  A   et...results  and  pitfalls.     Molecular  docking  experiments  were  performed  as   follows:   The   molecular  docking  was...al,  2010;Salsbury.  2010).  However,  for  this  work  more  extensive   simulations

THE IMPACT OF MOLECULAR GAS ON MASS MODELS OF NEARBY GALAXIES

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

Frank, B. S.; Blok, W. J. G. de; Walter, F.

2016-04-15

We present CO velocity fields and rotation curves for a sample of nearby galaxies, based on data from HERACLES. We combine our data with THINGS, SINGS, and KINGFISH results to provide a comprehensive sample of mass models of disk galaxies inclusive of molecular gas. We compare the kinematics of the molecular (CO from HERACLES) and atomic (H i from THINGS) gas distributions to determine the extent to which CO may be used to probe the dynamics in the inner part of galaxies. In general, we find good agreement between the CO and H i kinematics, with small differences in themore » inner part of some galaxies. We add the contribution of the molecular gas to the mass models in our galaxies by using two different conversion factors α{sub CO} to convert CO luminosity to molecular gas mass surface density—the constant Milky Way value and the radially varying profiles determined in recent work based on THINGS, HERACLES, and KINGFISH data. We study the relative effect that the addition of the molecular gas has on the halo rotation curves for Navarro–Frenk–White and the observationally motivated pseudo-isothermal halos. The contribution of the molecular gas varies for galaxies in our sample—for those galaxies where there is a substantial molecular gas content, using different values of α{sub CO} can result in significant differences to the relative contribution of the molecular gas and hence the shape of the dark matter halo rotation curves in the central regions of galaxies.« less

Adsorption of dissolved organics in lake water by aluminum oxide. Effect of molecular weight

USGS Publications Warehouse

Davis, J.A.; Gloor, R.

1981-01-01

Dissolved organic compounds in a Swiss lake were fractionated into three molecular size classes by gel exclusion chromatography, and adsorption of each fraction on colloidal alumina was studied as a function of pH. Organic compounds with molecular weight (Mr) greater than 1000 formed strong complexes with the alumina surface, but low molecular weight compounds were weakly adsorbed. Electrophoretic mobility measurements indicated that alumina particles suspended in the original lake water were highly negatively charged because of adsorbed organic matter. Most of the adsorbed organic compounds were in the Mr range 1000 < Mr < 3000. Adsorption of these compounds during the treatment of drinking water by alum coagulation may be responsible for the preferential removal of trihalomethane precursors. Adsorption may also influence the molecular-weight distribution of dissolved organic material in lakes. surface, the present work will focus on the influence of molecular size and pH on the adsorption behavior of dissolved organic material of a Swiss lake. From a geochemical point of view, it is important to know the molecular-weight distribution of adsorbed organic matter so that we may better assess its reactivity with trace elements. The study also serves as a first step in quantifying the role of adsorption in the geochemical cycle of organic carbon in lacustrine environments. For water-treatment practice, we need to determine whether molecular weight fractionation occurs during adsorption by aluminum oxide. Such a fractionation could be significant in the light of recent reports that chloroform and other organochlorine compounds are preferentially produced by particular molecular-weight fractions (25-27). ?? 1981 American Chemical Society.

Molecular phylogeny of Pasiphaeidae (Crustacea, Decapoda, Caridea) reveals systematic incongruence of the current classification.

PubMed

Liao, Yunshi; De Grave, Sammy; Ho, Tsz Wai; Ip, Brian H Y; Tsang, Ling Ming; Chan, Tin-Yam; Chu, Ka Hou

2017-10-01

Caridean shrimps constitute one of the most diverse groups of decapod crustaceans, notwithstanding their poorly resolved infraordinal relationships. One of the systematically controversial families in Caridea is the predominantly pelagic Pasiphaeidae, comprises 101 species in seven genera. Pasiphaeidae species exhibit high morphological disparity, as well as ecological niche width, inhabiting shallow to very deep waters (>4000m). The present work presents the first molecular phylogeny of the family, based on a combined dataset of six mitochondrial and nuclear gene markers (12S rDNA, 16S rDNA, histone 3, sodium-potassium ATPase α-subunit, enolase and ATP synthase β-subunit) from 33 species belonged to six genera of Pasiphaeidae with 19 species from 12 other caridean families as outgroup taxa. Maximum likelihood and Bayesian inference analyses conducted on the concatenated dataset of 2265bp suggest the family Pasiphaeidae is not monophyletic, with Psathyrocaris more closely related to other carideans than to the other five pasiphaeid genera included in this analysis. Leptochela occupies a sister position to the remaining genera and is genetically quite distant from them. At the generic level, the analysis supports the monophyly of Pasiphaea, Leptochela and Psathyrocaris, while Eupasiphae is shown to be paraphyletic, closely related to Parapasiphae and Glyphus. The present molecular result strongly implies that certain morphological characters used in the present systematic delineation within Pasiphaeidae may not be synapomorphies and the classification within the family needs to be urgently revised. Copyright © 2017 Elsevier Inc. All rights reserved.

Possibility designing half-wave and full-wave molecular rectifiers by using single benzene molecule

NASA Astrophysics Data System (ADS)

Abbas, Mohammed A.; Hanoon, Falah H.; Al-Badry, Lafy F.

2018-02-01

This work focused on possibility designing half-wave and full-wave molecular rectifiers by using single and two benzene rings, respectively. The benzene rings were threaded by a magnetic flux that changes over time. The quantum interference effect was considered as the basic idea in the rectification action, the para and meta configurations were investigated. All the calculations are performed by using steady-state theoretical model, which is based on the time-dependent Hamiltonian model. The electrical conductance and the electric current are considered as DC output signals of half-wave and full-wave molecular rectifiers. The finding in this work opens up the exciting potential to use these molecular rectifiers in molecular electronics.

How much structuring is beneficial with regard to examination scores? A prospective study of three forms of active learning.

PubMed

Reinhardt, Claus H; Rosen, Evelyne N

2012-09-01

Many studies have demonstrated a superiority of active learning forms compared with traditional lecture. However, there is still debate as to what degree structuring is necessary with regard to high exam outcomes. Seventy-five students from a premedical school were randomly attributed to an active lecture group, a cooperative group, or a collaborative learning group. The active lecture group received lectures with questions to resolve at the end of the lecture. At the same time, the cooperative group and the collaborative group had to work on a problem and prepare presentations for their answers. The collaborative group worked in a mostly self-directed manner; the cooperative group had to follow a time schedule. For the additional work of preparing the poster presentation, the collaborative and cooperative groups were allowed 50% more working time. In part 1, all groups worked on the citric acid cycle, and in part 2, all groups worked on molecular genetics. Collaborative groups had to work on tasks and prepare presentations for their answers. At the end of each part, all three groups were subjected to the same exam. Additionally, in the collaborative and cooperative groups, the presentations were marked. All evaluations were performed by two independent examiners. Exam results of the active lecture groups were highest. Results of the cooperative group were nonsignificantly lower than the active lecture group and significantly higher than the collaborative group. The presentation quality was nonsignificantly higher in the collaborative group compared with the cooperative group. This study shows that active lecturing produced the highest exam results, which significantly differed from collaborative learning results. The additional elaboration in the cooperative and collaborative learning setting yielded the high presentation quality but apparently could not contribute further to exam scores. Cooperative learning seems to be a good compromise if high exam and presentation scores are expected.

The Effect of Water on the Work of Adhesion at Epoxy Interfaces by Molecular Dynamics Simulation

NASA Technical Reports Server (NTRS)

Hinkley, J.A.; Frankland, S.J.V.; Clancy, T.C.

2009-01-01

Molecular dynamics simulation can be used to explore the detailed effects of chemistry on properties of materials. In this paper, two different epoxies found in aerospace resins are modeled using molecular dynamics. The first material, an amine-cured tetrafunctional epoxy, represents a composite matrix resin, while the second represents a 177 C-cured adhesive. Surface energies are derived for both epoxies and the work of adhesion values calculated for the epoxy/epoxy interfaces agree with experiment. Adding water -- to simulate the effect of moisture exposure -- reduced the work of adhesion in one case, and increased it in the other. To explore the difference, the various energy terms that make up the net work of adhesion were compared and the location of the added water was examined.

ECUT (Energy Conversion and Utilization Technologies) program: Biocatalysis Project

NASA Technical Reports Server (NTRS)

1988-01-01

Fiscal year 1987 research activities and accomplishments for the Biocatalysis Project of the U.S. Department of Energy, Energy Conversion and Utilization Technologies (ECUT) Division are presented. The project's technical activities were organized into three work elements. The Molecular Modeling and Applied Genetics work element includes modeling and simulation studies to verify a dynamic model of the enzyme carboxypeptidase; plasmid stabilization by chromosomal integration; growth and stability characteristics of plasmid-containing cells; and determination of optional production parameters for hyper-production of polyphenol oxidase. The Bioprocess Engineering work element supports efforts in novel bioreactor concepts that are likely to lead to substantially higher levels of reactor productivity, product yields, and lower separation energetics. The Bioprocess Design and Assessment work element attempts to develop procedures (via user-friendly computer software) for assessing the economics and energetics of a given biocatalyst process.

Ground-water contamination at an inactive coal and oil gasification plant site, Gas Works Park, Seattle, Washington

USGS Publications Warehouse

Turney, G.L.; Goerlitz, D.F.

1989-01-01

Gas Works Park, in Seattle, Washington, is located on the site of a coal and oil gasification plant that ceased operation in 1956. During operation, many types of wastes, including coal, tar, and oil, accumulated on site. The park soil is presently (1986) contaminated with compounds such as polynuclear aromatic hydrocarbons, volatile organic compounds, trace metals, and cyanide. Analyses of water samples from a network of observation wells in the park indicate that these compounds are also present in the groundwater. Polynuclear aromatic hydrocarbons and volatile organic compounds were identified in groundwater samples in concentrations as large as 200 mg/L. Concentrations of organic compounds were largest where groundwater was in contact with a nonaqueous phase liquid in the soil. Concentrations in groundwater were much smaller where no nonaqueous phase liquid was present, even if the groundwater was in contact with contaminated soils. This condition is attributed to weathering processes at the site, such as dissolution, volatilization, and biodegradation. Soluble, volatile, low-molecular-weight organic compounds are preferentially dissolved from the nonaqueous phase liquid into the groundwater. Where no nonaqueous phase liquid is present, only stained soils containing relatively insoluble, high-molecular-weight compounds remain; therefore, contaminant concentrations in the groundwater are much smaller. Concentrations of organic contaminants in the soils may still remain large. Values of specific conductance were as large as 5,280 microsiemens/cm, well above a background of 242 microsiemens/cm, suggesting large concentrations of minerals in the groundwater. Trace metal concentrations, however , were generally < 0.010 mg/L, and below limits of US EPA drinking water standards. Cyanide was present in groundwater samples from throughout the park, ranging in concentration from 0.01 to 8.6 mg/L. (Author 's abstract)

An anatomic transcriptional atlas of human glioblastoma.

PubMed

Puchalski, Ralph B; Shah, Nameeta; Miller, Jeremy; Dalley, Rachel; Nomura, Steve R; Yoon, Jae-Guen; Smith, Kimberly A; Lankerovich, Michael; Bertagnolli, Darren; Bickley, Kris; Boe, Andrew F; Brouner, Krissy; Butler, Stephanie; Caldejon, Shiella; Chapin, Mike; Datta, Suvro; Dee, Nick; Desta, Tsega; Dolbeare, Tim; Dotson, Nadezhda; Ebbert, Amanda; Feng, David; Feng, Xu; Fisher, Michael; Gee, Garrett; Goldy, Jeff; Gourley, Lindsey; Gregor, Benjamin W; Gu, Guangyu; Hejazinia, Nika; Hohmann, John; Hothi, Parvinder; Howard, Robert; Joines, Kevin; Kriedberg, Ali; Kuan, Leonard; Lau, Chris; Lee, Felix; Lee, Hwahyung; Lemon, Tracy; Long, Fuhui; Mastan, Naveed; Mott, Erika; Murthy, Chantal; Ngo, Kiet; Olson, Eric; Reding, Melissa; Riley, Zack; Rosen, David; Sandman, David; Shapovalova, Nadiya; Slaughterbeck, Clifford R; Sodt, Andrew; Stockdale, Graham; Szafer, Aaron; Wakeman, Wayne; Wohnoutka, Paul E; White, Steven J; Marsh, Don; Rostomily, Robert C; Ng, Lydia; Dang, Chinh; Jones, Allan; Keogh, Bart; Gittleman, Haley R; Barnholtz-Sloan, Jill S; Cimino, Patrick J; Uppin, Megha S; Keene, C Dirk; Farrokhi, Farrokh R; Lathia, Justin D; Berens, Michael E; Iavarone, Antonio; Bernard, Amy; Lein, Ed; Phillips, John W; Rostad, Steven W; Cobbs, Charles; Hawrylycz, Michael J; Foltz, Greg D

2018-05-11

Glioblastoma is an aggressive brain tumor that carries a poor prognosis. The tumor's molecular and cellular landscapes are complex, and their relationships to histologic features routinely used for diagnosis are unclear. We present the Ivy Glioblastoma Atlas, an anatomically based transcriptional atlas of human glioblastoma that aligns individual histologic features with genomic alterations and gene expression patterns, thus assigning molecular information to the most important morphologic hallmarks of the tumor. The atlas and its clinical and genomic database are freely accessible online data resources that will serve as a valuable platform for future investigations of glioblastoma pathogenesis, diagnosis, and treatment. Copyright © 2018 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works.

Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila.

PubMed

Ishemgulova, Aygul; Butenko, Anzhelika; Kortišová, Lucie; Boucinha, Carolina; Grybchuk-Ieremenko, Anastasiia; Morelli, Karina A; Tesařová, Martina; Kraeva, Natalya; Grybchuk, Danyil; Pánek, Tomáš; Flegontov, Pavel; Lukeš, Julius; Votýpka, Jan; Pavan, Márcio Galvão; Opperdoes, Fred R; Spodareva, Viktoria; d'Avila-Levy, Claudia M; Kostygov, Alexei Yu; Yurchenko, Vyacheslav

2017-01-01

In the present work, we investigated molecular mechanisms governing thermal resistance of a monoxenous trypanosomatid Crithidia luciliae thermophila, which we reclassified as a separate species C. thermophila. We analyzed morphology, growth kinetics, and transcriptomic profiles of flagellates cultivated at low (23°C) and elevated (34°C) temperature. When maintained at high temperature, they grew significantly faster, became shorter, with genes involved in sugar metabolism and mitochondrial stress protection significantly upregulated. Comparison with another thermoresistant monoxenous trypanosomatid, Leptomonas seymouri, revealed dramatic differences in transcription profiles of the two species with only few genes showing the same expression pattern. This disparity illustrates differences in the biology of these two parasites and distinct mechanisms of their thermotolerance, a prerequisite for living in warm-blooded vertebrates.

Electronic properties of diphenyl-s-tetrazine and some related oligomers. An spectroscopic and theoretical study

NASA Astrophysics Data System (ADS)

Moral, Mónica; García, Gregorio; Peñas, Antonio; Garzón, Andrés; Granadino-Roldán, José M.; Melguizo, Manuel; Fernández-Gómez, Manuel

2012-10-01

This work presents a theoretical and spectroscopic study on the electronic and structural properties of the diphenyl-s-tetrazine molecule (Ph2Tz) and some oligomeric derivatives. Ph2Tz was synthesized through a variation of Pinner-type reaction which uses N-acetylcysteine as catalyst. Insight into the structure and electronic properties of the title compound was obtained through IR, Raman, UV-Vis spectra in different solvents, and theoretical calculations. Theoretical studies have been extended to different n-mers derivatives up to an ideal molecular wire through the oligomeric approximation, predicting this way electronic properties such as LUMO energy levels, electron affinity and reorganization energy in order to assess their possible applications in molecular electronics.

Trends in Karyotype Evolution in Astyanax (Teleostei, Characiformes, Characidae): Insights From Molecular Data

PubMed Central

Pazza, Rubens; Dergam, Jorge A.; Kavalco, Karine F.

2018-01-01

The study of patterns and evolutionary processes in neotropical fish is not always an easy task due the wide distribution of major fish groups in large and extensive river basins. Thus, it is not always possible to detect or correlate possible effects of chromosome rearrangements in the evolution of biodiversity. In the Astyanax genus, chromosome data obtained since the 1970s have shown evidence of cryptic species, karyotypic plasticity, supernumerary chromosomes, triploidies, and minor chromosomal rearrangements. In the present work, we map and discuss the main chromosomal events compatible with the molecular evolution of the genus Astyanax (Characiformes, Characidae) using mitochondrial DNA sequence data, in the search for major chromosome evolutionary trends within this taxon. PMID:29713335

Molecular modeling and biological evaluation of 2-N,N-dimethylaminecyclohexyl 1-N‧,N‧-dimethylcarbamate isomers and their methylsulfate salts as cholinesterases inhibitors

NASA Astrophysics Data System (ADS)

Bocca, Cleverson C.; Rittner, Roberto; Höehr, Nelci F.; Pinheiro, Glaucia M. S.; Abiko, Layara A.; Basso, Ernani A.

2010-11-01

This work presents a detailed theoretical and experimental study on the inhibitory properties of 2- N,N-dimethylaminecyclohexyl 1- N',N'-dimethylcarbamate isomers and their methylsulfate salts against the cholinesterases enzymes. The in vitro inhibition test performed by the Ellman's method showed that the salt form compounds were more active than the neutral ones in cholinesterases inhibition. The trans salt showed good selectivity towards the inhibition of erythrocyte cholinesterase with a maximum limit around 90% and 55% for the plasma cholinesterase inhibition. Molecular modeling, docking and experimental results performed in this study showed to be important initial steps toward the development of a novel pharmaceuticals in the fight against Alzheimer's disease.

Molecular beam epitaxy growth of SmB6+/-δ thin films

NASA Astrophysics Data System (ADS)

Hoffman, Jason; Saleem, Muhammad; Day, James; Bonn, Doug; Hoffman, Jennifer

SmB6 has emerged as a leading candidate in the search for exotic topological states generated by strong interactions. The synthesis of epitaxial SmB6 thin films presents new avenues to control surface termination, thickness, and strain in this system. In this work, we use molecular beam epitaxy (MBE) to deposit SmB6+/-δ films on insulating (001)-oriented MgO substrates. We use ex-situ x-ray diffraction and magnetotransport measurements to assess the properties of the samples and compare them to previously reported values for single crystals. We also discuss the prospects of using rare-earth substitution to control the correlation strength and alter the topology of the bulk and surface electronic states.

Ionized and Molecular Gas in IC 860: Evidence for an Outflow

NASA Astrophysics Data System (ADS)

Adams, Carson; Alatalo, Katherine; Medling, Anne M.

2018-01-01

Galaxies at present-day fall predominantly in two distinct populations, as either blue, star-forming spirals or red, quiescent early-type galaxies. Blue galaxies appear to evolve onto the red sequence as star formation is quenched. The absence of a significant population falling in the intermediate ‘green valley’ implies that these transitions must occur rapidly. Identifying the initial properties of and pathways taken by these ‘dying galaxies’ is essential to building a complete understanding of galactic evolution. In this work, we investigate these phenomena in action within IC860 — a nearby, early-type spiral in the initial stages of undergoing a rapid transition in the presence of a powerful AGN-driven molecular outflow. As a shocked, post-starburst galaxy with an intermediate-age stellar population which lies on the blue end of the green valley, IC860 provides a window into the early stages of galaxy transition and AGN feedback. We present Hubble Space Telescope imaging of IC860 showing a violent, dusty outflow originating from a compact core. We find that the mean velocity map of the CO(1-0) from CARMA suggests a dynamically excited bar funneling molecular gas into the galactic center. Finally, we present kinematic maps of ionized gas emission lines as well as sodium D absorption tracing neutral winds obtained by the Wide-Field Spectrograph.

Controlling Proton Delivery through Catalyst Structural Dynamics

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

Cardenas, Allan Jay P.; Ginovska, Bojana; Kumar, Neeraj

The fastest synthetic molecular catalysts for production and oxidation of H2 emulate components of the active site of natural hydrogenases. The role of controlled structural dynamics is recognized as a critical component in the catalytic performance of many enzymes, including hydrogenases, but is largely neglected in the design of synthetic molecular cata-lysts. In this work, the impact of controlling structural dynamics on the rate of production of H2 was studied for a series of [Ni(PPh2NC6H4-R2)2]2+ catalysts including R = n-hexyl, n-decyl, n-tetradecyl, n-octadecyl, phenyl, or cyclohexyl. A strong correlation was observed between the ligand structural dynamics and the rates ofmore » electrocatalytic hydrogen production in acetonitrile, acetonitrile-water, and protic ionic liquid-water mixtures. Specifically, the turnover frequencies correlate inversely with the rates of ring inversion of the amine-containing ligand, as this dynamic process dictates the positioning of the proton relay in the second coordination sphere and therefore governs protonation at either catalytically productive or non-productive sites. This study demonstrates that the dynamic processes involved in proton delivery can be controlled through modifications of the outer coordination sphere of the catalyst, similar to the role of the protein architecture in many enzymes. The present work provides new mechanistic insight into the large rate enhancements observed in aqueous protic ionic liquid media for the [Ni(PPh2NR2)]2+ family of catalysts. The incorporation of controlled structural dynamics as a design parameter to modulate proton delivery in molecular catalysts has enabled H2 production rates that are up to three orders of magnitude faster than the [Ni(PPh2NPh2)]2+complex. The observed turnover frequencies are up to 106 s-1 in acetonitrile-water, and over 107 s-1 in protic ionic liquid-water mixtures, with a minimal increase in overpotential. This material is based upon work supported as part of the Center for Molecular Electrocatalysis, an Energy Frontier Research Center funded by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, and was performed in part using the Molecular Science Computing Facility (MSCF) in the William R. Wiley Environmental Molecular Sciences Laboratory, a DOE national scientific user facility located at Pacific Northwest National Laboratory (PNNL). PNNL is operated by Battelle for DOE.« less

Molecular and supramolecular control of the work function of an inorganic electrode with self-assembled monolayer of umbrella-shaped fullerene derivatives.

PubMed

Lacher, Sebastian; Matsuo, Yutaka; Nakamura, Eiichi

2011-10-26

The surface properties of inorganic substrates can be altered by coating with organic molecules, which may result in the improvement of the properties suitable for electronic or biological applications. This article reports a systematic experimental study on the influence of the molecular and supramolecular properties of umbrella-shaped penta(organo)[60]fullerene derivatives, and on the work function and the water contact angle of indium-tin oxide (ITO) and gold surfaces. We could relate these macroscopic characteristics to single-molecular level properties, such as ionization potential and molecular dipole. The results led us to conclude that the formation of a SAM of a polar compound generates an electronic field through intermolecular interaction of the molecular charges, and this field makes the overall dipole of the SAM much smaller than the one expected from the simple sum of the dipoles of all molecules in the SAM. This effect, which was called depolarization and previously discussed theoretically, is now quantitatively probed by experiments. The important physical properties in surface science such as work function, ionization potential, and water contact angles have been mutually correlated at the level of molecular structures and molecular orientations on the substrate surface. We also found that the SAMs on ITO and gold operate under the same principle except that the "push-back" effect operates specifically for gold. The study also illustrates the ability of the photoelectron yield spectroscopy technique to rapidly measure the work function of a SAM-covered substrate and the ionization potential value of a molecule on the surface.

Thermoelectricity in fullerene-metal heterojunctions.

PubMed

Yee, Shannon K; Malen, Jonathan A; Majumdar, Arun; Segalman, Rachel A

2011-10-12

Thermoelectricty in heterojunctions, where a single-molecule is trapped between metal electrodes, has been used to understand transport properties at organic-inorganic interfaces. (1) The transport in these systems is highly dependent on the energy level alignment between the molecular orbitals and the Fermi level (or work function) of the metal contacts. To date, the majority of single-molecule measurements have focused on simple small molecules where transport is dominated through the highest occupied molecular orbital. (2, 3) In these systems, energy level alignment is limited by the absence of electrode materials with low Fermi levels (i.e., large work functions). Alternatively, more controllable alignment between molecular orbitals and the Fermi level can be achieved with molecules whose transport is dominated by the lowest unoccupied molecular orbital (LUMO) because of readily available metals with lower work functions. Herein, we report molecular junction thermoelectric measurements of fullerene molecules (i.e., C(60), PCBM, and C(70)) trapped between metallic electrodes (i.e., Pt, Au, Ag). Fullerene junctions demonstrate the first strongly n-type molecular thermopower corresponding to transport through the LUMO, and the highest measured magnitude of molecular thermopower to date. While the electronic conductance of fullerenes is highly variable, due to fullerene's variable bonding geometries with the electrodes, the thermopower shows predictable trends based on the alignment of the LUMO with the work function of the electrodes. Both the magnitude and trend of the thermopower suggest that heterostructuring organic and inorganic materials at the nanoscale can further enhance thermoelectric performance, therein providing a new pathway for designing thermoelectric materials.

EDITORIAL: 18th European Conference on Dynamics of Molecular Systems 18th European Conference on Dynamics of Molecular Systems

NASA Astrophysics Data System (ADS)

Varandas, A. J. C.

2011-08-01

This special section of Comments on Atomic, Molecular and Optical Physics (CAMOP) in Physica Scripta collects some of the papers that have been presented at the 18th European Conference on Dynamics of Molecular Systems MOLEC 2010 held in September 2010 in Curia, Portugal, as part of a series of biennial MOLEC conferences. This started in 1976 in Trento, Italy, and has continued, visiting 17 cities in 11 countries, namely Denmark, The Netherlands, Israel, France, Italy, Germany, Czech Republic, Spain, United Kingdom, Turkey and Russia. Following the MOLEC tradition, the scientific programme of the Curia meeting focused on experimental and theoretical studies of molecular interactions, collision dynamics, spectroscopy, and related fields. It included invited speakers from 22 countries, who were asked to summarize the problems reported in their presentations with the objective of revealing the current thinking of leading researchers in atomic, molecular and optical physics. It is hoped that their authoritative contributions presented in this CAMOP special section will also appeal to non-specialists through their clear and broad introductions to the field as well as references to the accessible literature. This CAMOP special section comprises ten contributions, which cover theoretical studies on the electronic structure of molecules and clusters as well as dynamics of elastic, inelastic and reactive encounters between atoms, molecules, ions, clusters and surfaces. Specifically, it includes electronic structure calculations using the traditional coupled-cluster method (Barreto et al 028111), the electron-attached equation-of-motion coupled cluster method (Hansen et al 028110), the diffusion Monte Carlo method (López-Durán et al 028107) and the path-integral Monte Carlo method (Barragán et al 028109). The contributions on molecular dynamics include on-the-fly quasi-classical trajectories on a five-atom molecule (Yu 028104), quantum reaction dynamics on triatomics (Bovino et al 028103, and Hankel et al 028102) and statistical reaction dynamics using a model based on the long-range interaction potential (McCarroll 028106). A contribution on gas-surface interactions is also included (Sahoo et al 028105) as well as first-principles ab initio calculations to explore the hydrogen-graphene interaction (Irving et al 028108). These articles reflect the recent progress made in this field and constructively build on work described in the previous three MOLEC special sections of CAMOP published in Physica Scripta. I thank, on behalf of the scientific organizing committee of MOLEC, all the authors who contributed and Physica Scripta for providing a platform for the publication of this special section dedicated to MOLEC 2010. A special thanks goes to the CAMOP Editor, Harold Linarz, for the excellent guidance in handling the editorial work. I hope that the articles catalyze the attention of the readers towards the topics covered and contribute in attracting them to attend MOLEC 2012 in Oxford, UK.

Theory of complicated liquids. Investigation of liquids, solvents and solvent effects with modern theoretical methods

NASA Astrophysics Data System (ADS)

Kirchner, Barbara

2007-03-01

It is the aim of this work to elucidate the usefulness and feasibility of the first-principles approach and to extend it to the regime of liquid molecular substances of complex structure. Physical and thermodynamic properties of complicated liquids are investigated by means of Car-Parrinello molecular dynamics (CPMD) and also with static quantum chemical methods. The connection between the dynamic and static approach is given by the quantum cluster equilibrium (QCE) theory. Since the QCE theory is not yet well established, a new implementation in the MD post-processing program P EACEMAKER is presented. It can be shown that it is by far more important to include cooperative effects rather than to concentrate the effort on the inclusion of weak dispersion forces not present in current density functionals. Traditionally, investigations of complicated liquids were also undertaken with the tools of simple liquids, because for some problems the size of the system does not allow for a more accurate description. Although linear-scaling techniques are simplifications from the point of view of quantum chemistry, they might be severe improvements when compared to traditional molecular dynamics simulations. For the interpretation of the liquid state the introduction of local properties is inevitable. New methods are presented for the calculation of local dipole moments and for the estimation of hydrogen bond energies in quantum mechanically nondecomposable systems. The latter also allows for the detection of hydrogen bonds in simulations through a wavefunction-based criterion instead of one which is solely grounded on the geometric structure of the atomic nuclei involved. The article then discusses prominent liquids which show properties that are not yet understood. Another part of the work analyzes the effect of solvent molecules on solutes and their reactions in the solvent. Finaly, neoteric solvents, such as ionic liquids are discussed.

[Modern methods application of genotyping of infectious diseases pathogens in the context of operational work of specialized anti-epidemic team during the XXII Olympic Winter Games and XI Paralympic Winter Games].

PubMed

Kuzkin, B P; Kulichenko, A N; Volynkina, A S; Efremenko, D V; Kuznetsova, I V; Kotenev, E S; Lyamkin, G I; Kartsev, N N; Klindukhov, V P

2015-01-01

This paper considers the experience of genotyping and sequencing technologies in laboratories of specialized anti-epidemic team (SAET) during the XXII Olympic Winter Games and XI Paralympic Winter Games of 2014 in Sochi. The work carried out during the pre-Olympic period on performance of readiness by SAET for these studies is analyzed. The results of genotyping strains of pathogens during the Olympic Games are presented. A conclusion about the effectiveness of the use of molecular genetic techniques in terms of SAET is made.

Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) Simulations of the Molecular Crystal alphaRDX

DTIC Science & Technology

2013-08-01

potential for HMX / RDX (3, 9). ...................................................................................8 1 1. Purpose This work...6 dispersion and electrostatic interactions. Constants for the SB potential are given in table 1. 8 Table 1. SB potential for HMX / RDX (3, 9...modeling dislocations in the energetic molecular crystal RDX using the Large-Scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) molecular

Nanoscale Insight and Control of Structural and Electronic Properties of Organic Semiconductor / Metal Interfaces

NASA Astrophysics Data System (ADS)

Maughan, Bret

Organic semiconductor interfaces are promising materials for use in next-generation electronic and optoelectronic devices. Current models for metal-organic interfacial electronic structure and dynamics are inadequate for strongly hybridized systems. This work aims to address this issue by identifying the factors most important for understanding chemisorbed interfaces with an eye towards tuning the interfacial properties. Here, I present the results of my research on chemisorbed interfaces formed between thin-films of phthalocyanine molecules grown on monocrystalline Cu(110). Using atomically-resolved nanoscale imaging in combination with surface-sensitive photoemission techniques, I show that single-molecule level interactions control the structural and electronic properties of the interface. I then demonstrate that surface modifications aimed at controlling interfacial interactions are an effective way to tailor the physical and electronic structure of the interface. This dissertation details a systematic investigation of the effect of molecular and surface functionalization on interfacial interactions. To understand the role of molecular structure, two types of phthalocyanine (Pc) molecules are studied: non-planar, dipolar molecules (TiOPc), and planar, non-polar molecules (H2Pc and CuPc). Multiple adsorption configurations for TiOPc lead to configuration-dependent self-assembly, Kondo screening, and electronic energy-level alignment. To understand the role of surface structure, the Cu(110) surface is textured and passivated by oxygen chemisorption prior to molecular deposition, which gives control over thin-film growth and interfacial electronic structure in H2Pc and CuPc films. Overall, the work presented here demonstrates a method for understanding interfacial electronic structure of strongly hybridized interfaces, an important first step towards developing more robust models for metal-organic interfaces, and reliable, predictive tuning of interfacial properties.

Discovery of oxidative burst in the field of plant immunity

PubMed Central

Yoshioka, Hirofumi; Bouteau, François

2008-01-01

This article is introductory to the series of works presented in this special issue on the homeostasis and the signaling roles of reactive oxygen species (ROS) in plants. Upper half of this article briefly describes the history of the ROS study in the field of plant immunity research initiated by the observation that the attacks by pathogenic microorganisms possibly stimulate the burst of ROS production in the plant tissues. The topics covered in the series of works presented here include the plants' responses to abiotic oxidative stress (atmospheric ozone), regulation of seed germination, chemical interaction between parasitic and host plants and the draught tolerance, all controlled through homeostasis of ROS at biochemical and molecular biological levels. Lastly a discussion forum was proposed to further deepen our understanding of ROS behaviors in plants. PMID:19513209

Application of Renyi entropy for ultrasonic molecular imaging

PubMed Central

Hughes, M. S.; Marsh, J. N.; Arbeit, J. M.; Neumann, R. G.; Fuhrhop, R. W.; Wallace, K. D.; Thomas, L.; Smith, J.; Agyem, K.; Lanza, G. M.; Wickline, S. A.; McCarthy, J. E.

2009-01-01

Previous work has demonstrated that a signal receiver based on a limiting form of the Shannon entropy is, in certain settings, more sensitive to subtle changes in scattering architecture than conventional energy-based signal receivers [M. S. Hughes et al., J. Acoust. Soc. Am. 121, 3542–3557 (2007)]. In this paper new results are presented demonstrating further improvements in sensitivity using a signal receiver based on the Renyi entropy. PMID:19425656

A model to estimate the relative position of sites for ligands in serum albumins

NASA Astrophysics Data System (ADS)

Motta, Art Adriel Emidio de Araújo; Grassini, Maria Carolina Vilela; Cortez, Célia Martins; Silva, Dilson

2017-11-01

In this work, we present a mathematical-computational model developed to estimate the relative position of ligand binding sites in HSA and BSA, based on the theory of fluorescence quenching, considering the molecular and spectrofluorimetric differences and similarities between these two albumins. Albumin is the largest and the most abundant serum protein in vertebrates. The ability to bind xenobiotics makes albumin important to the bioavailability and effectiveness of drugs.

Round Robin Study: Molecular Simulation of Thermodynamic Properties from Models with Internal Degrees of Freedom.

PubMed

Schappals, Michael; Mecklenfeld, Andreas; Kröger, Leif; Botan, Vitalie; Köster, Andreas; Stephan, Simon; García, Edder J; Rutkai, Gabor; Raabe, Gabriele; Klein, Peter; Leonhard, Kai; Glass, Colin W; Lenhard, Johannes; Vrabec, Jadran; Hasse, Hans

2017-09-12

Thermodynamic properties are often modeled by classical force fields which describe the interactions on the atomistic scale. Molecular simulations are used for retrieving thermodynamic data from such models, and many simulation techniques and computer codes are available for that purpose. In the present round robin study, the following fundamental question is addressed: Will different user groups working with different simulation codes obtain coinciding results within the statistical uncertainty of their data? A set of 24 simple simulation tasks is defined and solved by five user groups working with eight molecular simulation codes: DL_POLY, GROMACS, IMC, LAMMPS, ms2, NAMD, Tinker, and TOWHEE. Each task consists of the definition of (1) a pure fluid that is described by a force field and (2) the conditions under which that property is to be determined. The fluids are four simple alkanes: ethane, propane, n-butane, and iso-butane. All force fields consider internal degrees of freedom: OPLS, TraPPE, and a modified OPLS version with bond stretching vibrations. Density and potential energy are determined as a function of temperature and pressure on a grid which is specified such that all states are liquid. The user groups worked independently and reported their results to a central instance. The full set of results was disclosed to all user groups only at the end of the study. During the study, the central instance gave only qualitative feedback. The results reveal the challenges of carrying out molecular simulations. Several iterations were needed to eliminate gross errors. For most simulation tasks, the remaining deviations between the results of the different groups are acceptable from a practical standpoint, but they are often outside of the statistical errors of the individual simulation data. However, there are also cases where the deviations are unacceptable. This study highlights similarities between computer experiments and laboratory experiments, which are both subject not only to statistical error but also to systematic error.

Molecular identification of the Sporothrix schenckii complex.

PubMed

Oliveira, Manoel Marques Evangelista; Almeida-Paes, Rodrigo; Gutierrez-Galhardo, Maria Clara; Zancope-Oliveira, Rosely M

2014-01-01

Sporothrix schenckii, an ascomycetous dimorphic organism that for over a century was recognized as the sole agent of sporotrichosis, a subcutaneous mycosis with a worldwide distribution. However, it has been proposed, based on physiologic and molecular aspects, that S. schenckii is a complex of distinct species: Sporothrix brasiliensis, Sporothrix mexicana, Sporothrix globosa, S. schenckii sensu strictu, Sporothrix luriei, and Sporothrix albicans (formerly Sporothrix pallida). Human disease has a broad range of clinical manifestations and can be classified into fixed cutaneous, lymphocutaneous, disseminated cutaneous, and extracutaneous sporotrichosis. The gold standard for the diagnosis of sporotrichosis is the culture; however, serologic, histopathologic and molecular approaches have been recently adopted for the diagnosis of this mycosis. Few molecular methods have been applied to the diagnosis of sporotrichosis to detect S. schenckii DNA from clinical specimens, and to identify Sporothrix spp. in culture. Until now, Sporothrix is the unique clinically relevant dimorphic fungus without an elucidated genome sequence, thus limiting molecular knowledge about the cryptic species of this complex, and the sexual form of all S. schenckii complex species. In this review we shall focus on the current diagnosis of the sporotrichosis, and discuss the current molecular tools applied to the diagnosis and identification of the Sporothrix complex species. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

MEvoLib v1.0: the first molecular evolution library for Python.

PubMed

Álvarez-Jarreta, Jorge; Ruiz-Pesini, Eduardo

2016-10-28

Molecular evolution studies involve many different hard computational problems solved, in most cases, with heuristic algorithms that provide a nearly optimal solution. Hence, diverse software tools exist for the different stages involved in a molecular evolution workflow. We present MEvoLib, the first molecular evolution library for Python, providing a framework to work with different tools and methods involved in the common tasks of molecular evolution workflows. In contrast with already existing bioinformatics libraries, MEvoLib is focused on the stages involved in molecular evolution studies, enclosing the set of tools with a common purpose in a single high-level interface with fast access to their frequent parameterizations. The gene clustering from partial or complete sequences has been improved with a new method that integrates accessible external information (e.g. GenBank's features data). Moreover, MEvoLib adjusts the fetching process from NCBI databases to optimize the download bandwidth usage. In addition, it has been implemented using parallelization techniques to cope with even large-case scenarios. MEvoLib is the first library for Python designed to facilitate molecular evolution researches both for expert and novel users. Its unique interface for each common task comprises several tools with their most used parameterizations. It has also included a method to take advantage of biological knowledge to improve the gene partition of sequence datasets. Additionally, its implementation incorporates parallelization techniques to enhance computational costs when handling very large input datasets.

Understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates

NASA Technical Reports Server (NTRS)

Etters, R. D.

1985-01-01

Work directed toward understanding the high pressure properties of molecular solids and molecular surfaces deposited on hetrogeneous substrates is reported. The motivation, apart from expanding our basic knowledge about these systems, was to understand and predict the properties of new materials synthesized at high pressure, including pressure induced metallic and superconducting states. As a consequence, information about the states of matter of the Jovian planets and their satellites, which are natural high pressure laboratories was also provided. The work on molecular surfaces and finite two and three dimensional clusters of atoms and molecules was connected with the composition and behavior of planetary atmospheres and on the processes involved in forming surface layers, which is vital to the development of composite materials and microcircuitry.

Study of reactive collisions between electrons and molecular cations using multichannel quantum defect theory: Application to HD{sup +} and BeH{sup +}

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

Pop, N., E-mail: nicolina.pop@upt.ro; Ilie, S.; Motapon, O.

2014-11-24

The present work is aimed at performing the computation of cross sections and Maxwell rate coefficients in the framework of the stepwise version of the Multichannel Quantum Defect Theory (MQDT). Cross sections and rate coefficients suitable for the modelling of the kinetics of HD{sup +} and BeH{sup +} in fusion plasmas and in the stellar atmospheres are presented and discussed. A very good agreement is found between our results for rotational transitions for HD{sup +} and other computations, as well as with experiment.

Thermally controlled preferential molecular aggregation state in a thiacarbocyanine dye

NASA Astrophysics Data System (ADS)

Passier, Rémy; Ritchie, James P.; Toro, Carlos; Diaz, Carlos; Masunov, Artëm E.; Belfield, Kevin D.; Hernandez, Florencio E.

2010-10-01

Herein we report the experimental and theoretical study of the temperature dependence of a thiacarbocyanine dye in its monomer, H- and J-aggregates states. We demonstrate the ability to control the ratio of monomer, H- and/or J-aggregates with heat. We link such a control to the conformation dependence of the molecule. An alternative way to gain access to the dominating species without changing the concentration as a complete switching mechanism between all the present species is proposed. The results presented in this work lead to a better understanding of thiacarbocyanine dye's behavior.

Particulate Pictures and Kinetic-Molecular Theory Concepts: Seizing an Opportunity

ERIC Educational Resources Information Center

Waner, Mark J.

2010-01-01

This work examines commonly used particulate-level pictures meant to illustrate gases. These pictures are found throughout textbooks in the middle grades through the college level, as well as in questions frequently used to assess conceptual learning in students. This work uses the kinetic-molecular theory of gases to demonstrate the inaccuracies…

Molecular markers in the epidemiology and diagnosis of coccidioidomycosis.

PubMed

Duarte-Escalante, Esperanza; Frías-De-León, María Guadalupe; Zúñiga, Gerardo; Martínez-Herrera, Erick; Acosta-Altamirano, Gustavo; Reyes-Montes, María Del Rocío

2014-01-01

The prevalence of coccidioidomycosis in endemic areas has been observed to increase daily. To understand the causes of the spread of the disease and design strategies for fungal detection in clinical and environmental samples, scientists have resorted to molecular tools that allow fungal detection in a natural environment, reliable identification in clinical cases and the study of biological characteristics, such as reproductive and genetic structure, demographic history and diversification. We conducted a review of the most important molecular markers in the epidemiology of Coccidioides spp. and the diagnosis of coccidioidomycosis. A literature search was performed for scientific publications concerning the application of molecular tools for the epidemiology and diagnosis of coccidioidomycosis. The use of molecular markers in the epidemiological study and diagnosis of coccidioidomycosis has allowed for the typing of Coccidioides spp. isolates, improved understanding of their mode of reproduction, genetic variation and speciation and resulted in the development specific, rapid and sensitive strategies for detecting the fungus in environmental and clinical samples. Molecular markers have revealed genetic variability in Coccidioides spp. This finding influences changes in the epidemiology of coccidioidomycosis, such as the emergence of more virulent or antifungal resistant genotypes. Furthermore, the molecular markers currently used to identify Coccidioides immitis and Coccidioides posadasii are specific and sensitive. However, they must be validated to determine their application in diagnosis. This manuscript is part of the series of works presented at the "V International Workshop: Molecular genetic approaches to the study of human pathogenic fungi" (Oaxaca, Mexico, 2012). Copyright © 2013 Revista Iberoamericana de Micología. Published by Elsevier Espana. All rights reserved.

Introducing a new methodology for the calculation of local philicity and multiphilic descriptor: an alternative to the finite difference approximation

NASA Astrophysics Data System (ADS)

Sánchez-Márquez, Jesús; Zorrilla, David; García, Víctor; Fernández, Manuel

2018-07-01

This work presents a new development based on the condensation scheme proposed by Chamorro and Pérez, in which new terms to correct the frozen molecular orbital approximation have been introduced (improved frontier molecular orbital approximation). The changes performed on the original development allow taking into account the orbital relaxation effects, providing equivalent results to those achieved by the finite difference approximation and leading also to a methodology with great advantages. Local reactivity indices based on this new development have been obtained for a sample set of molecules and they have been compared with those indices based on the frontier molecular orbital and finite difference approximations. A new definition based on the improved frontier molecular orbital methodology for the dual descriptor index is also shown. In addition, taking advantage of the characteristics of the definitions obtained with the new condensation scheme, the descriptor local philicity is analysed by separating the components corresponding to the frontier molecular orbital approximation and orbital relaxation effects, analysing also the local parameter multiphilic descriptor in the same way. Finally, the effect of using the basis set is studied and calculations using DFT, CI and Möller-Plesset methodologies are performed to analyse the consequence of different electronic-correlation levels.

Systematics of spiny predatory katydids (Tettigoniidae: Listroscelidinae) from the Brazilian Atlantic Forest based on morphology and molecular data.

PubMed

Fialho, Verônica Saraiva; Chamorro-Rengifo, Juliana; Lopes-Andrade, Cristiano; Yotoko, Karla Suemy Clemente

2014-01-01

Listroscelidinae (Orthoptera: Tettigoniidae) are insectivorous Pantropical katydids whose taxonomy presents a long history of controversy, with several genera incertae sedis. This work focused on species occurring in the Brazilian Atlantic Forest, one of the world's most threatened biomes. We examined material deposited in scientific collections and visited 15 conservation units from Rio de Janeiro to southern Bahia between November 2011 and January 2012, catching 104 specimens from 10 conservation units. Based on morphological and molecular data we redefined Listroscelidini, adding a new tribe, new genus and eight new species to the subfamily. Using morphological analysis, we redescribed and added new geographic records for six species, synonymized two species and built a provisional identification key for the Atlantic Forest Listroscelidinae. Molecular results suggest two new species and a new genus to be described, possibly by the fission of the genus Hamayulus. We also proposed a 500 bp region in the final portion of the COI to be used as a molecular barcode. Our data suggest that the Atlantic Forest Listroscelidinae are seriously endangered, because they occur in highly preserved forest remnants, show high rates of endemism and have a narrow geographic distribution. Based on our results, we suggest future collection efforts must take into account the molecular barcode data to accelerate species recognition.

Molecular modeling and molecular dynamics simulation studies on the interactions of hydroxylated polychlorinated biphenyls with estrogen receptor-β.

PubMed

Li, Xiaolin; Ye, Li; Wang, Xiaoxiang; Shi, Wei; Qian, XiangPing; Zhu, YongLiang; Yu, HongXia

2013-10-01

Endocrine-disrupting chemicals have attracted great concern. As major metabolites of polychlorinated biphenyls (PCBs), hydroxylated polychlorinated biphenyls (HO-PCBs) may disrupt estrogen hormone status because of their structural similarity to estrogen endogenous compounds. However, interactions between HO-PCBs and estrogen receptors (ERs) are not fully understood. In the present work, a molecular modeling study combining molecular docking, molecular dynamics simulations, and binding free energy calculations was performed to characterize the interactions of three HO-PCBs (4'-HO-PCB50, 2'-HO-PCB65, and 4'-HO-PCB69) having much different estrogenic activities with ERβ. Docking results showed that binding between ligands and ERβ was stabilized by hydrogen bond and hydrophobic interactions. The binding free energies of three ligands with ERβ were calculated, and further binding free energy decomposition analysis indicated that the dominating driving force of the binding between the ligands and ERβ was the van der Waals interaction. Some key residues, such as Leu298, Phe356, Gly472, His475, and Leu476, played important roles in ligand-receptor interactions by forming hydrophobic and hydrogen bond interactions with ligands. The results may be beneficial to increase understanding of the interactions between HO-PCBs and ERβ.

Preserving and vouchering butterflies and moths for large-scale museum-based molecular research

PubMed Central

Epstein, Samantha W.; Mitter, Kim; Hamilton, Chris A.; Plotkin, David; Mitter, Charles

2016-01-01

Butterflies and moths (Lepidoptera) comprise significant portions of the world’s natural history collections, but a standardized tissue preservation protocol for molecular research is largely lacking. Lepidoptera have traditionally been spread on mounting boards to display wing patterns and colors, which are often important for species identification. Many molecular phylogenetic studies have used legs from pinned specimens as the primary source for DNA in order to preserve a morphological voucher, but the amount of available tissue is often limited. Preserving an entire specimen in a cryogenic freezer is ideal for DNA preservation, but without an easily accessible voucher it can make specimen identification, verification, and morphological work difficult. Here we present a procedure that creates accessible and easily visualized “wing vouchers” of individual Lepidoptera specimens, and preserves the remainder of the insect in a cryogenic freezer for molecular research. Wings are preserved in protective holders so that both dorsal and ventral patterns and colors can be easily viewed without further damage. Our wing vouchering system has been implemented at the University of Maryland (AToL Lep Collection) and the University of Florida (Florida Museum of Natural History, McGuire Center of Lepidoptera and Biodiversity), which are among two of the largest Lepidoptera molecular collections in the world. PMID:27366654

Laser Spectroscopy of Radicals, Carbenes, and Ions in Superfluid Helium Droplets

NASA Astrophysics Data System (ADS)

Douberly, Gary E.

2015-06-01

The first beam of helium droplets was reported in the 1961 paper Strahlen aus kondensiertem Helium im Hochvakuum by Von E. W. Becker and co-workers. However, molecular spectroscopy of helium-solvated dopants wasn't realized until 30 years later in the laboratories of Scoles and Toennies. It has now been two decades since this early, seminal work on doped helium droplets, yet the field of helium droplet spectroscopy is still fresh with vast potential. Analogous in many ways to cryogenic matrix isolation spectroscopy, the helium droplet is an ideal environment to spectroscopically probe difficult to prepare molecular species, such as radicals, carbenes and ions. The quantum nature of helium at 0.35 K often results in molecular spectra that are sufficiently resolved to evoke an analysis of line shapes and fine-structure that is worthy of the International Symposium on Molecular Spectroscopy. The present talk will focus on our recent successful attempts to efficiently dope the title molecular species into helium droplets and probe their properties with infrared laser Stark and Zeeman spectroscopies. E. W. Becker, R. Klingelhöfer, P. Lohse, Z. Naturforsch. A 16A, 1259 (1961). S. Goyal, D. L. Schutt, G. Scoles, Phys. Rev. Lett. 69, 933 (1992). M. Hartmann, R. E. Miller, J. P. Toennies, A. F. Vilesov, Phys. Rev. Lett. 75, 1566, (1995).

NREL Research Advances Hydrogen Production Efforts | News | NREL

Science.gov Websites

-effective, however. The use of cheaper molecular catalysts instead of precious metals has been proposed, but -based catalysts. Instead, the NREL researchers decided to examine molecular catalysts outside of the the semiconductor and bond the molecular catalyst to the TiO2. Their work showed molecular catalysts

Molecular cloning and characterization of sea bass (Dicentrarchus labrax, L.) calreticulin.

PubMed

Pinto, Rute D; Moreira, Ana R; Pereira, Pedro J B; dos Santos, Nuno M S

2013-06-01

Mammalian calreticulin (CRT) is a key molecular chaperone and regulator of Ca(2+) homeostasis in endoplasmic reticulum (ER), also being implicated in a variety of physiological/pathological processes outside the ER. Importantly, it is involved in assembly of MHC class I molecules. In this work, sea bass (Dicentrarchus labrax) CRT (Dila-CRT) gene and cDNA have been isolated and characterized. The mature protein retains two conserved motifs, three structural/functional domains (N, P and C), three type 1 and 2 motifs repeated in tandem, a conserved pair of cysteines and ER-retention motif. It is a single-copy gene composed of 9 exons. Dila-CRT three-dimensional homology models are consistent with the structural features described for mammalian molecules. Together, these results are supportive of a highly conserved structure of CRT through evolution. Moreover, the present data provides information that will allow further studies on sea bass CRT involvement in immunity and in particular class I antigen presentation. Copyright © 2013 Elsevier Ltd. All rights reserved.

Toward a nanoimprinted nanoantenna to perform optical rectification through molecular diodes

NASA Astrophysics Data System (ADS)

Reynaud, C. A.; Duché, D.; Ruiz, C. M.; Palanchoke, U.; Patrone, L.; Le Rouzo, J.; Labau, S.; Frolet, N.; Gourgon, C.; Alfonso, C.; Charaï, A.; Lebouin, C.; Simon, J.-J.; Escoubas, L.

2017-12-01

This work presents investigations about the realization and modelization of rectenna solar cells. Rectennas are antennas coupled with a rectifier to convert the alternative current originating from the antenna into direct current that can be harvested and stored. By reducing the size of the antennas to the nanoscale, interactions with visible and near-infrared light become possible. If techniques such as nanoimprint lithography make possible the fabrication of sufficiently small plasmonic structures to act as optical antennas, the concept of rectenna still faces several challenges. One of the most critical point is to achieve rectification at optical frequencies. To address this matter, we propose to use molecular diodes (ferrocenyl-alkanethiol) that can be self-assembled on metallic surfaces such as gold or silver. In this paper, we present a basic rectenna theory as well as finite-difference time-domain (FDTD) optical simulations of plasmonic structures and experimental results of both nanoimprint fabrication of samples and characterizations by electron microscopy, Raman spectroscopy, and cyclic voltammetry techniques.

Towards Breath Gas Analysis Based on Millimeter-Wave Molecular Spectroscopy

NASA Astrophysics Data System (ADS)

Rothbart, Nick; Hübers, Heinz-Wilhelm; Schmalz, Klaus; Borngräber, Johannes; Kissinger, Dietmar

2018-03-01

Breath gas analysis is a promising non-invasive tool for medical diagnosis as there are thousands of Volatile Organic Compounds (VOCs) in human breath that can be used as health monitoring markers. Millimeter-wave/terahertz molecular spectroscopy is highly suitable for breath gas analysis due to unique fingerprint spectra of many VOCs in that frequency range. We present our recent work on sensor systems for gas spectroscopy based on integrated transmitters (TX) and receivers (RX) fabricated in IHP's 0.13 μm SiGe BiCMOS technology. For a single-band system, spectroscopic measurements and beam profiles are presented. The frequency is tuned by direct voltage-frequency tuning and by a fractional-n PLL, respectively. The spectroscopic system includes a folded gas absorption cell with gas pre-concentration abilities demonstrating the detection of a 50 ppm mixture of ethanol in ambient air corresponding to a minimum detectable concentration of 260 ppb. Finally, the design of a 3-band system covering frequencies from 225 to 273 GHz is introduced.

Dimer model for Tau proteins bound in microtubule bundles

NASA Astrophysics Data System (ADS)

Hall, Natalie; Kluber, Alexander; Hayre, N. Robert; Singh, Rajiv; Cox, Daniel

2013-03-01

The microtubule associated protein tau is important in nucleating and maintaining microtubule spacing and structure in neuronal axons. Modification of tau is implicated as a later stage process in Alzheimer's disease, but little is known about the structure of tau in microtubule bundles. We present preliminary work on a proposed model for tau dimers in microtubule bundles (dimers are the minimal units since there is one microtubule binding domain per tau). First, a model of tau monomer was created and its characteristics explored using implicit solvent molecular dynamics simulation. Multiple simulations yield a partially collapsed form with separate positively/negatively charged clumps, but which are a factor of two smaller than required by observed microtubule spacing. We argue that this will elongate in dimer form to lower electrostatic energy at a cost of entropic ``spring'' energy. We will present preliminary results on steered molecular dynamics runs on tau dimers to estimate the actual force constant. Supported by US NSF Grant DMR 1207624.

Middle/high school students in the research laboratory: A summer internship program emphasizing the interdisciplinary nature of biology.

PubMed

McMiller, Tracee; Lee, Tameshia; Saroop, Ria; Green, Tyra; Johnson, Casonya M

2006-03-01

We describe an eight-week summer Young Scientist in Training (YSIT) internship program involving middle and high school students. This program exposed students to current basic research in molecular genetics, while introducing or reinforcing principles of the scientific method and demonstrating the uses of mathematics and chemistry in biology. For the laboratory-based program, selected students from Baltimore City Schools working in groups of three were teamed with undergraduate research assistants at Morgan State University. Teams were assigned a project that was indirectly related to our laboratory research on the characterization of gene expression in Caenorhabditis elegans. At the end of the program, teams prepared posters detailing their accomplishments, and presented their findings to parents and faculty members during a mini-symposium. The posters were also submitted to the respective schools and the interns were offered a presentation of their research at local high school science fairs. Copyright © 2006 International Union of Biochemistry and Molecular Biology, Inc.

In vitro penetration through the skin layers of topically applied glucocorticoids.

PubMed

Carrer, Victor; Alonso, Cristina; Oliver, Marc Adrià; Coderch, Luisa

2018-05-22

Corticoids are actives widely used in the treatment of skin diseases. This work aims to study the penetration of three corticoids (betamethasone, clobetasol and flurandrenolide), their relationship with their Log D values and the effects of the vehicles. The three compounds were applied on a Franz-type diffusion cell in propylene glycol solution and their respective commercial creams and ointments. The active amounts found in the stratum corneum, epidermal and dermal layers of the skin were investigated. Their diffusions were greatly affected by the formulation, moreover higher amounts of substance in the epidermis and dermis were detected in ointments than in creams. The enhancement effect of propylene glycol was also observed. Moreover, the differences between the three substances could be related to their lipophilicity, molecular structure and molecular weight. The more hydrophobic compounds (clobetasol and betamethasone) are present in higher amounts in the epidermis and dermis, while the hydrophilic compound (flurandrenolide) is mostly present in the receptor fluid. This article is protected by copyright. All rights reserved.

Reversed-phase ion-pair ultra-high-performance-liquid chromatography-mass spectrometry for fingerprinting low-molecular-weight heparins.

PubMed

Langeslay, Derek J; Urso, Elena; Gardini, Cristina; Naggi, Annamaria; Torri, Giangiacomo; Larive, Cynthia K

2013-05-31

Heparin is a complex mixture of sulfated linear carbohydrate polymers. It is widely used as an antithrombotic drug, though it has been shown to have a myriad of additional biological activities. Heparin is often partially depolymerized in order to decrease the average molecular weight, as it has been shown that low molecular weight heparins (LMWH) possess more desirable pharmacokinetic and pharmacodynamic properties than unfractionated heparin (UFH). Due to the prevalence of LMWHs in the market and the emerging availability of generic LMWH products, it is important that analytical methods be developed to ensure the drug quality. This work explores the use of tributylamine (TrBA), dibutylamine (DBA), and pentylamine (PTA) as ion-pairing reagents in conjunction with acetonitrile and methanol modified mobile phases for reversed-phase ion-pairing ultraperformance liquid chromatography coupled to mass spectrometry (RPIP-UPLC-MS) for fingerprint analysis of LMWH preparations. RPIP-UPLC-MS fingerprints are presented and compared for tinzaparinand enoxaparin. Copyright © 2013 Elsevier B.V. All rights reserved.

The Ascorbate-glutathione-α-tocopherol Triad in Abiotic Stress Response

PubMed Central

Szarka, András; Tomasskovics, Bálint; Bánhegyi, Gábor

2012-01-01

The life of any living organism can be defined as a hurdle due to different kind of stresses. As with all living organisms, plants are exposed to various abiotic stresses, such as drought, salinity, extreme temperatures and chemical toxicity. These primary stresses are often interconnected, and lead to the overproduction of reactive oxygen species (ROS) in plants, which are highly reactive and toxic and cause damage to proteins, lipids, carbohydrates and DNA, which ultimately results in oxidative stress. Stress-induced ROS accumulation is counteracted by enzymatic antioxidant systems and non-enzymatic low molecular weight metabolites, such as ascorbate, glutathione and α-tocopherol. The above mentioned low molecular weight antioxidants are also capable of chelating metal ions, reducing thus their catalytic activity to form ROS and also scavenge them. Hence, in plant cells, this triad of low molecular weight antioxidants (ascorbate, glutathione and α-tocopherol) form an important part of abiotic stress response. In this work we are presenting a review of abiotic stress responses connected to these antioxidants. PMID:22605990

Molecular pathogenesis of precursor lesions of pancreatic ductal adenocarcinoma.

PubMed

Biankin, Andrew V; Kench, James G; Dijkman, Floriaan P; Biankin, Sandra A; Henshall, Susan M

2003-02-01

Precursor lesions are assuming greater importance in the study of pancreatic ductal adenocarcinoma. As pancreatic cancer is almost universally fatal due to late clinical presentation and biological aggressiveness, characterisation of its precursor lesions may create scope for early diagnosis and improved outcome with conventional therapies as well as the development of novel therapeutic and preventative strategies. Pancreatic intraepithelial neoplasia (PanIN) and intraductal papillary mucinous tumours (IPMTs) are thought to be precursor lesions of ductal adenocarcinoma of the pancreas. Recent work has focused on the molecular aberrations associated with these lesions leading to the formulation of a progression model for pancreatic cancer. Progressive histopathological changes along the progression model are associated with aberrations of cell cycle regulatory and growth factor signalling molecules that occur in pancreatic cancer at high frequency and are common to many cancers. Characterisation of these molecular aberrations provides scope for the development of novel diagnostic and treatment strategies that will ultimately impact on the outcome for people who develop pancreatic cancer.

Proposed morphologic classification of prostate cancer with neuroendocrine differentiation.

PubMed

Epstein, Jonathan I; Amin, Mahul B; Beltran, Himisha; Lotan, Tamara L; Mosquera, Juan-Miguel; Reuter, Victor E; Robinson, Brian D; Troncoso, Patricia; Rubin, Mark A

2014-06-01

On July 31, 2013, the Prostate Cancer Foundation assembled a working committee on the molecular biology and pathologic classification of neuroendocrine (NE) differentiation in prostate cancer. New clinical and molecular data emerging from prostate cancers treated by contemporary androgen deprivation therapies, as well as primary lesions, have highlighted the need for refinement of diagnostic terminology to encompass the full spectrum of NE differentiation. The classification system consists of: Usual prostate adenocarcinoma with NE differentiation; 2) Adenocarcinoma with Paneth cell NE differentiation; 3) Carcinoid tumor; 4) Small cell carcinoma; 5) Large cell NE carcinoma; and 5) Mixed NE carcinoma - acinar adenocarcinoma. The article also highlights "prostate carcinoma with overlapping features of small cell carcinoma and acinar adenocarcinoma" and "castrate-resistant prostate cancer with small cell cancer-like clinical presentation". It is envisioned that specific criteria associated with the refined diagnostic terminology will lead to clinically relevant pathologic diagnoses that will stimulate further clinical and molecular investigation and identification of appropriate targeted therapies.

Copy Number Alterations and Methylation in Ewing's Sarcoma

PubMed Central

Jahromi, Mona S.; Jones, Kevin B.; Schiffman, Joshua D.

2011-01-01

Ewing's sarcoma is the second most common bone malignancy affecting children and young adults. The prognosis is especially poor in metastatic or relapsed disease. The cell of origin remains elusive, but the EWS-FLI1 fusion oncoprotein is present in the majority of cases. The understanding of the molecular basis of Ewing's sarcoma continues to progress slowly. EWS-FLI1 affects gene expression, but other factors must also be at work such as mutations, gene copy number alterations, and promoter methylation. This paper explores in depth two molecular aspects of Ewing's sarcoma: copy number alterations (CNAs) and methylation. While CNAs consistently have been reported in Ewing's sarcoma, their clinical significance has been variable, most likely due to small sample size and tumor heterogeneity. Methylation is thought to be important in oncogenesis and balanced karyotype cancers such as Ewing's, yet it has received only minimal attention in prior studies. Future CNA and methylation studies will help to understand the molecular basis of this disease. PMID:21437220

An experimental study of the putative mechanism of a synthetic autonomous rotary DNA nanomotor

NASA Astrophysics Data System (ADS)

Dunn, K. E.; Leake, M. C.; Wollman, A. J. M.; Trefzer, M. A.; Johnson, S.; Tyrrell, A. M.

2017-03-01

DNA has been used to construct a wide variety of nanoscale molecular devices. Inspiration for such synthetic molecular machines is frequently drawn from protein motors, which are naturally occurring and ubiquitous. However, despite the fact that rotary motors such as ATP synthase and the bacterial flagellar motor play extremely important roles in nature, very few rotary devices have been constructed using DNA. This paper describes an experimental study of the putative mechanism of a rotary DNA nanomotor, which is based on strand displacement, the phenomenon that powers many synthetic linear DNA motors. Unlike other examples of rotary DNA machines, the device described here is designed to be capable of autonomous operation after it is triggered. The experimental results are consistent with operation of the motor as expected, and future work on an enhanced motor design may allow rotation to be observed at the single-molecule level. The rotary motor concept presented here has potential applications in molecular processing, DNA computing, biosensing and photonics.

Interfacing the Ab initio multiple spawning method with electronic structure methods in GAMESS: Photodecay of trans-Azomethane

DOE PAGES

Gaenko, Alexander; DeFusco, Albert; Varganov, Sergey A.; ...

2014-10-20

This work presents a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane, using the ab initio multiple spawning (AIMS) program that has been interfaced with the General Atomic and Molecular Electronic Structure System (GAMESS) quantum chemistry package for on-the-fly electronic structure evaluation. The interface strategy is discussed, and the capabilities of the combined programs are demonstrated with a nonadiabatic molecular dynamics study of the nonradiative decay of photoexcited trans-azomethane. Energies, gradients, and nonadiabatic coupling matrix elements were obtained with the state-averaged complete active space self-consistent field method, as implemented in GAMESS. The influence of initial vibrational excitationmore » on the outcome of the photoinduced isomerization is explored. Increased vibrational excitation in the CNNC torsional mode shortens the excited state lifetime. Depending on the degree of vibrational excitation, the excited state lifetime varies from ~60–200 fs. As a result, these short lifetimes are in agreement with time-resolved photoionization mass spectroscopy experiments.« less

Aero-Thermo-Dynamic Mass Analysis

NASA Astrophysics Data System (ADS)

Shiba, Kota; Yoshikawa, Genki

2016-07-01

Each gas molecule has its own molecular weight, while such a microscopic characteristic is generally inaccessible, and thus, it is measured indirectly through e.g. ionization in conventional mass analysis. Here, we present a novel approach to the direct measurement of molecular weight through a nanoarchitectonic combination of aerodynamics, thermodynamics, and mechanics, transducing microscopic events into macroscopic phenomena. It is confirmed that this approach can provide molecular weight of virtually any gas or vaporizable liquid sample in real-time without ionization. Demonstrations through analytical calculations, numerical simulations, and experiments verify the validity and versatility of the novel mass analysis realized by a simple setup with a flexible object (e.g. with a bare cantilever and even with a business card) placed in a laminar jet. Owing to its unique and simple working principle, this aero-thermo-dynamic mass analysis (AMA) can be integrated into various analytical devices, production lines, and consumer mobile platforms, opening new chapters in aerodynamics, thermodynamics, mechanics, and mass analysis.

Study of ground state optical transfer for ultracold alkali dimers

NASA Astrophysics Data System (ADS)

Bouloufa-Maafa, Nadia; Londono, Beatriz; Borsalino, Dimitri; Vexiau, Romain; Mahecha, Jorge; Dulieu, Olivier; Luc-Koenig, Eliane

2013-05-01

Control of molecular states by laser pulses offer promising potential applications. The manipulation of molecules by external fields requires precise knowledge of the molecular structure. Our motivation is to perform a detailed analysis of the spectroscopic properties of alkali dimers, with the aim to determine efficient optical paths to form molecules in the absolute ground state and to determine the optimal parameters of the optical lattices where those molecules are manipulated to avoid losses by collisions. To this end, we use state of the art molecular potentials, R-dependent spin-orbit coupling and transition dipole moment to perform our calculations. R-dependent SO coupling are of crucial importance because the transitions occur at internuclear distances where they are affected by this R-dependence. Efficient schemes to transfer RbCs, KRb and KCs to the absolute ground state as well as the optimal parameters of the optical lattices will be presented. This work was supported in part by ``Triangle de la Physique'' under contract 2008-007T-QCCM (Quantum Control of Cold Molecules).

[When history meets molecular medicine: molecular history of human tuberculosis].

PubMed

Ottini, Laura; Falchetti, Mario

2010-01-01

Tuberculosis represents one of the humankind's most socially devastating diseases. Despite a long history of medical research and the development of effective therapies, this disease remains a global health danger even in the 21st century. Tuberculosis may cause death but infected people with effective immunity may remain healthy for years, suggesting long-term host-pathogen co-existence. Because of its antiquity, a supposed association with human settlements and the tendency to leave typical lesions on skeletal and mummified remains, tuberculosis has been the object of intensive multidisciplinary studies, including paleo-pathological research. During the past 10 years molecular paleo-pathology developed as a new scientific discipline allowing the study of ancient pathogens by direct detection of their DNA. In this work, we reviewed evidences for tuberculosis in ancient human remains, current methods for identifying ancient mycobacterial DNA and explored current theories of Mycobacterium tuberculosis evolution and their implications in the global development of tuberculosis looking into the past and present at the same time.

Using computer-aided drug design and medicinal chemistry strategies in the fight against diabetes.

PubMed

Semighini, Evandro P; Resende, Jonathan A; de Andrade, Peterson; Morais, Pedro A B; Carvalho, Ivone; Taft, Carlton A; Silva, Carlos H T P

2011-04-01

The aim of this work is to present a simple, practical and efficient protocol for drug design, in particular Diabetes, which includes selection of the illness, good choice of a target as well as a bioactive ligand and then usage of various computer aided drug design and medicinal chemistry tools to design novel potential drug candidates in different diseases. We have selected the validated target dipeptidyl peptidase IV (DPP-IV), whose inhibition contributes to reduce glucose levels in type 2 diabetes patients. The most active inhibitor with complex X-ray structure reported was initially extracted from the BindingDB database. By using molecular modification strategies widely used in medicinal chemistry, besides current state-of-the-art tools in drug design (including flexible docking, virtual screening, molecular interaction fields, molecular dynamics, ADME and toxicity predictions), we have proposed 4 novel potential DPP-IV inhibitors with drug properties for Diabetes control, which have been supported and validated by all the computational tools used herewith.

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome.

PubMed

Pucheta-Martinez, Encarna; D'Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

2016-07-26

WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.

Molecular genetics of dyslexia: an overview.

PubMed

Carrion-Castillo, Amaia; Franke, Barbara; Fisher, Simon E

2013-11-01

Dyslexia is a highly heritable learning disorder with a complex underlying genetic architecture. Over the past decade, researchers have pinpointed a number of candidate genes that may contribute to dyslexia susceptibility. Here, we provide an overview of the state of the art, describing how studies have moved from mapping potential risk loci, through identification of associated gene variants, to characterization of gene function in cellular and animal model systems. Work thus far has highlighted some intriguing mechanistic pathways, such as neuronal migration, axon guidance, and ciliary biology, but it is clear that we still have much to learn about the molecular networks that are involved. We end the review by highlighting the past, present, and future contributions of the Dutch Dyslexia Programme to studies of genetic factors. In particular, we emphasize the importance of relating genetic information to intermediate neurobiological measures, as well as the value of incorporating longitudinal and developmental data into molecular designs. Copyright © 2013 John Wiley & Sons, Ltd.

Changes in the folding landscape of the WW domain provide a molecular mechanism for an inherited genetic syndrome

NASA Astrophysics Data System (ADS)

Pucheta-Martinez, Encarna; D'Amelio, Nicola; Lelli, Moreno; Martinez-Torrecuadrada, Jorge L.; Sudol, Marius; Saladino, Giorgio; Gervasio, Francesco Luigi

2016-07-01

WW domains are small domains present in many human proteins with a wide array of functions and acting through the recognition of proline-rich sequences. The WW domain belonging to polyglutamine tract-binding protein 1 (PQBP1) is of particular interest due to its direct involvement in several X chromosome-linked intellectual disabilities, including Golabi-Ito-Hall (GIH) syndrome, where a single point mutation (Y65C) correlates with the development of the disease. The mutant cannot bind to its natural ligand WBP11, which regulates mRNA processing. In this work we use high-field high-resolution NMR and enhanced sampling molecular dynamics simulations to gain insight into the molecular causes the disease. We find that the wild type protein is partially unfolded exchanging among multiple beta-strand-like conformations in solution. The Y65C mutation further destabilizes the residual fold and primes the protein for the formation of a disulphide bridge, which could be at the origin of the loss of function.

Quantitative computational models of molecular self-assembly in systems biology

PubMed Central

Thomas, Marcus; Schwartz, Russell

2017-01-01

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally. PMID:28535149

Geometric and electrostatic modeling using molecular rigidity functions

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

Mu, Lin; Xia, Kelin; Wei, Guowei

Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins.more » Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.« less

Computational and experimental investigation of molecular imprinted polymers for selective extraction of dimethoate and its metabolite omethoate from olive oil.

PubMed

Bakas, Idriss; Oujji, Najwa Ben; Moczko, Ewa; Istamboulie, Georges; Piletsky, Sergey; Piletska, Elena; Ait-Addi, Elhabib; Ait-Ichou, Ihya; Noguer, Thierry; Rouillon, Régis

2013-01-25

This work presents the development of molecularly imprinted polymers (MIPs) for the selective extraction of dimethoate from olive oil. Computational simulations allowed selecting itaconic acid as the monomer showing the highest affinity towards dimethoate. Experimental validation confirmed modelling predictions and showed that the polymer based on IA as functional monomer and omethoate as template molecule displays the highest selectivity for the structurally similar pesticides dimethoate, omethoate and monocrotophos. Molecularly imprinted solid phase extraction (MISPE) method was developed and applied to the clean-up of olive oil extracts. It was found that the most suitable solvents for loading, washing and elution step were respectively hexane, hexane-dichloromethane (85:15%) and methanol. The developed MIPSE was successfully applied to extraction of dimethoate from olive oil, with recovery rates up to 94%. The limits of detection and quantification of the described method were respectively 0.012 and 0.05 μg g(-1). Copyright © 2012 Elsevier B.V. All rights reserved.

Quantitative computational models of molecular self-assembly in systems biology.

PubMed

Thomas, Marcus; Schwartz, Russell

2017-05-23

Molecular self-assembly is the dominant form of chemical reaction in living systems, yet efforts at systems biology modeling are only beginning to appreciate the need for and challenges to accurate quantitative modeling of self-assembly. Self-assembly reactions are essential to nearly every important process in cell and molecular biology and handling them is thus a necessary step in building comprehensive models of complex cellular systems. They present exceptional challenges, however, to standard methods for simulating complex systems. While the general systems biology world is just beginning to deal with these challenges, there is an extensive literature dealing with them for more specialized self-assembly modeling. This review will examine the challenges of self-assembly modeling, nascent efforts to deal with these challenges in the systems modeling community, and some of the solutions offered in prior work on self-assembly specifically. The review concludes with some consideration of the likely role of self-assembly in the future of complex biological system models more generally.

Characterization of galactomannan derivatives in roasted coffee beverages.

PubMed

Nunes, Fernando M; Reis, Ana; Domingues, M Rosário M; Coimbra, Manuel A

2006-05-03

In this work, the galactomannans from roasted coffee infusions were purified by 50% ethanol precipitation, anion exchange chromatography, and phenylboronic acid-immobilized Sepharose chromatography. Specific enzymatic hydrolysis of the beta-(1-->4)-D-mannan backbone allowed us to conclude that the galactomannans of roasted coffee infusions are high molecular weight supports of low molecular weight brown compounds. Also, the molecular weight of the brown compounds linked to the galactomannan increases with the increase of the coffee degree of roast. The reaction pathways of galactomannans during the coffee roasting process were inferred from the detection of specific chemical markers by gas chromatography-electron impact mass spectrometry and/or electrospray ionization tandem mass spectrometry. Maillard reaction, caramelization, isomerization, oxidation, and decarboxylation pathways were identified by detection of Amadori compounds, 1,6-beta-anhydromannose, fructose, glucose, mannonic acid, 2-ketogluconic acid, and arabinonic acid in the reducing end of the obtained oligosaccharides. The implication of the several competitive reaction pathways is discussed and related to the structural changes of the galactomannans present in the roasted coffee infusions.

Geometric and electrostatic modeling using molecular rigidity functions

DOE PAGES

Mu, Lin; Xia, Kelin; Wei, Guowei

2017-03-01

Geometric and electrostatic modeling is an essential component in computational biophysics and molecular biology. Commonly used geometric representations admit geometric singularities such as cusps, tips and self-intersecting facets that lead to computational instabilities in the molecular modeling. Our present work explores the use of flexibility and rigidity index (FRI), which has a proved superiority in protein B-factor prediction, for biomolecular geometric representation and associated electrostatic analysis. FRI rigidity surfaces are free of geometric singularities. We propose a rigidity based Poisson–Boltzmann equation for biomolecular electrostatic analysis. These approaches to surface and electrostatic modeling are validated by a set of 21 proteins.more » Our results are compared with those of established methods. Finally, being smooth and analytically differentiable, FRI rigidity functions offer excellent curvature analysis, which characterizes concave and convex regions on protein surfaces. Polarized curvatures constructed by using the product of minimum curvature and electrostatic potential is shown to predict potential protein–ligand binding sites.« less

Investigation of oxygen self-diffusion in PuO 2 by combining molecular dynamics with thermodynamic calculations

DOE PAGES

Saltas, V.; Chroneos, A.; Cooper, Michael William D.; ...

2016-01-01

In the present work, the defect properties of oxygen self-diffusion in PuO 2 are investigated over a wide temperature (300–1900 K) and pressure (0–10 GPa) range, by combining molecular dynamics simulations and thermodynamic calculations. Based on the well-established cBΩ thermodynamic model which connects the activation Gibbs free energy of diffusion with the bulk elastic and expansion properties, various point defect parameters such as activation enthalpy, activation entropy, and activation volume were calculated as a function of T and P. Molecular dynamics calculations provided the necessary bulk properties for the proper implementation of the thermodynamic model, in the lack of anymore » relevant experimental data. The estimated compressibility and the thermal expansion coefficient of activation volume are found to be more than one order of magnitude greater than the corresponding values of the bulk plutonia. As a result, the diffusion mechanism is discussed in the context of the temperature and pressure dependence of the activation volume.« less

Ferroelectric molecular field-switch based on double proton transfer process: Static and dynamical simulations

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

Rode, Michał F.; Sobolewski, Andrzej L.; Jankowska, Joanna

2016-04-07

In this work, we present a reversible ferroelectric molecular switch controlled by an external electric field. The studied (2Z)-1-(6-((Z)-2-hydroxy-2-phenylvinyl)pyridin-3-yl)-2-(pyridin-2(1H) -ylidene)ethanone (DSA) molecule is polarized by two uniaxial intramolecular hydrogen bonds. Two protons can be transferred along hydrogen bonds upon an electric field applied along the main molecular axis. The process results in reversion of the dipole moment of the system. Static ab initio and on-the-fly dynamical simulations of the DSA molecule placed in an external electric field give insight into the mechanism of the double proton transfer (DPT) in the system and allow for estimation of the time scale ofmore » this process. The results indicate that with increasing strength of the electric field, the step-wise mechanism of DPT changes into the downhill barrierless process in which the synchronous and asynchronous DPTs compete with each other.« less

Electroosmotic Mixing in Nanochannels

NASA Astrophysics Data System (ADS)

Conlisk, A. T.; Chen, Lei

2004-11-01

Electroosmotic flow in nanochannels is characterized by low Reynolds number in which flow mixing is difficult because of the dominance of molecular diffusion. Previous work shows that heterogenerous surface potential could generate a circulation region within the bulk flow near the surface. But all of this work requires that the ionic species be pairs of ions of equal and opposite valence and the distribution of ions is not considered. In the present work the electroosmotic flow in a rectangular channel with non-uniform zeta potential is examined. A model for the two dimensional electroosmotic flow problem is established. The distributions of potential, velocity and mole fractions are calculated numerically. Vortex formation is observed within the bulk flow near the the region of non-uniform zeta potential which suggests mixing can be induced.

Investigating rare events with nonequilibrium work measurements. I. Nonequilibrium transition path probabilities

NASA Astrophysics Data System (ADS)

Moradi, Mahmoud; Sagui, Celeste; Roland, Christopher

2014-01-01

We have developed a formalism for investigating transition pathways and transition probabilities for rare events in biomolecular systems. In this paper, we set the theoretical framework for employing nonequilibrium work relations to estimate the relative reaction rates associated with different classes of transition pathways. Particularly, we derive an extension of Crook's transient fluctuation theorem, which relates the relative transition rates of driven systems in the forward and reverse directions, and allows for the calculation of these relative rates using work measurements (e.g., in Steered Molecular Dynamics). The formalism presented here can be combined with Transition Path Theory to relate the equilibrium and driven transition rates. The usefulness of this framework is illustrated by means of a Gaussian model and a driven proline dimer.

Optimizing Energy Conversion: Magnetic Nano-materials

NASA Astrophysics Data System (ADS)

McIntyre, Dylan; Dann, Martin; Ilie, Carolina C.

2015-03-01

We present herein the work started at SUNY Oswego as a part of a SUNY 4E grant. The SUNY 4E Network of Excellence has awarded SUNY Oswego and collaborators a grant to carry out extensive studies on magnetic nanoparticles. The focus of the study is to develop cost effective rare-earth-free magnetic materials that will enhance energy transmission performance of various electrical devices (solar cells, electric cars, hard drives, etc.). The SUNY Oswego team has started the preliminary work for the project and graduate students from the rest of the SUNY 4E team (UB, Alfred College, Albany) will continue the project. The preliminary work concentrates on analyzing the properties of magnetic nanoparticle candidates, calculating molecular orbitals and band gap, and the fabrication of thin films. SUNY 4E Network of Excellence Grant.

Extensive Evaluation of the Conductor-like Screening Model for Real Solvents Method in Predicting Liquid-Liquid Equilibria in Ternary Systems of Ionic Liquids with Molecular Compounds.

PubMed

Paduszyński, Kamil

2018-04-12

A conductor-like screening model for real solvents (COSMO-RS) is nowadays one of the most popular and commonly applied tools for the estimation of thermodynamic properties of complex fluids. The goal of this work is to provide a comprehensive review and analysis of the performance of this approach in calculating liquid-liquid equilibrium (LLE) phase diagrams in ternary systems composed of ionic liquid and two molecular compounds belonging to diverse families of chemicals (alkanes, aromatics, S/N-compounds, alcohols, ketones, ethers, carboxylic acid, esters, and water). The predictions are presented for extensive experimental database, including 930 LLE data sets and more than 9000 data points (LLE tie lines) reported for 779 unique ternary mixtures. An impact of the type of molecular binary subsystem on the accuracy of predictions is demonstrated and discussed on the basis of representative examples. The model's capability of capturing qualitative trends in the LLE distribution ratio and selectivity is also checked for a number of structural effects. Comparative analysis of two levels of quantum chemical theory (BP-TZVP-COSMO vs BP-TZVPD-FINE) for the input molecular data for COSMO-RS is presented. Finally, some general recommendations for the applicability of the model are indicated based on the analysis of the global performance as well as on the results obtained for systems relevant from the point of view of important separation problems.

Molecular and Cellular Characterization of Space Flight Effects on Microvascular Endothelial Cell Function - PreparatoryWork for the SFEF Project

NASA Astrophysics Data System (ADS)

Balsamo, Michele; Barravecchia, Ivana; Mariotti, Sara; Merenda, Alessandra; De Cesari, Chiara; Vukich, Marco; Angeloni, Debora

2014-12-01

Exposure to microgravity during space flight (SF) of variable length induces suffering of the endothelium (the cells lining all blood vessels), mostly responsible for health problems found in astronauts and animals returning from space. Of interest to pre-nosological medicine, the effects of microgravity on astronauts are strikingly similar to the consequences of sedentary life, senescence and degenerative diseases on Earth, although SF effects are accelerated and reversible. Thus, microgravity is a significant novel model for better understanding of common pathologies. A comprehensive cell and molecular biology study is needed in order to explain pathophysiological findings after SFs. This project will study the effects of microgravity and cosmic radiation on endothelial cells (ECs) cultured on the International Space Station through analysis of 1) cell transcriptome, 2) DNA methylome, 3) DNA damage and cell senescence, 4) variations in cell cycle and cell morphology. This project has been selected by the European Space Agency and the Italian Space Agency and is presently in preparation. The ground study presented here was performed to determine the biological and engineering requirements that will allow us to retrieve suitable samples after culturing, fixing and storing ECs in space. We expect to identify molecular pathways activated by space microgravity in microvascular ECs, which may shed light on pathogenic molecular mechanisms responsible for endothelial suffering shared by astronauts and individuals affected with aging, degenerative and sedentary life-associated pathologies on Earth.

Critical comparison of the on-line and off-line molecularly imprinted solid-phase extraction of patulin coupled with liquid chromatography.

PubMed

Lhotská, Ivona; Holznerová, Anežka; Solich, Petr; Šatínský, Dalibor

2017-12-01

Reaching trace amounts of mycotoxin contamination requires sensitive and selective analytical tools for their determination. Improving the selectivity of sample pretreatment steps covering new and modern extraction techniques is one way to achieve it. Molecularly imprinted polymers as selective sorbent for extraction undoubtedly meet these criteria. The presented work is focused on the hyphenation of on-line molecularly imprinted solid-phase extraction with a chromatography system using a column-switching approach. Making a critical comparison with a simultaneously developed off-line extraction procedure, evaluation of pros and cons of each method, and determining the reliability of both methods on a real sample analysis were carried out. Both high-performance liquid chromatography methods, using off-line extraction on molecularly imprinted polymer and an on-line column-switching approach, were validated, and the validation results were compared against each other. Although automation leads to significant time savings, fewer human errors, and required no handling of toxic solvents, it reached worse detection limits (15 versus 6 μg/L), worse recovery values (68.3-123.5 versus 81.2-109.9%), and worse efficiency throughout the entire clean-up process in comparison with the off-line extraction method. The difficulties encountered, the compromises made during the optimization of on-line coupling and their critical evaluation are presented in detail. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Atomic Forces for Geometry-Dependent Point Multipole and Gaussian Multipole Models

PubMed Central

Elking, Dennis M.; Perera, Lalith; Duke, Robert; Darden, Thomas; Pedersen, Lee G.

2010-01-01

In standard treatments of atomic multipole models, interaction energies, total molecular forces, and total molecular torques are given for multipolar interactions between rigid molecules. However, if the molecules are assumed to be flexible, two additional multipolar atomic forces arise due to 1) the transfer of torque between neighboring atoms, and 2) the dependence of multipole moment on internal geometry (bond lengths, bond angles, etc.) for geometry-dependent multipole models. In the current study, atomic force expressions for geometry-dependent multipoles are presented for use in simulations of flexible molecules. The atomic forces are derived by first proposing a new general expression for Wigner function derivatives ∂Dlm′m/∂Ω. The force equations can be applied to electrostatic models based on atomic point multipoles or Gaussian multipole charge density. Hydrogen bonded dimers are used to test the inter-molecular electrostatic energies and atomic forces calculated by geometry-dependent multipoles fit to the ab initio electrostatic potential (ESP). The electrostatic energies and forces are compared to their reference ab initio values. It is shown that both static and geometry-dependent multipole models are able to reproduce total molecular forces and torques with respect to ab initio, while geometry-dependent multipoles are needed to reproduce ab initio atomic forces. The expressions for atomic force can be used in simulations of flexible molecules with atomic multipoles. In addition, the results presented in this work should lead to further development of next generation force fields composed of geometry-dependent multipole models. PMID:20839297

Systems Biology Methods for Alzheimer's Disease Research Toward Molecular Signatures, Subtypes, and Stages and Precision Medicine: Application in Cohort Studies and Trials.

PubMed

Castrillo, Juan I; Lista, Simone; Hampel, Harald; Ritchie, Craig W

2018-01-01

Alzheimer's disease (AD) is a complex multifactorial disease, involving a combination of genomic, interactome, and environmental factors, with essential participation of (a) intrinsic genomic susceptibility and (b) a constant dynamic interplay between impaired pathways and central homeostatic networks of nerve cells. The proper investigation of the complexity of AD requires new holistic systems-level approaches, at both the experimental and computational level. Systems biology methods offer the potential to unveil new fundamental insights, basic mechanisms, and networks and their interplay. These may lead to the characterization of mechanism-based molecular signatures, and AD hallmarks at the earliest molecular and cellular levels (and beyond), for characterization of AD subtypes and stages, toward targeted interventions according to the evolving precision medicine paradigm. In this work, an update on advanced systems biology methods and strategies for holistic studies of multifactorial diseases-particularly AD-is presented. This includes next-generation genomics, neuroimaging and multi-omics methods, experimental and computational approaches, relevant disease models, and latest genome editing and single-cell technologies. Their progressive incorporation into basic research, cohort studies, and trials is beginning to provide novel insights into AD essential mechanisms, molecular signatures, and markers toward mechanism-based classification and staging, and tailored interventions. Selected methods which can be applied in cohort studies and trials, with the European Prevention of Alzheimer's Dementia (EPAD) project as a reference example, are presented and discussed.

Predicting gene regulatory networks by combining spatial and temporal gene expression data in Arabidopsis root stem cells

PubMed Central

de Luis Balaguer, Maria Angels; Fisher, Adam P.; Clark, Natalie M.; Fernandez-Espinosa, Maria Guadalupe; Möller, Barbara K.; Weijers, Dolf; Williams, Cranos; Lorenzo, Oscar; Sozzani, Rosangela

2017-01-01

Identifying the transcription factors (TFs) and associated networks involved in stem cell regulation is essential for understanding the initiation and growth of plant tissues and organs. Although many TFs have been shown to have a role in the Arabidopsis root stem cells, a comprehensive view of the transcriptional signature of the stem cells is lacking. In this work, we used spatial and temporal transcriptomic data to predict interactions among the genes involved in stem cell regulation. To accomplish this, we transcriptionally profiled several stem cell populations and developed a gene regulatory network inference algorithm that combines clustering with dynamic Bayesian network inference. We leveraged the topology of our networks to infer potential major regulators. Specifically, through mathematical modeling and experimental validation, we identified PERIANTHIA (PAN) as an important molecular regulator of quiescent center function. The results presented in this work show that our combination of molecular biology, computational biology, and mathematical modeling is an efficient approach to identify candidate factors that function in the stem cells. PMID:28827319

Differential expression and emerging functions of non-coding RNAs in cold adaptation.

PubMed

Frigault, Jacques J; Morin, Mathieu D; Morin, Pier Jr

2017-01-01

Several species undergo substantial physiological and biochemical changes to confront the harsh conditions associated with winter. Small mammalian hibernators and cold-hardy insects are examples of natural models of cold adaptation that have been amply explored. While the molecular picture associated with cold adaptation has started to become clearer in recent years, notably through the use of high-throughput experimental approaches, the underlying cold-associated functions attributed to several non-coding RNAs, including microRNAs (miRNAs) and long non-coding RNAs (lncRNAs), remain to be better characterized. Nevertheless, key pioneering work has provided clues on the likely relevance of these molecules in cold adaptation. With an emphasis on mammalian hibernation and insect cold hardiness, this work first reviews various molecular changes documented so far in these processes. The cascades leading to miRNA and lncRNA production as well as the mechanisms of action of these non-coding RNAs are subsequently described. Finally, we present examples of differentially expressed non-coding RNAs in models of cold adaptation and elaborate on the potential significance of this modulation with respect to low-temperature adaptation.

Small endogenous molecules as moiety to improve targeting of CNS drugs.

PubMed

Sutera, Flavia Maria; De Caro, Viviana; Giannola, Libero Italo

2017-01-01

A major challenge in the development of novel neuro-therapeutic agents is to effectively overcome the blood-brain barrier (BBB), which acts as a 'working dynamic barrier'. The core problem in the treatment of neurodegenerative diseases is failed delivery of potential medicines due to their inadequate permeation rate. Areas covered: The present review gives a summary of endogenous moieties used in synthesizing prodrugs, derivatives and bioisosteric drugs appositely designed to structurally resemble physiological molecular entities able to be passively absorbed or carried by specific carrier proteins expressed at BBB level. In particular, this overview focuses on aminoacidic, glycosyl, purinergic, ureic and acidic fragments derivatives, most of which can take advantage from BBB carrier-mediated transporters, where passive diffusion is not permitted. Expert opinion: In the authors' perspective, further progress in this field could expedite successful translation of new chemical entities into clinical trials. Careful rationalization of the linkage between endogenous molecular structures and putative transporters binding sites could allow to useful work-flows and libraries for synthesizing new BBB-crossing therapeutic substances and/or multifunctional drugs for treatments of central disorders.

Optimization strategies for molecular dynamics programs on Cray computers and scalar work stations

NASA Astrophysics Data System (ADS)

Unekis, Michael J.; Rice, Betsy M.

1994-12-01

We present results of timing runs and different optimization strategies for a prototype molecular dynamics program that simulates shock waves in a two-dimensional (2-D) model of a reactive energetic solid. The performance of the program may be improved substantially by simple changes to the Fortran or by employing various vendor-supplied compiler optimizations. The optimum strategy varies among the machines used and will vary depending upon the details of the program. The effect of various compiler options and vendor-supplied subroutine calls is demonstrated. Comparison is made between two scalar workstations (IBM RS/6000 Model 370 and Model 530) and several Cray supercomputers (X-MP/48, Y-MP8/128, and C-90/16256). We find that for a scientific application program dominated by sequential, scalar statements, a relatively inexpensive high-end work station such as the IBM RS/60006 RISC series will outperform single processor performance of the Cray X-MP/48 and perform competitively with single processor performance of the Y-MP8/128 and C-9O/16256.

[The specific bronchial provocation test in the diagnosis of occupational asthma].

PubMed

Fraj, J; Duce, F; Lezaun, A; Colás, C; Domínguez, M A; Abadía, M C

1997-10-01

Specific bronchial challenge (SBC) testing is a key technique for diagnosing the origin of occupational asthma (OA). SBC is indicated in specific circumstances, including whenever several agents present in the work environment may be the cause of OA, when new or unusual occupational agents need to be identified, when evidence for legal action is required, or when research is conducted. SBC procedures are not standardized, because of the great diversity of occupational agents and the variety of physical and chemical properties involved. Thus, SBC testing with agents found in fumes, gases or vapors can be administered in special cabins or in closed circuits with continuous monitoring of sub-irritant concentrations. Agents found in dust, most but not all of which have high molecular weights, may be appropriate for routine SBC testing in an allergy laboratory. This paper will treat only these cases. SBC must be formed in specialized centers by experienced personnel, as it is a sophisticated and potentially dangerous technique. We describe a series of 20 patients diagnosed of OA in our unit over the past two years in whom SBC provided an etiologic diagnosis. All were exposed to dust or aerosols at work. The cause was a substance of high molecular weight in 17 cases, and low molecular weight in 3. The procedure used is described and models of bronchial response are discussed.

Automated bond order assignment as an optimization problem.

PubMed

Dehof, Anna Katharina; Rurainski, Alexander; Bui, Quang Bao Anh; Böcker, Sebastian; Lenhof, Hans-Peter; Hildebrandt, Andreas

2011-03-01

Numerous applications in Computational Biology process molecular structures and hence strongly rely not only on correct atomic coordinates but also on correct bond order information. For proteins and nucleic acids, bond orders can be easily deduced but this does not hold for other types of molecules like ligands. For ligands, bond order information is not always provided in molecular databases and thus a variety of approaches tackling this problem have been developed. In this work, we extend an ansatz proposed by Wang et al. that assigns connectivity-based penalty scores and tries to heuristically approximate its optimum. In this work, we present three efficient and exact solvers for the problem replacing the heuristic approximation scheme of the original approach: an A*, an ILP and an fixed-parameter approach (FPT) approach. We implemented and evaluated the original implementation, our A*, ILP and FPT formulation on the MMFF94 validation suite and the KEGG Drug database. We show the benefit of computing exact solutions of the penalty minimization problem and the additional gain when computing all optimal (or even suboptimal) solutions. We close with a detailed comparison of our methods. The A* and ILP solution are integrated into the open-source C++ LGPL library BALL and the molecular visualization and modelling tool BALLView and can be downloaded from our homepage www.ball-project.org. The FPT implementation can be downloaded from http://bio.informatik.uni-jena.de/software/.

Molecularly imprinted polymer/cryogel composites for solid-phase extraction of bisphenol A from river water and wine.

PubMed

Baggiani, Claudio; Baravalle, Patrizia; Giovannoli, Cristina; Anfossi, Laura; Giraudi, Gianfranco

2010-05-01

Superporous monolithic hydrogels (cryogel monoliths) are elastic, sponge-like materials that can be prepared in an aqueous medium through a cryotropic gelation technique. These monoliths show interesting properties for the development of high-throughput solid-phase extraction supports to treat large volumes of aqueous samples. In this work, a cryogel-supported molecularly imprinted solid-phase extraction approach for the endocrine disruptor bisphenol A (BPA) from river water and wine samples is presented. An imprinted polymer with molecular recognition properties for BPA was prepared in acetonitrile by thermal polymerization of a mixture of 4,4'-dihydroxy-2,2-diphenyl-1,1,1,3,3,3-trifluoropropane as a mimic template of BPA, 4-vinylpyridine and trimethylolpropane trimethacrylate in a molar ratio of 1 + 6 + 6. Fine imprinted particles (<10 microm) were embedded in a poly-acrylamide-co-N,N'-methylenbisacrylamide cryogel obtained by ammonium persulfate-induced cryopolymerization at -18 degrees C. The resulting monolithic gel was evaluated for its use as a sorbent support in an off-line solid-phase extraction approach to recover BPA from dilute aqueous samples with minimum pre-loading work-up. The optimized extraction protocol resulted in a reliable MISPE method suitable to selectively extract and preconcentrate BPA from river water and red wine samples, demonstrating the practical feasibility of cryogel-trapped imprinted polymers as solid-phase extraction materials.

Predicting Biological Information Flow in a Model Oxygen Minimum Zone

NASA Astrophysics Data System (ADS)

Louca, S.; Hawley, A. K.; Katsev, S.; Beltran, M. T.; Bhatia, M. P.; Michiels, C.; Capelle, D.; Lavik, G.; Doebeli, M.; Crowe, S.; Hallam, S. J.

2016-02-01

Microbial activity drives marine biochemical fluxes and nutrient cycling at global scales. Geochemical measurements as well as molecular techniques such as metagenomics, metatranscriptomics and metaproteomics provide great insight into microbial activity. However, an integration of molecular and geochemical data into mechanistic biogeochemical models is still lacking. Recent work suggests that microbial metabolic pathways are, at the ecosystem level, strongly shaped by stoichiometric and energetic constraints. Hence, models rooted in fluxes of matter and energy may yield a holistic understanding of biogeochemistry. Furthermore, such pathway-centric models would allow a direct consolidation with meta'omic data. Here we present a pathway-centric biogeochemical model for the seasonal oxygen minimum zone in Saanich Inlet, a fjord off the coast of Vancouver Island. The model considers key dissimilatory nitrogen and sulfur fluxes, as well as the population dynamics of the genes that mediate them. By assuming a direct translation of biocatalyzed energy fluxes to biosynthesis rates, we make predictions about the distribution and activity of the corresponding genes. A comparison of the model to molecular measurements indicates that the model explains observed DNA, RNA, protein and cell depth profiles. This suggests that microbial activity in marine ecosystems such as oxygen minimum zones is well described by DNA abundance, which, in conjunction with geochemical constraints, determines pathway expression and process rates. Our work further demonstrates how meta'omic data can be mechanistically linked to environmental redox conditions and biogeochemical processes.

Quantum nuclear effects in water using centroid molecular dynamics

NASA Astrophysics Data System (ADS)

Kondratyuk, N. D.; Norman, G. E.; Stegailov, V. V.

2018-01-01

The quantum nuclear effects are studied in water using the method of centroid molecular dynamics (CMD). The aim is the calibration of CMD implementation in LAMMPS. The calculated intramolecular energy, atoms gyration radii and radial distribution functions are shown in comparison with previous works. The work is assumed to be the step toward to solution of the discrepancy between the simulation results and the experimental data of liquid n-alkane properties in our previous works.

Science | Argonne National Laboratory

Science.gov Websites

Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at Argonne Work with Scientific Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at understand, predict, and ultimately control matter and energy at the electronic, atomic, and molecular levels

Argonne Research Library | Argonne National Laboratory

Science.gov Websites

Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at Argonne Work with Scientific Publications Researchers Postdocs Exascale Computing Institute for Molecular Engineering at IMEInstitute for Molecular Engineering JCESRJoint Center for Energy Storage Research MCSGMidwest Center for

1978 bibliography of atomic and molecular processes. [Bibliography

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

Not Available

This annotated bibliography lists 2557 works on atomic and molecular processes reported in publications dated 1978. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

1979 bibliography of atomic and molecular processes. [Bibliography

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

None

1980-08-01

This annotated bibliography lists 2146 works on atomic and molecular processes reported in publications dated 1979. Sources include scientific journals, conference proceedings, and books. Each entry is designated by one or more of the 114 categories of atomic and molecular processes used by the Controlled Fusion Atomic Data Center, Oak Ridge National Laboratory, to classify data. Also indicated is whether the work was experimental or theoretical, what energy range was covered, what reactants were investigated, and the country of origin of the first author. Following the bibliographical listing are indexes of reactants and authors.

Fabrication and characterization of a solid state nanopore with self-aligned carbon nanoelectrodes for molecular detection

NASA Astrophysics Data System (ADS)

Spinney, Patrick; Collins, Scott D.; Howitt, David G.; Smith, Rosemary L.

2012-06-01

Rapid and cost-effective DNA sequencing is a pivotal prerequisite for the genomics era. Many of the recent advances in forensics, medicine, agriculture, taxonomy, and drug discovery have paralleled critical advances in DNA sequencing technology. Nanopore modalities for DNA sequencing have recently surfaced including the electrical interrogation of protein ion channels and/or solid-state nanopores during translocation of DNA. However to date, most of this work has met with mixed success. In this work, we present a unique nanofabrication strategy that realizes an artificial nanopore articulated with carbon electrodes to sense the current modulations during the transport of DNA through the nanopore. This embodiment overcomes most of the technical difficulties inherent in other artificial nanopore embodiments and present a versatile platform for the testing of DNA single nucleotide detection. Characterization of the device using gold nanoparticles, silica nanoparticles, lambda dsDNA and 16-mer ssDNA are presented. Although single molecule DNA sequencing is still not demonstrated, the device shows a path towards this goal.

Drosophila immunity research on the move.

PubMed

Eleftherianos, Ioannis; Schneider, David

2011-01-01

Drosophila has been established as useful model for infectious diseases because it allows large numbers of whole animals to be studied and provides powerful genetic tools and conservation with signaling and pathogenesis mechanisms in vertebrates. During the past twenty years, significant progress has been made on the characterization of innate immune responses against various pathogenic organisms in flies (Fig. 1). In this year's Drosophila Research Conference, which was held in San Diego (March 30-April 3) and sponsored by the Genetics Society of America, the immunity and pathogenesis session comprised seven platform presentations and 34 posters that highlighted the latest advances in Drosophila infection and immunity field. The presented work covered a wide range of studies from immune signaling pathways and the molecular basis of humoral and cellular immune mechanisms to the role of endosymbionts in fly immune function and effects of immune priming. Here, we give an overview of the presented work and we explain how these findings will open new avenues in Drosophila immunity research.

Understanding the role of Ti in reversible hydrogen storage as sodium alanate: a combined experimental and density functional theoretical approach.

PubMed

Chaudhuri, Santanu; Graetz, Jason; Ignatov, Alex; Reilly, James J; Muckerman, James T

2006-09-06

We report the results of an experimental and theoretical study of hydrogen storage in sodium alanate (NaAlH(4)). Reversible hydrogen storage in this material is dependent on the presence of 2-4% Ti dopant. Our combined study shows that the role of Ti may be linked entirely to Ti-containing active catalytic sites in the metallic Al phase present in the dehydrogenated NaAlH(4). The EXAFS data presented here show that dehydrogenated samples contain a highly disordered distribution of Ti-Al distances with no long-range order beyond the second coordination sphere. We have used density functional theory techniques to calculate the chemical potential of possible Ti arrangements on an Al(001) surface for Ti coverages ranging from 0.125 to 0.5 monolayer (ML) and have identified those that can chemisorb molecular hydrogen via spontaneous or only moderately activated pathways. The chemisorption process exhibits a characteristic nodal symmetry property for the low-barrier sites: the incipient doped surface-H(2) adduct's highest occupied molecular orbital (HOMO) incorporates the sigma antibonding molecular orbital of hydrogen, allowing the transfer of charge density from the surface to dissociate the molecular hydrogen. This work also proposes a plausible mechanism for the transport of an aluminum hydride species back into the NaH lattice that is supported by Car-Parrinello molecular dynamics (CPMD) simulations of the stability and mobility of aluminum clusters (alanes) on Al(001). As an experimental validation of the proposed role of titanium and the subsequent diffusion of alanes, we demonstrate experimentally that AlH(3) reacts with NaH to form NaAlH(4) without any requirement of a catalyst or hydrogen overpressure.

Pharmacophore generation, atom-based 3D-QSAR, molecular docking and molecular dynamics simulation studies on benzamide analogues as FtsZ inhibitors.

PubMed

Tripathy, Swayansiddha; Azam, Mohammed Afzal; Jupudi, Srikanth; Sahu, Susanta Kumar

2017-10-11

FtsZ is an appealing target for the design of antimicrobial agent that can be used to defeat the multidrug-resistant bacterial pathogens. Pharmacophore modelling, molecular docking and molecular dynamics (MD) simulation studies were performed on a series of three-substituted benzamide derivatives. In the present study a five-featured pharmacophore model with one hydrogen bond acceptors, one hydrogen bond donors, one hydrophobic and two aromatic rings was developed using 97 molecules having MIC values ranging from .07 to 957 μM. A statistically significant 3D-QSAR model was obtained using this pharmacophore hypothesis with a good correlation coefficient (R 2  = .8319), cross validated coefficient (Q 2  = .6213) and a high Fisher ratio (F = 103.9) with three component PLS factor. A good correlation between experimental and predicted activity of the training (R 2  = .83) and test set (R 2  = .67) molecules were displayed by ADHRR.1682 model. The generated model was further validated by enrichment studies using the decoy test and MAE-based criteria to measure the efficiency of the model. The docking studies of all selected inhibitors in the active site of FtsZ protein showed crucial hydrogen bond interactions with Val 207, Asn 263, Leu 209, Gly 205 and Asn-299 residues. The binding free energies of these inhibitors were calculated by the molecular mechanics/generalized born surface area VSGB 2.0 method. Finally, a 15 ns MD simulation was done to confirm the stability of the 4DXD-ligand complex. On a wider scope, the prospect of present work provides insight in designing molecules with better selective FtsZ inhibitory potential.

Quantum mechanical force field for water with explicit electronic polarization.

PubMed

Han, Jaebeom; Mazack, Michael J M; Zhang, Peng; Truhlar, Donald G; Gao, Jiali

2013-08-07

A quantum mechanical force field (QMFF) for water is described. Unlike traditional approaches that use quantum mechanical results and experimental data to parameterize empirical potential energy functions, the present QMFF uses a quantum mechanical framework to represent intramolecular and intermolecular interactions in an entire condensed-phase system. In particular, the internal energy terms used in molecular mechanics are replaced by a quantum mechanical formalism that naturally includes electronic polarization due to intermolecular interactions and its effects on the force constants of the intramolecular force field. As a quantum mechanical force field, both intermolecular interactions and the Hamiltonian describing the individual molecular fragments can be parameterized to strive for accuracy and computational efficiency. In this work, we introduce a polarizable molecular orbital model Hamiltonian for water and for oxygen- and hydrogen-containing compounds, whereas the electrostatic potential responsible for intermolecular interactions in the liquid and in solution is modeled by a three-point charge representation that realistically reproduces the total molecular dipole moment and the local hybridization contributions. The present QMFF for water, which is called the XP3P (explicit polarization with three-point-charge potential) model, is suitable for modeling both gas-phase clusters and liquid water. The paper demonstrates the performance of the XP3P model for water and proton clusters and the properties of the pure liquid from about 900 × 10(6) self-consistent-field calculations on a periodic system consisting of 267 water molecules. The unusual dipole derivative behavior of water, which is incorrectly modeled in molecular mechanics, is naturally reproduced as a result of an electronic structural treatment of chemical bonding by XP3P. We anticipate that the XP3P model will be useful for studying proton transport in solution and solid phases as well as across biological ion channels through membranes.

Molecular status of human immunodeficiency virus, hepatitis B virus, and hepatitis C virus among transgender commercial sex workers in Surakarta, Indonesia

NASA Astrophysics Data System (ADS)

Prasetyo, Afiono Agung; Sari, Yulia; Dharmawan, Ruben; Marwoto

2017-02-01

Sexual contact and other risk behavior among transgender working as commercial sex workers are important factors for sexual and blood-borne virus (BBV) infections. However, there no data concerning the molecular status of human immunodeficiency virus (HIV), hepatitis B virus (HBV) and hepatitis C virus (HCV) circulated among transgender working as commercial sex workers. Blood samples obtained from transgender working as commercial sex workers in Surakarta were examined for HIV antibodies, HBsAg and HCV antibodies, respectively, by immunological assays. All blood samples were also subjected for viral nucleic acid extraction and molecular detection of HIV, HBV and HCV by nested RT-PCR. The PCR products were purified from agarose gels, and the nucleotide sequences were retrieved and molecular analyzed. HIV, HBV and HCV was detected in 26.9% (7/26), 19.2% (5/26) and 46.2% (12/26), respectively. HIV CRF01_AE and B were found to be circulating in the community. HBV genotype B3 predominated, followed by C1. HCV genotype 1a predominated among HCV-infected transgender working as commercial sex workers, followed by 1c, 3a, and 4a. HIV, HBV, and HCV were found circulating in the transgender working as commercial sex workers in Surakarta, Indonesia.

Unravelling polar lipids dynamics during embryonic development of two sympatric brachyuran crabs (Carcinus maenas and Necora puber) using lipidomics

PubMed Central

Rey, Felisa; Alves, Eliana; Melo, Tânia; Domingues, Pedro; Queiroga, Henrique; Rosa, Rui; Domingues, M. Rosário M.; Calado, Ricardo

2015-01-01

Embryogenesis is an important stage of marine invertebrates with bi-phasic life cycles, as it conditions their larval and adult life. Throughout embryogenesis, phospholipids (PL) play a key role as an energy source, as well as constituents of biological membranes. However, the dynamics of PL during embryogenesis in marine invertebrates is still poorly studied. The present work used a lipidomic approach to determine how polar lipid profiles shift during embryogenesis in two sympatric estuarine crabs, Carcinus maenas and Necora puber. The combination of thin layer chromatography, liquid chromatography – mass spectrometry and gas chromatography – mass spectrometry allowed us to achieve an unprecedented resolution on PL classes and molecular species present on newly extruded embryos (stage 1) and those near hatching (stage 3). Embryogenesis proved to be a dynamic process, with four PL classes being recorded in stage 1 embryos (68 molecular species in total) and seven PL classes at stage 3 embryos (98 molecular species in total). The low interspecific difference recorded in the lipidomic profiles of stage 1 embryos appears to indicate the existence of similar maternal investment. The same pattern was recorded for stage 3 embryos revealing a similar catabolism of embryonic resources during incubation for both crab species. PMID:26419891

Shedding light on the puzzle of drug-membrane interactions: Experimental techniques and molecular dynamics simulations.

PubMed

Lopes, Daniela; Jakobtorweihen, Sven; Nunes, Cláudia; Sarmento, Bruno; Reis, Salette

2017-01-01

Lipid membranes work as barriers, which leads to inevitable drug-membrane interactions in vivo. These interactions affect the pharmacokinetic properties of drugs, such as their diffusion, transport, distribution, and accumulation inside the membrane. Furthermore, these interactions also affect their pharmacodynamic properties with respect to both therapeutic and toxic effects. Experimental membrane models have been used to perform in vitro assessment of the effects of drugs on the biophysical properties of membranes by employing different experimental techniques. In in silico studies, molecular dynamics simulations have been used to provide new insights at an atomistic level, which enables the study of properties that are difficult or even impossible to measure experimentally. Each model and technique has its advantages and disadvantages. Hence, combining different models and techniques is necessary for a more reliable study. In this review, the theoretical backgrounds of these (in vitro and in silico) approaches are presented, followed by a discussion of the pharmacokinetic and pharmacodynamic properties of drugs that are related to their interactions with membranes. All approaches are discussed in parallel to present for a better connection between experimental and simulation studies. Finally, an overview of the molecular dynamics simulation studies used for drug-membrane interactions is provided. Copyright © 2016 Elsevier Ltd. All rights reserved.

Rodent Brain Microinjection to Study Molecular Substrates of Motivated Behavior

PubMed Central

Poland, Ryan S.; Bull, Cecilia; Syed, Wahab A.; Bowers, M. Scott

2015-01-01

Brain microinjection can aid elucidation of the molecular substrates of complex behaviors, such as motivation. For this purpose rodents can serve as appropriate models, partly because the response to behaviorally relevant stimuli and the circuitry parsing stimulus-action outcomes is astonishingly similar between humans and rodents. In studying molecular substrates of complex behaviors, the microinjection of reagents that modify, augment, or silence specific systems is an invaluable technique. However, it is crucial that the microinjection site is precisely targeted in order to aid interpretation of the results. We present a method for the manufacture of surgical implements and microinjection needles that enables accurate microinjection and unlimited customizability with minimal cost. Importantly, this technique can be successfully completed in awake rodents if conducted in conjunction with other JoVE articles that covered requisite surgical procedures. Additionally, there are many behavioral paradigms that are well suited for measuring motivation. The progressive ratio is a commonly used method that quantifies the efficacy of a reinforcer to maintain responding despite an (often exponentially) increasing work requirement. This assay is sensitive to reinforcer magnitude and pharmacological manipulations, which allows reinforcing efficacy and/ or motivation to be determined. We also present a straightforward approach to program operant software to accommodate a progressive ratio reinforcement schedule. PMID:26437131

Characteristics of the mixing volume model with the interactions among spatially distributed particles for Lagrangian simulations of turbulent mixing

NASA Astrophysics Data System (ADS)

Watanabe, Tomoaki; Nagata, Koji

2016-11-01

The mixing volume model (MVM), which is a mixing model for molecular diffusion in Lagrangian simulations of turbulent mixing problems, is proposed based on the interactions among spatially distributed particles in a finite volume. The mixing timescale in the MVM is derived by comparison between the model and the subgrid scale scalar variance equation. A-priori test of the MVM is conducted based on the direct numerical simulations of planar jets. The MVM is shown to predict well the mean effects of the molecular diffusion under various conditions. However, a predicted value of the molecular diffusion term is positively correlated to the exact value in the DNS only when the number of the mixing particles is larger than two. Furthermore, the MVM is tested in the hybrid implicit large-eddy-simulation/Lagrangian-particle-simulation (ILES/LPS). The ILES/LPS with the present mixing model predicts well the decay of the scalar variance in planar jets. This work was supported by JSPS KAKENHI Nos. 25289030 and 16K18013. The numerical simulations presented in this manuscript were carried out on the high performance computing system (NEC SX-ACE) in the Japan Agency for Marine-Earth Science and Technology.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of a biomolecule: 5-Hydroxymethyluracil.

PubMed

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2014-06-05

In the present work, the experimental and theoretical vibrational spectra of 5-hydroxymethyluracil were investigated. The FT-IR (4000-400cm(-1)) spectrum of the molecule in the solid phase was recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared intensities of the title molecule in the ground state were calculated using density functional B3LYP and M06-2X methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data, and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 5-hydroxymethyluracil molecule was also simulated to evaluate the effect of intermolecular hydrogen bonding on its vibrational frequencies. It was observed that the NH stretching modes shifted to lower frequencies, while its in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular NH⋯O hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented. Copyright © 2014 Elsevier B.V. All rights reserved.

Effect of intermolecular hydrogen bonding, vibrational analysis and molecular structure of 4-chlorobenzothioamide

NASA Astrophysics Data System (ADS)

Çırak, Çağrı; Sert, Yusuf; Ucun, Fatih

2013-09-01

In the present work, the experimental and theoretical vibrational spectra of 4-chlorobenzothioamide were investigated. The FT-IR (400-4000 cm-1) and μ-Raman spectra (100-4000 cm-1) of 4-chlorobenzothioamide in the solid phase were recorded. The geometric parameters (bond lengths and bond angles), vibrational frequencies, Infrared and Raman intensities of the title molecule in the ground state were calculated using ab initio Hartree-Fock and density functional theory (B3LYP) methods with the 6-311++G(d,p) basis set for the first time. The optimized geometric parameters and the theoretical vibrational frequencies were found to be in good agreement with the corresponding experimental data and with the results found in the literature. The vibrational frequencies were assigned based on the potential energy distribution using the VEDA 4 program. The dimeric form of 4-chlorobenzothioamide was also simulated to evaluate the effect of intermolecular hydrogen bonding on the vibrational frequencies. It was observed that the Nsbnd H stretching modes shifted to lower frequencies, while the in-plane and out-of-plane bending modes shifted to higher frequencies due to the intermolecular Nsbnd H⋯S hydrogen bond. Also, the highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO) energies and diagrams were presented.

On the optimal design of molecular sensing interfaces with lipid bilayer assemblies - A knowledge based approach

NASA Astrophysics Data System (ADS)

Siontorou, Christina G.

2012-12-01

Biosensors are analytic devices that incorporate a biochemical recognition system (biological, biologicalderived or biomimic: enzyme, antibody, DNA, receptor, etc.) in close contact with a physicochemical transducer (electrochemical, optical, piezoelectric, conductimetric, etc.) that converts the biochemical information, produced by the specific biological recognition reaction (analyte-biomolecule binding), into a chemical or physical output signal, related to the concentration of the analyte in the measuring sample. The biosensing concept is based on natural chemoreception mechanisms, which are feasible over/within/by means of a biological membrane, i.e., a structured lipid bilayer, incorporating or attached to proteinaceous moieties that regulate molecular recognition events which trigger ion flux changes (facilitated or passive) through the bilayer. The creation of functional structures that are similar to natural signal transduction systems, correlating and interrelating compatibly and successfully the physicochemical transducer with the lipid film that is self-assembled on its surface while embedding the reconstituted biological recognition system, and at the same time manage to satisfy the basic conditions for measuring device development (simplicity, easy handling, ease of fabrication) is far from trivial. The aim of the present work is to present a methodological framework for designing such molecular sensing interfaces, functioning within a knowledge-based system built on an ontological platform for supplying sub-systems options, compatibilities, and optimization parameters.

Diagnosis of lubricating oil by evaluating cyanide and carbon molecular emission lines in laser induced breakdown spectra

NASA Astrophysics Data System (ADS)

Elnasharty, I. Y.; Kassem, A. K.; Sabsabi, M.; Harith, M. A.

2011-08-01

To prevent engine failure it is essential to change lubricating oil regularly before it loses its protective properties. It is also necessary to monitor the physical and chemical conditions of the oil to reliably determine the optimum oil-change intervals. The present work focuses on studying evolution of the cyanide (CN) and carbon (C 2) molecular spectral emission lines in the laser induced breakdown spectra of lubricating oil as a function of its consumption. The intensities of these molecular bands have been taken as indicator of engine oil degradation at certain mileage. Furthermore, the percentage of decay of CN and C 2 integral intensity values at the corresponding mileage was calculated in order to relate it to the degree of consumption of the motor oil. Such percentage decay of the CN and C 2 integral intensities have been found to increase gradually with increasing mileage which is accompanied with increasing depletion of engine oil. The results of using LIBS technique in the present measurements proved that it is possible to have a direct, straightforward and easy method for prediction of lubricating oil degree of consumption. This may facilitate scheduling the proper time and/or mileage intervals for changing the oil to avoid any possibility of engine failure.

Molecular typing of Sporothrix schenckii isolates from cats in Malaysia.

PubMed

Kano, Rui; Okubo, Miki; Siew, Han Hock; Kamata, Hiroshi; Hasegawa, Atsuhiko

2015-04-01

Epidemiological data on the aetiologic agents of feline sporotrichosis in Malaysia have not been reported, though human sporotrichosis in Malaysia is reported to be transmitted primarily via cat scratch. To the best of our knowledge, the present report is the first study of the molecular epidemiology of Sporothrix schenckii isolates from cats with sporotrichosis in Malaysia. In the present work, we characterised 18 clinical isolates from cats in Malaysia based on molecular properties, including sequence analyses of the calmodulin gene and the rDNA ITS region and selective PCR of mating type (MAT) loci. In this study, isolates from feline sporotrichosis were identified as a S. schenckii sensu stricto by sequence analyses of the calmodulin gene and the internal transcribed spacer (ITS) region. Notably, phylogenetic analysis of the ITS confirmed assignment to clinical clade D (and not C) of S. schenckii sensu stricto. Therefore, clinical clade D of S. schenckii sensu stricto appeared to be the prevailing source of feline sporotrichosis in Malaysia. The ratio of MAT1-1-1:MAT1-2-1 in these Malaysian isolates was found to be 1 : 0. This result suggested that a clonal strain of S. schenckii is the prevailing causative agent of feline sporotrichosis in Malaysia. © 2015 Blackwell Verlag GmbH.

Developments in the CCP4 molecular-graphics project.

PubMed

Potterton, Liz; McNicholas, Stuart; Krissinel, Eugene; Gruber, Jan; Cowtan, Kevin; Emsley, Paul; Murshudov, Garib N; Cohen, Serge; Perrakis, Anastassis; Noble, Martin

2004-12-01

Progress towards structure determination that is both high-throughput and high-value is dependent on the development of integrated and automatic tools for electron-density map interpretation and for the analysis of the resulting atomic models. Advances in map-interpretation algorithms are extending the resolution regime in which fully automatic tools can work reliably, but at present human intervention is required to interpret poor regions of macromolecular electron density, particularly where crystallographic data is only available to modest resolution [for example, I/sigma(I) < 2.0 for minimum resolution 2.5 A]. In such cases, a set of manual and semi-manual model-building molecular-graphics tools is needed. At the same time, converting the knowledge encapsulated in a molecular structure into understanding is dependent upon visualization tools, which must be able to communicate that understanding to others by means of both static and dynamic representations. CCP4 mg is a program designed to meet these needs in a way that is closely integrated with the ongoing development of CCP4 as a program suite suitable for both low- and high-intervention computational structural biology. As well as providing a carefully designed user interface to advanced algorithms of model building and analysis, CCP4 mg is intended to present a graphical toolkit to developers of novel algorithms in these fields.

Multiresolution molecular mechanics: Implementation and efficiency

NASA Astrophysics Data System (ADS)

Biyikli, Emre; To, Albert C.

2017-01-01

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

Work of adhesion between mucin macromolecule and calcium-alginate gels on molecular level.

PubMed

Popeski-Dimovski, Riste

2015-06-05

The bioadhesion of biopolymers to mucus layers is of great interest for the development of drug delivery systems. Herein we use AFM force measurements to evaluate the interaction on molecular level between a mucin macromolecule attached to an AFM tip and a calcium-alginate gel layer. The total work of adhesion is measured from the AFM force curves depending on different parameters: time of contact, G/M ratio of the alginate, and crosslink ratio of the gel. The total work of adhesion is found to be in the range of 1×10(-19) to 6×10(-18)J. The results show that the work of adhesion increases with the time of contact but it is independent from the molecular mass of the alginate, the G/M ratio of the alginate and crosslink ratio of the gel. Copyright © 2015 Elsevier Ltd. All rights reserved.

The Effect of Two Receivers on Broadcast Molecular Communication Systems.

PubMed

Lu, Yi; Higgins, Matthew D; Noel, Adam; Leeson, Mark S; Chen, Yunfei

2016-12-01

Molecular communication is a paradigm that utilizes molecules to exchange information between nano-machines. When considering such systems where multiple receivers are present, prior work has assumed for simplicity that they do not interfere with each other. This paper aims to address this issue and shows to what extent an interfering receiver, [Formula: see text], will have an impact on the target receiver, [Formula: see text], with respect to Bit Error Rate (BER) and capacity. Furthermore, approximations of the Binomial distribution are applied to reduce the complexity of calculations. Results show the sensitivity in communication performance due to the relative location of the interfering receiver. Critically, placing [Formula: see text] between the transmitter [Formula: see text] and [Formula: see text] causes a significant increase in BER or decrease in capacity.

Molecular mechanisms of thermal resistance of the insect trypanosomatid Crithidia thermophila

PubMed Central

Ishemgulova, Aygul; Butenko, Anzhelika; Kortišová, Lucie; Boucinha, Carolina; Grybchuk-Ieremenko, Anastasiia; Morelli, Karina A.; Tesařová, Martina; Kraeva, Natalya; Grybchuk, Danyil; Pánek, Tomáš; Flegontov, Pavel; Lukeš, Julius; Votýpka, Jan; Pavan, Márcio Galvão; Opperdoes, Fred R.; Spodareva, Viktoria; d'Avila-Levy, Claudia M.; Kostygov, Alexei Yu.

2017-01-01

In the present work, we investigated molecular mechanisms governing thermal resistance of a monoxenous trypanosomatid Crithidia luciliae thermophila, which we reclassified as a separate species C. thermophila. We analyzed morphology, growth kinetics, and transcriptomic profiles of flagellates cultivated at low (23°C) and elevated (34°C) temperature. When maintained at high temperature, they grew significantly faster, became shorter, with genes involved in sugar metabolism and mitochondrial stress protection significantly upregulated. Comparison with another thermoresistant monoxenous trypanosomatid, Leptomonas seymouri, revealed dramatic differences in transcription profiles of the two species with only few genes showing the same expression pattern. This disparity illustrates differences in the biology of these two parasites and distinct mechanisms of their thermotolerance, a prerequisite for living in warm-blooded vertebrates. PMID:28328988

Vibrational spectroscopic investigation of p-, m- and o-nitrobenzonitrile by using Hartree-Fock and density functional theory

NASA Astrophysics Data System (ADS)

Sert, Y.; Ucun, F.

2013-08-01

In the present work, the theoretical vibrational spectra of p-, m- and o-nitrobenzonitrile molecules have been analyzed. The harmonic vibrational frequencies and geometric parameters (bond lengths and bond angles) of these molecules have been calculated using ab initio Hartree-Fock and density functional theory methods with 6-311++G(d,p) basis set by Gaussian 03 W, for the first time. Assignments of the vibrational frequencies have been performed by potential energy distribution by using VEDA 4 program. The optimized geometric parameters and harmonic vibrational frequencies have been compared with the corresponding experimental data and seen to be in a good agreement with each other. Also, the highest occupied molecular orbital and lowest unoccupied molecular orbital energies have been obtained.

Catalytic transformation of dinitrogen into ammonia and hydrazine by iron-dinitrogen complexes bearing pincer ligand

PubMed Central

Kuriyama, Shogo; Arashiba, Kazuya; Nakajima, Kazunari; Matsuo, Yuki; Tanaka, Hiromasa; Ishii, Kazuyuki; Yoshizawa, Kazunari; Nishibayashi, Yoshiaki

2016-01-01

Synthesis and reactivity of iron-dinitrogen complexes have been extensively studied, because the iron atom plays an important role in the industrial and biological nitrogen fixation. As a result, iron-catalyzed reduction of molecular dinitrogen into ammonia has recently been achieved. Here we show that an iron-dinitrogen complex bearing an anionic PNP-pincer ligand works as an effective catalyst towards the catalytic nitrogen fixation, where a mixture of ammonia and hydrazine is produced. In the present reaction system, molecular dinitrogen is catalytically and directly converted into hydrazine by using transition metal-dinitrogen complexes as catalysts. Because hydrazine is considered as a key intermediate in the nitrogen fixation in nitrogenase, the findings described in this paper provide an opportunity to elucidate the reaction mechanism in nitrogenase. PMID:27435503

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics.

PubMed

de Buyl, Pierre; Nies, Erik

2015-04-07

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

A parallel algorithm for step- and chain-growth polymerization in molecular dynamics

NASA Astrophysics Data System (ADS)

de Buyl, Pierre; Nies, Erik

2015-04-01

Classical Molecular Dynamics (MD) simulations provide insight into the properties of many soft-matter systems. In some situations, it is interesting to model the creation of chemical bonds, a process that is not part of the MD framework. In this context, we propose a parallel algorithm for step- and chain-growth polymerization that is based on a generic reaction scheme, works at a given intrinsic rate and produces continuous trajectories. We present an implementation in the ESPResSo++ simulation software and compare it with the corresponding feature in LAMMPS. For chain growth, our results are compared to the existing simulation literature. For step growth, a rate equation is proposed for the evolution of the crosslinker population that compares well to the simulations for low crosslinker functionality or for short times.

Nanodevices in diagnostics

PubMed Central

Hu, Ye; Fine, Daniel H.; Tasciotti, Ennio; Bouamrani, Ali; Ferrari, Mauro

2010-01-01

The real-time, personalized and highly sensitive early-stage diagnosis of disease remains an important challenge in modern medicine. With the ability to interact with matter at the nanoscale, the development of nanotechnology architectures and materials could potentially extend subcellular and molecular detection beyond the limits of conventional diagnostic modalities. At the very least, nanotechnology should be able to dramatically accelerate biomarker discovery, as well as facilitate disease monitoring, especially of maladies presenting a high degree of molecular and compositional heterogeneity. This article gives an overview of several of the most promising nanodevices and nanomaterials along with their applications in clinical practice. Significant work to adapt nanoscale materials and devices to clinical applications involving large interdisciplinary collaborations is already underway with the potential for nanotechnology to become an important enabling diagnostic technology. PMID:20229595

Synthesis and molecular characterization of chitosan based polyurethane elastomers using aromatic diisocyanate.

PubMed

Zia, Khalid Mahmood; Anjum, Sohail; Zuber, Mohammad; Mujahid, Muhammad; Jamil, Tahir

2014-05-01

The present research work was performed to synthesize a new series of chitosan based polyurethane elastomers (PUEs) using poly(ɛ-caprolactone) (PCL). The chitosan based PUEs were prepared by step-growth polymerization technique using poly(ɛ-caprolactone) (PCL) and 2,4-toluene diisocyanate (TDI). In the second step the PU prepolymer was extended with different mole ratios of chitosan and 1,4-butane diol (BDO). Molecular engineering was carried out during the synthesis. The conventional spectroscopic characterization of the synthesized samples using FT-IR confirms the existence of the proposed chitosan based PUEs structure. Internal morphology of the prepared PUEs was studied using SEM analysis. The SEM images confirmed the incorporation of chitosan molecules into the PU backbone. Copyright © 2014 Elsevier B.V. All rights reserved.

Comment on "Spontaneous liquid-liquid phase separation of water"

NASA Astrophysics Data System (ADS)

Limmer, David T.; Chandler, David

2015-01-01

Yagasaki et al. [Phys. Rev. E 89, 020301 (2014), 10.1103/PhysRevE.89.020301] present results from a molecular dynamics trajectory illustrating coarsening of ice, which they interpret as evidence of transient coexistence between two distinct supercooled phases of liquid water. We point out that neither two distinct liquids nor criticality are demonstrated in this simulation study. Instead, the illustrated trajectory is consistent with coarsening behaviors analyzed and predicted in earlier work by others.

Spotting and designing promiscuous ligands for drug discovery.

PubMed

Schneider, P; Röthlisberger, M; Reker, D; Schneider, G

2016-01-21

The promiscuous binding behavior of bioactive compounds forms a mechanistic basis for understanding polypharmacological drug action. We present the development and prospective application of a computational tool for identifying potential promiscuous drug-like ligands. In combination with computational target prediction methods, the approach provides a working concept for rationally designing such molecular structures. We could confirm the multi-target binding of a de novo generated compound in a proof-of-concept study relying on the new method.

Diode Laser Measurements of Concentration and Temperature in Microgravity Combustion

NASA Technical Reports Server (NTRS)

Silver, Joel A.; Kane, Daniel J.

1999-01-01

Diode laser absorption spectroscopy provides a direct method of determinating species concentration and local gas temperature in combustion flames. Under microgravity conditions, diode lasers are particularly suitable, given their compact size, low mass and low power requirements. The development of diode laser-based sensors for gas detection in microgravity is presented, detailing measurements of molecular oxygen. Current progress of this work and future application possibilities for these methods on the International Space Station are discussed.

The intermolecular interaction in D2 - CX4 and O2 - CX4 (X = F, Cl) systems: Molecular beam scattering experiments as a sensitive probe of the selectivity of charge transfer component.

PubMed

Cappelletti, David; Falcinelli, Stefano; Pirani, Fernando

2016-10-07

Gas phase collisions of a D 2 projectile by CF 4 and by CCl 4 targets have been investigated with the molecular beam technique. The integral cross section, Q, has been measured for both collisional systems in the thermal energy range and oscillations due to the quantum "glory" interference have been resolved in the velocity dependence of Q. The analysis of the measured Q(v) data provided novel information on the anisotropic potential energy surfaces of the studied systems at intermediate and large separation distances. The relative role of the most relevant types of contributions to the global interaction has been characterized. Extending the phenomenology of a weak intermolecular halogen bond, the present work demonstrates that while D 2 - CF 4 is basically bound through the balance between size (Pauli) repulsion and dispersion attraction, an appreciable intermolecular bond stabilization by charge transfer is operative in D 2 - CCl 4 . We also demonstrated that the present analysis is consistent with that carried out for the F( 2 P)-D 2 and Cl( 2 P)-D 2 systems, previously characterized by scattering experiments performed with state-selected halogen atom beams. A detailed comparison of the present and previous results on O 2 -CF 4 and O 2 -CCl 4 systems pinpointed striking differences in the behavior of hydrogen and oxygen molecules when they interact with the same partner, mainly due to the selectivity of the charge transfer component. The present work contributes to cast light on the nature and role of the intermolecular interaction in prototype systems, involving homo-nuclear diatoms and symmetric halogenated molecules.

Contracaecum osculatum and other anisakid nematodes in grey seals and cod in the Baltic Sea: molecular and ecological links.

PubMed

Zuo, S; Kania, P W; Mehrdana, F; Marana, M H; Buchmann, K

2018-01-01

Populations of grey seals (Halichoerus grypus), sprats (Sprattus sprattus) and cod (Gadus morhua) in the Baltic Sea are relatively stationary. The present work, applying classical and molecular helminthological techniques, documents that seals and cod also share a common parasite, the anisakid nematode Contracaecum osculatum, which uses seals as the final host and fish as transport hosts. Sequencing mitochondrial genes (COX1 and COX2) in adult worms from seals and third-stage larvae from livers of Baltic fish (sprats and cod), showed that all gene variants occur in both seals and fish. Other anisakid nematodes Pseudoterranova decipiens and Anisakis simplex are also found in both seals and cod in the Baltic Sea, but at much lower rates. The Baltic grey seal population was left at a critically low level (comprising a few hundred individuals) during the latter part of the 20th century, but since the year 2000 a marked increase in the population has been observed, reaching more than 40,000 individuals at present. Ecological consequences of the increased seal abundance may result from increased predation on fish stocks, but recent evidence also points to the influence of elevated parasitism on fish performance. Contracaecum osculatum larvae preferentially infect the liver of Baltic cod, considered a vital organ of the host. Whereas low prevalences and intensities in cod were reported during the 1980s and 1990s, the present study documents 100% prevalence and a mean intensity of above 80 worms per fish. Recent studies have also indicated the zoonotic potential of C. osculatum larvae in fish, following the consumption of raw or under-cooked fish. Therefore the present work discusses the impact of parasitism on the cod stock and the increasing risk for consumer health, and lists possible solutions for control.

Molecular characterization of Hepatozoon sp. in cats from São Luís Island, Maranhão, Northeastern Brazil.

PubMed

de Bortoli, Caroline P; André, Marcos R; Braga, Maria do Socorro C; Machado, Rosangela Zacarias

2011-10-01

Few molecular studies have been done concerning the molecular characterization of Hepatozoon species among domestic and wild felids. The present work aimed to characterize molecularly the presence of Hepatozoon sp. DNA in cat blood samples from São Luís Island, Maranhão state, Northeastern Brazil. EDTA-whole blood samples were collected from 200 domestic cats with outdoor and wood areas access from São Luís, Maranhão, Brazil. Each sample of extracted DNA was used as a template in PCR reactions aiming to amplify a partial sequence of 18S rRNA of Hepatozoon spp. We also performed sequence alignment to establish the identity of the parasite species infecting these animals using DNA sequences based on 18S rRNA. From 200 sampled cats, Hepatozoon DNA was only found in one animal (0.5%). The found Hepatozoon DNA showed 97% of identity with Hemobartonella felis isolates 1 and 2 from Spain. When analyzing the phylogenetic tree, the found Hepatozoon DNA was in the same clade than H. felis isolates. Our findings suggest that more than one species of Hepatozoon could infect felids in Brazil.

Protonation free energy levels in complex molecular systems.

PubMed

Antosiewicz, Jan M

2008-04-01

All proteins, nucleic acids, and other biomolecules contain residues capable of exchanging protons with their environment. These proton transfer phenomena lead to pH sensitivity of many molecular processes underlying biological phenomena. In the course of biological evolution, Nature has invented some mechanisms to use pH gradients to regulate biomolecular processes inside cells or in interstitial fluids. Therefore, an ability to model protonation equilibria in molecular systems accurately would be of enormous value for our understanding of biological processes and for possible rational influence on them, like in developing pH dependent drugs to treat particular diseases. This work presents a derivation, by thermodynamic and statistical mechanical methods, of an expression for the free energy of a complex molecular system at arbitrary ionization state of its titratable residues. This constitutes one of the elements of modeling protonation equilibria. Starting from a consideration of a simple acid-base equilibrium of a model compound with a single tritratable group, we arrive at an expression which is of general validity for complex systems. The only approximation used in this derivation is the postulating that the interaction energy between any pair of titratable sites does not depend on the protonation states of all the remaining ionizable groups.

Understanding the interactions of human follicle stimulating hormone with single-walled carbon nanotubes by molecular dynamics simulation and free energy analysis.

PubMed

Mahmoodi, Yasaman; Mehrnejad, Faramarz; Khalifeh, Khosrow

2018-01-01

Interactions of carbon nanotubes (CNTs) and blood proteins are of interest for nanotoxicology and nanomedicine. It is believed that the interactions of blood proteins and glycoproteins with CNTs may have important biological effects. In spite of many experimental studies of single-walled carbon nanotubes (SWCNT) and glycoproteins with different methods, little is known about the atomistic details of their association process or of structural alterations occurring in adsorbed glycoproteins. In this study, we have applied molecular dynamics simulation to investigate the interaction of follicle stimulating hormone (hFSH) with SWCNT. The aim of this work is to investigate possible mechanisms of nanotoxicity at a molecular level. We present details of the molecular dynamics, structure, and free energy of binding of hFSH on the surface of SWCNT. We find that hFSH in aqueous solution strongly adsorbs onto SWCNT via their concave surface as evidenced by high binding free energies for residues in both protein subunits. It was found that hydrophobic, π-cation, and π-π stacking interactions are the main driving forces for the adsorption of the protein at the nanotube surface.